WorldWideScience

Sample records for linear nucleosomal arrays

  1. Characterization of Dnmt1 Binding and DNA Methylation on Nucleosomes and Nucleosomal Arrays.

    Anna Schrader

    Full Text Available The packaging of DNA into nucleosomes and the organisation into higher order structures of chromatin limits the access of sequence specific DNA binding factors to DNA. In cells, DNA methylation is preferentially occuring in the linker region of nucleosomes, suggesting a structural impact of chromatin on DNA methylation. These observations raise the question whether DNA methyltransferases are capable to recognize the nucleosomal substrates and to modify the packaged DNA. Here, we performed a detailed analysis of nucleosome binding and nucleosomal DNA methylation by the maintenance DNA methyltransferase Dnmt1. Our binding studies show that Dnmt1 has a DNA length sensing activity, binding cooperatively to DNA, and requiring a minimal DNA length of 20 bp. Dnmt1 needs linker DNA to bind to nucleosomes and most efficiently recognizes nucleosomes with symmetric DNA linkers. Footprinting experiments reveal that Dnmt1 binds to both DNA linkers exiting the nucleosome core. The binding pattern correlates with the efficient methylation of DNA linkers. However, the enzyme lacks the ability to methylate nucleosomal CpG sites on mononucleosomes and nucleosomal arrays, unless chromatin remodeling enzymes create a dynamic chromatin state. In addition, our results show that Dnmt1 functionally interacts with specific chromatin remodeling enzymes to enable complete methylation of hemi-methylated DNA in chromatin.

  2. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation.

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-06-07

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.

  3. Removal of histone tails from nucleosome dissects the physical mechanisms of salt-induced aggregation, linker histone H1-induced compaction, and 30-nm fiber formation of the nucleosome array

    Hizume, Kohji; Nakai, Tonau; Araki, Sumiko; Prieto, Eloise; Yoshikawa, Kenichi; Takeyasu, Kunio

    2009-01-01

    In order to reveal the roles of histone tails in the formation of higher-order chromatin structures, we employed atomic force microscopy (AFM), and an in vitro reconstitution system to examine the properties of reconstituted chromatin composed of tail-less histones and a long DNA (106-kb plasmid) template. The tail-less nucleosomes did not aggregate at high salt concentrations or with an excess amount of core histones, in contrast with the behavior of nucleosomal arrays composed of nucleosomes containing normal, N-terminal tails. Analysis of our nucleosome distributions reveals that the attractive interaction between tail-less nucleosomes is weakened. Addition of linker histone H1 into the tail-less nucleosomal array failed to promote the formation of 30 nm chromatin fibers that are usually formed in the normal nucleosomal array. These results demonstrate that the attractive interaction between nucleosomes via histone tails plays a critical role in the formation of the uniform 30-nm chromatin fiber.

  4. Dynamic Conformations of Nucleosome Arrays in Solution from Small-Angle X-ray Scattering

    Howell, Steven C. [George Washington Univ., Washington, DC (United States)

    2016-01-31

    We set out to determine quantitative information regarding the dynamic conformation of nucleosome arrays in solution using experimental SAXS. Toward this end, we developed a CG simulation algorithm for dsDNA which rapidly generates ensembles of structures through Metropolis MC sampling of a Markov chain.

  5. ESPRIT And Uniform Linear Arrays

    Roy, R. H.; Goldburg, M.; Ottersten, B. E.; Swindlehurst, A. L.; Viberg, M.; Kailath, T.

    1989-11-01

    Abstract ¬â€?ESPRIT is a recently developed and patented technique for high-resolution estimation of signal parameters. It exploits an invariance structure designed into the sensor array to achieve a reduction in computational requirements of many orders of magnitude over previous techniques such as MUSIC, Burg's MEM, and Capon's ML, and in addition achieves performance improvement as measured by parameter estimate error variance. It is also manifestly more robust with respect to sensor errors (e.g. gain, phase, and location errors) than other methods as well. Whereas ESPRIT only requires that the sensor array possess a single invariance best visualized by considering two identical but other-wise arbitrary arrays of sensors displaced (but not rotated) with respect to each other, many arrays currently in use in various applications are uniform linear arrays of identical sensor elements. Phased array radars are commonplace in high-resolution direction finding systems, and uniform tapped delay lines (i.e., constant rate A/D converters) are the rule rather than the exception in digital signal processing systems. Such arrays possess many invariances, and are amenable to other types of analysis, which is one of the main reasons such structures are so prevalent. Recent developments in high-resolution algorithms of the signal/noise subspace genre including total least squares (TLS) ESPRIT applied to uniform linear arrays are summarized. ESPRIT is also shown to be a generalization of the root-MUSIC algorithm (applicable only to the case of uniform linear arrays of omni-directional sensors and unimodular cisoids). Comparisons with various estimator bounds, including CramerRao bounds, are presented.

  6. Directivity of basic linear arrays

    Bach, Henning

    1970-01-01

    For a linear uniform array ofnelements, an expression is derived for the directivity as a function of the spacing and the phase constants. The cases of isotropic elements, collinear short dipoles, and parallel short dipoles are included. The formula obtained is discussed in some detail and contour...

  7. An adjustable linear Halbach array

    Hilton, J.E., E-mail: James.Hilton@csiro.au [CSIRO Mathematics, Informatics and Statistics, Clayton South, VIC 3169 (Australia); McMurry, S.M. [School of Physics, Trinity College, Dublin (Ireland)

    2012-07-15

    The linear Halbach array is a well-known planar magnetic structure capable, in the idealized case, of generating a one-sided magnetic field. We show that such a field can be created from an array of uniformly magnetized rods, and rotating these rods in an alternating fashion can smoothly transfer the resultant magnetic field through the plane of the device. We examine an idealized model composed of infinite line dipoles and carry out computational simulations on a realizable device using a magnetic boundary element method. Such an arrangement can be used for an efficient latching device, or to produce a highly tunable field in the space above the device. - Highlights: Black-Right-Pointing-Pointer We model an adjustable 'one-sided' flux sheet made up of a series of dipolar magnetic field sources. Black-Right-Pointing-Pointer We show that magnetic field can be switched from one side of sheet to other by a swap rotation of each of magnetic sources. Black-Right-Pointing-Pointer Investigations show that such an arrangement is practical and can easily be fabricated. Black-Right-Pointing-Pointer The design has a wide range of potential applications.

  8. An adjustable linear Halbach array

    Hilton, J.E.; McMurry, S.M.

    2012-01-01

    The linear Halbach array is a well-known planar magnetic structure capable, in the idealized case, of generating a one-sided magnetic field. We show that such a field can be created from an array of uniformly magnetized rods, and rotating these rods in an alternating fashion can smoothly transfer the resultant magnetic field through the plane of the device. We examine an idealized model composed of infinite line dipoles and carry out computational simulations on a realizable device using a magnetic boundary element method. Such an arrangement can be used for an efficient latching device, or to produce a highly tunable field in the space above the device. - Highlights: ► We model an adjustable ‘one-sided’ flux sheet made up of a series of dipolar magnetic field sources. ► We show that magnetic field can be switched from one side of sheet to other by a swap rotation of each of magnetic sources. ► Investigations show that such an arrangement is practical and can easily be fabricated. ► The design has a wide range of potential applications.

  9. Statistical monitoring of linear antenna arrays

    Harrou, Fouzi; Sun, Ying

    2016-01-01

    The paper concerns the problem of monitoring linear antenna arrays using the generalized likelihood ratio (GLR) test. When an abnormal event (fault) affects an array of antenna elements, the radiation pattern changes and significant deviation from

  10. Statistical monitoring of linear antenna arrays

    Harrou, Fouzi

    2016-11-03

    The paper concerns the problem of monitoring linear antenna arrays using the generalized likelihood ratio (GLR) test. When an abnormal event (fault) affects an array of antenna elements, the radiation pattern changes and significant deviation from the desired design performance specifications can resulted. In this paper, the detection of faults is addressed from a statistical point of view as a fault detection problem. Specifically, a statistical method rested on the GLR principle is used to detect potential faults in linear arrays. To assess the strength of the GLR-based monitoring scheme, three case studies involving different types of faults were performed. Simulation results clearly shown the effectiveness of the GLR-based fault-detection method to monitor the performance of linear antenna arrays.

  11. Linear-array systems for aerospace NDE

    Smith, Robert A.; Willsher, Stephen J.; Bending, Jamie M.

    1999-01-01

    Rapid large-area inspection of composite structures for impact damage and multi-layered aluminum skins for corrosion has been a recognized priority for several years in both military and civil aerospace applications. Approaches to this requirement have followed two clearly different routes: the development of novel large-area inspection systems, and the enhancement of current ultrasonic or eddy-current methods to reduce inspection times. Ultrasonic inspection is possible with standard flaw detection equipment but the addition of a linear ultrasonic array could reduce inspection times considerably. In order to investigate their potential, 9-element and 17-element linear ultrasonic arrays for composites, and 64-element arrays for aluminum skins, have been developed to DERA specifications for use with the ANDSCAN area scanning system. A 5 m 2 composite wing surface has been scanned with a scan resolution of approximately 3 mm in 6 hours. With subsequent software and hardware improvements all four composite wing surfaces (top/bottom, left/right) of a military fighter aircraft can potentially be inspected in less than a day. Array technology has been very widely used in the medical ultrasound field although rarely above 10 MHz, whereas lap-joint inspection requires a pulse center-frequency of 12 to 20 MHz in order to resolve the separate interfaces in the lap joint. A 128 mm-long multi-element array of 5 mmx2 mm ultrasonic elements for use with the ANDSCAN scanning software was produced to a DERA specification by an NDT manufacturer with experience in the medical imaging field. This paper analyses the performance of the transducers that have been produced and evaluates their use in scanning systems of different configurations

  12. Improved linear pyroelectric IR detector arrays

    Twiney, R.C.; Robinson, M.K.; Porter, S.G.

    1987-01-01

    Good agreement has been found between theoretical models and measured performance for a range of array geometries. A 64-element 80 x 140-micron element array with integral MOSFET IC buffer preamplifiers shows improved source voltage uniformity, a J-FET buffered array, and low-frequency specific detectivity (SD) of 1.7 x 10 to the 8th cm sq rt Hz/W at 40 Hz. The MOSFET array shows reduced degradation of SD at high temperatures, retaining an SD of not less than 1 x 10 to the 8th cm sq rt Hz/W at +70 C across much of the band. A 64-element array has been designed using onboard multiplexers, thus greatly reducing the connections needed to run the array

  13. Linearly tapered slot antenna circular array for mobile communications

    Simons, Rainee N.; Kelly, Eron; Lee, Richard Q.; Taub, Susan R.

    1993-01-01

    The design, fabrication and testing of a conformal K-band circular array is presented. The array consists of sixteen linearly tapered slot antennas (LTSA). It is fed by a 1:16 microstrip line power splitter via electromagnetic coupling. The array has an omni-directional pattern in the azimuth plane. In the elevation plane the beam is displaced above the horizon.

  14. Linear Array Ultrasonic Transducers: Sensitivity and Resolution Study

    Kramb, V.A.

    2005-01-01

    The University of Dayton Research Institute (UDRI) under contract by the US Air Force has designed and integrated a fully automated inspection system for the inspection of turbine engines that incorporates linear phased array ultrasonic transducers. Phased array transducers have been successfully implemented into weld and turbine blade root inspections where the defect types are well known and characterized. Embedded defects in aerospace turbine engine components are less well defined, however. In order to determine the applicability of linear arrays to aerospace inspections the sensitivity of array transducers to embedded defects in engine materials must be characterized. In addition, the implementation of array transducers into legacy inspection procedures must take into account any differences in sensitivity between the array transducer and that of the single element transducer currently used. This paper discusses preliminary results in a study that compares the sensitivity of linear array and conventional single element transducers to synthetic hard alpha defects in a titanium alloy

  15. Displacement measurement system for linear array detector

    Zhang Pengchong; Chen Ziyu; Shen Ji

    2011-01-01

    It presents a set of linear displacement measurement system based on encoder. The system includes displacement encoders, optical lens and read out circuit. Displacement read out unit includes linear CCD and its drive circuit, two amplifier circuits, second order Butterworth low-pass filter and the binarization circuit. The coding way is introduced, and various parts of the experimental signal waveforms are given, and finally a linear experimental test results are given. The experimental results are satisfactory. (authors)

  16. A novel method to design sparse linear arrays for ultrasonic phased array.

    Yang, Ping; Chen, Bin; Shi, Ke-Ren

    2006-12-22

    In ultrasonic phased array testing, a sparse array can increase the resolution by enlarging the aperture without adding system complexity. Designing a sparse array involves choosing the best or a better configuration from a large number of candidate arrays. We firstly designed sparse arrays by using a genetic algorithm, but found that the arrays have poor performance and poor consistency. So, a method based on the Minimum Redundancy Linear Array was then adopted. Some elements are determined by the minimum-redundancy array firstly in order to ensure spatial resolution and then a genetic algorithm is used to optimize the remaining elements. Sparse arrays designed by this method have much better performance and consistency compared to the arrays designed only by a genetic algorithm. Both simulation and experiment confirm the effectiveness.

  17. Determination of wave direction from linear and polygonal arrays

    Fernandes, A.A; Gouveia, A; Nagarajan, R.

    documentation of Borgman (1974) in case of linear arrays; and the second issue being the failure of Esteva (1976, 1977) to correctly determine wave directions over the design range 25 to 7 sec of his polygonal array. This paper presents requisite documentation...

  18. Multispectral linear array (MLA) focal plane mechanical and thermal design

    Mitchell, A. S.; Kaminski, E. F.

    1982-01-01

    The mechanical and thermal design of an integrated focal plane subsystem of a Multispectral Linear Array (MLA) instrument is discussed in terms of focal-plane alignment, thermoelastic performance, and thermal requirements. The modular construction and thermal control of the focal plane array are discussed.

  19. Fiber optic spectrophotometer with photodiode linear array

    Blanc, F.; Vernet, P.

    1988-01-01

    Spectrophotometric measurements are used in a great number of industrial processes, in nuclear environment and with optical precision components. Especially the evolution of a chemical process or of an optical coating could be followed by these measurements. Spectrophotometers, using optical fibers to transport the signal out of the instrument make possible the measurement ''in-situ'' and in real time. The advantage of using a diode array to detect the signal is an instantaneous measurement all over the spectral range without moving parts. It allows an excellent reproductibility. The instrument is controlled by a micro computer. The spectrophotometer is described and technical performance presented. An extension using optical fibers on a ''classical'' spectrophotometer (a H.P. one) is also described and technical performance presented

  20. Linear complexity for multidimensional arrays - a numerical invariant

    Gomez-Perez, Domingo; Høholdt, Tom; Moreno, Oscar

    2015-01-01

    Linear complexity is a measure of how complex a one dimensional sequence can be. In this paper we extend the concept of linear complexity to multiple dimensions and present a definition that is invariant under well-orderings of the arrays. As a result we find that our new definition for the proce...

  1. Characterization of Kerfless Linear Arrays Based on PZT Thick Film.

    Zawada, Tomasz; Bierregaard, Louise Moller; Ringgaard, Erling; Xu, Ruichao; Guizzetti, Michele; Levassort, Franck; Certon, Dominique

    2017-09-01

    Multielement transducers enabling novel cost-effective fabrication of imaging arrays for medical applications have been presented earlier. Due to the favorable low lateral coupling of the screen-printed PZT, the elements can be defined by the top electrode pattern only, leading to a kerfless design with low crosstalk between the elements. The thick-film-based linear arrays have proved to be compatible with a commercial ultrasonic scanner and to support linear array beamforming as well as phased array beamforming. The main objective of the presented work is to investigate the performance of the devices at the transducer level by extensive measurements of the test structures. The arrays have been characterized by several different measurement techniques. First, electrical impedance measurements on several elements in air and liquid have been conducted in order to support material parameter identification using the Krimholtz-Leedom-Matthaei model. It has been found that electromechanical coupling is at the level of 35%. The arrays have also been characterized by a pulse-echo system. The measured sensitivity is around -60 dB, and the fractional bandwidth is close to 60%, while the center frequency is about 12 MHz over the whole array. Finally, laser interferometry measurements have been conducted indicating very good displacement level as well as pressure. The in-depth characterization of the array structure has given insight into the performance parameters for the array based on PZT thick film, and the obtained information will be used to optimize the key parameters for the next generation of cost-effective arrays based on piezoelectric thick film.

  2. Nucleosome Positioning and Epigenetics

    Schwab, David; Bruinsma, Robijn

    2008-03-01

    The role of chromatin structure in gene regulation has recently taken center stage in the field of epigenetics, phenomena that change the phenotype without changing the DNA sequence. Recent work has also shown that nucleosomes, a complex of DNA wrapped around a histone octamer, experience a sequence dependent energy landscape due to the variation in DNA bend stiffness with sequence composition. In this talk, we consider the role nucleosome positioning might play in the formation of heterochromatin, a compact form of DNA generically responsible for gene silencing. In particular, we discuss how different patterns of nucleosome positions, periodic or random, could either facilitate or suppress heterochromatin stability and formation.

  3. Electromagnetic linear machines with dual Halbach array design and analysis

    Yan, Liang; Peng, Juanjuan; Zhang, Lei; Jiao, Zongxia

    2017-01-01

    This book extends the conventional two-dimensional (2D) magnet arrangement into 3D pattern for permanent magnet linear machines for the first time, and proposes a novel dual Halbach array. It can not only effectively increase the radial component of magnetic flux density and output force of tubular linear machines, but also significantly reduce the axial flux density, radial force and thus system vibrations and noises. The book is also the first to address the fundamentals and provide a summary of conventional arrays, as well as novel concepts for PM pole design in electric linear machines. It covers theoretical study, numerical simulation, design optimization and experimental works systematically. The design concept and analytical approaches can be implemented to other linear and rotary machines with similar structures. The book will be of interest to academics, researchers, R&D engineers and graduate students in electronic engineering and mechanical engineering who wish to learn the core principles, met...

  4. Design and Analysis of MEMS Linear Phased Array

    Guoxiang Fan

    2016-01-01

    Full Text Available A structure of micro-electro-mechanical system (MEMS linear phased array based on “multi-cell” element is designed to increase radiation sound pressure of transducer working in bending vibration mode at high frequency. In order to more accurately predict the resonant frequency of an element, the theoretical analysis of the dynamic equation of a fixed rectangular composite plate and finite element method simulation are adopted. The effects of the parameters both in the lateral and elevation direction on the three-dimensional beam directivity characteristics are comprehensively analyzed. The key parameters in the analysis include the “cell” number of element, “cell” size, “inter-cell” spacing and the number of elements, element width. The simulation results show that optimizing the linear array parameters both in the lateral and elevation direction can greatly improve the three-dimensional beam focusing for MEMS linear phased array, which is obviously different from the traditional linear array.

  5. Penalized Estimation in Large-Scale Generalized Linear Array Models

    Lund, Adam; Vincent, Martin; Hansen, Niels Richard

    2017-01-01

    Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension...

  6. Position sensor for linear synchronous motors employing halbach arrays

    Post, Richard Freeman

    2014-12-23

    A position sensor suitable for use in linear synchronous motor (LSM) drive systems employing Halbach arrays to create their magnetic fields is described. The system has several advantages over previously employed ones, especially in its simplicity and its freedom from being affected by weather conditions, accumulated dirt, or electrical interference from the LSM system itself.

  7. Baculoviruses and nucleosome management

    Volkman, Loy E.

    2015-01-01

    Negatively-supercoiled-ds DNA molecules, including the genomes of baculoviruses, spontaneously wrap around cores of histones to form nucleosomes when present within eukaryotic nuclei. Hence, nucleosome management should be essential for baculovirus genome replication and temporal regulation of transcription, but this has not been documented. Nucleosome mobilization is the dominion of ATP-dependent chromatin-remodeling complexes. SWI/SNF and INO80, two of the best-studied complexes, as well as chromatin modifier TIP60, all contain actin as a subunit. Retrospective analysis of results of AcMNPV time course experiments wherein actin polymerization was blocked by cytochalasin D drug treatment implicate actin-containing chromatin modifying complexes in decatenating baculovirus genomes, shutting down host transcription, and regulating late and very late phases of viral transcription. Moreover, virus-mediated nuclear localization of actin early during infection may contribute to nucleosome management. - Highlights: • Baculoviruses have negatively-supercoiled, circular ds DNA. • Negatively-supercoiled DNA spontaneously forms nucleosomes in the nucleus. • Nucleosomes must be mobilized for replication and transcription to proceed. • Actin-containing chromatin modifiers participate in baculovirus replication

  8. Baculoviruses and nucleosome management

    Volkman, Loy E., E-mail: lvolkman@berkeley.edu

    2015-02-15

    Negatively-supercoiled-ds DNA molecules, including the genomes of baculoviruses, spontaneously wrap around cores of histones to form nucleosomes when present within eukaryotic nuclei. Hence, nucleosome management should be essential for baculovirus genome replication and temporal regulation of transcription, but this has not been documented. Nucleosome mobilization is the dominion of ATP-dependent chromatin-remodeling complexes. SWI/SNF and INO80, two of the best-studied complexes, as well as chromatin modifier TIP60, all contain actin as a subunit. Retrospective analysis of results of AcMNPV time course experiments wherein actin polymerization was blocked by cytochalasin D drug treatment implicate actin-containing chromatin modifying complexes in decatenating baculovirus genomes, shutting down host transcription, and regulating late and very late phases of viral transcription. Moreover, virus-mediated nuclear localization of actin early during infection may contribute to nucleosome management. - Highlights: • Baculoviruses have negatively-supercoiled, circular ds DNA. • Negatively-supercoiled DNA spontaneously forms nucleosomes in the nucleus. • Nucleosomes must be mobilized for replication and transcription to proceed. • Actin-containing chromatin modifiers participate in baculovirus replication.

  9. Very high frequency (beyond 100 MHz) PZT kerfless linear arrays.

    Wu, Da-Wei; Zhou, Qifa; Geng, Xuecang; Liu, Chang-Geng; Djuth, Frank; Shung, K Kirk

    2009-10-01

    This paper presents the design, fabrication, and measurements of very high frequency kerfless linear arrays prepared from PZT film and PZT bulk material. A 12-microm PZT thick film fabricated from PZT-5H powder/solution composite and a piece of 15-microm PZT-5H sheet were used to fabricate 32-element kerfless high-frequency linear arrays with photolithography. The PZT thick film was prepared by spin-coating of PZT sol-gel composite solution. The thin PZT-5H sheet sample was prepared by lapping a PZT-5H ceramic with a precision lapping machine. The measured results of the 2 arrays were compared. The PZT film array had a center frequency of 120 MHz, a bandwidth of 60% with a parylene matching layer, and an insertion loss of 41 dB. The PZT ceramic sheet array was found to have a center frequency of 128 MHz with a poorer bandwidth (40% with a parylene matching layer) but a better sensitivity (28 dB insertion loss).

  10. Linear micromechanical stepping drive for pinhole array positioning

    Endrödy, Csaba; Mehner, Hannes; Hoffmann, Martin; Grewe, Adrian

    2015-01-01

    A compact linear micromechanical stepping drive for positioning a 7 × 5.5 mm 2 optical pinhole array is presented. The system features a step size of 13.2 µm and a full displacement range of 200 µm. The electrostatic inch-worm stepping mechanism shows a compact design capable of positioning a payload 50% of its own weight. The stepping drive movement, step sizes and position accuracy are characterized. The actuated pinhole array is integrated in a confocal chromatic hyperspectral imaging system, where coverage of the object plane, and therefore the useful picture data, can be multiplied by 14 in contrast to a non-actuated array. (paper)

  11. An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions.

    Yanping Fan

    Full Text Available In the eukaryotic cell nucleus, DNA exists as chromatin, a compact but dynamic complex with histone proteins. The first level of DNA organization is the linear array of nucleosome core particles (NCPs. The NCP is a well-defined complex of 147 bp DNA with an octamer of histones. Interactions between NCPs are of paramount importance for higher levels of chromatin compaction. The polyelectrolyte nature of the NCP implies that nucleosome-nucleosome interactions must exhibit a great influence from both the ionic environment as well as the positively charged and highly flexible N-terminal histone tails, protruding out from the NCP. The large size of the system precludes a modelling analysis of chromatin at an all-atom level and calls for coarse-grained approximations. Here, a model of the NCP that include the globular histone core and the flexible histone tails described by one particle per each amino acid and taking into account their net charge is proposed. DNA wrapped around the histone core was approximated at the level of two base pairs represented by one bead (bases and sugar plus four beads of charged phosphate groups. Computer simulations, using a Langevin thermostat, in a dielectric continuum with explicit monovalent (K(+, divalent (Mg(2+ or trivalent (Co(NH(3(6 (3+ cations were performed for systems with one or ten NCPs. Increase of the counterion charge results in a switch from repulsive NCP-NCP interaction in the presence of K(+, to partial aggregation with Mg(2+ and to strong mutual attraction of all 10 NCPs in the presence of CoHex(3+. The new model reproduced experimental results and the structure of the NCP-NCP contacts is in agreement with available data. Cation screening, ion-ion correlations and tail bridging contribute to the NCP-NCP attraction and the new NCP model accounts for these interactions.

  12. Spatial Signature Estimation with an Uncalibrated Uniform Linear Array

    Xiang Cao

    2015-06-01

    Full Text Available In this paper, the problem of spatial signature estimation using a uniform linear array (ULA with unknown sensor gain and phase errors is considered. As is well known, the directions-of-arrival (DOAs can only be determined within an unknown rotational angle in this array model. However, the phase ambiguity has no impact on the identification of the spatial signature. Two auto-calibration methods are presented for spatial signature estimation. In our methods, the rotational DOAs and model error parameters are firstly obtained, and the spatial signature is subsequently calculated. The first method extracts two subarrays from the ULA to construct an estimator, and the elements of the array can be used several times in one subarray. The other fully exploits multiple invariances in the interior of the sensor array, and a multidimensional nonlinear problem is formulated. A Gauss–Newton iterative algorithm is applied for solving it. The first method can provide excellent initial inputs for the second one. The effectiveness of the proposed algorithms is demonstrated by several simulation results.

  13. Low-redundancy linear arrays in mirrored interferometric aperture synthesis.

    Zhu, Dong; Hu, Fei; Wu, Liang; Li, Jun; Lang, Liang

    2016-01-15

    Mirrored interferometric aperture synthesis (MIAS) is a novel interferometry that can improve spatial resolution compared with that of conventional IAS. In one-dimensional (1-D) MIAS, antenna array with low redundancy has the potential to achieve a high spatial resolution. This Letter presents a technique for the direct construction of low-redundancy linear arrays (LRLAs) in MIAS and derives two regular analytical patterns that can yield various LRLAs in short computation time. Moreover, for a better estimation of the observed scene, a bi-measurement method is proposed to handle the rank defect associated with the transmatrix of those LRLAs. The results of imaging simulation demonstrate the effectiveness of the proposed method.

  14. Logical Qubit in a Linear Array of Semiconductor Quantum Dots

    Cody Jones

    2018-06-01

    Full Text Available We design a logical qubit consisting of a linear array of quantum dots, we analyze error correction for this linear architecture, and we propose a sequence of experiments to demonstrate components of the logical qubit on near-term devices. To avoid the difficulty of fully controlling a two-dimensional array of dots, we adapt spin control and error correction to a one-dimensional line of silicon quantum dots. Control speed and efficiency are maintained via a scheme in which electron spin states are controlled globally using broadband microwave pulses for magnetic resonance, while two-qubit gates are provided by local electrical control of the exchange interaction between neighboring dots. Error correction with two-, three-, and four-qubit codes is adapted to a linear chain of qubits with nearest-neighbor gates. We estimate an error correction threshold of 10^{-4}. Furthermore, we describe a sequence of experiments to validate the methods on near-term devices starting from four coupled dots.

  15. Wake Vortex Detection: Phased Microphone vs. Linear Infrasonic Array

    Shams, Qamar A.; Zuckerwar, Allan J.; Sullivan, Nicholas T.; Knight, Howard K.

    2014-01-01

    infrasonic array at the Newport News-Williamsburg International Airport early in the year 2013. A pattern of pressure burst, high-coherence intervals, and diminishing-coherence intervals was observed for all takeoff and landing events without exception. The results of a phased microphone vs. linear infrasonic array comparison will be presented.

  16. A 128 pixel linear array for radiotherapy quality assurance

    Franco, L. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain); Gomez, F. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain)]. E-mail: faustgr@usc.es; Iglesias, A. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain); Lobato, R. [Hospital Clinico Universitario de Santiago, 15706 Santiago (Spain); Marin, J. [CIEMAT, Laboratorio de Electronica y Automatica, 28040 Madrid Spain (Spain); Mosquera, J. [Hospital Clinico Universitario de Santiago, 15706 Santiago (Spain); Pardo, J. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain)]. E-mail: juanpm@usc.es; Pazos, A. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain); Pena, J. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain); Pombar, M. [Hospital Clinico Universitario de Santiago, 15706 Santiago (Spain); Rodriguez, A. [Departmento de Fisica de Particulas, Facultade de Fisica, Universidade de Santiago, campus sur s/n, 15782 Santiago de Compostela (Spain); Saavedra, D. [Universidade da Coruna, Dpto. de Enxeneria Industrial II, 15403 Ferrol Spain (Spain); Sendon, J. [Hospital Clinico Universitario de Santiago, 15706 Santiago (Spain); Yanez, A. [Universidade da Coruna, Dpto. de Enxeneria Industrial II, 15403 Ferrol Spain (Spain)

    2004-12-11

    New radiotherapy techniques require detectors able to verify and monitor the clinical beam with high spatial resolution and fast response. Room temperature organic liquid ionization detectors are becoming an alternative to standard air ionization chambers, due to their tissue equivalent behavior, their sensibility and small directional dependence. A liquid isooctane filled ionization linear array for radiotherapy quality assurance has been designed, built and tested. The detector consists of 128 pixels, each of them with an area of 1.7mmx1.7mm and a gap of 0.5mm. The small pixel size makes the detector ideal for high gradient beam profiles like those present in Intensity Modulated Radiation Therapy. The gap and the polarization voltage have been chosen in order to guarantee a linear relationship between the dose rate and the readout signal at high dose rates. As readout electronics we use the X-ray Data Acquisition System with the Xchip developed by the CCLRC.In the first device tests we have confirmed linearity up to a 6.7Gy/min dose rate with a deviation less than 1%. A profile with a signal-to-noise ratio around 500 can be obtained for a 4Gy/min dose rate with a 10 ms integration time.

  17. A 128 pixel linear array for radiotherapy quality assurance

    Franco, L.; Gomez, F.; Iglesias, A.; Lobato, R.; Marin, J.; Mosquera, J.; Pardo, J.; Pazos, A.; Pena, J.; Pombar, M.; Rodriguez, A.; Saavedra, D.; Sendon, J.; Yanez, A.

    2004-01-01

    New radiotherapy techniques require detectors able to verify and monitor the clinical beam with high spatial resolution and fast response. Room temperature organic liquid ionization detectors are becoming an alternative to standard air ionization chambers, due to their tissue equivalent behavior, their sensibility and small directional dependence. A liquid isooctane filled ionization linear array for radiotherapy quality assurance has been designed, built and tested. The detector consists of 128 pixels, each of them with an area of 1.7mmx1.7mm and a gap of 0.5mm. The small pixel size makes the detector ideal for high gradient beam profiles like those present in Intensity Modulated Radiation Therapy. The gap and the polarization voltage have been chosen in order to guarantee a linear relationship between the dose rate and the readout signal at high dose rates. As readout electronics we use the X-ray Data Acquisition System with the Xchip developed by the CCLRC.In the first device tests we have confirmed linearity up to a 6.7Gy/min dose rate with a deviation less than 1%. A profile with a signal-to-noise ratio around 500 can be obtained for a 4Gy/min dose rate with a 10 ms integration time

  18. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  19. Comparison of heating deposition patterns for stacked linear phased array and fixed focus ultrasonic hyperthermia applicators

    Ocheltree, K.B.; Benkeser, P.J.; Frizzell, L.A.; Cain, C.A.

    1985-01-01

    An ultrasonic stacked linear phased array applicator for hyperthermia has been designed to heat tumors at depths from 5 to 10 cm. The power deposition pattern for this applicator is compared to that for a fixed focus applicator for several different scan paths. The power deposition pattern for the stacked linear phased array shows hot spots that are not observed for the mechanically scanned fixed focus applicator. These hot spots are related to the skewed power deposition pattern resulting from scanning the focus off the center of the linear arrays. The overall performance of the stacked linear phased array applicator is compared to that of a fixed focus applicator

  20. Enhanced linear-array photoacoustic beamforming using modified coherence factor.

    Mozaffarzadeh, Moein; Yan, Yan; Mehrmohammadi, Mohammad; Makkiabadi, Bahador

    2018-02-01

    Photoacoustic imaging (PAI) is a promising medical imaging modality providing the spatial resolution of ultrasound imaging and the contrast of optical imaging. For linear-array PAI, a beamformer can be used as the reconstruction algorithm. Delay-and-sum (DAS) is the most prevalent beamforming algorithm in PAI. However, using DAS beamformer leads to low-resolution images as well as high sidelobes due to nondesired contribution of off-axis signals. Coherence factor (CF) is a weighting method in which each pixel of the reconstructed image is weighted, based on the spatial spectrum of the aperture, to mainly improve the contrast. We demonstrate that the numerator of the formula of CF contains a DAS algebra and propose the use of a delay-multiply-and-sum beamformer instead of the available DAS on the numerator. The proposed weighting technique, modified CF (MCF), has been evaluated numerically and experimentally compared to CF. It was shown that MCF leads to lower sidelobes and better detectable targets. The quantitative results of the experiment (using wire targets) show that MCF leads to for about 45% and 40% improvement, in comparison with CF, in the terms of signal-to-noise ratio and full-width-half-maximum, respectively. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  1. Enhanced linear-array photoacoustic beamforming using modified coherence factor

    Mozaffarzadeh, Moein; Yan, Yan; Mehrmohammadi, Mohammad; Makkiabadi, Bahador

    2018-02-01

    Photoacoustic imaging (PAI) is a promising medical imaging modality providing the spatial resolution of ultrasound imaging and the contrast of optical imaging. For linear-array PAI, a beamformer can be used as the reconstruction algorithm. Delay-and-sum (DAS) is the most prevalent beamforming algorithm in PAI. However, using DAS beamformer leads to low-resolution images as well as high sidelobes due to nondesired contribution of off-axis signals. Coherence factor (CF) is a weighting method in which each pixel of the reconstructed image is weighted, based on the spatial spectrum of the aperture, to mainly improve the contrast. We demonstrate that the numerator of the formula of CF contains a DAS algebra and propose the use of a delay-multiply-and-sum beamformer instead of the available DAS on the numerator. The proposed weighting technique, modified CF (MCF), has been evaluated numerically and experimentally compared to CF. It was shown that MCF leads to lower sidelobes and better detectable targets. The quantitative results of the experiment (using wire targets) show that MCF leads to for about 45% and 40% improvement, in comparison with CF, in the terms of signal-to-noise ratio and full-width-half-maximum, respectively.

  2. G+C content dominates intrinsic nucleosome occupancy

    Hughes Timothy R

    2009-12-01

    Full Text Available Abstract Background The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences. Results We find that a simple linear combination of only 14 simple DNA sequence attributes (G+C content, two transformations of dinucleotide composition, and the frequency of eleven 4-bp sequences explains nucleosome occupancy in vitro and in vivo in a manner comparable to the Kaplan model. G+C content and frequency of AAAA are the most important features. G+C content is dominant, alone explaining ~50% of the variation in nucleosome occupancy in vitro. Conclusions Our findings provide a dramatically simplified means to predict and understand intrinsic nucleosome occupancy. G+C content may dominate because it both reduces frequency of poly-A-like stretches and correlates with many other DNA structural characteristics. Since G+C content is enriched or depleted at many types of features in diverse eukaryotic genomes, our results suggest that variation in nucleotide composition may have a widespread and direct influence on chromatin structure.

  3. An in vitro-identified high-affinity nucleosome-positioning signal is capable of transiently positioning a nucleosome in vivo

    Gracey Lia E

    2010-07-01

    Full Text Available Abstract Background The physiological function of eukaryotic DNA occurs in the context of nucleosomal arrays that can expose or obscure defined segments of the genome. Certain DNA sequences are capable of strongly positioning a nucleosome in vitro, suggesting the possibility that favorable intrinsic signals might reproducibly structure chromatin segments. As high-throughput sequencing analyses of nucleosome coverage in vitro and in vivo have become possible, a vigorous debate has arisen over the degree to which intrinsic DNA:nucleosome affinities orchestrate the in vivo positions of nucleosomes, thereby controlling physical accessibility of specific sequences in DNA. Results We describe here the in vivo consequences of placing a synthetic high-affinity nucleosome-positioning signal, the 601 sequence, into a DNA plasmid vector in mice. Strikingly, the 601 sequence was sufficient to position nucleosomes during an early phase after introduction of the DNA into the mice (when the plasmid vector transgene was active. This positioning capability was transient, with a loss of strong positioning at a later time point when the transgenes had become silent. Conclusions These results demonstrate an ability of DNA sequences selected solely for nucleosome affinity to organize chromatin in vivo, and the ability of other mechanisms to overcome these interactions in a dynamic nuclear environment.

  4. Comparison of Thrust Characteristics in Pencil Sized Cylinder-type Linear Motors with Different Magnet Arrays

    Nakaiwa, K; Yamada, A; Tashiro, K; Wakiwaka, H

    2009-01-01

    From a strong demand on the miniaturization of a chip mounter or a semiconductor device, the thrust improvement considering the magnets arrangement is studied. We accept a core stator with a Halbach type magnet array for a current linear motor. The thrust characteristics are compared with two kinds of mover, a NS magnet array and a Halbach magnet array.

  5. Optimal array factor radiation pattern synthesis for linear antenna array using cat swarm optimization: validation by an electromagnetic simulator

    Gopi RAM; Durbadal MANDAL; Sakti Prasad GHOSHAL; Rajib KAR

    2017-01-01

    In this paper, an optimal design of linear antenna arrays having microstrip patch antenna elements has been carried out. Cat swarm optimization (CSO) has been applied for the optimization of the control parameters of radiation pattern of an antenna array. The optimal radiation patterns of isotropic antenna elements are obtained by optimizing the current excitation weight of each element and the inter-element spacing. The antenna arrays of 12, 16, and 20 elements are taken as examples. The arrays are de-signed by using MATLAB computation and are validated through Computer Simulation Technology-Microwave Studio (CST-MWS). From the simulation results it is evident that CSO is able to yield the optimal design of linear antenna arrays of patch antenna elements.

  6. Active cancellation of probing in linear dipole phased array

    Singh, Hema; Jha, Rakesh Mohan

    2015-01-01

    In this book, a modified improved LMS algorithm is employed for weight adaptation of dipole array for the generation of beam pattern in multiple signal environments. In phased arrays, the generation of adapted pattern according to the signal scenario requires an efficient adaptive algorithm. The antenna array is expected to maintain sufficient gain towards each of the desired source while at the same time suppress the probing sources. This cancels the signal transmission towards each of the hostile probing sources leading to active cancellation. In the book, the performance of dipole phased array is demonstrated in terms of fast convergence, output noise power and output signal-to-interference-and noise ratio. The mutual coupling effect and role of edge elements are taken into account. It is established that dipole array along with an efficient algorithm is able to maintain multilobe beamforming with accurate and deep nulls towards each probing source. This work has application to the active radar cross secti...

  7. Assessment of the Roche Linear Array HPV Genotyping Test within the VALGENT framework.

    Xu, Lan; Oštrbenk, Anja; Poljak, Mario; Arbyn, Marc

    2018-01-01

    Cervical cancer screening programs are switching from cytology-based screening to high-risk (hr) HPV testing. Only clinically validated tests should be used in clinical practice. To assess the clinical performance of the Roche Linear Array HPV genotyping test (Linear Array) within the VALGENT-3 framework. The VALGENT framework is designed for comprehensive comparison and clinical validation of HPV tests that have limited to extended genotyping capacity. The Linear Array enables type-specific detection of 37 HPV types. For the purpose of this study, Linear Array results were designated as positive only if one of the 13 hrHPV types also included in the Hybrid Capture 2 (HC2) was detected. The VALGENT-3 framework comprised 1600 samples obtained from Slovenian women (1300 sequential cases from routine cervical cancer screening enriched with 300 cytological abnormal samples). Sensitivity for cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) (n=127) and specificity for Linear Array and for HC2 and non-inferiority of Linear Array relative to HC2 was checked. In addition, the prevalence of separate hrHPV types in the screening population, as well as the concordance for presence of HPV16, HPV18 and other hrHPV types between Linear Array and the Abbott RealTime High Risk HPV test (RealTime) were assessed. The clinical sensitivity and specificity for CIN2+ of the Linear Array in the total study population was 97.6% (95% CI, 93.3-99.5%) and 91.7% (95% CI, 90.0-93.2%), respectively. The relative sensitivity and specificity of Linear Array vs HC2 was 1.02 [95% CI, 0.98-1.05, (pLinear Array in the screening population was 10.5% (95% CI, 8.9-12.3%) with HPV16 and HPV18 detected in 2.3% and 0.9% of the samples, respectively. Excellent agreement for presence or absence of HPV16, HPV18 and other hrHPV between Linear Array and RealTime was observed. Linear Array showed similar sensitivity with higher specificity to detect CIN2+ compared to HC2. Detection of 13 hrHPV types

  8. Finding Traps in Non-linear Spin Arrays

    Wiesniak, Marcin; Markiewicz, Marcin

    2009-01-01

    Precise knowledge of the Hamiltonian of a system is a key to many of its applications. Tasks such state transfer or quantum computation have been well studied with a linear chain, but hardly with systems, which do not possess a linear structure. While this difference does not disturb the end-to-end dynamics of a single excitation, the evolution is significantly changed in other subspaces. Here we quantify the difference between a linear chain and a pseudo-chain, which have more than one spin ...

  9. Compression dynamics of quasi-spherical wire arrays with different linear mass profiles

    Mitrofanov, K. N.; Aleksandrov, V. V.; Gritsuk, A. N.; Grabovski, E. V.; Frolov, I. N.; Laukhin, Ya. N.; Oleinik, G. M.; Ol’khovskaya, O. G.

    2016-01-01

    Results of experimental studies of the implosion of quasi-spherical wire (or metalized fiber) arrays are presented. The goal of the experiments was to achieve synchronous three-dimensional compression of the plasma produced in different regions of a quasi-spherical array into its geometrical center. To search for optimal synchronization conditions, quasi-spherical arrays with different initial profiles of the linear mass were used. The following dependences of the linear mass on the poloidal angle were used: m_l(θ) ∝ sin"–"1θ and m_l(θ) ∝ sin"–"2θ. The compression dynamics of such arrays was compared with that of quasi-spherical arrays without linear mass profiling, m_l(θ) = const. To verify the experimental data, the spatiotemporal dynamics of plasma compression in quasi-spherical arrays was studied using various diagnostics. The experiments on three-dimensional implosion of quasi-spherical arrays made it possible to study how the frozen-in magnetic field of the discharge current penetrates into the array. By measuring the magnetic field in the plasma of a quasi-spherical array, information is obtained on the processes of plasma production and formation of plasma flows from the wire/fiber regions with and without an additionally deposited mass. It is found that penetration of the magnetic flux depends on the initial linear mass profile m_l(θ) of the quasi-spherical array. From space-resolved spectral measurements and frame imaging of plasma X-ray emission, information is obtained on the dimensions and shape of the X-ray source formed during the implosion of a quasi-spherical array. The intensity of this source is estimated and compared with that of the Z-pinch formed during the implosion of a cylindrical array.

  10. Nucleosome Organization in Human Embryonic Stem Cells.

    Puya G Yazdi

    Full Text Available The fundamental repeating unit of eukaryotic chromatin is the nucleosome. Besides being involved in packaging DNA, nucleosome organization plays an important role in transcriptional regulation and cellular identity. Currently, there is much debate about the major determinants of the nucleosome architecture of a genome and its significance with little being known about its role in stem cells. To address these questions, we performed ultra-deep sequencing of nucleosomal DNA in two human embryonic stem cell lines and integrated our data with numerous epigenomic maps. Our analyses have revealed that the genome is a determinant of nucleosome organization with transcriptionally inactive regions characterized by a "ground state" of nucleosome profiles driven by underlying DNA sequences. DNA sequence preferences are associated with heterogeneous chromatin organization around transcription start sites. Transcription, histone modifications, and DNA methylation alter this "ground state" by having distinct effects on both nucleosome positioning and occupancy. As the transcriptional rate increases, nucleosomes become better positioned. Exons transcribed and included in the final spliced mRNA have distinct nucleosome profiles in comparison to exons not included at exon-exon junctions. Genes marked by the active modification H3K4m3 are characterized by lower nucleosome occupancy before the transcription start site compared to genes marked by the inactive modification H3K27m3, while bivalent domains, genes associated with both marks, lie exactly in the middle. Combinatorial patterns of epigenetic marks (chromatin states are associated with unique nucleosome profiles. Nucleosome organization varies around transcription factor binding in enhancers versus promoters. DNA methylation is associated with increasing nucleosome occupancy and different types of methylations have distinct location preferences within the nucleosome core particle. Finally, computational

  11. Pattern Synthesis of Dual-band Shared Aperture Interleaved Linear Antenna Arrays

    H. Guo

    2014-09-01

    Full Text Available This paper presents an approach to improve the efficiency of an array aperture by interleaving two different arrays in the same aperture area. Two sub-arrays working at different frequencies are interleaved in the same linear aperture area. The available aperture area is efficiently used. The element positions of antenna array are optimized by using Invasive Weed Optimization (IWO to reduce the peak side lobe level (PSLL of the radiation pattern. To overcome the shortness of traditional methods which can only fulfill the design of shared aperture antenna array working at the same frequency, this method can achieve the design of dual-band antenna array with wide working frequency range. Simulation results show that the proposed method is feasible and efficient in the synthesis of dual-band shared aperture antenna array.

  12. RCS estimation of linear and planar dipole phased arrays approximate model

    Singh, Hema; Jha, Rakesh Mohan

    2016-01-01

    In this book, the RCS of a parallel-fed linear and planar dipole array is derived using an approximate method. The signal propagation within the phased array system determines the radar cross section (RCS) of phased array. The reflection and transmission coefficients for a signal at different levels of the phased-in scattering array system depend on the impedance mismatch and the design parameters. Moreover the mutual coupling effect in between the antenna elements is an important factor. A phased array system comprises of radiating elements followed by phase shifters, couplers, and terminating load impedance. These components lead to respective impedances towards the incoming signal that travels through them before reaching receive port of the array system. In this book, the RCS is approximated in terms of array factor, neglecting the phase terms. The mutual coupling effect is taken into account. The dependence of the RCS pattern on the design parameters is analyzed. The approximate model is established as a...

  13. Voltage splay modes and enhanced phase locking in a modified linear Josephson array

    Harris, E. B.; Garland, J. C.

    1997-02-01

    We analyze a modified linear Josephson-junction array in which additional unbiased junctions are used to greatly enhance phase locking. This geometry exhibits strong correlated behavior, with an external magnetic field tuning the voltage splay angle between adjacent Josephson oscillators. The array displays a coherent in-phase mode for f=, where f is the magnetic frustration, while for 0tolerant of critical current disorder approaching 100%. The stability of the array has also been studied by computing Floquet exponents. These exponents are found to be negative for all array lengths, with a 1/N2 dependence, N being the number of series-connected junctions.

  14. Micro-machined high-frequency (80 MHz) PZT thick film linear arrays.

    Zhou, Qifa; Wu, Dawei; Liu, Changgeng; Zhu, Benpeng; Djuth, Frank; Shung, K

    2010-10-01

    This paper presents the development of a micromachined high-frequency linear array using PZT piezoelectric thick films. The linear array has 32 elements with an element width of 24 μm and an element length of 4 mm. Array elements were fabricated by deep reactive ion etching of PZT thick films, which were prepared from spin-coating of PZT sol-gel composite. Detailed fabrication processes, especially PZT thick film etching conditions and a novel transferring-and-etching method, are presented and discussed. Array designs were evaluated by simulation. Experimental measurements show that the array had a center frequency of 80 MHz and a fractional bandwidth (-6 dB) of 60%. An insertion loss of -41 dB and adjacent element crosstalk of -21 dB were found at the center frequency.

  15. Weighted thinned linear array design with the iterative FFT technique

    Du Plessis, WP

    2011-09-01

    Full Text Available techniques utilise simulated annealing [3]?[5], [10], mixed integer linear programming [7], genetic algorithms [9], and a hyrid approach combining a genetic algorithm and a local optimiser [8]. The iterative Fourier technique (IFT) developed by Keizer [2... algorithm being well- suited to obtaining low CTRs. Test problems from the literature are considered, and the results obtained with the IFT considerably exceed those achieved with other algorithms. II. DESCRIPTION OF THE ALGORITHM A flowchart describing...

  16. The size of the nucleosome

    Bohr, Jakob; Olsen, Kasper

    2011-01-01

    is a necessity when allowing for transient tensile stresses during the reorganization of DNA, e.g., during the reposition, or sliding, of a nucleosome along the DNA double helix. The mathematical model we apply is based on a tubular description of double helices assuming hard walls. When the base...

  17. Isotropic-resolution linear-array-based photoacoustic computed tomography through inverse Radon transform

    Li, Guo; Xia, Jun; Li, Lei; Wang, Lidai; Wang, Lihong V.

    2015-03-01

    Linear transducer arrays are readily available for ultrasonic detection in photoacoustic computed tomography. They offer low cost, hand-held convenience, and conventional ultrasonic imaging. However, the elevational resolution of linear transducer arrays, which is usually determined by the weak focus of the cylindrical acoustic lens, is about one order of magnitude worse than the in-plane axial and lateral spatial resolutions. Therefore, conventional linear scanning along the elevational direction cannot provide high-quality three-dimensional photoacoustic images due to the anisotropic spatial resolutions. Here we propose an innovative method to achieve isotropic resolutions for three-dimensional photoacoustic images through combined linear and rotational scanning. In each scan step, we first elevationally scan the linear transducer array, and then rotate the linear transducer array along its center in small steps, and scan again until 180 degrees have been covered. To reconstruct isotropic three-dimensional images from the multiple-directional scanning dataset, we use the standard inverse Radon transform originating from X-ray CT. We acquired a three-dimensional microsphere phantom image through the inverse Radon transform method and compared it with a single-elevational-scan three-dimensional image. The comparison shows that our method improves the elevational resolution by up to one order of magnitude, approaching the in-plane lateral-direction resolution. In vivo rat images were also acquired.

  18. 5G antenna array with wide-angle beam steering and dual linear polarizations

    Klionovski, Kirill; Shamim, Atif; Sharawi, Mohammad Said

    2017-01-01

    In this paper, we present the design of a switched-beam antenna array at millimeter-wave frequencies for future 5G applications. The proposed antenna array is based on wideband patch antenna elements and a Butler matrix feed network. The patch antenna has a broad radiation pattern for wide-angle beam steering and allows the simultaneous operation with two orthogonal linear polarizations. A combination of two separated Butler matrices provides independent beam steering for both polarizations in the wide operating band. The antenna array has a simple multilayer construction, and it is made on a low-cost Rogers laminate.

  19. 5G antenna array with wide-angle beam steering and dual linear polarizations

    Klionovski, Kirill

    2017-10-25

    In this paper, we present the design of a switched-beam antenna array at millimeter-wave frequencies for future 5G applications. The proposed antenna array is based on wideband patch antenna elements and a Butler matrix feed network. The patch antenna has a broad radiation pattern for wide-angle beam steering and allows the simultaneous operation with two orthogonal linear polarizations. A combination of two separated Butler matrices provides independent beam steering for both polarizations in the wide operating band. The antenna array has a simple multilayer construction, and it is made on a low-cost Rogers laminate.

  20. New fabrication of high-frequency (100-MHz) ultrasound PZT film kerfless linear array.

    Zhu, Benpeng; Chan, Ngai Yui; Dai, Jiyan; Shung, K Kirk; Takeuchi, Shinichi; Zhou, Qifa

    2013-04-01

    The paper describes the design, fabrication, and measurements of a high-frequency ultrasound kerfless linear array prepared from hydrothermal lead zirconate titanate (PZT) thick film. The 15-μm hydrothermal PZT thick film with an area of 1 × 1 cm, obtained through a self-separation process from Ti substrate, was used to fabricate a 32-element 100-MHz kerfless linear array with photolithography. The bandwidth at -6 dB without matching layer, insertion loss around center frequency, and crosstalk between adjacent elements were measured to be 39%, -30 dB, and -15 dB, respectively.

  1. A METHOD FOR SELF-CALIBRATION IN SATELLITE WITH HIGH PRECISION OF SPACE LINEAR ARRAY CAMERA

    W. Liu

    2016-06-01

    Full Text Available At present, the on-orbit calibration of the geometric parameters of a space surveying camera is usually processed by data from a ground calibration field after capturing the images. The entire process is very complicated and lengthy and cannot monitor and calibrate the geometric parameters in real time. On the basis of a large number of on-orbit calibrations, we found that owing to the influence of many factors, e.g., weather, it is often difficult to capture images of the ground calibration field. Thus, regular calibration using field data cannot be ensured. This article proposes a real time self-calibration method for a space linear array camera on a satellite using the optical auto collimation principle. A collimating light source and small matrix array CCD devices are installed inside the load system of the satellite; these use the same light path as the linear array camera. We can extract the location changes of the cross marks in the matrix array CCD to determine the real-time variations in the focal length and angle parameters of the linear array camera. The on-orbit status of the camera is rapidly obtained using this method. On one hand, the camera’s change regulation can be mastered accurately and the camera’s attitude can be adjusted in a timely manner to ensure optimal photography; in contrast, self-calibration of the camera aboard the satellite can be realized quickly, which improves the efficiency and reliability of photogrammetric processing.

  2. A Low-Complexity ESPRIT-Based DOA Estimation Method for Co-Prime Linear Arrays.

    Sun, Fenggang; Gao, Bin; Chen, Lizhen; Lan, Peng

    2016-08-25

    The problem of direction-of-arrival (DOA) estimation is investigated for co-prime array, where the co-prime array consists of two uniform sparse linear subarrays with extended inter-element spacing. For each sparse subarray, true DOAs are mapped into several equivalent angles impinging on the traditional uniform linear array with half-wavelength spacing. Then, by applying the estimation of signal parameters via rotational invariance technique (ESPRIT), the equivalent DOAs are estimated, and the candidate DOAs are recovered according to the relationship among equivalent and true DOAs. Finally, the true DOAs are estimated by combining the results of the two subarrays. The proposed method achieves a better complexity-performance tradeoff as compared to other existing methods.

  3. MTF measurement and analysis of linear array HgCdTe infrared detectors

    Zhang, Tong; Lin, Chun; Chen, Honglei; Sun, Changhong; Lin, Jiamu; Wang, Xi

    2018-01-01

    The slanted-edge technique is the main method for measurement detectors MTF, however this method is commonly used on planar array detectors. In this paper the authors present a modified slanted-edge method to measure the MTF of linear array HgCdTe detectors. Crosstalk is one of the major factors that degrade the MTF value of such an infrared detector. This paper presents an ion implantation guard-ring structure which was designed to effectively absorb photo-carriers that may laterally defuse between adjacent pixels thereby suppressing crosstalk. Measurement and analysis of the MTF of the linear array detectors with and without a guard-ring were carried out. The experimental results indicated that the ion implantation guard-ring structure effectively suppresses crosstalk and increases MTF value.

  4. Fast photoacoustic imaging system based on 320-element linear transducer array

    Yin Bangzheng; Xing Da; Wang Yi; Zeng Yaguang; Tan Yi; Chen Qun

    2004-01-01

    A fast photoacoustic (PA) imaging system, based on a 320-transducer linear array, was developed and tested on a tissue phantom. To reconstruct a test tomographic image, 64 time-domain PA signals were acquired from a tissue phantom with embedded light-absorption targets. A signal acquisition was accomplished by utilizing 11 phase-controlled sub-arrays, each consisting of four transducers. The results show that the system can rapidly map the optical absorption of a tissue phantom and effectively detect the embedded light-absorbing target. By utilizing the multi-element linear transducer array and phase-controlled imaging algorithm, we thus can acquire PA tomography more efficiently, compared to other existing technology and algorithms. The methodology and equipment thus provide a rapid and reliable approach to PA imaging that may have potential applications in noninvasive imaging and clinic diagnosis

  5. Diode array pumped, non-linear mirror Q-switched and mode-locked

    A non-linear mirror consisting of a lithium triborate crystal and a dichroic output coupler are used to mode-lock (passively) an Nd : YVO4 laser, pumped by a diode laser array. The laser can operate both in cw mode-locked and simultaneously Q-switched and mode-locked (QML) regime. The peak power of the laser while ...

  6. Linear array implementation of the EM algorithm for PET image reconstruction

    Rajan, K.; Patnaik, L.M.; Ramakrishna, J.

