Blind information-theoretic multiuser detection algorithms for DS-CDMA and WCDMA downlink systems.

PubMed

Waheed, Khuram; Salem, Fathi M

2005-07-01

Code division multiple access (CDMA) is based on the spread-spectrum technology and is a dominant air interface for 2.5G, 3G, and future wireless networks. For the CDMA downlink, the transmitted CDMA signals from the base station (BS) propagate through a noisy multipath fading communication channel before arriving at the receiver of the user equipment/mobile station (UE/MS). Classical CDMA single-user detection (SUD) algorithms implemented in the UE/MS receiver do not provide the required performance for modern high data-rate applications. In contrast, multi-user detection (MUD) approaches require a lot of a priori information not available to the UE/MS. In this paper, three promising adaptive Riemannian contra-variant (or natural) gradient based user detection approaches, capable of handling the highly dynamic wireless environments, are proposed. The first approach, blind multiuser detection (BMUD), is the process of simultaneously estimating multiple symbol sequences associated with all the users in the downlink of a CDMA communication system using only the received wireless data and without any knowledge of the user spreading codes. This approach is applicable to CDMA systems with relatively short spreading codes but becomes impractical for systems using long spreading codes. We also propose two other adaptive approaches, namely, RAKE -blind source recovery (RAKE-BSR) and RAKE-principal component analysis (RAKE-PCA) that fuse an adaptive stage into a standard RAKE receiver. This adaptation results in robust user detection algorithms with performance exceeding the linear minimum mean squared error (LMMSE) detectors for both Direct Sequence CDMA (DS-CDMA) and wide-band CDMA (WCDMA) systems under conditions of congestion, imprecise channel estimation and unmodeled multiple access interference (MAI).

Distributed reservation-based code division multiple access

NASA Astrophysics Data System (ADS)

Wieselthier, J. E.; Ephremides, A.

1984-11-01

The use of spread spectrum signaling, motivated primarily by its antijamming capabilities in military applications, leads naturally to the use of Code Division Multiple Access (CDMA) techniques that permit the successful simultaneous transmission by a number of users over a wideband channel. In this paper we address some of the major issues that are associated with the design of multiple access protocols for spread spectrum networks. We then propose, analyze, and evaluate a distributed reservation-based multiple access protocol that does in fact exploit CDMA properties. Especially significant is the fact that no acknowledgment or feedback information from the destination is required (thus facilitating communication with a radio-silent mode), nor is any form of coordination among the users necessary.

Adaptive data rate SSMA system for personal and mobile satellite communications

NASA Technical Reports Server (NTRS)

Ikegami, Tetsushi; Takahashi, Takashi; Arakaki, Yoshiya; Wakana, Hiromitsu

1995-01-01

An adaptive data rate SSMA (spread spectrum multiple access) system is proposed for mobile and personal multimedia satellite communications without the aid of system control earth stations. This system has a constant occupied bandwidth and has variable data rates and processing gains to mitigate communication link impairments such as fading, rain attenuation and interference as well as to handle variable data rate on demand. Proof of concept hardware for 6MHz bandwidth transponder is developed, that uses offset-QPSK (quadrature phase shift keying) and MSK (minimum shift keying) for direct sequence spread spectrum modulation and handle data rates of 4k to 64kbps. The RS422 data interface, low rate voice and H.261 video codecs are installed. The receiver is designed with coherent matched filter technique to achieve fast code acquisition, AFC (automatic frequency control) and coherent detection with minimum hardware losses in a single matched filter circuit. This receiver structure facilitates variable data rate on demand during a call. This paper shows the outline of the proposed system and the performance of the prototype equipment.

Digital Construction and Characterization of Noise-like Spread Spectrum Signals

DTIC Science & Technology

2016-11-01

Digital Construction and Characterization of Noise -like Spread Spectrum Signals Donald C. Buzanowski II, Frederick J. Block, Thomas C. Royster MIT...Lincoln Laboratory Lexington, MA 02420 Abstract—A new method for generating digital noise -like spread spectrum signals is proposed. A standard binary...employing signals that are noise -like (e.g., [1]). Direct sequence spread spectrum (DSSS) signals provide benefits such as protection against jamming, low

Quadriphase DS-CDMA wireless communication systems employing the generalized detector

NASA Astrophysics Data System (ADS)

Tuzlukov, Vyacheslav

2012-05-01

Probability of bit-error Per performance of asynchronous direct-sequence code-division multiple-access (DS-CDMA) wireless communication systems employing the generalized detector (GD) constructed based on the generalized approach to signal processing in noise is analyzed. The effects of pulse shaping, quadriphase or direct sequence quadriphase shift keying (DS-QPSK) spreading, aperiodic spreading sequences are considered in DS-CDMA based on GD and compared with the coherent Neyman-Pearson receiver. An exact Per expression and several approximations: one using the characterristic function method, a simplified expression for the improved Gaussian approximation (IGA) and the simplified improved Gaussian approximation are derived. Under conditions typically satisfied in practice and even with a small number of interferers, the standard Gaussian approximation (SGA) for the multiple-access interference component of the GD statistic and Per performance is shown to be accurate. Moreover, the IGA is shown to reduce to the SGA for pulses with zero excess bandwidth. Second, the GD Per performance of quadriphase DS-CDMA is shown to be superior to that of bi-phase DS-CDMA. Numerical examples by Monte Carlo simulation are presented to illustrate the GD Per performance for square-root raised-cosine pulses and spreading factors of moderate to large values. Also, a superiority of GD employment in CDMA systems over the Neyman-Pearson receiver is demonstrated

Why is CDMA the solution for mobile satellite communication

NASA Technical Reports Server (NTRS)

Gilhousen, Klein S.; Jacobs, Irwin M.; Padovani, Roberto; Weaver, Lindsay A.

1989-01-01

It is demonstrated that spread spectrum Code Division Multiple Access (CDMA) systems provide an economically superior solution to satellite mobile communications by increasing the system maximum capacity with respect to single channel per carrier Frequency Division Multiple Access (FDMA) systems. Following the comparative analysis of CDMA and FDMA systems, the design of a model that was developed to test the feasibility of the approach and the performance of a spread spectrum system in a mobile environment. Results of extensive computer simulations as well as laboratory and field tests results are presented.

Short range spread-spectrum radiolocation system and method

DOEpatents

Smith, Stephen F.

2003-04-29

A short range radiolocation system and associated methods that allow the location of an item, such as equipment, containers, pallets, vehicles, or personnel, within a defined area. A small, battery powered, self-contained tag is provided to an item to be located. The tag includes a spread-spectrum transmitter that transmits a spread-spectrum code and identification information. A plurality of receivers positioned about the area receive signals from a transmitting tag. The position of the tag, and hence the item, is located by triangulation. The system employs three different ranging techniques for providing coarse, intermediate, and fine spatial position resolution. Coarse positioning information is provided by use of direct-sequence code phase transmitted as a spread-spectrum signal. Intermediate positioning information is provided by the use of a difference signal transmitted with the direct-sequence spread-spectrum code. Fine positioning information is provided by use of carrier phase measurements. An algorithm is employed to combine the three data sets to provide accurate location measurements.

Spectrum Sharing in an ISM Band: Outage Performance of a Hybrid DS/FH Spread Spectrum System with Beamforming

NASA Astrophysics Data System (ADS)

Li, Hanyu; Syed, Mubashir; Yao, Yu-Dong; Kamakaris, Theodoros

2009-12-01

This paper investigates spectrum sharing issues in the unlicensed industrial, scientific, and medical (ISM) bands. It presents a radio frequency measurement setup and measurement results in 2.4 GHz. It then develops an analytical model to characterize the coexistence interference in the ISM bands, based on radio frequency measurement results in the 2.4 GHz. Outage performance using the interference model is examined for a hybrid direct-sequence frequency-hopping spread spectrum system. The utilization of beamforming techniques in the system is also investigated, and a simplified beamforming model is proposed to analyze the system performance using beamforming. Numerical results show that beamforming significantly improves the system outage performance. The work presented in this paper provides a quantitative evaluation of signal outages in a spectrum sharing environment. It can be used as a tool in the development process for future dynamic spectrum access models as well as engineering designs for applications in unlicensed bands.

Space-Time Processing for Tactical Mobile Ad Hoc Networks

DTIC Science & Technology

2010-05-01

Spatial Diversity and Imperfect Channel Estimation on Wideband MC- DS - CDMA and MC- CDMA " IEEE Transactions on Communications, Vol. 57, No. 10, pp. 2988...include direct sequence code division multiple access ( DS - CDMA ), Frequency Hopped (FH) CDMA and Orthogonal Frequency Division Multiple Access (OFDMA...capability, LPD/LPI, and operability in non-continuous spectrum. In addition, FH- CDMA is robust to the near-far problem, while DS - CDMA requires

Utilizing Spectrum Efficiently (USE)

DTIC Science & Technology

2011-02-28

18 4.8 Space-Time Coded Asynchronous DS - CDMA with Decentralized MAI Suppression: Performance and...numerical results. 4.8 Space-Time Coded Asynchronous DS - CDMA with Decentralized MAI Suppression: Performance and Spectral Efficiency In [60] multiple...supported at a given signal-to-interference ratio in asynchronous direct-sequence code-division multiple-access ( DS - CDMA ) sys- tems was examined. It was

Full Duplex, Spread Spectrum Radio System

NASA Technical Reports Server (NTRS)

Harvey, Bruce A.

2000-01-01

The goal of this project was to support the development of a full duplex, spread spectrum voice communications system. The assembly and testing of a prototype system consisting of a Harris PRISM spread spectrum radio, a TMS320C54x signal processing development board and a Zilog Z80180 microprocessor was underway at the start of this project. The efforts under this project were the development of multiple access schemes, analysis of full duplex voice feedback delays, and the development and analysis of forward error correction (FEC) algorithms. The multiple access analysis involved the selection between code division multiple access (CDMA), frequency division multiple access (FDMA) and time division multiple access (TDMA). Full duplex voice feedback analysis involved the analysis of packet size and delays associated with full loop voice feedback for confirmation of radio system performance. FEC analysis included studies of the performance under the expected burst error scenario with the relatively short packet lengths, and analysis of implementation in the TMS320C54x digital signal processor. When the capabilities and the limitations of the components used were considered, the multiple access scheme chosen was a combination TDMA/FDMA scheme that will provide up to eight users on each of three separate frequencies. Packets to and from each user will consist of 16 samples at a rate of 8,000 samples per second for a total of 2 ms of voice information. The resulting voice feedback delay will therefore be 4 - 6 ms. The most practical FEC algorithm for implementation was a convolutional code with a Viterbi decoder. Interleaving of the bits of each packet will be required to offset the effects of burst errors.

Spread-Spectrum Beamforming and Clutter Filtering for Plane-Wave Color Doppler Imaging.

PubMed

Mansour, Omar; Poepping, Tamie L; Lacefield, James C

2016-07-21

Plane-wave imaging is desirable for its ability to achieve high frame rates, allowing the capture of fast dynamic events and continuous Doppler data. In most implementations of plane-wave imaging, multiple low-resolution images from different plane wave tilt angles are compounded to form a single high-resolution image, thereby reducing the frame rate. Compounding improves the lateral beam profile in the high-resolution image, but it also acts as a low-pass filter in slow time that causes attenuation and aliasing of signals with high Doppler shifts. This paper introduces a spread-spectrum color Doppler imaging method that produces high-resolution images without the use of compounding, thereby eliminating the tradeoff between beam quality, maximum unaliased Doppler frequency, and frame rate. The method uses a long, random sequence of transmit angles rather than a linear sweep of plane wave directions. The random angle sequence randomizes the phase of off-focus (clutter) signals, thereby spreading the clutter power in the Doppler spectrum, while keeping the spectrum of the in-focus signal intact. The ensemble of randomly tilted low-resolution frames also acts as the Doppler ensemble, so it can be much longer than a conventional linear sweep, thereby improving beam formation while also making the slow-time Doppler sampling frequency equal to the pulse repetition frequency. Experiments performed using a carotid artery phantom with constant flow demonstrate that the spread-spectrum method more accurately measures the parabolic flow profile of the vessel and outperforms conventional plane-wave Doppler in both contrast resolution and estimation of high flow velocities. The spread-spectrum method is expected to be valuable for Doppler applications that require measurement of high velocities at high frame rates.

Direct-Sequence Spread Spectrum System

DTIC Science & Technology

1990-06-01

by directly modulating a conventional narrowband frequency-modulated (FM) carrier by a high rate digital code. The direct modulation is binary phase ...specification of the DSSS system will not be developed. The results of the evaluation phase of this research will be compared against theoretical...spread spectrum is called binary phase -shift keying 19 (BPSK). BPSK is a modulation in which a binary Ŕ" represents a 0-degree relative phase

Adaptive Digital Signature Design and Short-Data-Record Adaptive Filtering

DTIC Science & Technology

2008-04-01

rate BPSK binary phase shift keying CA − CFAR cell averaging− constant false alarm rate CDMA code − division multiple − access CFAR constant false...Cotae, “Spreading sequence design for multiple cell synchronous DS-CDMA systems under total weighted squared correlation criterion,” EURASIP Journal...415-428, Mar. 2002. [6] P. Cotae, “Spreading sequence design for multiple cell synchronous DS-CDMA systems under total weighted squared correlation

Theoretical analysis of the performance of code division multiple access communications over multimode optical fiber channels. Part 1: Transmission and detection

NASA Astrophysics Data System (ADS)

Walker, Ernest L.

1994-05-01

This paper presents results of a theoretical investigation to evaluate the performance of code division multiple access communications over multimode optical fiber channels in an asynchronous, multiuser communication network environment. The system is evaluated using Gold sequences for spectral spreading of the baseband signal from each user employing direct-sequence biphase shift keying and intensity modulation techniques. The transmission channel model employed is a lossless linear system approximation of the field transfer function for the alpha -profile multimode optical fiber. Due to channel model complexity, a correlation receiver model employing a suboptimal receive filter was used in calculating the peak output signal at the ith receiver. In Part 1, the performance measures for the system, i.e., signal-to-noise ratio and bit error probability for the ith receiver, are derived as functions of channel characteristics, spectral spreading, number of active users, and the bit energy to noise (white) spectral density ratio. In Part 2, the overall system performance is evaluated.

DS-SS with de Bruijn sequences for secure Inter Satellite Links

NASA Astrophysics Data System (ADS)

Spinsante, S.; Warty, C.; Gambi, E.

Today, both the military and commercial sectors are placing an increased emphasis on global communications. This has prompted the development of several Low Earth Orbit satellite systems that promise a worldwide connectivity and real-time voice, data and video communications. Constellations that avoid repeated uplink and downlink work by exploiting Inter Satellite Links have proved to be very economical in space routing. However, traditionally Inter Satellite Links were considered to be out of reach for any malicious activity and thus little, or no security was employed. This paper proposes a secured Inter Satellite Links based network, built upon the adoption of the Direct Sequence Spread Spectrum technique, with binary de Bruijn sequences used as spreading codes. Selected sequences from the de Bruijn family may be used over directional spot beams. The main intent of the paper is to propose a secure and robust communication link for the next generation of satellite communications, relying on a classical spread spectrum approach employing innovative sequences.

Investigating effects of communications modulation technique on targeting performance

NASA Astrophysics Data System (ADS)

Blasch, Erik; Eusebio, Gerald; Huling, Edward

2006-05-01

One of the key challenges facing the global war on terrorism (GWOT) and urban operations is the increased need for rapid and diverse information from distributed sources. For users to get adequate information on target types and movements, they would need reliable data. In order to facilitate reliable computational intelligence, we seek to explore the communication modulation tradeoffs affecting information distribution and accumulation. In this analysis, we explore the modulation techniques of Orthogonal Frequency Division Multiplexing (OFDM), Direct Sequence Spread Spectrum (DSSS), and statistical time-division multiple access (TDMA) as a function of the bit error rate and jitter that affect targeting performance. In the analysis, we simulate a Link 16 with a simple bandpass frequency shift keying (PSK) technique using different Signal-to-Noise ratios. The communications transfer delay and accuracy tradeoffs are assessed as to the effects incurred in targeting performance.

Wireless rake-receiver using adaptive filter with a family of partial update algorithms in noise cancellation applications

NASA Astrophysics Data System (ADS)

Fayadh, Rashid A.; Malek, F.; Fadhil, Hilal A.; Aldhaibani, Jaafar A.; Salman, M. K.; Abdullah, Farah Salwani

2015-05-01

For high data rate propagation in wireless ultra-wideband (UWB) communication systems, the inter-symbol interference (ISI), multiple-access interference (MAI), and multiple-users interference (MUI) are influencing the performance of the wireless systems. In this paper, the rake-receiver was presented with the spread signal by direct sequence spread spectrum (DS-SS) technique. The adaptive rake-receiver structure was shown with adjusting the receiver tap weights using least mean squares (LMS), normalized least mean squares (NLMS), and affine projection algorithms (APA) to support the weak signals by noise cancellation and mitigate the interferences. To minimize the data convergence speed and to reduce the computational complexity by the previous algorithms, a well-known approach of partial-updates (PU) adaptive filters were employed with algorithms, such as sequential-partial, periodic-partial, M-max-partial, and selective-partial updates (SPU) in the proposed system. The simulation results of bit error rate (BER) versus signal-to-noise ratio (SNR) are illustrated to show the performance of partial-update algorithms that have nearly comparable performance with the full update adaptive filters. Furthermore, the SPU-partial has closed performance to the full-NLMS and full-APA while the M-max-partial has closed performance to the full-LMS updates algorithms.

Spread-Spectrum Carrier Estimation With Unknown Doppler Shift

NASA Technical Reports Server (NTRS)

DeLeon, Phillip L.; Scaife, Bradley J.

1998-01-01

We present a method for the frequency estimation of a BPSK modulated, spread-spectrum carrier with unknown Doppler shift. The approach relies on a classic periodogram in conjunction with a spectral matched filter. Simulation results indicate accurate carrier estimation with processing gains near 40. A DSP-based prototype has been implemented for real-time carrier estimation for use in New Mexico State University's proposal for NASA's Demand Assignment Multiple Access service.

High security chaotic multiple access scheme for visible light communication systems with advanced encryption standard interleaving

NASA Astrophysics Data System (ADS)

Qiu, Junchao; Zhang, Lin; Li, Diyang; Liu, Xingcheng

2016-06-01

Chaotic sequences can be applied to realize multiple user access and improve the system security for a visible light communication (VLC) system. However, since the map patterns of chaotic sequences are usually well known, eavesdroppers can possibly derive the key parameters of chaotic sequences and subsequently retrieve the information. We design an advanced encryption standard (AES) interleaving aided multiple user access scheme to enhance the security of a chaotic code division multiple access-based visible light communication (C-CDMA-VLC) system. We propose to spread the information with chaotic sequences, and then the spread information is interleaved by an AES algorithm and transmitted over VLC channels. Since the computation complexity of performing inverse operations to deinterleave the information is high, the eavesdroppers in a high speed VLC system cannot retrieve the information in real time; thus, the system security will be enhanced. Moreover, we build a mathematical model for the AES-aided VLC system and derive the theoretical information leakage to analyze the system security. The simulations are performed over VLC channels, and the results demonstrate the effectiveness and high security of our presented AES interleaving aided chaotic CDMA-VLC system.

Thermal signature identification system (TheSIS): a spread spectrum temperature cycling method

NASA Astrophysics Data System (ADS)

Merritt, Scott

2015-03-01

NASA GSFC's Thermal Signature Identification System (TheSIS) 1) measures the high order dynamic responses of optoelectronic components to direct sequence spread-spectrum temperature cycling, 2) estimates the parameters of multiple autoregressive moving average (ARMA) or other models the of the responses, 3) and selects the most appropriate model using the Akaike Information Criterion (AIC). Using the AIC-tested model and parameter vectors from TheSIS, one can 1) select high-performing components on a multivariate basis, i.e., with multivariate Figures of Merit (FOMs), 2) detect subtle reversible shifts in performance, and 3) investigate irreversible changes in component or subsystem performance, e.g. aging. We show examples of the TheSIS methodology for passive and active components and systems, e.g. fiber Bragg gratings (FBGs) and DFB lasers with coupled temperature control loops, respectively.

Information hiding technique

NASA Astrophysics Data System (ADS)

Younger, Michael; Budulas, Peter P.; Young, Stuart H.

2002-08-01

Spread spectrum communication techniques have been recognized as a viable method to gain an advantage in interference environments. Many military-oriented systems have been initiated, and some civil systems have been attempted. Spread spectrum allows the ability to hide the signal of interest below or in the noise floor, so as not to be detected. A spread spectrum system is one in which the transmitted signal is spread over a wide frequency band, much wider, in fact, than the minimum bandwidth required to transmit the information being sent. We at Army Research Lab (ARL) are proposing using the same technique on the Internet with port hopping. The information would be transmitted in data packets over multiple ports. The port used would vary per packet or per session basis. This port hopping gives you and the recipients the ability to take datagram's and spread them out over a multitude of ports. This will hide information among the Internet noise. This will allow trusted communications between the transmitter and receiver because of the port coding sequence. There are 64K possible ports to span datagram. Jamming of transmission would be limiting the ability of the sniffer/listener. Also, the listener will find it difficult to use a man in the middle attach, since the data will be spread over multiple ports and only the receiver and transmitter will know the specific port sequencing for the datagram.

Orthogonal Multi-Carrier DS-CDMA with Frequency-Domain Equalization

NASA Astrophysics Data System (ADS)

Tanaka, Ken; Tomeba, Hiromichi; Adachi, Fumiyuki

Orthogonal multi-carrier direct sequence code division multiple access (orthogonal MC DS-CDMA) is a combination of orthogonal frequency division multiplexing (OFDM) and time-domain spreading, while multi-carrier code division multiple access (MC-CDMA) is a combination of OFDM and frequency-domain spreading. In MC-CDMA, a good bit error rate (BER) performance can be achieved by using frequency-domain equalization (FDE), since the frequency diversity gain is obtained. On the other hand, the conventional orthogonal MC DS-CDMA fails to achieve any frequency diversity gain. In this paper, we propose a new orthogonal MC DS-CDMA that can obtain the frequency diversity gain by applying FDE. The conditional BER analysis is presented. The theoretical average BER performance in a frequency-selective Rayleigh fading channel is evaluated by the Monte-Carlo numerical computation method using the derived conditional BER and is confirmed by computer simulation of the orthogonal MC DS-CDMA signal transmission.

Energy efficiency in wireless communication systems

DOEpatents

Caffrey, Michael Paul; Palmer, Joseph McRae

2012-12-11

Wireless communication systems and methods utilize one or more remote terminals, one or more base terminals, and a communication channel between the remote terminal(s) and base terminal(s). The remote terminal applies a direct sequence spreading code to a data signal at a spreading factor to provide a direct sequence spread spectrum (DSSS) signal. The DSSS signal is transmitted over the communication channel to the base terminal which can be configured to despread the received DSSS signal by a spreading factor matching the spreading factor utilized to spread the data signal. The remote terminal and base terminal can dynamically vary the matching spreading factors to adjust the data rate based on an estimation of operating quality over time between the remote terminal and base terminal such that the amount of data being transmitted is substantially maximized while providing a specified quality of service.

Spread Spectrum Receiver Electromagnetic Interference (EMI) Test Guide

NASA Technical Reports Server (NTRS)

Wheeler, Mark L.

1998-01-01

This program consisted of: (1) a study to define appropriate EMI test guidelines and test methods for direct sequence (DS) spread spectrum receivers; and (2) preparation of a written test guide to document the recommended test methods. The scope of this test guide includes: (1) a discussion of generic DS receiver performance characteristics; (2) a summary of S-band TDRSS receiver operation; (3) a discussion of DS receiver EMI susceptibility mechanisms and characteristics; (4) a summary of military standard test guidelines; (5) recommended test approach and methods; and (6) general conclusions and recommendations for future studies in the area of spread spectrum receiver testing.

FIR Filter of DS-CDMA UWB Modem Transmitter

NASA Astrophysics Data System (ADS)

Kang, Kyu-Min; Cho, Sang-In; Won, Hui-Chul; Choi, Sang-Sung

This letter presents low-complexity digital pulse shaping filter structures of a direct sequence code division multiple access (DS-CDMA) ultra wide-band (UWB) modem transmitter with a ternary spreading code. The proposed finite impulse response (FIR) filter structures using a look-up table (LUT) have the effect of saving the amount of memory by about 50% to 80% in comparison to the conventional FIR filter structures, and consequently are suitable for a high-speed parallel data process.

Spread-Spectrum Communications.

DTIC Science & Technology

1984-08-07

Articles M. B. Parsley and H. F. A. Roefs, "Numerical evaluation of correlation parameters for optimal phases of binary shift-register sequences," IEEE...Transactions on Communications, Vol. COM-27, pp. 1597-1604, October 1979. D. V. Sarwate and M. B. Parsley , "Crcuecorrehation proets Of psuoadmand related...Signal Processing, Vol. 128, pp. 104-109, April 1981. * M. B. Parsley , D. V. Sarwate, and W. E. Stark, ’Error probability for direct-sequence spread

Novel Maximum-based Timing Acquisition for Spread-Spectrum Communications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sibbetty, Taylor; Moradiz, Hussein; Farhang-Boroujeny, Behrouz

This paper proposes and analyzes a new packet detection and timing acquisition method for spread spectrum systems. The proposed method provides an enhancement over the typical thresholding techniques that have been proposed for direct sequence spread spectrum (DS-SS). The effective implementation of thresholding methods typically require accurate knowledge of the received signal-to-noise ratio (SNR), which is particularly difficult to estimate in spread spectrum systems. Instead, we propose a method which utilizes a consistency metric of the location of maximum samples at the output of a filter matched to the spread spectrum waveform to achieve acquisition, and does not require knowledgemore » of the received SNR. Through theoretical study, we show that the proposed method offers a low probability of missed detection over a large range of SNR with a corresponding probability of false alarm far lower than other methods. Computer simulations that corroborate our theoretical results are also presented. Although our work here has been motivated by our previous study of a filter bank multicarrier spread-spectrum (FB-MC-SS) system, the proposed method is applicable to DS-SS systems as well.« less

Interuser Interference Analysis for Direct-Sequence Spread-Spectrum Systems Part I: Partial-Period Cross-Correlation

NASA Technical Reports Server (NTRS)

Ni, Jianjun (David)

2012-01-01

This presentation discusses an analysis approach to evaluate the interuser interference for Direct-Sequence Spread-Spectrum (DSSS) Systems for Space Network (SN) Users. Part I of this analysis shows that the correlation property of pseudo noise (PN) sequences is the critical factor which determines the interuser interference performance of the DSSS system. For non-standard DSSS systems in which PN sequence s period is much larger than one data symbol duration, it is the partial-period cross-correlation that determines the system performance. This study reveals through an example that a well-designed PN sequence set (e.g. Gold Sequence, in which the cross-correlation for a whole-period is well controlled) may have non-controlled partial-period cross-correlation which could cause severe interuser interference for a DSSS system. Since the analytical derivation of performance metric (bit error rate or signal-to-noise ratio) based on partial-period cross-correlation is prohibitive, the performance degradation due to partial-period cross-correlation will be evaluated using simulation in Part II of this analysis in the future.

Low-Power Direct-Sequence Spread-Spectrum Modem Architecture for Distributed Wireless Sensor Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chien, C; Elgorriaga, I; McConaghy, C

2001-07-03

Emerging CMOS and MEMS technologies enable the implementation of a large number of wireless distributed microsensors that can be easily and rapidly deployed to form highly redundant, self-configuring, and ad hoc sensor networks. To facilitate ease of deployment, these sensors should operate on battery for extended periods of time. A particular challenge in maintaining extended battery lifetime lies in achieving communications with low power. This paper presents a direct-sequence spread-spectrum modem architecture that provides robust communications for wireless sensor networks while dissipating very low power. The modem architecture has been verified in an FPGA implementation that dissipates only 33 mWmore » for both transmission and reception. The implementation can be easily mapped to an ASIC technology, with an estimated power performance of less than 1 mW.« less

Spread Spectrum Receiver Electromagnetic Interference (EMI) Test Guide

NASA Technical Reports Server (NTRS)

Wheeler, M. L.

1998-01-01

The objective of this test guide is to document appropriate unit level test methods and techniques for the performance of EMI testing of Direct Sequence (DS) spread spectrum receivers. Consideration of EMI test methods tailored for spread spectrum receivers utilizing frequency spreading, techniques other than direct sequence (such as frequency hopping, frequency chirping, and various hybrid methods) is beyond the scope of this test guide development program and is not addressed as part of this document EMI test requirements for NASA programs are primarily developed based on the requirements contained in MIL-STD-46 1 D (or earlier revisions of MIL-STD-46 1). The corresponding test method guidelines for the MIL-STD-461 D tests are provided in MIL-STD-462D. These test methods are well documented with the exception of the receiver antenna port susceptibility tests (intermodulation, cross modulation, and rejection of undesired signals) which must be tailored to the specific type of receiver that is being tested. Thus, test methods addressed in this guide consist only of antenna port tests designed to evaluate receiver susceptibility characteristics. MIL-STD-462D should be referred for guidance pertaining to test methods for EMI tests other than the antenna port tests. The scope of this test guide includes: (1) a discussion of generic DS receiver performance characteristics; (2) a summary of S-band TDRSS receiver operation; (3) a discussion of DS receiver EMI susceptibility mechanisms and characteristics; (4) a summary of military standard test guidelines; (5) recommended test approach and methods; and (6) general conclusions and recommendations for future studies in the area of spread spectrum receiver testing.

Optimization of training sequence for DFT-spread DMT signal in optical access network with direct detection utilizing DML.

PubMed

Li, Fan; Li, Xinying; Yu, Jianjun; Chen, Lin

2014-09-22

We experimentally demonstrated the transmission of 79.86-Gb/s discrete-Fourier-transform spread 32 QAM discrete multi-tone (DFT-spread 32 QAM-DMT) signal over 20-km standard single-mode fiber (SSMF) utilizing directly modulated laser (DML). The experimental results show DFT-spread effectively reduces Peak-to-Average Power Ratio (PAPR) of DMT signal, and also well overcomes narrowband interference and high frequencies power attenuation. We compared different types of training sequence (TS) symbols and found that the optimized TS for channel estimation is the symbol with digital BPSK/QPSK modulation format due to its best performance against optical link noise during channel estimation.

Wideband Channel Modeling in Real Atmospheric Environments with Experimental Evaluation

DTIC Science & Technology

2013-04-01

5] D. F. Gingras and P. Gerstoft. 1997. “The Effect of Propagation on Wideband DS - CDMA Systems in the Suburban Environment,” The First IEEE...are commonly used in spread spectrum communication systems such as Code Division Multiple Access ( CDMA ) systems. Narrowband interference mitigation

Predicting impact of multi-paths on phase change in map-based vehicular ad hoc networks

NASA Astrophysics Data System (ADS)

Rahmes, Mark; Lemieux, George; Sonnenberg, Jerome; Chester, David B.

2014-05-01

Dynamic Spectrum Access, which through its ability to adapt the operating frequency of a radio, is widely believed to be a solution to the limited spectrum problem. Mobile Ad Hoc Networks (MANETs) can extend high capacity mobile communications over large areas where fixed and tethered-mobile systems are not available. In one use case with high potential impact cognitive radio employs spectrum sensing to facilitate identification of allocated frequencies not currently accessed by their primary users. Primary users own the rights to radiate at a specific frequency and geographic location, secondary users opportunistically attempt to radiate at a specific frequency when the primary user is not using it. We quantify optimal signal detection in map based cognitive radio networks with multiple rapidly varying phase changes and multiple orthogonal signals. Doppler shift occurs due to reflection, scattering, and rapid vehicle movement. Path propagation as well as vehicle movement produces either constructive or destructive interference with the incident wave. Our signal detection algorithms can assist the Doppler spread compensation algorithm by deciding how many phase changes in signals are present in a selected band of interest. Additionally we can populate a spatial radio environment map (REM) database with known information that can be leveraged in an ad hoc network to facilitate Dynamic Spectrum Access. We show how topography can help predict the impact of multi-paths on phase change, as well as about the prediction from dense traffic areas. Utilization of high resolution geospatial data layers in RF propagation analysis is directly applicable.

FBMC receiver for multi-user asynchronous transmission on fragmented spectrum

NASA Astrophysics Data System (ADS)

Doré, Jean-Baptiste; Berg, Vincent; Cassiau, Nicolas; Kténas, Dimitri

2014-12-01

Relaxed synchronization and access to fragmented spectrum are considered for future generations of wireless networks. Frequency division multiple access for filter bank multicarrier (FBMC) modulation provides promising performance without strict synchronization requirements contrary to conventional orthogonal frequency division multiplexing (OFDM). The architecture of a FBMC receiver suitable for this scenario is considered. Carrier frequency offset (CFO) compensation is combined with intercarrier interference (ICI) cancellation and performs well under very large frequency offsets. Channel estimation and interpolation had to be adapted and proved effective even for heavily fragmented spectrum usage. Channel equalization can sustain large delay spread. Because all the receiver baseband signal processing functionalities are proposed in the frequency domain, the overall architecture is suitable for multiuser asynchronous transmission on fragmented spectrum.

Performance analysis of an all-digital BPSK direct sequence spread-spectrum IF receiver architecture

NASA Astrophysics Data System (ADS)

Chung, Bong-Young; Chien, Charles; Samueli, Henry; Jain, Rajeev

1993-09-01

A VLSI architecture for an all-digital binary phase shift keyed (BPSK) direct-sequence (DS) spread spectrum (SS) IF receiver is presented, and an in-depth performance analysis is given. The all-digital architecture incorporates a Costar loop for carrier recovery and a delay-locked loop for clock recovery. For the PN acquisition block, a robust energy detection scheme is proposed to reduce false PN locks over a broad range of signal-to-noise ratios. The proposed architecture is intended for use in the 902-928 MHz unlicensed spread spectrum radio band. A 100 kbs information rate and a 12.7 Mchips/second PN code rate are assumed. The IF center frequency is 12.7 MHz and the IF sampling rate is 50.8 Msamples/ second, which is the Nyquist rate for the 25.4 MHz bandwidth signal. Finite wordlength effects have been simulated to optimize the architecture, thereby minimizing the chip area, and results of the finite wordlength simulations demonstrate that the chip architecture achieves a bit error rate performance within 1 dB of theory in an additive white Gaussian noise channel. The probability of PN acquisition within 5 ms is approximately 56% at -17 dB IF input SNR and 82% at -11 dB IF input SNR.

100 Gbps Wireless System and Circuit Design Using Parallel Spread-Spectrum Sequencing

NASA Astrophysics Data System (ADS)

Scheytt, J. Christoph; Javed, Abdul Rehman; Bammidi, Eswara Rao; KrishneGowda, Karthik; Kallfass, Ingmar; Kraemer, Rolf

2017-09-01

In this article mixed analog/digital signal processing techniques based on parallel spread-spectrum sequencing (PSSS) and radio frequency (RF) carrier synchronization for ultra-broadband wireless communication are investigated on system and circuit level.

Direct Sequence Spread Spectrum (DSSS) Receiver, User Manual

DTIC Science & Technology

2008-01-01

sampled data is clocked in to correlator data registers and a comparison is made between the code and data register contents, producing a correlation ...symbol (equal to the processing gain Gp ) but need not be otherwise synchronised with the spreading codes . This allows a very long and noise- like PRBS...and Q channels are independently but synchronously sampled . Complex Real ADC FIR Filter Interpolator Acquisition Correlators

Multiple Signal Classification for Determining Direction of Arrival of Frequency Hopping Spread Spectrum Signals

DTIC Science & Technology

2014-03-27

42 4.2.3 Number of Hops Hs . . . . . . . . . . . . . . . . . . . . . . . . . 45 4.2.4 Number of Sensors M... 45 4.5 Standard deviation vs. Ns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4.6 Bias...laboratory MTM multiple taper method MUSIC multiple signal classification MVDR minimum variance distortionless reposnse PSK phase shift keying QAM

Channel coding for underwater acoustic single-carrier CDMA communication system

NASA Astrophysics Data System (ADS)

Liu, Lanjun; Zhang, Yonglei; Zhang, Pengcheng; Zhou, Lin; Niu, Jiong

2017-01-01

CDMA is an effective multiple access protocol for underwater acoustic networks, and channel coding can effectively reduce the bit error rate (BER) of the underwater acoustic communication system. For the requirements of underwater acoustic mobile networks based on CDMA, an underwater acoustic single-carrier CDMA communication system (UWA/SCCDMA) based on the direct-sequence spread spectrum is proposed, and its channel coding scheme is studied based on convolution, RA, Turbo and LDPC coding respectively. The implementation steps of the Viterbi algorithm of convolutional coding, BP and minimum sum algorithms of RA coding, Log-MAP and SOVA algorithms of Turbo coding, and sum-product algorithm of LDPC coding are given. An UWA/SCCDMA simulation system based on Matlab is designed. Simulation results show that the UWA/SCCDMA based on RA, Turbo and LDPC coding have good performance such that the communication BER is all less than 10-6 in the underwater acoustic channel with low signal to noise ratio (SNR) from -12 dB to -10dB, which is about 2 orders of magnitude lower than that of the convolutional coding. The system based on Turbo coding with Log-MAP algorithm has the best performance.

Adaptive spread spectrum receiver using acoustic surface wave technology

NASA Astrophysics Data System (ADS)

Das, P.; Milstein, L. B.