    1995-01-01

    The PET image reconstruction based on the EM algorithm has several attractive advantages over the conventional convolution back projection algorithms. However, the PET image reconstruction based on the EM algorithm is computationally burdensome for today's single processor systems. In addition, a large memory is required for the storage of the image, projection data, and the probability matrix. Since the computations are easily divided into tasks executable in parallel, multiprocessor configurations are the ideal choice for fast execution of the EM algorithms. In tis study, the authors attempt to overcome these two problems by parallelizing the EM algorithm on a multiprocessor systems. The parallel EM algorithm on a linear array topology using the commercially available fast floating point digital signal processor (DSP) chips as the processing elements (PE's) has been implemented. The performance of the EM algorithm on a 386/387 machine, IBM 6000 RISC workstation, and on the linear array system is discussed and compared. The results show that the computational speed performance of a linear array using 8 DSP chips as PE's executing the EM image reconstruction algorithm is about 15.5 times better than that of the IBM 6000 RISC workstation. The novelty of the scheme is its simplicity. The linear array topology is expandable with a larger number of PE's. The architecture is not dependant on the DSP chip chosen, and the substitution of the latest DSP chip is straightforward and could yield better speed performance

  7. A proof of the Woodward-Lawson sampling method for a finite linear array

    Somers, Gary A.

    1993-01-01

    An extension of the continuous aperture Woodward-Lawson sampling theorem has been developed for a finite linear array of equidistant identical elements with arbitrary excitations. It is shown that by sampling the array factor at a finite number of specified points in the far field, the exact array factor over all space can be efficiently reconstructed in closed form. The specified sample points lie in real space and hence are measurable provided that the interelement spacing is greater than approximately one half of a wavelength. This paper provides insight as to why the length parameter used in the sampling formulas for discrete arrays is larger than the physical span of the lattice points in contrast with the continuous aperture case where the length parameter is precisely the physical aperture length.

  8. Voltage splay modes and enhanced phase locking in a modified linear Josephson array

    Harris, E.B.; Garland, J.C.

    1997-01-01

    We analyze a modified linear Josephson-junction array in which additional unbiased junctions are used to greatly enhance phase locking. This geometry exhibits strong correlated behavior, with an external magnetic field tuning the voltage splay angle between adjacent Josephson oscillators. The array displays a coherent in-phase mode for f=(1)/(2), where f is the magnetic frustration, while for 0 p (f)=2aV dc /Φ 0 (1-2f). The locked splay modes are found to be tolerant of critical current disorder approaching 100%. The stability of the array has also been studied by computing Floquet exponents. These exponents are found to be negative for all array lengths, with a 1/N 2 dependence, N being the number of series-connected junctions. copyright 1996 The American Physical Society

  9. Research on geometric rectification of the Large FOV Linear Array Whiskbroom Image

    Liu, Dia; Liu, Hui-tong; Dong, Hao; Liu, Xiao-bo

    2015-08-01

    To solve the geometric distortion problem of large FOV linear array whiskbroom image, a model of multi center central projection collinearity equation was founded considering its whiskbroom and linear CCD imaging feature, and the principle of distortion was analyzed. Based on the rectification method with POS, we introduced the angular position sensor data of the servo system, and restored the geometric imaging process exactly. An indirect rectification scheme aiming at linear array imaging with best scanline searching method was adopted, matrixes for calculating the exterior orientation elements was redesigned. We improved two iterative algorithms for this device, and did comparison and analysis. The rectification for the images of airborne imaging experiment showed ideal effect.

  10. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples

    Alyssa M. Cornall

    2017-12-01

    Full Text Available Purpose: To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene and EuroArray HPV (EuroImmun, with Linear Array HPV (Roche. Methods: DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic, from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Results: Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 − 1.00 for most genotypes, and was almost perfect (κ = 0.81 – 0.98 for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497, HPV52 (Anyplex II; p = 0.039 and HPV61 (Anyplex II; p=0.047. EuroArray detected signficantly more HPV26 (p = 0.002 and Anyplex II detected more HPV42 (p = 0.035 than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively, but were in poor disagreement with each other (κ = −0.01. Conclusions: EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Keywords: Human papillomavirus, Genotyping, Linear Array, Anyplex II, EuroArray, Cervix

  11. Pattern Nulling of Linear Antenna Arrays Using Backtracking Search Optimization Algorithm

    Kerim Guney

    2015-01-01

    Full Text Available An evolutionary method based on backtracking search optimization algorithm (BSA is proposed for linear antenna array pattern synthesis with prescribed nulls at interference directions. Pattern nulling is obtained by controlling only the amplitude, position, and phase of the antenna array elements. BSA is an innovative metaheuristic technique based on an iterative process. Various numerical examples of linear array patterns with the prescribed single, multiple, and wide nulls are given to illustrate the performance and flexibility of BSA. The results obtained by BSA are compared with the results of the following seventeen algorithms: particle swarm optimization (PSO, genetic algorithm (GA, modified touring ant colony algorithm (MTACO, quadratic programming method (QPM, bacterial foraging algorithm (BFA, bees algorithm (BA, clonal selection algorithm (CLONALG, plant growth simulation algorithm (PGSA, tabu search algorithm (TSA, memetic algorithm (MA, nondominated sorting GA-2 (NSGA-2, multiobjective differential evolution (MODE, decomposition with differential evolution (MOEA/D-DE, comprehensive learning PSO (CLPSO, harmony search algorithm (HSA, seeker optimization algorithm (SOA, and mean variance mapping optimization (MVMO. The simulation results show that the linear antenna array synthesis using BSA provides low side-lobe levels and deep null levels.

  12. Noise analysis and performance of a selfscanned linear InSb detector array

    Finger, G.; Meyer, M.; Moorwood, A.F.M.

    1987-01-01

    A noise model for detectors operated in the capacitive discharge mode is presented. It is used to analyze the noise performance of the ESO nested timing readout technique applied to a linear 32-element InSb array which is multiplexed by a silicon switched-FET shift register. Analysis shows that KTC noise of the videoline is the major noise contribution; it can be eliminated by weighted double-correlated sampling. Best noise performance of this array is achieved at the smallest possible reverse bias voltage (not more than 20 mV) whereas excess noise is observed at higher reverse bias voltages. 5 references

  13. Pulse Splitting for Harmonic Beamforming in Time-Modulated Linear Arrays

    Lorenzo Poli

    2014-01-01

    Full Text Available A novel strategy for harmonic beamforming in time-modulated linear arrays is proposed. The pulse splitting technique is exploited to simultaneously generate two harmonic patterns, one at the central frequency and another at a preselected harmonic of arbitrary order, while controlling the maximum level of the remaining sideband radiations. An optimization strategy based on the particle swarm optimizer is developed in order to determine the optimal parameters describing the pulse sequence used to modulate the excitation weights of the array elements. Representative numerical results are reported and discussed to point out potentialities and limitations of the proposed approach.

  14. Linear and nonlinear excitations in two stacks of parallel arrays of long Josephson junctions

    Carapella, G.; Constabile, Giovanni; Latempa, R.

    2000-01-01

    We investigate a structure consisting of two parallel arrays of long Josephson junctions sharing a common electrode that allows inductive coupling between the arrays. A model for this structure is derived starting from the description of its continuous limit. The excitation of linear cavity modes...... known from continuous and discrete systems as well as the excitation of a new state exhibiting synchronization in two dimensions are inferred from the mathematical model of the system. The stable nonlinear solution of the coupled sine-Gordon equations describing the system is found to consist...

  15. CFD Analysis of a Finite Linear Array of Savonius Wind Turbines

    Belkacem, Belabes; Paraschivoiu, Marius

    2016-09-01

    Vertical axis wind turbines such as Savonius rotors have been shown to be suitable for low wind speeds normally associated with wind resources in all corners of the world. However, the efficiency of the rotor is low. This paper presents results of Computational Fluid Dynamics (CFD) simulations for an array of Savonius rotors that show a significant increase in efficiency. It looks at identifying the effect on the energy yield of a number of turbines placed in a linear array. Results from this investigation suggest that an increase in the energy yield could be achieved which can reach almost two times than the conventional Savonius wind turbine in the case of an array of 11turbines with a distance of 1.4R in between them. The effect of different TSR values and different wind inlet speeds on the farm has been studied for both a synchronous and asynchronous wind farm.

  16. CFD Analysis of a Finite Linear Array of Savonius Wind Turbines

    Belkacem, Belabes; Paraschivoiu, Marius

    2016-01-01

    Vertical axis wind turbines such as Savonius rotors have been shown to be suitable for low wind speeds normally associated with wind resources in all corners of the world. However, the efficiency of the rotor is low. This paper presents results of Computational Fluid Dynamics (CFD) simulations for an array of Savonius rotors that show a significant increase in efficiency. It looks at identifying the effect on the energy yield of a number of turbines placed in a linear array. Results from this investigation suggest that an increase in the energy yield could be achieved which can reach almost two times than the conventional Savonius wind turbine in the case of an array of 11turbines with a distance of 1.4R in between them. The effect of different TSR values and different wind inlet speeds on the farm has been studied for both a synchronous and asynchronous wind farm. (paper)

  17. Small-angle tomography algorithm for transmission inspection of acoustic linear array

    Soldatov Alexey

    2016-01-01

    Full Text Available The paper describes the algorithm of reconstruction of tomographic image used in the through-transition method in a small angle sounding of acoustic linear arrays and the results of practical application of the proposed algorithm. In alternate probing of each element of emitting array and simultaneous reception of all elements of the receiving array is a collection of shadow images of the testing zone. The testing zone is divided into small local areas and using the collection of shadow images computed matrix normalized transmission coefficients for each of the small local area. Tomographic image control zone is obtained by submitting the resulting matrix of normalized transmission coefficients in grayscale or colors.

  18. Two-dimensional Fast ESPRIT Algorithm for Linear Array SAR Imaging

    Zhao Yi-chao

    2015-10-01

    Full Text Available The linear array Synthetic Aperture Radar (SAR system is a popular research tool, because it can realize three-dimensional imaging. However, owning to limitations of the aircraft platform and actual conditions, resolution improvement is difficult in cross-track and along-track directions. In this study, a twodimensional fast Estimation of Signal Parameters by Rotational Invariance Technique (ESPRIT algorithm for linear array SAR imaging is proposed to overcome these limitations. This approach combines the Gerschgorin disks method and the ESPRIT algorithm to estimate the positions of scatterers in cross and along-rack directions. Moreover, the reflectivity of scatterers is obtained by a modified pairing method based on “region growing”, replacing the least-squares method. The simulation results demonstrate the applicability of the algorithm with high resolution, quick calculation, and good real-time response.

  19. Optimal linear generator with Halbach array for harvesting of vibration energy during human walking

    Joonsoo Jun

    2016-05-01

    Full Text Available In IT business, the capacity of the battery in smartphone was drastically improved to digest various functions such as communication, Internet, e-banking, and entertainment. Although the capacity of the battery is improved, it still needs to be upgraded due to customer’s demands. In this article, we optimize the design of the linear generator with the Halbach array to improve the efficiency of harvesting vibration energy during human walking for the battery capacitance. We propose the optimal design of the tubular permanent magnet with the linear generator that uses a Halbach array. The approximate model is established using generic algorithm. Furthermore, we performed electromagnetic finite element analysis to predict the induced voltage.

  20. Nature-inspired Cuckoo Search Algorithm for Side Lobe Suppression in a Symmetric Linear Antenna Array

    K. N. Abdul Rani

    2012-09-01

    Full Text Available In this paper, we proposed a newly modified cuckoo search (MCS algorithm integrated with the Roulette wheel selection operator and the inertia weight controlling the search ability towards synthesizing symmetric linear array geometry with minimum side lobe level (SLL and/or nulls control. The basic cuckoo search (CS algorithm is primarily based on the natural obligate brood parasitic behavior of some cuckoo species in combination with the Levy flight behavior of some birds and fruit flies. The CS metaheuristic approach is straightforward and capable of solving effectively general N-dimensional, linear and nonlinear optimization problems. The array geometry synthesis is first formulated as an optimization problem with the goal of SLL suppression and/or null prescribed placement in certain directions, and then solved by the newly MCS algorithm for the optimum element or isotropic radiator locations in the azimuth-plane or xy-plane. The study also focuses on the four internal parameters of MCS algorithm specifically on their implicit effects in the array synthesis. The optimal inter-element spacing solutions obtained by the MCS-optimizer are validated through comparisons with the standard CS-optimizer and the conventional array within the uniform and the Dolph-Chebyshev envelope patterns using MATLABTM. Finally, we also compared the fine-tuned MCS algorithm with two popular evolutionary algorithm (EA techniques include particle swarm optimization (PSO and genetic algorithms (GA.

  1. Kalman filter-based tracking of moving objects using linear ultrasonic sensor array for road vehicles

    Li, Shengbo Eben; Li, Guofa; Yu, Jiaying; Liu, Chang; Cheng, Bo; Wang, Jianqiang; Li, Keqiang

    2018-01-01

    Detection and tracking of objects in the side-near-field has attracted much attention for the development of advanced driver assistance systems. This paper presents a cost-effective approach to track moving objects around vehicles using linearly arrayed ultrasonic sensors. To understand the detection characteristics of a single sensor, an empirical detection model was developed considering the shapes and surface materials of various detected objects. Eight sensors were arrayed linearly to expand the detection range for further application in traffic environment recognition. Two types of tracking algorithms, including an Extended Kalman filter (EKF) and an Unscented Kalman filter (UKF), for the sensor array were designed for dynamic object tracking. The ultrasonic sensor array was designed to have two types of fire sequences: mutual firing or serial firing. The effectiveness of the designed algorithms were verified in two typical driving scenarios: passing intersections with traffic sign poles or street lights, and overtaking another vehicle. Experimental results showed that both EKF and UKF had more precise tracking position and smaller RMSE (root mean square error) than a traditional triangular positioning method. The effectiveness also encourages the application of cost-effective ultrasonic sensors in the near-field environment perception in autonomous driving systems.

  2. Broadband implementation of coprime linear microphone arrays for direction of arrival estimation.

    Bush, Dane; Xiang, Ning

    2015-07-01

    Coprime arrays represent a form of sparse sensing which can achieve narrow beams using relatively few elements, exceeding the spatial Nyquist sampling limit. The purpose of this paper is to expand on and experimentally validate coprime array theory in an acoustic implementation. Two nested sparse uniform linear subarrays with coprime number of elements ( M and N) each produce grating lobes that overlap with one another completely in just one direction. When the subarray outputs are combined it is possible to retain the shared beam while mostly canceling the other superfluous grating lobes. In this way a small number of microphones ( N+M-1) creates a narrow beam at higher frequencies, comparable to a densely populated uniform linear array of MN microphones. In this work beampatterns are simulated for a range of single frequencies, as well as bands of frequencies. Narrowband experimental beampatterns are shown to correspond with simulated results even at frequencies other than the arrays design frequency. Narrowband side lobe locations are shown to correspond to the theoretical values. Side lobes in the directional pattern are mitigated by increasing bandwidth of analyzed signals. Direction of arrival estimation is also implemented for two simultaneous noise sources in a free field condition.

  3. 3D Analytical Calculation of Forces between Linear Halbach-Type Permanent Magnet Arrays

    Allag , Hicham; Yonnet , Jean-Paul; Latreche , Mohamed E. H.

    2009-01-01

    International audience; Usely, in analytical calculation of magnetic and mechanical quantities of Halbach systems, the authors use the Fourier series approximation because the exact calculations are more difficult. In this work the interaction forces between linear Halbach arrays are analytically calculated thanks to our recent development 3D exact calculation of forces between two cuboïdal magnets with parallel and perpendicular magnetization. We essentially describe the way to separately ca...

  4. An Optimal DEM Reconstruction Method for Linear Array Synthetic Aperture Radar Based on Variational Model

    Shi Jun

    2015-02-01

    Full Text Available Downward-looking Linear Array Synthetic Aperture Radar (LASAR has many potential applications in the topographic mapping, disaster monitoring and reconnaissance applications, especially in the mountainous area. However, limited by the sizes of platforms, its resolution in the linear array direction is always far lower than those in the range and azimuth directions. This disadvantage leads to the blurring of Three-Dimensional (3D images in the linear array direction, and restricts the application of LASAR. To date, the research on 3D SAR image enhancement has focused on the sparse recovery technique. In this case, the one-to-one mapping of Digital Elevation Model (DEM brakes down. To overcome this, an optimal DEM reconstruction method for LASAR based on the variational model is discussed in an effort to optimize the DEM and the associated scattering coefficient map, and to minimize the Mean Square Error (MSE. Using simulation experiments, it is found that the variational model is more suitable for DEM enhancement applications to all kinds of terrains compared with the Orthogonal Matching Pursuit (OMPand Least Absolute Shrinkage and Selection Operator (LASSO methods.

  5. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples.

    Cornall, Alyssa M; Poljak, Marin; Garland, Suzanne M; Phillips, Samuel; Machalek, Dorothy A; Tan, Jeffrey H; Quinn, Michael A; Tabrizi, Sepehr N

    2017-12-01

    To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene) and EuroArray HPV (EuroImmun), with Linear Array HPV (Roche). DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic), from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 - 1.00) for most genotypes, and was almost perfect (κ = 0.81 - 0.98) for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497), HPV52 (Anyplex II; p = 0.039) and HPV61 (Anyplex II; p=0.047). EuroArray detected signficantly more HPV26 (p = 0.002) and Anyplex II detected more HPV42 (p = 0.035) than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively), but were in poor disagreement with each other (κ = -0.01). EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  6. Design of a linear detector array unit for high energy x-ray helical computed tomography and linear scanner

    Lee, Jeong Tae; Park, Jong Hwan; Kim, Gi Yoon [Dept. of Nuclear and Quantum Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon (Korea, Republic of); Kim, Dong Geun [Medical Imaging Department, ASTEL Inc., Seongnam (Korea, Republic of); Park, Shin Woong; Yi, Yun [Dept. of Electronics and Information Eng, Korea University, Seoul (Korea, Republic of); Kim, Hyun Duk [Research Center, Luvantix ADM Co., Ltd., Daejeon (Korea, Republic of)

    2016-11-15

    A linear detector array unit (LdAu) was proposed and designed for the high energy X-ray 2-d and 3-d imaging systems for industrial non-destructive test. Specially for 3-d imaging, a helical CT with a 15 MeV linear accelerator and a curved detector is proposed. the arc-shape detector can be formed by many LdAus all of which are arranged to face the focal spot when the source-to-detector distance is fixed depending on the application. An LdAu is composed of 10 modules and each module has 48 channels of CdWO{sub 4} (CWO) blocks and Si PIn photodiodes with 0.4 mm pitch. this modular design was made for easy manufacturing and maintenance. through the Monte carlo simulation, the CWO detector thickness of 17 mm was optimally determined. the silicon PIn photodiodes were designed as 48 channel arrays and fabricated with NTD (neutron transmutation doping) wafers of high resistivity and showed excellent leakage current properties below 1 nA at 10 V reverse bias. to minimize the low-voltage breakdown, the edges of the active layer and the guard ring were designed as a curved shape. the data acquisition system was also designed and fabricated as three independent functional boards; a sensor board, a capture board and a communication board to a Pc. this paper describes the design of the detectors (CWO blocks and Si PIn photodiodes) and the 3-board data acquisition system with their simulation results.

  7. The investigation of the phase-locking stability in linear arrays of Josephson junctions and arrays closed into a superconducting loop

    Darula, M.; Seidel, P.; Misanik, B.; Busse, F.; Heinz, E.; Benacka, S.

    1994-01-01

    The phase-locking stability is investigated theoretically in two structures: linear arrays of Josephson junctions shunted by resistive load and arrays closed into superconducting loop. In both cases the quasi-identical junctions are supposed to be in arrays. The stability as a function of spread in Josephson junction parameters as well as a function of other circuit parameters is investigated. Using Floquet theory it is shown that spread in critical currents of Josephson junction limit the stability of phase-locking state. From the simulations it follows that the phase-locking in arrays closed into superconducting loop is more stable against the spread in junction parameters than in the case of linear array of Josephson junctions. (orig.)

  8. The DNA-encoded nucleosome organization of a eukaryotic genome.

    Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne; Gossett, Andrea J; Tillo, Desiree; Field, Yair; LeProust, Emily M; Hughes, Timothy R; Lieb, Jason D; Widom, Jonathan; Segal, Eran

    2009-03-19

    Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for approximately 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

  9. Study on the near-field non-linearity (SMILE) of high power diode laser arrays

    Zhang, Hongyou; Jia, Yangtao; Li, Changxuan; Zah, Chung-en; Liu, Xingsheng

    2018-02-01

    High power laser diodes have been found a wide range of industrial, space, medical applications, characterized by high conversion efficiency, small size, light weight and a long lifetime. However, due to thermal induced stress, each emitter in a semiconductor laser bar or array is displaced along p-n junction, resulting of each emitter is not in a line, called Near-field Non-linearity. Near-field Non-linearity along laser bar (also known as "SMILE") determines the outcome of optical coupling and beam shaping [1]. The SMILE of a laser array is the main obstacle to obtain good optical coupling efficiency and beam shaping from a laser array. Larger SMILE value causes a larger divergence angle and a wider line after collimation and focusing, respectively. In this letter, we simulate two different package structures based on MCC (Micro Channel Cooler) with Indium and AuSn solders, including the distribution of normal stress and the SMILE value. According to the theoretical results, we found the distribution of normal stress on laser bar shows the largest in the middle and drops rapidly near both ends. At last, we did another experiment to prove that the SMILE value of a laser bar was mainly affected by the die bonding process, rather than the operating condition.

  10. Distributed 3D Source Localization from 2D DOA Measurements Using Multiple Linear Arrays

    Antonio Canclini

    2017-01-01

    Full Text Available This manuscript addresses the problem of 3D source localization from direction of arrivals (DOAs in wireless acoustic sensor networks. In this context, multiple sensors measure the DOA of the source, and a central node combines the measurements to yield the source location estimate. Traditional approaches require 3D DOA measurements; that is, each sensor estimates the azimuth and elevation of the source by means of a microphone array, typically in a planar or spherical configuration. The proposed methodology aims at reducing the hardware and computational costs by combining measurements related to 2D DOAs estimated from linear arrays arbitrarily displaced in the 3D space. Each sensor measures the DOA in the plane containing the array and the source. Measurements are then translated into an equivalent planar geometry, in which a set of coplanar equivalent arrays observe the source preserving the original DOAs. This formulation is exploited to define a cost function, whose minimization leads to the source location estimation. An extensive simulation campaign validates the proposed approach and compares its accuracy with state-of-the-art methodologies.

  11. Polarized Uniform Linear Array System: Beam Radiation Pattern, Beamforming Diversity Order, and Channel Capacity

    Xin Su

    2015-01-01

    Full Text Available There have been many studies regarding antenna polarization; however, there have been few publications on the analysis of the channel capacity for polarized antenna systems using the beamforming technique. According to Chung et al., the channel capacity is determined by the density of scatterers and the transmission power, which is obtained based on the assumption that scatterers are uniformly distributed on a 3D spherical scattering model. However, it contradicts the practical scenario, where scatterers may not be uniformly distributed under outdoor environment, and lacks the consideration of fading channel gain. In this study, we derive the channel capacity of polarized uniform linear array (PULA systems using the beamforming technique in a practical scattering environment. The results show that, for PULA systems, the channel capacity, which is boosted by beamforming diversity, can be determined using the channel gain, beam radiation pattern, and beamforming diversity order (BDO, where the BDO is dependent on the antenna characteristics and array configurations.

  12. Improving emission uniformity and linearizing band dispersion in nanowire arrays using quasi-aperiodicity

    Anderson, P. Duke [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Univ. of Southern California, Los Angeles, CA (United States). Ming Hsieh Dept. of Electrical Engineering; Koleske, Daniel D. [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States); Povinelli, Michelle L. [Univ. of Southern California, Los Angeles, CA (United States). Ming Hsieh Dept. of Electrical Engineering; Subramania, Ganapathi [Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

    2017-10-01

    For this study, we experimentally investigate a new class of quasi-aperiodic structures for improving the emission pattern in nanowire arrays. Efficient normal emission, as well as lasing, can be obtained from III-nitride photonic crystal (PhC) nanowire arrays that utilize slow group velocity modes near the Γ-point in reciprocal space. However, due to symmetry considerations, the emitted far-field pattern of such modes are often ‘donut’-like. Many applications, including lighting for displays or lasers, require a more uniform beam profile in the far-field. Previous work has improved far-field beam uniformity of uncoupled modes by changing the shape of the emitting structure. However, in nanowire systems, the shape of nanowires cannot always be arbitrarily changed due to growth or etch considerations. Here, we investigate breaking symmetry by instead changing the position of emitters. Using a quasi-aperiodic geometry, which changes the emitter position within a photonic crystal supercell (2x2), we are able to linearize the photonic bandstructure near the Γ-point and greatly improve emitted far-field uniformity. We realize the III-nitride nanowires structures using a top-down fabrication procedure that produces nanowires with smooth, vertical sidewalls. Comparison of room-temperature micro-photoluminescence (µ-PL) measurements between periodic and quasi-aperiodic nanowire arrays reveal resonances in each structure, with the simple periodic structure producing a donut beam in the emitted far-field and the quasi-aperiodic structure producing a uniform Gaussian-like beam. We investigate the input pump power vs. output intensity in both systems and observe the simple periodic array exhibiting a non-linear relationship, indicative of lasing. We believe that the quasi-aperiodic approach studied here provides an alternate and promising strategy for shaping the emission pattern of nanoemitter systems.

  13. Mixed Linear/Square-Root Encoded Single Slope Ramp Provides a Fast, Low Noise Analog to Digital Converter with Very High Linearity for Focal Plane Arrays

    Wrigley, Christopher James (Inventor); Hancock, Bruce R. (Inventor); Newton, Kenneth W. (Inventor); Cunningham, Thomas J. (Inventor)

    2014-01-01

    An analog-to-digital converter (ADC) converts pixel voltages from a CMOS image into a digital output. A voltage ramp generator generates a voltage ramp that has a linear first portion and a non-linear second portion. A digital output generator generates a digital output based on the voltage ramp, the pixel voltages, and comparator output from an array of comparators that compare the voltage ramp to the pixel voltages. A return lookup table linearizes the digital output values.

  14. Characterization and linear array LA48 Commissioner for measuring the position of the multi leaf collimator

    Conles Picos, I.; Cenizo de Castro, E.; Aparicio martin, A. R.; Barrio Lazo, F.; Cesteros Morante, M. J.

    2011-01-01

    The protocol of Quality Control of electron accelerators for medical use of SEFM proposed for multi leaf collimation system (MLC) to verify the positioning of the blades connect. To do this you must find a system with sufficient accuracy and precision and, if possible, easy to assemble and offers real-time results. One of these teams is the Linear Array of PTW-Freiburg (LA48), which consists of a row of 47 ionization chambers, of 0008 cc and 8 mm apart from each other. In this paper, we describe our process of characterization and LA48 commissioner. (Author)

  15. A Multibeam Dual-Band Orthogonal Linearly Polarized Antenna Array for Satellite Communication on the Move

    Yi Liu

    2015-01-01

    Full Text Available The design and simulation of a 10 × 8 multibeam dual-band orthogonal linearly polarized antenna array operating at Ku-band are presented for transmit-receive applications. By using patches with different coupling methods as elements, both perpendicular polarization in 12.25–12.75 GHz band and horizontal polarization in 14.0–14.5 GHz band are realized in a shared antenna aperture. A microstrip Rotman lens is employed as the beamforming network with 7 input ports, which can generate a corresponding number of beams to cover −30°–30° with 5 dB beamwidth along one dimension. This type of multibeam orthogonal linearly polarized planar antenna is a good candidate for satellite communication (SatCom.

  16. Dynamic wedge, electron energy and beam profile Q.A. using an ionization chamber linear array

    Kenny, M.B.; Todd, S.P.

    1996-01-01

    Since the introduction of multi-modal linacs the quality assurance workload of a Physical Sciences department has increased dramatically. The advent of dynamic wedges has further complicated matters because of the need to invent accurate methods to perform Q.A. in a reasonable time. We have been using an ionization chamber linear array, the Thebes 7000 TM by Victoreen, Inc., for some years to measure X-ray and electron beam profiles. Two years ago we developed software to perform Q.A. on our dynamic wedges using the array and more recently included a routine to check electron beam energies using the method described by Rosenow, U.F. et al., Med. Phys. 18(1) 19-25. The integrated beam and profile management system has enabled us to maintain a comprehensive quality assurance programme on all our linaccs. Both our efficiency and accuracy have increased to the point where we are able to keep up with the greater number of tests required without an increase in staff or hours spent in quality assurance. In changing the processor from the Z80 of the Thebes console to the 486 of the PC we have also noticed a marked increase in the calibration stability of the array. (author)

  17. Choosing processor array configuration by performance modeling for a highly parallel linear algebra algorithm

    Littlefield, R.J.; Maschhoff, K.J.

    1991-04-01

    Many linear algebra algorithms utilize an array of processors across which matrices are distributed. Given a particular matrix size and a maximum number of processors, what configuration of processors, i.e., what size and shape array, will execute the fastest? The answer to this question depends on tradeoffs between load balancing, communication startup and transfer costs, and computational overhead. In this paper we analyze in detail one algorithm: the blocked factored Jacobi method for solving dense eigensystems. A performance model is developed to predict execution time as a function of the processor array and matrix sizes, plus the basic computation and communication speeds of the underlying computer system. In experiments on a large hypercube (up to 512 processors), this model has been found to be highly accurate (mean error ∼ 2%) over a wide range of matrix sizes (10 x 10 through 200 x 200) and processor counts (1 to 512). The model reveals, and direct experiment confirms, that the tradeoffs mentioned above can be surprisingly complex and counterintuitive. We propose decision procedures based directly on the performance model to choose configurations for fastest execution. The model-based decision procedures are compared to a heuristic strategy and shown to be significantly better. 7 refs., 8 figs., 1 tab

  18. Magnetic Flux Distribution of Linear Machines with Novel Three-Dimensional Hybrid Magnet Arrays

    Nan Yao

    2017-11-01

    Full Text Available The objective of this paper is to propose a novel tubular linear machine with hybrid permanent magnet arrays and multiple movers, which could be employed for either actuation or sensing technology. The hybrid magnet array produces flux distribution on both sides of windings, and thus helps to increase the signal strength in the windings. The multiple movers are important for airspace technology, because they can improve the system’s redundancy and reliability. The proposed design concept is presented, and the governing equations are obtained based on source free property and Maxwell equations. The magnetic field distribution in the linear machine is thus analytically formulated by using Bessel functions and harmonic expansion of magnetization vector. Numerical simulation is then conducted to validate the analytical solutions of the magnetic flux field. It is proved that the analytical model agrees with the numerical results well. Therefore, it can be utilized for the formulation of signal or force output subsequently, depending on its particular implementation.

  19. Ultrasound pulse-echo measurements on rough surfaces with linear array transducers

    Sjøj, Sidsel M. N.; Blanco, Esther N.; Wilhjelm, Jens E.

    2012-01-01

    The echo from planar surfaces with rms roughness, Rq, in the range from 0-155 μm was measured with a clinical linear array transducer at different angles of incidence at 6 MHz and 12 MHz. The echo-pulse from the surfaces was isolated with an equal sized window and the power of the echo-pulse was ......The echo from planar surfaces with rms roughness, Rq, in the range from 0-155 μm was measured with a clinical linear array transducer at different angles of incidence at 6 MHz and 12 MHz. The echo-pulse from the surfaces was isolated with an equal sized window and the power of the echo......-pulse was calculated. The power of the echo from the smooth surface (Rq = 0) is highly angle-dependent due to a high degree of specular reflection. Within the angular range considered here, -10° to 10°, the variation spans a range of 18 dB at both 6 MHz and 12 MHz. When roughness increases, the angle......-dependence decreases, as the echo process gradually changes from pure reflection to being predominantly governed by backscattering. The power of the echoes from the two roughest surfaces (Rq = 115 μm and 155 μm) are largely independent of angle at both 6 MHz and 12 MHz with a variation of 2 dB in the angular range...

  20. Linear Array Ambient Noise Adjoint Tomography Reveals Intense Crust-Mantle Interactions in North China Craton

    Zhang, Chao; Yao, Huajian; Liu, Qinya; Zhang, Ping; Yuan, Yanhua O.; Feng, Jikun; Fang, Lihua

    2018-01-01

    We present a 2-D ambient noise adjoint tomography technique for a linear array with a significant reduction in computational cost and show its application to an array in North China. We first convert the observed data for 3-D media, i.e., surface-wave empirical Green's functions (EGFs) to the reconstructed EGFs (REGFs) for 2-D media using a 3-D/2-D transformation scheme. Different from the conventional steps of measuring phase dispersion, this technology refines 2-D shear wave speeds along the profile directly from REGFs. With an initial model based on traditional ambient noise tomography, adjoint tomography updates the model by minimizing the frequency-dependent Rayleigh wave traveltime delays between the REGFs and synthetic Green functions calculated by the spectral-element method. The multitaper traveltime difference measurement is applied in four-period bands: 20-35 s, 15-30 s, 10-20 s, and 6-15 s. The recovered model shows detailed crustal structures including pronounced low-velocity anomalies in the lower crust and a gradual crust-mantle transition zone beneath the northern Trans-North China Orogen, which suggest the possible intense thermo-chemical interactions between mantle-derived upwelling melts and the lower crust, probably associated with the magmatic underplating during the Mesozoic to Cenozoic evolution of this region. To our knowledge, it is the first time that ambient noise adjoint tomography is implemented for a 2-D medium. Compared with the intensive computational cost and storage requirement of 3-D adjoint tomography, this method offers a computationally efficient and inexpensive alternative to imaging fine-scale crustal structures beneath linear arrays.

  1. Shift of the Acoustic Center of a Closed-Box Loudspeaker in a Linear Array: Investigation Using the Beamforming Technique

    Chang, Ji-Ho; Jensen, Joe; Agerkvist, Finn T.

    2015-01-01

    The center of the spherical waves radiated from a loudspeaker is defined as its acoustic center. This study aims to investigate how the acoustic center of a closed-box loudspeaker is shifted when the loudspeaker is placed in a linear array. That is, the acoustic center of the loudspeaker is estim......The center of the spherical waves radiated from a loudspeaker is defined as its acoustic center. This study aims to investigate how the acoustic center of a closed-box loudspeaker is shifted when the loudspeaker is placed in a linear array. That is, the acoustic center of the loudspeaker...... is estimated when the loudspeaker is placed alone and then the loudspeaker is placed in a linear array composed of two or three identical loudspeakers. The acoustic center of each loudspeaker in the linear arrays is estimated with the other loudspeakers turned off and compared with that in the single...... that the acoustic center is shifted differently depending on the relative position of the loudspeaker in the array. This implies that the performance of sound field control with a linear array of loudspeakers can be improved by taking the shift of the acoustic center into account....

  2. A CMOS 128-APS linear array integrated with a LVOF for highsensitivity and high-resolution micro-spectrophotometry

    Liu, C.; Emadi, A.; Wu, H.; De Graaf, G.; Wolffenbuttel, R.F.

    2010-01-01

    A linear array of 128 Active Pixel Sensors has been developed in standard CMOS technology and a Linear Variable Optical Filter (LVOF) is added using CMOS-compatible post-process, resulting in a single chip highly-integrated highresolution microspectrometer. The optical requirements imposed by the

  3. Design Methodology of a Dual-Halbach Array Linear Actuator with Thermal-Electromagnetic Coupling.

    Eckert, Paulo Roberto; Flores Filho, Aly Ferreira; Perondi, Eduardo; Ferri, Jeferson; Goltz, Evandro

    2016-03-11

    This paper proposes a design methodology for linear actuators, considering thermal and electromagnetic coupling with geometrical and temperature constraints, that maximizes force density and minimizes force ripple. The method allows defining an actuator for given specifications in a step-by-step way so that requirements are met and the temperature within the device is maintained under or equal to its maximum allowed for continuous operation. According to the proposed method, the electromagnetic and thermal models are built with quasi-static parametric finite element models. The methodology was successfully applied to the design of a linear cylindrical actuator with a dual quasi-Halbach array of permanent magnets and a moving-coil. The actuator can produce an axial force of 120 N and a stroke of 80 mm. The paper also presents a comparative analysis between results obtained considering only an electromagnetic model and the thermal-electromagnetic coupled model. This comparison shows that the final designs for both cases differ significantly, especially regarding its active volume and its electrical and magnetic loading. Although in this paper the methodology was employed to design a specific actuator, its structure can be used to design a wide range of linear devices if the parametric models are adjusted for each particular actuator.

  4. Low nucleosome occupancy is encoded around functional human transcription factor binding sites

    Daenen Floris

    2008-07-01

    Full Text Available Abstract Background Transcriptional regulation of genes in eukaryotes is achieved by the interactions of multiple transcription factors with arrays of transcription factor binding sites (TFBSs on DNA and with each other. Identification of these TFBSs is an essential step in our understanding of gene regulatory networks, but computational prediction of TFBSs with either consensus or commonly used stochastic models such as Position-Specific Scoring Matrices (PSSMs results in an unacceptably high number of hits consisting of a few true functional binding sites and numerous false non-functional binding sites. This is due to the inability of the models to incorporate higher order properties of sequences including sequences surrounding TFBSs and influencing the positioning of nucleosomes and/or the interactions that might occur between transcription factors. Results Significant improvement can be expected through the development of a new framework for the modeling and prediction of TFBSs that considers explicitly these higher order sequence properties. It would be particularly interesting to include in the new modeling framework the information present in the nucleosome positioning sequences (NPSs surrounding TFBSs, as it can be hypothesized that genomes use this information to encode the formation of stable nucleosomes over non-functional sites, while functional sites have a more open chromatin configuration. In this report we evaluate the usefulness of the latter feature by comparing the nucleosome occupancy probabilities around experimentally verified human TFBSs with the nucleosome occupancy probabilities around false positive TFBSs and in random sequences. Conclusion We present evidence that nucleosome occupancy is remarkably lower around true functional human TFBSs as compared to non-functional human TFBSs, which supports the use of this feature to improve current TFBS prediction approaches in higher eukaryotes.

  5. Nucleosome dynamics: HMGB1 facilitates nucleosome restructuring and collaborates in estrogen-responsive gene expression

    William M. Scovell

    2016-12-01

    Full Text Available The genome in the human cell is extraordinarily compacted in the nucleus. As a result, much of the DNA is inaccessible and functionally inert. Notwithstanding the highly efficient packaging, mechanisms have evolved to render DNA sites accessible that then enable a multitude of factors to carry out ongoing and vital functions. The compaction is derived from DNA complexation within nucleosomes, which can further consolidate into a higher-order chromatin structure. The nucleosome and nucleosomal DNA are not static in nature, but are dynamic, undergoing structural and functional changes as the cell responds to stresses and/or metabolic or environmental cues. We are only beginning to understand the forces and the complexes that engage the nucleosome to unearth the tightly bound and inaccessible DNA sequences and provide an opening to more accessible target sites. In many cases, current findings support a major role for the action of ATP-dependent chromatin remodeling complexes (CRCs in providing an avenue to factor accessibility that leads to the activation of transcription. The estrogen receptor α (ERα does not bind to the estrogen response element (ERE in the canonical nucleosome. However, evidence will be presented that HMGB1 restructures the nucleosome in an ATP-independent manner and also facilitates access and strong binding of ERα to ERE. The features that appear important in the mechanism of action for HMGB1 will be highlighted, in addition to the characteristic features of the restructured nucleosome. These findings, together with previous evidence, suggest a collaborative role for HMGB1 in the step-wise transcription of estrogen-responsive genes. In addition, alternate mechanistic pathways will be discussed, with consideration that “HMGB1 restructuring” of the nucleosome may generally be viewed as a perturbation of the equilibrium of an ensemble of nearly isoenergetic nucleosome states in an energy landscape that is driven by

  6. Linear array of photodiodes to track a human speaker for video recording

    DeTone, D; Neal, H; Lougheed, R

    2012-01-01

    Communication and collaboration using stored digital media has garnered more interest by many areas of business, government and education in recent years. This is due primarily to improvements in the quality of cameras and speed of computers. An advantage of digital media is that it can serve as an effective alternative when physical interaction is not possible. Video recordings that allow for viewers to discern a presenter's facial features, lips and hand motions are more effective than videos that do not. To attain this, one must maintain a video capture in which the speaker occupies a significant portion of the captured pixels. However, camera operators are costly, and often do an imperfect job of tracking presenters in unrehearsed situations. This creates motivation for a robust, automated system that directs a video camera to follow a presenter as he or she walks anywhere in the front of a lecture hall or large conference room. Such a system is presented. The system consists of a commercial, off-the-shelf pan/tilt/zoom (PTZ) color video camera, a necklace of infrared LEDs and a linear photodiode array detector. Electronic output from the photodiode array is processed to generate the location of the LED necklace, which is worn by a human speaker. The computer controls the video camera movements to record video of the speaker. The speaker's vertical position and depth are assumed to remain relatively constant– the video camera is sent only panning (horizontal) movement commands. The LED necklace is flashed at 70Hz at a 50% duty cycle to provide noise-filtering capability. The benefit to using a photodiode array versus a standard video camera is its higher frame rate (4kHz vs. 60Hz). The higher frame rate allows for the filtering of infrared noise such as sunlight and indoor lighting–a capability absent from other tracking technologies. The system has been tested in a large lecture hall and is shown to be effective.

  7. Linear array of photodiodes to track a human speaker for video recording

    DeTone, D.; Neal, H.; Lougheed, R.

    2012-12-01

    Communication and collaboration using stored digital media has garnered more interest by many areas of business, government and education in recent years. This is due primarily to improvements in the quality of cameras and speed of computers. An advantage of digital media is that it can serve as an effective alternative when physical interaction is not possible. Video recordings that allow for viewers to discern a presenter's facial features, lips and hand motions are more effective than videos that do not. To attain this, one must maintain a video capture in which the speaker occupies a significant portion of the captured pixels. However, camera operators are costly, and often do an imperfect job of tracking presenters in unrehearsed situations. This creates motivation for a robust, automated system that directs a video camera to follow a presenter as he or she walks anywhere in the front of a lecture hall or large conference room. Such a system is presented. The system consists of a commercial, off-the-shelf pan/tilt/zoom (PTZ) color video camera, a necklace of infrared LEDs and a linear photodiode array detector. Electronic output from the photodiode array is processed to generate the location of the LED necklace, which is worn by a human speaker. The computer controls the video camera movements to record video of the speaker. The speaker's vertical position and depth are assumed to remain relatively constant- the video camera is sent only panning (horizontal) movement commands. The LED necklace is flashed at 70Hz at a 50% duty cycle to provide noise-filtering capability. The benefit to using a photodiode array versus a standard video camera is its higher frame rate (4kHz vs. 60Hz). The higher frame rate allows for the filtering of infrared noise such as sunlight and indoor lighting-a capability absent from other tracking technologies. The system has been tested in a large lecture hall and is shown to be effective.

  8. Design and optimization of multi-class series-parallel linear electromagnetic array artificial muscle.

    Li, Jing; Ji, Zhenyu; Shi, Xuetao; You, Fusheng; Fu, Feng; Liu, Ruigang; Xia, Junying; Wang, Nan; Bai, Jing; Wang, Zhanxi; Qin, Xiansheng; Dong, Xiuzhen

    2014-01-01

    Skeletal muscle exhibiting complex and excellent precision has evolved for millions of years. Skeletal muscle has better performance and simpler structure compared with existing driving modes. Artificial muscle may be designed by analyzing and imitating properties and structure of skeletal muscle based on bionics, which has been focused on by bionic researchers, and a structure mode of linear electromagnetic array artificial muscle has been designed in this paper. Half sarcomere is the minimum unit of artificial muscle and electromagnetic model has been built. The structural parameters of artificial half sarcomere actuator were optimized to achieve better movement performance. Experimental results show that artificial half sarcomere actuator possesses great motion performance such as high response speed, great acceleration, small weight and size, robustness, etc., which presents a promising application prospect of artificial half sarcomere actuator.

  9. Innervation zones of fasciculating motor units: observations by a linear electrode array.

    Jahanmiri-Nezhad, Faezeh; Barkhaus, Paul E; Rymer, William Z; Zhou, Ping

    2015-01-01

    This study examines the innervation zone (IZ) in the biceps brachii muscle in healthy subjects and those with amyotrophic lateral sclerosis (ALS) using a 20-channel linear electromyogram (EMG) electrode array. Raster plots of individual waveform potentials were studied to estimate the motor unit IZ. While this work mainly focused on fasciculation potentials (FPs), a limited number of motor unit potentials (MUPs) from voluntary activity of 12 healthy and seven ALS subjects were also examined. Abnormal propagation of MUPs and scattered IZs were observed in fasciculating units, compared with voluntarily activated MUPs in healthy and ALS subjects. These findings can be related to muscle fiber reinnervation following motor neuron degeneration in ALS and the different origin sites of FPs compared with voluntary MUPs.

  10. Enhanced 2D-DOA Estimation for Large Spacing Three-Parallel Uniform Linear Arrays

    Dong Zhang

    2018-01-01

    Full Text Available An enhanced two-dimensional direction of arrival (2D-DOA estimation algorithm for large spacing three-parallel uniform linear arrays (ULAs is proposed in this paper. Firstly, we use the propagator method (PM to get the highly accurate but ambiguous estimation of directional cosine. Then, we use the relationship between the directional cosine to eliminate the ambiguity. This algorithm not only can make use of the elements of the three-parallel ULAs but also can utilize the connection between directional cosine to improve the estimation accuracy. Besides, it has satisfied estimation performance when the elevation angle is between 70° and 90° and it can automatically pair the estimated azimuth and elevation angles. Furthermore, it has low complexity without using any eigen value decomposition (EVD or singular value decompostion (SVD to the covariance matrix. Simulation results demonstrate the effectiveness of our proposed algorithm.

  11. Electromagnetic Linear Vibration Energy Harvester Using Sliding Permanent Magnet Array and Ferrofluid as a Lubricant

    Song Hee Chae

    2017-09-01

    Full Text Available We present an electromagnetic linear vibration energy harvester with an array of rectangular permanent magnets as a springless proof mass. Instead of supporting the magnet assembly with spring element, ferrofluid has been used as a lubricating material. When external vibration is applied laterally to the harvester, magnet assembly slides back and forth on the channel with reduced friction and wear due to ferrofluid, which significantly improves the long-term reliability of the device. Electric power is generated across an array of copper windings formed at the bottom of the aluminum housing. A proof-of-concept harvester has been fabricated and tested with a vibration exciter at various input frequencies and accelerations. For the device where 5 μL of ferrofluid was used for lubrication, maximum output power of 493 μW has been generated, which was 4.37% higher than that without ferrofluid. Long-term reliability improvement due to ferrofluid lubrication has also been verified. For the device with ferrofluid, 1.02% decrease of output power has been observed, in contrast to 59.73% decrease of output power without ferrofluid after 93,600 cycles.

  12. Development and operation of a pixel segmented liquid-filled linear array for radiotherapy quality assurance

    Pardo, J [Departamento de Fisica de Particulas, Facultade de Fisica, 15782 Santiago de Compostela (Spain); Franco, L [Departamento de Fisica de Particulas, Facultade de Fisica, 15782 Santiago de Compostela (Spain); Gomez, F [Departamento de Fisica de Particulas, Facultade de Fisica, 15782 Santiago de Compostela (Spain); Iglesias, A [Departamento de Fisica de Particulas, Facultade de Fisica, 15782 Santiago de Compostela (Spain); Pazos, A [Departamento de Fisica de Particulas, Facultade de Fisica, 15782 Santiago de Compostela (Spain); Pena, J [Departamento de Fisica de Particulas, Facultade de Fisica, 15782 Santiago de Compostela (Spain); Lobato, R [Hospital Clinico Universitario de Santiago, Santiago (Spain); Mosquera, J [Hospital Clinico Universitario de Santiago, Santiago (Spain); Pombar, M [Hospital Clinico Universitario de Santiago, Santiago (Spain); Sendon, J [Hospital Clinico Universitario de Santiago, Santiago (Spain)

    2005-04-21

    A liquid isooctane (C{sub 8}H{sub 18}) filled ionization linear array for radiotherapy quality assurance has been designed, built and tested. The detector consists of 128 pixels, each of them with an area of 1.7 mm x 1.7 mm and a gap of 0.5 mm. The small pixel size makes the detector ideal for high gradient beam profiles such as those present in intensity modulated radiation therapy (IMRT) and radiosurgery. As the read-out electronics we use the X-ray Data Acquisition System with the Xchip developed by the CCLRC. Studies concerning the collection efficiency dependence on the polarization voltage and on the dose rate have been made in order to optimize the device operation. In the first tests, we have studied dose rate and energy dependences. Dose rate dependence was found to be lower than 2.1% up to 5 Gy min{sup -1}, and energy dependence lower than 2.5% up to 20 cm depth in solid water. Output factors and penumbras for several rectangular fields have been measured with the linear array and were compared with the results obtained with a 0.125 cm{sup 3} air ionization chamber and radiographic film, respectively. Finally, we have acquired profiles for an IMRT field and for a virtual wedge. These profiles have also been compared with radiographic film measurements. All the comparisons show a good correspondence. The device has proved its capability to verify on-line therapy beams with good spatial resolution and signal-to-noise ratio.

  13. Development and operation of a pixel segmented liquid-filled linear array for radiotherapy quality assurance

    Pardo, J; Franco, L; Gomez, F; Iglesias, A; Pazos, A; Pena, J; Lobato, R; Mosquera, J; Pombar, M; Sendon, J

    2005-01-01

    A liquid isooctane (C 8 H 18 ) filled ionization linear array for radiotherapy quality assurance has been designed, built and tested. The detector consists of 128 pixels, each of them with an area of 1.7 mm x 1.7 mm and a gap of 0.5 mm. The small pixel size makes the detector ideal for high gradient beam profiles such as those present in intensity modulated radiation therapy (IMRT) and radiosurgery. As the read-out electronics we use the X-ray Data Acquisition System with the Xchip developed by the CCLRC. Studies concerning the collection efficiency dependence on the polarization voltage and on the dose rate have been made in order to optimize the device operation. In the first tests, we have studied dose rate and energy dependences. Dose rate dependence was found to be lower than 2.1% up to 5 Gy min -1 , and energy dependence lower than 2.5% up to 20 cm depth in solid water. Output factors and penumbras for several rectangular fields have been measured with the linear array and were compared with the results obtained with a 0.125 cm 3 air ionization chamber and radiographic film, respectively. Finally, we have acquired profiles for an IMRT field and for a virtual wedge. These profiles have also been compared with radiographic film measurements. All the comparisons show a good correspondence. The device has proved its capability to verify on-line therapy beams with good spatial resolution and signal-to-noise ratio

  14. Performance study of monochromatic synchrotron X-ray computed tomography using a linear array detector

    Kazama, Masahiro; Takeda, Tohoru; Itai, Yuji [Tsukuba Univ., Ibaraki (Japan). Inst. of Clinical Medicine; Akiba, Masahiro; Yuasa, Tetsuya; Hyodo, Kazuyuki; Ando, Masami; Akatsuka, Takao

    1997-09-01

    Monochromatic x-ray computed tomography (CT) using synchrotron radiation (SR) is being developed for detection of non-radioactive contrast materials at low concentration for application in clinical diagnosis. A new SR-CT system with improved contrast resolution, was constructed using a linear array detector which provides wide dynamic ranges and a double monochromator. The performance of this system was evaluated in a phantom and a rat model of brain ischemia. This system consists of a silicon (111) double crystal monochromator, an x-ray shutter, an ionization chamber, x-ray slits, a scanning table for the target organ, and an x-ray linear array detector. The research was carried out at the BLNE-5A bending magnet beam line of the Tristan Accumulation Ring in KEK, Japan. In this experiment, the reconstructed image of the spatial-resolution phantom clearly showed the 1 mm holes. At 1 mm slice thickness, the above K-edge image of the phantom showed contrast resolution at the concentration of 200 {mu}g/ml iodine-based contrast materials whereas the K-edge energy subtraction image showed contrast resolution at the concentration of 500 {mu}g/ml contrast materials. The cerebral arteries filled with iodine microspheres were clearly revealed, and the ischemic regions at the right temporal lobe and frontal lobe were depicted as non-vascular regions. The measured minimal detectable concentration of iodine on the above K-edge image is about 6 times higher than the expected value of 35.3 {mu}g/ml because of the high dark current of this detector. Thus, the use of a CCD detector which is cooled by liquid nitrogen to improve the dynamic range of the detector, is being under construction. (author)

  15. Theoretical analysis of epigenetic cell memory by nucleosome modification

    Dodd, Ian B; Micheelsen, Mille A; Sneppen, Kim

    2007-01-01

    to involve positive feedback where modified nucleosomes recruit enzymes that similarly modify nearby nucleosomes. We developed a simplified stochastic model for dynamic nucleosome modification based on the silent mating-type region of the yeast Schizosaccharomyces pombe. We show that the mechanism can give...

  16. Bearing Estimation Using Double Frequency Reassignment for a Linear Passive Array

    Czarnecki Krzysztof

    2017-09-01

    Full Text Available The paper demonstrates the use of frequency reassignment for bearing estimation. For this task, signals derived from a linear equispaced passive array are used. The presented method makes use of Fourier transformation based spatial spectrum estimation. It is further developed through the application of two-dimensional reassignment, which leads to obtaining highly concentrated energy distributions in the joint frequency-angle domain and sharp graphical imaging. The introduced method can be used for analysing, a priori, unknown signals of broadband, nonstationary, and/or multicomponent type. For such signals, the direction of arrival is obtained based upon the marginal energy distribution in the angle domain, through searching for arguments of its maxima. In the paper, bearing estimation of three popular types of sonar pulses, including linear and hyperbolic frequency modulated pulses, as well as no frequency modulation at all, is considered. The results of numerical experiments performed in the presence of additive white Gaussian noise are presented and compared to conventional digital sum-delay beamforming performed in the time domain. The root-mean-square error and the peak-to-average power ratio, also known as the crest factor, are introduced in order to estimate, respectively, the accuracy of the methods and the sharpness of the obtained energy distributions in the angle domain.

  17. Linear Array Ultrasonic Testing Of A Thick Concrete Specimens For Non-Destructive Evaluation

    Clayton, Dwight A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Khazanovich, Lev [Univ. of Minnesota, Minneapolis, MN (United States); Zammerachi, Mattia [Univ. of Minnesota, Minneapolis, MN (United States); Ezell, N. Dianne Bull [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-04-01

    The University of Minnesota and Oak Ridge National Laboratory are collaborating on the design and construction of a concrete specimen with sufficient reinforcement density and cross-sectional size to represent a light water reactor (LWR) containment wall with various defects. The preliminary analysis of the collected data using extended synthetic aperture focussin technique (SAFT) reconstruction indicated a great potential of the ultrasound array technology for locating relatively shallow distresses. However, the resolution and reliability of the analysis is inversely proportional to the defect depth and the amount of reinforcement between the measurement point and the defect location. The objective of this round of testing is to evaluate repeatability of the obtained reconstructions from measurements with different frequencies as well as to examine the effect of the duration of the sending ultrasound signal on the resulting reconstructions. Two series of testing are performed in this study. The objective of the first series is to evaluate repeatability of the measurements and resulting reconstructed images. The measurements use three center frequencies. Five measurements are performed at each location with and without lifting the device. The analysis of the collected data suggested that a linear array ultrasound system can produce reliably repeatable reconstructions using 50 kHz signals for relatively shallow depths (less than 0.5 m). However, for reconstructions at the greater depths the use of lower frequency and/or signal filtering to reduce the effect of signal noise may be required. The objective of the second series of testing is to obtain measurements with various impulse signal durations. The entire grid on the smooth surface is tested with four different various impulse signal durations. An analysis of the resulting extended SAFT reconstructions suggested that Kirchhoff-based migration leads to easier interpreting reconstructions when shorter duration

  18. Measurement of changes in linear accelerator photon energy through flatness variation using an ion chamber array

    Gao Song; Balter, Peter A.; Rose, Mark; Simon, William E.

    2013-01-01

    Purpose: To compare the use of flatness versus percent depth dose (PDD) for determining changes in photon beam energy for a megavoltage linear accelerator. Methods: Energy changes were accomplished by adjusting the bending magnet current by up to ±15% in 5% increments away from the value used clinically. Two metrics for flatness, relative flatness in the central 80% of the field (Flat) and average maximum dose along the diagonals normalized by central axis dose (F DN ), were measured using a commercially available planner ionization chamber array. PDD was measured in water at depths of 5 and 10 cm in 3 × 3 cm 2 and 10 × 10 cm 2 fields using a cylindrical chamber. Results: PDD was more sensitive to changes in energy when the beam energy was increased than when it was decreased. For the 18-MV beam in particular, PDD was not sensitive to energy reductions below the nominal energy. The value of Flat was found to be more sensitive to decreases in energy than to increases, with little sensitivity to energy increases above the nominal energy for 18-MV beams. F DN was the only metric that was found to be sensitive to both increases and reductions of energy for both the 6- and 18-MV beams. Conclusions: Flatness based metrics were found to be more sensitive to energy changes than PDD, In particular, F DN was found to be the most sensitive metric to energy changes for photon beams of 6 and 18 MV. The ionization chamber array allows this metric to be conveniently measured as part of routine accelerator quality assurance.