1984-05-01

This technical report summarizes the results of the research we have been engaged in regarding the use of surface acoustic wave devices in direct sequence spread spectrum receivers. The heart of this research has been the use of the device as a real-time Fourier transformer. A system of this type is sometimes referred to as a compressive receiver, and our use of the system has been primarily as a means to implement a narrowband interference rejection filter. In addition, we have studied many other topics such as rapid acquisition, Hilbert transform generation, etc. and these topics are all overviewed in this report.

Performance Analysis of Direct-Sequence Code-Division Multiple-Access Communications with Asymmetric Quadrature Phase-Shift-Keying Modulation

NASA Technical Reports Server (NTRS)

Wang, C.-W.; Stark, W.

2005-01-01

This article considers a quaternary direct-sequence code-division multiple-access (DS-CDMA) communication system with asymmetric quadrature phase-shift-keying (AQPSK) modulation for unequal error protection (UEP) capability. Both time synchronous and asynchronous cases are investigated. An expression for the probability distribution of the multiple-access interference is derived. The exact bit-error performance and the approximate performance using a Gaussian approximation and random signature sequences are evaluated by extending the techniques used for uniform quadrature phase-shift-keying (QPSK) and binary phase-shift-keying (BPSK) DS-CDMA systems. Finally, a general system model with unequal user power and the near-far problem is considered and analyzed. The results show that, for a system with UEP capability, the less protected data bits are more sensitive to the near-far effect that occurs in a multiple-access environment than are the more protected bits.

GLOBECOM '86 - Global Telecommunications Conference, Houston, TX, Dec. 1-4, 1986, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

Papers are presented on local area networks; formal methods for communication protocols; computer simulation of communication systems; spread spectrum and coded communications; tropical radio propagation; VLSI for communications; strategies for increasing software productivity; multiple access communications; advanced communication satellite technologies; and spread spectrum systems. Topics discussed include Space Station communication and tracking development and design; transmission networks; modulation; data communications; computer network protocols and performance; and coding and synchronization. Consideration is given to free space optical communications systems; VSAT communication networks; network topology design; advances in adaptive filtering echo cancellation and adaptive equalization; advanced signal processing for satellite communications; the elements, design, and analysis of fiber-optic networks; and advances in digital microwave systems.

Coherent direct sequence optical code multiple access encoding-decoding efficiency versus wavelength detuning.

PubMed

Pastor, D; Amaya, W; García-Olcina, R; Sales, S

2007-07-01

We present a simple theoretical model of and the experimental verification for vanishing of the autocorrelation peak due to wavelength detuning on the coding-decoding process of coherent direct sequence optical code multiple access systems based on a superstructured fiber Bragg grating. Moreover, the detuning vanishing effect has been explored to take advantage of this effect and to provide an additional degree of multiplexing and/or optical code tuning.

Soldier communication net for the 21st century digitized battlespace

NASA Astrophysics Data System (ADS)

Mu, Libo; Zhang, Yutian

1999-07-01

This paper present soldier communication net scheme, which survives and operates in the 21st century battlefield environment. First, it analyzes the features, the need, function of the soldier communication net on the 21st century battlefield environment. Secondly it presents a layered model of the soldier communication net, derived from the OSI theory, and discusses the design of the 3 layers, link layer, link controller and input/output applications layer. Thirdly, it present some key technical discussion concerning with the direct-sequence-spread-spectrum communication, code/decode and low power consumption. Finally, it gives the conclusion that spread spectrum time division system is the best scheme of soldier communication net.

Interference Cancellation Technique Based on Discovery of Spreading Codes of Interference Signals and Maximum Correlation Detection for DS-CDMA System

NASA Astrophysics Data System (ADS)

Hettiarachchi, Ranga; Yokoyama, Mitsuo; Uehara, Hideyuki

This paper presents a novel interference cancellation (IC) scheme for both synchronous and asynchronous direct-sequence code-division multiple-access (DS-CDMA) wireless channels. In the DS-CDMA system, the multiple access interference (MAI) and the near-far problem (NFP) are the two factors which reduce the capacity of the system. In this paper, we propose a new algorithm that is able to detect all interference signals as an individual MAI signal by maximum correlation detection. It is based on the discovery of all the unknowing spreading codes of the interference signals. Then, all possible MAI patterns so called replicas are generated as a summation of interference signals. And the true MAI pattern is found by taking correlation between the received signal and the replicas. Moreover, the receiver executes MAI cancellation in a successive manner, removing all interference signals by single-stage. Numerical results will show that the proposed IC strategy, which alleviates the detrimental effect of the MAI and the near-far problem, can significantly improve the system performance. Especially, we can obtain almost the same receiving characteristics as in the absense of interference for asynchrnous system when received powers are equal. Also, the same performances can be seen under any received power state for synchronous system.

Layered video transmission over multirate DS-CDMA wireless systems

NASA Astrophysics Data System (ADS)

Kondi, Lisimachos P.; Srinivasan, Deepika; Pados, Dimitris A.; Batalama, Stella N.

2003-05-01

n this paper, we consider the transmission of video over wireless direct-sequence code-division multiple access (DS-CDMA) channels. A layered (scalable) video source codec is used and each layer is transmitted over a different CDMA channel. Spreading codes with different lengths are allowed for each CDMA channel (multirate CDMA). Thus, a different number of chips per bit can be used for the transmission of each scalable layer. For a given fixed energy value per chip and chip rate, the selection of a spreading code length affects the transmitted energy per bit and bit rate for each scalable layer. An MPEG-4 source encoder is used to provide a two-layer SNR scalable bitstream. Each of the two layers is channel-coded using Rate-Compatible Punctured Convolutional (RCPC) codes. Then, the data are interleaved, spread, carrier-modulated and transmitted over the wireless channel. A multipath Rayleigh fading channel is assumed. At the other end, we assume the presence of an antenna array receiver. After carrier demodulation, multiple-access-interference suppressing despreading is performed using space-time auxiliary vector (AV) filtering. The choice of the AV receiver is dictated by realistic channel fading rates that limit the data record available for receiver adaptation and redesign. Indeed, AV filter short-data-record estimators have been shown to exhibit superior bit-error-rate performance in comparison with LMS, RLS, SMI, or 'multistage nested Wiener' adaptive filter implementations. Our experimental results demonstrate the effectiveness of multirate DS-CDMA systems for wireless video transmission.

Performance of cellular frequency-hopped spread-spectrum radio networks

NASA Astrophysics Data System (ADS)

Gluck, Jeffrey W.; Geraniotis, Evaggelos

1989-10-01

Multiple access interference is characterized for cellular mobile networks, in which users are assumed to be Poisson-distributed in the plane and employ frequency-hopped spread-spectrum signaling with transmitter-oriented assignment of frequency-hopping patterns. Exact expressions for the bit error probabilities are derived for binary coherently demodulated systems without coding. Approximations for the packet error probability are derived for coherent and noncoherent systems and these approximations are applied when forward-error-control coding is employed. In all cases, the effects of varying interference power are accurately taken into account according to some propagation law. Numerical results are given in terms of bit error probability for the exact case and throughput for the approximate analyses. Comparisons are made with previously derived bounds and it is shown that these tend to be very pessimistic.

Approximate equiangular tight frames for compressed sensing and CDMA applications

NASA Astrophysics Data System (ADS)

Tsiligianni, Evaggelia; Kondi, Lisimachos P.; Katsaggelos, Aggelos K.

2017-12-01

Performance guarantees for recovery algorithms employed in sparse representations, and compressed sensing highlights the importance of incoherence. Optimal bounds of incoherence are attained by equiangular unit norm tight frames (ETFs). Although ETFs are important in many applications, they do not exist for all dimensions, while their construction has been proven extremely difficult. In this paper, we construct frames that are close to ETFs. According to results from frame and graph theory, the existence of an ETF depends on the existence of its signature matrix, that is, a symmetric matrix with certain structure and spectrum consisting of two distinct eigenvalues. We view the construction of a signature matrix as an inverse eigenvalue problem and propose a method that produces frames of any dimensions that are close to ETFs. Due to the achieved equiangularity property, the so obtained frames can be employed as spreading sequences in synchronous code-division multiple access (s-CDMA) systems, besides compressed sensing.

Methods and apparatuses using filter banks for multi-carrier spread-spectrum signals

DOEpatents

Moradi, Hussein; Farhang, Behrouz; Kutsche, Carl A

2014-10-14

A transmitter includes a synthesis filter bank to spread a data symbol to a plurality of frequencies by encoding the data symbol on each frequency, apply a common pulse-shaping filter, and apply gains to the frequencies such that a power level of each frequency is less than a noise level of other communication signals within the spectrum. Each frequency is modulated onto a different evenly spaced subcarrier. A demodulator in a receiver converts a radio frequency input to a spread-spectrum signal in a baseband. A matched filter filters the spread-spectrum signal with a common filter having characteristics matched to the synthesis filter bank in the transmitter by filtering each frequency to generate a sequence of narrow pulses. A carrier recovery unit generates control signals responsive to the sequence of narrow pulses suitable for generating a phase-locked loop between the demodulator, the matched filter, and the carrier recovery unit.

Methods and apparatuses using filter banks for multi-carrier spread-spectrum signals

DOEpatents

Moradi, Hussein; Farhang, Behrouz; Kutsche, Carl A

2014-05-20

A transmitter includes a synthesis filter bank to spread a data symbol to a plurality of frequencies by encoding the data symbol on each frequency, apply a common pulse-shaping filter, and apply gains to the frequencies such that a power level of each frequency is less than a noise level of other communication signals within the spectrum. Each frequency is modulated onto a different evenly spaced subcarrier. A demodulator in a receiver converts a radio frequency input to a spread-spectrum signal in a baseband. A matched filter filters the spread-spectrum signal with a common filter having characteristics matched to the synthesis filter bank in the transmitter by filtering each frequency to generate a sequence of narrow pulses. A carrier recovery unit generates control signals responsive to the sequence of narrow pulses suitable for generating a phase-locked loop between the demodulator, the matched filter, and the carrier recovery unit.

The Performance of a PN Spread Spectrum Receiver Preceded by an Adaptive Interference Suppression Filter.

DTIC Science & Technology

1982-12-01

Sequence dj Estimate of the Desired Signal DEL Sampling Time Interval DS Direct Sequence c Sufficient Statistic E/T Signal Power Erfc Complimentary Error...Namely, a white Gaussian noise (WGN) generator was added. Also, a statistical subroutine was added in order to assess performance improvement at the...reference code and then passed through a correlation detector whose output is the sufficient 1 statistic , e . Using a threshold device and the sufficient

Actinobase: Database on molecular diversity, phylogeny and biocatalytic potential of salt tolerant alkaliphilic actinomycetes.

PubMed

Sharma, Amit K; Gohel, Sangeeta; Singh, Satya P

2012-01-01

Actinobase is a relational database of molecular diversity, phylogeny and biocatalytic potential of haloalkaliphilic actinomycetes. The main objective of this data base is to provide easy access to range of information, data storage, comparison and analysis apart from reduced data redundancy, data entry, storage, retrieval costs and improve data security. Information related to habitat, cell morphology, Gram reaction, biochemical characterization and molecular features would allow researchers in understanding identification and stress adaptation of the existing and new candidates belonging to salt tolerant alkaliphilic actinomycetes. The PHP front end helps to add nucleotides and protein sequence of reported entries which directly help researchers to obtain the required details. Analysis of the genus wise status of the salt tolerant alkaliphilic actinomycetes indicated 6 different genera among the 40 classified entries of the salt tolerant alkaliphilic actinomycetes. The results represented wide spread occurrence of salt tolerant alkaliphilic actinomycetes belonging to diverse taxonomic positions. Entries and information related to actinomycetes in the database are publicly accessible at http://www.actinobase.in. On clustalW/X multiple sequence alignment of the alkaline protease gene sequences, different clusters emerged among the groups. The narrow search and limit options of the constructed database provided comparable information. The user friendly access to PHP front end facilitates would facilitate addition of sequences of reported entries. The database is available for free at http://www.actinobase.in.

Electromagnetic interference-aware transmission scheduling and power control for dynamic wireless access in hospital environments.

PubMed

Phunchongharn, Phond; Hossain, Ekram; Camorlinga, Sergio

2011-11-01

We study the multiple access problem for e-Health applications (referred to as secondary users) coexisting with medical devices (referred to as primary or protected users) in a hospital environment. In particular, we focus on transmission scheduling and power control of secondary users in multiple spatial reuse time-division multiple access (STDMA) networks. The objective is to maximize the spectrum utilization of secondary users and minimize their power consumption subject to the electromagnetic interference (EMI) constraints for active and passive medical devices and minimum throughput guarantee for secondary users. The multiple access problem is formulated as a dual objective optimization problem which is shown to be NP-complete. We propose a joint scheduling and power control algorithm based on a greedy approach to solve the problem with much lower computational complexity. To this end, an enhanced greedy algorithm is proposed to improve the performance of the greedy algorithm by finding the optimal sequence of secondary users for scheduling. Using extensive simulations, the tradeoff in performance in terms of spectrum utilization, energy consumption, and computational complexity is evaluated for both the algorithms.

Iterative Overlap FDE for Multicode DS-CDMA

NASA Astrophysics Data System (ADS)

Takeda, Kazuaki; Tomeba, Hiromichi; Adachi, Fumiyuki

Recently, a new frequency-domain equalization (FDE) technique, called overlap FDE, that requires no GI insertion was proposed. However, the residual inter/intra-block interference (IBI) cannot completely be removed. In addition to this, for multicode direct sequence code division multiple access (DS-CDMA), the presence of residual interchip interference (ICI) after FDE distorts orthogonality among the spreading codes. In this paper, we propose an iterative overlap FDE for multicode DS-CDMA to suppress both the residual IBI and the residual ICI. In the iterative overlap FDE, joint minimum mean square error (MMSE)-FDE and ICI cancellation is repeated a sufficient number of times. The bit error rate (BER) performance with the iterative overlap FDE is evaluated by computer simulation.

Images multiplexing by code division technique

NASA Astrophysics Data System (ADS)

Kuo, Chung J.; Rigas, Harriett

Spread Spectrum System (SSS) or Code Division Multiple Access System (CDMAS) has been studied for a long time, but most of the attention was focused on the transmission problems. In this paper, we study the results when the code division technique is applied to the image at the source stage. The idea is to convolve the N different images with the corresponding m-sequence to obtain the encrypted image. The superimposed image (summation of the encrypted images) is then stored or transmitted. The benefit of this is that no one knows what is stored or transmitted unless the m-sequence is known. The recovery of the original image is recovered by correlating the superimposed image with corresponding m-sequence. Two cases are studied in this paper. First, the two-dimensional image is treated as a long one-dimensional vector and the m-sequence is employed to obtain the results. Secondly, the two-dimensional quasi m-array is proposed and used for the code division multiplexing. It is shown that quasi m-array is faster when the image size is 256 x 256. The important features of the proposed technique are not only the image security but also the data compactness. The compression ratio depends on how many images are superimposed.

Images Multiplexing By Code Division Technique

NASA Astrophysics Data System (ADS)

Kuo, Chung Jung; Rigas, Harriett B.

1990-01-01

Spread Spectrum System (SSS) or Code Division Multiple Access System (CDMAS) has been studied for a long time, but most of the attention was focused on the transmission problems. In this paper, we study the results when the code division technique is applied to the image at the source stage. The idea is to convolve the N different images with the corresponding m-sequence to obtain the encrypted image. The superimposed image (summation of the encrypted images) is then stored or transmitted. The benefit of this is that no one knows what is stored or transmitted unless the m-sequence is known. The recovery of the original image is recovered by correlating the superimposed image with corresponding m-sequence. Two cases are studied in this paper. First, the 2-D image is treated as a long 1-D vector and the m-sequence is employed to obtained the results. Secondly, the 2-D quasi m-array is proposed and used for the code division multiplexing. It is showed that quasi m-array is faster when the image size is 256x256. The important features of the proposed technique are not only the image security but also the data compactness. The compression ratio depends on how many images are superimposed.

On the performance of a code division multiple access scheme with transmit/receive conflicts

NASA Astrophysics Data System (ADS)

Silvester, J. A.

One of the benefits of spread spectrum is that by assigning each user a different orthogonal signal set, multiple transmissions can occur simultaneously. This possibility is utilized in new access schemes called Code Division Multiple Access (CDMA). The present investigation is concerned with a particular CDMA implementation in which the transmit times for each symbol are exactly determined in a distributed manner such that both sender and receiver know them. In connection with a decision whether to transmit or receive, the loss of a symbol in one of the channels results. The system employs thus a coding technique which permits correct decoding of a codeword even if some constituent symbols are missing or in error. The technique used is Reed Solomon coding. The performance of this system is analyzed, and attention is given to the optimum strategy which should be used in deciding whether to receive or transmit.

Several Families of Sequences with Low Correlation and Large Linear Span

NASA Astrophysics Data System (ADS)

Zeng, Fanxin; Zhang, Zhenyu

In DS-CDMA systems and DS-UWB radios, low correlation of spreading sequences can greatly help to minimize multiple access interference (MAI) and large linear span of spreading sequences can reduce their predictability. In this letter, new sequence sets with low correlation and large linear span are proposed. Based on the construction Trm1[Trnm(αbt+γiαdt)]r for generating p-ary sequences of period pn-1, where n=2m, d=upm±v, b=u±v, γi∈GF(pn), and p is an arbitrary prime number, several methods to choose the parameter d are provided. The obtained sequences with family size pn are of four-valued, five-valued, six-valued or seven-valued correlation and the maximum nontrivial correlation value is (u+v-1)pm-1. The simulation by a computer shows that the linear span of the new sequences is larger than that of the sequences with Niho-type and Welch-type decimations, and similar to that of [10].

3D Indoor Positioning of UAVs with Spread Spectrum Ultrasound and Time-of-Flight Cameras

PubMed Central

Aguilera, Teodoro

2017-01-01

This work proposes the use of a hybrid acoustic and optical indoor positioning system for the accurate 3D positioning of Unmanned Aerial Vehicles (UAVs). The acoustic module of this system is based on a Time-Code Division Multiple Access (T-CDMA) scheme, where the sequential emission of five spread spectrum ultrasonic codes is performed to compute the horizontal vehicle position following a 2D multilateration procedure. The optical module is based on a Time-Of-Flight (TOF) camera that provides an initial estimation for the vehicle height. A recursive algorithm programmed on an external computer is then proposed to refine the estimated position. Experimental results show that the proposed system can increase the accuracy of a solely acoustic system by 70–80% in terms of positioning mean square error. PMID:29301211

Wavelet versus DCT-based spread spectrum watermarking of image databases

NASA Astrophysics Data System (ADS)

Mitrea, Mihai P.; Zaharia, Titus B.; Preteux, Francoise J.; Vlad, Adriana

2004-05-01

This paper addresses the issue of oblivious robust watermarking, within the framework of colour still image database protection. We present an original method which complies with all the requirements nowadays imposed to watermarking applications: robustness (e.g. low-pass filtering, print & scan, StirMark), transparency (both quality and fidelity), low probability of false alarm, obliviousness and multiple bit recovering. The mark is generated from a 64 bit message (be it a logo, a serial number, etc.) by means of a Spread Spectrum technique and is embedded into DWT (Discrete Wavelet Transform) domain, into certain low frequency coefficients, selected according to the hierarchy of their absolute values. The best results were provided by the (9,7) bi-orthogonal transform. The experiments were carried out on 1200 image sequences, each of them of 32 images. Note that these sequences represented several types of images: natural, synthetic, medical, etc. and each time we obtained the same good results. These results are compared with those we already obtained for the DCT domain, the differences being pointed out and discussed.

Multiple Access Interference Reduction Using Received Response Code Sequence for DS-CDMA UWB System

NASA Astrophysics Data System (ADS)

Toh, Keat Beng; Tachikawa, Shin'ichi

This paper proposes a combination of novel Received Response (RR) sequence at the transmitter and a Matched Filter-RAKE (MF-RAKE) combining scheme receiver system for the Direct Sequence-Code Division Multiple Access Ultra Wideband (DS-CDMA UWB) multipath channel model. This paper also demonstrates the effectiveness of the RR sequence in Multiple Access Interference (MAI) reduction for the DS-CDMA UWB system. It suggests that by using conventional binary code sequence such as the M sequence or the Gold sequence, there is a possibility of generating extra MAI in the UWB system. Therefore, it is quite difficult to collect the energy efficiently although the RAKE reception method is applied at the receiver. The main purpose of the proposed system is to overcome the performance degradation for UWB transmission due to the occurrence of MAI during multiple accessing in the DS-CDMA UWB system. The proposed system improves the system performance by improving the RAKE reception performance using the RR sequence which can reduce the MAI effect significantly. Simulation results verify that significant improvement can be obtained by the proposed system in the UWB multipath channel models.

Methods and apparatuses using filter banks for multi-carrier spread spectrum signals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moradi, Hussein; Farhang, Behrouz; Kutsche, Carl A

2017-01-31

A transmitter includes a synthesis filter bank to spread a data symbol to a plurality of frequencies by encoding the data symbol on each frequency, apply a common pulse-shaping filter, and apply gains to the frequencies such that a power level of each frequency is less than a noise level of other communication signals within the spectrum. Each frequency is modulated onto a different evenly spaced subcarrier. A demodulator in a receiver converts a radio frequency input to a spread-spectrum signal in a baseband. A matched filter filters the spread-spectrum signal with a common filter having characteristics matched to themore » synthesis filter bank in the transmitter by filtering each frequency to generate a sequence of narrow pulses. A carrier recovery unit generates control signals responsive to the sequence of narrow pulses suitable for generating a phase-locked loop between the demodulator, the matched filter, and the carrier recovery unit.« less

Methods and apparatuses using filter banks for multi-carrier spread spectrum signals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moradi, Hussein; Farhang, Behrouz; Kutsche, Carl A.

2016-06-14

A transmitter includes a synthesis filter bank to spread a data symbol to a plurality of frequencies by encoding the data symbol on each frequency, apply a common pulse-shaping filter, and apply gains to the frequencies such that a power level of each frequency is less than a noise level of other communication signals within the spectrum. Each frequency is modulated onto a different evenly spaced subcarrier. A demodulator in a receiver converts a radio frequency input to a spread-spectrum signal in a baseband. A matched filter filters the spread-spectrum signal with a common filter having characteristics matched to themore » synthesis filter bank in the transmitter by filtering each frequency to generate a sequence of narrow pulses. A carrier recovery unit generates control signals responsive to the sequence of narrow pulses suitable for generating a phase-locked loop between the demodulator, the matched filter, and the carrier recovery unit.« less

Neisseria gonorrhoeae Strain with Reduced Susceptibilities to Extended-Spectrum Cephalosporins

PubMed Central

Gose, Severin; Castro, Lina; Chung, Kathleen; Bernstein, Kyle; Samuel, Micheal; Bauer, Heidi; Pandori, Mark

2014-01-01

The spread of Neisseria gonorrhoeae strains with reduced susceptibility to extended-spectrum cephalosporins is an increasing public health threat. Using Etest and multiantigen sequence typing, we detected sequence type 1407, which is associated with reduced susceptibilities to extended-spectrum cephalosporins, in 4 major populated regions in California, USA, in 2012. PMID:24964277

Neisseria gonorrhoeae strain with reduced susceptibilities to extended-spectrum cephalosporins.

PubMed

Nguyen, Duylinh; Gose, Severin; Castro, Lina; Chung, Kathleen; Bernstein, Kyle; Samuel, Micheal; Bauer, Heidi; Pandori, Mark

2014-07-01

The spread of Neisseria gonorrhoeae strains with reduced susceptibility to extended-spectrum cephalosporins is an increasing public health threat. Using Etest and multiantigen sequence typing, we detected sequence type 1407, which is associated with reduced susceptibilities to extended-spectrum cephalosporins, in 4 major populated regions in California, USA, in 2012.

Cognitive Radio for Tactical Wireless Communication Networks

DTIC Science & Technology

2011-10-09

Pursley. Demodulator Statistics for Enhanced Soft-Decision Decoding in CDMA Packet Radio Systems, ICC 2010 - 2010 IEEE International Conference on...likelihood ratio (LLR) metrics and distance metrics. In [BPR08], [BoP09], and [BPR11], we investigated direct-sequence spread-spectrum ( DS -SS...modulation formats, which are among the most robust formats for tactical cognitive radio networks. DS -SS modulation with adaptive soft-decision decoding is

Carrier Estimation Using Classic Spectral Estimation Techniques for the Proposed Demand Assignment Multiple Access Service

NASA Technical Reports Server (NTRS)

Scaife, Bradley James

1999-01-01

In any satellite communication, the Doppler shift associated with the satellite's position and velocity must be calculated in order to determine the carrier frequency. If the satellite state vector is unknown then some estimate must be formed of the Doppler-shifted carrier frequency. One elementary technique is to examine the signal spectrum and base the estimate on the dominant spectral component. If, however, the carrier is spread (as in most satellite communications) this technique may fail unless the chip rate-to-data rate ratio (processing gain) associated with the carrier is small. In this case, there may be enough spectral energy to allow peak detection against a noise background. In this thesis, we present a method to estimate the frequency (without knowledge of the Doppler shift) of a spread-spectrum carrier assuming a small processing gain and binary-phase shift keying (BPSK) modulation. Our method relies on an averaged discrete Fourier transform along with peak detection on spectral match filtered data. We provide theory and simulation results indicating the accuracy of this method. In addition, we will describe an all-digital hardware design based around a Motorola DSP56303 and high-speed A/D which implements this technique in real-time. The hardware design is to be used in NMSU's implementation of NASA's demand assignment, multiple access (DAMA) service.

Design study of a HEAO-C spread spectrum transponder telemetry system for use with the TDRSS subnet

NASA Technical Reports Server (NTRS)

Weathers, G.

1975-01-01

The results of a design study of a spread spectrum transponder for use on the HEAO-C satellite were given. The transponder performs the functions of code turn-around for ground range and range-rate determination, ground command receiver, and telemetry data transmitter. The spacecraft transponder and associated communication system components will allow the HEAO-C satellite to utilize the Tracking and Data Relay Satellite System (TDRSS) subnet of the post 1978 STDN. The following areas were discussed in the report: TDRSS Subnet Description, TDRSS-HEAO-C System Configuration, Gold Code Generator, Convolutional Encoder Design and Decoder Algorithm, High Speed Sequence Generators, Statistical Evaluation of Candidate Code Sequences using Amplitude and Phase Moments, Code and Carrier Phase Lock Loops, Total Spread Spectrum Transponder System, and Reference Literature Search.

Self-organizing feature maps for dynamic control of radio resources in CDMA microcellular networks

NASA Astrophysics Data System (ADS)

Hortos, William S.

1998-03-01

The application of artificial neural networks to the channel assignment problem for cellular code-division multiple access (CDMA) cellular networks has previously been investigated. CDMA takes advantage of voice activity and spatial isolation because its capacity is only interference limited, unlike time-division multiple access (TDMA) and frequency-division multiple access (FDMA) where capacities are bandwidth-limited. Any reduction in interference in CDMA translates linearly into increased capacity. To satisfy the high demands for new services and improved connectivity for mobile communications, microcellular and picocellular systems are being introduced. For these systems, there is a need to develop robust and efficient management procedures for the allocation of power and spectrum to maximize radio capacity. Topology-conserving mappings play an important role in the biological processing of sensory inputs. The same principles underlying Kohonen's self-organizing feature maps (SOFMs) are applied to the adaptive control of radio resources to minimize interference, hence, maximize capacity in direct-sequence (DS) CDMA networks. The approach based on SOFMs is applied to some published examples of both theoretical and empirical models of DS/CDMA microcellular networks in metropolitan areas. The results of the approach for these examples are informally compared to the performance of algorithms, based on Hopfield- Tank neural networks and on genetic algorithms, for the channel assignment problem.

Robust statistical methods for impulse noise suppressing of spread spectrum induced polarization data, with application to a mine site, Gansu province, China

NASA Astrophysics Data System (ADS)

Liu, Weiqiang; Chen, Rujun; Cai, Hongzhu; Luo, Weibin

2016-12-01

In this paper, we investigated the robust processing of noisy spread spectrum induced polarization (SSIP) data. SSIP is a new frequency domain induced polarization method that transmits pseudo-random m-sequence as source current where m-sequence is a broadband signal. The potential information at multiple frequencies can be obtained through measurement. Removing the noise is a crucial problem for SSIP data processing. Considering that if the ordinary mean stack and digital filter are not capable of reducing the impulse noise effectively in SSIP data processing, the impact of impulse noise will remain in the complex resistivity spectrum that will affect the interpretation of profile anomalies. We implemented a robust statistical method to SSIP data processing. The robust least-squares regression is used to fit and remove the linear trend from the original data before stacking. The robust M estimate is used to stack the data of all periods. The robust smooth filter is used to suppress the residual noise for data after stacking. For robust statistical scheme, the most appropriate influence function and iterative algorithm are chosen by testing the simulated data to suppress the outliers' influence. We tested the benefits of the robust SSIP data processing using examples of SSIP data recorded in a test site beside a mine in Gansu province, China.

Analysis, optimization, and implementation of a hybrid DS/FFH spread-spectrum technique for smart grid communications

DOE PAGES

Olama, Mohammed M.; Ma, Xiao; Killough, Stephen M.; ...

2015-03-12

In recent years, there has been great interest in using hybrid spread-spectrum (HSS) techniques for commercial applications, particularly in the Smart Grid, in addition to their inherent uses in military communications. This is because HSS can accommodate high data rates with high link integrity, even in the presence of significant multipath effects and interfering signals. A highly useful form of this transmission technique for many types of command, control, and sensing applications is the specific code-related combination of standard direct sequence modulation with fast frequency hopping, denoted hybrid DS/FFH, wherein multiple frequency hops occur within a single data-bit time. Inmore » this paper, error-probability analyses are performed for a hybrid DS/FFH system over standard Gaussian and fading-type channels, progressively including the effects from wide- and partial-band jamming, multi-user interference, and varying degrees of Rayleigh and Rician fading. In addition, an optimization approach is formulated that minimizes the bit-error performance of a hybrid DS/FFH communication system and solves for the resulting system design parameters. The optimization objective function is non-convex and can be solved by applying the Karush-Kuhn-Tucker conditions. We also present our efforts toward exploring the design, implementation, and evaluation of a hybrid DS/FFH radio transceiver using a single FPGA. Numerical and experimental results are presented under widely varying design parameters to demonstrate the adaptability of the waveform for varied harsh smart grid RF signal environments.« less

Pilot-Assisted Channel Estimation for Orthogonal Multi-Carrier DS-CDMA with Frequency-Domain Equalization

NASA Astrophysics Data System (ADS)

Shima, Tomoyuki; Tomeba, Hiromichi; Adachi, Fumiyuki

Orthogonal multi-carrier direct sequence code division multiple access (orthogonal MC DS-CDMA) is a combination of time-domain spreading and orthogonal frequency division multiplexing (OFDM). In orthogonal MC DS-CDMA, the frequency diversity gain can be obtained by applying frequency-domain equalization (FDE) based on minimum mean square error (MMSE) criterion to a block of OFDM symbols and can improve the bit error rate (BER) performance in a severe frequency-selective fading channel. FDE requires an accurate estimate of the channel gain. The channel gain can be estimated by removing the pilot modulation in the frequency domain. In this paper, we propose a pilot-assisted channel estimation suitable for orthogonal MC DS-CDMA with FDE and evaluate, by computer simulation, the BER performance in a frequency-selective Rayleigh fading channel.

DoS detection in IEEE 802.11 with the presence of hidden nodes

PubMed Central

Soryal, Joseph; Liu, Xijie; Saadawi, Tarek

2013-01-01

The paper presents a novel technique to detect Denial of Service (DoS) attacks applied by misbehaving nodes in wireless networks with the presence of hidden nodes employing the widely used IEEE 802.11 Distributed Coordination Function (DCF) protocols described in the IEEE standard [1]. Attacker nodes alter the IEEE 802.11 DCF firmware to illicitly capture the channel via elevating the probability of the average number of packets transmitted successfully using up the bandwidth share of the innocent nodes that follow the protocol standards. We obtained the theoretical network throughput by solving two-dimensional Markov Chain model as described by Bianchi [2], and Liu and Saadawi [3] to determine the channel capacity. We validated the results obtained via the theoretical computations with the results obtained by OPNET simulator [4] to define the baseline for the average attainable throughput in the channel under standard conditions where all nodes follow the standards. The main goal of the DoS attacker is to prevent the innocent nodes from accessing the channel and by capturing the channel’s bandwidth. In addition, the attacker strives to appear as an innocent node that follows the standards. The protocol resides in every node to enable each node to police other nodes in its immediate wireless coverage area. All innocent nodes are able to detect and identify the DoS attacker in its wireless coverage area. We applied the protocol to two Physical Layer technologies: Direct Sequence Spread Spectrum (DSSS) and Frequency Hopping Spread Spectrum (FHSS) and the results are presented to validate the algorithm. PMID:25685510

DoS detection in IEEE 802.11 with the presence of hidden nodes.

PubMed

Soryal, Joseph; Liu, Xijie; Saadawi, Tarek

2014-07-01

The paper presents a novel technique to detect Denial of Service (DoS) attacks applied by misbehaving nodes in wireless networks with the presence of hidden nodes employing the widely used IEEE 802.11 Distributed Coordination Function (DCF) protocols described in the IEEE standard [1]. Attacker nodes alter the IEEE 802.11 DCF firmware to illicitly capture the channel via elevating the probability of the average number of packets transmitted successfully using up the bandwidth share of the innocent nodes that follow the protocol standards. We obtained the theoretical network throughput by solving two-dimensional Markov Chain model as described by Bianchi [2], and Liu and Saadawi [3] to determine the channel capacity. We validated the results obtained via the theoretical computations with the results obtained by OPNET simulator [4] to define the baseline for the average attainable throughput in the channel under standard conditions where all nodes follow the standards. The main goal of the DoS attacker is to prevent the innocent nodes from accessing the channel and by capturing the channel's bandwidth. In addition, the attacker strives to appear as an innocent node that follows the standards. The protocol resides in every node to enable each node to police other nodes in its immediate wireless coverage area. All innocent nodes are able to detect and identify the DoS attacker in its wireless coverage area. We applied the protocol to two Physical Layer technologies: Direct Sequence Spread Spectrum (DSSS) and Frequency Hopping Spread Spectrum (FHSS) and the results are presented to validate the algorithm.

Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type 131 Strains from Nepal and Japan

PubMed Central

Miyoshi-Akiyama, Tohru; Sherchan, Jatan Bahadur; Doi, Yohei; Nagamatsu, Maki; Sherchand, Jeevan B.; Tandukar, Sarmila; Ohmagari, Norio; Kirikae, Teruo; Ohara, Hiroshi

2016-01-01

ABSTRACT The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region. IMPORTANCE The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia. PMID:27830191

Airborne Network Data Availability Using Peer to Peer Database Replication on a Distributed Hash Table

DTIC Science & Technology

2013-03-01

DSR Dynamic Source Routing DSSS Direct -sequence spread spectrum GUID Globally Unique ID MANET Mobile Ad-hoc Network NS3 Network Simulator 3 OLSR...networking schemes for safe maneuvering and data communication. Imagine needing to maintain an operational picture of an overall environment using a...as simple as O(n) where every node is sequentially queried to O log(n), or O(1). These schemes will be discussed with each individual DHT. Four of the

On Achieving Network LPI (Link Parameter Interactions) for Spread Spectrum Communications.

DTIC Science & Technology

1985-10-01

Direct Sequence,Longley-Rice Model, Adaptive Control, LPI, Scenario Snapshots,Interference Limi ted , Wi deband Propagation Modell1ing. . i idL COU This...0; a. ..- ,2 w N a11 N z , <:X --. t ,0 II fr Zo 7 10m I II P:3 ZZXUO. (3O U 𔃻. 0 WUN 4 - 0 4,U w 0-N~lrC~C (fjwW -w 2 -. OI- C) I- I Li tjU (A xf

Adaptive Transmission and Channel Modeling for Frequency Hopping Communications

DTIC Science & Technology

2009-09-21

proposed adaptive transmission method has much greater system capacity than conventional non-adaptive MC direct- sequence ( DS )- CDMA system. • We...several mobile radio systems. First, a new improved allocation algorithm was proposed for multicarrier code-division multiple access (MC- CDMA ) system...Multicarrier code-division multiple access (MC- CDMA ) system with adaptive frequency hopping (AFH) has attracted attention of researchers due to its

Spread of Plasmids Carrying Multiple GES Variants

PubMed Central

Cuzon, Gaelle; Bogaerts, Pierre; Bauraing, Caroline; Huang, Te-Din; Glupczynski, Youri

2016-01-01

Five GES-producing Enterobacteriaceae isolates that displayed an extended-spectrum β-lactamase (ESBL) phenotype harbored two GES variants: GES-7 ESBL and GES-6 carbapenemase. In all isolates, the two GES alleles were located on the same integron that was inserted into an 80-kb IncM1 self-conjugative plasmid. Whole-genome sequencing suggested in vivo horizontal gene transfer of the plasmid along with clonal diffusion of Enterobacter cloacae. To our knowledge, this is the first description in Europe of clustered Enterobacteriaceae isolates carrying two GES β-lactamases, of which one has extended activity toward carbapenems. PMID:27216071

Topology-selective jamming of fully-connected, code-division random-access networks

NASA Technical Reports Server (NTRS)

Polydoros, Andreas; Cheng, Unjeng

1990-01-01

The purpose is to introduce certain models of topology selective stochastic jamming and examine its impact on a class of fully-connected, spread-spectrum, slotted ALOHA-type random access networks. The theory covers dedicated as well as half-duplex units. The dominant role of the spatial duty factor is established, and connections with the dual concept of time selective jamming are discussed. The optimal choices of coding rate and link access parameters (from the users' side) and the jamming spatial fraction are numerically established for DS and FH spreading.