  19. P-S & S-P Elastic Wave Conversions from Linear Arrays of Oriented Microcracks

    Jiang, L.; Modiriasari, A.; Bobet, A.; Pyrak-Nolte, L. J.

    2017-12-01

    Natural and induced processes can produce oriented mechanical discontinuities such as en echelon cracks, fractures and faults. Previous research has shown that compressional to shear (P-S) wave conversions occur at normal incidence to a fracture because of cross-coupling fracture compliances (Nakagawa et al., 2000). Here, experiments and computer simulation are presented to demonstrate the link among cross-coupling stiffness, microcrack orientation and energy partitioning among P, S, and P-S/S-P waves. A FormLabs 2 3D printer was used to fabricate 7 samples (50 mm x 50 mm x 100 mm) with linear arrays of microcracks oriented at 0, 15, 30, 45, 60, 75, and 900 with a print resolution of 0.025 mm. The microcracks were elliptical in cross-sections (2 mm long by 1 mm wide), through the 50 mm thickness of sample, and spaced 3 mm (center-to-center for adjacent cracks). A 25 mm length of each sample contained no microcracks to act as a reference material. Broadband transducers (0.2-1.5 MHz) were used to transmit and receive P and polarized S wave signals that were propagated at normal incidence to the linear array of microcracks. P-wave amplitude increased, while S-wave amplitude remained relatively constant, as the microcrack orientation increased from 0o to 90o. At normal incidence, P-S and S-P wave conversions emerged and increased in amplitude as the crack inclination increased from 00 to 450. From 450 to 900, the amplitude of these converted modes decreased. Between negative and positive crack angles, the P-to-S and S-to-P waves were 1800 phase reversed. The observed energy partitioning matched the computed compliances obtained from numerical simulations with ABAQUS. The cross-coupling compliance for cracks inclined at 450 was found to be the smallest magnitude. 3D printing enabled the study of microstructural effects on macro-scale wave measurements. Information on the orientation of microcracks or even en echelon fractures and faults is contained in P-S conversions

  20. Dynamic nucleosome organization at hox promoters during zebrafish embryogenesis.

    Steven E Weicksel

    Full Text Available Nucleosome organization at promoter regions plays an important role in regulating gene activity. Genome-wide studies in yeast, flies, worms, mammalian embryonic stem cells and transformed cell lines have found well-positioned nucleosomes flanking a nucleosome depleted region (NDR at transcription start sites. This nucleosome arrangement depends on DNA sequence (cis-elements as well as DNA binding factors and ATP-dependent chromatin modifiers (trans-factors. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome must undergo a broad reprogramming event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development, we map nucleosome positions at the promoter region of 37 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a progressive process that takes place over several stages. At stages immediately after fertilization, nucleosomes appear to be largely disordered at hox promoter regions. At stages after activation of the embryonic genome, nucleosomes are detectable at hox promoters, with positions becoming more uniform and more highly occupied. Since the genomic sequence is invariant during embryogenesis, this progressive change in nucleosome arrangement suggests that trans-factors play an important role in organizing nucleosomes during embryogenesis. Separating hox genes into expressed and non-expressed groups shows that expressed promoters have better positioned and occupied nucleosomes, as well as distinct NDRs, than non-expressed promoters. Finally, by blocking the retinoic acid-signaling pathway, we disrupt early hox gene transcription, but observe no effect on nucleosome positions, suggesting that active hox transcription is not a driving force behind the arrangement of nucleosomes at the promoters of hox genes during early development.

  1. Using a 2D detector array for meaningful and efficient linear accelerator beam property validations.

    Ritter, Timothy A; Gallagher, Ian; Roberson, Peter L

    2014-11-08

    Following linear accelerator commissioning, the qualified medical physicist is responsible for monitoring the machine's ongoing performance, detecting and investigating any changes in beam properties, and assessing the impact of unscheduled repairs. In support of these responsibilities, the authors developed a method of using a 2D ionization chamber array to efficiently test and validate important linear accelerator photon beam properties. A team of three physicists identified critical properties of the accelerator and developed constancy tests that were sensitive to each of the properties. The result was a 14-field test plan. The test plan includes large and small fields at varying depths, a reduced SSD field at shallow depth for sensitivity to extra focal photon and electron components, and analysis of flatness, symmetry, dose, dose profiles, and dose ratios. Constancy tests were repeated five times over a period of six weeks and used to set upper and lower investigation levels at ± 3 SDs. Deliberate variations in output, penumbra, and energy were tested to determine the suitability of the proposed method. Measurements were also performed on a similar, but distinct, machine to assess test sensitivity. The results demonstrated upper and lower investigation levels significantly smaller than the comparable TG-142 annual recommendations, with the exception of the surrogate used for output calibration, which still fell within the TG-142 monthly recommendation. Subtle changes in output, beam energy, and penumbra were swiftly identified for further investigation. The test set identified the distinct nature of the second accelerator. The beam properties of two photon energies can be validated in approximately 1.5 hrs using this method. The test suite can be used to evaluate the impact of minor repairs, detect changes in machine performance over time, and supplement other machine quality assurance testing.

  2. [A capillary blood flow velocity detection system based on linear array charge-coupled devices].

    Zhou, Houming; Wang, Ruofeng; Dang, Qi; Yang, Li; Wang, Xiang

    2017-12-01

    In order to detect the flow characteristics of blood samples in the capillary, this paper introduces a blood flow velocity measurement system based on field-programmable gate array (FPGA), linear charge-coupled devices (CCD) and personal computer (PC) software structure. Based on the analysis of the TCD1703C and AD9826 device data sheets, Verilog HDL hardware description language was used to design and simulate the driver. Image signal acquisition and the extraction of the real-time edge information of the blood sample were carried out synchronously in the FPGA. Then a series of discrete displacement were performed in a differential operation to scan each of the blood samples displacement, so that the sample flow rate could be obtained. Finally, the feasibility of the blood flow velocity detection system was verified by simulation and debugging. After drawing the flow velocity curve and analyzing the velocity characteristics, the significance of measuring blood flow velocity is analyzed. The results show that the measurement of the system is less time-consuming and less complex than other flow rate monitoring schemes.

  3. MLAOS: A Multi-Point Linear Array of Optical Sensors for Coniferous Foliage Clumping Index Measurement

    Yonghua Qu

    2014-05-01

    Full Text Available The canopy foliage clumping effect is primarily caused by the non-random distribution of canopy foliage. Currently, measurements of clumping index (CI by handheld instruments is typically time- and labor-intensive. We propose a low-cost and low-power automatic measurement system called Multi-point Linear Array of Optical Sensors (MLAOS, which consists of three above-canopy and nine below-canopy optical sensors that capture plant transmittance at different times of the day. Data communication between the MLAOS node is facilitated by using a ZigBee network, and the data are transmitted from the field MLAOS to a remote data server using the Internet. The choice of the electronic element and design of the MLAOS software is aimed at reducing costs and power consumption. A power consumption test showed that, when a 4000 mAH Li-ion battery is used, a maximum of 8–10 months of work can be achieved. A field experiment on a coniferous forest revealed that the CI of MLAOS may reveal a clumping effect that occurs within the canopy. In further work, measurement of the multi-scale clumping effect can be achieved by utilizing a greater number of MLAOS devices to capture the heterogeneity of the plant canopy.

  4. Application of Hybrid Optimization Algorithm in the Synthesis of Linear Antenna Array

    Ezgi Deniz Ülker

    2014-01-01

    Full Text Available The use of hybrid algorithms for solving real-world optimization problems has become popular since their solution quality can be made better than the algorithms that form them by combining their desirable features. The newly proposed hybrid method which is called Hybrid Differential, Particle, and Harmony (HDPH algorithm is different from the other hybrid forms since it uses all features of merged algorithms in order to perform efficiently for a wide variety of problems. In the proposed algorithm the control parameters are randomized which makes its implementation easy and provides a fast response. This paper describes the application of HDPH algorithm to linear antenna array synthesis. The results obtained with the HDPH algorithm are compared with three merged optimization techniques that are used in HDPH. The comparison shows that the performance of the proposed algorithm is comparatively better in both solution quality and robustness. The proposed hybrid algorithm HDPH can be an efficient candidate for real-time optimization problems since it yields reliable performance at all times when it gets executed.

  5. Three-dimensional optoacoustic tomography using a conventional ultrasound linear detector array: whole-body tomographic system for small animals.

    Gateau, Jerome; Caballero, Miguel Angel Araque; Dima, Alexander; Ntziachristos, Vasilis

    2013-01-01

    Optoacoustic imaging relies on the detection of ultrasonic waves induced by laser pulse excitations to map optical absorption in biological tissue. A tomographic geometry employing a conventional ultrasound linear detector array for volumetric optoacoustic imaging is reported. The geometry is based on a translate-rotate scanning motion of the detector array, and capitalizes on the geometrical characteristics of the transducer assembly to provide a large solid angular detection aperture. A system for three-dimensional whole-body optoacoustic tomography of small animals is implemented. The detection geometry was tested using a 128-element linear array (5.0∕7.0 MHz, Acuson L7, Siemens), moved by steps with a rotation∕translation stage assembly. Translation and rotation range of 13.5 mm and 180°, respectively, were implemented. Optoacoustic emissions were induced in tissue-mimicking phantoms and ex vivo mice using a pulsed laser operating in the near-IR spectral range at 760 nm. Volumetric images were formed using a filtered backprojection algorithm. The resolution of the optoacoustic tomography system was measured to be better than 130 μm in-plane and 330 μm in elevation (full width half maximum), and to be homogenous along a 15 mm diameter cross section due to the translate-rotate scanning geometry. Whole-body volumetric optoacoustic images of mice were performed ex vivo, and imaged organs and blood vessels through the intact abdominal and head regions were correlated to the mouse anatomy. Overall, the feasibility of three-dimensional and high-resolution whole-body optoacoustic imaging of small animal using a conventional linear array was demonstrated. Furthermore, the scanning geometry may be used for other linear arrays and is therefore expected to be of great interest for optoacoustic tomography at macroscopic and mesoscopic scale. Specifically, conventional detector arrays with higher central frequencies may be investigated.

  6. Sonography of the chest using linear-array versus sector transducers: Correlation with auscultation, chest radiography, and computed tomography.

    Tasci, Ozlem; Hatipoglu, Osman Nuri; Cagli, Bekir; Ermis, Veli

    2016-07-08

    The primary purpose of our study was to compare the efficacies of two sonographic (US) probes, a high-frequency linear-array probe and a lower-frequency phased-array sector probe in the diagnosis of basic thoracic pathologies. The secondary purpose was to compare the diagnostic performance of thoracic US with auscultation and chest radiography (CXR) using thoracic CT as a gold standard. In total, 55 consecutive patients scheduled for thoracic CT were enrolled in this prospective study. Four pathologic entities were evaluated: pneumothorax, pleural effusion, consolidation, and interstitial syndrome. A portable US scanner was used with a 5-10-MHz linear-array probe and a 1-5-MHz phased-array sector probe. The first probe used was chosen randomly. US, CXR, and auscultation results were compared with the CT results. The linear-array probe had the highest performance in the identification of pneumothorax (83% sensitivity, 100% specificity, and 99% diagnostic accuracy) and pleural effusion (100% sensitivity, 97% specificity, and 98% diagnostic accuracy); the sector probe had the highest performance in the identification of consolidation (89% sensitivity, 100% specificity, and 95% diagnostic accuracy) and interstitial syndrome (94% sensitivity, 93% specificity, and 94% diagnostic accuracy). For all pathologies, the performance of US was superior to those of CXR and auscultation. The linear probe is superior to the sector probe for identifying pleural pathologies, whereas the sector probe is superior to the linear probe for identifying parenchymal pathologies. Thoracic US has better diagnostic performance than CXR and auscultation for the diagnosis of common pathologic conditions of the chest. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 44:383-389, 2016. © 2016 Wiley Periodicals, Inc.

  7. Nucleosome-coupled expression differences in closely-related species

    Gebbia Marinella

    2011-09-01

    Full Text Available Abstract Background Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown. Results We address this challenge by generating nucleosome positioning and cell cycle expression data for Saccharomyces bayanus and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, S. bayanus and S. cerevisiae. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs. Conclusions Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.

  8. Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution.

    Pawandeep Dhami

    2010-08-01

    Full Text Available It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II occupancy show preferential association with exons ("exon-intron marking", linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.

  9. Exploring the Link between Nucleosome Occupancy and DNA Methylation

    Cecilia Lövkvist

    2018-01-01

    Full Text Available Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies imply a causal link where CpG methylation might induce nucleosome formation, whereas others argue the opposite, i.e., that nucleosome occupancy might influence CpG methylation. Correlations are indeed evident between nucleosomes, CpG density and CpG methylation—at least near promoter sites. It is however less established whether there is an immediate causal relation between nucleosome occupancy and the presence of CpG sites—or if nucleosome occupancy could be influenced by other factors. In this work, we test for such causality in human genomes by analyzing the three quantities both near and away from promoter sites. For data from the human genome we compare promoter regions with given CpG densities with genomic regions without promoters but of similar CpG densities. We find the observed correlation between nucleosome occupancy and CpG density, respectively CpG methylation, to be specific to promoter regions. In other regions along the genome nucleosome occupancy is statistically independent of the positioning of CpGs or their methylation levels. Anti-correlation between CpG density and methylation level is however similarly strong in both regions. On promoters, nucleosome occupancy is more strongly affected by the level of gene expression than CpG density or CpG methylation—calling into question any direct causal relation between nucleosome occupancy and CpG organization. Rather, our results suggest that for organisms with cytosine methylation nucleosome occupancy might be primarily linked to gene expression, with no strong impact on methylation.

  10. Interaction of influenza virus proteins with nucleosomes

    Garcia-Robles, Inmaculada; Akarsu, Hatice; Mueller, Christoph W.; Ruigrok, Rob W.H.; Baudin, Florence

    2005-01-01

    During influenza virus infection, transcription and replication of the viral RNA take place in the cell nucleus. Directly after entry in the nucleus the viral ribonucleoproteins (RNPs, the viral subunits containing vRNA, nucleoprotein and the viral polymerase) are tightly associated with the nuclear matrix. Here, we have analysed the binding of RNPs, M1 and NS2/NEP proteins to purified nucleosomes, reconstituted histone octamers and purified single histones. RNPs and M1 both bind to the chromatin components but at two different sites, RNP to the histone tails and M1 to the globular domain of the histone octamer. NS2/NEP did not bind to nucleosomes at all. The possible consequences of these findings for nuclear release of newly made RNPs and for other processes during the infection cycle are discussed

  11. Optimal design of a double-sided linear motor with a multi-segmented trapezoidal magnet array for a high precision positioning system

    Lee, Moon G.; Gweon, Dae-Gab

    2004-01-01

    A comparative analysis is performed for linear motors adopting conventional and multi-segmented trapezoidal (MST) magnet arrays, respectively, for a high-precision positioning system. The proposed MST magnet array is a modified version of a Halbach magnet array. The MST array has trapezoidal magnets with variable shape and dimensions while the Halbach magnet array generally has a rectangular magnet with identical dimensions. We propose a new model that can describe the magnetic field resulting from the complex-shaped magnets. The model can be applied to both MST and conventional magnet arrays. Using the model, a design optimization of the two types of linear motors is performed and compared. The magnet array with trapezoidal magnets can produce more force than one with rectangular magnets when they are arrayed in a linear motor where there is a yoke with high permeability. After the optimization and comparison, we conclude that the linear motor with the MST magnet array can generate more actuating force per volume than the motor with the conventional array. In order to satisfy the requirements of next generation systems such as high resolution, high speed, and long stroke, the use of a linear motor with a MST array as an actuator in a high precision positioning system is recommended from the results obtained here

  12. Geometric Potential Assessment for ZY3-02 Triple Linear Array Imagery

    Kai Xu

    2017-06-01

    Full Text Available ZiYuan3-02 (ZY3-02 is the first remote sensing satellite for the development of China’s civil space infrastructure (CCSI and the second satellite in the ZiYuan3 series; it was launched successfully on 30 May 2016, aboard the CZ-4B rocket at the Taiyuan Satellite Launch Center (TSLC in China. Core payloads of ZY3-02 include a triple linear array camera (TLC and a multi-spectral camera, and this equipment will be used to acquire space geographic information with high-resolution and stereoscopic observations. Geometric quality is a key factor that affects the performance and potential of satellite imagery. For the purpose of evaluating comprehensively the geometric potential of ZY3-02, this paper introduces the method used for geometric calibration of the TLC onboard the satellite and a model for sensor corrected (SC products that serve as basic products delivered to users. Evaluation work was conducted by making a full assessment of the geometric performance. Furthermore, images of six regions and corresponding reference data were collected to implement the geometric calibration technique and evaluate the resulting geometric accuracy. Experimental results showed that the direct location performance and internal accuracy of SC products increased remarkably after calibration, and the planimetric and vertical accuracies with relatively few ground control points (GCPs were demonstrated to be better than 2.5 m and 2 m, respectively. Additionally, the derived digital surface model (DSM accuracy was better than 3 m (RMSE for flat terrain and 5 m (RMSE for mountainous terrain. However, given that several variations such as changes in the thermal environment can alter the camera’s installation angle, geometric performance will vary with the geographical location and imaging time changes. Generally, ZY3-02 can be used for 1:50,000 stereo mapping and can produce (and update larger-scale basic geographic information products.

  13. Numerical implementation of magneto-acousto-electrical tomography (MAET) using a linear phased array transducer

    Soner Gözü, Mehmet; Zengin, Reyhan; Güneri Gençer, Nevzat

    2018-02-01

    In this study, the performance and implementation of magneto-acousto-electrical tomography (MAET) is investigated using a linear phased array (LPA) transducer. The goal of MAET is to image the conductivity distribution in biological bodies. It uses the interaction between ultrasound and a static magnetic field to generate velocity current density distribution inside the body. The resultant voltage due to velocity current density is sensed by surface electrodes attached on the body. In this study, the theory of MAET is reviewed. A 16-element LPA transducer with 1 MHz excitation frequency is used to provide beam directivity and steerability of acoustic waves. Different two-dimensional numerical models of breast and tumour are formed to analyze the multiphysics problem coupled with acoustics and electromagnetic fields. In these models, velocity current density distributions are obtained for pulse type ultrasound excitations. The static magnetic field is assumed as 1 T. To sense the resultant voltage caused by the velocity current density, it is assumed that two electrodes are attached on the surface of the body. The performance of MAET is shown through sensitivity matrix analysis. The sensitivity matrix is obtained for two transducer positions with 13 steering angles between -30\\circ to 30\\circ with 5\\circ angular intervals. For the reconstruction of the images, truncated singular value decomposition method is used with different signal-to-noise ratio (SNR) values (20 dB, 40 dB, 60 dB and 80 dB). The resultant images show that the perturbation (5 mm  ×  5 mm) placed 35 mm depth can be detected even if the SNR is 20 dB.

  14. Disappearance of nucleosome positioning in mitotic chromatin in vivo.

    Komura, Jun-ichiro; Ono, Tetsuya

    2005-04-15

    During mitosis, transcription is silenced and most transcription factors are displaced from their recognition sequences. By in vivo footprinting analysis, we have confirmed and extended previous studies showing loss of transcription factors from an RNA polymerase II promoter (c-FOS) and, for the first time, an RNA polymerase III promoter (U6) in HeLa cells. Because little was known about nucleosomal organization in mitotic chromosomes, we performed footprinting analysis for nucleosomes on these promoters in interphase and mitotic cells. During interphase, each of the promoters had a positioned nucleosome in the region intervening between proximal promoter elements and distal enhancer elements, but the strong nucleosome positioning disappeared during mitosis. Thus, the nucleosomal organization that appears to facilitate transcription in interphase cells may be lost in mitotic cells, and nucleosome positioning during mitosis does not seem to be a major component of the epigenetic mechanisms to mark genes for rapid reactivation after this phase.

  15. Efficient Narrowband Direction of Arrival Estimation Based on a Combination of Uniform Linear/Shirvani-Akbari Arrays

    Shahriar Shirvani Moghaddam

    2012-01-01

    Full Text Available Uniform linear array (ULA geometry does not perform well for direction of arrival (DOA estimation at directions close to the array endfires. Shirvani and Akbari solved this problem by displacing two elements from both ends of the ULA to the top and/or bottom of the array axis. Shirvani-Akbari array (SAA presents a considerable improvement in the DOA estimation of narrowband sources arriving at endfire directions in terms of DOA estimation accuracy and angular resolution. In this paper, all new proposed SAA configurations are modelled and also examined, numerically. In this paper, two well-known DOA estimation algorithms, multiple signal classification (MUSIC and minimum variance distortionless response (MVDR, are used to evaluate the effectiveness of proposed arrays using total root mean square error (RMSE criterion. In addition, two new scenarios are proposed which divide angular search to two parts, directions close to array endfires as well as middle angles. For middle angles, which belong to (−70∘≤≤70∘, ULA is considered, and for endfire angles, the angles which belong to (−90∘≤≤−70∘ and (70∘≤≤90∘, SAA is considered. Simulation results of new proposed scenarios for DOA estimation of narrowband signals show the better performance with lower computational load.

  16. Routes to DNA Accessibility: Alternative Pathways for Nucleosome Unwinding

    Schlingman, Daniel J.; Mack, Andrew H.; Kamenetska, Masha; Mochrie, Simon G.J.; Regan, Lynne

    2014-01-01

    The dynamic packaging of DNA into chromatin is a key determinant of eukaryotic gene regulation and epigenetic inheritance. Nucleosomes are the basic unit of chromatin, and therefore the accessible states of the nucleosome must be the starting point for mechanistic models regarding these essential processes. Although the existence of different unwound nucleosome states has been hypothesized, there have been few studies of these states. The consequences of multiple states are far reaching. Thes...

  17. Prediction of nucleosome positioning based on transcription factor binding sites.

    Xianfu Yi

    Full Text Available BACKGROUND: The DNA of all eukaryotic organisms is packaged into nucleosomes, the basic repeating units of chromatin. The nucleosome consists of a histone octamer around which a DNA core is wrapped and the linker histone H1, which is associated with linker DNA. By altering the accessibility of DNA sequences, the nucleosome has profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is of great importance for the study of genomic control mechanisms. Transcription factors (TFs have been suggested to play a role in nucleosome positioning in vivo. PRINCIPAL FINDINGS: Here, the minimum redundancy maximum relevance (mRMR feature selection algorithm, the nearest neighbor algorithm (NNA, and the incremental feature selection (IFS method were used to identify the most important TFs that either favor or inhibit nucleosome positioning by analyzing the numbers of transcription factor binding sites (TFBSs in 53,021 nucleosomal DNA sequences and 50,299 linker DNA sequences. A total of nine important families of TFs were extracted from 35 families, and the overall prediction accuracy was 87.4% as evaluated by the jackknife cross-validation test. CONCLUSIONS: Our results are consistent with the notion that TFs are more likely to bind linker DNA sequences than the sequences in the nucleosomes. In addition, our results imply that there may be some TFs that are important for nucleosome positioning but that play an insignificant role in discriminating nucleosome-forming DNA sequences from nucleosome-inhibiting DNA sequences. The hypothesis that TFs play a role in nucleosome positioning is, thus, confirmed by the results of this study.

  18. Modelling of the thermal parameters of high-power linear laser-diode arrays. Two-dimensional transient model

    Bezotosnyi, V V; Kumykov, Kh Kh

    1998-01-01

    A two-dimensional transient thermal model of an injection laser is developed. This model makes it possible to analyse the temperature profiles in pulsed and cw stripe lasers with an arbitrary width of the stripe contact, and also in linear laser-diode arrays. This can be done for any durations and repetition rates of the pump pulses. The model can also be applied to two-dimensional laser-diode arrays operating quasicontinuously. An analysis is reported of the influence of various structural parameters of a diode array on the thermal regime of a single laser. The temperature distributions along the cavity axis are investigated for different variants of mounting a crystal on a heat sink. It is found that the temperature drop along the cavity length in cw and quasi-cw laser diodes may exceed 20%. (lasers)

  19. Surgical Workflow Analysis: Ideal Application of Navigated Linear Array Ultrasound in Low-Grade Glioma Surgery.

    Lothes, Thomas Ernst; Siekmann, Max; König, Ralph Werner; Wirtz, Christian Rainer; Coburger, Jan

    2016-11-01

    Background  Intraoperative imaging in low-grade glioma (LGG) surgery can facilitate residual tumor control and improve surgical outcome. The aim of the study was to evaluate the ideal application and typical interactions of intraoperative MRI (iMRI), conventional low-frequency intraoperative ultrasound (cioUS), and high-frequency linear array intraoperative ultrasound (lioUS) to optimize surgical workflow. Methods  Prospectively, we included 11 patients with an LGG. Typical procedural workflow in the iMRI suite was recorded with a compatible software. We took notes of duration, frequency of application, the surgeon's evaluation of image quality, and the respective benefit of lioUS (15 MHz), cioUS (7 MHz), and iMRI (1.5 T). With the help of the workflow software, we meticulously analyzed ∼ 55 hours of surgery. Results  During the interventions, lioUS was used more often (76.3%) than cioUS (23.7%) and showed a better mean image quality (1 = best to 6 = worst) of 2.08 versus 3.26 with cioUS. The benefit of the lioUS application was rated with an average of 2.27, whereas the cioUS probe only reached a mean value of 3.83. The most common application of lioUS was resection control (42.6%); cioUS was used mainly for orientation (63.2%). Overall, lioUS was used more often and was rated better for both the purposes just described regarding image quality and benefit. Estimated residual tumor based on lioUS alone was lower than the final residual tumor detected with iMRI (7.5% versus 14.5%). The latter technique was rated as the best imaging modality for resection control in all cases followed by lioUS. Conclusion  We provide proof of principle for workflow assessment in cranial neurosurgery. Although iMRI remains the imaging method of choice, lioUS has shown to be beneficial in a combined setup. Evaluation of lioUS was significantly superior to cioUS in most indications except for subcortical lesions. Georg Thieme Verlag KG Stuttgart · New York.

  20. Ambient noise adjoint tomography for a linear array in North China

    Zhang, C.; Yao, H.; Liu, Q.; Yuan, Y. O.; Zhang, P.; Feng, J.; Fang, L.

    2017-12-01

    Ambient noise tomography based on dispersion data and ray theory has been widely utilized for imaging crustal structures. In order to improve the inversion accuracy, ambient noise tomography based on the 3D adjoint approach or full waveform inversion has been developed recently, however, the computational cost is tremendous. In this study we present 2D ambient noise adjoint tomography for a linear array in north China with significant computational efficiency compared to 3D ambient noise adjoint tomography. During the preprocessing, we first convert the observed data in 3D media, i.e., surface-wave empirical Green's functions (EGFs) from ambient noise cross-correlation, to the reconstructed EGFs in 2D media using a 3D/2D transformation scheme. Different from the conventional steps of measuring phase dispersion, the 2D adjoint tomography refines 2D shear wave speeds along the profile directly from the reconstructed Rayleigh wave EGFs in the period band 6-35s. With the 2D initial model extracted from the 3D model from traditional ambient noise tomography, adjoint tomography updates the model by minimizing the frequency-dependent Rayleigh wave traveltime misfits between the reconstructed EGFs and synthetic Green function (SGFs) in 2D media generated by the spectral-element method (SEM), with a preconditioned conjugate gradient method. The multitaper traveltime difference measurement is applied in four period bands during the inversion: 20-35s, 15-30s, 10-20s and 6-15s. The recovered model shows more detailed crustal structures with pronounced low velocity anomaly in the mid-lower crust beneath the junction of Taihang Mountains and Yin-Yan Mountains compared with the initial model. This low velocity structure may imply the possible intense crust-mantle interactions, probably associated with the magmatic underplating during the Mesozoic to Cenozoic evolution of the region. To our knowledge, it's first time that ambient noise adjoint tomography is implemented in 2D media

  1. Fabrication of long linear arrays of plastic optical fibers with squared ends for the use of code mark printing lithography

    Horiuchi, Toshiyuki; Watanabe, Jun; Suzuki, Yuta; Iwasaki, Jun-ya

    2017-05-01

    Two dimensional code marks are often used for the production management. In particular, in the production lines of liquid-crystal-display panels and others, data on fabrication processes such as production number and process conditions are written on each substrate or device in detail, and they are used for quality managements. For this reason, lithography system specialized in code mark printing is developed. However, conventional systems using lamp projection exposure or laser scan exposure are very expensive. Therefore, development of a low-cost exposure system using light emitting diodes (LEDs) and optical fibers with squared ends arrayed in a matrix is strongly expected. In the past research, feasibility of such a new exposure system was demonstrated using a handmade system equipped with 100 LEDs with a central wavelength of 405 nm, a 10×10 matrix of optical fibers with 1 mm square ends, and a 10X projection lens. Based on these progresses, a new method for fabricating large-scale arrays of finer fibers with squared ends was developed in this paper. At most 40 plastic optical fibers were arranged in a linear gap of an arraying instrument, and simultaneously squared by heating them on a hotplate at 120°C for 7 min. Fiber sizes were homogeneous within 496+/-4 μm. In addition, average light leak was improved from 34.4 to 21.3% by adopting the new method in place of conventional one by one squaring method. Square matrix arrays necessary for printing code marks will be obtained by piling the newly fabricated linear arrays up.

  2. Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

    Lajla Bruntse Hansen

    Full Text Available We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2. Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA and from rabbit serum albumin (RSA were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

  3. Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays.

    Hansen, Lajla Bruntse; Buus, Soren; Schafer-Nielsen, Claus

    2013-01-01

    We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm(2). Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.

  4. Synthesis of Phase-Only Reconfigurable Linear Arrays Using Multiobjective Invasive Weed Optimization Based on Decomposition

    Yan Liu

    2014-01-01

    Full Text Available Synthesis of phase-only reconfigurable array aims at finding a common amplitude distribution and different phase distributions for the array to form different patterns. In this paper, the synthesis problem is formulated as a multiobjective optimization problem and solved by a new proposed algorithm MOEA/D-IWO. First, novel strategies are introduced in invasive weed optimization (IWO to make original IWO fit for solving multiobjective optimization problems; then, the modified IWO is integrated into the framework of the recently well proved competitive multiobjective optimization algorithm MOEA/D to form a new competitive MOEA/D-IWO algorithm. At last, two sets of experiments are carried out to illustrate the effectiveness of MOEA/D-IWO. In addition, MOEA/D-IWO is compared with MOEA/D-DE, a new version of MOEA/D. The comparing results show the superiority of MOEA/D-IWO and indicate its potential for solving the antenna array synthesis problems.

  5. Study on data acquisition circuit used in SSPA linear array detector X-ray detection

    Wei Biao; Che Zhen Ping

    2002-01-01

    After SSPA used as X-ray array detector is developed, the authors take a research on the data acquisition circuit applied to the detector. The experiment designed has verified the feasibility of application of this array detector and its data acquisition circuit to X-ray computed tomography (X-CT). The preliminary test results indicate that the method of the X-ray detection is feasible for industry X-CT nondestructive testing, which brings about advantage for detecting and measuring with high resolution, good efficiency and low cost

  6. Improvement of resolution in full-view linear-array photoacoustic computed tomography using a novel adaptive weighting method

    Omidi, Parsa; Diop, Mamadou; Carson, Jeffrey; Nasiriavanaki, Mohammadreza

    2017-03-01

    Linear-array-based photoacoustic computed tomography is a popular methodology for deep and high resolution imaging. However, issues such as phase aberration, side-lobe effects, and propagation limitations deteriorate the resolution. The effect of phase aberration due to acoustic attenuation and constant assumption of the speed of sound (SoS) can be reduced by applying an adaptive weighting method such as the coherence factor (CF). Utilizing an adaptive beamforming algorithm such as the minimum variance (MV) can improve the resolution at the focal point by eliminating the side-lobes. Moreover, invisibility of directional objects emitting parallel to the detection plane, such as vessels and other absorbing structures stretched in the direction perpendicular to the detection plane can degrade resolution. In this study, we propose a full-view array level weighting algorithm in which different weighs are assigned to different positions of the linear array based on an orientation algorithm which uses the histogram of oriented gradient (HOG). Simulation results obtained from a synthetic phantom show the superior performance of the proposed method over the existing reconstruction methods.

  7. Characterization and linear array LA48 Commissioner for measuring the position of the multi leaf collimator; Caracterizacion y comisionado del linear array LA48 para medir el posicionamiento del colimador multilaminas

    Conles Picos, I.; Cenizo de Castro, E.; Aparicio martin, A. R.; Barrio Lazo, F.; Cesteros Morante, M. J.

    2011-07-01

    The protocol of Quality Control of electron accelerators for medical use of SEFM proposed for multi leaf collimation system (MLC) to verify the positioning of the blades connect. To do this you must find a system with sufficient accuracy and precision and, if possible, easy to assemble and offers real-time results. One of these teams is the Linear Array of PTW-Freiburg (LA48), which consists of a row of 47 ionization chambers, of 0008 cc and 8 mm apart from each other. In this paper, we describe our process of characterization and LA48 commissioner. (Author)

  8. Two-dimensional mapping of needle visibility with linear and curved array for ultrasound-guided interventional procedure

    Susanti, Hesty; Suprijanto, Kurniadi, Deddy

    2018-02-01

    Needle visibility in ultrasound-guided technique has been a crucial factor for successful interventional procedure. It has been affected by several factors, i.e. puncture depth, insertion angle, needle size and material, and imaging technology. The influences of those factors made the needle not always well visible. 20 G needles of 15 cm length (Nano Line, facet) were inserted into water bath with variation of insertion angles and depths. Ultrasound measurements are performed with BK-Medical Flex Focus 800 using 12 MHz linear array and 5 MHz curved array in Ultrasound Guided Regional Anesthesia mode. We propose 3 criteria to evaluate needle visibility, i.e. maximum intensity, mean intensity, and the ratio between minimum and maximum intensity. Those criteria were then depicted into representative maps for practical purpose. The best criterion candidate for representing the needle visibility was criterion 1. Generally, the appearance pattern of the needle from this criterion was relatively consistent, i.e. for linear array, it was relatively poor visibility in the middle part of the shaft, while for curved array, it is relatively better visible toward the end of the shaft. With further investigations, for example with the use of tissue-mimicking phantom, the representative maps can be built for future practical purpose, i.e. as a tool for clinicians to ensure better needle placement in clinical application. It will help them to avoid the "dead" area where the needle is not well visible, so it can reduce the risks of vital structures traversing and the number of required insertion, resulting in less patient morbidity. Those simple criteria and representative maps can be utilized to evaluate general visibility patterns of the needle in vast range of needle types and sizes in different insertion media. This information is also important as an early investigation for future research of needle visibility improvement, i.e. the development of beamforming strategies and

  9. Nature of the Nucleosomal Barrier to RNA Polymerase II | Center for Cancer Research

    In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation (arrest) of the pol II core enzyme. To determine potential mechanisms making nucleosomes transparent to transcription in vivo, we analyzed the nature of the nucleosome-induced arrest. We found that the arrests

  10. A Mixed-Integer Linear Programming approach to wind farm layout and inter-array cable routing

    Fischetti, Martina; Leth, John-Josef; Borchersen, Anders Bech

    2015-01-01

    A Mixed-Integer Linear Programming (MILP) approach is proposed to optimize the turbine allocation and inter-array offshore cable routing. The two problems are considered with a two steps strategy, solving the layout problem first and then the cable problem. We give an introduction to both problems...... and present the MILP models we developed to solve them. To deal with interference in the onshore cases, we propose an adaptation of the standard Jensen’s model, suitable for 3D cases. A simple Stochastic Programming variant of our model allows us to consider different wind scenarios in the optimization...

  11. Linear distributed source modeling of local field potentials recorded with intra-cortical electrode arrays.

    Rikkert Hindriks

    Full Text Available Planar intra-cortical electrode (Utah arrays provide a unique window into the spatial organization of cortical activity. Reconstruction of the current source density (CSD underlying such recordings, however, requires "inverting" Poisson's equation. For inter-laminar recordings, this is commonly done by the CSD method, which consists in taking the second-order spatial derivative of the recorded local field potentials (LFPs. Although the CSD method has been tremendously successful in mapping the current generators underlying inter-laminar LFPs, its application to planar recordings is more challenging. While for inter-laminar recordings the CSD method seems reasonably robust against violations of its assumptions, is it unclear as to what extent this holds for planar recordings. One of the objectives of this study is to characterize the conditions under which the CSD method can be successfully applied to Utah array data. Using forward modeling, we find that for spatially coherent CSDs, the CSD method yields inaccurate reconstructions due to volume-conducted contamination from currents in deeper cortical layers. An alternative approach is to "invert" a constructed forward model. The advantage of this approach is that any a priori knowledge about the geometrical and electrical properties of the tissue can be taken into account. Although several inverse methods have been proposed for LFP data, the applicability of existing electroencephalographic (EEG and magnetoencephalographic (MEG inverse methods to LFP data is largely unexplored. Another objective of our study therefore, is to assess the applicability of the most commonly used EEG/MEG inverse methods to Utah array data. Our main conclusion is that these inverse methods provide more accurate CSD reconstructions than the CSD method. We illustrate the inverse methods using event-related potentials recorded from primary visual cortex of a macaque monkey during a motion discrimination task.

  12. Performance of a high-resolution depth-encoding PET detector module using linearly-graded SiPM arrays

    Du, Junwei; Bai, Xiaowei; Gola, Alberto; Acerbi, Fabio; Ferri, Alessandro; Piemonte, Claudio; Yang, Yongfeng; Cherry, Simon R.

    2018-02-01

    The goal of this study was to exploit the excellent spatial resolution characteristics of a position-sensitive silicon photomultiplier (SiPM) and develop a high-resolution depth-of-interaction (DOI) encoding positron emission tomography (PET) detector module. The detector consists of a 30  ×  30 array of 0.445  ×  0.445  ×  20 mm3 polished LYSO crystals coupled to two 15.5  ×  15.5 mm2 linearly-graded SiPM (LG-SiPM) arrays at both ends. The flood histograms show that all the crystals in the LYSO array can be resolved. The energy resolution, the coincidence timing resolution and the DOI resolution were 21.8  ±  5.8%, 1.23  ±  0.10 ns and 3.8  ±  1.2 mm, respectively, at a temperature of -10 °C and a bias voltage of 35.0 V. The performance did not degrade significantly for event rates of up to 130 000 counts s-1. This detector represents an attractive option for small-bore PET scanner designs that simultaneously emphasize high spatial resolution and high detection efficiency, important, for example, in preclinical imaging of the rodent brain with neuroreceptor ligands.

  13. Design and experimental validation of Unilateral Linear Halbach magnet arrays for single-sided magnetic resonance.

    Bashyam, Ashvin; Li, Matthew; Cima, Michael J

    2018-07-01

    Single-sided NMR has the potential for broad utility and has found applications in healthcare, materials analysis, food quality assurance, and the oil and gas industry. These sensors require a remote, strong, uniform magnetic field to perform high sensitivity measurements. We demonstrate a new permanent magnet geometry, the Unilateral Linear Halbach, that combines design principles from "sweet-spot" and linear Halbach magnets to achieve this goal through more efficient use of magnetic flux. We perform sensitivity analysis using numerical simulations to produce a framework for Unilateral Linear Halbach design and assess tradeoffs between design parameters. Additionally, the use of hundreds of small, discrete magnets within the assembly allows for a tunable design, improved robustness to variability in magnetization strength, and increased safety during construction. Experimental validation using a prototype magnet shows close agreement with the simulated magnetic field. The Unilateral Linear Halbach magnet increases the sensitivity, portability, and versatility of single-sided NMR. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Diode array pumped, non-linear mirror Q-switched and mode-locked ...

    A non-linear mirror consisting of a lithium triborate crystal and a dichroic ... effects such as all-optical switching [7,8], nearly degenerate four-wave mixing [9,10], .... is driven by a radio frequency signal of 27.2MHz with a modulation available in.

  15. Quantum criticality of geometric phase in coupled optical cavity arrays under linear quench

    Sarkar, Sujit

    2013-01-01

    The atoms trapped in microcavities and interacting through the exchange of virtual photons can be modeled as an anisotropic Heisenberg spin-1/2 lattice. We study the dynamics of the geometric phase of this system under the linear quenching process of laser field detuning which shows the XX criticality of the geometric phase in presence of single Rabi frequency oscillation. We also study the quantum criticality for different quenching rate in the presence of single or two Rabi frequencies osci...

  16. A linear laser-driver array for optical transmission in the LHC experiments

    Cervelli, G; Moreira, P; Vasey, F

    2000-01-01

    A 4-way linear laser driver has been designed and implemented in a commercial 0.25 mu m CMOS technology. The full-custom IC is intended for analogue and digital data transmission as part of the 50 000 optical fibre links of the CMS particle tracking system. Intrinsic radiation tolerance and specific design methodologies enable the device to operate over 10 years in the harsh radiation environment of the innermost LHC detectors. Although optimised for analogue operation the driver is compatible with LVDS digital signalling. A combination of linearization methods achieves good analogue performance (8-bit equivalent dynamic range with a bandwidth of 100 MHz), while maintaining wide input common-mode range (+or-350 mV) and limited power dissipation. The linearly amplified signal is added to a DC current, which can be set over a wide range (-60 mA to +60 mA). The latter capability allows tracking of changes in laser threshold due to ageing or radiation damage. The driver gain and bias current are set via a serial ...

  17. Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells

    Saera Hihara

    2012-12-01

    Full Text Available Genome information, which is three-dimensionally organized within cells as chromatin, is searched and read by various proteins for diverse cell functions. Although how the protein factors find their targets remains unclear, the dynamic and flexible nature of chromatin is likely crucial. Using a combined approach of fluorescence correlation spectroscopy, single-nucleosome imaging, and Monte Carlo computer simulations, we demonstrate local chromatin dynamics in living mammalian cells. We show that similar to interphase chromatin, dense mitotic chromosomes also have considerable chromatin accessibility. For both interphase and mitotic chromatin, we observed local fluctuation of individual nucleosomes (∼50 nm movement/30 ms, which is caused by confined Brownian motion. Inhibition of these local dynamics by crosslinking impaired accessibility in the dense chromatin regions. Our findings show that local nucleosome dynamics drive chromatin accessibility. We propose that this local nucleosome fluctuation is the basis for scanning genome information.

  18. Role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders

    Alberto J Lopez

    2015-04-01

    Full Text Available It is becoming increasingly important to understand how epigenetic mechanisms control gene expression during neurodevelopment. Two epigenetic mechanisms that have received considerable attention are DNA methylation and histone acetylation. Human exome sequencing and genome-wide association studies have linked several neurobiological disorders to genes whose products actively regulate DNA methylation and histone acetylation. More recently, a third major epigenetic mechanism, nucleosome remodeling, has been implicated in human developmental and intellectual disability disorders. Nucleosome remodeling is driven primarily through nucleosome remodeling complexes with specialized ATP-dependent enzymes. These enzymes directly interact with DNA or chromatin structure, as well as histone subunits, to restructure the shape and organization of nucleosome positioning to ultimately regulate gene expression. Of particular interest is the neuron-specific Brg1/hBrm Associated Factor (nBAF complex. Mutations in nBAF subunit genes have so far been linked to Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, schizophrenia, and Autism Spectrum Disorder. Together, these human developmental and intellectual disability disorders are powerful examples of the impact of epigenetic modulation on gene expression. This review focuses on the new and emerging role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders and whether nucleosome remodeling affects gene expression required for cognition independently of its role in regulating gene expression required for development.

  19. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

    Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, Ricardo

    2016-01-01

    The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo. DOI: http://dx.doi.org/10.7554/eLife.13450.001 PMID:27130520

  20. Role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders.

    López, Alberto J; Wood, Marcelo A

    2015-01-01

    It is becoming increasingly important to understand how epigenetic mechanisms control gene expression during neurodevelopment. Two epigenetic mechanisms that have received considerable attention are DNA methylation and histone acetylation. Human exome sequencing and genome-wide association studies have linked several neurobiological disorders to genes whose products actively regulate DNA methylation and histone acetylation. More recently, a third major epigenetic mechanism, nucleosome remodeling, has been implicated in human developmental and intellectual disability (ID) disorders. Nucleosome remodeling is driven primarily through nucleosome remodeling complexes with specialized ATP-dependent enzymes. These enzymes directly interact with DNA or chromatin structure, as well as histone subunits, to restructure the shape and organization of nucleosome positioning to ultimately regulate gene expression. Of particular interest is the neuron-specific Brg1/hBrm Associated Factor (nBAF) complex. Mutations in nBAF subunit genes have so far been linked to Coffin-Siris syndrome (CSS), Nicolaides-Baraitser syndrome (NBS), schizophrenia, and Autism Spectrum Disorder (ASD). Together, these human developmental and ID disorders are powerful examples of the impact of epigenetic modulation on gene expression. This review focuses on the new and emerging role of nucleosome remodeling in neurodevelopmental and ID disorders and whether nucleosome remodeling affects gene expression required for cognition independently of its role in regulating gene expression required for development.

  1. Evaluation of linear array MOSFET detectors for in vivo dosimetry to measure rectal dose in HDR brachytherapy.

    Haughey, Aisling; Coalter, George; Mugabe, Koki

    2011-09-01

    The study aimed to assess the suitability of linear array metal oxide semiconductor field effect transistor detectors (MOSFETs) as in vivo dosimeters to measure rectal dose in high dose rate brachytherapy treatments. The MOSFET arrays were calibrated with an Ir192 source and phantom measurements were performed to check agreement with the treatment planning system. The angular dependence, linearity and constancy of the detectors were evaluated. For in vivo measurements two sites were investigated, transperineal needle implants for prostate cancer and Fletcher suites for cervical cancer. The MOSFETs were inserted into the patients' rectum in theatre inside a modified flatus tube. The patients were then CT scanned for treatment planning. Measured rectal doses during treatment were compared with point dose measurements predicted by the TPS. The MOSFETs were found to require individual calibration factors. The calibration was found to drift by approximately 1% ±0.8 per 500 mV accumulated and varies with distance from source due to energy dependence. In vivo results for prostate patients found only 33% of measured doses agreed with the TPS within ±10%. For cervix cases 42% of measured doses agreed with the TPS within ±10%, however of those not agreeing variations of up to 70% were observed. One of the most limiting factors in this study was found to be the inability to prevent the MOSFET moving internally between the time of CT and treatment. Due to the many uncertainties associated with MOSFETs including calibration drift, angular dependence and the inability to know their exact position at the time of treatment, we consider them to be unsuitable for in vivo dosimetry in rectum for HDR brachytherapy.

  2. Evaluation of linear array MOSFET detectors for in vivo dosimetry to measure rectal dose in DHR brachytherapy

    Haughey, A.; Coalter, G.; Mugabe, K.

    2011-01-01

    Full text: The study aimed to assess the suitability of linear array metal oxide semiconductor field effect transistor detectors (MOSFETs) as in vivo dosimeters to measure rectal dose in high dose rate brachytherapy treatments. The MOSFET arrays were calibrated with an Ir192 source and phantom measurements were performed to check agreement with the treatment planning system. The angular dependence, linearity and constancy of the detectors were evaluated. For in vivo measurements two sites were investigated, transperineal needle implants for prostate cancer and Fletcher suites for cervical cancer. The MOSFETs were inserted into the patients' rectum in theatre inside a modified flatus tube. The patients were then CT scanned for treatment planning. Measured rectal doses during treatment were compared with point dose measurements predicted by the TPS. The MOSFETs were found to require individual calibration factors. The calibration was found to drift by approximately 1% ±0.8 per 500 mV accumulated and varies with distance from source due to energy dependence. In vivo results for prostate patients found only 33% of measured doses agreed with the TPS within ±1O%. For cervix cases 42% of measured doses agreed with the TPS within ± 10%, however of those not agreeing variations of up to 70% were observed. One of the most limiting factors in this study was found to be the inability to prevent the MOSFET moving internally between the time of CT and treatment. Due to the many uncertainties associated with MOSFETs including calibration drift, angular dependence and the inability to know their exact position at the time of treatment, we consider them to be unsuitable for in vivo dosimetry in rectum for HDR brachytherapy. (author)

  3. Real time image synthesis on a SIMD linear array processor: algorithms and architectures

    Letellier, Laurent

    1993-01-01

    Nowadays, image synthesis has become a widely used technique. The impressive computing power required for real time applications necessitates the use of parallel architectures. In this context, we evaluate an SIMD linear parallel architecture, SYMPATI2, dedicated to image processing. The objective of this study is to propose a cost-effective graphics accelerator relying on SYMPATI2's modular and programmable structure. The parallelization of basic image synthesis algorithms on SYMPATI2 enables us to determine its limits in this application field. These limits lead us to evaluate a new structure with a fast intercommunication network between processors, but processors have to support the message consistency, which brings about a strong decrease in performance. To solve this problem, we suggest a simple network whose access priorities are represented by tokens. The simulations of this new architecture indicate that the SIMD mode causes a drastic cut in parallelism. To cope with this drawback, we propose a context switching procedure which reduces the SIMD rigidity and increases the parallelism rate significantly. Then, the graphics accelerator we propose is compared with existing graphics workstations. This comparison indicates that our structure, which is able to accelerate both image synthesis and image processing, is competitive and well-suited for multimedia applications. (author) [fr

  4. Multiple distinct stimuli increase measured nucleosome occupancy around human promoters.

    Chuong D Pham

    Full Text Available Nucleosomes can block access to transcription factors. Thus the precise localization of nucleosomes relative to transcription start sites and other factor binding sites is expected to be a critical component of transcriptional regulation. Recently developed microarray approaches have allowed the rapid mapping of nucleosome positions over hundreds of kilobases (kb of human genomic DNA, although these approaches have not yet been widely used to measure chromatin changes associated with changes in transcription. Here, we use custom tiling microarrays to reveal changes in nucleosome positions and abundance that occur when hormone-bound glucocorticoid receptor (GR binds to sites near target gene promoters in human osteosarcoma cells. The most striking change is an increase in measured nucleosome occupancy at sites spanning ∼1 kb upstream and downstream of transcription start sites, which occurs one hour after addition of hormone, but is lost at 4 hours. Unexpectedly, this increase was seen both on GR-regulated and GR-non-regulated genes. In addition, the human SWI/SNF chromatin remodeling factor (a GR co-activator was found to be important for increased occupancy upon hormone treatment and also for low nucleosome occupancy without hormone. Most surprisingly, similar increases in nucleosome occupancy were also seen on both regulated and non-regulated promoters during differentiation of human myeloid leukemia cells and upon activation of human CD4+ T-cells. These results indicate that dramatic changes in chromatin structure over ∼2 kb of human promoters may occur genomewide and in response to a variety of stimuli, and suggest novel models for transcriptional regulation.

  5. Acetylation curtails nucleosome binding, not stable nucleosome remodeling, by FoxO1

    Hatta, M.; Liu, F.; Cirillo, L.A.

    2009-01-01

    Transcriptional activity of FoxO factors is controlled through the actions of multiple growth factors signaling through protein kinase B, whereby phosphorylation of FoxO factors inhibits FoxO-mediated transactivation by promoting nuclear export. Phosphorylation of FoxO factors is enhanced by p300-mediated acetylation, which decreases their affinity for DNA. The negative effect of acetylation on FoxO DNA binding, together with nuclear FoxO mobility, is eliminated by over-expression of the de-acetylase Sirt1, suggesting that acetylation mobilizes FoxO factors in chromatin for inducible gene expression. Here, we show that acetylation significantly curtails the affinity of FoxO1 for its binding sites in nucleosomal DNA but has no effect on either stable nucleosome binding or remodeling by this factor. We suggest that, while acetylation provides a first, essential step toward mobilizing FoxO factors for inducible gene repression, additional mechanisms exist for overcoming their inherent capacity to stably bind and remodel nuclear chromatin.

  6. The nucleosome: orchestrating DNA damage signaling and repair within chromatin.

    Agarwal, Poonam; Miller, Kyle M

    2016-10-01

    DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

  7. Structural Mechanisms of Nucleosome Recognition by Linker Histones.

    Zhou, Bing-Rui; Jiang, Jiansheng; Feng, Hanqiao; Ghirlando, Rodolfo; Xiao, T Sam; Bai, Yawen

    2015-08-20

    Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, the structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal structure of the globular domain of chicken linker histone H5 in complex with the nucleosome at 3.5 Å resolution, which is validated using nuclear magnetic resonance spectroscopy. The globular domain sits on the dyad of the nucleosome and interacts with both DNA linkers. Our structure integrates results from mutation analyses and previous cross-linking and fluorescence recovery after photobleach experiments, and it helps resolve the long debate on structural mechanisms of nucleosome recognition by linker histones. The on-dyad binding mode of the H5 globular domain is different from the recently reported off-dyad binding mode of Drosophila linker histone H1. We demonstrate that linker histones with different binding modes could fold chromatin to form distinct higher-order structures. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Reconstitution of Nucleosomes with Differentially Isotope-labeled Sister Histones.

    Liokatis, Stamatios

    2017-03-26

    Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones. The generated complex can be also asymmetrically modified, after including a premodified histone pool during refolding of histone subcomplexes. These asymmetric nucleosome preparations can be readily reacted with histone-modifying enzymes to study modification cross-talk mechanisms imposed by the asymmetrically pre-incorporated PTM using nuclear magnetic resonance (NMR) spectroscopy. Particularly, the modification reactions in real-time can be mapped independently on the two sister histones by performing different types of NMR correlation experiments, tailored for the respective isotope type. This methodology provides the means to study crosstalk mechanisms that contribute to the formation and propagation of asymmetric PTM patterns on nucleosomal complexes.

  9. Design of a 5-MA 100-ns linear-transformer-driver accelerator for wire array Z-pinch experiments

    Zhou, Lin; Li, Zhenghong; Wang, Zhen; Liang, Chuan; Li, Mingjia; Qi, Jianmin; Chu, Yanyun

    2016-03-01

    The linear-transformer-driver (LTD) is a recently developed pulsed-power technology that shows great promise for a number of applications. These include a Z -pinch-driven fission-fusion-hybrid reactor that is being developed by the Chinese Academy of Engineering Physics. In support of the reactor development effort, we are planning to build an LTD-based accelerator that is optimized for driving wire-array Z -pinch loads. The accelerator comprises six modules in parallel, each of which has eight series 0.8-MA LTD cavities in a voltage-adder configuration. Vacuum transmission lines are used from the interior of the adder to the central vacuum chamber where the load is placed. Thus the traditional stack-flashover problem is eliminated. The machine is 3.2 m tall and 12 m in outer diameter including supports. A prototype cavity was built and tested for more than 6000 shots intermittently at a repetition rate of 0.1 Hz. A novel trigger, in which only one input trigger pulse is needed by utilizing an internal trigger brick, was developed and successfully verified in these shots. A full circuit modeling was conducted for the accelerator. The simulation result shows that a current pulse rising to 5.2 MA in 91 ns (10%-90%) can be delivered to the wire-array load, which is 1.5 cm in height, 1.2 cm in initial radius, and 1 mg in mass. The maximum implosion velocity of the load is 32 cm /μ s when compressed to 0.1 of the initial radius. The maximum kinetic energy is 78 kJ, which is 11.7% of the electric energy stored in the capacitors. This accelerator is supposed to enable a radiation energy efficiency of 20%-30%, providing a high efficient facility for research on the fast Z pinch and technologies for repetition-rate-operated accelerators.

  10. Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes

    Vlijm, R.; Lee, M.; Lipfert, J.; Lusser, A.; Dekker, C.; Dekker, N.H.

    2015-01-01

    DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length

  11. EMG-Torque Relation in Chronic Stroke: A Novel EMG Complexity Representation With a Linear Electrode Array.

    Zhang, Xu; Wang, Dongqing; Yu, Zaiyang; Chen, Xiang; Li, Sheng; Zhou, Ping

    2017-11-01

    This study examines the electromyogram (EMG)-torque relation for chronic stroke survivors using a novel EMG complexity representation. Ten stroke subjects performed a series of submaximal isometric elbow flexion tasks using their affected and contralateral arms, respectively, while a 20-channel linear electrode array was used to record surface EMG from the biceps brachii muscles. The sample entropy (SampEn) of surface EMG signals was calculated with both global and local tolerance schemes. A regression analysis was performed between SampEn of each channel's surface EMG and elbow flexion torque. It was found that a linear regression can be used to well describe the relation between surface EMG SampEn and the torque. Each channel's root mean square (RMS) amplitude of surface EMG signal in the different torque level was computed to determine the channel with the highest EMG amplitude. The slope of the regression (observed from the channel with the highest EMG amplitude) was smaller on the impaired side than on the nonimpaired side in 8 of the 10 subjects, regardless of the tolerance scheme (global or local) and the range of torques (full or matched range) used for comparison. The surface EMG signals from the channels above the estimated muscle innervation zones demonstrated significantly lower levels of complexity compared with other channels between innervation zones and muscle tendons. The study provides a novel point of view of the EMG-torque relation in the complexity domain, and reveals its alterations post stroke, which are associated with complex neural and muscular changes post stroke. The slope difference between channels with regard to innervation zones also confirms the relevance of electrode position in surface EMG analysis.