Steganography on multiple MP3 files using spread spectrum and Shamir's secret sharing

NASA Astrophysics Data System (ADS)

Yoeseph, N. M.; Purnomo, F. A.; Riasti, B. K.; Safiie, M. A.; Hidayat, T. N.

2016-11-01

The purpose of steganography is how to hide data into another media. In order to increase security of data, steganography technique is often combined with cryptography. The weakness of this combination technique is the data was centralized. Therefore, a steganography technique is develop by using combination of spread spectrum and secret sharing technique. In steganography with secret sharing, shares of data is created and hidden in several medium. Medium used to concealed shares were MP3 files. Hiding technique used was Spread Spectrum. Secret sharing scheme used was Shamir's Secret Sharing. The result showed that steganography with spread spectrum combined with Shamir's Secret Share using MP3 files as medium produce a technique that could hid data into several cover. To extract and reconstruct the data hidden in stego object, it is needed the amount of stego object which more or equal to its threshold. Furthermore, stego objects were imperceptible and robust.

Coded spread spectrum digital transmission system design study

NASA Technical Reports Server (NTRS)

Heller, J. A.; Odenwalder, J. P.; Viterbi, A. J.

1974-01-01

Results are presented of a comprehensive study of the performance of Viterbi-decoded convolutional codes in the presence of nonideal carrier tracking and bit synchronization. A constraint length 7, rate 1/3 convolutional code and parameters suitable for the space shuttle coded communications links are used. Mathematical models are developed and theoretical and simulation results are obtained to determine the tracking and acquisition performance of the system. Pseudorandom sequence spread spectrum techniques are also considered to minimize potential degradation caused by multipath.

Research on parallel combinatory spread spectrum communication system with double information matching

NASA Astrophysics Data System (ADS)

Xue, Wei; Wang, Qi; Wang, Tianyu

2018-04-01

This paper presents an improved parallel combinatory spread spectrum (PC/SS) communication system with the method of double information matching (DIM). Compared with conventional PC/SS system, the new model inherits the advantage of high transmission speed, large information capacity and high security. Besides, the problem traditional system will face is the high bit error rate (BER) and since its data-sequence mapping algorithm. Hence the new model presented shows lower BER and higher efficiency by its optimization of mapping algorithm.

Evolution of a Directional Wave Spectrum in a 3D Marginal Ice Zone with Random Floe Size Distribution

NASA Astrophysics Data System (ADS)

Montiel, F.; Squire, V. A.

2013-12-01

A new ocean wave/sea-ice interaction model is proposed that simulates how a directional wave spectrum evolves as it travels through a realistic marginal ice zone (MIZ), where wave/ice dynamics are entirely governed by coherent conservative wave scattering effects. Field experiments conducted by Wadhams et al. (1986) in the Greenland Sea generated important data on wave attenuation in the MIZ and, particularly, on whether the wave spectrum spreads directionally or collimates with distance from the ice edge. The data suggest that angular isotropy, arising from multiple scattering by ice floes, occurs close to the edge and thenceforth dominates wave propagation throughout the MIZ. Although several attempts have been made to replicate this finding theoretically, including by the use of numerical models, none have confronted this problem in a 3D MIZ with fully randomised floe distribution properties. We construct such a model by subdividing the discontinuous ice cover into adjacent infinite slabs of finite width parallel to the ice edge. Each slab contains an arbitrary (but finite) number of circular ice floes with randomly distributed properties. Ice floes are modeled as thin elastic plates with uniform thickness and finite draught. We consider a directional wave spectrum with harmonic time dependence incident on the MIZ from the open ocean, defined as a continuous superposition of plane waves traveling at different angles. The scattering problem within each slab is then solved using Graf's interaction theory for an arbitrary incident directional plane wave spectrum. Using an appropriate integral representation of the Hankel function of the first kind (see Cincotti et al., 1993), we map the outgoing circular wave field from each floe on the slab boundaries into a directional spectrum of plane waves, which characterizes the slab reflected and transmitted fields. Discretizing the angular spectrum, we can obtain a scattering matrix for each slab. Standard recursive techniques are then used to solve the problem for the full MIZ. Wave attenuation data are obtained using ensemble averaging and preliminary comparisons with field experiment data will be given in the presentation. The model also offers important insights in regards to the spreading of the directional wave spectrum as it penetrates deeper into the MIZ. Cincotti, G., Gori, F., Santarsiero, M., Frezza, F., Furno, F., and Schettini, G. (1993). Plane wave expansion of cylindrical functions. Opt. Commun., 95(4):192-198. Wadhams, P., Squire, V. A., Ewing, J. A., and Pascal, R. W. (1986). The effect of the marginal ice zone on the directional wave spectrum of the ocean. J. Phys. Oceanogr., 16:358-376.

Evaluation of CDMA system capacity for mobile satellite system applications

NASA Technical Reports Server (NTRS)

Smith, Partrick O.; Geraniotis, Evaggelos A.

1988-01-01

A specific Direct-Sequence/Pseudo-Noise (DS/PN) Code-Division Multiple-Access (CDMA) mobile satellite system (MSAT) architecture is discussed. The performance of this system is evaluated in terms of the maximum number of active MSAT subscribers that can be supported at a given uncoded bit-error probability. The evaluation decouples the analysis of the multiple-access capability (i.e., the number of instantaneous user signals) from the analysis of the multiple-access mutliplier effect allowed by the use of CDMA with burst-modem operation. We combine the results of these two analyses and present numerical results for scenarios of interest to the mobile satellite system community.

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

PubMed

Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Optimum decoding and detection of a multiplicative amplitude-encoded watermark

NASA Astrophysics Data System (ADS)

Barni, Mauro; Bartolini, Franco; De Rosa, Alessia; Piva, Alessandro

2002-04-01

The aim of this paper is to present a novel approach to the decoding and the detection of multibit, multiplicative, watermarks embedded in the frequency domain. Watermark payload is conveyed by amplitude modulating a pseudo-random sequence, thus resembling conventional DS spread spectrum techniques. As opposed to conventional communication systems, though, the watermark is embedded within the host DFT coefficients by using a multiplicative rule. The watermark decoding technique presented in the paper is an optimum one, in that it minimizes the bit error probability. The problem of watermark presence assessment, which is often underestimated by state-of-the-art research on multibit watermarking, is addressed too, and the optimum detection rule derived according to the Neyman-Pearson criterion. Experimental results are shown both to demonstrate the validity of the theoretical analysis and to highlight the good performance of the proposed system.

Pseudorandom binary injection of levitons for electron quantum optics

NASA Astrophysics Data System (ADS)

Glattli, D. C.; Roulleau, P.

2018-03-01

The recent realization of single-electron sources lets us envision performing electron quantum optics experiments, where electrons can be viewed as flying qubits propagating in a ballistic conductor. To date, all electron sources operate in a periodic electron injection mode, leading to energy spectrum singularities in various physical observables which sometimes hide the bare nature of physical effects. To go beyond this, we propose a spread-spectrum approach where electron flying qubits are injected in a nonperiodic manner following a pseudorandom binary bit pattern. Extending the Floquet scattering theory approach from periodic to spread-spectrum drive, the shot noise of pseudorandom binary sequences of single-electron injection can be calculated for leviton and nonleviton sources. Our new approach allows us to disentangle the physics of the manipulated excitations from that of the injection protocol. In particular, the spread-spectrum approach is shown to provide better knowledge of electronic Hong-Ou-Mandel correlations and to clarify the nature of the pulse train coherence and the role of the dynamical orthogonality catastrophe for noninteger charge injection.

Narrow field electromagnetic sensor system and method

DOEpatents

McEwan, Thomas E.

1996-01-01

A narrow field electromagnetic sensor system and method of sensing a characteristic of an object provide the capability to realize a characteristic of an object such as density, thickness, or presence, for any desired coordinate position on the object. One application is imaging. The sensor can also be used as an obstruction detector or an electronic trip wire with a narrow field without the disadvantages of impaired performance when exposed to dirt, snow, rain, or sunlight. The sensor employs a transmitter for transmitting a sequence of electromagnetic signals in response to a transmit timing signal, a receiver for sampling only the initial direct RF path of the electromagnetic signal while excluding all other electromagnetic signals in response to a receive timing signal, and a signal processor for processing the sampled direct RF path electromagnetic signal and providing an indication of the characteristic of an object. Usually, the electromagnetic signal is a short RF burst and the obstruction must provide a substantially complete eclipse of the direct RF path. By employing time-of-flight techniques, a timing circuit controls the receiver to sample only the initial direct RF path of the electromagnetic signal while not sampling indirect path electromagnetic signals. The sensor system also incorporates circuitry for ultra-wideband spread spectrum operation that reduces interference to and from other RF services while allowing co-location of multiple electronic sensors without the need for frequency assignments.

Narrow field electromagnetic sensor system and method

DOEpatents

McEwan, T.E.

1996-11-19

A narrow field electromagnetic sensor system and method of sensing a characteristic of an object provide the capability to realize a characteristic of an object such as density, thickness, or presence, for any desired coordinate position on the object. One application is imaging. The sensor can also be used as an obstruction detector or an electronic trip wire with a narrow field without the disadvantages of impaired performance when exposed to dirt, snow, rain, or sunlight. The sensor employs a transmitter for transmitting a sequence of electromagnetic signals in response to a transmit timing signal, a receiver for sampling only the initial direct RF path of the electromagnetic signal while excluding all other electromagnetic signals in response to a receive timing signal, and a signal processor for processing the sampled direct RF path electromagnetic signal and providing an indication of the characteristic of an object. Usually, the electromagnetic signal is a short RF burst and the obstruction must provide a substantially complete eclipse of the direct RF path. By employing time-of-flight techniques, a timing circuit controls the receiver to sample only the initial direct RF path of the electromagnetic signal while not sampling indirect path electromagnetic signals. The sensor system also incorporates circuitry for ultra-wideband spread spectrum operation that reduces interference to and from other RF services while allowing co-location of multiple electronic sensors without the need for frequency assignments. 12 figs.

Concept For Generation Of Long Pseudorandom Sequences

NASA Technical Reports Server (NTRS)

Wang, C. C.

1990-01-01

Conceptual very-large-scale integrated (VLSI) digital circuit performs exponentiation in finite field. Algorithm that generates unusually long sequences of pseudorandom numbers executed by digital processor that includes such circuits. Concepts particularly advantageous for such applications as spread-spectrum communications, cryptography, and generation of ranging codes, synthetic noise, and test data, where usually desirable to make pseudorandom sequences as long as possible.

A comparison of in situ and airborne radar observations of ocean wave directionality

NASA Technical Reports Server (NTRS)

Jackson, F. C.; Walton, W. T.; Peng, C. Y.

1985-01-01

The directional spectrum of a fully arisen, about 3 m sea as measured by an experimental airborne radar, the NASA K(u)-band radar ocean wave spectrometer (ROWS), is compared to reference pitch-roll buoy data and to the classical SWOP (stereo wave observations project) spectrum for fully developed conditions. The ROWS spectrum, inferred indirectly from backscattered power measurements at 5-km altitude, is shown to be in excellent agreement with the buoy spectrum. Specifically, excellent agreement is found between the two nondirectional height spectra, and mean wave directions and directional spreads as functions of frequency. A comparison of the ROWS and SWOP spectra shows the two spectra to be very similar, in detailed shape as well as in terms of the gross spreading characteristics. Both spectra are seen to exhibit bimodal structures which accord with the Phillips' (1958) resonance mechanism. This observation is thus seen to support Phillips' contention that the SWOP modes were indeed resonance modes, not statistical artifacts.

Hybrid spread spectrum radio system

DOEpatents

Smith, Stephen F.; Dress, William B.

2010-02-02

Systems and methods are described for hybrid spread spectrum radio systems. A method includes modulating a signal by utilizing a subset of bits from a pseudo-random code generator to control an amplification circuit that provides a gain to the signal. Another method includes: modulating a signal by utilizing a subset of bits from a pseudo-random code generator to control a fast hopping frequency synthesizer; and fast frequency hopping the signal with the fast hopping frequency synthesizer, wherein multiple frequency hops occur within a single data-bit time.

De novo protein sequencing by combining top-down and bottom-up tandem mass spectra.

PubMed

Liu, Xiaowen; Dekker, Lennard J M; Wu, Si; Vanduijn, Martijn M; Luider, Theo M; Tolić, Nikola; Kou, Qiang; Dvorkin, Mikhail; Alexandrova, Sonya; Vyatkina, Kira; Paša-Tolić, Ljiljana; Pevzner, Pavel A

2014-07-03

There are two approaches for de novo protein sequencing: Edman degradation and mass spectrometry (MS). Existing MS-based methods characterize a novel protein by assembling tandem mass spectra of overlapping peptides generated from multiple proteolytic digestions of the protein. Because each tandem mass spectrum covers only a short peptide of the target protein, the key to high coverage protein sequencing is to find spectral pairs from overlapping peptides in order to assemble tandem mass spectra to long ones. However, overlapping regions of peptides may be too short to be confidently identified. High-resolution mass spectrometers have become accessible to many laboratories. These mass spectrometers are capable of analyzing molecules of large mass values, boosting the development of top-down MS. Top-down tandem mass spectra cover whole proteins. However, top-down tandem mass spectra, even combined, rarely provide full ion fragmentation coverage of a protein. We propose an algorithm, TBNovo, for de novo protein sequencing by combining top-down and bottom-up MS. In TBNovo, a top-down tandem mass spectrum is utilized as a scaffold, and bottom-up tandem mass spectra are aligned to the scaffold to increase sequence coverage. Experiments on data sets of two proteins showed that TBNovo achieved high sequence coverage and high sequence accuracy.

Bounds on the cross-correlation functions of state m-sequences

NASA Astrophysics Data System (ADS)

Woodcock, C. F.; Davies, Phillip A.; Shaar, Ahmed A.

1987-03-01

Lower and upper bounds on the peaks of the periodic Hamming cross-correlation function for state m-sequences, which are often used in frequency-hopped spread-spectrum systems, are derived. The state position mapped (SPM) sequences of the state m-sequences are described. The use of SPM sequences for OR-channel code division multiplexing is studied. The relation between the Hamming cross-correlation function and the correlation function of SPM sequence is examined. Numerical results which support the theoretical data are presented.

Fast converging minimum probability of error neural network receivers for DS-CDMA communications.

PubMed

Matyjas, John D; Psaromiligkos, Ioannis N; Batalama, Stella N; Medley, Michael J

2004-03-01

We consider a multilayer perceptron neural network (NN) receiver architecture for the recovery of the information bits of a direct-sequence code-division-multiple-access (DS-CDMA) user. We develop a fast converging adaptive training algorithm that minimizes the bit-error rate (BER) at the output of the receiver. The adaptive algorithm has three key features: i) it incorporates the BER, i.e., the ultimate performance evaluation measure, directly into the learning process, ii) it utilizes constraints that are derived from the properties of the optimum single-user decision boundary for additive white Gaussian noise (AWGN) multiple-access channels, and iii) it embeds importance sampling (IS) principles directly into the receiver optimization process. Simulation studies illustrate the BER performance of the proposed scheme.

Genomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough.

PubMed

Bouchez, Valérie; Guglielmini, Julien; Dazas, Mélody; Landier, Annie; Toubiana, Julie; Guillot, Sophie; Criscuolo, Alexis; Brisse, Sylvain

2018-06-01

Bordetella pertussis causes whooping cough, a highly contagious respiratory disease that is reemerging in many world regions. The spread of antigen-deficient strains may threaten acellular vaccine efficacy. Dynamics of strain transmission are poorly defined because of shortcomings in current strain genotyping methods. Our objective was to develop a whole-genome genotyping strategy with sufficient resolution for local epidemiologic questions and sufficient reproducibility to enable international comparisons of clinical isolates. We defined a core genome multilocus sequence typing scheme comprising 2,038 loci and demonstrated its congruence with whole-genome single-nucleotide polymorphism variation. Most cases of intrafamilial groups of isolates or of multiple isolates recovered from the same patient were distinguished from temporally and geographically cocirculating isolates. However, epidemiologically unrelated isolates were sometimes nearly undistinguishable. We set up a publicly accessible core genome multilocus sequence typing database to enable global comparisons of B. pertussis isolates, opening the way for internationally coordinated surveillance.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration.

PubMed

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K; Martin, Daniel B

2011-06-03

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate-limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper, we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching), is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA, which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment.

Rapid code acquisition algorithms employing PN matched filters

NASA Technical Reports Server (NTRS)

Su, Yu T.

1988-01-01

The performance of four algorithms using pseudonoise matched filters (PNMFs), for direct-sequence spread-spectrum systems, is analyzed. They are: parallel search with fix dwell detector (PL-FDD), parallel search with sequential detector (PL-SD), parallel-serial search with fix dwell detector (PS-FDD), and parallel-serial search with sequential detector (PS-SD). The operation characteristic for each detector and the mean acquisition time for each algorithm are derived. All the algorithms are studied in conjunction with the noncoherent integration technique, which enables the system to operate in the presence of data modulation. Several previous proposals using PNMF are seen as special cases of the present algorithms.

On the instability of wave-fields with JONSWAP spectra to inhomogeneous disturbances, and the consequent long-time evolution

NASA Astrophysics Data System (ADS)

Ribal, A.; Stiassnie, M.; Babanin, A.; Young, I.

2012-04-01

The instability of two-dimensional wave-fields and its subsequent evolution in time are studied by means of the Alber equation for narrow-banded random surface-waves in deep water subject to inhomogeneous disturbances. A linear partial differential equation (PDE) is obtained after applying an inhomogeneous disturbance to the Alber's equation and based on the solution of this PDE, the instability of the ocean wave surface is studied for a JONSWAP spectrum, which is a realistic ocean spectrum with variable directional spreading and steepness. The steepness of the JONSWAP spectrum depends on γ and α which are the peak-enhancement factor and energy scale of the spectrum respectively and it is found that instability depends on the directional spreading, α and γ. Specifically, if the instability stops due to the directional spreading, increase of the steepness by increasing α or γ can reactivate it. This result is in qualitative agreement with the recent large-scale experiment and new theoretical results. In the instability area of α-γ plane, a long-time evolution has been simulated by integrating Alber's equation numerically and recurrent evolution is obtained which is the stochastic counterpart of the Fermi-Pasta-Ulam recurrence obtained for the cubic Schrödinger equation.

High data rate modem simulation for the space station multiple-access communications system

NASA Technical Reports Server (NTRS)

Horan, Stephen

1987-01-01

The communications system for the space station will require a space based multiple access component to provide communications between the space based program elements and the station. A study was undertaken to investigate two of the concerns of this multiple access system, namely, the issues related to the frequency spectrum utilization and the possibilities for higher order (than QPSK) modulation schemes for use in possible modulators and demodulators (modems). As a result of the investigation, many key questions about the frequency spectrum utilization were raised. At this point, frequency spectrum utilization is seen as an area requiring further work. Simulations were conducted using a computer aided communications system design package to provide a straw man modem structure to be used for both QPSK and 8-PSK channels.

Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium.

PubMed

Li, Cheng-Lin Frank; Santhanam, Balaji; Webb, Amanda Nicole; Zupan, Blaž; Shaulsky, Gad

2016-09-01

Whole-genome sequencing is a useful approach for identification of chemical-induced lesions, but previous applications involved tedious genetic mapping to pinpoint the causative mutations. We propose that saturation mutagenesis under low mutagenic loads, followed by whole-genome sequencing, should allow direct implication of genes by identifying multiple independent alleles of each relevant gene. We tested the hypothesis by performing three genetic screens with chemical mutagenesis in the social soil amoeba Dictyostelium discoideum Through genome sequencing, we successfully identified mutant genes with multiple alleles in near-saturation screens, including resistance to intense illumination and strong suppressors of defects in an allorecognition pathway. We tested the causality of the mutations by comparison to published data and by direct complementation tests, finding both dominant and recessive causative mutations. Therefore, our strategy provides a cost- and time-efficient approach to gene discovery by integrating chemical mutagenesis and whole-genome sequencing. The method should be applicable to many microbial systems, and it is expected to revolutionize the field of functional genomics in Dictyostelium by greatly expanding the mutation spectrum relative to other common mutagenesis methods. © 2016 Li et al.; Published by Cold Spring Harbor Laboratory Press.

Sequence harmony: detecting functional specificity from alignments

PubMed Central

Feenstra, K. Anton; Pirovano, Walter; Krab, Klaas; Heringa, Jaap

2007-01-01

Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww. PMID:17584793

Young inversion with multiple linked QTLs under selection in a hybrid zone.

PubMed

Lee, Cheng-Ruei; Wang, Baosheng; Mojica, Julius P; Mandáková, Terezie; Prasad, Kasavajhala V S K; Goicoechea, Jose Luis; Perera, Nadeesha; Hellsten, Uffe; Hundley, Hope N; Johnson, Jenifer; Grimwood, Jane; Barry, Kerrie; Fairclough, Stephen; Jenkins, Jerry W; Yu, Yeisoo; Kudrna, Dave; Zhang, Jianwei; Talag, Jayson; Golser, Wolfgang; Ghattas, Kathryn; Schranz, M Eric; Wing, Rod; Lysak, Martin A; Schmutz, Jeremy; Rokhsar, Daniel S; Mitchell-Olds, Thomas

2017-04-03

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.

Young inversion with multiple linked QTLs under selection in a hybrid zone

PubMed Central

Lee, Cheng-Ruei; Wang, Baosheng; Mojica, Julius; Mandáková, Terezie; Prasad, Kasavajhala V. S. K.; Goicoechea, Jose Luis; Perera, Nadeesha; Hellsten, Uffe; Hundley, Hope N.; Johnson, Jenifer; Grimwood, Jane; Barry, Kerrie; Fairclough, Stephen; Jenkins, Jerry W.; Yu, Yeisoo; Kudrna, Dave; Zhang, Jianwei; Talag, Jayson; Golser, Wolfgang; Ghattas, Katherine; Schranz, M. Eric; Wing, Rod; Lysak, Martin A.; Schmutz, Jeremy; Rokhsar, Daniel S.; Mitchell-Olds, Thomas

2017-01-01

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favored alleles at multiple loci. However, it is unknown whether favored mutations slowly accumulate on older inversions or if young inversions spread because they capture preexisting adaptive Quantitative Trait Loci (QTLs). By genetic mapping, chromosome painting and genome sequencing we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation. PMID:28812690

A sequence database allowing automated genotyping of Classical swine fever virus isolates.

PubMed

Dreier, Sabrina; Zimmermann, Bernd; Moennig, Volker; Greiser-Wilke, Irene

2007-03-01

Classical swine fever (CSF) is a highly contagious viral disease of pigs. According to the OIE classification of diseases it is classified as a notifiable (previously List A) disease, thus having the potential for causing severe socio-economic problems and affecting severely the international trade of pigs and pig products. Effective control measures are compulsory, and to expose weaknesses a reliable tracing of the spread of the virus is necessary. Genetic typing has proved to be the method of choice. However, genotyping involves the use of multiple software applications, which is laborious and complex. The implementation of a sequence database, which is accessible by the World Wide Web with the option to type automatically new CSF virus isolates once the sequence is available is described. The sequence to be typed is tested for correct orientation and, if necessary, adjusted to the right length. The alignment and the neighbor-joining phylogenetic analysis with a standard set of sequences can then be calculated. The results are displayed as a graph. As an example, the determination is shown of the genetic subgroup of the isolate obtained from the outbreaks registered in Russia, in 2005. After registration (Irene.greiser-wilke@tiho-hannover.de) the database including the module for genotyping are accessible under http://viro08.tiho-hannover.de/eg/eurl_virus_db.htm.

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

PubMed

Smith, R F; Wiese, B A; Wojzynski, M K; Davison, D B; Worley, K C

1996-05-01

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

Performance of DS-CDMA with imperfect power control operating over a low earth orbiting satellite link

NASA Astrophysics Data System (ADS)

Vojcic, Branimir R.; Pickholtz, Raymond L.; Milstein, Laurence B.

1994-05-01

The analysis of both performance and capacity of direct sequence CDMA in terrestrial cellular systems has been addressed in the technical literature. It has been suggested that CDMA be used as a multiple access method for satellite systems as well, in particular for multispot beam Low Earth Orbit Satellites (LEOS). One is tempted to argue that since CDMA works well on terrestrial links, it will nominally work as well on satellite links. However, because there are fundamental differences in the characteristics of the two channels, such as larger time delays from the mobile to the base station and smaller multipath delay spreads on the satellite channels, the performance of CDMA on satellite links cannot always be accurately predicted from its performance on terrestrial channels. In this paper, we analytically derive the performance of a CDMA system which operates over a low earth orbiting satellite channel. We incorporate such effects as imperfect power control and dual-order diversity to obtain the average probability of error of a single user.

Center for Space Telemetering and Telecommunications Systems, New Mexico State University

NASA Technical Reports Server (NTRS)

Horan, Stephen; DeLeon, Phillip; Borah, Deva; Lyman, Ray

2002-01-01

This viewgraph presentation gives an overview of the Center for Space Telemetering and Telecommunications Systems activities at New Mexico State University. Presentations cover the following topics: (1) small satellite communications, including nanosatellite radio and virtual satellite development; (2) modulation and detection studies, including details on smooth phase interpolated keying (SPIK) spectra and highlights of an adaptive turbo multiuser detector; (3) decoupled approaches to nonlinear ISI compensation; (4) space internet testing; (4) optical communication; (5) Linux-based receiver for lightweight optical communications without a laser in space, including software design, performance analysis, and the receiver algorithm; (6) carrier tracking hardware; and (7) subband transforms for adaptive direct sequence spread spectrum receivers.

Multi-Point Hermes Acoustic Modem for High-Speed, High-Frequency Acoustic Communications with Low-Frequency Acoustic Control Loop for Real-Time Transmission of AUV-Carried High-Resolution Images and Navigation Data in Support of Ship Hulls Inspection

DTIC Science & Technology

2013-08-31

13.3 µs) used in the data frame. The preamble uses direct-sequence spread spectrum (DSSS) to reduce the negative impact of fading. Three bits... ifr t covers one of the allocated hops of index  h i . The received reference symbol transmitted in hop   1,2,..., Hh i N is    ( )h...are recovered based on the phase difference between the constellation points demodulated from the sub-band m of the information symbol  ( ) ifr t

Coexistence Analysis of Civil Unmanned Aircraft Systems at Low Altitudes

NASA Astrophysics Data System (ADS)

Zhou, Yuzhe

2016-11-01

The requirement of unmanned aircraft systems in civil areas is growing. However, provisioning of flight efficiency and safety of unmanned aircraft has critical requirements on wireless communication spectrum resources. Current researches mainly focus on spectrum availability. In this paper, the unmanned aircraft system communication models, including the coverage model and data rate model, and two coexistence analysis procedures, i. e. the interference and noise ratio criterion and frequency-distance-direction criterion, are proposed to analyze spectrum requirements and interference results of the civil unmanned aircraft systems at low altitudes. In addition, explicit explanations are provided. The proposed coexistence analysis criteria are applied to assess unmanned aircraft systems' uplink and downlink interference performances and to support corresponding spectrum planning. Numerical results demonstrate that the proposed assessments and analysis procedures satisfy requirements of flexible spectrum accessing and safe coexistence among multiple unmanned aircraft systems.

Three children with autism spectrum disorder learn to perform a three-step communication sequence using an iPad®-based speech-generating device.

PubMed

Waddington, Hannah; Sigafoos, Jeff; Lancioni, Giulio E; O'Reilly, Mark F; van der Meer, Larah; Carnett, Amarie; Stevens, Michelle; Roche, Laura; Hodis, Flaviu; Green, Vanessa A; Sutherland, Dean; Lang, Russell; Marschik, Peter B

2014-12-01

Many children with autism spectrum disorder (ASD) have limited or absent speech and might therefore benefit from learning to use a speech-generating device (SGD). The purpose of this study was to evaluate a procedure aimed at teaching three children with ASD to use an iPad(®)-based SGD to make a general request for access to toys, then make a specific request for one of two toys, and then communicate a thank-you response after receiving the requested toy. A multiple-baseline across participants design was used to determine whether systematic instruction involving least-to-most-prompting, time delay, error correction, and reinforcement was effective in teaching the three children to engage in this requesting and social communication sequence. Generalization and follow-up probes were conducted for two of the three participants. With intervention, all three children showed improvement in performing the communication sequence. This improvement was maintained with an unfamiliar communication partner and during the follow-up sessions. With systematic instruction, children with ASD and severe communication impairment can learn to use an iPad-based SGD to complete multi-step communication sequences that involve requesting and social communication functions. Copyright © 2014 ISDN. Published by Elsevier Ltd. All rights reserved.

Multiple alignment analysis on phylogenetic tree of the spread of SARS epidemic using distance method

NASA Astrophysics Data System (ADS)

Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.

2017-09-01

Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.

Direct RNA-Based Detection and Differentiation of CTX-M-Type Extended-Spectrum β-Lactamases (ESBL)

PubMed Central

Stein, Claudia; Makarewicz, Oliwia; Pfeifer, Yvonne; Brandt, Christian; Ramos, João Costa; Klinger, Mareike; Pletz, Mathias W.

2013-01-01

The current global spread of multi-resistant Gram-negatives, particularly extended spectrum β-lactamases expressing bacteria, increases the likelihood of inappropriate empiric treatment of critically ill patients with subsequently increased mortality. From a clinical perspective, fast detection of resistant pathogens would allow a pre-emptive correction of an initially inappropriate treatment. Here we present diagnostic amplification-sequencing approach as proof of principal based on the fast molecular detection and correct discrimination of CTX-M-β-lactamases, the most frequent ESBL family. The workflow consists of the isolation of total mRNA and CTX-M-specific reverse transcription (RT), amplification and pyrosequencing. Due to the high variability of the CTX-M-β-lactamase-genes, degenerated primers for RT, qRT as well as for pyrosequencing, were used and the suitability and discriminatory performance of two conserved positions within the CTX-M genes were analyzed, using one protocol for all isolates and positions, respectively. Using this approach, no information regarding the expected CTX-M variant is needed since all sequences are covered by these degenerated primers. The presented workflow can be conducted within eight hours and has the potential to be expanded to other β-lactamase families. PMID:24224038

Non-Orthogonal Multiple Access for Ubiquitous Wireless Sensor Networks.

PubMed

Anwar, Asim; Seet, Boon-Chong; Ding, Zhiguo

2018-02-08

Ubiquitous wireless sensor networks (UWSNs) have become a critical technology for enabling smart cities and other ubiquitous monitoring applications. Their deployment, however, can be seriously hampered by the spectrum available to the sheer number of sensors for communication. To support the communication needs of UWSNs without requiring more spectrum resources, the power-domain non-orthogonal multiple access (NOMA) technique originally proposed for 5th Generation (5G) cellular networks is investigated for UWSNs for the first time in this paper. However, unlike 5G networks that operate in the licensed spectrum, UWSNs mostly operate in unlicensed spectrum where sensors also experience cross-technology interferences from other devices sharing the same spectrum. In this paper, we model the interferences from various sources at the sensors using stochastic geometry framework. To evaluate the performance, we derive a theorem and present new closed form expression for the outage probability of the sensors in a downlink scenario under interference limited environment. In addition, diversity analysis for the ordered NOMA users is performed. Based on the derived outage probability, we evaluate the average link throughput and energy consumption efficiency of NOMA against conventional orthogonal multiple access (OMA) technique in UWSNs. Further, the required computational complexity for the NOMA users is presented.

Fast parallel tandem mass spectral library searching using GPU hardware acceleration

PubMed Central

Baumgardner, Lydia Ashleigh; Shanmugam, Avinash Kumar; Lam, Henry; Eng, Jimmy K.; Martin, Daniel B.

2011-01-01

Mass spectrometry-based proteomics is a maturing discipline of biologic research that is experiencing substantial growth. Instrumentation has steadily improved over time with the advent of faster and more sensitive instruments collecting ever larger data files. Consequently, the computational process of matching a peptide fragmentation pattern to its sequence, traditionally accomplished by sequence database searching and more recently also by spectral library searching, has become a bottleneck in many mass spectrometry experiments. In both of these methods, the main rate limiting step is the comparison of an acquired spectrum with all potential matches from a spectral library or sequence database. This is a highly parallelizable process because the core computational element can be represented as a simple but arithmetically intense multiplication of two vectors. In this paper we present a proof of concept project taking advantage of the massively parallel computing available on graphics processing units (GPUs) to distribute and accelerate the process of spectral assignment using spectral library searching. This program, which we have named FastPaSS (for Fast Parallelized Spectral Searching) is implemented in CUDA (Compute Unified Device Architecture) from NVIDIA which allows direct access to the processors in an NVIDIA GPU. Our efforts demonstrate the feasibility of GPU computing for spectral assignment, through implementation of the validated spectral searching algorithm SpectraST in the CUDA environment. PMID:21545112

A Brief Survey of Media Access Control, Data Link Layer, and Protocol Technologies for Lunar Surface Communications

NASA Technical Reports Server (NTRS)

Wallett, Thomas M.

2009-01-01

This paper surveys and describes some of the existing media access control and data link layer technologies for possible application in lunar surface communications and the advanced wideband Direct Sequence Code Division Multiple Access (DSCDMA) conceptual systems utilizing phased-array technology that will evolve in the next decade. Time Domain Multiple Access (TDMA) and Code Division Multiple Access (CDMA) are standard Media Access Control (MAC) techniques that can be incorporated into lunar surface communications architectures. Another novel hybrid technique that is recently being developed for use with smart antenna technology combines the advantages of CDMA with those of TDMA. The relatively new and sundry wireless LAN data link layer protocols that are continually under development offer distinct advantages for lunar surface applications over the legacy protocols which are not wireless. Also several communication transport and routing protocols can be chosen with characteristics commensurate with smart antenna systems to provide spacecraft communications for links exhibiting high capacity on the surface of the Moon. The proper choices depend on the specific communication requirements.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

All-Optical Fibre Networks For Coal Mines

NASA Astrophysics Data System (ADS)

Zientkiewicz, Jacek K.

1987-09-01

A topic of the paper is fiber-optic integrated network (FOIN) suited to the most hostile environments existing in coal mines. The use of optical fibres for transmission of mine instrumentation data offers the prospects of improved safety and immunity to electromagnetic interference (EMI). The feasibility of optically powered sensors has opened up new opportunities for research into optical signal processing architectures. This article discusses a new fibre-optic sensor network involving a time domain multiplexing(TDM)scheme and optical signal processing techniques. The pros and cons of different FOIN topologies with respect to coal mine applications are considered. The emphasis has been placed on a recently developed all-optical fibre network using spread spectrum code division multiple access (COMA) techniques. The all-optical networks have applications in explosive environments where electrical isolation is required.

A Unified Directional Spectrum for Long and Short Wind-Driven Waves

NASA Technical Reports Server (NTRS)

Elfouhaily, T.; Chapron, B.; Katsaros, K.; Vandemark, D.

1997-01-01

Review of several recent ocean surface wave models finds that while comprehensive in many regards, these spectral models do not satisfy certain additional, but fundamental, criteria. We propose that these criteria include the ability to properly describe diverse fetch conditions and to provide agreement with in situ observations of Cox and Munk [1954] and Jiihne and Riemer [1990] and Hara et al. [1994] data in the high-wavenumber regime. Moreover, we find numerous analytically undesirable aspects such as discontinuities across wavenumber limits, nonphysical tuning or adjustment parameters, and noncentrosymmetric directional spreading functions. This paper describes a two-dimensional wavenumber spectrum valid over all wavenumbers and analytically amenable to usage in electromagnetic models. The two regime model is formulated based on the Joint North Sea Wave Project (JONSWAP) in the long-wave regime and on the work of Phillips [1985] and Kitaigorodskii [1973] at the high wavenumbers. The omnidirectional and wind-dependent spectrum is constructed to agree with past and recent observations including the criteria mentioned above. The key feature of this model is the similarity of description for the high- and low-wavenumber regimes; both forms are posed to stress that the air-sea interaction process of friction between wind and waves (i.e., generalized wave age, u/c) is occurring at all wavelengths simultaneously. This wave age parameterization is the unifying feature of the spectrum. The spectrum's directional spreading function is symmetric about the wind direction and has both wavenumber and wind speed dependence. A ratio method is described that enables comparison of this spreading function with previous noncentrosymmetric forms. Radar data are purposefully excluded from this spectral development. Finally, a test of the spectrum is made by deriving roughness length using the boundary layer model of Kitaigorodskii. Our inference of drag coefficient versus wind speed and wave age shows encouraging agreement with Humidity Exchange Over the Sea (HEXOS) campaign results.

Evaluation of electrosurgical interference to low-power spread-spectrum local area net transceivers.