  12. An intelligent sensor array distributed system for vibration analysis and acoustic noise characterization of a linear switched reluctance actuator.

    Salvado, José; Espírito-Santo, António; Calado, Maria

    2012-01-01

    This paper proposes a distributed system for analysis and monitoring (DSAM) of vibrations and acoustic noise, which consists of an array of intelligent modules, sensor modules, communication bus and a host PC acting as data center. The main advantages of the DSAM are its modularity, scalability, and flexibility for use of different type of sensors/transducers, with analog or digital outputs, and for signals of different nature. Its final cost is also significantly lower than other available commercial solutions. The system is reconfigurable, can operate either with synchronous or asynchronous modes, with programmable sampling frequencies, 8-bit or 12-bit resolution and a memory buffer of 15 kbyte. It allows real-time data-acquisition for signals of different nature, in applications that require a large number of sensors, thus it is suited for monitoring of vibrations in Linear Switched Reluctance Actuators (LSRAs). The acquired data allows the full characterization of the LSRA in terms of its response to vibrations of structural origins, and the vibrations and acoustic noise emitted under normal operation. The DSAM can also be used for electrical machine condition monitoring, machine fault diagnosis, structural characterization and monitoring, among other applications.

  13. An Intelligent Sensor Array Distributed System for Vibration Analysis and Acoustic Noise Characterization of a Linear Switched Reluctance Actuator

    Maria Calado

    2012-06-01

    Full Text Available This paper proposes a distributed system for analysis and monitoring (DSAM of vibrations and acoustic noise, which consists of an array of intelligent modules, sensor modules, communication bus and a host PC acting as data center. The main advantages of the DSAM are its modularity, scalability, and flexibility for use of different type of sensors/transducers, with analog or digital outputs, and for signals of different nature. Its final cost is also significantly lower than other available commercial solutions. The system is reconfigurable, can operate either with synchronous or asynchronous modes, with programmable sampling frequencies, 8-bit or 12-bit resolution and a memory buffer of 15 kbyte. It allows real-time data-acquisition for signals of different nature, in applications that require a large number of sensors, thus it is suited for monitoring of vibrations in Linear Switched Reluctance Actuators (LSRAs. The acquired data allows the full characterization of the LSRA in terms of its response to vibrations of structural origins, and the vibrations and acoustic noise emitted under normal operation. The DSAM can also be used for electrical machine condition monitoring, machine fault diagnosis, structural characterization and monitoring, among other applications.

  14. A Series-Fed Linear Substrate-Integrated Dielectric Resonator Antenna Array for Millimeter-Wave Applications

    Ke Gong

    2018-01-01

    Full Text Available A series-fed linear substrate-integrated dielectric resonator antenna array (SIDRAA is presented for millimeter-wave applications, in which the substrate-integrated dielectric resonator antenna (SIDRA elements and the feeding structure can be codesigned and fabricated using the same planar process. A prototype 4 × 1 SIDRAA is designed at Ka-band and fabricated with a two-layer printed circuit board (PCB technology. Four SIDRAs are implemented in the Rogers RT6010 substrate using the perforation technique and fed by a compact substrate-integrated waveguide (SIW through four longitudinal coupling slots within the Rogers RT5880 substrate. The return loss, radiation patterns, and antenna gain were experimentally studied, and good agreement between the measured and simulated results is observed. The SIDRAA example provides a bandwidth of about 10% around 34.5 GHz for 10 dB return loss and stable broadside radiation patterns with the peak gain of 10.5–11.5 dBi across the band.

  15. Design of a 5-MA 100-ns linear-transformer-driver accelerator for wire array Z-pinch experiments

    Zhou Lin

    2016-03-01

    Full Text Available The linear-transformer-driver (LTD is a recently developed pulsed-power technology that shows great promise for a number of applications. These include a Z-pinch-driven fission-fusion-hybrid reactor that is being developed by the Chinese Academy of Engineering Physics. In support of the reactor development effort, we are planning to build an LTD-based accelerator that is optimized for driving wire-array Z-pinch loads. The accelerator comprises six modules in parallel, each of which has eight series 0.8-MA LTD cavities in a voltage-adder configuration. Vacuum transmission lines are used from the interior of the adder to the central vacuum chamber where the load is placed. Thus the traditional stack-flashover problem is eliminated. The machine is 3.2 m tall and 12 m in outer diameter including supports. A prototype cavity was built and tested for more than 6000 shots intermittently at a repetition rate of 0.1 Hz. A novel trigger, in which only one input trigger pulse is needed by utilizing an internal trigger brick, was developed and successfully verified in these shots. A full circuit modeling was conducted for the accelerator. The simulation result shows that a current pulse rising to 5.2 MA in 91 ns (10%–90% can be delivered to the wire-array load, which is 1.5 cm in height, 1.2 cm in initial radius, and 1 mg in mass. The maximum implosion velocity of the load is 32  cm/μs when compressed to 0.1 of the initial radius. The maximum kinetic energy is 78 kJ, which is 11.7% of the electric energy stored in the capacitors. This accelerator is supposed to enable a radiation energy efficiency of 20%–30%, providing a high efficient facility for research on the fast Z pinch and technologies for repetition-rate-operated accelerators.

  16. A comparative study of the work involved in measuring profiles using ion chambers, a linear diode array and film

    Rykers, K.L.; RMIT University, Melbourne, VIC; Royal North Shore Hospital, St Leonards, NSW; Geso, M.; Brown, G.M.; Olilver, L.D.

    1996-01-01

    Full text: The usefulness of film to perform dosimetric measurement is a topic often discussed and not clearly agreed upon. While single point measurement detectors give consistent and reliable results for physically wedged fields they cannot be easily used to measure intensity modulated fields. In this work a method of using film to measure profiles for dynamically wedged (DW) fields is presented. The method of positioning film for the subsequent generation of a conversion function to allow for the variation in films' response with energy is outlined. Furthermore, the profiles determined by film measurement are compared with those measured with single point measurement detector and an array of silicon diodes. Both Leavitt et. al. 8 and Weber et. al. 7 have reported on the successful use of the linear diode array (LDA) in measuring dynamic wedge data. This claim will be investigated. The film used in this work was Kodak X-Omat V. The solid water was RW3 with high water equivalency in the range from 137 CS to 50 MV for photons and electrons. All films were processed in an automatic processor. Both the Wellhoefer and the Scanditronix RFA 300 densitometers were used to take film readings. Wedged field and open field profiles measurements were taken in water using both the Wellhoefer IC-10 chamber, the Scanditronix RFA 300 RK chamber and the Scanditronix LDA . The energy investigated was 6 MV at 1.5, 5.0, 10.0, 15.0 and 20.0 cm for a Varian 2100C machine. More consistent density readings were obtained when films were processed with the edge of the film that was parallel to the beam axis was fed into the processor first; rather than when the beam incident edge was fed into the processor first. Comparing the position of the central axis (CAX) of open films from the geometric method developed in this work to the software determined CAX (as available with the Wellhoefer software), it was found that the difference in CAX positions varied between -0.03 to +0.04 cm at 2.5 cm

  17. Routes to DNA accessibility: alternative pathways for nucleosome unwinding.

    Schlingman, Daniel J; Mack, Andrew H; Kamenetska, Masha; Mochrie, Simon G J; Regan, Lynne

    2014-07-15

    The dynamic packaging of DNA into chromatin is a key determinant of eukaryotic gene regulation and epigenetic inheritance. Nucleosomes are the basic unit of chromatin, and therefore the accessible states of the nucleosome must be the starting point for mechanistic models regarding these essential processes. Although the existence of different unwound nucleosome states has been hypothesized, there have been few studies of these states. The consequences of multiple states are far reaching. These states will behave differently in all aspects, including their interactions with chromatin remodelers, histone variant exchange, and kinetic properties. Here, we demonstrate the existence of two distinct states of the unwound nucleosome, which are accessible at physiological forces and ionic strengths. Using optical tweezers, we measure the rates of unwinding and rewinding for these two states and show that the rewinding rates from each state are different. In addition, we show that the probability of unwinding into each state is dependent on the applied force and ionic strength. Our results demonstrate not only that multiple unwound states exist but that their accessibility can be differentially perturbed, suggesting possible roles for these states in gene regulation. For example, different histone variants or modifications may facilitate or suppress access to DNA by promoting unwinding into one state or the other. We anticipate that the two unwound states reported here will be the basis for future models of eukaryotic transcriptional control. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  18. Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

    Helbo, Alexandra Søgaard; Lay, Fides D; Jones, Peter A

    2017-01-01

    Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high...

  19. Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.

    Bameta, Tripti; Das, Dibyendu; Padinhateeri, Ranjith

    2018-06-01

    Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich 'phase diagram' having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.

  20. The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer

    Qiu, Yupeng; Levendosky, Robert F.; Chakravarthy, Srinivas; Patel, Ashok; Bowman, Gregory D.; Myong, Sua

    2017-10-01

    Chromatin remodelers catalyze dynamic packaging of the genome by carrying out nucleosome assembly/disassembly, histone exchange, and nucleosome repositioning. Remodeling results in evenly spaced nucleosomes, which requires probing both sides of the nucleosome, yet the way remodelers organize sliding activity to achieve this task is not understood. Here, we show that the monomeric Chd1 remodeler shifts DNA back and forth by dynamically alternating between different segments of the nucleosome. During sliding, Chd1 generates unstable remodeling intermediates that spontaneously relax to a pre-remodeled position. We demonstrate that nucleosome sliding is tightly controlled by two regulatory domains: the DNA-binding domain, which interferes with sliding when its range is limited by a truncated linking segment, and the chromodomains, which play a key role in substrate discrimination. We propose that active interplay of the ATPase motor with the regulatory domains may promote dynamic nucleosome structures uniquely suited for histone exchange and chromatin reorganization during transcription.

  1. Unfolding of core nucleosomes by PARP-1 revealed by spFRET microscopy

    Daniel Sultanov

    2017-01-01

    Full Text Available DNA accessibility to various protein complexes is essential for various processes in the cell and is affected by nucleosome structure and dynamics. Protein factor PARP-1 (poly(ADP-ribose polymerase 1 increases the accessibility of DNA in chromatin to repair proteins and transcriptional machinery, but the mechanism and extent of this chromatin reorganization are unknown. Here we report on the effects of PARP-1 on single nucleosomes revealed by spFRET (single-particle Förster Resonance Energy Transfer microscopy. PARP-1 binding to a double-strand break in the vicinity of a nucleosome results in a significant increase of the distance between the adjacent gyres of nucleosomal DNA. This partial uncoiling of the entire nucleosomal DNA occurs without apparent loss of histones and is reversed after poly(ADP-ribosylation of PARP-1. Thus PARP-1-nucleosome interactions result in reversible, partial uncoiling of the entire nucleosomal DNA.

  2. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

    Duan, Zhao-Wen; Li, Wei; Xie, Ping; Dou, Shuo-Xing; Wang, Peng-Ye

    2010-04-01

    Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking" interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon.

  3. Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

    Zhao-Wen, Duan; Wei, Li; Ping, Xie; Shuo-Xing, Dou; Peng-Ye, Wang

    2010-01-01

    Using Brownian dynamics simulation, we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin. The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA, thus involving the “cross-talking” interactions among the histones. Each state can stay for a sufficiently long time. These conformational states are essential for gene expression or gene silence. The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication, giving a theoretical explanation of the epigenetic phenomenon. (cross-disciplinary physics and related areas of science and technology)

  4. [Development of a portable mid-infrared rapid analyzer for oil concentration in water based on MEMS linear sensor array].

    Gao, Zhi-fan; Zeng, Li-bo; Shi, Lei; Li, Kai; Yang, Yuan-zhou; Wu, Qiong-shui

    2014-06-01

    Aiming at the existing problems such as weak environmental adaptability, low analytic efficiency and poor measuring repeatability in the traditional spectral oil analyzers, the present paper designed a portable mid-infrared rapid analyzer for oil concentration in water. To reduce the volume of the instrument, the non-symmetrical folding M-type Czerny-Turner optical structure was adopted in the core optical path. With a periodically rotating chopper, controlled by digital PID algorithm, applied for infrared light modulation, the modulating accuracy reached ±0.5%. Different from traditional grating-scanning spectrophotometers, this instrument used a fixed grating for light dispersion and avoided rotating error in the course of the measuring procedures. A new-type MEMS infrared linear sensor array was applied for modulated spectral signals detection, which improved the measuring efficiency remarkably. Optical simulation and experimental results indicate that the spectral range is 2 800 - 3 200 cm(-1), the spectral resolution is 6 cm(-1) (@3 130 cm(-1)), and the signal to noise ratio is up to 5 200 : 1. The acquisition time is 13 milliseconds per spectrogram, and the standard deviation of absorbance is less than 3 x 10(-3). These performances meet the standards of oil concentration measurements perfectly. Compared with traditional infrared spectral analyzers for oil concentration, the instrument demonstrated in this paper has many advantages such as smaller size, more efficiency, higher precision, and stronger vibration & moisture isolation. In addition, the proposed instrument is especially suitable for the environmental monitoring departments to implement real-time measurements in the field for oil concentration in water, hence it has broad prospects of application in the field of water quality monitoring.

  5. Screening of Carotenoids in Tomato Fruits by Using Liquid Chromatography with Diode Array-Linear Ion Trap Mass Spectrometry Detection.

    Gentili, Alessandra; Caretti, Fulvia; Ventura, Salvatore; Pérez-Fernández, Virginia; Venditti, Alessandro; Curini, Roberta

    2015-08-26

    This paper presents an analytical strategy for a large-scale screening of carotenoids in tomato fruits by exploiting the potentialities of the triple quadrupole-linear ion trap hybrid mass spectrometer (QqQLIT). The method involves separation on C30 reversed-phase column and identification by means of diode array detection (DAD) and atmospheric pressure chemical ionization-mass spectrometry (APCI-MS). The authentic standards of six model compounds were used to optimize the separative conditions and to predict the chromatographic behavior of untargeted carotenoids. An information dependent acquisition (IDA) was performed with (i) enhanced-mass scan (EMS) as the survey scan, (ii) enhanced-resolution (ER) scan to obtain the exact mass of the precursor ions (16-35 ppm), and (iii) enhanced product ion (EPI) scan as dependent scan to obtain structural information. LC-DAD-multiple reaction monitoring (MRM) chromatograms were also acquired for the identification of targeted carotenoids occurring at low concentrations; for the first time, the relative abundance between the MRM transitions (ion ratio) was used as an extra tool for the MS distinction of structural isomers and the related families of geometrical isomers. The whole analytical strategy was high-throughput, because a great number of experimental data could be acquired with few analytical steps, and cost-effective, because only few standards were used; when applied to characterize some tomato varieties ('Tangerine', 'Pachino', 'Datterino', and 'Camone') and passata of 'San Marzano' tomatoes, our method succeeded in identifying up to 44 carotenoids in the 'Tangerine'" variety.

  6. Comparison of the cobas Human Papillomavirus (HPV) Test with the Hybrid Capture 2 and Linear Array HPV DNA Tests

    Sadorra, Mark; LaMere, Brandon J.; Kail, Randi; Aldrich, Carrie; Kinney, Walter; Fetterman, Barbara; Lorey, Thomas; Schiffman, Mark; Castle, Philip E.

    2012-01-01

    The cobas human papillomavirus (HPV) test (cobas) was recently approved by the U.S. Food and Drug Administration (FDA) and identifies HPV16 and HPV18 separately as well as detecting a pool of 11 HR-HPV genotypes (HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -68) and also HPV66. We compared cobas, Linear Array (LA), and Hybrid Capture 2 (HC2) assays for detection of carcinogenic HPV DNA, and cobas and LA for detection of HPV16 and HPV18 DNA, among the first 1,852 women enrolled in the HPV Persistence and Progression Cohort (PaP Cohort) study. Specimens were tested by all 3 assays 1 year after an HC2-positive result. In 1,824 specimens with cobas results, cobas had an 85.9% agreement with HC2 and 91.0% agreement with LA for carcinogenic HPV detection. When results between cobas and HC2 disagreed, cobas tended to call more women HPV positive (P < 0.01). Categorizing cobas and LA results hierarchically according to cancer risk (HPV16, HPV18, other carcinogenic HPV genotypes, or carcinogen negative), there was a 90% agreement for all categories of HPV (n = 1,824). We found good agreement between the two U.S. FDA-approved HPV tests, with discrepancies between the two assays due to specific characteristics of the individual assays. Additional studies are needed to compare HC2 and cobas for detecting and predicting CIN3 to understand the clinical implications of the discrepant test results between the two tests. PMID:22075592

  7. Comparison of Thrust Characteristics in Pencil Sized Cylinder-type Linear Motors with Different Magnet Arrays(Asia-Pacific Symposium on Applied Electromagnetics and Mechanics (APSAEM08))

    K., Nakaiwa; A., Yamada; K., Tashiro; H., Wakiwaka; Tamagawa-Seiki Co., Ltd; Shinshu University; Shinshu University; Shinshu University

    2009-01-01

    From a strong demand on the miniaturization of a chip mounter or a semiconductor device, the thrust improvement considering the magnets arrangement is studied. We accept a core stator with a Halbach type magnet array for a current linear motor. The thrust characteristics are compared with two kinds of mover, a NS magnet array and a Halbach magnet array.

  8. Sequence periodicity in nucleosomal DNA and intrinsic curvature.

    Nair, T Murlidharan

    2010-05-17

    Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.

  9. Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory.

    Norman, Patrick; Parello, Joseph; Polavarapu, Prasad L; Linares, Mathieu

    2015-09-14

    It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles. At the DFT/B3LYP level of theory, the ECD signal response is reduced by a factor of 6.7 in going from the B-DNA to the N-DNA form, and it is illustrated how more than 90% of the individual base-pair dimers contribute to this strong hypochromic effect. Of the several inter-base pair parameters, an increase in twist angles is identified as to strongly contribute to a reduced ellipticity. The present work provides first evidence that first-principles calculations can elucidate changes in DNA dichroism due to the supramolecular organization of the nucleoprotein particle and associates these changes with the local structural features of nucleosomal DNA.

  10. Imaging San Jacinto Fault damage zone structure using dense linear arrays: application of ambient noise tomography, Rayleigh wave ellipticity, and site amplification

    Wang, Y.; Lin, F. C.; Allam, A. A.; Ben-Zion, Y.

    2017-12-01

    The San Jacinto fault is presently the most seismically active component of the San Andreas Transform system in Southern California. To study the damage zone structure, two dense linear geophone arrays (BS and RR) were deployed across the Clark segment of the San Jacinto Fault between Anza and Hemet during winter 2015 and Fall 2016, respectively. Both arrays were 2 km long with 20 m station spacing. Month-long three-component ambient seismic noise data were recorded and used to calculate multi-channel cross-correlation functions. All three-component noise records of each array were normalized simultaneously to retain relative amplitude information between different stations and different components. We observed clear Rayleigh waves and Love waves on the cross-correlations of both arrays at 0.3 - 1 s period. The phase travel times of the Rayleigh waves on both arrays were measured by frequency-time analysis (FTAN), and inverted for Rayleigh wave phase velocity profiles of the upper 500 m depth. For both arrays, we observe prominent asymmetric low velocity zones which narrow with depth. At the BS array near the Hemet Stepover, an approximately 250m wide slow zone is observed to be offset by 75m to the northeast of the surface fault trace. At the RR array near the Anza segment of the fault, a similar low velocity zone width and offset are observed, along with a 10% across-fault velocity contrast. Analyses of Rayleigh wave ellipticity (H/V ratio), Love wave phase travel times, and site amplification are in progress. By using multiple measurements from ambient noise cross-correlations, we can obtain strong constraints on the local damage zone structure of the San Jacinto Fault. The results contribute to improved understanding of rupture directivity, maximum earthquake magnitude and more generally seismic hazard associated with the San Jacinto fault zone.

  11. Time-dependent transport of a localized surface plasmon through a linear array of metal nanoparticles: Precursor and normal mode contributions

    Compaijen, P. J.; Malyshev, V. A.; Knoester, J.

    2018-02-01

    We theoretically investigate the time-dependent transport of a localized surface plasmon excitation through a linear array of identical and equidistantly spaced metal nanoparticles. Two different signals propagating through the array are found: one traveling with the group velocity of the surface plasmon polaritons of the system and damped exponentially, and the other running with the speed of light and decaying in a power-law fashion, as x-1 and x-2 for the transversal and longitudinal polarizations, respectively. The latter resembles the Sommerfeld-Brillouin forerunner and has not been identified in previous studies. The contribution of this signal dominates the plasmon transport at large distances. In addition, even though this signal is spread in the propagation direction and has the lateral dimension larger than the wavelength, the field profile close to the chain axis does not change with distance, indicating that this part of the signal is confined to the array.

  12. Nuclear resonant scattering measurements on (57)Fe by multichannel scaling with a 64-pixel silicon avalanche photodiode linear-array detector.

    Kishimoto, S; Mitsui, T; Haruki, R; Yoda, Y; Taniguchi, T; Shimazaki, S; Ikeno, M; Saito, M; Tanaka, M

    2014-11-01

    We developed a silicon avalanche photodiode (Si-APD) linear-array detector for use in nuclear resonant scattering experiments using synchrotron X-rays. The Si-APD linear array consists of 64 pixels (pixel size: 100 × 200 μm(2)) with a pixel pitch of 150 μm and depletion depth of 10 μm. An ultrafast frontend circuit allows the X-ray detector to obtain a high output rate of >10(7) cps per pixel. High-performance integrated circuits achieve multichannel scaling over 1024 continuous time bins with a 1 ns resolution for each pixel without dead time. The multichannel scaling method enabled us to record a time spectrum of the 14.4 keV nuclear radiation at each pixel with a time resolution of 1.4 ns (FWHM). This method was successfully applied to nuclear forward scattering and nuclear small-angle scattering on (57)Fe.

  13. Effect of the plasma production rate on the implosion dynamics of cylindrical wire/fiber arrays with a profiled linear mass

    Aleksandrov, V. V.; Mitrofanov, K. N.; Gritsuk, A. N.; Frolov, I. N.; Grabovski, E. V.; Laukhin, Ya. N.

    2013-01-01

    Results are presented from experimental studies on the implosion of arrays made of wires and metalized fibers under the action of current pulses with an amplitude of up to 3.5 MA at the Angara-5-1 facility. The effect of the parameters of an additional linear mass of bismuth and gold deposited on the wires/fibers is investigated. It is examined how the material of the wires/fibers and the metal coating deposited on them affect the penetration of the plasma with the frozen-in magnetic field into a cylindrical array. Information on the plasma production rate for different metals is obtained by analyzing optical streak images of imploding arrays. The plasma production rate m-dot m for cylindrical arrays made of the kapron fibers coated with bismuth is determined. For the initial array radius of R 0 = 1 cm and discharge current of I = 1 MA, the plasma production rate is found to be m-dot m approx. 0.095 ± 0.015 μg/(cm 2 ns)

  14. Nucleosome mediated crosstalk between transcription factors at eukaryotic enhancers

    Teif, Vladimir B; Rippe, Karsten

    2011-01-01

    A recent study of transcription regulation in Drosophila embryonic development revealed a complex non-monotonic dependence of gene expression on the distance between binding sites of repressor and activator proteins at the corresponding enhancer cis-regulatory modules (Fakhouri et al 2010 Mol. Syst. Biol. 6 341). The repressor efficiency was high at small separations, low around 30 bp, reached a maximum at 50–60 bp, and decreased at larger distances to the activator binding sites. Here, we propose a straightforward explanation for the distance dependence of repressor activity by considering the effect of the presence of a nucleosome. Using a method that considers partial unwrapping of nucleosomal DNA from the histone octamer core, we calculated the dependence of activator binding on the repressor–activator distance and found a quantitative agreement with the distance dependence reported for the Drosophila enhancer element. In addition, the proposed model offers explanations for other distance-dependent effects at eukaryotic enhancers. (communication)

  15. Linker histones: novel insights into structure-specific recognition of the nucleosome.

    Cutter, Amber R; Hayes, Jeffrey J

    2017-04-01

    Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.

  16. A Discrete Component Low-Noise Preamplifier Readout for a Linear (1x16) SiC Photodiode Array

    Kahle, Duncan; Aslam, Shahid; Herrero, Frederico A.; Waczynski, Augustyn

    2016-01-01

    A compact, low-noise and inexpensive preamplifier circuit has been designed and fabricated to optimally readout a common cathode (1x16) channel 4H-SiC Schottky photodiode array for use in ultraviolet experiments. The readout uses an operational amplifier with 10 pF capacitor in the feedback loop in parallel with a low leakage switch for each of the channels. This circuit configuration allows for reiterative sample, integrate and reset. A sampling technique is given to remove Johnson noise, enabling a femtoampere level readout noise performance. Commercial-off-the-shelf acquisition electronics are used to digitize the preamplifier analogue signals. The data logging acquisition electronics has a different integration circuit, which allows the bandwidth and gain to be independently adjusted. Using this readout, photoresponse measurements across the array between spectral wavelengths 200 nm and 370 nm are made to establish the array pixels external quantum efficiency, current responsivity and noise equivalent power.

  17. A discrete component low-noise preamplifier readout for a linear (1×16) SiC photodiode array

    Kahle, Duncan [NASA, Goddard Space Flight Center, Detector Systems Branch, Greenbelt, MD 20771 (United States); Aslam, Shahid, E-mail: shahid.aslam-1@nasa.gov [NASA, Goddard Space Flight Center, Planetary Systems Laboratory, Greenbelt, MD 20771 (United States); Herrero, Federico A.; Waczynski, Augustyn [NASA, Goddard Space Flight Center, Detector Systems Branch, Greenbelt, MD 20771 (United States)

    2016-09-11

    A compact, low-noise and inexpensive preamplifier circuit has been designed and fabricated to optimally readout a common cathode (1×16) channel 4H-SiC Schottky photodiode array for use in ultraviolet experiments. The readout uses an operational amplifier with 10 pF capacitor in the feedback loop in parallel with a low leakage switch for each of the channels. This circuit configuration allows for reiterative sample, integrate and reset. A sampling technique is given to remove Johnson noise, enabling a femtoampere level readout noise performance. Commercial-off-the-shelf acquisition electronics are used to digitize the preamplifier analog signals. The data logging acquisition electronics has a different integration circuit, which allows the bandwidth and gain to be independently adjusted. Using this readout, photoresponse measurements across the array between spectral wavelengths 200 nm and 370 nm are made to establish the array pixels external quantum efficiency, current responsivity and noise equivalent power.

  18. The Nucleosome Assembly Activity of NAP1 Is Enhanced by Alien▿

    Eckey, Maren; Hong, Wei; Papaioannou, Maria; Baniahmad, Aria

    2007-01-01

    The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitam...

  19. Abo1, a conserved bromodomain AAA?ATPase, maintains global nucleosome occupancy and organisation

    Gal, Csenge; Murton, Heather E; Subramanian, Lakxmi; Whale, Alex J; Moore, Karen M; Paszkiewicz, Konrad; Codlin, Sandra; B?hler, J?rg; Creamer, Kevin M; Partridge, Janet F; Allshire, Robin C; Kent, Nicholas A; Whitehall, Simon K

    2015-01-01

    Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA-ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1+ experience both a reduction and mis-positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re-establishment behind RNA polymerase II. Abo1 is rec...

  20. Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy

    Maria E. Valieva

    2017-01-01

    Full Text Available A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD and the high mobility group (HMG domain of the structure-specific recognition protein 1 (SSRP1 subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16 and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3. Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar.

  1. Insertion of linear 8.4 μm diameter 16 channel carbon fiber electrode arrays for single unit recordings

    Patel, Paras R.; Na, Kyounghwan; Zhang, Huanan; Kozai, Takashi D. Y.; Kotov, Nicholas A.; Yoon, Euisik; Chestek, Cynthia A.

    2016-01-01

    Objective Single carbon fiber electrodes (d=8.4 μm) insulated with parylene-c and functionalized with PEDOT:pTS have been shown to record single unit activity but manual implantation of these devices with forceps can be difficult. Without an improvement in the insertion method any increase in the channel count by fabricating carbon fiber arrays would be impractical. In this study, we utilize a water soluble coating and structural backbones that allow us to create, implant, and record from fully functionalized arrays of carbon fibers with ~150 μm pitch. Approach Two approaches were tested for the insertion of carbon fiber arrays. The first method used a PEG coating that temporarily stiffened the fibers while leaving a small portion at the tip exposed. The small exposed portion (500 μm – 1 mm) readily penetrated the brain allowing for an insertion that did not require the handling of each fiber by forceps. The second method involved the fabrication of silicon support structures with individual shanks spaced 150 μm apart. Each shank consisted of a small groove that held an individual carbon fiber. Main results Our results showed that the PEG coating allowed for the chronic implantation of carbon fiber arrays in 5 rats with unit activity detected at 31 days post-implant. The silicon support structures recorded single unit activity in 3 acute rat surgeries. In one of those surgeries a stacked device with 3 layers of silicon support structures and carbon fibers was built and shown to readily insert into the brain with unit activity on select sites. Significance From these studies we have found that carbon fibers spaced at ~150 μm readily insert into the brain. This greatly increases the recording density of chronic neural probes and paves the way for even higher density devices that have a minimal scarring response. PMID:26035638

  2. Fully Integrated Linear Single Photon Avalanche Diode (SPAD) Array with Parallel Readout Circuit in a Standard 180 nm CMOS Process

    Isaak, S.; Bull, S.; Pitter, M. C.; Harrison, Ian.

    2011-05-01

    This paper reports on the development of a SPAD device and its subsequent use in an actively quenched single photon counting imaging system, and was fabricated in a UMC 0.18 μm CMOS process. A low-doped p- guard ring (t-well layer) encircling the active area to prevent the premature reverse breakdown. The array is a 16×1 parallel output SPAD array, which comprises of an active quenched SPAD circuit in each pixel with the current value being set by an external resistor RRef = 300 kΩ. The SPAD I-V response, ID was found to slowly increase until VBD was reached at excess bias voltage, Ve = 11.03 V, and then rapidly increase due to avalanche multiplication. Digital circuitry to control the SPAD array and perform the necessary data processing was designed in VHDL and implemented on a FPGA chip. At room temperature, the dark count was found to be approximately 13 KHz for most of the 16 SPAD pixels and the dead time was estimated to be 40 ns.

  3. Increased Nucleosomes and Neutrophil Activation Link to Disease Progression in Patients with Scrub Typhus but Not Murine Typhus in Laos

    Paris, Daniel H.; Stephan, Femke; Bulder, Ingrid; Wouters, Diana; van der Poll, Tom; Newton, Paul N.; Day, Nicholas P. J.; Zeerleder, Sacha

    2015-01-01

    Cell-mediated immunity is essential in protection against rickettsial illnesses, but the role of neutrophils in these intracellular vasculotropic infections remains unclear. This study analyzed the plasma levels of nucleosomes, FSAP-activation (nucleosome-releasing factor), and neutrophil

  4. Transcription factor binding sites prediction based on modified nucleosomes.

    Mohammad Talebzadeh

    Full Text Available In computational methods, position weight matrices (PWMs are commonly applied for transcription factor binding site (TFBS prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, "modified nucleosomes neighboring" and "modified nucleosomes occupancy", to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method

  5. The nucleosome assembly activity of NAP1 is enhanced by Alien.

    Eckey, Maren; Hong, Wei; Papaioannou, Maria; Baniahmad, Aria

    2007-05-01

    The assembly of nucleosomes into chromatin is essential for the compaction of DNA and inactivation of the DNA template to modulate and repress gene expression. The nucleosome assembly protein 1, NAP1, assembles nucleosomes independent of DNA synthesis and was shown to enhance coactivator-mediated gene expression, suggesting a role for NAP1 in transcriptional regulation. Here, we show that Alien, known to harbor characteristics of a corepressor of nuclear hormone receptors such as of the vitamin D receptor (VDR), binds in vivo and in vitro to NAP1 and modulates its activity by enhancing NAP1-mediated nucleosome assembly on DNA. Furthermore, Alien reduces the accessibility of the histones H3 and H4 for NAP1-promoted assembly reaction. This indicates that Alien sustains and reinforces the formation of nucleosomes. Employing deletion mutants of Alien suggests that different regions of Alien are involved in enhancement of NAP1-mediated nucleosome assembly and in inhibiting the accessibility of the histones H3 and H4. In addition, we provide evidence that Alien is associated with chromatin and with micrococcus nuclease-prepared nucleosome fractions and interacts with the histones H3 and H4. Furthermore, chromatin immunoprecipitation and reimmunoprecipitation experiments suggest that NAP1 and Alien localize to the endogenous CYP24 promoter in vivo, a VDR target gene. Based on these findings, we present here a novel pathway linking corepressor function with nucleosome assembly activity.

  6. Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes

    van den Berg, A.A.; Depken, S.M.

    2017-01-01

    During eukaryotic transcription, RNA polymerase (RNAP) translocates along DNA molecules covered with nucleosomes and other DNA binding proteins. Though the interactions between a single nucleosome and RNAP are by now fairly well understood, this understanding has not been synthesized into a

  7. Deposition of nucleosomal antigens (histones and DNA) in the epidermal basement membrane in human lupus nephritis.

    Grootscholten, C.; Bruggen, M.C.J. van; Pijl, J.W. van der; Jong, E.M.G.J. de; Ligtenberg, G.; Derksen, R.H.W.M.; Berden, J.H.M.

    2003-01-01

    OBJECTIVE: Antinuclear autoantibodies complexed to nucleosomes can bind to heparan sulfate (HS) in the glomerular basement membrane. This binding is due to the binding of the positively charged histones to the strongly anionic HS. Nucleosomes and histones have been identified in glomerular deposits

  8. Nucleosomes and histones are present in glomerular deposits in human lupus nephritis

    vanBruggen, MCJ; Kramers, C; Walgreen, B; Elema, JD; Kallenberg, CGM; vandenBorn, J; Smeenk, RJT; Assmann, KJM; Muller, S; Monestier, M; Berden, JHM

    Background. Recently we showed that antinuclear autoantibodies complexed to nucleosomes can bind to heparan sulphate (HS) in the glomerular basement membrane (GEM) via the histone part of the nucleosome. Histones have been identified in glomerular deposits in human and murine lupus nephritis. In

  9. Nitrated nucleosome levels and neuropsychiatric events in systemic lupus erythematosus;

    Ferreira, Isabel; Croca, Sara; Raimondo, Maria Gabriella

    2017-01-01

    BACKGROUND: In patients with systemic lupus erythematosus (SLE) there is no serological test that will reliably distinguish neuropsychiatric (NP) events due to active SLE from those due to other causes. Previously we showed that serum levels of nitrated nucleosomes (NN) were elevated in a small...... number of patients with NPSLE. Here we measured serum NN in samples from a larger population of patients with SLE and NP events to see whether elevated serum NN could be a marker for NPSLE. METHODS: We obtained serum samples from patients in the Systemic Lupus International Collaborative Clinics (SLICC...

  10. PARP-1 Interaction with and Activation by Histones and Nucleosomes.

    Thomas, Colin; Kotova, Elena; Tulin, Alexei V

    2017-01-01

    Poly(ADP-ribose) Polymerase 1 (PARP-1) is an abundant chromatin associated protein, typical for most eukaryotic nuclei. The localization of PARP-1 in chromatin and its enzymatic activation involves multiple interactions of PARP-1 with nucleosomal histones, other proteins, and DNA. We report a set of methods designed to reconstitute PARP-1 regulation in vitro. These methods involve the expression of PARP-1 and PARP-1-regulating proteins using bacterial and eukaryotic systems, purification of these proteins using chromatography, testing of individual interactions in vitro, assembly of active complexes, and reconstitution of PARP-1 regulating reactions in vitro.

  11. RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly.

    Liu, Shaofeng; Xu, Zhiyun; Leng, He; Zheng, Pu; Yang, Jiayi; Chen, Kaifu; Feng, Jianxun; Li, Qing

    2017-01-27

    DNA replication-coupled nucleosome assembly is essential to maintain genome integrity and retain epigenetic information. Multiple involved histone chaperones have been identified, but how nucleosome assembly is coupled to DNA replication remains elusive. Here we show that replication protein A (RPA), an essential replisome component that binds single-stranded DNA, has a role in replication-coupled nucleosome assembly. RPA directly binds free H3-H4. Assays using a synthetic sequence that mimics freshly unwound single-stranded DNA at replication fork showed that RPA promotes DNA-(H3-H4) complex formation immediately adjacent to double-stranded DNA. Further, an RPA mutant defective in H3-H4 binding exhibited attenuated nucleosome assembly on nascent chromatin. Thus, we propose that RPA functions as a platform for targeting histone deposition to replication fork, through which RPA couples nucleosome assembly with ongoing DNA replication. Copyright © 2017, American Association for the Advancement of Science.

  12. Circulatory nucleosome levels are significantly increased in early and late-onset preeclampsia.

    Zhong, Xiao Yan; Gebhardt, Stefan; Hillermann, Renate; Tofa, Kashefa Carelse; Holzgreve, Wolfgang; Hahn, Sinuhe

    2005-08-01

    Elevations in circulatory DNA, as measured by real-time PCR, have been observed in pregnancies with manifest preeclampsia. Recent reports have indicated that circulatory nucleosome levels are elevated in the periphery of cancer patients. We have now examined whether circulatory nucleosome levels are similarly elevated in cases with preeclampsia. Maternal plasma samples were prepared from 17 cases with early onset preeclampsia (34 weeks gestation) with 10 matched normotensive controls. Levels of circulatory nucleosomes were quantified by commercial ELISA (enzyme-linked immunosorbant assay). The level of circulatory nucleosomes was significantly elevated in both study preeclampsia groups, compared to the matched normotensive control group (p = 0.000 and p = 0.001, respectively). Our data suggests that preeclampsia is associated with the elevated presence of circulatory nucleosomes, and that this phenomenon occurs in both early- and late-onset forms of the disorder. Copyright 2005 John Wiley & Sons, Ltd.

  13. A Design Of Feeding Network For A Dual-Linear Polarization, Stacked, Probe-Fed Microstrip Patch Antenna Array

    Jaworski, G.; Krozer, Viktor

    2004-01-01

    Components of multilayer feed network are presented for application in broad-band dual-linear polarized stacked C-band antenna. Measurement results of wide band matching circuits and different types of power divider networks constituting parts of BFN demonstrate wideband operation. Suitable...

  14. Links between DNA methylation and nucleosome occupancy in the human genome.

    Collings, Clayton K; Anderson, John N

    2017-01-01

    DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome. The results demonstrated that increasing methylated CpG density is correlated with nucleosome occupancy in the total genome and within nearly all subgenomic regions. Features with elevated methylated CpG density such as exons, SINE-Alu sequences, H3K36-trimethylated peaks, and methylated CpG islands are among the highest nucleosome occupied elements in the genome, while some of the lowest occupancies are displayed by unmethylated CpG islands and unmethylated transcription factor binding sites. Additionally, outside of CpG islands, the density of CpGs within nucleosomes was shown to be important for the nucleosomal location of DNA methylation with low CpG frequencies favoring linker methylation and high CpG frequencies favoring core particle methylation. Prominent exceptions to the correlations between methylated CpG density and nucleosome occupancy include CpG islands marked by H3K27me3 and CpG-poor heterochromatin marked by H3K9me3, and these modifications, along with DNA methylation, distinguish the major silencing mechanisms of the human epigenome. Thus, the relationship between DNA methylation and nucleosome occupancy is influenced by the density of methylated CpG dinucleotides and by other epigenomic components in chromatin.

  15. Core nucleosomes by digestion of reconstructed histone-DNA complexes

    Bryan, P N; Wright, E B; Olins, D E

    1979-04-01

    Reconstructed complexes of the inner histones (H2A, H2B, H3, H4) and a variety of DNAs were digested with micrococcal nuclease to yield very homogeneous populations of core nucleosomes (..nu../sub 1/). Nucleosomes containing Micrococcus luteus DNA (72% G+C); chicken DNA (43% G+C), Clostridium perfringens DNA (29% G+C); or poly(dA-dT).poly(dA-dT) have been examined by circular dichroism, thermal denaturation, electron microscopy, and DNAse I digestion. Circular dichroism spectra of all particles show a typically suppressed ellipticity at 260 to 280 nm and a prominent ..cap alpha..-helix signal at 222 nm. All particles show biphasic melting except ..nu../sub 1/(dA-dT), which show three prominent melting transitions at ionic strength less than or equal to 1 mM. DNAse I digestion of ..nu../sub 1/ (dA-dT) produces a ladder of DNA fragments differing in length by one base residue. ..nu../sub 1/ (dA-dT) contain 146 base pairs of DNA and exhibit an average DNA helix pitch of 10.4 to 10.5 bases per turn. There appear to be two regions of different DNA pitch within ..nu../sub 1/ (dA-dT). It is suggested that the two regions of DNA pitch might correspond to the two regions of the melting profiles.

  16. In silico evidence for sequence-dependent nucleosome sliding

    Lequieu, Joshua; Schwartz, David C.; de Pablo, Juan J.

    2017-10-18

    Nucleosomes represent the basic building block of chromatin and provide an important mechanism by which cellular processes are controlled. The locations of nucleosomes across the genome are not random but instead depend on both the underlying DNA sequence and the dynamic action of other proteins within the nucleus. These processes are central to cellular function, and the molecular details of the interplay between DNA sequence and nudeosome dynamics remain poorly understood. In this work, we investigate this interplay in detail by relying on a molecular model, which permits development of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of nudeosome repositioning. The mechanism of nudeosome repositioning is shown to be strongly linked to DNA sequence and directly related to the binding energy of a given DNA sequence to the histone core. It is also demonstrated that chromatin remodelers can override DNA-sequence preferences by exerting torque, and the histone H4 tail is then identified as a key component by which DNA-sequence, histone modifications, and chromatin remodelers could in fact be coupled.

  17. TH-CD-207B-05: Measurement of CT Bow-Tie Profiles Using a Linear Array Detector

    Yang, K; Li, X; Liu, B [Massachusetts General Hospital, Boston, MA (United States)

    2016-06-15

    Purpose: To accurately measure CT bow-tie profiles from various manufacturers and to provide non-proprietary information for CT system modeling. Methods: A GOS-based linear detector (0.8 mm per pixel and 51.2 cm in length) with a fast data sampling speed (0.24 ms/sample) was used to measure the relative profiles of bow-tie filters from a collection of eight CT scanners by three different vendors, GE (LS Xtra, LS VCT, Discovery HD750), Siemens (Sensation 64, Edge, Flash, Force), and Philips (iBrilliance 256). The linear detector was first calibrated for its energy response within typical CT beam quality ranges and compared with an ion chamber and analytical modeling (SPECTRA and TASMIP). A geometrical calibration process was developed to determine key parameters including the distance from the focal spot to the linear detector, the angular increment of the gantry at each data sampling, the location of the central x-ray on the linear detector, and the angular response of the detector pixel. Measurements were performed under axial-scan modes for most representative bow-tie filters and kV selections from each scanner. Bow-tie profiles were determined by re-binning the measured rotational data with an angular accuracy of 0.1 degree using the calibrated geometrical parameters. Results: The linear detector demonstrated an energy response as a solid state detector, which is close to the CT imaging detector. The geometrical calibration was proven to be sufficiently accurate (< 1mm in error for distances >550 mm) and the bow-tie profiles measured from rotational mode matched closely to those from the gantry-stationary mode. Accurate profiles were determined for a total of 21 bow-tie filters and 83 filter/kV combinations from the abovementioned scanner models. Conclusion: A new improved approach of CT bow-tie measurement was proposed and accurate bow-tie profiles were provided for a broad list of CT scanner models.

  18. Non-destructive visualization of linear explosive-induced Pyroshock using phase arrayed laser-induced shock in a space launcher composite

    Jang, Jae Kyeong; Lee, Jung Ryul

    2015-01-01

    Separation mechanism of Space launch vehicles are used in various separation systems and pyrotechnic devices. The operation of these pyrotechnic devices generates Pyroshock that can cause failures in electronic components. The prediction of high frequency structural response, especially the shock response spectrum (SRS), is important. This paper presents a non-destructive visualization and simulation of linear explosive-induced Pyroshock using phase arrayed Laser-induced shock. The proposed method includes a laser shock test based on laser beam and filtering zone conditioning to predict the SRS of Pyroshock. A ballistic test based on linear explosive and non-contact Laser Doppler Vibrometers and a nondestructive Laser shock measurement using laser excitation and several PZT sensors, are performed using a carbon composite sandwich panel. The similarity of the SRS of the conditioned laser shock to that of the real explosive Pyroshock is evaluated with the Mean Acceleration Difference. The average of MADs over the two training points was 33.64%. And, MAD at verification point was improved to 31.99%. After that, experimentally found optimal conditions are applied to any arbitrary points in laser scanning area. Finally, it is shown that linear explosive-induced real Pyroshock wave propagation can be visualized with high similarity based on the proposed laser technology. (paper)

  19. Attenuated total internal reflection infrared microspectroscopic imaging using a large-radius germanium internal reflection element and a linear array detector.

    Patterson, Brian M; Havrilla, George J

    2006-11-01

    The number of techniques and instruments available for Fourier transform infrared (FT-IR) microspectroscopic imaging has grown significantly over the past few years. Attenuated total internal reflectance (ATR) FT-IR microspectroscopy reduces sample preparation time and has simplified the analysis of many difficult samples. FT-IR imaging has become a powerful analytical tool using either a focal plane array or a linear array detector, especially when coupled with a chemometric analysis package. The field of view of the ATR-IR microspectroscopic imaging area can be greatly increased from 300 x 300 microm to 2500 x 2500 microm using a larger internal reflection element of 12.5 mm radius instead of the typical 1.5 mm radius. This gives an area increase of 70x before aberrant effects become too great. Parameters evaluated include the change in penetration depth as a function of beam displacement, measurements of the active area, magnification factor, and change in spatial resolution over the imaging area. Drawbacks such as large file size will also be discussed. This technique has been successfully applied to the FT-IR imaging of polydimethylsiloxane foam cross-sections, latent human fingerprints, and a model inorganic mixture, which demonstrates the usefulness of the method for pharmaceuticals.

  20. Solid phase microextraction of diclofenac using molecularly imprinted polymer sorbent in hollow fiber combined with fiber optic-linear array spectrophotometry.

    Pebdani, Arezou Amiri; Shabani, Ali Mohammad Haji; Dadfarnia, Shayessteh; Khodadoust, Saeid

    2015-08-05

    A simple solid phase microextraction method based on molecularly imprinted polymer sorbent in the hollow fiber (MIP-HF-SPME) combined with fiber optic-linear array spectrophotometer has been applied for the extraction and determination of diclofenac in environmental and biological samples. The effects of different parameters such as pH, times of extraction, type and volume of the organic solvent, stirring rate and donor phase volume on the extraction efficiency of the diclofenac were investigated and optimized. Under the optimal conditions, the calibration graph was linear (r(2)=0.998) in the range of 3.0-85.0 μg L(-1) with a detection limit of 0.7 μg L(-1) for preconcentration of 25.0 mL of the sample and the relative standard deviation (n=6) less than 5%. This method was applied successfully for the extraction and determination of diclofenac in different matrices (water, urine and plasma) and accuracy was examined through the recovery experiments. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Solid phase microextraction of diclofenac using molecularly imprinted polymer sorbent in hollow fiber combined with fiber optic-linear array spectrophotometry

    Pebdani, Arezou Amiri; Shabani, Ali Mohammad Haji; Dadfarnia, Shayessteh; Khodadoust, Saeid

    2015-08-01

    A simple solid phase microextraction method based on molecularly imprinted polymer sorbent in the hollow fiber (MIP-HF-SPME) combined with fiber optic-linear array spectrophotometer has been applied for the extraction and determination of diclofenac in environmental and biological samples. The effects of different parameters such as pH, times of extraction, type and volume of the organic solvent, stirring rate and donor phase volume on the extraction efficiency of the diclofenac were investigated and optimized. Under the optimal conditions, the calibration graph was linear (r2 = 0.998) in the range of 3.0-85.0 μg L-1 with a detection limit of 0.7 μg L-1 for preconcentration of 25.0 mL of the sample and the relative standard deviation (n = 6) less than 5%. This method was applied successfully for the extraction and determination of diclofenac in different matrices (water, urine and plasma) and accuracy was examined through the recovery experiments.

  2. A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins.

    Quintales, Luis; Soriano, Ignacio; Vázquez, Enrique; Segurado, Mónica; Antequera, Francisco

    2015-04-01

    Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

  3. nuMap: a web platform for accurate prediction of nucleosome positioning.

    Alharbi, Bader A; Alshammari, Thamir H; Felton, Nathan L; Zhurkin, Victor B; Cui, Feng

    2014-10-01

    Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site. Copyright © 2014 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  4. nuMap: A Web Platform for Accurate Prediction of Nucleosome Positioning

    Bader A. Alharbi

    2014-10-01

    Full Text Available Nucleosome positioning is critical for gene expression and of major biological interest. The high cost of experimentally mapping nucleosomal arrangement signifies the need for computational approaches to predict nucleosome positions at high resolution. Here, we present a web-based application to fulfill this need by implementing two models, YR and W/S schemes, for the translational and rotational positioning of nucleosomes, respectively. Our methods are based on sequence-dependent anisotropic bending that dictates how DNA is wrapped around a histone octamer. This application allows users to specify a number of options such as schemes and parameters for threading calculation and provides multiple layout formats. The nuMap is implemented in Java/Perl/MySQL and is freely available for public use at http://numap.rit.edu. The user manual, implementation notes, description of the methodology and examples are available at the site.

  5. Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations.

    Guillem Portella

    Full Text Available Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression. Here, we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models. We found that methylation of CpG steps destabilizes nucleosomes, especially when these are placed in sites where the DNA minor groove faces the histone core. The larger stiffness of methylated CpG steps is a crucial factor behind the decrease in nucleosome stability. Methylation changes the positioning and phasing of the nucleosomal DNA, altering the accessibility of DNA to regulatory proteins, and accordingly gene functionality. Our theoretical calculations highlight a simple physical-based explanation on the foundations of epigenetic signaling.

  6. Altered nucleosomes of active nucleolar chromatin contain accessible histone H3 in its hyperacetylated forms

    Johnson, E.M.; Sterner, R.; Allfrey, V.G.

    1987-01-01

    Chromatin of the organism Physarum polycephalum contains a class of conformationally altered nucleosomes previously localized to the transcribing regions of ribosomal genes in nucleoli. When nuclei are treated with 2-iodo[2-tritium]acetate, the histone H3 sulfhydryl group of the altered nucleosomes is derivatized while that of folded nucleosomes is not, and the labeled histones can then be identified by autoradiography of gels that separate H3 isoforms. The H3 derivatized is predominantly of tri- and tetraacetylated forms. In contrast, total free histone reacted with iodoacetate shows no preferential labeling of isoforms. Selective reaction of acetylated H3 is prevalent in both nucleolar and non-nucleolar chromatin. The results link specific patterns of H3 acetylation to changes in nucleosome conformation that occur during transcription

  7. Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines

    Aaron L. Statham

    2015-03-01

    Full Text Available DNA methylation and nucleosome positioning are two key mechanisms that contribute to the epigenetic control of gene expression. During carcinogenesis, the expression of many genes is altered alongside extensive changes in the epigenome, with repressed genes often being associated with local DNA hypermethylation and gain of nucleosomes at their promoters. However the spectrum of alterations that occur at distal regulatory regions has not been extensively studied. To address this we used Nucleosome Occupancy and Methylation sequencing (NOMe-seq to compare the genome-wide DNA methylation and nucleosome occupancy profiles between normal and cancer cell line models of the breast and prostate. Here we describe the bioinformatic pipeline and methods that we developed for the processing and analysis of the NOMe-seq data published by (Taberlay et al., 2014 [1] and deposited in the Gene Expression Omnibus with accession GSE57498.

  8. Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers.

    Tao, Yu; Zheng, Weisheng; Jiang, Yonghua; Ding, Guitao; Hou, Xinfeng; Tang, Yitao; Li, Yueying; Gao, Shuai; Chang, Gang; Zhang, Xiaobai; Liu, Wenqiang; Kou, Xiaochen; Wang, Hong; Jiang, Cizhong; Gao, Shaorong

    2014-12-21

    Nucleosome organization determines the chromatin state, which in turn controls gene expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it is still unclear to what degree the re-established nucleosome organization of induced pluripotent stem cells (iPSCs) resembles embryonic stem cells (ESCs), and whether the iPSCs inherit some residual gene expression from the parental fibroblast cells. We generated genome-wide nucleosome maps in mouse ESCs and in iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. Pairwise comparisons showed that the nucleosome organizations in the iPSCs, regardless of the iPSCs' tissue of origin, were nearly identical to the ESCs, but distinct from mouse embryonic fibroblasts (MEF). There is a canonical nucleosome arrangement of -1, nucleosome depletion region, +1, +2, +3, and so on nucleosomes around the transcription start sites of active genes whereas only a nucleosome occupies silent transcriptional units. Transcription factor binding sites possessed characteristic nucleosomal architecture, such that their access was governed by the rotational and translational settings of the nucleosome. Interestingly, the tissue-specific genes were highly expressed only in the parental somatic cells of the corresponding iPS cell line before reprogramming, but had a similar expression level in all the resultant iPSCs and ESCs. The re-established nucleosome landscape during nuclear reprogramming provides a conserved setting for accessibility of DNA sequences in mouse pluripotent stem cells. No persistent residual expression program or nucleosome positioning of the parental somatic cells that reflected their tissue of origin was passed on to the resulting mouse iPSCs.

  9. Soft skills turned into hard facts: nucleosome remodelling at developmental switches.

    Chioda, M; Becker, P B

    2010-07-01

    Nucleosome remodelling factors are regulators of DNA accessibility in chromatin and lubricators of all major functions of eukaryotic genomes. Their action is transient and reversible, yet can be decisive for irreversible cell-fate decisions during development. In addition to the well-known local actions of nucleosome remodelling factors during transcription initiation, more global and fundamental roles for remodelling complexes in shaping the epigenome during development are emerging.

  10. A role for FACT in repopulation of nucleosomes at inducible genes.

    Warren P Voth

    Full Text Available Xenobiotic drugs induce Pleiotropic Drug Resistance (PDR genes via the orthologous Pdr1/Pdr3 transcription activators. We previously identified the Mediator transcription co-activator complex as a key target of Pdr1 orthologs and demonstrated that Pdr1 interacts directly with the Gal11/Med15 subunit of the Mediator complex. Based on an interaction between Pdr1 and the FACT complex, we show that strains with spt16 or pob3 mutations are sensitive to xenobiotic drugs and display diminished PDR gene induction. Although FACT acts during the activation of some genes by assisting in the nucleosomes eviction at promoters, PDR promoters already contain nucleosome-depleted regions (NDRs before induction. To determine the function of FACT at PDR genes, we examined the kinetics of RNA accumulation and changes in nucleosome occupancy following exposure to a xenobiotic drug in wild type and FACT mutant yeast strains. In the presence of normal FACT, PDR genes are transcribed within 5 minutes of xenobiotic stimulation and transcription returns to basal levels by 30-40 min. Nucleosomes are constitutively depleted in the promoter regions, are lost from the open reading frames during transcription, and the ORFs are wholly repopulated with nucleosomes as transcription ceases. While FACT mutations cause minor delays in activation of PDR genes, much more pronounced and significant defects in nucleosome repopulation in the ORFs are observed in FACT mutants upon transcription termination. FACT therefore has a major role in nucleosome redeposition following cessation of transcription at the PDR genes, the opposite of its better-known function in nucleosome disassembly.

  11. Anti-nucleosome antibodies complexed to nucleosomal antigens show anti-DNA reactivity and bind to rat glomerular basement membrane in vivo.