PubMed

Gibby, G L; Schwab, W K; Miller, W C

1997-11-01

To study whether an electrosurgery device interferes with the operation of a low-power spread-spectrum wireless network adapter. Nonrandomized, unblinded trials with controls, conducted in the corridor of our institution's operating suite using two portable computers equipped with RoamAbout omnidirectional 250 mW spread-spectrum 928 MHz wireless network adapters. To simulate high power electrosurgery interference, a 100-watt continuous electrocoagulation arc was maintained five feet from the receiving adapter, while device reported signal to noise values were measured at 150 feet and 400 feet distance between the wireless-networked computers. At 150 feet range, and with continuous 100-watt electrocoagulation arc five feet from one computer, error-corrected local area net throughput was measured by sending and receiving a large file multiple times. The reported signal to noise (N = 50) decreased with electrocoagulation from 36.42+/-3.47 (control) to 31.85+/-3.64 (electrocoagulation) (p < 0.001) at 400 feet inter-adapter distance, and from 64.53+/-1.43 (control) to 60.12+/-3.77 (electrocoagulation) (p < 0.001) at 150 feet inter-adapter distance. There was no statistically significant change in network throughput (average 93 kbyte/second) at 150 feet inter-adapter distance, either transmitting or receiving during continuous 100 Watt electrocoagulation arc. The manufacturer indicates "acceptable" performance will be obtained with signal to noise values as low as 20. In view of this, while electrocoagulation affects this spread spectrum network adapter, the effects are small even at 400 feet. At a distance of 150 feet, no discernible effect on network communications was found, suggesting that if other obstructions are minimal, within a wide range on one floor of an operating suite, network communications may be maintained using the technology of this wireless spread spectrum network adapter. The impact of such adapters on cardiac pacemakers should be studied. Wireless spread spectrum network adapters are an attractive technology for mobile computer communications in the operating room.

Detection and identification of cutaneous leishmaniasis isolates by culture, Polymerase chain reaction and sequence analyses in Syrian and Central Anatolia patients.

PubMed

Beyhan, Yunus E; Karakus, Mehmet; Karagoz, Alper; Mungan, Mesut; Ozkan, Aysegul T; Hokelek, Murat

2017-09-01

To characterize the cutaneous leishmaniasis (CL) isolates of Syrian and Central Anatolia patients at species levels. Methods: Skin scrapings of 3 patients (2 Syrian, 1 Turkish) were taken and examined by direct examination, culture in Novy-MacNeal-Nicole (NNN) medium, internal transcribed spacer polymerase chain reaction and sequence analysis (PCR). Results:According to microscopic examination, culture and PCR methods, 3 samples were detected positive. The sequencing results of all isolates in the study were identified as Leishmania tropica. The same genotypes were detected in the 3 isolates and nucleotide sequence submitted into GenBank with the accession number: KP689599. Conclusion: This finding could give information about the transmission of CL between Turkey and Syria. Because of the Syrian civil war, most of the Syrian citizens circulating in Turkey and different part of Europe, this can be increase the risk of spreading the disease. So, prevention measurements must be taken urgently.

Regional Spread of CTX-M-2-Producing Proteus mirabilis with the Identical Genetic Structure in Japan.

PubMed

Kato, Karin; Matsumura, Yasufumi; Yamamoto, Masaki; Nagao, Miki; Takakura, Shunji; Ichiyama, Satoshi

2017-07-01

In this study, we analyzed the molecular epidemiology of extended-spectrum β-lactamase (ESBL)-producing Proteus mirabilis isolates collected from the central region of Japan. Between 2005 and 2012, 820 clinical P. mirabilis isolates were obtained from ten acute care hospitals in Japan. We characterized ESBL confirmatory test-positive isolates by sequencing the ESBL genes and their flanking regions, detecting plasmid replicons, and performing pulsed-field gel electrophoresis (PFGE). Ninety-six isolates (12%) were positive according to the ESBL confirmatory test; all these isolates possessed bla CTX-M-2 with the same flanking structure of upstream ΔISEcp1 and a downstream region identical to downstream bla KLUA-1 . IncT was the prevalent, and only, replicon found in 63 isolates. PFGE analysis detected eight clusters with more than one isolate, among which three included 56 isolates and six included isolates from multiple hospitals. CTX-M-2-producing P. mirabilis with an identical genetic structure flanking bla CTX-M-2 is dominant in this Japanese region, and there is evidence for the clonal spread of isolates.

FD/DAMA Scheme For Mobile/Satellite Communications

NASA Technical Reports Server (NTRS)

Yan, Tsun-Yee; Wang, Charles C.; Cheng, Unjeng; Rafferty, William; Dessouky, Khaled I.

1992-01-01

Integrated-Adaptive Mobile Access Protocol (I-AMAP) proposed to allocate communication channels to subscribers in first-generation MSAT-X mobile/satellite communication network. Based on concept of frequency-division/demand-assigned multiple access (FD/DAMA) where partition of available spectrum adapted to subscribers' demands for service. Requests processed, and competing requests resolved according to channel-access protocol, or free-access tree algorithm described in "Connection Protocol for Mobile/Satellite Communications" (NPO-17735). Assigned spectrum utilized efficiently.

The Effects of Spatial Diversity and Imperfect Channel Estimation on Wideband MC-DS-CDMA and MC-CDMA

DTIC Science & Technology

2009-10-01

In our previous work, we compared the theoretical bit error rates of multi-carrier direct sequence code division multiple access (MC- DS - CDMA ) and...consider only those cases where MC- CDMA has higher frequency diversity than MC- DS - CDMA . Since increases in diversity yield diminishing gains, we conclude

Verification and Validation of the Coastal Modeling System. Report 3: CMS-Flow: Hydrodynamics

DTIC Science & Technology

2011-12-01

Jansen (1978) Spectrum TMA Directional spreading distribution Cosine Power Directional spreading parameter γ 3.3 Bottom friction Off (default...Ramp duration 3 hr The wave breaking formula applied was Battjes and Jansen (1978) because it is the recommended wave breaking formula when using...Li, Z.H., K.D. Nguyen , J.C. Brun-Cottan and J.M. Martin. 1994. Numerical simulation of the turbidity maximum transport in the Gironde Estuary (France

Narrowband Interference Suppression in Spread Spectrum Communication Systems

DTIC Science & Technology

1995-12-01

receiver input. As stated earlier, these waveforms must be sampled to obtain the discrete time sequences. The sampling theorem states: A bandlimited...From the FFT chips, the data is passed to a Plessey PDSP16330 Pythagoras Processor. The 16330 is a high-speed digital CMOS IC that converts real and

The NASA data systems standardization program - Radio frequency and modulation

NASA Technical Reports Server (NTRS)

Martin, W. L.

1983-01-01

The modifications being considered by the NASA-ESA Working Group (NEWG) for space-data-systems standardization to maximize the commonality of the NASA and ESA RF and modulation systems linking spaceborne scientific experiments with ground stations are summarized. The first phase of the NEWG project shows that the NASA MK-IVA Deep Space Network and Shuttle Interrogator (SI) systems in place or planned for 1985 are generally compatible with the ESA Network, but that communications involving the Tracking and Data Relay Satellite (TDRS) are incompatible due to its use of spread-spectrum modulation, pseudonoise ranging, multiple-access channels, and Mbit/s data rates. Topics under study for the post-1985 period include low-bit-rate capability for the ESA Network, an optional 8-kHz command subcarrier for the SI, fixing the spacecraft-transponder frequency-multiplication ratios for possible X-band uplinks or X-band nondeep-space downlinks, review of incompatible TDRS features, and development of the 32-GHz band.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

PubMed

Zeng, Victor; Extavour, Cassandra G

2012-01-01

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.

Iterative MMSE Detection for MIMO/BLAST DS-CDMA Systems in Frequency Selective Fading Channels - Achieving High Performance in Fully Loaded Systems

NASA Astrophysics Data System (ADS)

Silva, João Carlos; Souto, Nuno; Cercas, Francisco; Dinis, Rui

A MMSE (Minimum Mean Square Error) DS-CDMA (Direct Sequence-Code Division Multiple Access) receiver coupled with a low-complexity iterative interference suppression algorithm was devised for a MIMO/BLAST (Multiple Input, Multiple Output / Bell Laboratories Layered Space Time) system in order to improve system performance, considering frequency selective fading channels. The scheme is compared against the simple MMSE receiver, for both QPSK and 16QAM modulations, under SISO (Single Input, Single Output) and MIMO systems, the latter with 2Tx by 2Rx and 4Tx by 4Rx (MIMO order 2 and 4 respectively) antennas. To assess its performance in an existing system, the uncoded UMTS HSDPA (High Speed Downlink Packet Access) standard was considered.

An Investigation of the Effects of CRA Instruction and Students with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Stroizer, Shaunita; Hinton, Vanessa; Flores, Margaret; Terry, LaTonya

2015-01-01

Students with Autism Spectrum Disorders (ASD) have unique educational needs. The concrete representational abstract (CRA) instructional sequence has been shown effective in teaching students with mathematical difficulties. The purpose of this study was to examine the effects of the CRA sequence in teaching students with ASD. A multiple baseline…

The detection error of thermal test low-frequency cable based on M sequence correlation algorithm

NASA Astrophysics Data System (ADS)

Wu, Dongliang; Ge, Zheyang; Tong, Xin; Du, Chunlin

2018-04-01

The problem of low accuracy and low efficiency of off-line detecting on thermal test low-frequency cable faults could be solved by designing a cable fault detection system, based on FPGA export M sequence code(Linear feedback shift register sequence) as pulse signal source. The design principle of SSTDR (Spread spectrum time-domain reflectometry) reflection method and hardware on-line monitoring setup figure is discussed in this paper. Testing data show that, this detection error increases with fault location of thermal test low-frequency cable.

New Sequences with Low Correlation and Large Family Size

NASA Astrophysics Data System (ADS)

Zeng, Fanxin

In direct-sequence code-division multiple-access (DS-CDMA) communication systems and direct-sequence ultra wideband (DS-UWB) radios, sequences with low correlation and large family size are important for reducing multiple access interference (MAI) and accepting more active users, respectively. In this paper, a new collection of families of sequences of length pn-1, which includes three constructions, is proposed. The maximum number of cyclically distinct families without GMW sequences in each construction is φ(pn-1)/n·φ(pm-1)/m, where p is a prime number, n is an even number, and n=2m, and these sequences can be binary or polyphase depending upon choice of the parameter p. In Construction I, there are pn distinct sequences within each family and the new sequences have at most d+2 nontrivial periodic correlation {-pm-1, -1, pm-1, 2pm-1,…,dpm-1}. In Construction II, the new sequences have large family size p2n and possibly take the nontrivial correlation values in {-pm-1, -1, pm-1, 2pm-1,…,(3d-4)pm-1}. In Construction III, the new sequences possess the largest family size p(d-1)n and have at most 2d correlation levels {-pm-1, -1,pm-1, 2pm-1,…,(2d-2)pm-1}. Three constructions are near-optimal with respect to the Welch bound because the values of their Welch-Ratios are moderate, WR_??_d, WR_??_3d-4 and WR_??_2d-2, respectively. Each family in Constructions I, II and III contains a GMW sequence. In addition, Helleseth sequences and Niho sequences are special cases in Constructions I and III, and their restriction conditions to the integers m and n, pm≠2 (mod 3) and n≅0 (mod 4), respectively, are removed in our sequences. Our sequences in Construction III include the sequences with Niho type decimation 3·2m-2, too. Finally, some open questions are pointed out and an example that illustrates the performance of these sequences is given.

Quantum internet using code division multiple access

PubMed Central

Zhang, Jing; Liu, Yu-xi; Özdemir, Şahin Kaya; Wu, Re-Bing; Gao, Feifei; Wang, Xiang-Bin; Yang, Lan; Nori, Franco

2013-01-01

A crucial open problem inS large-scale quantum networks is how to efficiently transmit quantum data among many pairs of users via a common data-transmission medium. We propose a solution by developing a quantum code division multiple access (q-CDMA) approach in which quantum information is chaotically encoded to spread its spectral content, and then decoded via chaos synchronization to separate different sender-receiver pairs. In comparison to other existing approaches, such as frequency division multiple access (FDMA), the proposed q-CDMA can greatly increase the information rates per channel used, especially for very noisy quantum channels. PMID:23860488

Molecular characterization of two high-level ceftriaxone-resistant Neisseria gonorrhoeae isolates detected in Catalonia, Spain.

PubMed

Cámara, Jordi; Serra, Judit; Ayats, Josefina; Bastida, Teresa; Carnicer-Pont, Dolors; Andreu, Antònia; Ardanuy, Carmen

2012-08-01

The aim of this study was to characterize the first two extended-spectrum cephalosporin-resistant and multidrug-resistant (MDR) Neisseria gonorrhoeae isolates collected from two sexually related patients (men who have sex with men) in Spain. Antimicrobial susceptibility was studied by Etest. Genes involved in quinolone, ceftriaxone and multidrug resistance were amplified by PCR and sequenced in both directions. The isolates were typed by N. gonorrhoeae multi-antigen sequence typing (NG-MAST). The two isolates had the same MDR profile, showing resistance to penicillin (MIC 0.094 mg/L; β-lactamase negative), ceftriaxone (MIC 1.5 mg/L), cefixime (MIC 1.5 mg/L), cefotaxime (MIC 1 mg/L), ciprofloxacin (MIC >32 mg/L) and tetracycline (MIC 1.5 mg/L). NG-MAST showed that both isolates belonged to sequence type (ST) 1407 (porB-908 and tbpB-110). Ciprofloxacin resistance was due to amino acid substitutions in GyrA (S91F and D95G) and ParC (S87R). An A deletion in the promoter of the MtrCDE efflux pump (mtrR) was detected. No changes were detected in the pilQ gene. The outer membrane protein PorB showed two substitutions at G120K and A121N. An L421P substitution was observed in the PBP1A (ponA) sequence. The sequence of PBP2 (penA) showed a mosaic structure related to genotype XXXIV with a single additional amino acid substitution (A501P). This genotype was identical to a recently described French isolate (F89). This is the first reported case of high-level extended-spectrum cephalosporin-resistant N. gonorrhoeae transmission. The molecular typing and MDR genotype suggest possible European spread of this strain, highlighting the need for surveillance and the importance of testing the susceptibility of N. gonorrhoeae to extended-spectrum cephalosporins.

Multicarrier orthogonal spread-spectrum (MOSS) data communications

DOEpatents

Smith, Stephen F [London, TN; Dress, William B [Camas, WA

2008-01-01

Systems and methods are described for multicarrier orthogonal spread-spectrum (MOSS) data communication. A method includes individually spread-spectrum modulating at least two of a set of orthogonal frequency division multiplexed carriers, wherein the resulting individually spread-spectrum modulated at least two of a set of orthogonal frequency division multiplexed carriers are substantially mutually orthogonal with respect to both frequency division multiplexing and spread-spectrum modulation.

Optical Processing Techniques For Pseudorandom Sequence Prediction

NASA Astrophysics Data System (ADS)

Gustafson, Steven C.

1983-11-01

Pseudorandom sequences are series of apparently random numbers generated, for example, by linear or nonlinear feedback shift registers. An important application of these sequences is in spread spectrum communication systems, in which, for example, the transmitted carrier phase is digitally modulated rapidly and pseudorandomly and in which the information to be transmitted is incorporated as a slow modulation in the pseudorandom sequence. In this case the transmitted information can be extracted only by a receiver that uses for demodulation the same pseudorandom sequence used by the transmitter, and thus this type of communication system has a very high immunity to third-party interference. However, if a third party can predict in real time the probable future course of the transmitted pseudorandom sequence given past samples of this sequence, then interference immunity can be significantly reduced.. In this application effective pseudorandom sequence prediction techniques should be (1) applicable in real time to rapid (e.g., megahertz) sequence generation rates, (2) applicable to both linear and nonlinear pseudorandom sequence generation processes, and (3) applicable to error-prone past sequence samples of limited number and continuity. Certain optical processing techniques that may meet these requirements are discussed in this paper. In particular, techniques based on incoherent optical processors that perform general linear transforms or (more specifically) matrix-vector multiplications are considered. Computer simulation examples are presented which indicate that significant prediction accuracy can be obtained using these transforms for simple pseudorandom sequences. However, the useful prediction of more complex pseudorandom sequences will probably require the application of more sophisticated optical processing techniques.

Learning with Technology: Video Modeling with Concrete-Representational-Abstract Sequencing for Students with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Yakubova, Gulnoza; Hughes, Elizabeth M.; Shinaberry, Megan

2016-01-01

The purpose of this study was to determine the effectiveness of a video modeling intervention with concrete-representational-abstract instructional sequence in teaching mathematics concepts to students with autism spectrum disorder (ASD). A multiple baseline across skills design of single-case experimental methodology was used to determine the…

On Transform Domain Communication Systems under Spectrum Sensing Mismatch: A Deterministic Analysis.

PubMed

Jin, Chuanxue; Hu, Su; Huang, Yixuan; Luo, Qu; Huang, Dan; Li, Yi; Gao, Yuan; Cheng, Shaochi

2017-07-08

Towards the era of mobile Internet and the Internet of Things (IoT), numerous sensors and devices are being introduced and interconnected. To support such an amount of data traffic, traditional wireless communication technologies are facing challenges both in terms of the increasing shortage of spectrum resources and massive multiple access. The transform-domain communication system (TDCS) is considered as an alternative multiple access system, where 5G and mobile IoT are mainly focused. However, previous studies about TDCS are under the assumption that the transceiver has the global spectrum information, without the consideration of spectrum sensing mismatch (SSM). In this paper, we present the deterministic analysis of TDCS systems under arbitrary given spectrum sensing scenarios, especially the influence of the SSM pattern to the signal to noise ratio (SNR) performance. Simulation results show that arbitrary SSM pattern can lead to inferior bit error rate (BER) performance.

On Transform Domain Communication Systems under Spectrum Sensing Mismatch: A Deterministic Analysis

PubMed Central

Jin, Chuanxue; Hu, Su; Huang, Yixuan; Luo, Qu; Huang, Dan; Li, Yi; Cheng, Shaochi

2017-01-01

Towards the era of mobile Internet and the Internet of Things (IoT), numerous sensors and devices are being introduced and interconnected. To support such an amount of data traffic, traditional wireless communication technologies are facing challenges both in terms of the increasing shortage of spectrum resources and massive multiple access. The transform-domain communication system (TDCS) is considered as an alternative multiple access system, where 5G and mobile IoT are mainly focused. However, previous studies about TDCS are under the assumption that the transceiver has the global spectrum information, without the consideration of spectrum sensing mismatch (SSM). In this paper, we present the deterministic analysis of TDCS systems under arbitrary given spectrum sensing scenarios, especially the influence of the SSM pattern to the signal to noise ratio (SNR) performance. Simulation results show that arbitrary SSM pattern can lead to inferior bit error rate (BER) performance. PMID:28698477

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

PubMed

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

GLOBECOM '88 - IEEE Global Telecommunications Conference and Exhibition, Hollywood, FL, Nov. 28-Dec. 1, 1988, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

Various papers on communications for the information age are presented. Among the general topics considered are: telematic services and terminals, satellite communications, telecommunications mangaement network, control of integrated broadband networks, advances in digital radio systems, the intelligent network, broadband networks and services deployment, future switch architectures, performance analysis of computer networks, advances in spread spectrum, optical high-speed LANs, and broadband switching and networks. Also addressed are: multiple access protocols, video coding techniques, modulation and coding, photonic switching, SONET terminals and applications, standards for video coding, digital switching, progress in MANs, mobile and portable radio, software design for improved maintainability, multipath propagation and advanced countermeasure, data communication, network control and management, fiber in the loop, network algorithm and protocols, and advances in computer communications.