    Kramers, C; Hylkema, M N; van Bruggen, M C; van de Lagemaat, R; Dijkman, H B; Assmann, K J; Smeenk, R J; Berden, J H

    1994-01-01

    Histones can mediate the binding of DNA and anti-DNA to the glomerular basement membrane (GBM). In ELISA histone/DNA/anti-DNA complexes are able to bind to heparan sulfate (HS), an intrinsic constituent of the GBM. We questioned whether histone containing immune complexes are able to bind to the GBM, and if so, whether the ligand in the GBM is HS. Monoclonal antibodies (mAbs) complexed to nucleosomal antigens and noncomplexed mAbs were isolated from culture supernatants of four IgG anti-nuclear mAbs. All noncomplexed mAbs showed strong anti-nucleosome reactivity in ELISA. One of them showed in addition anti-DNA reactivity in noncomplexed form. The other three mAbs only showed anti-DNA reactivity when they were complexed to nucleosomal antigens. After renal perfusion a fine granular binding of complexed mAbs to the glomerular capillary wall and activation of complement was observed in immunofluorescence, whereas noncomplexed mAbs did not bind. Immuno-electron microscopy showed binding of complexes to the whole width of the GBM. When HS in the GBM was removed by renal heparinase perfusion the binding of complexed mAb decreased, but did not disappear completely. We conclude that anti-nucleosome mAbs, which do not bind DNA, become DNA reactive once complexed to nucleosomal antigens. These complexed mAbs can bind to the GBM. The binding ligand in the GBM is partly, but not solely, HS. Binding to the GBM of immune complexes containing nucleosomal material might be an important event in the pathogenesis of lupus nephritis. Images PMID:8040312

  12. In vitro reconstitution and biochemical analyses of the Schizosaccharomyces pombe nucleosome

    Koyama, Masako; Nagakura, Wataru; Tanaka, Hiroki; Kujirai, Tomoya; Chikashige, Yuji; Haraguchi, Tokuko; Hiraoka, Yasushi; Kurumizaka, Hitoshi

    2017-01-01

    Schizosaccharomyces pombe, which has a small genome but shares many physiological functions with higher eukaryotes, is a useful single-cell, model eukaryotic organism. In particular, many features concerning chromatin structure and dynamics, including heterochromatin, centromeres, telomeres, and DNA replication origins, are well conserved between S. pombe and higher eukaryotes. However, the S. pombe nucleosome, the fundamental structural unit of chromatin, has not been reconstituted in vitro. In the present study, we established the method to purify S. pombe histones H2A, H2B, H3, and H4, and successfully reconstituted the S. pombe nucleosome in vitro. Our thermal stability assay and micrococcal nuclease treatment assay revealed that the S. pombe nucleosome is markedly unstable and its DNA ends are quite accessible, as compared to the canonical human nucleosome. These findings are important to understand the mechanisms of epigenetic genomic DNA regulation in fission yeast. - Highlights: • S. pombe histones were purified as recombinant proteins. • The recombinant S. pombe histones efficiently form nucleosomes in vitro. • The S. pombe nucleosome has distinct stability and DNA dynamics.

  13. Inducible nucleosome depletion at OREBP-binding-sites by hypertonic stress.

    Edith H Y Tong

    Full Text Available BACKGROUND: Osmotic Response Element-Binding Protein (OREBP, also known as TonEBP or NFAT5, is a unique transcription factor. It is hitherto the only known mammalian transcription factor that regulates hypertonic stress-induced gene transcription. In addition, unlike other monomeric members of the NFAT family, OREBP exists as a homodimer and it is the only transcription factor known to bind naked DNA targets by complete encirclement in vitro. Nevertheless, how OREBP interacts with target DNA, also known as ORE/TonE, and how it elicits gene transcription in vivo, remains unknown. METHODOLOGY: Using hypertonic induction of the aldose reductase (AR gene activation as a model, we showed that OREs contained dynamic nucleosomes. Hypertonic stress induced a rapid and reversible loss of nucleosome(s around the OREs. The loss of nucleosome(s was found to be initiated by an OREBP-independent mechanism, but was significantly potentiated in the presence of OREBP. Furthermore, hypertonic induction of AR gene was associated with an OREBP-dependent hyperacetylation of histones that spanned the 5' upstream sequences and at least some exons of the gene. Nevertheless, nucleosome loss was not regulated by the acetylation status of histone. SIGNIFICANCE: Our findings offer novel insights into the mechanism of OREBP-dependent transcriptional regulation and provide a basis for understanding how histone eviction and transcription factor recruitment are coupled.

  14. Nucleosome Repositioning: A Novel Mechanism for Nicotine- and Cocaine-Induced Epigenetic Changes.

    Amber N Brown

    Full Text Available Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug naïve positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.

  15. Evaluation of fiber Bragg grating sensor interrogation using InGaAs linear detector arrays and Gaussian approximation on embedded hardware

    Kumar, Saurabh; Amrutur, Bharadwaj; Asokan, Sundarrajan

    2018-02-01

    Fiber Bragg Grating (FBG) sensors have become popular for applications related to structural health monitoring, biomedical engineering, and robotics. However, for successful large scale adoption, FBG interrogation systems are as important as sensor characteristics. Apart from accuracy, the required number of FBG sensors per fiber and the distance between the device in which the sensors are used and the interrogation system also influence the selection of the interrogation technique. For several measurement devices developed for applications in biomedical engineering and robotics, only a few sensors per fiber are required and the device is close to the interrogation system. For these applications, interrogation systems based on InGaAs linear detector arrays provide a good choice. However, their resolution is dependent on the algorithms used for curve fitting. In this work, a detailed analysis of the choice of algorithm using the Gaussian approximation for the FBG spectrum and the number of pixels used for curve fitting on the errors is provided. The points where the maximum errors occur have been identified. All comparisons for wavelength shift detection have been made against another interrogation system based on the tunable swept laser. It has been shown that maximum errors occur when the wavelength shift is such that one new pixel is included for curve fitting. It has also been shown that an algorithm with lower computation cost compared to the more popular methods using iterative non-linear least squares estimation can be used without leading to the loss of accuracy. The algorithm has been implemented on embedded hardware, and a speed-up of approximately six times has been observed.

  16. Increased Nucleosomes and Neutrophil Activation Link to Disease Progression in Patients with Scrub Typhus but Not Murine Typhus in Laos.

    Paris, Daniel H; Stephan, Femke; Bulder, Ingrid; Wouters, Diana; van der Poll, Tom; Newton, Paul N; Day, Nicholas P J; Zeerleder, Sacha

    2015-01-01

    Cell-mediated immunity is essential in protection against rickettsial illnesses, but the role of neutrophils in these intracellular vasculotropic infections remains unclear. This study analyzed the plasma levels of nucleosomes, FSAP-activation (nucleosome-releasing factor), and neutrophil activation, as evidenced by neutrophil-elastase (ELA) complexes, in sympatric Lao patients with scrub typhus and murine typhus. In acute scrub typhus elevated nucleosome levels correlated with lower GCS scores, raised respiratory rate, jaundice and impaired liver function, whereas neutrophil activation correlated with fibrinolysis and high IL-8 plasma levels, a recently identified predictor of severe disease and mortality. Nucleosome and ELA complex levels were associated with a 4.8-fold and 4-fold increased risk of developing severe scrub typhus, beyond cut off values of 1,040 U/ml for nucleosomes and 275 U/ml for ELA complexes respectively. In murine typhus, nucleosome levels associated with pro-inflammatory cytokines and the duration of illness, while ELA complexes correlated strongly with inflammation markers, jaundice and increased respiratory rates. This study found strong correlations between circulating nucleosomes and neutrophil activation in patients with scrub typhus, but not murine typhus, providing indirect evidence that nucleosomes could originate from neutrophil extracellular trap (NET) degradation. High circulating plasma nucleosomes and ELA complexes represent independent risk factors for developing severe complications in scrub typhus. As nucleosomes and histones exposed on NETs are highly cytotoxic to endothelial cells and are strongly pro-coagulant, neutrophil-derived nucleosomes could contribute to vascular damage, the pro-coagulant state and exacerbation of disease in scrub typhus, thus indicating a detrimental role of neutrophil activation. The data suggest that increased neutrophil activation relates to disease progression and severe complications, and

  17. Experimental study of sector and linear array ultrasound accuracy and the influence of navigated 3D-reconstruction as compared to MRI in a brain tumor model.

    Siekmann, Max; Lothes, Thomas; König, Ralph; Wirtz, Christian Rainer; Coburger, Jan

    2018-03-01

    Currently, intraoperative ultrasound in brain tumor surgery is a rapidly propagating option in imaging technology. We examined the accuracy and resolution limits of different ultrasound probes and the influence of 3D-reconstruction in a phantom and compared these results to MRI in an intraoperative setting (iMRI). An agarose gel phantom with predefined gel targets was examined with iMRI, a sector (SUS) and a linear (LUS) array probe with two-dimensional images. Additionally, 3D-reconstructed sweeps in perpendicular directions were made of every target with both probes, resulting in 392 measurements. Statistical calculations were performed, and comparative boxplots were generated. Every measurement of iMRI and LUS was more precise than SUS, while there was no apparent difference in height of iMRI and 3D-reconstructed LUS. Measurements with 3D-reconstructed LUS were always more accurate than in 2D-LUS, while 3D-reconstruction of SUS showed nearly no differences to 2D-SUS in some measurements. We found correlations of 3D-reconstructed SUS and LUS length and width measurements with 2D results in the same image orientation. LUS provides an accuracy and resolution comparable to iMRI, while SUS is less exact than LUS and iMRI. 3D-reconstruction showed the potential to distinctly improve accuracy and resolution of ultrasound images, although there is a strong correlation with the sweep direction during data acquisition.

  18. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array.

    Godínez, Jose M; Tous, Sara; Baixeras, Nuria; Moreno-Crespi, Judith; Alejo, María; Lejeune, Marylène; Bravo, Ignacio G; Bosch, F Xavier; de Sanjosé, Silvia

    2011-11-18

    Certain Human Papillomaviruses (HPVs) are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA) technologies. The concordances and kappa statistics (k) for each technique compared with HC2 were 98.69% (k = 0.94) for LQ, 98.03% (k = 0.91) for RH and 91.80% (k = 0.82) for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90), HPV18 (k.r.= 0.74-0.80) and HPV45 (k.r.= 0.82-0.90). The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  19. Rapid long-wave infrared laser-induced breakdown spectroscopy measurements using a mercury-cadmium-telluride linear array detection system.

    Yang, Clayton S-C; Brown, Eiei; Kumi-Barimah, Eric; Hommerich, Uwe; Jin, Feng; Jia, Yingqing; Trivedi, Sudhir; D'souza, Arvind I; Decuir, Eric A; Wijewarnasuriya, Priyalal S; Samuels, Alan C

    2015-11-20

    In this work, we develop a mercury-cadmium-telluride linear array detection system that is capable of rapidly capturing (∼1-5  s) a broad spectrum of atomic and molecular laser-induced breakdown spectroscopy (LIBS) emissions in the long-wave infrared (LWIR) region (∼5.6-10  μm). Similar to the conventional UV-Vis LIBS, a broadband emission spectrum of condensed phase samples covering the whole 5.6-10 μm region can be acquired from just a single laser-induced microplasma or averaging a few single laser-induced microplasmas. Atomic and molecular signature emission spectra of solid inorganic and organic tablets and thin liquid films deposited on a rough asphalt surface are observed. This setup is capable of rapidly probing samples "as is" without the need of elaborate sample preparation and also offers the possibility of a simultaneous UV-Vis and LWIR LIBS measurement.

  20. Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are directed by the underlying DNA sequence.

    Joke J F A van Vugt

    Full Text Available BACKGROUND: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. METHODOLOGY/PRINCIPAL FINDINGS: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type and native RSC from yeast (SWI/SNF-type repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. CONCLUSIONS/SIGNIFICANCE: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase

  1. Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact

    Taylor, Jared F.; Khattab, Omar S.; Chen, Yu-Han; Chen, Yumay; Jacobsen, Steven E.; Wang, Ping H.

    2015-01-01

    Deciphering the multitude of epigenomic and genomic factors that influence the mutation rate is an area of great interest in modern biology. Recently, chromatin has been shown to play a part in this process. To elucidate this relationship further, we integrated our own ultra-deep sequenced human nucleosomal DNA data set with a host of published human genomic and cancer genomic data sets. Our results revealed, that differences in nucleosome occupancy are associated with changes in base-specific mutation rates. Increasing nucleosome occupancy is associated with an increasing transition to transversion ratio and an increased germline mutation rate within the human genome. Additionally, cancer single nucleotide variants and microindels are enriched within nucleosomes and both the coding and non-coding cancer mutation rate increases with increasing nucleosome occupancy. There is an enrichment of cancer indels at the theoretical start (74 bp) and end (115 bp) of linker DNA between two nucleosomes. We then hypothesized that increasing nucleosome occupancy decreases access to DNA by DNA repair machinery and could account for the increasing mutation rate. Such a relationship should not exist in DNA repair knockouts, and we thus repeated our analysis in DNA repair machinery knockouts to test our hypothesis. Indeed, our results revealed no correlation between increasing nucleosome occupancy and increasing mutation rate in DNA repair knockouts. Our findings emphasize the linkage of the genome and epigenome through the nucleosome whose properties can affect genome evolution and genetic aberrations such as cancer. PMID:26308346

  2. Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact.

    Puya G Yazdi

    Full Text Available Deciphering the multitude of epigenomic and genomic factors that influence the mutation rate is an area of great interest in modern biology. Recently, chromatin has been shown to play a part in this process. To elucidate this relationship further, we integrated our own ultra-deep sequenced human nucleosomal DNA data set with a host of published human genomic and cancer genomic data sets. Our results revealed, that differences in nucleosome occupancy are associated with changes in base-specific mutation rates. Increasing nucleosome occupancy is associated with an increasing transition to transversion ratio and an increased germline mutation rate within the human genome. Additionally, cancer single nucleotide variants and microindels are enriched within nucleosomes and both the coding and non-coding cancer mutation rate increases with increasing nucleosome occupancy. There is an enrichment of cancer indels at the theoretical start (74 bp and end (115 bp of linker DNA between two nucleosomes. We then hypothesized that increasing nucleosome occupancy decreases access to DNA by DNA repair machinery and could account for the increasing mutation rate. Such a relationship should not exist in DNA repair knockouts, and we thus repeated our analysis in DNA repair machinery knockouts to test our hypothesis. Indeed, our results revealed no correlation between increasing nucleosome occupancy and increasing mutation rate in DNA repair knockouts. Our findings emphasize the linkage of the genome and epigenome through the nucleosome whose properties can affect genome evolution and genetic aberrations such as cancer.

  3. Functional conservation of nucleosome formation selectively biases presumably neutral molecular variation in yeast genomes.

    Babbitt, Gregory A; Cotter, C R

    2011-01-01

    One prominent pattern of mutational frequency, long appreciated in comparative genomics, is the bias of purine/pyrimidine conserving substitutions (transitions) over purine/pyrimidine altering substitutions (transversions). Traditionally, this transitional bias has been thought to be driven by the underlying rates of DNA mutation and/or repair. However, recent sequencing studies of mutation accumulation lines in model organisms demonstrate that substitutions generally do not accumulate at rates that would indicate a transitional bias. These observations have called into question a very basic assumption of molecular evolution; that naturally occurring patterns of molecular variation in noncoding regions accurately reflect the underlying processes of randomly accumulating neutral mutation in nuclear genomes. Here, in Saccharomyces yeasts, we report a very strong inverse association (r = -0.951, P < 0.004) between the genome-wide frequency of substitutions and their average energetic effect on nucleosome formation, as predicted by a structurally based energy model of DNA deformation around the nucleosome core. We find that transitions occurring at sites positioned nearest the nucleosome surface, which are believed to function most importantly in nucleosome formation, alter the deformation energy of DNA to the nucleosome core by only a fraction of the energy changes typical of most transversions. When we examined the same substitutions set against random background sequences as well as an existing study reporting substitutions arising in mutation accumulation lines of Saccharomyces cerevisiae, we failed to find a similar relationship. These results support the idea that natural selection acting to functionally conserve chromatin organization may contribute significantly to genome-wide transitional bias, even in noncoding regions. Because nucleosome core structure is highly conserved across eukaryotes, our observations may also help to further explain locally elevated

  4. Nucleosome Assembly Dynamics Involve Spontaneous Fluctuations in the Handedness of Tetrasomes

    Rifka Vlijm

    2015-01-01

    Full Text Available DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length of single DNA molecules, we monitor the real-time loading of tetramers or complete histone octamers onto DNA by Nucleosome Assembly Protein-1 (NAP1. Remarkably, we find that tetrasomes exhibit spontaneous flipping between a preferentially occupied left-handed state (ΔLk = −0.73 and a right-handed state (ΔLk = +1.0, separated by a free energy difference of 2.3 kBT (1.5 kcal/mol. This flipping occurs without concomitant changes in DNA end-to-end length. The application of weak positive torque converts left-handed tetrasomes into right-handed tetrasomes, whereas nucleosomes display more gradual conformational changes. Our findings reveal unexpected dynamical rearrangements of the nucleosomal structure, suggesting that chromatin can serve as a “twist reservoir,” offering a mechanistic explanation for the regulation of DNA supercoiling in chromatin.

  5. Chromatin Regulation of Estrogen-Mediated Transcription in Breast Cancer: Rules for Binding Sites in Nucleosomes and Modified Histones that Enhance ER Binding

    Chrivia, John C

    2005-01-01

    .... Using gel shift assays, we tested whether ER can bind these nucleosomes. We have also found that the non-histone chromatin protein HMOB2 enhances binding of ER to an ERE located at the center of the nucleosome...

  6. Automation of the linear array HPV genotyping test and its application for routine typing of human papillomaviruses in cervical specimens of women without cytological abnormalities in Switzerland.

    Dobec, Marinko; Bannwart, Fridolin; Kaeppeli, Franz; Cassinotti, Pascal

    2009-05-01

    There is a need for reliable, automated high throughput HPV detection and genotyping methods for pre- and post-prophylactic vaccine intervention analyses. To optimize the linear array (LA) HPV genotyping test (Roche Diagnostics, Rotkreuz) in regard to possible automation steps for the routine laboratory diagnosis of HPV infections and to analyze the HPV genotype distribution in cervical specimens of women without cytological abnormalities in Switzerland. 680 cervical cell specimens with normal cytology, obtained from women undergoing routine cervical screening by liquid-based Pap smear, were analyzed by the LA HPV genotyping test for HPV-DNA. The automation of the LA HPV genotyping test resulted in a total hands-on time reduction of 255 min (from 480 to 225 min; 53%). Any of 37 HPV genotypes were detected in 117 (17.2%) and high-risk (HR) HPV in 55 (8.1%) of 680 women with normal cytology. The highest prevalence of any HPV (28.1%) and HR-HPV (15.1%) was observed in age-group 21-30 and showed a continuous decrease in older age-groups. The most common HR-HPV genotypes were HPV-16 (12%), HPV-31 (9.4%), HPV-52 (6%), HPV-51 (5.1%), HPV-45 (4.3%), HPV-58 (4.3%) and HPV-59 (4.3%). The optimization and automation of the LA HPV genotyping test makes it suited for high throughput HPV detection and typing. The epidemiological data provides information about distribution of HPV genotypes in women without cytological abnormalities in Switzerland and may be important for determining the future impact of vaccines and potential changes in the country's epidemiological HPV profile.

  7. Performance of the digene LQ, RH and PS HPVs genotyping systems on clinical samples and comparison with HC2 and PCR-based Linear Array

    Godínez Jose M

    2011-11-01

    Full Text Available Abstract Background Certain Human Papillomaviruses (HPVs are the infectious agents involved in cervical cancer development. Detection of HPVs DNA is part of the cervical cancer screening protocols and HPVs genotyping has been proposed for its inclusion in these preventive programs. The aim of this study was to evaluate three novel genotyping tests, namely Qiagen LQ, RH and PS, in clinical samples with and without abnormalities. For this, 305 cervical samples were processed and the results of the evaluated techniques were compared with those obtained in the HPVs diagnostic process in our lab, by using HC2 and Linear Array (LA technologies. Results The concordances and kappa statistics (k for each technique compared with HC2 were 98.69% (k = 0.94 for LQ, 98.03% (k = 0.91 for RH and 91.80% (k = 0.82 for PS. There was a very good agreement in HPVs type-specific concordance for the most prevalent types HPV16 (kappa range = 0.83-0.90, HPV18 (k.r.= 0.74-0.80 and HPV45 (k.r.= 0.82-0.90. Conclusions The three tests showed an overall good concordance for HPVs detection when compared with HR-HC2 system. LQ and RH rendered lower detection rate for multiple infections than LA genotyping. However, our understanding of the clinical significance of multiple HPVs infections is still incomplete and therefore the relevance of the lower ability to detect multiple infections needs to be evaluated.

  8. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

    Soler-López Montserrat

    2011-10-01

    Full Text Available Abstract Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site and TTS (Transcription Termination Site (at least in yeast is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression.

  9. Asymmetric binding of histone H1 stabilizes MMTV nucleosomes and the interaction of progesterone receptor with the exposed HRE.

    Vicent, Guillermo P; Meliá, María J; Beato, Miguel

    2002-11-29

    Packaging of mouse mammary tumor virus (MMTV) promoter sequences in nucleosomes modulates access of DNA binding proteins and influences the interaction among DNA bound transcription factors. Here we analyze the binding of histone H1 to MMTV mononucleosomes assembled with recombinant histones and study its influence on nucleosome structure and stability as well as on progesterone receptor (PR) binding to the hormone responsive elements (HREs). The MMTV nucleosomes can be separated into three main populations, two of which exhibited precise translational positioning. Histone H1 bound preferentially to the 5' distal nucleosomal DNA protecting additional 27-28 nt from digestion by micrococcal nuclease. Binding of histone H1 was unaffected by prior crosslinking of protein and DNA in nucleosomes with formaldehyde. Neither the translational nor the rotational nucleosome positioning was altered by histone H1 binding, but the nucleosomes were stabilized as judged by the kinetics of nuclease cleavage. Unexpectedly, binding of recombinant PR to the exposed distal HRE-I in nucleosomes was enhanced in the presence of histone H1, as demonstrated by band shift and footprinting experiments. This enhanced PR affinity may contribute to the reported positive effect of histone H1 on the hormonal activation of MMTV reporter genes.

  10. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails.

    Benleulmi, Mohamed S; Matysiak, Julien; Robert, Xavier; Miskey, Csaba; Mauro, Eric; Lapaillerie, Delphine; Lesbats, Paul; Chaignepain, Stéphane; Henriquez, Daniel R; Calmels, Christina; Oladosu, Oyindamola; Thierry, Eloïse; Leon, Oscar; Lavigne, Marc; Andreola, Marie-Line; Delelis, Olivier; Ivics, Zoltán; Ruff, Marc; Gouet, Patrice; Parissi, Vincent

    2017-11-28

    Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein-protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin.

  11. ATP-Dependent Chromatin Remodeling Factors and Their Roles in Affecting Nucleosome Fiber Composition

    Alexandra Lusser

    2011-10-01

    Full Text Available ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.

  12. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

    Pedersen, Jakob Skou; Valen, Eivind; Velazquez, Amhed Missael Vargas

    2014-01-01

    Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence...... data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery...

  13. Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae.

    Soriano, Ignacio; Morafraile, Esther C; Vázquez, Enrique; Antequera, Francisco; Segurado, Mónica

    2014-09-13

    Eukaryotic genomes are replicated during S phase according to a temporal program. Several determinants control the timing of origin firing, including the chromatin environment and epigenetic modifications. However, how chromatin structure influences the timing of the activation of specific origins is still poorly understood. By performing high-resolution analysis of genome-wide nucleosome positioning we have identified different chromatin architectures at early and late replication origins. These different patterns are already established in G1 and are tightly correlated with the organization of adjacent transcription units. Moreover, specific early and late nucleosomal patterns are fixed robustly, even in rpd3 mutants in which histone acetylation and origin timing have been significantly altered. Nevertheless, higher histone acetylation levels correlate with the local modulation of chromatin structure, leading to increased origin accessibility. In addition, we conducted parallel analyses of replication and nucleosome dynamics that revealed that chromatin structure at origins is modulated during origin activation. Our results show that early and late replication origins present distinctive nucleosomal configurations, which are preferentially associated to different genomic regions. Our data also reveal that origin structure is dynamic and can be locally modulated by histone deacetylation, as well as by origin activation. These data offer novel insight into the contribution of chromatin structure to origin selection and firing in budding yeast.

  14. Extracellular histones, cell-free DNA, or nucleosomes: differences in immunostimulation.

    Marsman, Gerben; Zeerleder, Sacha; Luken, Brenda M

    2016-12-08

    In inflammation, extensive cell death may occur, which results in the release of chromatin components into the extracellular environment. Individually, the purified chromatin components double stranded (ds)DNA and histones have been demonstrated, both in vitro and in vivo, to display various immunostimulatory effects, for example, histones induce cytotoxicity and proinflammatory signaling through toll-like receptor (TLR)2 and 4, while DNA induces signaling through TLR9 and intracellular nucleic acid sensing mechanisms. However, DNA and histones are organized in nucleosomes in the nucleus, and evidence suggests that nucleosomes are released as such in inflammation. The cytotoxicity and proinflammatory signaling induced by nucleosomes have not been studied as extensively as the separate effects brought about by histones and dsDNA, and there appear to be some marked differences. Remarkably, little distinction between the different forms in which histones circulate has been made throughout literature. This is partly due to the limitations of existing techniques to differentiate between histones in their free or DNA-bound form. Here we review the current understanding of immunostimulation induced by extracellular histones, dsDNA and nucleosomes, and discuss the importance of techniques that in their detection differentiate between these different chromatin components.

  15. Extranuclear detection of histones and nucleosomes in activated human lymphoblasts as an early event in apoptosis.

    Gabler, C.; Blank, N.; Hieronymus, T.; Schiller, M.; Berden, J.H.M.; Kalden, J.R.; Lorenz, H.M.

    2004-01-01

    OBJECTIVE: To evaluate the presence of histones and nucleosomes in cell lysates of freshly isolated peripheral blood mononuclear cells (PBMC), fully activated lymphoblasts, or lymphoblasts after induction of apoptosis. METHODS: Each histone class (H1, H2A, H2B, H3, and H4) was detected by western

  16. Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.

    Xiong, Jie; Gao, Shan; Dui, Wen; Yang, Wentao; Chen, Xiao; Taverna, Sean D; Pearlman, Ronald E; Ashlock, Wendy; Miao, Wei; Liu, Yifan

    2016-12-01

    The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: the transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cis-determinants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis- and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. It's fun to transcribe with Fun30: A model for nucleosome dynamics during RNA polymerase II-mediated elongation.

    Lee, Junwoo; Choi, Eun Shik; Lee, Daeyoup

    2018-01-01

    The ability of elongating RNA polymerase II (RNAPII) to regulate the nucleosome barrier is poorly understood because we do not know enough about the involved factors and we lack a conceptual framework to model this process. Our group recently identified the conserved Fun30/SMARCAD1 family chromatin-remodeling factor, Fun30 Fft3 , as being critical for relieving the nucleosome barrier during RNAPII-mediated elongation, and proposed a model illustrating how Fun30 Fft3 may contribute to nucleosome disassembly during RNAPII-mediated elongation. Here, we present a model that describes nucleosome dynamics during RNAPII-mediated elongation in mathematical terms and addresses the involvement of Fun30 Fft3 in this process.

  18. Photodiode 1 × 64 linear array based on a double p-InAsSbP/n-InAs{sub 0.92}Sb{sub 0.08}/n{sup +}-InAs heterostructure

    Il’inskaya, N. D., E-mail: ioffeled@mail.ru; Karandashev, S. A. [Russian Academy of Sciences, Ioffe Institute (Russian Federation); Karpukhina, N. G. [Limited Liability Company Ioffe LED Ltd. (Russian Federation); Lavrov, A. A.; Matveev, B. A.; Remennyi, M. A.; Stus, N. M.; Usikova, A. A. [Russian Academy of Sciences, Ioffe Institute (Russian Federation)

    2016-05-15

    The results of studies of the current–voltage characteristics and of the photoelectric and luminescence properties of a monolithic diode 1 × 64 linear array based on p-InAsSbP/n-InAsSb/n{sup +}-InAs with the n{sup +}-InAs-substrate side illuminated and sensitive in the region of 4-μm are reported. An analysis is performed of the mechanisms of current flow in the temperature range of 77–353 K and also of the photosensitivity and the speed of response taking into account the spatial distribution of nonequilibrium radiation and the data of capacitance–voltage measurements.

  19. In vitro molecular magnetic resonance imaging detection and measurement of apoptosis using superparamagnetic iron oxide + antibody as ligands for nucleosomes

    Rapley, P. L.; Witiw, C.; Rich, K.; Niccoli, S.; Tassotto, M. L.; Th'ng, J.

    2012-11-01

    Recent research in cell biology as well as oncology research has focused on apoptosis or programmed cell death as a means of quantifying the induced effects of treatment. A hallmark of late-stage apoptosis is nuclear fragmentation in which DNA is degraded to release nucleosomes with their associated histones. In this work, a method was developed for detecting and measuring nucleosome concentration in vitro with magnetic resonance imaging (MRI). The indirect procedure used a commercially available secondary antibody-superparamagnetic iron oxide (SPIO) particle complex as a contrast agent that bound to primary antibodies against nucleosomal histones H4, H2A and H2B. Using a multiple-echo spin-echo sequence on a 1.5 T clinical MRI scanner, significant T2 relaxation enhancement as a function of in vitro nucleosomal concentration was measured. In addition, clustering or aggregation of the contrast agent was demonstrated with its associated enhancement in T2 effects. The T2 clustering enhancement showed a complex dependence on relative concentrations of nucleosomes, primary antibody and secondary antibody + SPIO. The technique supports the feasibility of using MRI measurements of nucleosome concentration in blood as a diagnostic, prognostic and predictive tool in the management of cancer.

  20. Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein.

    Kizaki, Seiichiro; Zou, Tingting; Li, Yue; Han, Yong-Woon; Suzuki, Yuki; Harada, Yoshie; Sugiyama, Hiroshi

    2016-11-07

    Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle.

    Hergeth, Sonja P; Schneider, Robert

    2015-11-01

    The linker histone H1 family members are a key component of chromatin and bind to the nucleosomal core particle around the DNA entry and exit sites. H1 can stabilize both nucleosome structure and higher-order chromatin architecture. In general, H1 molecules consist of a central globular domain with more flexible tail regions at both their N- and C-terminal ends. The existence of multiple H1 subtypes and a large variety of posttranslational modifications brings about a considerable degree of complexity and makes studying this protein family challenging. Here, we review recent progress in understanding the function of linker histones and their subtypes beyond their role as merely structural chromatin components. We summarize current findings on the role of H1 in heterochromatin formation, transcriptional regulation and embryogenesis with a focus on H1 subtypes and their specific modifications. © 2015 The Authors.

  2. Studies of torsional properties of DNA and nucleosomes using angular optical trapping

    Sheinin, Maxim Y.

    DNA in vivo is subjected to torsional stress due to the action of molecular motors and other DNA-binding proteins. Several decades of research have uncovered the fascinating diversity of DNA transformations under torsion and the important role they play in the regulation of vital cellular processes such as transcription and replication. Recent studies have also suggested that torsion can influence the structure and stability of nucleosomes---basic building blocks of the eukaryotic genome. However, our understanding of the impact of torsion is far from being complete due to significant experimental challenges. In this work we have used a powerful single-molecule experimental technique, angular optical trapping, to address several long-standing issues in the field of DNA and nucleosome mechanics. First, we utilized the high resolution and direct torque measuring capability of the angular optical trapping to precisely measure DNA twist-stretch coupling. Second, we characterized DNA melting under tension and torsion. We found that torsionally underwound DNA forms a left-handed structure, significantly more flexible compared to the regular B-DNA. Finally, we performed the first comprehensive investigation of the single nucleosome behavior under torque and force. Importantly, we discovered that positive torque causes significant dimer loss, which can have implications for transcription through chromatin.

  3. Nucleosome–nucleosome interactions via histone tails and linker DNA regulate nuclear rigidity

    Shimamoto, Yuta; Tamura, Sachiko; Masumoto, Hiroshi; Maeshima, Kazuhiro

    2017-01-01

    Cells, as well as the nuclei inside them, experience significant mechanical stress in diverse biological processes, including contraction, migration, and adhesion. The structural stability of nuclei must therefore be maintained in order to protect genome integrity. Despite extensive knowledge on nuclear architecture and components, however, the underlying physical and molecular mechanisms remain largely unknown. We address this by subjecting isolated human cell nuclei to microneedle-based quantitative micromanipulation with a series of biochemical perturbations of the chromatin. We find that the mechanical rigidity of nuclei depends on the continuity of the nucleosomal fiber and interactions between nucleosomes. Disrupting these chromatin features by varying cation concentration, acetylating histone tails, or digesting linker DNA results in loss of nuclear rigidity. In contrast, the levels of key chromatin assembly factors, including cohesin, condensin II, and CTCF, and a major nuclear envelope protein, lamin, are unaffected. Together with in situ evidence using living cells and a simple mechanical model, our findings reveal a chromatin-based regulation of the nuclear mechanical response and provide insight into the significance of local and global chromatin structures, such as those associated with interdigitated or melted nucleosomal fibers. PMID:28428255

  4. In vivo dosimetry using a linear Mosfet-array dosimeter to determine the urethra dose in 125I permanent prostate implants.

    Bloemen-van Gurp, Esther J; Murrer, Lars H P; Haanstra, Björk K C; van Gils, Francis C J M; Dekker, Andre L A J; Mijnheer, Ben J; Lambin, Philippe

    2009-01-01

    In vivo dosimetry during brachytherapy of the prostate with (125)I seeds is challenging because of the high dose gradients and low photon energies involved. We present the results of a study using metal-oxide-semiconductor field-effect transistor (MOSFET) dosimeters to evaluate the dose in the urethra after a permanent prostate implantation procedure. Phantom measurements were made to validate the measurement technique, determine the measurement accuracy, and define action levels for clinical measurements. Patient measurements were performed with a MOSFET array in the urinary catheter immediately after the implantation procedure. A CT scan was performed, and dose values, calculated by the treatment planning system, were compared to in vivo dose values measured with MOSFET dosimeters. Corrections for temperature dependence of the MOSFET array response and photon attenuation in the catheter on the in vivo dose values are necessary. The overall uncertainty in the measurement procedure, determined in a simulation experiment, is 8.0% (1 SD). In vivo dose values were obtained for 17 patients. In the high-dose region (> 100 Gy), calculated and measured dose values agreed within 1.7% +/- 10.7% (1 SD). In the low-dose region outside the prostate (MOSFET detectors are suitable for in vivo dosimetry during (125)I brachytherapy of prostate cancer. An action level of +/- 16% (2 SD) for detection of errors in the implantation procedure is achievable after validation of the detector system and measurement conditions.

  5. Carbon nanotube nanoelectrode arrays

    Ren, Zhifeng; Lin, Yuehe; Yantasee, Wassana; Liu, Guodong; Lu, Fang; Tu, Yi

    2008-11-18

    The present invention relates to microelectode arrays (MEAs), and more particularly to carbon nanotube nanoelectrode arrays (CNT-NEAs) for chemical and biological sensing, and methods of use. A nanoelectrode array includes a carbon nanotube material comprising an array of substantially linear carbon nanotubes each having a proximal end and a distal end, the proximal end of the carbon nanotubes are attached to a catalyst substrate material so as to form the array with a pre-determined site density, wherein the carbon nanotubes are aligned with respect to one another within the array; an electrically insulating layer on the surface of the carbon nanotube material, whereby the distal end of the carbon nanotubes extend beyond the electrically insulating layer; a second adhesive electrically insulating layer on the surface of the electrically insulating layer, whereby the distal end of the carbon nanotubes extend beyond the second adhesive electrically insulating layer; and a metal wire attached to the catalyst substrate material.

  6. Rational design of binder-free noble metal/metal oxide arrays with nanocauliflower structure for wide linear range nonenzymatic glucose detection

    Li, Zhenzhen

    2015-06-12

    One-dimensional nanocomposites of metal-oxide and noble metal were expected to present superior performance for nonenzymatic glucose detection due to its good conductivity and high catalytic activity inherited from noble metal and metal oxide respectively. As a proof of concept, we synthesized gold and copper oxide (Au/CuO) composite with unique one-dimensional nanocauliflowers structure. Due to the nature of the synthesis method, no any foreign binder was needed in keeping either Au or CuO in place. To the best of our knowledge, this is the first attempt in combining metal oxide and noble metal in a binder-free style for fabricating nonenzymatic glucose sensor. The Au/CuO nanocauliflowers with large electrochemical active surface and high electrolyte contact area would promise a wide linear range and high sensitive detection of glucose with good stability and reproducibility due to its good electrical conductivity of Au and high electrocatalytic activity of CuO.

  7. Linear self-assembly and grafting of gold nanorods into arrayed micrometer-long nanowires on a silicon wafer via a combined top-down/bottom-up approach.

    Lestini, Elena; Andrei, Codrin; Zerulla, Dominic

    2018-01-01

    Macroscopically long wire-like arrangements of gold nanoparticles were obtained by controlled evaporation and partial coalescence of an aqueous colloidal solution of capped CTAB-Au nanorods onto a functionalised 3-mercaptopropyl trimethoxysilane (MPTMS) silicon substrate, using a removable, silicon wafer with a hydrophobic surface that serves as a "handrail" for the initial nanorods' linear self-assembly. The wire-like structures display a quasi-continuous pattern by thermal annealing of the gold nanorods when the solvent (i.e. water) is evaporated at temperatures rising from 20°C to 140°C. Formation of both single and self-replicating parallel 1D-superstructures consisting of two or even three wires is observed and explained under such conditions.

  8. Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects.

    Erica M Hildebrand

    2016-03-01

    Full Text Available The exclusive localization of the histone H3 variant CENP-A to centromeres is essential for accurate chromosome segregation. Ubiquitin-mediated proteolysis helps to ensure that CENP-A does not mislocalize to euchromatin, which can lead to genomic instability. Consistent with this, overexpression of the budding yeast CENP-A(Cse4 is lethal in cells lacking Psh1, the E3 ubiquitin ligase that targets CENP-A(Cse4 for degradation. To identify additional mechanisms that prevent CENP-A(Cse4 misincorporation and lethality, we analyzed the genome-wide mislocalization pattern of overexpressed CENP-A(Cse4 in the presence and absence of Psh1 by chromatin immunoprecipitation followed by high throughput sequencing. We found that ectopic CENP-A(Cse4 is enriched at promoters that contain histone H2A.Z(Htz1 nucleosomes, but that H2A.Z(Htz1 is not required for CENP-A(Cse4 mislocalization. Instead, the INO80 complex, which removes H2A.Z(Htz1 from nucleosomes, promotes the ectopic deposition of CENP-A(Cse4. Transcriptional profiling revealed gene expression changes in the psh1Δ cells overexpressing CENP-A(Cse4. The down-regulated genes are enriched for CENP-A(Cse4 mislocalization to promoters, while the up-regulated genes correlate with those that are also transcriptionally up-regulated in an htz1Δ strain. Together, these data show that regulating centromeric nucleosome localization is not only critical for maintaining centromere function, but also for ensuring accurate promoter function and transcriptional regulation.

  9. Chromatin associated mechanisms in base excision repair - nucleosome remodeling and DNA transcription, two key players.

    Menoni, Hervé; Di Mascio, Paolo; Cadet, Jean; Dimitrov, Stefan; Angelov, Dimitar

    2017-06-01

    Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to overcome the general repression associated with the nucleosomal organization. It is broadly accepted that energy-dependent nucleosome remodeling factors disrupt histones-DNA interactions at the expense of ATP hydrolysis to favor transcription as well as DNA repair. Importantly, unlike transcription, BER is not part of a regulated developmental process but represents a maintenance system that should be efficient anytime and anywhere in the genome. In this review we will discuss how BER can deal with chromatin organization to maintain genetic information. Emphasis will be placed on the following challenging question: how BER is initiated within chromatin? Copyright © 2017 Elsevier Inc. All rights reserved.

  10. The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression

    Cui, Peng

    2011-08-19

    To further understand the relationship between nucleosome-space occupancy (NO) and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3)-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues-cerebrum, testis, and ESCs-and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK) genes and tissue-specific (TS) genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types. © 2011 Cui et al.

  11. The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression.

    Peng Cui

    Full Text Available To further understand the relationship between nucleosome-space occupancy (NO and global transcriptional activity in mammals, we acquired a set of genome-wide nucleosome distribution and transcriptome data from the mouse cerebrum and testis based on ChIP (H3-seq and RNA-seq, respectively. We identified a nearly consistent NO patterns among three mouse tissues--cerebrum, testis, and ESCs--and found, through clustering analysis for transcriptional activation, that the NO variations among chromosomes are closely associated with distinct expression levels between house-keeping (HK genes and tissue-specific (TS genes. Both TS and HK genes form clusters albeit the obvious majority. This feature implies that NO patterns, i.e. nucleosome binding and clustering, are coupled with gene clustering that may be functionally and evolutionarily conserved in regulating gene expression among different cell types.

  12. Subnucleosomes and their relationships to the arrangement of histone binding sites along nucleosome deoxyribonucleic acid

    Nelson, D.A.; Mencke, A.J.; Chambers, S.A.; Oosterhof, D.K.; Rill, R.L.

    1982-01-01

    Micrococcal nuclease cleaves within nucleosomes at sites spaced about 10.4 base pairs (bp) apart. Cleavages at sites equivalent to 30-35 bp from the ends of 146-bp cores cause spontaneous loss of an H2a-H2b pair associated with 30-40 bp length DNA. Cleavages at certain other sites do not affect the nucleosome integrity unless a solvent perturbant such as urea is added. Chromatin moderately digested with micrococcal nuclease, when fractionated by sedimentation or electrophoresis in the presence of 3 M urea, yielded four previously unobserved subnucleosomes with the following histone/DNA compositions: (H3) 2 (H4) 2 (H2a)(H2b)/95-115 bp; (H3)(H4)/70-80 bp DNA; (H2a)(H2b)/50-60 bp DNA; and (H1)/60-70 bp DNA. All but the latter subnucleosome were also obtained upon DNase I digestion of purified nucleosome cores labeled on the 5' ends with 32 P. Only subnucleosomes that retained H2a and H2b also retained labeled ends. These results show that H2a and H2b are paired on the terminal 30-40 bp of core DNA, as suggested from analyses of histone-DNA cross-link products by Mirzabekov and coworkers. Considerations of the orgins and compositions of subnucleosomes and of cross-linking data suggest an expanded model for the locations of histone binding sites along nucleosome core DNA. The principal features of this model are (i) strong electrostatic binding sites of H2a and H2b occur at positions approximately 20-30 bp from the core ends, (ii) strong electrostatic binding sites of H3 and H4 occur primarily on the central 40 bp of core DNA, (iii) strong nonelectrostatic, urea-sensitive binding sites of H3 and H4 occur at positions approximately 30-50 bp from the core ends, and (iv) urea-sensitive binding sites of H2a or H2b may occur on the terminal 10-20 bp of core DNA

  13. Analysis of the histone protein tail and DNA in nucleosome using molecular dynamics simulation

    Fujimori, R.; Komatsu, Y.; Fukuda, M.; Miyakawa, T.; Morikawa, R.; Takasu, M.

    2013-02-01

    We study the effect of the tails of H3 and H4 histones in the nucleosomes, where DNA and histones are packed in the form of chromatin. We perform molecular dynamics simulations of the complex of DNA and histones and calculate the mean square displacement and the gyration radius of the complex of DNA and histones for the cases with tails intact and the cases with tails missing. Our results show that the H3 tails are important for the motion of the histones. We also find that the motion of one tail is affected by other tails, although the tails are distanced apart, suggesting the correlated motion in biological systems.

  14. FEM-based linear inverse modeling using a 3D source array to image magma chambers with free geometry. Application to InSAR data from Rabaul Caldera (PNG).

    Ronchin, Erika; Masterlark, Timothy; Dawson, John; Saunders, Steve; Martí Molist, Joan

    2015-04-01

    In this study, we present a method to fully integrate a family of finite element models (FEMs) into the regularized linear inversion of InSAR data collected at Rabaul caldera (PNG) between February 2007 and December 2010. During this period the caldera experienced a long-term steady subsidence that characterized surface movement both inside the caldera and outside, on its western side. The inversion is based on an array of FEM sources in the sense that the Green's function matrix is a library of forward numerical displacement solutions generated by the sources of an array common to all FEMs. Each entry of the library is the LOS surface displacement generated by injecting a unity mass of fluid, of known density and bulk modulus, into a different source cavity of the array for each FEM. By using FEMs, we are taking advantage of their capability of including topography and heterogeneous distribution of elastic material properties. All FEMs of the family share the same mesh in which only one source is activated at the time by removing the corresponding elements and applying the unity fluid flux. The domain therefore only needs to be discretized once. This precludes remeshing for each activated source, thus reducing computational requirements, often a downside of FEM-based inversions. Without imposing an a-priori source, the method allows us to identify, from a least-squares standpoint, a complex distribution of fluid flux (or change in pressure) with a 3D free geometry within the source array, as dictated by the data. The results of applying the proposed inversion to Rabaul InSAR data show a shallow magmatic system under the caldera made of two interconnected lobes located at the two opposite sides of the caldera. These lobes could be consistent with feeding reservoirs of the ongoing Tavuvur volcano eruption of andesitic products, on the eastern side, and of the past Vulcan volcano eruptions of more evolved materials, on the western side. The interconnection and

  15. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    Sheila M Reynolds

    2010-07-01

    Full Text Available DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the

  16. Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens.

    Reynolds, Sheila M; Bilmes, Jeff A; Noble, William Stafford

    2010-07-08

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence-301 base pairs, centered at the position to be scored-with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  17. Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens

    Reynolds, Sheila M.; Bilmes, Jeff A.; Noble, William Stafford

    2010-01-01

    DNA in eukaryotes is packaged into a chromatin complex, the most basic element of which is the nucleosome. The precise positioning of the nucleosome cores allows for selective access to the DNA, and the mechanisms that control this positioning are important pieces of the gene expression puzzle. We describe a large-scale nucleosome pattern that jointly characterizes the nucleosome core and the adjacent linkers and is predominantly characterized by long-range oscillations in the mono, di- and tri-nucleotide content of the DNA sequence, and we show that this pattern can be used to predict nucleosome positions in both Homo sapiens and Saccharomyces cerevisiae more accurately than previously published methods. Surprisingly, in both H. sapiens and S. cerevisiae, the most informative individual features are the mono-nucleotide patterns, although the inclusion of di- and tri-nucleotide features results in improved performance. Our approach combines a much longer pattern than has been previously used to predict nucleosome positioning from sequence—301 base pairs, centered at the position to be scored—with a novel discriminative classification approach that selectively weights the contributions from each of the input features. The resulting scores are relatively insensitive to local AT-content and can be used to accurately discriminate putative dyad positions from adjacent linker regions without requiring an additional dynamic programming step and without the attendant edge effects and assumptions about linker length modeling and overall nucleosome density. Our approach produces the best dyad-linker classification results published to date in H. sapiens, and outperforms two recently published models on a large set of S. cerevisiae nucleosome positions. Our results suggest that in both genomes, a comparable and relatively small fraction of nucleosomes are well-positioned and that these positions are predictable based on sequence alone. We believe that the bulk of the

  18. Regulation of BAZ1A and nucleosome positioning in the nucleus accumbens in response to cocaine.

    Sun, HaoSheng; Damez-Werno, Diane M; Scobie, Kimberly N; Shao, Ning-Yi; Dias, Caroline; Rabkin, Jacqui; Wright, Katherine N; Mouzon, Ezekiell; Kabbaj, Mohamed; Neve, Rachael; Turecki, Gustavo; Shen, Li; Nestler, Eric J

    2017-06-14

    Chromatin regulation, in particular ATP-dependent chromatin remodelers, have previously been shown to be important in the regulation of reward-related behaviors in animal models of mental illnesses. Here we demonstrate that BAZ1A, an accessory subunit of the ISWI family of chromatin remodeling complexes, is downregulated in the nucleus accumbens (NAc) of mice exposed repeatedly to cocaine and of cocaine-addicted humans. Viral-mediated overexpression of BAZ1A in mouse NAc reduces cocaine reward as assessed by conditioned place preference (CPP), but increases cocaine-induced locomotor activation. Furthermore, we investigate nucleosome repositioning genome-wide by conducting chromatin immunoprecipitation (ChIP)-sequencing for total H3 in NAc of control mice and after repeated cocaine administration, and find extensive nucleosome occupancy and shift changes across the genome in response to cocaine exposure. These findings implicate BAZ1A in molecular and behavioral plasticity to cocaine and offer new insight into the pathophysiology of cocaine addiction. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

  19. The Cac2 subunit is essential for productive histone binding and nucleosome assembly in CAF-1

    Mattiroli, Francesca; Gu, Yajie; Balsbaugh, Jeremy L.; Ahn, Natalie G.; Luger, Karolin

    2017-04-18

    Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding. The large subunit, Cac1 organizes the assembly of CAF-1. Strikingly, H3-H4 binding is mediated by a composite interface, shaped by Cac1-bound Cac2 and the Cac1 acidic region. Cac2 is indispensable for productive histone binding, while deletion of Cac3 has only moderate effects on H3-H4 binding and nucleosome assembly. These results define direct structural roles for yeast CAF-1 subunits and uncover a previously unknown critical function of the middle subunit in CAF-1.

  20. A brief histone in time: understanding the combinatorial functions of histone PTMs in the nucleosome context.

    Ng, Marlee K; Cheung, Peter

    2016-02-01

    It has been over 50 years since Allfrey et al. proposed that histone acetylation regulates RNA synthesis, and the study of histone modifications has progressed at an extraordinary pace for the past two decades. In this review, we provide a perspective on some key events and advances in our understanding of histone modifications. We also highlight reagents and tools from past to present that facilitated progress in this research field. Using histone H3 phosphorylation as an underlying thread, we review the rationale that led to the proposal of the histone code hypothesis, as well as examples that illustrate the concepts of combinatorial histone modifications and cross-talk pathways. We further highlight the importance of investigating these mechanisms in the context of nucleosomes rather than just at the histone level and present current and developing approaches for such studies. Overall, research on histone modifications has yielded great mechanistic insights into the regulation of genomic functions, and extending these studies using nucleosomes will further elucidate the complexity of these pathways in a more physiologically relevant context.

  1. Scutellarein antagonizes the tumorigenesis by modulating cytokine VEGF mediated neoangiogenesis and DFF-40 actuated nucleosomal degradation

    Thirusangu, Prabhu; Vigneshwaran, V.; Vijay Avin, B.R.; Rakesh, H.; Vikas, H.M.; Prabhakar, B.T.

    2017-01-01

    Neoplastic cells often reside in distinctive tumor hypoxia armed with a series of adaptive responses including oxidative stress, defective apoptotic machinery and neoangiogenesis, through that further confer cell survival improvement. Plants still acts as reservoir of natural chemicals to provide newer active pharmacophores. Scutellarein is flavones which has wide range of pharmacophoral effects. In our current research, scutellarein employed for targeting oxidative stress mediated tumor angiogenesis and apoptotic nuclear fragmentation. Experimental results revealed that scutellarein has antiproliferative index against multiple cancer cell lines and diminished the oxidative stress and tumor development of murine ascitic lymphoma & inflammatory hepatocellular carcinoma. Eventual consequences lead to reduced neovessel formation by abrogating angiogeneic factors cytokine-VEGF-A, Flt-1, HIF-1α, MMP-2 and MMP-9 and reversing of evading apoptosis by activating caspase-3 activated DNA fragmentation factor (DFF-40) mediated nucleosomal degradation. In summary, our experimental evidences suggest that scutellarein has strong potentiality to attenuate the tumor development by modulating sprouting neovasculature and DFF-40 mediated apoptosis. - Highlights: • Scutellarein exhibits potent neoplastic effect against ascitic and DEN-induced liver carcinoma in-vivo. • Scutellarein reticence the oxidative stress and angiogenesis on tumor and non-tumor models. • Scutellarein modulates tumor vasculature by altering tumor angiogenic factor’s expressions. • Scutellarein actuates the DFF-40 mediated nucleosomal degradation in DLA tumor.

  2. Arginine-phosphate salt bridges between histones and DNA: Intermolecular actuators that control nucleosome architecture

    Yusufaly, Tahir I.; Li, Yun; Singh, Gautam; Olson, Wilma K.

    2014-10-01

    Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.

  3. FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation.

    Jennifer R Stevens

    Full Text Available Gene transcription is constrained by the nucleosomal nature of chromosomal DNA. This nucleosomal barrier is modulated by FACT, a conserved histone-binding heterodimer. FACT mediates transcription-linked nucleosome disassembly and also nucleosome reassembly in the wake of the RNA polymerase II transcription complex, and in this way maintains the repression of 'cryptic' promoters found within some genes. Here we focus on a novel mutant version of the yeast FACT subunit Spt16 that supplies essential Spt16 activities but impairs transcription-linked nucleosome reassembly in dominant fashion. This Spt16 mutant protein also has genetic effects that are recessive, which we used to show that certain Spt16 activities collaborate with histone acetylation and the activities of a Bur-kinase/Spt4-Spt5/Paf1C pathway that facilitate transcription elongation. These collaborating activities were opposed by the actions of Rpd3S, a histone deacetylase that restores a repressive chromatin environment in a transcription-linked manner. Spt16 activity paralleling that of HirC, a co-repressor of histone gene expression, was also found to be opposed by Rpd3S. Our findings suggest that Spt16, the Bur/Spt4-Spt5/Paf1C pathway, and normal histone abundance and/or stoichiometry, in mutually cooperative fashion, facilitate nucleosome disassembly during transcription elongation. The recessive nature of these effects of the mutant Spt16 protein on transcription-linked nucleosome disassembly, contrasted to its dominant negative effect on transcription-linked nucleosome reassembly, indicate that mutant FACT harbouring the mutant Spt16 protein competes poorly with normal FACT at the stage of transcription-linked nucleosome disassembly, but effectively with normal FACT for transcription-linked nucleosome reassembly. This functional difference is consistent with the idea that FACT association with the transcription elongation complex depends on nucleosome disassembly, and that the

  4. The incorporation of the novel histone variant H2AL2 confers unusual structural and functional properties of the nucleosome

    Syed, S.H.; Boulard, M.; Shukla, M.S.; Gautier, T.; Travers, A.; Bednár, Jan; Faivre-Moskalenko, C.; Dimitrov, S.; Angelov, D.

    2009-01-01

    Roč. 37, č. 14 (2009), s. 4684-4695 ISSN 0305-1048 Grant - others:GA MŠk(CZ) LC535; GA ČR(CZ) GA304/05/2168 Program:LC Institutional research plan: CEZ:AV0Z50110509 Keywords : nucleosome * histone * variant Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.479, year: 2009

  5. Sensor array signal processing

    Naidu, Prabhakar S

    2009-01-01

    Chapter One: An Overview of Wavefields 1.1 Types of Wavefields and the Governing Equations 1.2 Wavefield in open space 1.3 Wavefield in bounded space 1.4 Stochastic wavefield 1.5 Multipath propagation 1.6 Propagation through random medium 1.7 ExercisesChapter Two: Sensor Array Systems 2.1 Uniform linear array (ULA) 2.2 Planar array 2.3 Distributed sensor array 2.4 Broadband sensor array 2.5 Source and sensor arrays 2.6 Multi-component sensor array2.7 ExercisesChapter Three: Frequency Wavenumber Processing 3.1 Digital filters in the w-k domain 3.2 Mapping of 1D into 2D filters 3.3 Multichannel Wiener filters 3.4 Wiener filters for ULA and UCA 3.5 Predictive noise cancellation 3.6 Exercises Chapter Four: Source Localization: Frequency Wavenumber Spectrum4.1 Frequency wavenumber spectrum 4.2 Beamformation 4.3 Capon's w-k spectrum 4.4 Maximum entropy w-k spectrum 4.5 Doppler-Azimuth Processing4.6 ExercisesChapter Five: Source Localization: Subspace Methods 5.1 Subspace methods (Narrowband) 5.2 Subspace methods (B...

  6. Modular Matrix Multiplication on a Linear Array.

    1983-11-01

    is fl(n2). 2 Case e Irl __ (see Figure 5.2) 2 2 ,1 Y, " X2v- ’ Y2 -. x= -- ~ Y4 "i; Yin Figure 5Ŗ At t--xi, either all Gk, such that IkEA , have n...nat and Image Proceuing, IEEE Transactions on Computers, Vol. C-31, No. 10 22 (October, 1982), pp. IO0oo09. [41 H.T. Kung, Let’s Design Algorithms for...VLSI Systems, Proc. Caltech Conf. on Very Large Scale Integration: Architecture, Design , Fabrication (January, 1979), pp. 65. 90. 151 H.T. Kung, and

  7. Towards the theoretical bases of the folding of the 100-A nucleosome filament

    Chela Flores, J.

    1994-01-01

    We attempt to model DNA packaging at the various stages of ever increasing DNA folding from the 100-A nucleosome filament to various further stages leading up to the metaphase chromosome. We have assumed that a phase transition has induced chromatin into a condensed mode. The mean-field model allows the simultaneous discussion of chromatin with packaging ration η and DNA replication at various stages of folding. We derive a formula correlating (during the S phase of the cell cycle) the DNA polymerase velocity r f (measured in nucleotides per minute) in a relation of inverse proportionality with the degree of DNA packaging: r f = λη -1/2 , where the dimensional constant λ has been determined. This model suggests that in the heterochromatic regions of chromatin there is reduced activity of DNA polymerases. We discuss the possible relevance of our model to late replicating telomeres in yeast and several higher eukaryotes. (author). 28 refs, 3 tabs

  8. Thermomechanical damage of nucleosome by the shock wave initiated by ion passing through liquid water

    Yakubovich, Alexander V.; Surdutovich, Eugene; Solov’yov, Andrey V.

    2012-01-01

    We report on the results of full-atom molecular dynamics simulations of the heat spike in the water medium caused by the propagation of the heavy ion in the vicinity of its Bragg peak. High rate of energy transfer from an ion to the molecules of surrounding water environment leads to the rapid increase of the temperature of the molecules in the vicinity of ions trajectory. As a result of an abrupt increase of the temperature we observe the formation of the nanoscale shock wave propagating through the medium. We investigate the thermomechanical damage caused by the shock wave to the nucleosome located in the vicinity of heavy ion trajectory. We observe the substantial deformation of the DNA secondary structure. We show that the produced shock wave can lead to the thermomechanical breakage of the DNA backbone covalent bonds and present estimates for the number of such strand brakes per one cell nucleus.

  9. Conformal array design on arbitrary polygon surface with transformation optics

    Deng, Li, E-mail: dengl@bupt.edu.cn; Hong, Weijun, E-mail: hongwj@bupt.edu.cn; Zhu, Jianfeng; Peng, Biao; Li, Shufang [Beijing Key Laboratory of Network System Architecture and Convergence, School of Information and Communication Engineering, Beijing University of Posts and Telecommunications, 100876 Beijing (China); Wu, Yongle, E-mail: wuyongle138@gmail.com [Beijing Key Laboratory of Work Safety Intelligent Monitoring, School of Electronic Engineering, Beijing University of Posts and Telecommunications, 100876 Beijing (China)

    2016-06-15

    A transformation-optics based method to design a conformal antenna array on an arbitrary polygon surface is proposed and demonstrated in this paper. This conformal antenna array can be adjusted to behave equivalently as a uniformly spaced linear array by applying an appropriate transformation medium. An typical example of general arbitrary polygon conformal arrays, not limited to circular array, is presented, verifying the proposed approach. In summary, the novel arbitrary polygon surface conformal array can be utilized in array synthesis and beam-forming, maintaining all benefits of linear array.

  10. Conformal array design on arbitrary polygon surface with transformation optics

    Deng, Li; Hong, Weijun; Zhu, Jianfeng; Peng, Biao; Li, Shufang; Wu, Yongle

    2016-01-01

    A transformation-optics based method to design a conformal antenna array on an arbitrary polygon surface is proposed and demonstrated in this paper. This conformal antenna array can be adjusted to behave equivalently as a uniformly spaced linear array by applying an appropriate transformation medium. An typical example of general arbitrary polygon conformal arrays, not limited to circular array, is presented, verifying the proposed approach. In summary, the novel arbitrary polygon surface conformal array can be utilized in array synthesis and beam-forming, maintaining all benefits of linear array.

  11. Compact Spectrometers Based on Linear Variable Filters

    National Aeronautics and Space Administration — Demonstrate a linear-variable spectrometer with an H2RG array. Linear Variable Filter (LVF) spectrometers provide attractive resource benefits – high optical...

  12. Array capabilities and future arrays

    Radford, D.

    1993-01-01

    Early results from the new third-generation instruments GAMMASPHERE and EUROGAM are confirming the expectation that such arrays will have a revolutionary effect on the field of high-spin nuclear structure. When completed, GAMMASHPERE will have a resolving power am order of magnitude greater that of the best second-generation arrays. When combined with other instruments such as particle-detector arrays and fragment mass analysers, the capabilites of the arrays for the study of more exotic nuclei will be further enhanced. In order to better understand the limitations of these instruments, and to design improved future detector systems, it is important to have some intelligible and reliable calculation for the relative resolving power of different instrument designs. The derivation of such a figure of merit will be briefly presented, and the relative sensitivities of arrays currently proposed or under construction presented. The design of TRIGAM, a new third-generation array proposed for Chalk River, will also be discussed. It is instructive to consider how far arrays of Compton-suppressed Ge detectors could be taken. For example, it will be shown that an idealised open-quote perfectclose quotes third-generation array of 1000 detectors has a sensitivity an order of magnitude higher again than that of GAMMASPHERE. Less conventional options for new arrays will also be explored

  13. Acoustic emission linear pulse holography

    Collins, H.D.; Busse, L.J.; Lemon, D.K.

    1983-01-01

    This paper describes the emission linear pulse holography which produces a chronological linear holographic image of a flaw by utilizing the acoustic energy emitted during crack growth. A thirty two point sampling array is used to construct phase-only linear holograms of simulated acoustic emission sources on large metal plates. The concept behind the AE linear pulse holography is illustrated, and a block diagram of a data acquisition system to implement the concept is given. Array element spacing, synthetic frequency criteria, and lateral depth resolution are specified. A reference timing transducer positioned between the array and the inspection zone and which inititates the time-of-flight measurements is described. The results graphically illustrate the technique using a one-dimensional FFT computer algorithm (ie. linear backward wave) for an AE image reconstruction

  14. The enrichment of TATA box and the scarcity of depleted proximal nucleosome in the promoters of duplicated yeast genes.

    Kim, Yuseob; Lee, Jang H; Babbitt, Gregory A

    2010-01-01

    Population genetic theory of gene duplication suggests that the preservation of duplicate copies requires functional divergence upon duplication. Genes that can be readily modified to produce new gene expression patterns may thus be duplicated often. In yeast, genes exhibit dichotomous expression patterns based on their promoter architectures. The expression of genes that contain TATA box or occupied proximal nucleosome (OPN) tends to be variable and respond to external signals. On the other hand, genes without TATA box or with depleted proximal nucleosome (DPN) are expressed constitutively. We find that recent duplicates in the yeast genome are heavily biased to be TATA box containing genes and not to be DPN genes. This suggests that variably expressed genes, due to the functional organization in their promoters, have higher duplicability than constitutively expressed genes.

  15. The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in Saccharomyces cerevisiae.

    Christine E Cucinotta

    2015-08-01

    Full Text Available Eukaryotes regulate gene expression and other nuclear processes through the posttranslational modification of histones. In S. cerevisiae, the mono-ubiquitylation of histone H2B on lysine 123 (H2B K123ub affects nucleosome stability, broadly influences gene expression and other DNA-templated processes, and is a prerequisite for additional conserved histone modifications that are associated with active transcription, namely the methylation of lysine residues in H3. While the enzymes that promote these chromatin marks are known, regions of the nucleosome required for the recruitment of these enzymes are undefined. To identify histone residues required for H2B K123ub, we exploited a functional interaction between the ubiquitin-protein ligase, Rkr1/Ltn1, and H2B K123ub in S. cerevisiae. Specifically, we performed a synthetic lethal screen with cells lacking RKR1 and a comprehensive library of H2A and H2B residue substitutions, and identified H2A residues that are required for H2B K123ub. Many of these residues map to the nucleosome acidic patch. The substitutions in the acidic patch confer varying histone modification defects downstream of H2B K123ub, indicating that this region contributes differentially to multiple histone modifications. Interestingly, substitutions in the acidic patch result in decreased recruitment of H2B K123ub machinery to active genes and defects in transcription elongation and termination. Together, our findings reveal a role for the nucleosome acidic patch in recruitment of histone modification machinery and maintenance of transcriptional integrity.

  16. SNP Arrays

    Jari Louhelainen

    2016-10-01

    Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

  17. Hypoxia-induced oxidative base modifications in the VEGF hypoxia-response element are associated with transcriptionally active nucleosomes.

    Ruchko, Mykhaylo V; Gorodnya, Olena M; Pastukh, Viktor M; Swiger, Brad M; Middleton, Natavia S; Wilson, Glenn L; Gillespie, Mark N

    2009-02-01

    Reactive oxygen species (ROS) generated in hypoxic pulmonary artery endothelial cells cause transient oxidative base modifications in the hypoxia-response element (HRE) of the VEGF gene that bear a conspicuous relationship to induction of VEGF mRNA expression (K.A. Ziel et al., FASEB J. 19, 387-394, 2005). If such base modifications are indeed linked to transcriptional regulation, then they should be detected in HRE sequences associated with transcriptionally active nucleosomes. Southern blot analysis of the VEGF HRE associated with nucleosome fractions prepared by micrococcal nuclease digestion indicated that hypoxia redistributed some HRE sequences from multinucleosomes to transcriptionally active mono- and dinucleosome fractions. A simple PCR method revealed that VEGF HRE sequences harboring oxidative base modifications were found exclusively in mononucleosomes. Inhibition of hypoxia-induced ROS generation with myxathiozol prevented formation of oxidative base modifications but not the redistribution of HRE sequences into mono- and dinucleosome fractions. The histone deacetylase inhibitor trichostatin A caused retention of HRE sequences in compacted nucleosome fractions and prevented formation of oxidative base modifications. These findings suggest that the hypoxia-induced oxidant stress directed at the VEGF HRE requires the sequence to be repositioned into mononucleosomes and support the prospect that oxidative modifications in this sequence are an important step in transcriptional activation.

  18. The Scc2/Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions

    Lopez-Serra, Lidia; Kelly, Gavin; Patel, Harshil; Stewart, Aengus; Uhlmann, Frank

    2014-01-01

    The cohesin complex is at the heart of many chromosomal activities, including sister chromatid cohesion and transcriptional regulation1-3. Cohesin loading onto chromosomes depends on the Scc2/Scc4 cohesin loader complex4-6, but the chromatin features that form cohesin loading sites remain poorly understood. Here, we show that the RSC chromatin remodeling complex recruits budding yeast Scc2/Scc4 to broad nucleosome-free regions, that the cohesin loader itself helps to maintain. Consequently, inactivation of the cohesin loader or RSC complex have similar effects on nucleosome positioning, gene expression and sister chromatid cohesion. These results reveal an intimate link between local chromatin structure and higher order chromosome architecture. Our findings pertain to the similarities between two severe human disorders, Cornelia de Lange syndrome, caused by mutations in the human cohesin loader, and Coffin-Siris syndrome, resulting from mutations in human RSC complex components7-9. Both could arise from gene misregulation due to related changes in the nucleosome landscape. PMID:25173104

  19. electrode array

    PROF EKWUEME

    A geoelectric investigation employing vertical electrical soundings (VES) using the Ajayi - Makinde Two-Electrode array and the ... arrangements used in electrical D.C. resistivity survey. These include ..... Refraction Tomography to Study the.

  20. Binding of ethidium to the nucleosome core particle. 2. Internal and external binding modes

    McMurray, C.T.; Small, E.W.; van Holde, K.E.

    1991-01-01

    The authors have previously reported that the binding of ethidium bromide to the nucleosome core particle results in a stepwise dissociation of the structure which involves the initial release of one copy each of H2A and H2B. In this report, they have examined the absorbance and fluorescence properties of intercalated and outside bound forms of ethidium bromide. From these properties, they have measured the extent of external, electrostatic binding of the dye versus internal, intercalation binding to the core particle, free from contribution by linker DNA. They have established that dissociation is induced by the intercalation mode of binding to DNA within the core particle DNA, and not by binding to the histones or by nonintercalative binding to DNA. The covalent binding of [ 3 H]-8-azidoethidium to the core particle clearly shows that < 1.0 adduct is formed per histone octamer over a wide range of input ratios. Simultaneously, analyses of steady-state fluorescence enhancement and fluorescence lifetime data from bound ethidium complexes demonstrate extensive intercalation binding. Combined analyses from steady-state fluorescence intensity with equilibrium dialysis or fluorescence lifetime data revealed that dissociation began when ∼14 ethidium molecules are bound by intercalation to each core particle and < 1.0 nonintercalated ion pair was formed per core particle

  1. DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition.

    Liu, Xiao; Dang, Yunkun; Matsu-Ura, Toru; He, Yubo; He, Qun; Hong, Christian I; Liu, Yi

    2017-07-20

    Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism. Published by Elsevier Inc.

  2. Interaction of nucleosome assembly proteins abolishes nuclear localization of DGKζ by attenuating its association with importins

    Okada, Masashi; Hozumi, Yasukazu; Ichimura, Tohru; Tanaka, Toshiaki; Hasegawa, Hiroshi; Yamamoto, Masakazu; Takahashi, Nobuya; Iseki, Ken; Yagisawa, Hitoshi; Shinkawa, Takashi; Isobe, Toshiaki; Goto, Kaoru

    2011-01-01

    Diacylglycerol kinase (DGK) is involved in the regulation of lipid-mediated signal transduction through the metabolism of a second messenger diacylglycerol. Of the DGK family, DGKζ, which contains a nuclear localization signal, localizes mainly to the nucleus but translocates to the cytoplasm under pathological conditions. However, the detailed mechanism of translocation and its functional significance remain unclear. To elucidate these issues, we used a proteomic approach to search for protein targets that interact with DGKζ. Results show that nucleosome assembly protein (NAP) 1-like 1 (NAP1L1) and NAP1-like 4 (NAP1L4) are identified as novel DGKζ binding partners. NAP1Ls constitutively shuttle between the nucleus and the cytoplasm in transfected HEK293 cells. The molecular interaction of DGKζ and NAP1Ls prohibits nuclear import of DGKζ because binding of NAP1Ls to DGKζ blocks import carrier proteins, Qip1 and NPI1, to interact with DGKζ, leading to cytoplasmic tethering of DGKζ. In addition, overexpression of NAP1Ls exerts a protective effect against doxorubicin-induced cytotoxicity. These findings suggest that NAP1Ls are involved in a novel molecular basis for the regulation of nucleocytoplasmic shuttling of DGKζ and provide a clue to examine functional significance of its translocation under pathological conditions.

  3. Dengue Virus Capsid Protein Binds Core Histones and Inhibits Nucleosome Formation in Human Liver Cells

    Colpitts, Tonya M.; Barthel, Sebastian; Wang, Penghua; Fikrig, Erol

    2011-01-01

    Dengue virus (DENV) is a member of the Flaviviridae and a globally (re)emerging pathogen that causes serious human disease. There is no specific antiviral or vaccine for dengue virus infection. Flavivirus capsid (C) is a structural protein responsible for gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. Flaviviral replication is known to occur in the cytoplasm yet a large portion of capsid protein localizes to the nucleus during infection. The reasons for the nuclear presences of capsid are not completely understood. Here, we expressed mature DENV C in a tandem affinity purification assay to identify potential binding partners in human liver cells. DENV C targeted the four core histones, H2A, H2B, H3 and H4. DENV C bound recombinant histones in solution and colocalized with histones in the nucleus and cytoplasm of liver cells during DENV infection. We show that DENV C acts as a histone mimic, forming heterodimers with core histones, binding DNA and disrupting nucleosome formation. We also demonstrate that DENV infection increases the amounts of core histones in livers cells, which may be a cellular response to C binding away the histone proteins. Infection with DENV additionally alters levels of H2A phosphorylation in a time-dependent manner. The interactions of C and histones add an interesting new role for the presence of C in the nucleus during DENV infection. PMID:21909430

  4. Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization.

    González-Romero, Rodrigo; Eirín-López, José M; Ausió, Juan

    2015-01-01

    High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance-most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  5. Linear algebra

    Shilov, Georgi E

    1977-01-01

    Covers determinants, linear spaces, systems of linear equations, linear functions of a vector argument, coordinate transformations, the canonical form of the matrix of a linear operator, bilinear and quadratic forms, Euclidean spaces, unitary spaces, quadratic forms in Euclidean and unitary spaces, finite-dimensional space. Problems with hints and answers.

  6. Combination of solid phase extraction and dispersive liquid–liquid microextraction for separation/preconcentration of ultra trace amounts of uranium prior to its fiber optic-linear array spectrophotometry determination

    Dadfarnia, Shayessteh; Shabani, Ali Mohammad Haji; Shakerian, Farid; Shiralian Esfahani, Golnaz

    2013-01-01

    Graphical abstract: Pass the sample through the basic alumina column ⇒ elute retained uranium along with the cations ⇒ convert the uranium to its anionic benzoate complex ⇒ extract its ion pair with malachite green into small volume of chloroform by DLLME ⇒ measure its absorption at 621 nm using fiber optic-linear array detection spectrophotometry. -- Highlights: • By combination of SPE and DDLME a high preconcentration factor of 2500 was obtained. • Development of SPE-DDLME-Spectrophotometric method for det. of trace amounts of uranium. • Ultra trace amount of uranium in water samples was det. by the proposed method. • The detection limit of the proposed method is comparable to the most sensitive method. • The proposed method is a free interference spectrophotometric method for uranium det. -- Abstract: A simple and sensitive method for the separation and preconcentration of the ultra trace amounts of uranium and its determination by spectrophotometry was developed. The method is based on the combination of solid phase extraction and dispersive liquid–liquid microextraction. Thus, by passing the sample through the basic alumina column, the uranyl ion and some cations are separated from the sample matrix. The retained uranyl ion along with the cations are eluted with 5 mL of nitric acid (2 mol L −1 ) and after neutralization of the eluent, the extracted uranyl ion is converted to its anionic benzoate complex and is separated from other cations by extraction of its ion pair with malachite green into small volume of chloroform using dispersive liquid–liquid microextraction. The amount of uranium is then determined by the absorption measurement of the extracted ion pair at 621 nm using flow injection spectrophotometry. Under the optimum conditions, with 500 mL of the sample, a preconcentration factor of 1980, a detection limit of 40 ng L −1 , and a relative standard deviation of 4.1% (n = 6) at 400 ng L −1 were obtained. The method was

  7. Design of circular differential microphone arrays

    Benesty, Jacob; Cohen, Israel

    2015-01-01

    Recently, we proposed a completely novel and efficient way to design differential beamforming algorithms for linear microphone arrays. Thanks to this very flexible approach, any order of differential arrays can be designed. Moreover, they can be made robust against white noise amplification, which is the main inconvenience in these types of arrays. The other well-known problem with linear arrays is that electronic steering is not really feasible.  In this book, we extend all these fundamental ideas to circular microphone arrays and show that we can design small and compact differential arrays of any order that can be electronically steered in many different directions and offer a good degree of control of the white noise amplification problem, high directional gain, and frequency-independent response. We also present a number of practical examples, demonstrating that differential beamforming with circular microphone arrays is likely one of the best candidates for applications involving speech enhancement (i....

  8. Filter arrays

    Page, Ralph H.; Doty, Patrick F.

    2017-08-01

    The various technologies presented herein relate to a tiled filter array that can be used in connection with performance of spatial sampling of optical signals. The filter array comprises filter tiles, wherein a first plurality of filter tiles are formed from a first material, the first material being configured such that only photons having wavelengths in a first wavelength band pass therethrough. A second plurality of filter tiles is formed from a second material, the second material being configured such that only photons having wavelengths in a second wavelength band pass therethrough. The first plurality of filter tiles and the second plurality of filter tiles can be interspersed to form the filter array comprising an alternating arrangement of first filter tiles and second filter tiles.

  9. Fundamentals of ultrasonic phased arrays

    Schmerr, Lester W

    2014-01-01

    This book describes in detail the physical and mathematical foundations of ultrasonic phased array measurements.?The book uses linear systems theory to develop a comprehensive model of the signals and images that can be formed with phased arrays. Engineers working in the field of ultrasonic nondestructive evaluation (NDE) will find in this approach a wealth of information on how to design, optimize and interpret ultrasonic inspections with phased arrays. The fundamentals and models described in the book will also be of significant interest to other fields, including the medical ultrasound and

  10. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling.

    Justin W Leung

    2014-03-01

    Full Text Available Histone ubiquitinations are critical for the activation of the DNA damage response (DDR. In particular, RNF168 and RING1B/BMI1 function in the DDR by ubiquitinating H2A/H2AX on Lys-13/15 and Lys-118/119, respectively. However, it remains to be defined how the ubiquitin pathway engages chromatin to provide regulation of ubiquitin targeting of specific histone residues. Here we identify the nucleosome acid patch as a critical chromatin mediator of H2A/H2AX ubiquitination (ub. The acidic patch is required for RNF168- and RING1B/BMI1-dependent H2A/H2AXub in vivo. The acidic patch functions within the nucleosome as nucleosomes containing a mutated acidic patch exhibit defective H2A/H2AXub by RNF168 and RING1B/BMI1 in vitro. Furthermore, direct perturbation of the nucleosome acidic patch in vivo by the expression of an engineered acidic patch interacting viral peptide, LANA, results in defective H2AXub and RNF168-dependent DNA damage responses including 53BP1 and BRCA1 recruitment to DNA damage. The acidic patch therefore is a critical nucleosome feature that may serve as a scaffold to integrate multiple ubiquitin signals on chromatin to compose selective ubiquitinations on histones for DNA damage signaling.

  11. Detector array and method

    Timothy, J.G.; Bybee, R.L.

    1978-01-01

    A detector array and method are described in which sets of electrode elements are provided. Each set consists of a number of linear extending parallel electrodes. The sets of electrode elements are disposed at an angle (preferably orthogonal) with respect to one another so that the individual elements intersect and overlap individual elements of the other sets. Electrical insulation is provided between the overlapping elements. The detector array is exposed to a source of charged particles which in accordance with one embodiment comprise electrons derived from a microchannel array plate exposed to photons. Amplifier and discriminator means are provided for each individual electrode element. Detection means are provided to sense pulses on individual electrode elements in the sets, with coincidence of pulses on individual intersecting electrode elements being indicative of charged particle impact at the intersection of the elements. Electronic readout means provide an indication of coincident events and the location where the charged particle or particles impacted. Display means are provided for generating appropriate displays representative of the intensity and locaton of charged particles impacting on the detector array

  12. Array processors based on Gaussian fraction-free method

    Peng, S; Sedukhin, S [Aizu Univ., Aizuwakamatsu, Fukushima (Japan); Sedukhin, I

    1998-03-01

    The design of algorithmic array processors for solving linear systems of equations using fraction-free Gaussian elimination method is presented. The design is based on a formal approach which constructs a family of planar array processors systematically. These array processors are synthesized and analyzed. It is shown that some array processors are optimal in the framework of linear allocation of computations and in terms of number of processing elements and computing time. (author)

  13. Phase retrieval in near-field measurements by array synthesis

    Wu, Jian; Larsen, Flemming Holm

    1991-01-01

    The phase retrieval problem in near-field antenna measurements is formulated as an array synthesis problem. As a test case, a particular synthesis algorithm has been used to retrieve the phase of a linear array......The phase retrieval problem in near-field antenna measurements is formulated as an array synthesis problem. As a test case, a particular synthesis algorithm has been used to retrieve the phase of a linear array...

  14. Plane-wave scattering from half-wave dipole arrays

    Jensen, Niels E.

    1970-01-01

    A matrix equation for determination of plane-wave scattering from arrays of thin short-circuited dipoles of lengths about half a wavelength is derived. Numerical and experimental results are presented for linear, circular, and concentric circular arrays.......A matrix equation for determination of plane-wave scattering from arrays of thin short-circuited dipoles of lengths about half a wavelength is derived. Numerical and experimental results are presented for linear, circular, and concentric circular arrays....

  15. Directional spectrum of ocean waves from array measurements using phase/time/path difference methods

    Fernandes, A.A.; Sarma, Y.V.B.; Menon, H.B.

    Wave direction has for the first time been consistently, accurately and unambiguously evaluated from array measurements using the phase/time/path difference (PTPD) methods of Esteva in case of polygonal arrays and Borgman in case of linear arrays...

  16. Seismometer array station processors

    Key, F.A.; Lea, T.G.; Douglas, A.

    1977-01-01

    A description is given of the design, construction and initial testing of two types of Seismometer Array Station Processor (SASP), one to work with data stored on magnetic tape in analogue form, the other with data in digital form. The purpose of a SASP is to detect the short period P waves recorded by a UK-type array of 20 seismometers and to edit these on to a a digital library tape or disc. The edited data are then processed to obtain a rough location for the source and to produce seismograms (after optimum processing) for analysis by a seismologist. SASPs are an important component in the scheme for monitoring underground explosions advocated by the UK in the Conference of the Committee on Disarmament. With digital input a SASP can operate at 30 times real time using a linear detection process and at 20 times real time using the log detector of Weichert. Although the log detector is slower, it has the advantage over the linear detector that signals with lower signal-to-noise ratio can be detected and spurious large amplitudes are less likely to produce a detection. It is recommended, therefore, that where possible array data should be recorded in digital form for input to a SASP and that the log detector of Weichert be used. Trial runs show that a SASP is capable of detecting signals down to signal-to-noise ratios of about two with very few false detections, and at mid-continental array sites it should be capable of detecting most, if not all, the signals with magnitude above msub(b) 4.5; the UK argues that, given a suitable network, it is realistic to hope that sources of this magnitude and above can be detected and identified by seismological means alone. (author)

  17. Tomographic array

    1976-01-01

    The configuration of a tomographic array in which the object can rotate about its axis is described. The X-ray detector is a cylindrical screen perpendicular to the axis of rotation. The X-ray source has a line-shaped focus coinciding with the axis of rotation. The beam is fan-shaped with one side of this fan lying along the axis of rotation. The detector screen is placed inside an X-ray image multiplier tube

  18. Tomographic array

    1976-01-01

    A tomographic array with the following characteristics is described. An X-ray screen serving as detector is placed before a photomultiplier tube which itself is placed in front of a television camera connected to a set of image processors. The detector is concave towards the source and is replacable. Different images of the object are obtained simultaneously. Optical fibers and lenses are used for transmission within the system

  19. Linear gate

    Suwono.

    1978-01-01

    A linear gate providing a variable gate duration from 0,40μsec to 4μsec was developed. The electronic circuity consists of a linear circuit and an enable circuit. The input signal can be either unipolar or bipolar. If the input signal is bipolar, the negative portion will be filtered. The operation of the linear gate is controlled by the application of a positive enable pulse. (author)

  20. Linear Accelerators

    Vretenar, M

    2014-01-01

    The main features of radio-frequency linear accelerators are introduced, reviewing the different types of accelerating structures and presenting the main characteristics aspects of linac beam dynamics

  1. Phased array ultrasound testing on complex geometry

    Tuan Arif Tuan Mat; Khazali Mohd Zin

    2009-01-01

    Phase array ultrasonic inspection is used to investigate its response to complex welded joints geometry. A 5 MHz probe with 64 linear array elements was employed to scan mild steel T-joint, nozzle and node samples. These samples contain many defects such as cracks, lack of penetration and lack of fusion. Ultrasonic respond is analysed and viewed using the Tomoview software. The results show the actual phase array images on respective types of defect. (author)

  2. Halbach arrays in precision motion control

    Trumper, D.L.; Williams, M.E. [Massachusetts Institute of Technology, Cambridge, MA (United States)

    1995-02-01

    The Halbach array was developed for use as an optical element in particle accelerators. Following up on a suggestion from Klaus Halbach, the authors have investigated the utility of such arrays as the permanent magnet structure for synchronous machines in cartesian, polar, and cylindrical geometries. Their work has focused on the design of a novel Halbach array linear motor for use in a magnetic suspension stage for photolithography. This paper presents the details of the motor design and its force and power characteristics.

  3. Linearization Method and Linear Complexity

    Tanaka, Hidema

    We focus on the relationship between the linearization method and linear complexity and show that the linearization method is another effective technique for calculating linear complexity. We analyze its effectiveness by comparing with the logic circuit method. We compare the relevant conditions and necessary computational cost with those of the Berlekamp-Massey algorithm and the Games-Chan algorithm. The significant property of a linearization method is that it needs no output sequence from a pseudo-random number generator (PRNG) because it calculates linear complexity using the algebraic expression of its algorithm. When a PRNG has n [bit] stages (registers or internal states), the necessary computational cost is smaller than O(2n). On the other hand, the Berlekamp-Massey algorithm needs O(N2) where N(≅2n) denotes period. Since existing methods calculate using the output sequence, an initial value of PRNG influences a resultant value of linear complexity. Therefore, a linear complexity is generally given as an estimate value. On the other hand, a linearization method calculates from an algorithm of PRNG, it can determine the lower bound of linear complexity.

  4. lncRNA-Induced Nucleosome Repositioning Reinforces Transcriptional Repression of rRNA Genes upon Hypotonic Stress

    Zhongliang Zhao

    2016-03-01

    Full Text Available The activity of rRNA genes (rDNA is regulated by pathways that target the transcription machinery or alter the epigenetic state of rDNA. Previous work has established that downregulation of rRNA synthesis in quiescent cells is accompanied by upregulation of PAPAS, a long noncoding RNA (lncRNA that recruits the histone methyltransferase Suv4-20h2 to rDNA, thus triggering trimethylation of H4K20 (H4K20me3 and chromatin compaction. Here, we show that upregulation of PAPAS in response to hypoosmotic stress does not increase H4K20me3 because of Nedd4-dependent ubiquitinylation and proteasomal degradation of Suv4-20h2. Loss of Suv4-20h2 enables PAPAS to interact with CHD4, a subunit of the chromatin remodeling complex NuRD, which shifts the promoter-bound nucleosome into the transcriptional “off” position. Thus, PAPAS exerts a “stress-tailored” dual function in rDNA silencing, facilitating either Suv4-20h2-dependent chromatin compaction or NuRD-dependent changes in nucleosome positioning.

  5. DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers.

    Umeyama, Taichi; Ito, Takashi

    2017-10-03

    Protein-DNA interactions provide the basis for chromatin structure and gene regulation. Comprehensive identification of protein-occupied sites is thus vital to an in-depth understanding of genome function. Dimethyl sulfate (DMS) is a chemical probe that has long been used to detect footprints of DNA-bound proteins in vitro and in vivo. Here, we describe a genomic footprinting method, dimethyl sulfate sequencing (DMS-seq), which exploits the cell-permeable nature of DMS to obviate the need for nuclear isolation. This feature makes DMS-seq simple in practice and removes the potential risk of protein re-localization during nuclear isolation. DMS-seq successfully detects transcription factors bound to cis-regulatory elements and non-canonical chromatin particles in nucleosome-free regions. Furthermore, an unexpected preference of DMS confers on DMS-seq a unique potential to directly detect nucleosome centers without using genetic manipulation. We expect that DMS-seq will serve as a characteristic method for genome-wide interrogation of in vivo protein-DNA interactions. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  6. Acoustic emission linear pulse holography

    Collins, H.D.; Busse, L.J.; Lemon, D.K.

    1983-10-25

    This device relates to the concept of and means for performing Acoustic Emission Linear Pulse Holography, which combines the advantages of linear holographic imaging and Acoustic Emission into a single non-destructive inspection system. This unique system produces a chronological, linear holographic image of a flaw by utilizing the acoustic energy emitted during crack growth. The innovation is the concept of utilizing the crack-generated acoustic emission energy to generate a chronological series of images of a growing crack by applying linear, pulse holographic processing to the acoustic emission data. The process is implemented by placing on a structure an array of piezoelectric sensors (typically 16 or 32 of them) near the defect location. A reference sensor is placed between the defect and the array.

  7. Linear algebra

    Said-Houari, Belkacem

    2017-01-01

    This self-contained, clearly written textbook on linear algebra is easily accessible for students. It begins with the simple linear equation and generalizes several notions from this equation for the system of linear equations and introduces the main ideas using matrices. It then offers a detailed chapter on determinants and introduces the main ideas with detailed proofs. The third chapter introduces the Euclidean spaces using very simple geometric ideas and discusses various major inequalities and identities. These ideas offer a solid basis for understanding general Hilbert spaces in functional analysis. The following two chapters address general vector spaces, including some rigorous proofs to all the main results, and linear transformation: areas that are ignored or are poorly explained in many textbooks. Chapter 6 introduces the idea of matrices using linear transformation, which is easier to understand than the usual theory of matrices approach. The final two chapters are more advanced, introducing t...

  8. Linear algebra

    Stoll, R R

    1968-01-01

    Linear Algebra is intended to be used as a text for a one-semester course in linear algebra at the undergraduate level. The treatment of the subject will be both useful to students of mathematics and those interested primarily in applications of the theory. The major prerequisite for mastering the material is the readiness of the student to reason abstractly. Specifically, this calls for an understanding of the fact that axioms are assumptions and that theorems are logical consequences of one or more axioms. Familiarity with calculus and linear differential equations is required for understand

  9. Co-Positivity for Anti-dsDNA, -Nucleosome and -Histone Antibodies in Lupus Nephritis Is Indicative of High Serum Levels and Severe Nephropathy.

    Jinfeng Yang

    Full Text Available To characterize the significance of correlated autoantibodies in systemic lupus erythematosus (SLE and its complication lupus nephritis (LN in a large cohort of patients.Clinical data were statistically analyzed in 1699 SLE patients with or without nephritis who were diagnosed and treated during 2002-2013 in the northeast region of China. Reactivity to a list of 16 autoantibodies was detected by the serum test Euroline ANA profile (IgG. Serum titers of the anti-nucleosome autoantibodies were measured by ELISA assays. Kidney biopsies were examined by pathologists. Immune complex deposition was identified by immunohistochemistry stain.Simultaneous positivity of anti-dsDNA, -nucleosome and -histone antibodies (3-pos was prevalent in SLE patients with LN compared to Non-renal SLE patients (41% vs 11%, p< 0.001. Significant correlations were found between any two of the above three anti-nucleosome antibodies in LN patients. In comparison to non-3-pos cohorts, 3-pos patients with LN had significantly higher serum levels of the three antibodies and more active disease; was associated with type IV disease; suffered from more severe renal damages; received more intensive treatment and had worse disease outcome. The serum levels of these three autoantibodies in 3-pos LN patients were significantly decreased when they underwent clinical recovery.Simultaneous reactivity to anti-dsDNA, -nucleosome and -histone antibodies by Euroline ANA profile (IgG may indicate severe nephropathy in patients with SLE.

  10. High mobility group protein number17 cross-links primarily to histone H2A in the reconstituted HMG 17 - nucleosome core particle complex

    Cook, G.R.; Yau, P.; Yasuda, H.; Traut, R.R.; Bradbury, E.M.

    1986-01-01

    The neighbor relationship of lamb thymus High Mobility Group (HMG) protein 17 to native HeLa nucleosome core particle histones in the reconstituted complex has been studied. 125 I-labeled HMG 17 was cross-linking to core histones using the protein-protein cross-linking reagent 2-iminothiolane. Specific cross-linked products were separated on a two-dimensional Triton-acid-urea/SDS gel system, located by autoradiography, excised and quantified. Disulfide bonds in the cross links were then cleaved and the protein constituents were identified by SDS gel electrophoresis. HMG 17 cross-linked primarily to histone H2A while lower levels of cross-linking occurred between HMG 17 and the other histones. In contrast, cross-linking between two HMG 17 molecules bound on the same nucleosome was relatively rare. It is concluded that the same nucleosome was relatively rare. It is concluded that H2A comprises part of the HMG 17 binding site but that HMG 17 is sufficiently elongated and mobile to permit cross-linking to the other histones and to a second HMG 17 molecule. These results are in agreement with the current model for the structure of the nucleosome and the proposed binding sites for HMG 17

  11. Dissociation of nucleosomal particles by chemical modification. Equivalence of the two binding sites for H2A.H2B dimers

    Jordano, J.; Nieto, M.A.; Palacian, E.

    1985-01-01

    Treatment of nucleosomal particles with dimethylmaleic anhydride, a reagent for protein amino groups, is accompanied by a biphasic release of histones H2A plus H2B; one H2A.H2B dimer is more easily released than the other. This behavior allows the preparation of nucleosomal particles containing only one H2A.H2B dimer, which were complemented with 125 I-labeled H2A.H2B. These reconstituted particles, which contain one labeled and one unlabeled H2A.H2B dimer, were treated with the amount of reagent needed to release one of the two H2A.H2B dimers. Radioactivity was equally distributed between residual particles and released proteins, which is consistent with equivalent binding sites in the nucleosomal particle for H2A.H2B dimers, rather than with intrinsically different sites. The asymmetric release of H2A.H2B dimers would be caused by a change in the binding site of one dimer following the release of the other. This behavior might be related to the structural dynamics of nucleosomes

  12. Linear programming

    Solow, Daniel

    2014-01-01

    This text covers the basic theory and computation for a first course in linear programming, including substantial material on mathematical proof techniques and sophisticated computation methods. Includes Appendix on using Excel. 1984 edition.

  13. Linear algebra

    Liesen, Jörg

    2015-01-01

    This self-contained textbook takes a matrix-oriented approach to linear algebra and presents a complete theory, including all details and proofs, culminating in the Jordan canonical form and its proof. Throughout the development, the applicability of the results is highlighted. Additionally, the book presents special topics from applied linear algebra including matrix functions, the singular value decomposition, the Kronecker product and linear matrix equations. The matrix-oriented approach to linear algebra leads to a better intuition and a deeper understanding of the abstract concepts, and therefore simplifies their use in real world applications. Some of these applications are presented in detailed examples. In several ‘MATLAB-Minutes’ students can comprehend the concepts and results using computational experiments. Necessary basics for the use of MATLAB are presented in a short introduction. Students can also actively work with the material and practice their mathematical skills in more than 300 exerc...

  14. Linear algebra

    Berberian, Sterling K

    2014-01-01

    Introductory treatment covers basic theory of vector spaces and linear maps - dimension, determinants, eigenvalues, and eigenvectors - plus more advanced topics such as the study of canonical forms for matrices. 1992 edition.

  15. Linear Models

    Searle, Shayle R

    2012-01-01

    This 1971 classic on linear models is once again available--as a Wiley Classics Library Edition. It features material that can be understood by any statistician who understands matrix algebra and basic statistical methods.

  16. LINEAR ACCELERATOR

    Christofilos, N.C.; Polk, I.J.

    1959-02-17

    Improvements in linear particle accelerators are described. A drift tube system for a linear ion accelerator reduces gap capacity between adjacent drift tube ends. This is accomplished by reducing the ratio of the diameter of the drift tube to the diameter of the resonant cavity. Concentration of magnetic field intensity at the longitudinal midpoint of the external sunface of each drift tube is reduced by increasing the external drift tube diameter at the longitudinal center region.

  17. Elastic interaction of a crack with a microcrack array. I - Formulation of the problem and general form of the solution. II - Elastic solution for two crack configurations (piecewise constant and linear approximations)

    Chudnovsky, A.; Dolgopolsky, A.; Kachanov, M.

    1987-01-01

    The elastic interactions of a two-dimensional configuration consisting of a crack with an array of microcracks located near the tip are studied. The general form of the solution is based on the potential representations and approximations of tractions on the microcracks by polynomials. In the second part, the technique is applied to two simple two-dimensional configurations involving one and two microcracks. The problems of stress shielding and stress amplification (the reduction or increase of the effective stress intensity factor due to the presence of microcracks) are discussed, and the refinements introduced by higher order polynomial approximations are illustrated.

  18. Predictive and prognostic value of circulating nucleosomes and serum biomarkers in patients with metastasized colorectal cancer undergoing Selective Internal Radiation Therapy

    Fahmueller, Yvonne Nadine; Nagel, Dorothea; Hoffmann, Ralf-Thorsten; Tatsch, Klaus; Jakobs, Tobias; Stieber, Petra; Holdenrieder, Stefan

    2012-01-01

    Selective Internal Radiation Therapy (SIRT) is a new and effective locoregional anticancer therapy for colorectal cancer patients with liver metastases. Markers for prediction of therapy response and prognosis are needed for the individual management of those patients undergoing SIRT. Blood samples were prospectively and consecutively taken from 49 colorectal cancer patients with extensive hepatic metastases before, three, six, 24 and 48 h after SIRT to analyze the concentrations of nucleosomes and further laboratory parameters, and to compare them with the response to therapy regularly determined 3 months after therapy and with overall survival. Circulating nucleosomes, cytokeratin-19 fragments (CYFRA 21-1), carcinoembryonic antigen (CEA), C-reactive protein (CRP) and various liver markers increased already 24 h after SIRT. Pretherapeutical levels of CYFRA 21-1, CEA, cancer antigen 19-9 (CA 19-9), asparate-aminotransferase (AST) and lactate dehydrogenase (LDH) as well as 24 h values of nucleosomes were significantly higher in patients suffering from disease progression (N = 35) than in non-progressive patients (N = 14). Concerning overall survival, CEA, CA 19-9, CYFRA 21-1, CRP, LDH, AST, choline esterase (CHE), gamma-glutamyl-transferase, alkaline phosphatase, and amylase (all 0 h, 24 h) and nucleosomes (24 h) were found to be prognostic relevant markers in univariate analyses. In multivariate Cox-Regression analysis, the best prognostic model was obtained for the combination of CRP and AST. When 24 h values were additionally included, nucleosomes (24 h) further improved the existing model. Panels of biochemical markers are helpful to stratify pretherapeutically colorectal cancer patients for SIR-therapy and to early estimate the response to SIR-therapy

  19. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  20. MARCC (Matrix-Assisted Reader Chromatin Capture): an antibody-free method to enrich and analyze combinatorial nucleosome modifications

    Su, Zhangli

    2016-01-01

    Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by western blotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications. PMID:26131849

  1. Linear regression

    Olive, David J

    2017-01-01

    This text covers both multiple linear regression and some experimental design models. The text uses the response plot to visualize the model and to detect outliers, does not assume that the error distribution has a known parametric distribution, develops prediction intervals that work when the error distribution is unknown, suggests bootstrap hypothesis tests that may be useful for inference after variable selection, and develops prediction regions and large sample theory for the multivariate linear regression model that has m response variables. A relationship between multivariate prediction regions and confidence regions provides a simple way to bootstrap confidence regions. These confidence regions often provide a practical method for testing hypotheses. There is also a chapter on generalized linear models and generalized additive models. There are many R functions to produce response and residual plots, to simulate prediction intervals and hypothesis tests, to detect outliers, and to choose response trans...

  2. Linear Colliders

    Alcaraz, J.

    2001-01-01

    After several years of study e''+ e''- linear colliders in the TeV range have emerged as the major and optimal high-energy physics projects for the post-LHC era. These notes summarize the present status form the main accelerator and detector features to their physics potential. The LHC era. These notes summarize the present status, from the main accelerator and detector features to their physics potential. The LHC is expected to provide first discoveries in the new energy domain, whereas an e''+ e''- linear collider in the 500 GeV-1 TeV will be able to complement it to an unprecedented level of precision in any possible areas: Higgs, signals beyond the SM and electroweak measurements. It is evident that the Linear Collider program will constitute a major step in the understanding of the nature of the new physics beyond the Standard Model. (Author) 22 refs

  3. Linear algebra

    Edwards, Harold M

    1995-01-01

    In his new undergraduate textbook, Harold M Edwards proposes a radically new and thoroughly algorithmic approach to linear algebra Originally inspired by the constructive philosophy of mathematics championed in the 19th century by Leopold Kronecker, the approach is well suited to students in the computer-dominated late 20th century Each proof is an algorithm described in English that can be translated into the computer language the class is using and put to work solving problems and generating new examples, making the study of linear algebra a truly interactive experience Designed for a one-semester course, this text adopts an algorithmic approach to linear algebra giving the student many examples to work through and copious exercises to test their skills and extend their knowledge of the subject Students at all levels will find much interactive instruction in this text while teachers will find stimulating examples and methods of approach to the subject

  4. Microfabricated linear Paul-Straubel ion trap

    Mangan, Michael A [Albuquerque, NM; Blain, Matthew G [Albuquerque, NM; Tigges, Chris P [Albuquerque, NM; Linker, Kevin L [Albuquerque, NM

    2011-04-19

    An array of microfabricated linear Paul-Straubel ion traps can be used for mass spectrometric applications. Each ion trap comprises two parallel inner RF electrodes and two parallel outer DC control electrodes symmetric about a central trap axis and suspended over an opening in a substrate. Neighboring ion traps in the array can share a common outer DC control electrode. The ions confined transversely by an RF quadrupole electric field potential well on the ion trap axis. The array can trap a wide array of ions.

  5. Nucleosomes correlate with in vivo progression pattern of de novo methylation of p16 CpG islands in human gastric carcinogenesis.

    Zhe-Ming Lu

    Full Text Available BACKGROUND: The exact relationship between nucleosome positioning and methylation of CpG islands in human pathogenesis is unknown. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we characterized the nucleosome position within the p16 CpG island and established a seeding methylation-specific PCR (sMSP assay based on bisulfite modification to enrich the p16 alleles containing methylated-CpG at the methylation "seeding" sites within its intron-1 in gastric carcinogenesis. The sMSP-positive rate in primary gastric carcinoma (GC samples (36/40 was significantly higher than that observed in gastritis (19/45 or normal samples (7/13 (P<0.01. Extensive clone sequencing of these sMSP products showed that the density of methylated-CpGs in p16 CpG islands increased gradually along with the severity of pathological changes in gastric tissues. In gastritis lesions the methylation was frequently observed in the region corresponding to the exon-1 coding-nucleosome and the 5'UTR-nucleosome; the methylation was further extended to the region corresponding to the promoter-nucleosome in GC samples. Only few methylated-CpG sites were randomly detected within p16 CpG islands in normal tissues. The significantly inversed relationship between the p16 exon-1 methylation and its transcription was observed in GC samples. An exact p16 promoter-specific 83 bp-MSP assay confirms the result of sMSP (33/55 vs. 1/6, P<0.01. In addition, p16 methylation in chronic gastritis lesions significantly correlated with H. pylori infection; however, such correlation was not observed in GC specimens. CONCLUSIONS/SIGNIFICANCE: It was determined that de novo methylation was initiated in the coding region of p16 exon-1 in gastritis, then progressed to its 5'UTR, and ultimately to the proximal promoter in GCs. Nucleosomes may function as the basic extension/progression unit of de novo methylation of p16 CpG islands in vivo.

  6. Degree-of-Freedom Strengthened Cascade Array for DOD-DOA Estimation in MIMO Array Systems.

    Yao, Bobin; Dong, Zhi; Zhang, Weile; Wang, Wei; Wu, Qisheng

    2018-05-14

    In spatial spectrum estimation, difference co-array can provide extra degrees-of-freedom (DOFs) for promoting parameter identifiability and parameter estimation accuracy. For the sake of acquiring as more DOFs as possible with a given number of physical sensors, we herein design a novel sensor array geometry named cascade array. This structure is generated by systematically connecting a uniform linear array (ULA) and a non-uniform linear array, and can provide more DOFs than some exist array structures but less than the upper-bound indicated by minimum redundant array (MRA). We further apply this cascade array into multiple input multiple output (MIMO) array systems, and propose a novel joint direction of departure (DOD) and direction of arrival (DOA) estimation algorithm, which is based on a reduced-dimensional weighted subspace fitting technique. The algorithm is angle auto-paired and computationally efficient. Theoretical analysis and numerical simulations prove the advantages and effectiveness of the proposed array structure and the related algorithm.

  7. Linear programming

    Karloff, Howard

    1991-01-01

    To this reviewer’s knowledge, this is the first book accessible to the upper division undergraduate or beginning graduate student that surveys linear programming from the Simplex Method…via the Ellipsoid algorithm to Karmarkar’s algorithm. Moreover, its point of view is algorithmic and thus it provides both a history and a case history of work in complexity theory. The presentation is admirable; Karloff's style is informal (even humorous at times) without sacrificing anything necessary for understanding. Diagrams (including horizontal brackets that group terms) aid in providing clarity. The end-of-chapter notes are helpful...Recommended highly for acquisition, since it is not only a textbook, but can also be used for independent reading and study. —Choice Reviews The reader will be well served by reading the monograph from cover to cover. The author succeeds in providing a concise, readable, understandable introduction to modern linear programming. —Mathematics of Computing This is a textbook intend...

  8. Coupling in reflector arrays

    Appel-Hansen, Jørgen

    1968-01-01

    In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present communic......In order to reduce the space occupied by a reflector array, it is desirable to arrange the array antennas as close to each other as possible; however, in this case coupling between the array antennas will reduce the reflecting properties of the reflector array. The purpose of the present...

  9. Josephson junctions array resonators

    Gargiulo, Oscar; Muppalla, Phani; Mirzaei, Iman; Kirchmair, Gerhard [Institute for Quantum Optics and Quantum Information, Innsbruck (Austria)

    2016-07-01

    We present an experimental analysis of the self- and cross-Kerr effect of extended plasma resonances in Josephson junction chains. The chain consists of 1600 individual junctions and we can measure quality factors in excess of 10000. The Kerr effect manifests itself as a frequency shift that depends linearly on the number of photons in a resonant mode. By changing the input power we are able to measure this frequency shift on a single mode (self-kerr). By changing the input power on another mode while measuring the same one, we are able to evaluate the cross-kerr effect. We can measure the cross-Kerr effect by probing the resonance frequency of one mode while exciting another mode of the array with a microwave drive.

  10. Skeletal Muscle PGC1α -1 Nucleosome Position and -260 nt DNA Methylation Determine Exercise Response and Prevent Ectopic Lipid Accumulation in Men.

    Bajpeyi, Sudip; Covington, Jeffrey D; Taylor, Erin M; Stewart, Laura K; Galgani, Jose E; Henagan, Tara M

    2017-07-01

    Endurance exercise has been shown to improve lipid oxidation and increase mitochondrial content in skeletal muscle, two features that have shown dependence on increased expression of the peroxisome proliferator-activated receptor-γ coactivator 1α (PGC1α). It is also hypothesized that exercise-related alterations in PGC1α expression occur through epigenetic regulation of nucleosome positioning in association with differential DNA methylation status within the PGC1α promoter. In this study, we show that when primary human myotubes from obese patients with type 2 diabetes are exposed to lipolytic stimulus (palmitate, forskolin, inomycin) in vitro, nucleosome occupancy surrounding the -260 nucleotide (nt) region, a known regulatory DNA methylation site, is reduced. This finding is reproduced in vivo in the vastus lateralis from 11 healthy males after a single, long endurance exercise bout in which participants expended 650 kcal. Additionally, we show a significant positive correlation between fold change of PGC1α messenger RNA expression and -1 nucleosome repositioning away from the -260 nt methylation site in skeletal muscle tissue following exercise. Finally, we found that when exercise participants are divided into high and low responders based on the -260 nt methylation status, the -1 nucleosome is repositioned away from the regulatory -260 nt methylation site in high responders, those exhibiting a significant decrease in -260 nt methylation, but not in low responders. Additionally, high but not low responders showed a significant decrease in intramyocellular lipid content after exercise. These findings suggest a potential target for epigenetic modification of the PGC1α promoter to stimulate the therapeutic effects of endurance exercise in skeletal muscle. Copyright © 2017 Endocrine Society.

  11. Combination of Hypomorphic Mutations of the Drosophila Homologues of Aryl Hydrocarbon Receptor and Nucleosome Assembly Protein Family Genes Disrupts Morphogenesis, Memory and Detoxification

    Kuzin, Boris A.; Nikitina, Ekaterina A.; Cherezov, Roman O.; Vorontsova, Julia E.; Slezinger, Mikhail S.; Zatsepina, Olga G.; Simonova, Olga B.; Enikolopov, Grigori N.; Savvateeva-Popova, Elena V.

    2014-01-01

    Aryl hydrocarbon receptor is essential for biological responses to endogenous and exogenous toxins in mammals. Its Drosophila homolog spineless plays an important role in fly morphogenesis. We have previously shown that during morphogenesis spineless genetically interacts with CG5017 gene, which encodes a nucleosome assembly factor and may affect cognitive function of the fly. We now demonstrate synergistic interactions of spineless and CG5017 in pathways controlling oxidative stress response...

  12. Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to methylated nucleosomes and maintenance of DNA methylation in somatic cells

    Sharma Shikhar

    2012-01-01

    Full Text Available Abstract Background DNA methylation, histone modifications and nucleosome occupancy act in concert for regulation of gene expression patterns in mammalian cells. Recently, G9a, a H3K9 methyltransferase, has been shown to play a role in establishment of DNA methylation at embryonic gene targets in ES cells through recruitment of de novo DNMT3A/3B enzymes. However, whether G9a plays a similar role in maintenance of DNA methylation in somatic cells is still unclear. Results Here we show that G9a is not essential for maintenance of DNA methylation in somatic cells. Knockdown of G9a has no measurable effect on DNA methylation levels at G9a-target loci. DNMT3A/3B remain stably anchored to nucleosomes containing methylated DNA even in the absence of G9a, ensuring faithful propagation of methylated states in cooperation with DNMT1 through somatic divisions. Moreover, G9a also associates with nucleosomes in a DNMT3A/3B and DNA methylation-independent manner. However, G9a knockdown synergizes with pharmacologic inhibition of DNMTs resulting in increased hypomethylation and inhibition of cell proliferation. Conclusions Taken together, these data suggest that G9a is not involved in maintenance of DNA methylation in somatic cells but might play a role in re-initiation of de novo methylation after treatment with hypomethylating drugs, thus serving as a potential target for combinatorial treatments strategies involving DNMTs inhibitors.

  13. Reduction of Linear Programming to Linear Approximation

    Vaserstein, Leonid N.

    2006-01-01

    It is well known that every Chebyshev linear approximation problem can be reduced to a linear program. In this paper we show that conversely every linear program can be reduced to a Chebyshev linear approximation problem.

  14. Parallel Access of Out-Of-Core Dense Extendible Arrays

    Otoo, Ekow J; Rotem, Doron

    2007-07-26

    Datasets used in scientific and engineering applications are often modeled as dense multi-dimensional arrays. For very large datasets, the corresponding array models are typically stored out-of-core as array files. The array elements are mapped onto linear consecutive locations that correspond to the linear ordering of the multi-dimensional indices. Two conventional mappings used are the row-major order and the column-major order of multi-dimensional arrays. Such conventional mappings of dense array files highly limit the performance of applications and the extendibility of the dataset. Firstly, an array file that is organized in say row-major order causes applications that subsequently access the data in column-major order, to have abysmal performance. Secondly, any subsequent expansion of the array file is limited to only one dimension. Expansions of such out-of-core conventional arrays along arbitrary dimensions, require storage reorganization that can be very expensive. Wepresent a solution for storing out-of-core dense extendible arrays that resolve the two limitations. The method uses a mapping function F*(), together with information maintained in axial vectors, to compute the linear address of an extendible array element when passed its k-dimensional index. We also give the inverse function, F-1*() for deriving the k-dimensional index when given the linear address. We show how the mapping function, in combination with MPI-IO and a parallel file system, allows for the growth of the extendible array without reorganization and no significant performance degradation of applications accessing elements in any desired order. We give methods for reading and writing sub-arrays into and out of parallel applications that run on a cluster of workstations. The axial-vectors are replicated and maintained in each node that accesses sub-array elements.

  15. BAF53b, a Neuron-Specific Nucleosome Remodeling Factor, Is Induced after Learning and Facilitates Long-Term Memory Consolidation.

    Yoo, Miran; Choi, Kwang-Yeon; Kim, Jieun; Kim, Mujun; Shim, Jaehoon; Choi, Jun-Hyeok; Cho, Hye-Yeon; Oh, Jung-Pyo; Kim, Hyung-Su; Kaang, Bong-Kiun; Han, Jin-Hee

    2017-03-29

    Although epigenetic mechanisms of gene expression regulation have recently been implicated in memory consolidation and persistence, the role of nucleosome-remodeling is largely unexplored. Recent studies show that the functional loss of BAF53b, a postmitotic neuron-specific subunit of the BAF nucleosome-remodeling complex, results in the deficit of consolidation of hippocampus-dependent memory and cocaine-associated memory in the rodent brain. However, it is unclear whether BAF53b expression is regulated during memory formation and how BAF53b regulates fear memory in the amygdala, a key brain site for fear memory encoding and storage. To address these questions, we used viral vector approaches to either decrease or increase BAF53b function specifically in the lateral amygdala of adult mice in auditory fear conditioning paradigm. Knockdown of Baf53b before training disrupted long-term memory formation with no effect on short-term memory, basal synaptic transmission, and spine structures. We observed in our qPCR analysis that BAF53b was induced in the lateral amygdala neurons at the late consolidation phase after fear conditioning. Moreover, transient BAF53b overexpression led to persistently enhanced memory formation, which was accompanied by increase in thin-type spine density. Together, our results provide the evidence that BAF53b is induced after learning, and show that such increase of BAF53b level facilitates memory consolidation likely by regulating learning-related spine structural plasticity. SIGNIFICANCE STATEMENT Recent works in the rodent brain begin to link nucleosome remodeling-dependent epigenetic mechanism to memory consolidation. Here we show that BAF53b, an epigenetic factor involved in nucleosome remodeling, is induced in the lateral amygdala neurons at the late phase of consolidation after fear conditioning. Using specific gene knockdown or overexpression approaches, we identify the critical role of BAF53b in the lateral amygdala neurons for

  16. Transcription factor 19 interacts with histone 3 lysine 4 trimethylation and controls gluconeogenesis via the nucleosome-remodeling-deacetylase complex.

    Sen, Sabyasachi; Sanyal, Sulagna; Srivastava, Dushyant Kumar; Dasgupta, Dipak; Roy, Siddhartha; Das, Chandrima

    2017-12-15

    Transcription factor 19 (TCF19) has been reported as a type 1 diabetes-associated locus involved in maintenance of pancreatic β cells through a fine-tuned regulation of cell proliferation and apoptosis. TCF19 also exhibits genomic association with type 2 diabetes, although the precise molecular mechanism remains unknown. It harbors both a plant homeodomain and a forkhead-associated domain implicated in epigenetic recognition and gene regulation, a phenomenon that has remained unexplored. Here, we show that TCF19 selectively interacts with histone 3 lysine 4 trimethylation through its plant homeodomain finger. Knocking down TCF19 under high-glucose conditions affected many metabolic processes, including gluconeogenesis. We found that TCF19 overexpression represses de novo glucose production in HepG2 cells. The transcriptional repression of key genes, induced by TCF19, coincided with NuRD (nucleosome-remodeling-deacetylase) complex recruitment to the promoters of these genes. TCF19 interacted with CHD4 (chromodomain helicase DNA-binding protein 4), which is a part of the NuRD complex, in a glucose concentration-independent manner. In summary, our results show that TCF19 interacts with an active transcription mark and recruits a co-repressor complex to regulate gluconeogenic gene expression in HepG2 cells. Our study offers critical insights into the molecular mechanisms of transcriptional regulation of gluconeogenesis and into the roles of chromatin readers in metabolic homeostasis. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Interaction of nucleosome assembly proteins abolishes nuclear localization of DGK{zeta} by attenuating its association with importins

    Okada, Masashi; Hozumi, Yasukazu [Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata 990-9585 (Japan); Ichimura, Tohru [Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); Tanaka, Toshiaki; Hasegawa, Hiroshi; Yamamoto, Masakazu; Takahashi, Nobuya [Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata 990-9585 (Japan); Iseki, Ken [Department of Emergency and Critical Care Medicine, Yamagata University School of Medicine, Yamagata 990-9585 (Japan); Yagisawa, Hitoshi [Laboratory of Biological Signaling, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297 (Japan); Shinkawa, Takashi; Isobe, Toshiaki [Department of Chemistry, Graduate School of Sciences and Engineering, Tokyo Metropolitan University, Hachioji 192-0397 (Japan); Goto, Kaoru, E-mail: kgoto@med.id.yamagata-u.ac.jp [Department of Anatomy and Cell Biology, Yamagata University School of Medicine, Yamagata 990-9585 (Japan)

    2011-12-10

    Diacylglycerol kinase (DGK) is involved in the regulation of lipid-mediated signal transduction through the metabolism of a second messenger diacylglycerol. Of the DGK family, DGK{zeta}, which contains a nuclear localization signal, localizes mainly to the nucleus but translocates to the cytoplasm under pathological conditions. However, the detailed mechanism of translocation and its functional significance remain unclear. To elucidate these issues, we used a proteomic approach to search for protein targets that interact with DGK{zeta}. Results show that nucleosome assembly protein (NAP) 1-like 1 (NAP1L1) and NAP1-like 4 (NAP1L4) are identified as novel DGK{zeta} binding partners. NAP1Ls constitutively shuttle between the nucleus and the cytoplasm in transfected HEK293 cells. The molecular interaction of DGK{zeta} and NAP1Ls prohibits nuclear import of DGK{zeta} because binding of NAP1Ls to DGK{zeta} blocks import carrier proteins, Qip1 and NPI1, to interact with DGK{zeta}, leading to cytoplasmic tethering of DGK{zeta}. In addition, overexpression of NAP1Ls exerts a protective effect against doxorubicin-induced cytotoxicity. These findings suggest that NAP1Ls are involved in a novel molecular basis for the regulation of nucleocytoplasmic shuttling of DGK{zeta} and provide a clue to examine functional significance of its translocation under pathological conditions.

  18. PGC1α −1 Nucleosome Position and Splice Variant Expression and Cardiovascular Disease Risk in Overweight and Obese Individuals

    Tara M. Henagan

    2014-01-01

    Full Text Available PGC1α, a transcriptional coactivator, interacts with PPARs and others to regulate skeletal muscle metabolism. PGC1α undergoes splicing to produce several mRNA variants, with the NTPGC1α variant having a similar biological function to the full length PGC1α (FLPGC1α. CVD is associated with obesity and T2D and a lower percentage of type 1 oxidative fibers and impaired mitochondrial function in skeletal muscle, characteristics determined by PGC1α expression. PGC1α expression is epigenetically regulated in skeletal muscle to determine mitochondrial adaptations, and epigenetic modifications may regulate mRNA splicing. We report in this paper that skeletal muscle PGC1α  −1 nucleosome (−1N position is associated with splice variant NTPGC1α but not FLPGC1α expression. Division of participants based on the −1N position revealed that those individuals with a −1N phased further upstream from the transcriptional start site (UP expressed lower levels of NTPGC1α than those with the −1N more proximal to TSS (DN. UP showed an increase in body fat percentage and serum total and LDL cholesterol. These findings suggest that the −1N may be a potential epigenetic regulator of NTPGC1α splice variant expression, and −1N position and NTPGC1α variant expression in skeletal muscle are linked to CVD risk. This trial is registered with clinicaltrials.gov, identifier NCT00458133.

  19. linear-quadratic-linear model

    Tanwiwat Jaikuna

    2017-02-01

    Full Text Available Purpose: To develop an in-house software program that is able to calculate and generate the biological dose distribution and biological dose volume histogram by physical dose conversion using the linear-quadratic-linear (LQL model. Material and methods : The Isobio software was developed using MATLAB version 2014b to calculate and generate the biological dose distribution and biological dose volume histograms. The physical dose from each voxel in treatment planning was extracted through Computational Environment for Radiotherapy Research (CERR, and the accuracy was verified by the differentiation between the dose volume histogram from CERR and the treatment planning system. An equivalent dose in 2 Gy fraction (EQD2 was calculated using biological effective dose (BED based on the LQL model. The software calculation and the manual calculation were compared for EQD2 verification with pair t-test statistical analysis using IBM SPSS Statistics version 22 (64-bit. Results: Two and three-dimensional biological dose distribution and biological dose volume histogram were displayed correctly by the Isobio software. Different physical doses were found between CERR and treatment planning system (TPS in Oncentra, with 3.33% in high-risk clinical target volume (HR-CTV determined by D90%, 0.56% in the bladder, 1.74% in the rectum when determined by D2cc, and less than 1% in Pinnacle. The difference in the EQD2 between the software calculation and the manual calculation was not significantly different with 0.00% at p-values 0.820, 0.095, and 0.593 for external beam radiation therapy (EBRT and 0.240, 0.320, and 0.849 for brachytherapy (BT in HR-CTV, bladder, and rectum, respectively. Conclusions : The Isobio software is a feasible tool to generate the biological dose distribution and biological dose volume histogram for treatment plan evaluation in both EBRT and BT.

  20. Matter-wave scattering and guiding by atomic arrays

    Vaishnav, J. Y.; Walls, J. D.; Apratim, M.; Heller, E. J.

    2007-01-01

    We investigate the possibility that linear arrays of atoms can guide matter waves, much as fiber optics guide light. We model the atomic line as a quasi-one-dimensional array of s-wave point scatterers embedded in two-dimensions. Our theoretical study reveals how matter-wave guiding arises from the interplay of scattering phenomena with bands and conduction along the array. We discuss the conditions under which a straight or curved array of atoms can guide a beam focused at one end of the array

  1. Fiber Laser Array

    Simpson, Thomas

    2002-01-01

    ...., field-dependent, loss within the coupled laser array. During this program, Jaycor focused on the construction and use of an experimental apparatus that can be used to investigate the coherent combination of an array of fiber lasers...

  2. Restoring Low Sidelobe Antenna Patterns with Failed Elements in a Phased Array Antenna

    2016-02-01

    optimum low sidelobes are demonstrated in several examples. Index Terms — Array signal processing, beams, linear algebra , phased arrays, shaped...beam antennas. I. INTRODUCTION For many phased array antenna applications , low spatial sidelobes are required, and it is desirable to maintain...represented by a linear combination of low sidelobe beamformers with no failed elements, ’s, in a neighborhood around under the constraint that the linear

  3. Coated carbon nanotube array electrodes

    Ren, Zhifeng [Newton, MA; Wen, Jian [Newton, MA; Chen, Jinghua [Chestnut Hill, MA; Huang, Zhongping [Belmont, MA; Wang, Dezhi [Wellesley, MA

    2008-10-28

    The present invention provides conductive carbon nanotube (CNT) electrode materials comprising aligned CNT substrates coated with an electrically conducting polymer, and the fabrication of electrodes for use in high performance electrical energy storage devices. In particular, the present invention provides conductive CNTs electrode material whose electrical properties render them especially suitable for use in high efficiency rechargeable batteries. The present invention also provides methods for obtaining surface modified conductive CNT electrode materials comprising an array of individual linear, aligned CNTs having a uniform surface coating of an electrically conductive polymer such as polypyrrole, and their use in electrical energy storage devices.

  4. Experimental Validation of a Wave Energy Converter Array Hydrodynamics Tool

    Ruiz, Pau Mercadé; Ferri, Francesco; Kofoed, Jens Peter

    2017-01-01

    This paper uses experimental data to validate a wave energy converter (WEC) array hydrodynamics tool developed within the context of linearized potential flow theory. To this end, wave forces and power absorption by an array of five-point absorber WECs in monochromatic and panchromatic waves were...

  5. Changes in nucleosome repeat lengths precede replication in the early replicating metallothionein II gene region of cells synchronized in early S phase

    D'Anna, J.A.; Tobey, R.A.

    1989-01-01

    Previous investigations showed that inhibition of DNA synthesis by hydroxyurea, aphidicolin, or 5-fluorodeoxyuridine produced large changes in the composition and nucleosome repeat lengths of bulk chromatin. There the authors report results of investigations to determine whether the changes in nucleosome repeat lengths might be localized in the initiated replicons, as postulated. In most experiments, Chinese hamster (line CHO) cells were synchronized in G1, or they were synchronized in early S phase by allowing G1 cells to enter S phase in medium containing 1 mM hydroxyurea or 5 μg mL -1 aphidicolin, a procedure believed to produce an accumulation of initiated replicons that arise from normally early replicating DNA. Measurements of nucleosome repeat lengths of bulk chromatin, the early replicating unexpressed metallothionein II (MTII) gene region, and a later replicating repeated sequence indicate that the changes in repeat lengths occur preferentially in the early replicating MTII gene region as G1 cells enter and become synchronized in early S phase. During that time, the MTII gene region is not replicated nor is there any evidence for induction of MTII messenger RNA. Thus, the results are consistent with the hypothesis that changes in chromatin structure occur preferentially in the early replicating (presumably initiated) replicons at initiation or that changes in chromatin structure can precede replication during inhibition of DNA synthesis. The shortened repeat lengths that precede MTII replication are, potentially, reversible, because they become elongated when the synchronized early S-phase cells are released to resume cell cycle progression

  6. Pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA or histone modification H3K9Me3

    Rasmussen, Louise; Herzog, Marielle; Rømer, Eva

    2016-01-01

    Aim: To evaluate pre-analytical variables of circulating cell-free nucleosomes containing 5-methylcytosine DNA (5mC) or histone modification H3K9Me3 (H3K9Me3). Materials and methods: Six studies were designed to assess the possible influence of pre-analytical variables. Study 1: influence of stasis...... significantly lower levels of 5mC or H3K9Me3 compared to levels in healthy individuals. Conclusion: Levels of 5mC or H3K9Me3 appear stable in most pre-analytical settings if blood samples are stored at room temperature until centrifugation....

  7. Direction-of-Arrival Estimation for Coprime Array Using Compressive Sensing Based Array Interpolation

    Aihua Liu

    2017-01-01

    Full Text Available A method of direction-of-arrival (DOA estimation using array interpolation is proposed in this paper to increase the number of resolvable sources and improve the DOA estimation performance for coprime array configuration with holes in its virtual array. The virtual symmetric nonuniform linear array (VSNLA of coprime array signal model is introduced, with the conventional MUSIC with spatial smoothing algorithm (SS-MUSIC applied on the continuous lags in the VSNLA; the degrees of freedom (DoFs for DOA estimation are obviously not fully exploited. To effectively utilize the extent of DoFs offered by the coarray configuration, a compressing sensing based array interpolation algorithm is proposed. The compressing sensing technique is used to obtain the coarse initial DOA estimation, and a modified iterative initial DOA estimation based interpolation algorithm (IMCA-AI is then utilized to obtain the final DOA estimation, which maps the sample covariance matrix of the VSNLA to the covariance matrix of a filled virtual symmetric uniform linear array (VSULA with the same aperture size. The proposed DOA estimation method can efficiently improve the DOA estimation performance. The numerical simulations are provided to demonstrate the effectiveness of the proposed method.

  8. Beam-Mode Piezoelectric Properties of Ternary Pb(In1/2Nb1/2)O3-Pb(Mg1/3Nb2/3)O3-PbTiO3 Single Crystals for Medical Linear Array Applications

    Wang, Wei; Wang, Sheng; Zhang, Yaoyao; Zhao, Xiangyong; Luo, Haosu

    2011-11-01

    In this work, the dielectric and beam-mode piezoelectric properties of ternary 0.35Pb(In1/2Nb1/2)O3-0.35Pb(Mg1/3Nb2/3)O3-0.30PbTiO3 (PIMNT35/35/30) piezoelectric single crystals were investigated. The Curie temperature ( T C) and rhombohedral-to-tetragonal phase-transition temperature ( T rt) are 187°C and 127°C, about 30°C higher than those of PMNT crystals. The beam-mode coupling coefficient k {33/ w } was found to be 90.3%. Furthermore, 3.5-MHz linear arrays based on PIMNT35/35/30 crystals and Pb(Zr1- x Ti x )O3 ceramic (PZT-5H) were simulated using PiezoCAD software. The results indicate that the sensitivity and -6 dB bandwidth of a PIMNT35/35/30 transducer would be approximately 4 dB and 20% higher, respectively, compared with a traditional PZT transducer.

  9. Linear Algebra and Smarandache Linear Algebra

    Vasantha, Kandasamy

    2003-01-01

    The present book, on Smarandache linear algebra, not only studies the Smarandache analogues of linear algebra and its applications, it also aims to bridge the need for new research topics pertaining to linear algebra, purely in the algebraic sense. We have introduced Smarandache semilinear algebra, Smarandache bilinear algebra and Smarandache anti-linear algebra and their fuzzy equivalents. Moreover, in this book, we have brought out the study of linear algebra and vector spaces over finite p...

  10. Topology optimization of Halbach magnet arrays using isoparametric projection

    Lee, Jaewook; Nomura, Tsuyoshi; Dede, Ercan M.

    2017-01-01

    Highlights: • Design method of Halbach magnet array is proposed using topology optimization. • Magnet strength and direction are simultaneously optimized by isoparametric projection. • For manufacturing feasibility of magnet, penalization and extrusion schemes are proposed. • Design results of circular shaped Halbach arrays are provided. • Halbach arrays in linear actuator are optimized to maximize magnetic force. - Abstract: Topology optimization using isoparametric projection for the design of permanent magnet patterns in Halbach arrays is proposed. Based on isoparametric shape functions used in the finite element analysis, the permanent magnet strength and magnetization directions in a Halbach array are simultaneously optimized for a given design goal. To achieve fabrication feasibility of a designed Halbach magnet array, two design schemes are combined with the isoparametric projection method. First, a penalization scheme is proposed for designing the permanent magnets to have discrete magnetization direction angles. Second, an extrusion scheme is proposed for the shape regularization of the permanent magnet segments. As a result, the method systematically finds the optimal permanent magnet patterns of a Halbach array considering manufacturing feasibility. In two numerical examples, a circular shaped permanent magnet Halbach array is designed to minimize the magnitude of the magnetic flux density and to maximize the upward direction magnetic flux density inside the magnet array. Logical extension of the method to the design of permanent magnet arrays in linear actuators is provided, where the design goal is to maximize the actuator magnetic force.

  11. Topology optimization of Halbach magnet arrays using isoparametric projection

    Lee, Jaewook, E-mail: jaewooklee@gist.ac.kr [School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005 (Korea, Republic of); Nomura, Tsuyoshi [Toyota Central R& D Labs., Inc., 41-1 Yokomichi, Aichi 480-1192 (Japan); Toyota Research Institute of North America, 1555 Woodridge Avenue, Ann Arbor, MI 48105 (United States); Dede, Ercan M. [Toyota Research Institute of North America, 1555 Woodridge Avenue, Ann Arbor, MI 48105 (United States)

    2017-06-15

    Highlights: • Design method of Halbach magnet array is proposed using topology optimization. • Magnet strength and direction are simultaneously optimized by isoparametric projection. • For manufacturing feasibility of magnet, penalization and extrusion schemes are proposed. • Design results of circular shaped Halbach arrays are provided. • Halbach arrays in linear actuator are optimized to maximize magnetic force. - Abstract: Topology optimization using isoparametric projection for the design of permanent magnet patterns in Halbach arrays is proposed. Based on isoparametric shape functions used in the finite element analysis, the permanent magnet strength and magnetization directions in a Halbach array are simultaneously optimized for a given design goal. To achieve fabrication feasibility of a designed Halbach magnet array, two design schemes are combined with the isoparametric projection method. First, a penalization scheme is proposed for designing the permanent magnets to have discrete magnetization direction angles. Second, an extrusion scheme is proposed for the shape regularization of the permanent magnet segments. As a result, the method systematically finds the optimal permanent magnet patterns of a Halbach array considering manufacturing feasibility. In two numerical examples, a circular shaped permanent magnet Halbach array is designed to minimize the magnitude of the magnetic flux density and to maximize the upward direction magnetic flux density inside the magnet array. Logical extension of the method to the design of permanent magnet arrays in linear actuators is provided, where the design goal is to maximize the actuator magnetic force.

  12. Development of a novel mixed hemimicelles dispersive micro solid phase extraction using 1-hexadecyl-3-methylimidazolium bromide coated magnetic graphene for the separation and preconcentration of fluoxetine in different matrices before its determination by fiber optic linear array spectrophotometry and mode-mismatched thermal lens spectroscopy

    Kazemi, Elahe; Haji Shabani, Ali Mohammad; Dadfarnia, Shayessteh; Abbasi, Amir; Rashidian Vaziri, Mohammad Reza; Behjat, Abbas

    2016-01-01

    This study aims at developing a novel, sensitive, fast, simple and convenient method for separation and preconcentration of trace amounts of fluoxetine before its spectrophotometric determination. The method is based on combination of magnetic mixed hemimicelles solid phase extraction and dispersive micro solid phase extraction using 1-hexadecyl-3-methylimidazolium bromide coated magnetic graphene as a sorbent. The magnetic graphene was synthesized by a simple coprecipitation method and characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM). The retained analyte was eluted using a 100 μL mixture of methanol/acetic acid (9:1) and converted into fluoxetine-β-cyclodextrin inclusion complex. The analyte was then quantified by fiber optic linear array spectrophotometry as well as mode-mismatched thermal lens spectroscopy (TLS). The factors affecting the separation, preconcentration and determination of fluoxetine were investigated and optimized. With a 50 mL sample and under optimized conditions using the spectrophotometry technique, the method exhibited a linear dynamic range of 0.4–60.0 μg L"−"1, a detection limit of 0.21 μg L"−"1, an enrichment factor of 167, and a relative standard deviation of 2.1% and 3.8% (n = 6) at 60 μg L"−"1 level of fluoxetine for intra- and inter-day analyses, respectively. However, with thermal lens spectrometry and a sample volume of 10 mL, the method exhibited a linear dynamic range of 0.05–300 μg L"−"1, a detection limit of 0.016 μg L"−"1 and a relative standard deviation of 3.8% and 5.6% (n = 6) at 60 μg L"−"1 level of fluoxetine for intra- and inter-day analyses, respectively. The method was successfully applied to determine fluoxetine in pharmaceutical formulation, human urine and environmental water samples. - Graphical abstract: A novel, sensitive, fast, simple and convenient mixed hemimicelles dispersive micro solid

  13. Development of a novel mixed hemimicelles dispersive micro solid phase extraction using 1-hexadecyl-3-methylimidazolium bromide coated magnetic graphene for the separation and preconcentration of fluoxetine in different matrices before its determination by fiber optic linear array spectrophotometry and mode-mismatched thermal lens spectroscopy

    Kazemi, Elahe; Haji Shabani, Ali Mohammad [Department of Chemistry, Yazd University, Safaieh, 89195-741, Yazd (Iran, Islamic Republic of); Dadfarnia, Shayessteh, E-mail: sdadfarnia@yazd.ac.ir [Department of Chemistry, Yazd University, Safaieh, 89195-741, Yazd (Iran, Islamic Republic of); Abbasi, Amir [Department of Physics, Yazd University, Safaieh, 89195-741, Yazd (Iran, Islamic Republic of); Rashidian Vaziri, Mohammad Reza [Laser and Optics Research School, 14155-1339, Tehran (Iran, Islamic Republic of); Behjat, Abbas [Department of Physics, Yazd University, Safaieh, 89195-741, Yazd (Iran, Islamic Republic of)

    2016-01-28

    This study aims at developing a novel, sensitive, fast, simple and convenient method for separation and preconcentration of trace amounts of fluoxetine before its spectrophotometric determination. The method is based on combination of magnetic mixed hemimicelles solid phase extraction and dispersive micro solid phase extraction using 1-hexadecyl-3-methylimidazolium bromide coated magnetic graphene as a sorbent. The magnetic graphene was synthesized by a simple coprecipitation method and characterized by X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM). The retained analyte was eluted using a 100 μL mixture of methanol/acetic acid (9:1) and converted into fluoxetine-β-cyclodextrin inclusion complex. The analyte was then quantified by fiber optic linear array spectrophotometry as well as mode-mismatched thermal lens spectroscopy (TLS). The factors affecting the separation, preconcentration and determination of fluoxetine were investigated and optimized. With a 50 mL sample and under optimized conditions using the spectrophotometry technique, the method exhibited a linear dynamic range of 0.4–60.0 μg L{sup −1}, a detection limit of 0.21 μg L{sup −1}, an enrichment factor of 167, and a relative standard deviation of 2.1% and 3.8% (n = 6) at 60 μg L{sup −1} level of fluoxetine for intra- and inter-day analyses, respectively. However, with thermal lens spectrometry and a sample volume of 10 mL, the method exhibited a linear dynamic range of 0.05–300 μg L{sup −1}, a detection limit of 0.016 μg L{sup −1} and a relative standard deviation of 3.8% and 5.6% (n = 6) at 60 μg L{sup −1} level of fluoxetine for intra- and inter-day analyses, respectively. The method was successfully applied to determine fluoxetine in pharmaceutical formulation, human urine and environmental water samples. - Graphical abstract: A novel, sensitive, fast, simple and convenient mixed hemimicelles

  14. Malvar-He-Cutler Linear Image Demosaicking

    Pascal Getreuer

    2011-08-01

    Full Text Available Image demosaicking (or demosaicing is the interpolation problem of estimating complete color information for an image that has been captured through a color filter array (CFA, particularly on the Bayer pattern. In this paper we review a simple linear method using 5 x 5 filters, proposed by Malvar, He, and Cutler in 2004, that shows surprisingly good results.

  15. Josephson junction arrays

    Bindslev Hansen, J.; Lindelof, P.E.

    1985-01-01

    In this review we intend to cover recent work involving arrays of Josephson junctions. The work on such arrays falls naturally into three main areas of interest: 1. Technical applications of Josephson junction arrays for high-frequency devices. 2. Experimental studies of 2-D model systems (Kosterlitz-Thouless phase transition, commensurate-incommensurate transition in frustrated (flux) lattices). 3. Investigations of phenomena associated with non-equilibrium superconductivity in and around Josephson junctions (with high current density). (orig./BUD)

  16. Phased-array radars

    Brookner, E.

    1985-02-01

    The operating principles, technology, and applications of phased-array radars are reviewed and illustrated with diagrams and photographs. Consideration is given to the antenna elements, circuitry for time delays, phase shifters, pulse coding and compression, and hybrid radars combining phased arrays with lenses to alter the beam characteristics. The capabilities and typical hardware of phased arrays are shown using the US military systems COBRA DANE and PAVE PAWS as examples.

  17. Storage array reflection considerations

    Haire, M.J.; Jordan, W.C.; Taylor, R.G.

    1997-01-01

    The assumptions used for reflection conditions of single containers are fairly well established and consistently applied throughout the industry in nuclear criticality safety evaluations. Containers are usually considered to be either fully water reflected (i.e., surrounded by 6 to 12 in. of water) for safety calculations or reflected by 1 in. of water for nominal (structural material and air) conditions. Tables and figures are usually available for performing comparative evaluations of containers under various loading conditions. Reflection considerations used for evaluating the safety of storage arrays of fissile material are not as well established. When evaluating arrays, it has become more common for analysts to use calculations to demonstrate the safety of the array configuration. In performing these calculations, the analyst has considerable freedom concerning the assumptions made for modeling the reflection of the array. Considerations are given for the physical layout of the array with little or no discussion (or demonstration) of what conditions are bounded by the assumed reflection conditions. For example, an array may be generically evaluated by placing it in a corner of a room in which the opposing walls are far away. Typically, it is believed that complete flooding of the room is incredible, so the array is evaluated for various levels of water mist interspersed among array containers. This paper discusses some assumptions that are made regarding storage array reflection

  18. The EUROBALL array

    Rossi Alvarez, C.

    1998-01-01

    The quality of the multidetector array EUROBALL is described, with emphasis on the history and formal organization of the related European collaboration. The detector layout is presented together with the electronics and Data Acquisition capabilities. The status of the instrument, its performances and the main features of some recently developed ancillary detectors will also be described. The EUROBALL array is operational in Legnaro National Laboratory (Italy) since April 1997 and is expected to run up to November 1998. The array represents a significant improvement in detector efficiency and sensitivity with respect to the previous generation of multidetector arrays

  19. Rectenna array measurement results

    Dickinson, R. M.

    1980-01-01

    The measured performance characteristics of a rectenna array are reviewed and compared to the performance of a single element. It is shown that the performance may be extrapolated from the individual element to that of the collection of elements. Techniques for current and voltage combining were demonstrated. The array performance as a function of various operating parameters is characterized and techniques for overvoltage protection and automatic fault clearing in the array demonstrated. A method for detecting failed elements also exists. Instrumentation for deriving performance effectiveness is described. Measured harmonic radiation patterns and fundamental frequency scattered patterns for a low level illumination rectenna array are presented.

  20. Arrayed waveguide Sagnac interferometer.

    Capmany, José; Muñoz, Pascual; Sales, Salvador; Pastor, Daniel; Ortega, Beatriz; Martinez, Alfonso

    2003-02-01

    We present a novel device, an arrayed waveguide Sagnac interferometer, that combines the flexibility of arrayed waveguides and the wide application range of fiber or integrated optics Sagnac loops. We form the device by closing an array of wavelength-selective light paths provided by two arrayed waveguides with a single 2 x 2 coupler in a Sagnac configuration. The equations that describe the device's operation in general conditions are derived. A preliminary experimental demonstration is provided of a fiber prototype in passive operation that shows good agreement with the expected theoretical performance. Potential applications of the device in nonlinear operation are outlined and discussed.

  1. Herpes simplex virus type 1 tegument protein VP22 interacts with TAF-I proteins and inhibits nucleosome assembly but not regulation of histone acetylation by INHAT.

    van Leeuwen, Hans; Okuwaki, Mitsuru; Hong, Rui; Chakravarti, Debabrata; Nagata, Kyosuke; O'Hare, Peter

    2003-09-01

    Affinity chromatography was used to identify cellular proteins that interact with the herpes simplex virus (HSV) tegument protein VP22. Among a small set of proteins that bind specifically to VP22, we identified TAF-I (template-activating factor I), a chromatin remodelling protein and close homologue of the histone chaperone protein NAP-1. TAF-I has been shown previously to promote more ordered transfer of histones to naked DNA through a direct interaction with histones. TAF-I, as a subunit of the INHAT (inhibitor of acetyltransferases) protein complex, also binds to histones and masks them from being substrates for the acetyltransferases p300 and PCAF. Using in vitro assays for TAF-I activity in chromatin assembly, we show that VP22 inhibits nucleosome deposition on DNA by binding to TAF-I. We also observed that VP22 binds non-specifically to DNA, an activity that is abolished by TAF-I. However, the presence of VP22 does not affect the property of INHAT in inhibiting the histone acetyltransferase activity of p300 or PCAF in vitro. We speculate that this interaction could be relevant to HSV DNA organization early in infection, for example, by interfering with nucleosomal deposition on the genome. Consistent with this possibility was the observation that overexpression of TAF-I in transfected cells interferes with the progression of HSV-1 infection.

  2. Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails.

    Stützer, Alexandra; Liokatis, Stamatios; Kiesel, Anja; Schwarzer, Dirk; Sprangers, Remco; Söding, Johannes; Selenko, Philipp; Fischle, Wolfgang

    2016-01-21

    Post-translational histone modifications and linker histone incorporation regulate chromatin structure and genome activity. How these systems interface on a molecular level is unclear. Using biochemistry and NMR spectroscopy, we deduced mechanistic insights into the modification behavior of N-terminal histone H3 tails in different nucleosomal contexts. We find that linker histones generally inhibit modifications of different H3 sites and reduce H3 tail dynamics in nucleosomes. These effects are caused by modulations of electrostatic interactions of H3 tails with linker DNA and largely depend on the C-terminal domains of linker histones. In agreement, linker histone occupancy and H3 tail modifications segregate on a genome-wide level. Charge-modulating modifications such as phosphorylation and acetylation weaken transient H3 tail-linker DNA interactions, increase H3 tail dynamics, and, concomitantly, enhance general modifiability. We propose that alterations of H3 tail-linker DNA interactions by linker histones and charge-modulating modifications execute basal control mechanisms of chromatin function. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Capacitive micromachined ultrasonic transducer arrays as tunable acoustic metamaterials

    Lani, Shane W., E-mail: shane.w.lani@gmail.com, E-mail: karim.sabra@me.gatech.edu, E-mail: levent.degertekin@me.gatech.edu; Sabra, Karim G. [George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801Ferst Drive, Georgia 30332-0405 (United States); Wasequr Rashid, M.; Hasler, Jennifer [School of Electrical and Computer Engineering, Georgia Institute of Technology, Van Leer Electrical Engineering Building, 777 Atlantic Drive NW, Atlanta, Georgia 30332-0250 (United States); Levent Degertekin, F. [George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, 801Ferst Drive, Georgia 30332-0405 (United States); School of Electrical and Computer Engineering, Georgia Institute of Technology, Van Leer Electrical Engineering Building, 777 Atlantic Drive NW, Atlanta, Georgia 30332-0250 (United States)

    2014-02-03

    Capacitive Micromachined Ultrasonic Transducers (CMUTs) operating in immersion support dispersive evanescent waves due to the subwavelength periodic structure of electrostatically actuated membranes in the array. Evanescent wave characteristics also depend on the membrane resonance which is modified by the externally applied bias voltage, offering a mechanism to tune the CMUT array as an acoustic metamaterial. The dispersion and tunability characteristics are examined using a computationally efficient, mutual radiation impedance based approach to model a finite-size array and realistic parameters of variation. The simulations are verified, and tunability is demonstrated by experiments on a linear CMUT array operating in 2-12 MHz range.

  4. Jammed-array wideband sawtooth filter.

    Tan, Zhongwei; Wang, Chao; Goda, Keisuke; Malik, Omer; Jalali, Bahram

    2011-11-21

    We present an all-optical passive low-cost spectral filter that exhibits a high-resolution periodic sawtooth spectral pattern without the need for active optoelectronic components. The principle of the filter is the partial masking of a phased array of virtual light sources with multiply jammed diffraction orders. We utilize the filter's periodic linear map between frequency and intensity to demonstrate fast sensitive interrogation of fiber Bragg grating sensor arrays and ultrahigh-frequency electrical sawtooth waveform generation. © 2011 Optical Society of America

  5. Focal plane array with modular pixel array components for scalability

    Kay, Randolph R; Campbell, David V; Shinde, Subhash L; Rienstra, Jeffrey L; Serkland, Darwin K; Holmes, Michael L

    2014-12-09

    A modular, scalable focal plane array is provided as an array of integrated circuit dice, wherein each die includes a given amount of modular pixel array circuitry. The array of dice effectively multiplies the amount of modular pixel array circuitry to produce a larger pixel array without increasing die size. Desired pixel pitch across the enlarged pixel array is preserved by forming die stacks with each pixel array circuitry die stacked on a separate die that contains the corresponding signal processing circuitry. Techniques for die stack interconnections and die stack placement are implemented to ensure that the desired pixel pitch is preserved across the enlarged pixel array.

  6. Multi-Beam Radio Frequency (RF) Aperture Arrays Using Multiplierless Approximate Fast Fourier Transform (FFT)

    2017-08-01

    Fourier transform, discrete Fourier transform, digital array processing , antenna beamformers 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...125 3.7 Simulation of 2-D Beams Cross Sections .................................................................... 125 3.7.1 8...unlimited. List of Figures Figure Page Figure 1: N-beam Array Processing System using a Linear Array

  7. Triggering the GRANDE array

    Wilson, C.L.; Bratton, C.B.; Gurr, J.; Kropp, W.; Nelson, M.; Sobel, H.; Svoboda, R.; Yodh, G.; Burnett, T.; Chaloupka, V.; Wilkes, R.J.; Cherry, M.; Ellison, S.B.; Guzik, T.G.; Wefel, J.; Gaidos, J.; Loeffler, F.; Sembroski, G.; Goodman, J.; Haines, T.J.; Kielczewska, D.; Lane, C.; Steinberg, R.; Lieber, M.; Nagle, D.; Potter, M.; Tripp, R.

    1990-01-01

    A brief description of the Gamma Ray And Neutrino Detector Experiment (GRANDE) is presented. The detector elements and electronics are described. The trigger logic for the array is then examined. The triggers for the Gamma Ray and the Neutrino portions of the array are treated separately. (orig.)

  8. ISS Solar Array Management

    Williams, James P.; Martin, Keith D.; Thomas, Justin R.; Caro, Samuel

    2010-01-01

    The International Space Station (ISS) Solar Array Management (SAM) software toolset provides the capabilities necessary to operate a spacecraft with complex solar array constraints. It monitors spacecraft telemetry and provides interpretations of solar array constraint data in an intuitive manner. The toolset provides extensive situational awareness to ensure mission success by analyzing power generation needs, array motion constraints, and structural loading situations. The software suite consists of several components including samCS (constraint set selector), samShadyTimers (array shadowing timers), samWin (visualization GUI), samLock (array motion constraint computation), and samJet (attitude control system configuration selector). It provides high availability and uptime for extended and continuous mission support. It is able to support two-degrees-of-freedom (DOF) array positioning and supports up to ten simultaneous constraints with intuitive 1D and 2D decision support visualizations of constraint data. Display synchronization is enabled across a networked control center and multiple methods for constraint data interpolation are supported. Use of this software toolset increases flight safety, reduces mission support effort, optimizes solar array operation for achieving mission goals, and has run for weeks at a time without issues. The SAM toolset is currently used in ISS real-time mission operations.

  9. Advanced statistical tools for SNP arrays : signal calibration, copy number estimation and single array genotyping

    Rippe, Ralph Christian Alexander

    2012-01-01

    Fluorescence bias in in signals from individual SNP arrays can be calibrated using linear models. Given the data, the system of equations is very large, so a specialized symbolic algorithm was developed. These models are also used to illustrate that genomic waves do not exist, but are merely an

  10. Fault Analysis in Solar Photovoltaic Arrays

    Zhao, Ye

    Fault analysis in solar photovoltaic (PV) arrays is a fundamental task to increase reliability, efficiency and safety in PV systems. Conventional fault protection methods usually add fuses or circuit breakers in series with PV components. But these protection devices are only able to clear faults and isolate faulty circuits if they carry a large fault current. However, this research shows that faults in PV arrays may not be cleared by fuses under some fault scenarios, due to the current-limiting nature and non-linear output characteristics of PV arrays. First, this thesis introduces new simulation and analytic models that are suitable for fault analysis in PV arrays. Based on the simulation environment, this thesis studies a variety of typical faults in PV arrays, such as ground faults, line-line faults, and mismatch faults. The effect of a maximum power point tracker on fault current is discussed and shown to, at times, prevent the fault current protection devices to trip. A small-scale experimental PV benchmark system has been developed in Northeastern University to further validate the simulation conclusions. Additionally, this thesis examines two types of unique faults found in a PV array that have not been studied in the literature. One is a fault that occurs under low irradiance condition. The other is a fault evolution in a PV array during night-to-day transition. Our simulation and experimental results show that overcurrent protection devices are unable to clear the fault under "low irradiance" and "night-to-day transition". However, the overcurrent protection devices may work properly when the same PV fault occurs in daylight. As a result, a fault under "low irradiance" and "night-to-day transition" might be hidden in the PV array and become a potential hazard for system efficiency and reliability.

  11. Ultrasound beam characteristics of a symmetric nodal origami based array

    Bilgunde, Prathamesh N.; Bond, Leonard J.

    2018-04-01

    Origami-the ancient art of paper folding-is being explored in acoustics for effective focusing of sound. In this short communication, we present a numerical investigation of beam characteristics for an origami based ultrasound array. A spatial re-configuration of array elements is performed based upon the symmetric nodal origami. The effect of fold angle on the ultrasound beam is evaluated using frequency domain and transient finite element analysis. It was found that increase in the fold angle reduces near field length by 58% and also doubles the beam intensity as compared to the linear array. Transient analysis also indicated 80% reduction in the -6dB beam width, which can improve the lateral resolution of phased array. Such a spatially re-configurable array could potentially be used in the future to reduce the cost of electronics in the phased array instrumentation.

  12. Linearly constrained minimax optimization

    Madsen, Kaj; Schjær-Jacobsen, Hans

    1978-01-01

    We present an algorithm for nonlinear minimax optimization subject to linear equality and inequality constraints which requires first order partial derivatives. The algorithm is based on successive linear approximations to the functions defining the problem. The resulting linear subproblems...

  13. Parallel algorithms for numerical linear algebra

    van der Vorst, H

    1990-01-01

    This is the first in a new series of books presenting research results and developments concerning the theory and applications of parallel computers, including vector, pipeline, array, fifth/future generation computers, and neural computers.All aspects of high-speed computing fall within the scope of the series, e.g. algorithm design, applications, software engineering, networking, taxonomy, models and architectural trends, performance, peripheral devices.Papers in Volume One cover the main streams of parallel linear algebra: systolic array algorithms, message-passing systems, algorithms for p

  14. Electronic correlations and disorder in transport through one-dimensional nanoparticle arrays

    Bascones, E.; Estevez, V.; Trinidad, J. A.; MacDonald, A. H.

    2007-01-01

    We analyze and clarify the transport properties of a one-dimensional metallic nanoparticle array with interaction between charges restricted to charges placed in the same conductor. We study the threshold voltage, the I-V curves and the potential drop through the array and their dependence on the array parameters including the effect of charge and resistance disorder. We show that very close to threshold the current depends linearly on voltage with a slope independent on the array size. At in...

  15. The data array, a tool to interface the user to a large data base

    Foster, G. H.

    1974-01-01

    Aspects of the processing of spacecraft data is considered. Use of the data array in a large address space as an intermediate form in data processing for a large scientific data base is advocated. Techniques for efficient indexing in data arrays are reviewed and the data array method for mapping an arbitrary structure onto linear address space is shown. A compromise between the two forms is given. The impact of the data array on the user interface are considered along with implementation.

  16. Introduction to adaptive arrays

    Monzingo, Bob; Haupt, Randy

    2011-01-01

    This second edition is an extensive modernization of the bestselling introduction to the subject of adaptive array sensor systems. With the number of applications of adaptive array sensor systems growing each year, this look at the principles and fundamental techniques that are critical to these systems is more important than ever before. Introduction to Adaptive Arrays, 2nd Edition is organized as a tutorial, taking the reader by the hand and leading them through the maze of jargon that often surrounds this highly technical subject. It is easy to read and easy to follow as fundamental concept

  17. Piezoelectric transducer array microspeaker

    Carreno, Armando Arpys Arevalo

    2016-12-19

    In this paper we present the fabrication and characterization of a piezoelectric micro-speaker. The speaker is an array of micro-machined piezoelectric membranes, fabricated on silicon wafer using advanced micro-machining techniques. Each array contains 2n piezoelectric transducer membranes, where “n” is the bit number. Every element of the array has a circular shape structure. The membrane is made out four layers: 300nm of platinum for the bottom electrode, 250nm or lead zirconate titanate (PZT), a top electrode of 300nm and a structural layer of 50

  18. Bearing estimation with acoustic vector-sensor arrays

    Hawkes, M.; Nehorai, A.

    1996-01-01

    We consider direction-of-arrival (DOA) estimation using arrays of acoustic vector sensors in free space, and derive expressions for the Cramacute er-Rao bound on the DOA parameters when there is a single source. The vector-sensor array is seen to have improved performance over the traditional scalar-sensor (pressure-sensor) array for two distinct reasons: its elements have an inherent directional sensitivity and the array makes a greater number of measurements. The improvement is greatest for small array apertures and low signal-to-noise ratios. Examination of the conventional beamforming and Capon DOA estimators shows that vector-sensor arrays can completely resolve the bearing, even with a linear array, and can remove the ambiguities associated with spatial undersampling. We also propose and analyze a diversely-oriented array of velocity sensors that possesses some of the advantages of the vector-sensor array without the increase in hardware and computation. In addition, in certain scenarios it can avoid problems with spatially correlated noise that the vector-sensor array may suffer. copyright 1996 American Institute of Physics

  19. Foundations of linear and generalized linear models

    Agresti, Alan

    2015-01-01

    A valuable overview of the most important ideas and results in statistical analysis Written by a highly-experienced author, Foundations of Linear and Generalized Linear Models is a clear and comprehensive guide to the key concepts and results of linear statistical models. The book presents a broad, in-depth overview of the most commonly used statistical models by discussing the theory underlying the models, R software applications, and examples with crafted models to elucidate key ideas and promote practical model building. The book begins by illustrating the fundamentals of linear models,

  20. Protein Functionalized Nanodiamond Arrays

    Liu YL

    2010-01-01

    Full Text Available Abstract Various nanoscale elements are currently being explored for bio-applications, such as in bio-images, bio-detection, and bio-sensors. Among them, nanodiamonds possess remarkable features such as low bio-cytotoxicity, good optical property in fluorescent and Raman spectra, and good photostability for bio-applications. In this work, we devise techniques to position functionalized nanodiamonds on self-assembled monolayer (SAMs arrays adsorbed on silicon and ITO substrates surface using electron beam lithography techniques. The nanodiamond arrays were functionalized with lysozyme to target a certain biomolecule or protein specifically. The optical properties of the nanodiamond-protein complex arrays were characterized by a high throughput confocal microscope. The synthesized nanodiamond-lysozyme complex arrays were found to still retain their functionality in interacting with E. coli.

  1. Photonic Crystal Nanocavity Arrays

    Altug, Hatice; Vuckovic, Jelena

    2006-01-01

    We recently proposed two-dimensional coupled photonic crystal nanocavity arrays as a route to achieve a slow-group velocity of light in all crystal directions, thereby enabling numerous applications...

  2. Carbon nanotube array actuators

    Geier, S; Mahrholz, T; Wierach, P; Sinapius, M

    2013-01-01

    Experimental investigations of highly vertically aligned carbon nanotubes (CNTs), also known as CNT-arrays, are the main focus of this paper. The free strain as result of an active material behavior is analyzed via a novel experimental setup. Previous test experiences of papers made of randomly oriented CNTs, also called Bucky-papers, reveal comparably low free strain. The anisotropy of aligned CNTs promises better performance. Via synthesis techniques like chemical vapor deposition (CVD) or plasma enhanced CVD (PECVD), highly aligned arrays of multi-walled carbon nanotubes (MWCNTs) are synthesized. Two different types of CNT-arrays are analyzed, morphologically first, and optically tested for their active characteristics afterwards. One type of the analyzed arrays features tube lengths of 750–2000 μm with a large variety of diameters between 20 and 50 nm and a wave-like CNT-shape. The second type features a maximum, almost uniform, length of 12 μm and a constant diameter of 50 nm. Different CNT-lengths and array types are tested due to their active behavior. As result of the presented tests, it is reported that the quality of orientation is the most decisive property for excellent active behavior. Due to their alignment, CNT-arrays feature the opportunity to clarify the actuation mechanism of architectures made of CNTs. (paper)

  3. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins.

    Foulk, Michael S; Urban, John M; Casella, Cinzia; Gerbi, Susan A

    2015-05-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand-independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo-controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na(+) instead of K(+) in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq. © 2015 Foulk et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Beam pattern improvement by compensating array nonuniformities in a guided wave phased array

    Kwon, Hyu-Sang; Lee, Seung-Seok; Kim, Jin-Yeon

    2013-01-01

    This paper presents a simple data processing algorithm which can improve the performance of a uniform circular array based on guided wave transducers. The algorithm, being intended to be used with the delay-and-sum beamformer, effectively eliminates the effects of nonuniformities that can significantly degrade the beam pattern. Nonuniformities can arise intrinsically from the array geometry when the circular array is transformed to a linear array for beam steering and extrinsically from unequal conditions of transducers such as element-to-element variations of sensitivity and directivity. The effects of nonuniformities are compensated by appropriately imposing weight factors on the elements in the projected linear array. Different cases are simulated, where the improvements of the beam pattern, especially the level of the highest sidelobe, are clearly seen, and related issues are discussed. An experiment is performed which uses A0 mode Lamb waves in a steel plate, to demonstrate the usefulness of the proposed method. The discrepancy between theoretical and experimental beam patterns is explained by accounting for near-field effects. (paper)

  5. BLAS- BASIC LINEAR ALGEBRA SUBPROGRAMS

    Krogh, F. T.

    1994-01-01

    The Basic Linear Algebra Subprogram (BLAS) library is a collection of FORTRAN callable routines for employing standard techniques in performing the basic operations of numerical linear algebra. The BLAS library was developed to provide a portable and efficient source of basic operations for designers of programs involving linear algebraic computations. The subprograms available in the library cover the operations of dot product, multiplication of a scalar and a vector, vector plus a scalar times a vector, Givens transformation, modified Givens transformation, copy, swap, Euclidean norm, sum of magnitudes, and location of the largest magnitude element. Since these subprograms are to be used in an ANSI FORTRAN context, the cases of single precision, double precision, and complex data are provided for. All of the subprograms have been thoroughly tested and produce consistent results even when transported from machine to machine. BLAS contains Assembler versions and FORTRAN test code for any of the following compilers: Lahey F77L, Microsoft FORTRAN, or IBM Professional FORTRAN. It requires the Microsoft Macro Assembler and a math co-processor. The PC implementation allows individual arrays of over 64K. The BLAS library was developed in 1979. The PC version was made available in 1986 and updated in 1988.

  6. Compressive Sensing for Millimeter Wave Antenna Array Diagnosis

    Eltayeb, Mohammed E.

    2018-01-08

    The radiation pattern of an antenna array depends on the excitation weights and the geometry of the array. Due to wind and atmospheric conditions, outdoor millimeter wave antenna elements are subject to full or partial blockages from a plethora of particles like dirt, salt, ice, and water droplets. Handheld devices are also subject to blockages from random finger placement and/or finger prints. These blockages cause absorption and scattering to the signal incident on the array, modify the array geometry, and distort the far-field radiation pattern of the array. This paper studies the effects of blockages on the far-field radiation pattern of linear arrays and proposes several array diagnosis techniques for millimeter wave antenna arrays. The proposed techniques jointly estimate the locations of the blocked antennas and the induced attenuation and phase-shifts given knowledge of the angles of arrival/departure. Numerical results show that the proposed techniques provide satisfactory results in terms of fault detection with reduced number of measurements (diagnosis time) provided that the number of blockages is small compared to the array size.

  7. Waferscale Electrostatic Quadrupole Array for Multiple Ion Beam Manipulation

    Vinayakumar, K. B.; Persaud, A.; Seidl, P. A.; Ji, Q.; Waldron, W. L.; Schenkel, T.; Ardanuc, S.; Lal, A.

    2018-01-01

    We report on the first through-wafer silicon-based Electrostatic Quadrupole Array (ESQA) to focus high energy ion beams. This device is a key enabler for a wafer based accelerator architecture that lends itself to orders-of-magnitude reduction in cost, volume and weight of charged particle accelerators. ESQs are a key building block in developing compact Multiple Electrostatic Quadrupole Array Linear Accelerator (MEQALAC) [1]. In a MEQALAC electrostatic forces are used to focus ions, and elec...

  8. Control Strategies for Arrays of Wave Energy Devices

    Westphalen, J; Bacelli, G; Balitsky, P; Ringwood, John

    2011-01-01

    In this paper, we investigate the differences between two control strategies for a two-device linear array of wave energy converters (WEC) for device spacings of 4 to 80 times the device diameter. The WECs operate in heave only and are controlled in real time. The control strategies, called the independent device and global array control, estimate the excitation forces and calculate the optimum vertical velocity trajectory and reactive power take off force to achieve the ...

  9. Testing of focal plane arrays

    Merriam, J.D.

    1988-01-01

    Problems associated with the testing of focal plane arrays are briefly examined with reference to the instrumentation and measurement procedures. In particular, the approach and instrumentation used as the Naval Ocean Systems Center is presented. Most of the measurements are made with flooded illumination on the focal plane array. The array is treated as an ensemble of individual pixels, data being taken on each pixel and array averages and standard deviations computed for the entire array. Data maps are generated, showing the pixel data in the proper spatial position on the array and the array statistics

  10. Non-linear Ultrasound Imaging

    Du, Yigang

    .3% relative to the measurement from a 1 inch diameter transducer. A preliminary study for harmonic imaging using synthetic aperture sequential beamforming (SASB) has been demonstrated. A wire phantom underwater measurement is made by an experimental synthetic aperture real-time ultrasound scanner (SARUS......) with a linear array transducer. The second harmonic imaging is obtained by a pulse inversion technique. The received data is beamformed by the SASB using a Beamformation Toolbox. In the measurements the lateral resolution at -6 dB is improved by 66% compared to the conventional imaging algorithm. There is also...... a 35% improvement for the lateral resolution at -6 dB compared with the sole harmonic imaging and a 46% improvement compared with merely using the SASB....

  11. Theory and applications of spherical microphone array processing

    Jarrett, Daniel P; Naylor, Patrick A

    2017-01-01

    This book presents the signal processing algorithms that have been developed to process the signals acquired by a spherical microphone array. Spherical microphone arrays can be used to capture the sound field in three dimensions and have received significant interest from researchers and audio engineers. Algorithms for spherical array processing are different to corresponding algorithms already known in the literature of linear and planar arrays because the spherical geometry can be exploited to great beneficial effect. The authors aim to advance the field of spherical array processing by helping those new to the field to study it efficiently and from a single source, as well as by offering a way for more experienced researchers and engineers to consolidate their understanding, adding either or both of breadth and depth. The level of the presentation corresponds to graduate studies at MSc and PhD level. This book begins with a presentation of some of the essential mathematical and physical theory relevant to ...

  12. Solving “Antenna Array Thinning Problem” Using Genetic Algorithm

    Rajashree Jain

    2012-01-01

    Full Text Available Thinning involves reducing total number of active elements in an antenna array without causing major degradation in system performance. Dynamic thinning is the process of achieving this under real-time conditions. It is required to find a strategic subset of antenna elements for thinning so as to have its optimum performance. From a mathematical perspective this is a nonlinear, multidimensional problem with multiple objectives and many constraints. Solution for such problem cannot be obtained by classical analytical techniques. It will be required to employ some type of search algorithm which can lead to a practical solution in an optimal. The present paper discusses an approach of using genetic algorithm for array thinning. After discussing the basic concept involving antenna array, array thinning, dynamic thinning, and application methodology, simulation results of applying the technique to linear and planar arrays are presented.

  13. A linear programming manual

    Tuey, R. C.

    1972-01-01

    Computer solutions of linear programming problems are outlined. Information covers vector spaces, convex sets, and matrix algebra elements for solving simultaneous linear equations. Dual problems, reduced cost analysis, ranges, and error analysis are illustrated.

  14. Wire Array Photovoltaics

    Turner-Evans, Dan

    Over the past five years, the cost of solar panels has dropped drastically and, in concert, the number of installed modules has risen exponentially. However, solar electricity is still more than twice as expensive as electricity from a natural gas plant. Fortunately, wire array solar cells have emerged as a promising technology for further lowering the cost of solar. Si wire array solar cells are formed with a unique, low cost growth method and use 100 times less material than conventional Si cells. The wires can be embedded in a transparent, flexible polymer to create a free-standing array that can be rolled up for easy installation in a variety of form factors. Furthermore, by incorporating multijunctions into the wire morphology, higher efficiencies can be achieved while taking advantage of the unique defect relaxation pathways afforded by the 3D wire geometry. The work in this thesis shepherded Si wires from undoped arrays to flexible, functional large area devices and laid the groundwork for multijunction wire array cells. Fabrication techniques were developed to turn intrinsic Si wires into full p-n junctions and the wires were passivated with a-Si:H and a-SiNx:H. Single wire devices yielded open circuit voltages of 600 mV and efficiencies of 9%. The arrays were then embedded in a polymer and contacted with a transparent, flexible, Ni nanoparticle and Ag nanowire top contact. The contact connected >99% of the wires in parallel and yielded flexible, substrate free solar cells featuring hundreds of thousands of wires. Building on the success of the Si wire arrays, GaP was epitaxially grown on the material to create heterostructures for photoelectrochemistry. These cells were limited by low absorption in the GaP due to its indirect bandgap, and poor current collection due to a diffusion length of only 80 nm. However, GaAsP on SiGe offers a superior combination of materials, and wire architectures based on these semiconductors were investigated for multijunction

  15. Linear shaped charge

    Peterson, David; Stofleth, Jerome H.; Saul, Venner W.

    2017-07-11

    Linear shaped charges are described herein. In a general embodiment, the linear shaped charge has an explosive with an elongated arrowhead-shaped profile. The linear shaped charge also has and an elongated v-shaped liner that is inset into a recess of the explosive. Another linear shaped charge includes an explosive that is shaped as a star-shaped prism. Liners are inset into crevices of the explosive, where the explosive acts as a tamper.

  16. Classifying Linear Canonical Relations

    Lorand, Jonathan

    2015-01-01

    In this Master's thesis, we consider the problem of classifying, up to conjugation by linear symplectomorphisms, linear canonical relations (lagrangian correspondences) from a finite-dimensional symplectic vector space to itself. We give an elementary introduction to the theory of linear canonical relations and present partial results toward the classification problem. This exposition should be accessible to undergraduate students with a basic familiarity with linear algebra.

  17. Linear-Algebra Programs

    Lawson, C. L.; Krogh, F. T.; Gold, S. S.; Kincaid, D. R.; Sullivan, J.; Williams, E.; Hanson, R. J.; Haskell, K.; Dongarra, J.; Moler, C. B.

    1982-01-01

    The Basic Linear Algebra Subprograms (BLAS) library is a collection of 38 FORTRAN-callable routines for performing basic operations of numerical linear algebra. BLAS library is portable and efficient source of basic operations for designers of programs involving linear algebriac computations. BLAS library is supplied in portable FORTRAN and Assembler code versions for IBM 370, UNIVAC 1100 and CDC 6000 series computers.

  18. A review of array radars

    Brookner, E.

    1981-10-01

    Achievements in the area of array radars are illustrated by such activities as the operational deployment of the large high-power, high-range-resolution Cobra Dane; the operational deployment of two all-solid-state high-power, large UHF Pave Paws radars; and the development of the SAM multifunction Patriot radar. This paper reviews the following topics: array radars steered in azimuth and elevation by phase shifting (phase-phase steered arrays); arrays steered + or - 60 deg, limited scan arrays, hemispherical coverage, and omnidirectional coverage arrays; array radars steering electronically in only one dimension, either by frequency or by phase steering; and array radar antennas which use no electronic scanning but instead use array antennas for achieving low antenna sidelobes.

  19. Diode lasers and arrays

    Streifer, W.

    1988-01-01

    This paper discusses the principles of operation of III-V semiconductor diode lasers, the use of distributed feedback, and high power laser arrays. The semiconductor laser is a robust, miniature, versatile device, which directly converts electricity to light with very high efficiency. Applications to pumping solid-state lasers and to fiber optic and point-to-point communications are reviewed

  20. Array Theory and Nial

    Falster, Peter; Jenkins, Michael

    1999-01-01

    This report is the result of collaboration between the authors during the first 8 months of 1999 when M. Jenkins was visiting professor at DTU. The report documents the development of a tool for the investigation of array theory concepts and in particular presents various approaches to choose...

  1. Piezoelectric transducer array microspeaker

    Carreno, Armando Arpys Arevalo; Conchouso Gonzalez, David; Castro, David; Kosel, Jü rgen; Foulds, Ian G.

    2016-01-01

    contains 2n piezoelectric transducer membranes, where “n” is the bit number. Every element of the array has a circular shape structure. The membrane is made out four layers: 300nm of platinum for the bottom electrode, 250nm or lead zirconate titanate (PZT

  2. Non linear system become linear system

    Petre Bucur

    2007-01-01

    Full Text Available The present paper refers to the theory and the practice of the systems regarding non-linear systems and their applications. We aimed the integration of these systems to elaborate their response as well as to highlight some outstanding features.

  3. Linear motor coil assembly and linear motor

    2009-01-01

    An ironless linear motor (5) comprising a magnet track (53) and a coil assembly (50) operating in cooperation with said magnet track (53) and having a plurality of concentrated multi-turn coils (31 a-f, 41 a-d, 51 a-k), wherein the end windings (31E) of the coils (31 a-f, 41 a-e) are substantially

  4. Wireless Sensor Array Network DoA Estimation from Compressed Array Data via Joint Sparse Representation.

    Yu, Kai; Yin, Ming; Luo, Ji-An; Wang, Yingguan; Bao, Ming; Hu, Yu-Hen; Wang, Zhi

    2016-05-23

    A compressive sensing joint sparse representation direction of arrival estimation (CSJSR-DoA) approach is proposed for wireless sensor array networks (WSAN). By exploiting the joint spatial and spectral correlations of acoustic sensor array data, the CSJSR-DoA approach provides reliable DoA estimation using randomly-sampled acoustic sensor data. Since random sampling is performed at remote sensor arrays, less data need to be transmitted over lossy wireless channels to the fusion center (FC), and the expensive source coding operation at sensor nodes can be avoided. To investigate the spatial sparsity, an upper bound of the coherence of incoming sensor signals is derived assuming a linear sensor array configuration. This bound provides a theoretical constraint on the angular separation of acoustic sources to ensure the spatial sparsity of the received acoustic sensor array signals. The Cram e ´ r-Rao bound of the CSJSR-DoA estimator that quantifies the theoretical DoA estimation performance is also derived. The potential performance of the CSJSR-DoA approach is validated using both simulations and field experiments on a prototype WSAN platform. Compared to existing compressive sensing-based DoA estimation methods, the CSJSR-DoA approach shows significant performance improvement.

  5. Concurrent array-based queue

    Heidelberger, Philip; Steinmacher-Burow, Burkhard

    2015-01-06

    According to one embodiment, a method for implementing an array-based queue in memory of a memory system that includes a controller includes configuring, in the memory, metadata of the array-based queue. The configuring comprises defining, in metadata, an array start location in the memory for the array-based queue, defining, in the metadata, an array size for the array-based queue, defining, in the metadata, a queue top for the array-based queue and defining, in the metadata, a queue bottom for the array-based queue. The method also includes the controller serving a request for an operation on the queue, the request providing the location in the memory of the metadata of the queue.

  6. Linear collider: a preview

    Wiedemann, H.

    1981-11-01

    Since no linear colliders have been built yet it is difficult to know at what energy the linear cost scaling of linear colliders drops below the quadratic scaling of storage rings. There is, however, no doubt that a linear collider facility for a center of mass energy above say 500 GeV is significantly cheaper than an equivalent storage ring. In order to make the linear collider principle feasible at very high energies a number of problems have to be solved. There are two kinds of problems: one which is related to the feasibility of the principle and the other kind of problems is associated with minimizing the cost of constructing and operating such a facility. This lecture series describes the problems and possible solutions. Since the real test of a principle requires the construction of a prototype I will in the last chapter describe the SLC project at the Stanford Linear Accelerator Center.

  7. Basic linear algebra

    Blyth, T S

    2002-01-01

    Basic Linear Algebra is a text for first year students leading from concrete examples to abstract theorems, via tutorial-type exercises. More exercises (of the kind a student may expect in examination papers) are grouped at the end of each section. The book covers the most important basics of any first course on linear algebra, explaining the algebra of matrices with applications to analytic geometry, systems of linear equations, difference equations and complex numbers. Linear equations are treated via Hermite normal forms which provides a successful and concrete explanation of the notion of linear independence. Another important highlight is the connection between linear mappings and matrices leading to the change of basis theorem which opens the door to the notion of similarity. This new and revised edition features additional exercises and coverage of Cramer's rule (omitted from the first edition). However, it is the new, extra chapter on computer assistance that will be of particular interest to readers:...

  8. Linear collider: a preview

    Wiedemann, H.

    1981-11-01

    Since no linear colliders have been built yet it is difficult to know at what energy the linear cost scaling of linear colliders drops below the quadratic scaling of storage rings. There is, however, no doubt that a linear collider facility for a center of mass energy above say 500 GeV is significantly cheaper than an equivalent storage ring. In order to make the linear collider principle feasible at very high energies a number of problems have to be solved. There are two kinds of problems: one which is related to the feasibility of the principle and the other kind of problems is associated with minimizing the cost of constructing and operating such a facility. This lecture series describes the problems and possible solutions. Since the real test of a principle requires the construction of a prototype I will in the last chapter describe the SLC project at the Stanford Linear Accelerator Center

  9. Radar techniques using array antennas

    Wirth, Wulf-Dieter

    2013-01-01

    Radar Techniques Using Array Antennas is a thorough introduction to the possibilities of radar technology based on electronic steerable and active array antennas. Topics covered include array signal processing, array calibration, adaptive digital beamforming, adaptive monopulse, superresolution, pulse compression, sequential detection, target detection with long pulse series, space-time adaptive processing (STAP), moving target detection using synthetic aperture radar (SAR), target imaging, energy management and system parameter relations. The discussed methods are confirmed by simulation stud

  10. Matrices and linear transformations

    Cullen, Charles G

    1990-01-01

    ""Comprehensive . . . an excellent introduction to the subject."" - Electronic Engineer's Design Magazine.This introductory textbook, aimed at sophomore- and junior-level undergraduates in mathematics, engineering, and the physical sciences, offers a smooth, in-depth treatment of linear algebra and matrix theory. The major objects of study are matrices over an arbitrary field. Contents include Matrices and Linear Systems; Vector Spaces; Determinants; Linear Transformations; Similarity: Part I and Part II; Polynomials and Polynomial Matrices; Matrix Analysis; and Numerical Methods. The first

  11. Efficient Non Linear Loudspeakers

    Petersen, Bo R.; Agerkvist, Finn T.

    2006-01-01

    Loudspeakers have traditionally been designed to be as linear as possible. However, as techniques for compensating non linearities are emerging, it becomes possible to use other design criteria. This paper present and examines a new idea for improving the efficiency of loudspeakers at high levels...... by changing the voice coil layout. This deliberate non-linear design has the benefit that a smaller amplifier can be used, which has the benefit of reducing system cost as well as reducing power consumption....

  12. Linear models with R

    Faraway, Julian J

    2014-01-01

    A Hands-On Way to Learning Data AnalysisPart of the core of statistics, linear models are used to make predictions and explain the relationship between the response and the predictors. Understanding linear models is crucial to a broader competence in the practice of statistics. Linear Models with R, Second Edition explains how to use linear models in physical science, engineering, social science, and business applications. The book incorporates several improvements that reflect how the world of R has greatly expanded since the publication of the first edition.New to the Second EditionReorganiz

  13. Linear integrated circuits

    Carr, Joseph

    1996-01-01

    The linear IC market is large and growing, as is the demand for well trained technicians and engineers who understand how these devices work and how to apply them. Linear Integrated Circuits provides in-depth coverage of the devices and their operation, but not at the expense of practical applications in which linear devices figure prominently. This book is written for a wide readership from FE and first degree students, to hobbyists and professionals.Chapter 1 offers a general introduction that will provide students with the foundations of linear IC technology. From chapter 2 onwa

  14. Fault tolerant linear actuator

    Tesar, Delbert

    2004-09-14

    In varying embodiments, the fault tolerant linear actuator of the present invention is a new and improved linear actuator with fault tolerance and positional control that may incorporate velocity summing, force summing, or a combination of the two. In one embodiment, the invention offers a velocity summing arrangement with a differential gear between two prime movers driving a cage, which then drives a linear spindle screw transmission. Other embodiments feature two prime movers driving separate linear spindle screw transmissions, one internal and one external, in a totally concentric and compact integrated module.

  15. Superconducting linear accelerator cryostat

    Ben-Zvi, I.; Elkonin, B.V.; Sokolowski, J.S.

    1984-01-01

    A large vertical cryostat for a superconducting linear accelerator using quarter wave resonators has been developed. The essential technical details, operational experience and performance are described. (author)

  16. The Big Optical Array

    Mozurkewich, D.; Johnston, K.J.; Simon, R.S.

    1990-01-01

    This paper describes the design and the capabilities of the Naval Research Laboratory Big Optical Array (BOA), an interferometric optical array for high-resolution imaging of stars, stellar systems, and other celestial objects. There are four important differences between the BOA design and the design of Mark III Optical Interferometer on Mount Wilson (California). These include a long passive delay line which will be used in BOA to do most of the delay compensation, so that the fast delay line will have a very short travel; the beam combination in BOA will be done in triplets, to allow measurement of closure phase; the same light will be used for both star and fringe tracking; and the fringe tracker will use several wavelength channels

  17. A 4 probe array

    Fernando, C E [CEGB, Marchwood Engineering Laboratories, Marchwood, Southampton, Hampshire (United Kingdom)

    1980-11-01

    A NDT system is described which moves away from the present manual method using a single send/receive transducer combination and uses instead an array of four transducers. Four transducers are shown sufficient to define a point reflector with a resolution of m{lambda}z/R where m{lambda} is the minimum detectable path difference in the system (corresponding to a m cycle time resolution), z the range and R the radius of the array. Signal averaging with an input ADC rate of 100 MHz is used with voice output for the range data. Typical resolution measurements in a water tank are presented. We expect a resolution of the order of mm in steel at a range of 80 mm. The system is expected to have applications in automated, high resolution, sizing of defects and in the inspection of austenitic stainless steel welds. (author)

  18. Timed arrays wideband and time varying antenna arrays

    Haupt, Randy L

    2015-01-01

    Introduces timed arrays and design approaches to meet the new high performance standards The author concentrates on any aspect of an antenna array that must be viewed from a time perspective. The first chapters briefly introduce antenna arrays and explain the difference between phased and timed arrays. Since timed arrays are designed for realistic time-varying signals and scenarios, the book also reviews wideband signals, baseband and passband RF signals, polarization and signal bandwidth. Other topics covered include time domain, mutual coupling, wideband elements, and dispersion. The auth

  19. Solar collector array

    Hall, John Champlin; Martins, Guy Lawrence

    2015-09-06

    A method and apparatus for efficient manufacture, assembly and production of solar energy. In one aspect, the apparatus may include a number of modular solar receiver assemblies that may be separately manufactured, assembled and individually inserted into a solar collector array housing shaped to receive a plurality of solar receivers. The housing may include optical elements for focusing light onto the individual receivers, and a circuit for electrically connecting the solar receivers.

  20. Photovoltaic cell array

    Eliason, J. T. (Inventor)

    1976-01-01

    A photovoltaic cell array consisting of parallel columns of silicon filaments is described. Each fiber is doped to produce an inner region of one polarity type and an outer region of an opposite polarity type to thereby form a continuous radial semi conductor junction. Spaced rows of electrical contacts alternately connect to the inner and outer regions to provide a plurality of electrical outputs which may be combined in parallel or in series.

  1. Phased array antenna control

    Doland, G. D. (Inventor)

    1978-01-01

    Several new and useful improvements in steering and control of phased array antennas having a small number of elements, typically on the order of 5 to 17 elements are provided. Among the improvements are increasing the number of beam steering positions, reducing the possibility of phase transients in signals received or transmitted with the antennas, and increasing control and testing capacity with respect to the antennas.

  2. Development of portable phased array UT system for real-time flaw imaging

    Goto, M.

    1995-01-01

    Many functions and features of phased array UT technology must be useful for NDE in the industrial field. Some phased array UT systems have been developed for the inspection of nuclear pressure vessel and turbine components. However, phased array UT is still a special NDE technique and it has not been used widely in the past. The reasons of that are system size, cost, operator performance, equipment design and others. TOSHIBA has newly developed PC controlled portable phased array system to solve those problems. The portable phased array UT system is very compact and light but it is able to drive up to 32-channel linear array probe, to display real-time linear/sector B-scan, to display accumulated B-scan with an encoder and to display profile overlaid B-scan. The first applications were turbine component inspections for precise flaw investigation and flaw image data recording

  3. Lectin-Array Blotting.

    Pazos, Raquel; Echevarria, Juan; Hernandez, Alvaro; Reichardt, Niels-Christian

    2017-09-01

    Aberrant protein glycosylation is a hallmark of cancer, infectious diseases, and autoimmune or neurodegenerative disorders. Unlocking the potential of glycans as disease markers will require rapid and unbiased glycoproteomics methods for glycan biomarker discovery. The present method is a facile and rapid protocol for qualitative analysis of protein glycosylation in complex biological mixtures. While traditional lectin arrays only provide an average signal for the glycans in the mixture, which is usually dominated by the most abundant proteins, our method provides individual lectin binding profiles for all proteins separated in the gel electrophoresis step. Proteins do not have to be excised from the gel for subsequent analysis via the lectin array but are transferred by contact diffusion from the gel to a glass slide presenting multiple copies of printed lectin arrays. Fluorescently marked glycoproteins are trapped by the printed lectins via specific carbohydrate-lectin interactions and after a washing step their binding profile with up to 20 lectin probes is analyzed with a fluorescent scanner. The method produces the equivalent of 20 lectin blots in a single experiment, giving detailed insight into the binding epitopes present in the fractionated proteins. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  4. Array processor architecture

    Barnes, George H. (Inventor); Lundstrom, Stephen F. (Inventor); Shafer, Philip E. (Inventor)

    1983-01-01

    A high speed parallel array data processing architecture fashioned under a computational envelope approach includes a data base memory for secondary storage of programs and data, and a plurality of memory modules interconnected to a plurality of processing modules by a connection network of the Omega gender. Programs and data are fed from the data base memory to the plurality of memory modules and from hence the programs are fed through the connection network to the array of processors (one copy of each program for each processor). Execution of the programs occur with the processors operating normally quite independently of each other in a multiprocessing fashion. For data dependent operations and other suitable operations, all processors are instructed to finish one given task or program branch before all are instructed to proceed in parallel processing fashion on the next instruction. Even when functioning in the parallel processing mode however, the processors are not locked-step but execute their own copy of the program individually unless or until another overall processor array synchronization instruction is issued.

  5. Bestimmung der optimalen Array-Apertur für die Ultraschallprüfung von faserverstärkten Kunststoffen

    Kurras, Martin

    2017-01-01

    Für die zerstörungsfreie Prüfung von Kohlenstofffaserverbundwerkstoffen (CFK) wird häufig die Ultraschallprüfung verwendet. Neben dem klassischen Ultraschallverfahren findet dabei auch die Phased Array Technologie Anwendung. Hierbei wird zwischen zwei Verfahren unterschieden: dem handelsüblichen Phased Array oder Conventional Phased Array (CPA) und dem tomographischen Sampling Phased Array (SPA). Der Einsatz von Phased Arrays im Zusammenhang mit Linear-Scan-Technik und das sich daraus ergeben...

  6. A role for the nucleosome assembly proteins TAF-Iβ and NAP1 in the activation of BZLF1 expression and Epstein-Barr virus reactivation.

    Mansouri, Sheila; Wang, Shan; Frappier, Lori

    2013-01-01

    The reactivation of Epstein-Barr virus (EBV) from latent to lytic infection begins with the expression of the viral BZLF1 gene, leading to a subsequent cascade of viral gene expression and amplification of the EBV genome. Using RNA interference, we show that nucleosome assembly proteins NAP1 and TAF-I positively contribute to EBV reactivation in epithelial cells through the induction of BZLF1 expression. In addition, overexpression of NAP1 or the β isoform of TAF-I (TAF-Iβ) in AGS cells latently infected with EBV was sufficient to induce BZLF1 expression. Chromatin immunoprecipitation experiments performed in AGS-EBV cells showed that TAF-I associated with the BZLF1 promoter upon lytic induction and affected local histone modifications by increasing H3K4 dimethylation and H4K8 acetylation. MLL1, the host protein known to dimethylate H3K4, was found to associate with the BZLF1 promoter upon lytic induction in a TAF-I-dependent manner, and MLL1 depletion decreased BZLF1 expression, confirming its contribution to lytic reactivation. The results indicate that TAF-Iβ promotes BZLF1 expression and subsequent lytic infection by affecting chromatin at the BZLF1 promoter.

  7. Combination of hypomorphic mutations of the Drosophila homologues of aryl hydrocarbon receptor and nucleosome assembly protein family genes disrupts morphogenesis, memory and detoxification.

    Kuzin, Boris A; Nikitina, Ekaterina A; Cherezov, Roman O; Vorontsova, Julia E; Slezinger, Mikhail S; Zatsepina, Olga G; Simonova, Olga B; Enikolopov, Grigori N; Savvateeva-Popova, Elena V

    2014-01-01

    Aryl hydrocarbon receptor is essential for biological responses to endogenous and exogenous toxins in mammals. Its Drosophila homolog spineless plays an important role in fly morphogenesis. We have previously shown that during morphogenesis spineless genetically interacts with CG5017 gene, which encodes a nucleosome assembly factor and may affect cognitive function of the fly. We now demonstrate synergistic interactions of spineless and CG5017 in pathways controlling oxidative stress response and long-term memory formation in Drosophila melanogaster. Oxidative stress was induced by low doses of X-ray irradiation of flies carrying hypomorphic mutation of spineless, mutation of CG5017, and their combination. To determine the sensitivity of these mutants to pharmacological modifiers of the irradiation effect, we irradiated flies growing on standard medium supplemented by radiosensitizer furazidin and radioprotector serotonin. The effects of irradiation were investigated by analyzing leg and antenna morphological structures and by using real-time PCR to measure mRNA expression levels for spineless, Cyp6g1 and Gst-theta genes. We also examined long-term memory in these mutants using conditioned courtship suppression paradigm. Our results show that the interaction of spineless and CG5017 is important for regulation of morphogenesis, long-term memory formation, and detoxification during oxidative stress. Since spineless and CG5017 are evolutionary conserved, these results must be considered when evaluating the risk of combining similar mutations in other organisms, including humans.

  8. Combination of hypomorphic mutations of the Drosophila homologues of aryl hydrocarbon receptor and nucleosome assembly protein family genes disrupts morphogenesis, memory and detoxification.

    Boris A Kuzin

    Full Text Available Aryl hydrocarbon receptor is essential for biological responses to endogenous and exogenous toxins in mammals. Its Drosophila homolog spineless plays an important role in fly morphogenesis. We have previously shown that during morphogenesis spineless genetically interacts with CG5017 gene, which encodes a nucleosome assembly factor and may affect cognitive function of the fly. We now demonstrate synergistic interactions of spineless and CG5017 in pathways controlling oxidative stress response and long-term memory formation in Drosophila melanogaster. Oxidative stress was induced by low doses of X-ray irradiation of flies carrying hypomorphic mutation of spineless, mutation of CG5017, and their combination. To determine the sensitivity of these mutants to pharmacological modifiers of the irradiation effect, we irradiated flies growing on standard medium supplemented by radiosensitizer furazidin and radioprotector serotonin. The effects of irradiation were investigated by analyzing leg and antenna morphological structures and by using real-time PCR to measure mRNA expression levels for spineless, Cyp6g1 and Gst-theta genes. We also examined long-term memory in these mutants using conditioned courtship suppression paradigm. Our results show that the interaction of spineless and CG5017 is important for regulation of morphogenesis, long-term memory formation, and detoxification during oxidative stress. Since spineless and CG5017 are evolutionary conserved, these results must be considered when evaluating the risk of combining similar mutations in other organisms, including humans.

  9. Linearity enigmas in ecology

    Patten, B.C.

    1983-04-01

    Two issues concerning linearity or nonlinearity of natural systems are considered. Each is related to one of the two alternative defining properties of linear systems, superposition and decomposition. Superposition exists when a linear combination of inputs to a system results in the same linear combination of outputs that individually correspond to the original inputs. To demonstrate this property it is necessary that all initial states and inputs of the system which impinge on the output in question be included in the linear combination manipulation. As this is difficult or impossible to do with real systems of any complexity, nature appears nonlinear even though it may be linear. A linear system that displays nonlinear behavior for this reason is termed pseudononlinear. The decomposition property exists when the dynamic response of a system can be partitioned into an input-free portion due to state plus a state-free portion due to input. This is a characteristic of all linear systems, but not of nonlinear systems. Without the decomposition property, it is not possible to distinguish which portions of a system's behavior are due to innate characteristics (self) vs. outside conditions (environment), which is an important class of questions in biology and ecology. Some philosophical aspects of these findings are then considered. It is suggested that those ecologists who hold to the view that organisms and their environments are separate entities are in effect embracing a linear view of nature, even though their belief systems and mathematical models tend to be nonlinear. On the other hand, those who consider that organism-environment complex forms a single inseparable unit are implictly involved in non-linear thought, which may be in conflict with the linear modes and models that some of them use. The need to rectify these ambivalences on the part of both groups is indicated.

  10. Linearity stabilizes discrete breathers

    themselves and with the boundaries leading to the eventual formation of an ... explored where these fascinating entities are being studied as, for example, ... Josephson-junction arrays, layered silicates, micromechanical cantilever ... velocities at late times (an expected result based on the Central Limit Theorem) and the.

  11. Element sharing in interleaved antenna arrays

    Du Plessis, WP

    2012-03-01

    Full Text Available , there is a large variation in the results for a small number of shared elements which reduces as the number of times the GA is run increases. Taken together, these points suggest that the GA implemented here does not provide consistently good results when... levels in linear arrays,? IEEE Antennas Wirel. Propag. Lett., vol. 9, pp. 771?774, 2010. [11] D. E. Goldberg, Genetic algorithms in search, optimization, and machine learning. Addison-Wesley, 1989. [12] T. Blickle and L. Thiele, ?A comparison...

  12. A 2x2 quantum dot array with controllable inter-dot tunnel couplings

    Mukhopadhyay, Uditendu; Dehollain, Juan Pablo; Reichl, Christian; Wegscheider, Werner; Vandersypen, Lieven M. K.

    2018-01-01

    The interaction between electrons in arrays of electrostatically defined quantum dots is naturally described by a Fermi-Hubbard Hamiltonian. Moreover, the high degree of tunability of these systems make them a powerful platform to simulate different regimes of the Hubbard model. However, most quantum dot array implementations have been limited to one-dimensional linear arrays. In this letter, we present a square lattice unit cell of 2$\\times$2 quantum dots defined electrostatically in a AlGaA...

  13. Limited Diffraction Maps for Pulsed Wave Annular Arrays

    Fox, Paul D.

    2002-01-01

    A procedure is provided for decomposing the linear field of flat pulsed wave annular arrays into an equivalent set of known limited diffraction Bessel beams. Each Bessel beam propagates with known characteristics, enabling good insight into the propagation of annular fields to be obtained...

  14. Collectively-enhanced optomechanical coupling in periodic arrays of scatterers

    Xuereb, André; Genes, Claudiu; Dantan, Aurelien Romain

    2013-01-01

    in linear optomechanical coupling strengths between the cavity field and collective motional modes of the array that may be several orders of magnitude larger than is possible with an equivalent reflective ensemble. We describe and interpret these effects in detail and investigate the nature of the scaling...... laws of the coupling strengths for the different transmissive points in various regimes....

  15. A Macintosh based data system for array spectrometers (Poster)

    Bregman, J.; Moss, N.

    An interactive data aquisition and reduction system has been assembled by combining a Macintosh computer with an instrument controller (an Apple II computer) via an RS-232 interface. The data system provides flexibility for operating different linear array spectrometers. The standard Macintosh interface is used to provide ease of operation and to allow transferring the reduced data to commercial graphics software.

  16. Linear colliders - prospects 1985

    Rees, J.

    1985-06-01

    We discuss the scaling laws of linear colliders and their consequences for accelerator design. We then report on the SLAC Linear Collider project and comment on experience gained on that project and its application to future colliders. 9 refs., 2 figs

  17. The SLAC linear collider

    Richter, B.

    1985-01-01

    A report is given on the goals and progress of the SLAC Linear Collider. The author discusses the status of the machine and the detectors and give an overview of the physics which can be done at this new facility. He also gives some ideas on how (and why) large linear colliders of the future should be built

  18. Linear Programming (LP)

    Rogner, H.H.

    1989-01-01

    The submitted sections on linear programming are extracted from 'Theorie und Technik der Planung' (1978) by W. Blaas and P. Henseler and reformulated for presentation at the Workshop. They consider a brief introduction to the theory of linear programming and to some essential aspects of the SIMPLEX solution algorithm for the purposes of economic planning processes. 1 fig

  19. Racetrack linear accelerators

    Rowe, C.H.; Wilton, M.S. de.

    1979-01-01

    An improved recirculating electron beam linear accelerator of the racetrack type is described. The system comprises a beam path of four straight legs with four Pretzel bending magnets at the end of each leg to direct the beam into the next leg of the beam path. At least one of the beam path legs includes a linear accelerator. (UK)

  20. Semidefinite linear complementarity problems

    Eckhardt, U.

    1978-04-01

    Semidefinite linear complementarity problems arise by discretization of variational inequalities describing e.g. elastic contact problems, free boundary value problems etc. In the present paper linear complementarity problems are introduced and the theory as well as the numerical treatment of them are described. In the special case of semidefinite linear complementarity problems a numerical method is presented which combines the advantages of elimination and iteration methods without suffering from their drawbacks. This new method has very attractive properties since it has a high degree of invariance with respect to the representation of the set of all feasible solutions of a linear complementarity problem by linear inequalities. By means of some practical applications the properties of the new method are demonstrated. (orig.) [de

  1. Linear algebra done right

    Axler, Sheldon

    2015-01-01

    This best-selling textbook for a second course in linear algebra is aimed at undergrad math majors and graduate students. The novel approach taken here banishes determinants to the end of the book. The text focuses on the central goal of linear algebra: understanding the structure of linear operators on finite-dimensional vector spaces. The author has taken unusual care to motivate concepts and to simplify proofs. A variety of interesting exercises in each chapter helps students understand and manipulate the objects of linear algebra. The third edition contains major improvements and revisions throughout the book. More than 300 new exercises have been added since the previous edition. Many new examples have been added to illustrate the key ideas of linear algebra. New topics covered in the book include product spaces, quotient spaces, and dual spaces. Beautiful new formatting creates pages with an unusually pleasant appearance in both print and electronic versions. No prerequisites are assumed other than the ...

  2. Iterative algorithms for large sparse linear systems on parallel computers

    Adams, L. M.

    1982-01-01

    Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.

  3. Optical analogue of relativistic Dirac solitons in binary waveguide arrays

    Tran, Truong X., E-mail: truong.tran@mpl.mpg.de [Department of Physics, Le Quy Don University, 236 Hoang Quoc Viet str., 10000 Hanoi (Viet Nam); Max Planck Institute for the Science of Light, Günther-Scharowsky str. 1, 91058 Erlangen (Germany); Longhi, Stefano [Department of Physics, Politecnico di Milano and Istituto di Fotonica e Nanotecnologie del Consiglio Nazionale delle Ricerche, Piazza L. da Vinci 32, I-20133 Milano (Italy); Biancalana, Fabio [Max Planck Institute for the Science of Light, Günther-Scharowsky str. 1, 91058 Erlangen (Germany); School of Engineering and Physical Sciences, Heriot-Watt University, EH14 4AS Edinburgh (United Kingdom)

    2014-01-15

    We study analytically and numerically an optical analogue of Dirac solitons in binary waveguide arrays in the presence of Kerr nonlinearity. Pseudo-relativistic soliton solutions of the coupled-mode equations describing dynamics in the array are analytically derived. We demonstrate that with the found soliton solutions, the coupled mode equations can be converted into the nonlinear relativistic 1D Dirac equation. This paves the way for using binary waveguide arrays as a classical simulator of quantum nonlinear effects arising from the Dirac equation, something that is thought to be impossible to achieve in conventional (i.e. linear) quantum field theory. -- Highlights: •An optical analogue of Dirac solitons in nonlinear binary waveguide arrays is suggested. •Analytical solutions to pseudo-relativistic solitons are presented. •A correspondence of optical coupled-mode equations with the nonlinear relativistic Dirac equation is established.

  4. Square pulse linear transformer driver

    A. A. Kim

    2012-04-01

    Full Text Available The linear transformer driver (LTD technological approach can result in relatively compact devices that can deliver fast, high current, and high-voltage pulses straight out of the LTD cavity without any complicated pulse forming and pulse compression network. Through multistage inductively insulated voltage adders, the output pulse, increased in voltage amplitude, can be applied directly to the load. The usual LTD architecture [A. A. Kim, M. G. Mazarakis, V. A. Sinebryukhov, B. M. Kovalchuk, V. A. Vizir, S. N Volkov, F. Bayol, A. N. Bastrikov, V. G. Durakov, S. V. Frolov, V. M. Alexeenko, D. H. McDaniel, W. E. Fowler, K. LeCheen, C. Olson, W. A. Stygar, K. W. Struve, J. Porter, and R. M. Gilgenbach, Phys. Rev. ST Accel. Beams 12, 050402 (2009PRABFM1098-440210.1103/PhysRevSTAB.12.050402; M. G. Mazarakis, W. E. Fowler, A. A. Kim, V. A. Sinebryukhov, S. T. Rogowski, R. A. Sharpe, D. H. McDaniel, C. L. Olson, J. L. Porter, K. W. Struve, W. A. Stygar, and J. R. Woodworth, Phys. Rev. ST Accel. Beams 12, 050401 (2009PRABFM1098-440210.1103/PhysRevSTAB.12.050401] provides sine shaped output pulses that may not be well suited for some applications like z-pinch drivers, flash radiography, high power microwaves, etc. A more suitable power pulse would have a flat or trapezoidal (rising or falling top. In this paper, we present the design and first test results of an LTD cavity that generates such a type of output pulse by including within its circular array a number of third harmonic bricks in addition to the main bricks. A voltage adder made out of a square pulse cavity linear array will produce the same shape output pulses provided that the timing of each cavity is synchronized with the propagation of the electromagnetic pulse.

  5. Handbook on linear motor application

    1988-10-01

    This book guides the application for Linear motor. It lists classification and speciality of Linear Motor, terms of linear-induction motor, principle of the Motor, types on one-side linear-induction motor, bilateral linear-induction motor, linear-DC Motor on basic of the motor, linear-DC Motor for moving-coil type, linear-DC motor for permanent-magnet moving type, linear-DC motor for electricity non-utility type, linear-pulse motor for variable motor, linear-pulse motor for permanent magneto type, linear-vibration actuator, linear-vibration actuator for moving-coil type, linear synchronous motor, linear electromagnetic motor, linear electromagnetic solenoid, technical organization and magnetic levitation and linear motor and sensor.

  6. Linear ubiquitination in immunity.

    Shimizu, Yutaka; Taraborrelli, Lucia; Walczak, Henning

    2015-07-01

    Linear ubiquitination is a post-translational protein modification recently discovered to be crucial for innate and adaptive immune signaling. The function of linear ubiquitin chains is regulated at multiple levels: generation, recognition, and removal. These chains are generated by the linear ubiquitin chain assembly complex (LUBAC), the only known ubiquitin E3 capable of forming the linear ubiquitin linkage de novo. LUBAC is not only relevant for activation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs) in various signaling pathways, but importantly, it also regulates cell death downstream of immune receptors capable of inducing this response. Recognition of the linear ubiquitin linkage is specifically mediated by certain ubiquitin receptors, which is crucial for translation into the intended signaling outputs. LUBAC deficiency results in attenuated gene activation and increased cell death, causing pathologic conditions in both, mice, and humans. Removal of ubiquitin chains is mediated by deubiquitinases (DUBs). Two of them, OTULIN and CYLD, are constitutively associated with LUBAC. Here, we review the current knowledge on linear ubiquitination in immune signaling pathways and the biochemical mechanisms as to how linear polyubiquitin exerts its functions distinctly from those of other ubiquitin linkage types. © 2015 The Authors. Immunological Reviews Published by John Wiley & Sons Ltd.

  7. Educational Cosmic Ray Arrays

    Soluk, R. A.

    2006-01-01

    In the last decade a great deal of interest has arisen in using sparse arrays of cosmic ray detectors located at schools as a means of doing both outreach and physics research. This approach has the unique advantage of involving grade school students in an actual ongoing experiment, rather then a simple teaching exercise, while at the same time providing researchers with the basic infrastructure for installation of cosmic ray detectors. A survey is made of projects in North America and Europe and in particular the ALTA experiment at the University of Alberta which was the first experiment operating under this paradigm

  8. Storage array reflection considerations

    Haire, M.J.; Jordan, W.C.; Taylor, R.G.

    1997-01-01

    The assumptions used for reflection conditions of single containers are fairly well established and consistently applied throughout the industry in nuclear criticality safety evaluations. Containers are usually considered to be either fully water-reflected (i.e. surrounded by 6 to 12 in. of water) for safety calculations or reflected by 1 in. of water for nominal (structural material and air) conditions. Tables and figures are usually available for performing comparative evaluations of containers under various loading conditions. Reflection considerations used for evaluating the safety of storage arrays of fissile material are not as well established

  9. Linearizing W-algebras

    Krivonos, S.O.; Sorin, A.S.

    1994-06-01

    We show that the Zamolodchikov's and Polyakov-Bershadsky nonlinear algebras W 3 and W (2) 3 can be embedded as subalgebras into some linear algebras with finite set of currents. Using these linear algebras we find new field realizations of W (2) 3 and W 3 which could be a starting point for constructing new versions of W-string theories. We also reveal a number of hidden relationships between W 3 and W (2) 3 . We conjecture that similar linear algebras can exist for other W-algebra as well. (author). 10 refs

  10. Matrices and linear algebra

    Schneider, Hans

    1989-01-01

    Linear algebra is one of the central disciplines in mathematics. A student of pure mathematics must know linear algebra if he is to continue with modern algebra or functional analysis. Much of the mathematics now taught to engineers and physicists requires it.This well-known and highly regarded text makes the subject accessible to undergraduates with little mathematical experience. Written mainly for students in physics, engineering, economics, and other fields outside mathematics, the book gives the theory of matrices and applications to systems of linear equations, as well as many related t

  11. Linearity in Process Languages

    Nygaard, Mikkel; Winskel, Glynn

    2002-01-01

    The meaning and mathematical consequences of linearity (managing without a presumed ability to copy) are studied for a path-based model of processes which is also a model of affine-linear logic. This connection yields an affine-linear language for processes, automatically respecting open......-map bisimulation, in which a range of process operations can be expressed. An operational semantics is provided for the tensor fragment of the language. Different ways to make assemblies of processes lead to different choices of exponential, some of which respect bisimulation....

  12. Elements of linear space

    Amir-Moez, A R; Sneddon, I N

    1962-01-01

    Elements of Linear Space is a detailed treatment of the elements of linear spaces, including real spaces with no more than three dimensions and complex n-dimensional spaces. The geometry of conic sections and quadric surfaces is considered, along with algebraic structures, especially vector spaces and transformations. Problems drawn from various branches of geometry are given.Comprised of 12 chapters, this volume begins with an introduction to real Euclidean space, followed by a discussion on linear transformations and matrices. The addition and multiplication of transformations and matrices a

  13. Applied linear regression

    Weisberg, Sanford

    2013-01-01

    Praise for the Third Edition ""...this is an excellent book which could easily be used as a course text...""-International Statistical Institute The Fourth Edition of Applied Linear Regression provides a thorough update of the basic theory and methodology of linear regression modeling. Demonstrating the practical applications of linear regression analysis techniques, the Fourth Edition uses interesting, real-world exercises and examples. Stressing central concepts such as model building, understanding parameters, assessing fit and reliability, and drawing conclusions, the new edition illus

  14. Measuring the linear heat generation rate of a nuclear reactor fuel pin

    Smith, R.D.

    1981-01-01

    A miniature gamma thermometer is described which is capable of travelling through bores distributed in an array through a nuclear reactor core and measure the linear heat generation rate of the fuel pins. (U.K.)

  15. Analyzing Responses of Chemical Sensor Arrays

    Zhou, Hanying

    2007-01-01

    NASA is developing a third-generation electronic nose (ENose) capable of continuous monitoring of the International Space Station s cabin atmosphere for specific, harmful airborne contaminants. Previous generations of the ENose have been described in prior NASA Tech Briefs issues. Sensor selection is critical in both (prefabrication) sensor material selection and (post-fabrication) data analysis of the ENose, which detects several analytes that are difficult to detect, or that are at very low concentration ranges. Existing sensor selection approaches usually include limited statistical measures, where selectivity is more important but reliability and sensitivity are not of concern. When reliability and sensitivity can be major limiting factors in detecting target compounds reliably, the existing approach is not able to provide meaningful selection that will actually improve data analysis results. The approach and software reported here consider more statistical measures (factors) than existing approaches for a similar purpose. The result is a more balanced and robust sensor selection from a less than ideal sensor array. The software offers quick, flexible, optimal sensor selection and weighting for a variety of purposes without a time-consuming, iterative search by performing sensor calibrations to a known linear or nonlinear model, evaluating the individual sensor s statistics, scoring the individual sensor s overall performance, finding the best sensor array size to maximize class separation, finding optimal weights for the remaining sensor array, estimating limits of detection for the target compounds, evaluating fingerprint distance between group pairs, and finding the best event-detecting sensors.

  16. Array Phase Shifters: Theory and Technology

    Romanofsky, Robert R.

    2007-01-01

    While there are a myriad of applications for microwave phase shifters in instrumentation and metrology, power combining, amplifier linearization, and so on, the most prevalent use is in scanning phased-array antennas. And while this market continues to be dominated by military radar and tracking platforms, many commercial applications have emerged in the past decade or so. These new and potential applications span low-Earth-orbit (LEO) communications satellite constellations and collision warning radar, an aspect of the Intelligent Vehicle Highway System or Automated Highway System. In any case, the phase shifters represent a considerable portion of the overall antenna cost, with some estimates approaching 40 percent for receive arrays. Ferrite phase shifters continue to be the workhorse in military-phased arrays, and while there have been advances in thin film ferrite devices, the review of this device technology in the previous edition of this book is still highly relevant. This chapter will focus on three types of phase shifters that have matured in the past decade: GaAs MESFET monolithic microwave integrated circuit (MMIC), micro-electromechanical systems (MEMS), and thin film ferroelectric-based devices. A brief review of some novel devices including thin film ferrite phase shifters and superconducting switches for phase shifter applications will be provided. Finally, the effects of modulo 2 phase shift limitations, phase errors, and transient response on bit error rate degradation will be considered.

  17. Beam-intensity limitations in linear accelerators

    Jameson, R.A.

    1981-01-01

    Recent demand for high-intensity beams of various particles has renewed interest in the investigation of beam current and beam quality limits in linear RF and induction accelerators and beam-transport channels. Previous theoretical work is reviewed, and new work on beam matching and stability is outlined. There is a real need for extending the theory to handle the time evolution of beam emittance; some present work toward this goal is described. The role of physical constraints in channel intensity limitation is emphasized. Work on optimizing channel performance, particularly at low particle velocities, has resulted in major technological advances. The opportunities for combining such channels into arrays are discussed. 50 references

  18. Selecting Sums in Arrays

    Brodal, Gerth Stølting; Jørgensen, Allan Grønlund

    2008-01-01

    In an array of n numbers each of the \\binomn2+nUnknown control sequence '\\binom' contiguous subarrays define a sum. In this paper we focus on algorithms for selecting and reporting maximal sums from an array of numbers. First, we consider the problem of reporting k subarrays inducing the k largest...... sums among all subarrays of length at least l and at most u. For this problem we design an optimal O(n + k) time algorithm. Secondly, we consider the problem of selecting a subarray storing the k’th largest sum. For this problem we prove a time bound of Θ(n · max {1,log(k/n)}) by describing...... an algorithm with this running time and by proving a matching lower bound. Finally, we combine the ideas and obtain an O(n· max {1,log(k/n)}) time algorithm that selects a subarray storing the k’th largest sum among all subarrays of length at least l and at most u....

  19. Programmable cellular arrays. Faults testing and correcting in cellular arrays

    Cercel, L.

    1978-03-01

    A review of some recent researches about programmable cellular arrays in computing and digital processing of information systems is presented, and includes both combinational and sequential arrays, with full arbitrary behaviour, or which can realize better implementations of specialized blocks as: arithmetic units, counters, comparators, control systems, memory blocks, etc. Also, the paper presents applications of cellular arrays in microprogramming, in implementing of a specialized computer for matrix operations, in modeling of universal computing systems. The last section deals with problems of fault testing and correcting in cellular arrays. (author)

  20. Linear system theory

    Callier, Frank M.; Desoer, Charles A.

    1991-01-01

    The aim of this book is to provide a systematic and rigorous access to the main topics of linear state-space system theory in both the continuous-time case and the discrete-time case; and the I/O description of linear systems. The main thrusts of the work are the analysis of system descriptions and derivations of their properties, LQ-optimal control, state feedback and state estimation, and MIMO unity-feedback systems.

  1. Friend of GATA (FOG interacts with the nucleosome remodeling and deacetylase complex (NuRD to support primitive erythropoiesis in Xenopus laevis.

    Mizuho S Mimoto

    Full Text Available Friend of GATA (FOG plays many diverse roles in adult and embryonic hematopoiesis, however the mechanisms by which it functions and the roles of potential interaction partners are not completely understood. Previous work has shown that overexpression of FOG in Xenopus laevis causes loss of blood suggesting that in contrast to its role in mammals, FOG might normally function to repress erythropoiesis in this species. Using loss-of-function analysis, we demonstrate that FOG is essential to support primitive red blood cell (RBC development in Xenopus. Moreover, we show that it is specifically required to prevent excess apoptosis of circulating primitive RBCs and that in the absence of FOG, the pro-apoptotic gene Bim-1 is strongly upregulated. To identify domains of FOG that are essential for blood development and, conversely, to begin to understand the mechanism by which overexpressed FOG represses primitive erythropoiesis, we asked whether FOG mutants that are unable to interact with known co-factors retain their ability to rescue blood formation in FOG morphants and whether they repress erythropoiesis when overexpressed in wild type embryos. We find that interaction of FOG with the Nucleosome Remodeling and Deacetylase complex (NuRD, but not with C-terminal Binding Protein, is essential for normal primitive RBC development. In contrast, overexpression of all mutant and wild type constructs causes a comparable repression of primitive erythropoiesis. Together, our data suggest that a requirement for FOG and its interaction with NuRD during primitive erythropoiesis are conserved in Xenopus and that loss of blood upon FOG overexpression is due to a dominant-interfering effect.

  2. Friend of GATA (FOG) interacts with the nucleosome remodeling and deacetylase complex (NuRD) to support primitive erythropoiesis in Xenopus laevis.

    Mimoto, Mizuho S; Christian, Jan L

    2012-01-01

    Friend of GATA (FOG) plays many diverse roles in adult and embryonic hematopoiesis, however the mechanisms by which it functions and the roles of potential interaction partners are not completely understood. Previous work has shown that overexpression of FOG in Xenopus laevis causes loss of blood suggesting that in contrast to its role in mammals, FOG might normally function to repress erythropoiesis in this species. Using loss-of-function analysis, we demonstrate that FOG is essential to support primitive red blood cell (RBC) development in Xenopus. Moreover, we show that it is specifically required to prevent excess apoptosis of circulating primitive RBCs and that in the absence of FOG, the pro-apoptotic gene Bim-1 is strongly upregulated. To identify domains of FOG that are essential for blood development and, conversely, to begin to understand the mechanism by which overexpressed FOG represses primitive erythropoiesis, we asked whether FOG mutants that are unable to interact with known co-factors retain their ability to rescue blood formation in FOG morphants and whether they repress erythropoiesis when overexpressed in wild type embryos. We find that interaction of FOG with the Nucleosome Remodeling and Deacetylase complex (NuRD), but not with C-terminal Binding Protein, is essential for normal primitive RBC development. In contrast, overexpression of all mutant and wild type constructs causes a comparable repression of primitive erythropoiesis. Together, our data suggest that a requirement for FOG and its interaction with NuRD during primitive erythropoiesis are conserved in Xenopus and that loss of blood upon FOG overexpression is due to a dominant-interfering effect.

  3. Combinatorial aspects of covering arrays

    Charles J. Colbourn

    2004-11-01

    Full Text Available Covering arrays generalize orthogonal arrays by requiring that t -tuples be covered, but not requiring that the appearance of t -tuples be balanced.Their uses in screening experiments has found application in software testing, hardware testing, and a variety of fields in which interactions among factors are to be identified. Here a combinatorial view of covering arrays is adopted, encompassing basic bounds, direct constructions, recursive constructions, algorithmic methods, and applications.

  4. A general technique for characterizing x-ray position sensitive arrays

    Dufresne, E.; Bruning, R.; Sutton, M.; Stephenson, G.B.

    1994-03-01

    We present a general statistical technique for characterizing x-ray sensitive linear diode arrays and CCD arrays. We apply this technique to characterize the response of a linear diode array, Princeton Instrument model X-PDA, and a virtual phase CCD array, TI 4849, to direct illumination by x-rays. We find that the response of the linear array is linearly proportional to the incident intensity and uniform over its length to within 2 %. Its quantum efficiency is 38 % for Cu K α x-rays. The resolution function is evaluated from the spatial autocorrelation function and falls to 10 % of its peak value after one pixel. On the other hand, the response of the CCD detecting system to direct x-ray exposure is non-linear. To properly quantify the scattered x-rays, one must correct for the non- linearity. The resolution is two pixels along the serial transfer direction. We characterize the noise of the CCD and propose a model that takes into account the non-linearity and the resolution function to estimate the quantum efficiency of the detector. The quantum efficiency is 20 %

  5. Nanoelectrode array for electrochemical analysis

    Yelton, William G [Sandia Park, NM; Siegal, Michael P [Albuquerque, NM

    2009-12-01

    A nanoelectrode array comprises a plurality of nanoelectrodes wherein the geometric dimensions of the electrode controls the electrochemical response, and the current density is independent of time. By combining a massive array of nanoelectrodes in parallel, the current signal can be amplified while still retaining the beneficial geometric advantages of nanoelectrodes. Such nanoelectrode arrays can be used in a sensor system for rapid, non-contaminating field analysis. For example, an array of suitably functionalized nanoelectrodes can be incorporated into a small, integrated sensor system that can identify many species rapidly and simultaneously under field conditions in high-resistivity water, without the need for chemical addition to increase conductivity.

  6. Array architectures for iterative algorithms

    Jagadish, Hosagrahar V.; Rao, Sailesh K.; Kailath, Thomas

    1987-01-01

    Regular mesh-connected arrays are shown to be isomorphic to a class of so-called regular iterative algorithms. For a wide variety of problems it is shown how to obtain appropriate iterative algorithms and then how to translate these algorithms into arrays in a systematic fashion. Several 'systolic' arrays presented in the literature are shown to be specific cases of the variety of architectures that can be derived by the techniques presented here. These include arrays for Fourier Transform, Matrix Multiplication, and Sorting.

  7. Solar photovoltaic water pumping system using a new linear actuator

    Andrada Gascón, Pedro; Castro, Javier

    2007-01-01

    In this paper a photovoltaic solar pumping system using a new linear actuator is presented. This linear actuator is a double-sided flat two-phase variable-reluctance linear stepper motor that moves a piston-type water pump with the help of a rope, a pulley and a counterweight. The entire actuator pump ensemble is controlled by a simple electronic unit that manages the electric power generated by a photovoltaic array. The proposed system is suitable for rural communities in developing...

  8. Diagnosable structured logic array

    Whitaker, Sterling (Inventor); Miles, Lowell (Inventor); Gambles, Jody (Inventor); Maki, Gary K. (Inventor)

    2009-01-01

    A diagnosable structured logic array and associated process is provided. A base cell structure is provided comprising a logic unit comprising a plurality of input nodes, a plurality of selection nodes, and an output node, a plurality of switches coupled to the selection nodes, where the switches comprises a plurality of input lines, a selection line and an output line, a memory cell coupled to the output node, and a test address bus and a program control bus coupled to the plurality of input lines and the selection line of the plurality of switches. A state on each of the plurality of input nodes is verifiably loaded and read from the memory cell. A trusted memory block is provided. The associated process is provided for testing and verifying a plurality of truth table inputs of the logic unit.

  9. Low Frequency Space Array

    Dennison, B.; Weiler, K.W.; Johnston, K.J.

    1987-01-01

    The Low Frequency Space Array (LFSA) is a conceptual mission to survey the entire sky and to image individual sources at frequencies between 1.5 and 26 MHz, a frequency range over which the earth's ionosphere transmits poorly or not at all. With high resolution, high sensitivity observations, a new window will be opened in the electromagnetic spectrum for astronomical investigation. Also, extending observations down to such low frequencies will bring astronomy to the fundamental limit below which the galaxy becomes optically thick due to free-free absorption. A number of major scientific goals can be pursued with such a mission, including mapping galactic emission and absorption, studies of individual source spectra in a frequency range where a number of important processes may play a role, high resolution imaging of extended sources, localization of the impulsive emission from Jupiter, and a search for coherent emission processes. 19 references

  10. Scintillator detector array

    Cusano, D.A.; Dibianca, F.A.

    1981-01-01

    This patent application relates to a scintillator detector array for use in computerized tomography and comprises a housing including a plurality of chambers, the said housing having a front wall transmissive to x-rays and side walls opaque to x-rays, such as of tungsten and tantalum, a liquid scintillation medium including a soluble fluor, the solvent for the fluor being disposed in the chambers. The solvent comprises either an intrinsically high Z solvent or a solvent which has dissolved therein a high Z compound e.g. iodo or bromonaphthalene; or toluene, xylene or trimethylbenzene with a lead or tin alkyl dissolved therein. Also disposed about the chambers are a plurality of photoelectric devices. (author)

  11. Cascading Constrained 2-D Arrays using Periodic Merging Arrays

    Forchhammer, Søren; Laursen, Torben Vaarby

    2003-01-01

    We consider a method for designing 2-D constrained codes by cascading finite width arrays using predefined finite width periodic merging arrays. This provides a constructive lower bound on the capacity of the 2-D constrained code. Examples include symmetric RLL and density constrained codes...

  12. Networked Sensor Arrays

    Tighe, R. J.

    2002-01-01

    A set of independent radiation sensors, coupled with real-time data telemetry, offers the opportunity to run correlation algorithms for the sensor array as well as to incorporate non-radiological data into the system. This may enhance the overall sensitivity of the sensors and provide an opportunity to project the location of a source within the array. In collaboration with Lawrence Livermore National Laboratory (LLNL) and Sandia National Laboratories (SNL), we have conducted field experiments to test a prototype system. Combining the outputs of a set of distributed sensors permits the correlation that the independent sensor outputs. Combined with additional information such as traffic patterns and velocities, this can reduce random/false detections and enhance detection capability. The principle components of such a system include: (1) A set of radiation sensors. These may be of varying type and complexity, including gamma and/or neutron detectors, gross count and spectral-capable sensors, and low to high energy-resolution sensors. (2) A set of non-radiation sensors. These may include sensors such as vehicle presence and imaging sensors. (3) A communications architecture for near real-time telemetry. Depending upon existing infrastructure and bandwidth requirements, this may be a radio or hard-wire based system. (4) A central command console to pole the sensors, correlate their output, and display the data in a meaningful form to the system operator. Both sensitivity and selectivity are important considerations when evaluating the performance of a detection system. Depending on the application, the optimization of sensitivity as well as the rejection of ''nuisance'' radioactive sources may or may not be critical

  13. Further linear algebra

    Blyth, T S

    2002-01-01

    Most of the introductory courses on linear algebra develop the basic theory of finite­ dimensional vector spaces, and in so doing relate the notion of a linear mapping to that of a matrix. Generally speaking, such courses culminate in the diagonalisation of certain matrices and the application of this process to various situations. Such is the case, for example, in our previous SUMS volume Basic Linear Algebra. The present text is a continuation of that volume, and has the objective of introducing the reader to more advanced properties of vector spaces and linear mappings, and consequently of matrices. For readers who are not familiar with the contents of Basic Linear Algebra we provide an introductory chapter that consists of a compact summary of the prerequisites for the present volume. In order to consolidate the student's understanding we have included a large num­ ber of illustrative and worked examples, as well as many exercises that are strategi­ cally placed throughout the text. Solutions to the ex...

  14. Acoustic field of focusing phased array probe and the scanning system

    Murai, J.; Miura, S.; Ida, T.; Shiraiwa, T.; Miya, T.

    1997-01-01

    Acoustic field of a point focusing cylindrical linear array probe, in which focusing in the axial direction of cylinder is done by the phased linear array and focusing in the orthogonal direction is done geometrically, was studied by numerical calculation and an optimum design of phased array probe for focusing has been obtained. In generally speaking, the beam width at focus point decreases with decrease of width of each transducer element and with increase of synthetic aperture made by total elements. If the number of total array elements excited as one pulse is limited, the above conditions are contradicted. Thus, an optimum element width exists for the best focusing. On the above consideration, we can get focusing ability of phased array nearly as same as geometrical focusing. A developed transducer is a linear array of polymer piezoelectric material of cylindrical shape, of which radius is from 50 mm to 75 mm. The frequency is 10 Mhz and the beam width of 0.5 mm (depending on aperture) in the orthogonal direction to the cylinder axis and 0.7 mm width in the cylinder axis (phased array focusing) have been obtained. A delay circuit for exciting the transducer was newly designed to give maximum performance to the array regarding to accuracy, stability, easy control and etc. A c-scan ultrasonic testing system equipped with this transducer has sixteen times inspection speed compared to the single probe instrument.

  15. Dual-polarization, wideband microstrip antenna array for airborne C-band SAR

    Granholm, Johan; Skou, Niels

    2000-01-01

    The paper describes the development of a C-band, dual linear polarization wideband antenna array, for use in the next-generation of the Danish airborne polarimetric synthetic aperture radar (SAR) system. The array is made of probe-fed, stacked microstrip patches. The design and performance of the...... of the basic stacked patch element, operating from 4.9 GHz to 5.7 GHz, and a 2×2 element test array of these, are described.......The paper describes the development of a C-band, dual linear polarization wideband antenna array, for use in the next-generation of the Danish airborne polarimetric synthetic aperture radar (SAR) system. The array is made of probe-fed, stacked microstrip patches. The design and performance...

  16. Ring-array processor distribution topology for optical interconnects

    Li, Yao; Ha, Berlin; Wang, Ting; Wang, Sunyu; Katz, A.; Lu, X. J.; Kanterakis, E.

    1992-01-01

    The existing linear and rectangular processor distribution topologies for optical interconnects, although promising in many respects, cannot solve problems such as clock skews, the lack of supporting elements for efficient optical implementation, etc. The use of a ring-array processor distribution topology, however, can overcome these problems. Here, a study of the ring-array topology is conducted with an aim of implementing various fast clock rate, high-performance, compact optical networks for digital electronic multiprocessor computers. Practical design issues are addressed. Some proof-of-principle experimental results are included.

  17. Application of optical processing to adaptive phased array radar

    Carroll, C. W.; Vijaya Kumar, B. V. K.

    1988-01-01

    The results of the investigation of the applicability of optical processing to Adaptive Phased Array Radar (APAR) data processing will be summarized. Subjects that are covered include: (1) new iterative Fourier transform based technique to determine the array antenna weight vector such that the resulting antenna pattern has nulls at desired locations; (2) obtaining the solution of the optimal Wiener weight vector by both iterative and direct methods on two laboratory Optical Linear Algebra Processing (OLAP) systems; and (3) an investigation of the effects of errors present in OLAP systems on the solution vectors.

  18. Linear mass reflectron

    Mamyrin, B.A.; Shmikk, D.V.

    1979-01-01

    A description and operating principle of a linear mass reflectron with V-form trajectory of ion motion -a new non-magnetic time-of-flight mass spectrometer with high resolution are presented. The ion-optical system of the device consists of an ion source with ionization by electron shock, of accelerating gaps, reflector gaps, a drift space and ion detector. Ions move in the linear mass refraction along the trajectories parallel to the axis of the analyzer chamber. The results of investigations into the experimental device are given. With an ion drift length of 0.6 m the device resolution is 1200 with respect to the peak width at half-height. Small-sized mass spectrometric transducers with high resolution and sensitivity may be designed on the base of the linear mass reflectron principle

  19. Applied linear algebra

    Olver, Peter J

    2018-01-01

    This textbook develops the essential tools of linear algebra, with the goal of imparting technique alongside contextual understanding. Applications go hand-in-hand with theory, each reinforcing and explaining the other. This approach encourages students to develop not only the technical proficiency needed to go on to further study, but an appreciation for when, why, and how the tools of linear algebra can be used across modern applied mathematics. Providing an extensive treatment of essential topics such as Gaussian elimination, inner products and norms, and eigenvalues and singular values, this text can be used for an in-depth first course, or an application-driven second course in linear algebra. In this second edition, applications have been updated and expanded to include numerical methods, dynamical systems, data analysis, and signal processing, while the pedagogical flow of the core material has been improved. Throughout, the text emphasizes the conceptual connections between each application and the un...

  20. Theory of linear operations

    Banach, S

    1987-01-01

    This classic work by the late Stefan Banach has been translated into English so as to reach a yet wider audience. It contains the basics of the algebra of operators, concentrating on the study of linear operators, which corresponds to that of the linear forms a1x1 + a2x2 + ... + anxn of algebra.The book gathers results concerning linear operators defined in general spaces of a certain kind, principally in Banach spaces, examples of which are: the space of continuous functions, that of the pth-power-summable functions, Hilbert space, etc. The general theorems are interpreted in various mathematical areas, such as group theory, differential equations, integral equations, equations with infinitely many unknowns, functions of a real variable, summation methods and orthogonal series.A new fifty-page section (``Some Aspects of the Present Theory of Banach Spaces'''') complements this important monograph.