Priority and Negotiation Based Dynamic Spectrum Allocation Scheme for Multiple Radio Access Network Operators

NASA Astrophysics Data System (ADS)

Kim, Hoon; Hyon, Taein; Lee, Yeonwoo

Most of previous works have presented the dynamic spectrum allocation (DSA) gain achieved by utilizing the time or regional variations in traffic demand between multi-network operators (NOs). In this paper, we introduce the functionalities required for the entities related with the spectrum sharing and allocation and propose a spectrum allocation algorithm while considering the long-term priority between NOs, the priority between multiple class services, and the urgent bandwidth request. To take into account the priorities among the NOs and the priorities of multiple class services, a spectrum sharing metric (SSM) is proposed, while a negotiation procedure is proposed to treat the urgent bandwidth request.

Wideband propagation measurement system using spread spectrum signaling and TDRS

NASA Technical Reports Server (NTRS)

Jenkins, Jeffrey D.; Fan, Yiping; Osborne, William P.

1995-01-01

In this paper, a wideband propagation measurement system, which consisted of a ground-based transmitter, a mobile receiver, and a data acquisition system, was constructed. This system has been employed in a study of the characteristics of different propagation environments, such as urban, suburban and rural areas, by using a pseudonoise spreading sequence transmitted over NASA's Tracking and Data Relay Satellite System. The hardware and software tests showed that it met overall system requirements and it was very robust during a 3-month-long outdoor data collection experiment.

An FPGA-based DS-CDMA multiuser demodulator employing adaptive multistage parallel interference cancellation

NASA Astrophysics Data System (ADS)

Li, Xinhua; Song, Zhenyu; Zhan, Yongjie; Wu, Qiongzhi

2009-12-01

Since the system capacity is severely limited, reducing the multiple access interfere (MAI) is necessary in the multiuser direct-sequence code division multiple access (DS-CDMA) system which is used in the telecommunication terminals data-transferred link system. In this paper, we adopt an adaptive multistage parallel interference cancellation structure in the demodulator based on the least mean square (LMS) algorithm to eliminate the MAI on the basis of overviewing various of multiuser dectection schemes. Neither a training sequence nor a pilot signal is needed in the proposed scheme, and its implementation complexity can be greatly reduced by a LMS approximate algorithm. The algorithm and its FPGA implementation is then derived. Simulation results of the proposed adaptive PIC can outperform some of the existing interference cancellation methods in AWGN channels. The hardware setup of mutiuser demodulator is described, and the experimental results based on it demonstrate that the simulation results shows large performance gains over the conventional single-user demodulator.

A Simple Exact Error Rate Analysis for DS-CDMA with Arbitrary Pulse Shape in Flat Nakagami Fading

NASA Astrophysics Data System (ADS)

Rahman, Mohammad Azizur; Sasaki, Shigenobu; Kikuchi, Hisakazu; Harada, Hiroshi; Kato, Shuzo

A simple exact error rate analysis is presented for random binary direct sequence code division multiple access (DS-CDMA) considering a general pulse shape and flat Nakagami fading channel. First of all, a simple model is developed for the multiple access interference (MAI). Based on this, a simple exact expression of the characteristic function (CF) of MAI is developed in a straight forward manner. Finally, an exact expression of error rate is obtained following the CF method of error rate analysis. The exact error rate so obtained can be much easily evaluated as compared to the only reliable approximate error rate expression currently available, which is based on the Improved Gaussian Approximation (IGA).

MAI statistics estimation and analysis in a DS-CDMA system

NASA Astrophysics Data System (ADS)

Alami Hassani, A.; Zouak, M.; Mrabti, M.; Abdi, F.

2018-05-01

A primary limitation of Direct Sequence Code Division Multiple Access DS-CDMA link performance and system capacity is multiple access interference (MAI). To examine the performance of CDMA systems in the presence of MAI, i.e., in a multiuser environment, several works assumed that the interference can be approximated by a Gaussian random variable. In this paper, we first develop a new and simple approach to characterize the MAI in a multiuser system. In addition to statistically quantifying the MAI power, the paper also proposes a statistical model for both variance and mean of the MAI for synchronous and asynchronous CDMA transmission. We show that the MAI probability density function (PDF) is Gaussian for the equal-received-energy case and validate it by computer simulations.

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

PubMed

Huynh, Tien; Rigoutsos, Isidore

2004-07-01

In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification--directly from sequence--of structural deviations from alpha-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

Sequence History Update Tool

NASA Technical Reports Server (NTRS)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

Synchronization in spread spectrum laser radar systems based on PMD-DLL

NASA Astrophysics Data System (ADS)

Buxbaum, Bernd; Schwarte, Rudolf; Ringbeck, Thorsten; Luan, Xuming; Zhang, Zhigang; Xu, Zhanping; Hess, H.

2000-09-01

This paper proposes a new optoelectronic delay locked loop (OE-DLL) and its use in optical ranging systems. The so called PMD-DLL receiver module is based on a novel electro-optical modulator (EOM), called the Photonic Mixer Device (PMD). This sensor element is a semiconductor device, which combines fast optical sensing and mixing of incoherent light signals in one component part by its unique and powerful principle of operation. Integration of some simple additional on-chip components offers a high integrated electro-optical correlation unit. Simulations and experimental results have already impressively verified the operation principle of PMD structures, all realized in CMOS technology so far. Although other technologies are also promising candidates for the PMD realization they should not be further discussed in this contribution. The principle of the new DLL approach is intensively discussed in this paper. Theoretical analysis as well as experimental results of a realized PMD-DLL system are demonstrated and judged. Due to the operation principle of sophisticated PMD devices and their unique features, a correlation process may be realized in order to synchronize a reflected incoherent light wave with an electronic reference signal. The phase shift between both signals represents the distance to an obstacle and may be determined by means of the synchronization process. This new approach, avoiding so far needed critical components such as broadband amplifiers and mixers for the detection of small photo currents in optical distance measurement, offers an extremely fast and precise phase determination in ranging applications based on the time- of-flight (TOF) principle. However, the optical measurement signal may be incoherent -- therefore a laser source is not needed imperatively. The kind of waveform used for the modulation of the light signal is variable and depends on the demands of every specific application. Even if there are plenty other alternatives (e.g., heterodyne techniques), in this contribution only so called quasi-heterodyne techniques - - also known as phase shifting methods -- are discussed and used for the implementation. The light modulation schemes described in this contribution are square-wave as well as pseudo-noise modulation. The latter approach, inspired by the wide spread use in communication as well as in position detection (e.g., IS-95 and GPS), offers essential advantages and is the most promising modulation method for the ranging approach. So called CDMA (code division multiple access) systems form a major task in communication technology investigations since the third generation mobile phone standard is also partly based on this principle. Fast and reliable synchronization in direct sequence spread spectrum communication systems (DSSS) differs hardly from the already mentioned ranging approach and will also be discussed. The possibility to integrate all components in a monolithic PMD based DLL design is also presented and discussed. This method might offer the feature to integrate complete lines or matrixes of PMD based DLLs for highly parallel, multidimensional ranging. Finally, an outlook is given with regard to further optimized PMD front ends. An estimation of the expected characteristics concerning accuracy and speed of the distance measurement is given in conclusion.

SAW correlator spread spectrum receiver

DOEpatents

Brocato, Robert W

2014-04-01

A surface acoustic wave (SAW) correlator spread-spectrum (SS) receiver is disclosed which utilizes a first demodulation stage with a chip length n and a second demodulation stage with a chip length m to decode a transmitted SS signal having a code length l=n.times.m which can be very long (e.g. up to 2000 chips or more). The first demodulation stage utilizes a pair of SAW correlators which demodulate the SS signal to generate an appropriate code sequence at an intermediate frequency which can then be fed into the second demodulation stage which can be formed from another SAW correlator, or by a digital correlator. A compound SAW correlator comprising two input transducers and a single output transducer is also disclosed which can be used to form the SAW correlator SS receiver, or for use in processing long code length signals.

Introduction of a new opto-electrical phase-locked loop in CMOS technology: the PMD-PLL

NASA Astrophysics Data System (ADS)

Ringbeck, Thorsten; Schwarte, Rudolf; Buxbaum, Bernd

1999-12-01

The huge and increasing need of information in the industrial world demands an enormous potential of bandwidth in telecommunication systems. Optical communication provides all participants with the whole spectrum of digital services like videophone, cable TV, video conferencing and online services. Especially fast and low cost opto-electrical receivers are badly needed in order to expand fiber networks to every home (FTTH--fiber to the home or FTTD--fiber to the desk, respectively). This paper proposes a new receiver structure which is designed to receiver optical data which are encoded by code division multiple access techniques (CDMA). For data recovery in such CDMA networks phase locked loops (PLL) are needed, which synchronize the local oscillator with the incoming clock. In optical code division multiple access networks these PLLs could be realized either with an electrical PLL after opto-electrical converting or directly in the optical path with a pure optical PLL.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

PubMed

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

The Degradome database: mammalian proteases and diseases of proteolysis.

PubMed

Quesada, Víctor; Ordóñez, Gonzalo R; Sánchez, Luis M; Puente, Xose S; López-Otín, Carlos

2009-01-01

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes.

The Degradome database: mammalian proteases and diseases of proteolysis

PubMed Central

Quesada, Víctor; Ordóñez, Gonzalo R.; Sánchez, Luis M.; Puente, Xose S.; López-Otín, Carlos

2009-01-01

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes. PMID:18776217

Clonally Related Neisseria gonorrhoeae Isolates with Decreased Susceptibility to the Extended-Spectrum Cephalosporin Cefotaxime in Amsterdam, the Netherlands

PubMed Central

Heymans, Raymond; Bruisten, Sylvia M.; Golparian, Daniel; Unemo, Magnus; de Vries, Henry J. C.

2012-01-01

From 2006 to 2008, Neisseria gonorrhoeae isolates were identified with decreased susceptibility to the extended-spectrum cephalosporin (ESC) cefotaxime among visitors of the Amsterdam sexually transmitted infections (STI) clinic, the Netherlands. Spread, clonality, and characteristics of 202 isolates were examined using antibiograms, conventional penA mosaic gene PCR, and N. gonorrhoeae multiple-locus variable-number tandem repeat analysis (NG-MLVA). A strictly defined subset was further characterized by N. gonorrhoeae multiantigen sequence typing (NG-MAST) and sequencing of ESC resistance determinants (penA, mtrR, and porB1b). Seventy-four N. gonorrhoeae isolates with a cefotaxime MIC of >0.125 μg/ml (group A), 54 with a cefotaxime MIC of 0.125 μg/ml (group B), and a control group of 74 with a cefotaxime MIC of <0.125 μg/ml (group C) were included. Fifty-three clonally related penA mosaic-positive isolates (penicillin-binding protein 2 type XXXIV) were identified in group A (n = 47 isolates; 64%) and B (n = 6 isolates; 11%). The 53 penA mosaic-positive isolates were predominantly NG-MAST ST1407 (87%) and contained an mtrR promoter A deletion (98%) and porB1b alterations G101K/A102N. All were assigned to the same NG-MLVA cluster that comprised in total 56 isolates. A correlation was found between decreased cefotaxime susceptibility and ST1407 that was highly prevalent among visitors of the Amsterdam STI clinic. The rapid spread of this strain, which also has been identified in many other countries, might be facilitated by high-risk sexual behavior and should be monitored closely to identify potential treatment failure. Quality-assured surveillance of ESC susceptibility on the national and international levels and exploration of new drugs and/or strategies for treatment of gonorrhea are crucial. PMID:22214779

Self-synchronization for spread spectrum audio watermarks after time scale modification

NASA Astrophysics Data System (ADS)

Nadeau, Andrew; Sharma, Gaurav

2014-02-01

De-synchronizing operations such as insertion, deletion, and warping pose significant challenges for watermarking. Because these operations are not typical for classical communications, watermarking techniques such as spread spectrum can perform poorly. Conversely, specialized synchronization solutions can be challenging to analyze/ optimize. This paper addresses desynchronization for blind spread spectrum watermarks, detected without reference to any unmodified signal, using the robustness properties of short blocks. Synchronization relies on dynamic time warping to search over block alignments to find a sequence with maximum correlation to the watermark. This differs from synchronization schemes that must first locate invariant features of the original signal, or estimate and reverse desynchronization before detection. Without these extra synchronization steps, analysis for the proposed scheme builds on classical SS concepts and allows characterizes the relationship between the size of search space (number of detection alignment tests) and intrinsic robustness (continuous search space region covered by each individual detection test). The critical metrics that determine the search space, robustness, and performance are: time-frequency resolution of the watermarking transform, and blocklength resolution of the alignment. Simultaneous robustness to (a) MP3 compression, (b) insertion/deletion, and (c) time-scale modification is also demonstrated for a practical audio watermarking scheme developed in the proposed framework.

ICC '86; Proceedings of the International Conference on Communications, Toronto, Canada, June 22-25, 1986, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

Papers are presented on ISDN, mobile radio systems and techniques for digital connectivity, centralized and distributed algorithms in computer networks, communications networks, quality assurance and impact on cost, adaptive filters in communications, the spread spectrum, signal processing, video communication techniques, and digital satellite services. Topics discussed include performance evaluation issues for integrated protocols, packet network operations, the computer network theory and multiple-access, microwave single sideband systems, switching architectures, fiber optic systems, wireless local communications, modulation, coding, and synchronization, remote switching, software quality, transmission, and expert systems in network operations. Consideration is given to wide area networks, image and speech processing, office communications application protocols, multimedia systems, customer-controlled network operations, digital radio systems, channel modeling and signal processing in digital communications, earth station/on-board modems, computer communications system performance evaluation, source encoding, compression, and quantization, and adaptive communications systems.

Transverse strain measurements using fiber optic grating based sensors

NASA Technical Reports Server (NTRS)

Udd, Eric (Inventor)

1998-01-01

A system and method to sense the application of transverse stress to an optical fiber which includes a light source that producing a relatively wide spectrum light beam. The light beam is reflected or transmitted off of an optical grating in the core of an optical fiber that is transversely stressed either directly or by the exposure to pressure when the fiber is bifringent so that the optical fiber responds to the pressure to transversely stress its core. When transversely stressed, the optical grating produces a reflection or transmission from the light beam that has two peaks or minimums in its frequency spectrum whose spacing and/or spread are indicative of the forces applied to the fiber. One or more detectors sense the reflection or transmissions from the optical grating to produce an output representative of the applied force. Multiple optical gratings and detectors may be employed to simultaneously measure temperature or the forces at different locations along the fiber.

xiSPEC: web-based visualization, analysis and sharing of proteomics data.

PubMed

Kolbowski, Lars; Combe, Colin; Rappsilber, Juri

2018-05-08

We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.

Unified tensor model for space-frequency spreading-multiplexing (SFSM) MIMO communication systems

NASA Astrophysics Data System (ADS)

de Almeida, André LF; Favier, Gérard

2013-12-01

This paper presents a unified tensor model for space-frequency spreading-multiplexing (SFSM) multiple-input multiple-output (MIMO) wireless communication systems that combine space- and frequency-domain spreadings, followed by a space-frequency multiplexing. Spreading across space (transmit antennas) and frequency (subcarriers) adds resilience against deep channel fades and provides space and frequency diversities, while orthogonal space-frequency multiplexing enables multi-stream transmission. We adopt a tensor-based formulation for the proposed SFSM MIMO system that incorporates space, frequency, time, and code dimensions by means of the parallel factor model. The developed SFSM tensor model unifies the tensorial formulation of some existing multiple-access/multicarrier MIMO signaling schemes as special cases, while revealing interesting tradeoffs due to combined space, frequency, and time diversities which are of practical relevance for joint symbol-channel-code estimation. The performance of the proposed SFSM MIMO system using either a zero forcing receiver or a semi-blind tensor-based receiver is illustrated by means of computer simulation results under realistic channel and system parameters.

Heterogeneity in multiple transmission pathways: modelling the spread of cholera and other waterborne disease in networks with a common water source.

PubMed

Robertson, Suzanne L; Eisenberg, Marisa C; Tien, Joseph H

2013-01-01

Many factors influencing disease transmission vary throughout and across populations. For diseases spread through multiple transmission pathways, sources of variation may affect each transmission pathway differently. In this paper we consider a disease that can be spread via direct and indirect transmission, such as the waterborne disease cholera. Specifically, we consider a system of multiple patches with direct transmission occurring entirely within patch and indirect transmission via a single shared water source. We investigate the effect of heterogeneity in dual transmission pathways on the spread of the disease. We first present a 2-patch model for which we examine the effect of variation in each pathway separately and propose a measure of heterogeneity that incorporates both transmission mechanisms and is predictive of R(0). We also explore how heterogeneity affects the final outbreak size and the efficacy of intervention measures. We conclude by extending several results to a more general n-patch setting.

Quantifying spillover spreading for comparing instrument performance and aiding in multicolor panel design.

PubMed

Nguyen, Richard; Perfetto, Stephen; Mahnke, Yolanda D; Chattopadhyay, Pratip; Roederer, Mario

2013-03-01

After compensation, the measurement errors arising from multiple fluorescences spilling into each detector become evident by the spreading of nominally negative distributions. Depending on the instrument configuration and performance, and reagents used, this "spillover spreading" (SS) affects sensitivity in any given parameter. The degree of SS had been predicted theoretically to increase with measurement error, i.e., by the square root of fluorescence intensity, as well as directly related to the spectral overlap matrix coefficients. We devised a metric to quantify SS between any pair of detectors. This metric is intrinsic, as it is independent of fluorescence intensity. The combination of all such values for one instrument can be represented as a spillover spreading matrix (SSM). Single-stained controls were used to determine the SSM on multiple instruments over time, and under various conditions of signal quality. SSM values reveal fluorescence spectrum interactions that can limit the sensitivity of a reagent in the presence of brightly-stained cells on a different color. The SSM was found to be highly reproducible; its non-trivial values show a CV of less than 30% across a 2-month time frame. In addition, the SSM is comparable between similarly-configured instruments; instrument-specific differences in the SSM reveal underperforming detectors. Quantifying and monitoring the SSM can be a useful tool in instrument quality control to ensure consistent sensitivity and performance. In addition, the SSM is a key element for predicting the performance of multicolor immunofluorescence panels, which will aid in the optimization and development of new panels. We propose that the SSM is a critical component of QA/QC in evaluation of flow cytometer performance. Published 2013 Wiley Periodicals, Inc.

Video watermarking for mobile phone applications

NASA Astrophysics Data System (ADS)

Mitrea, M.; Duta, S.; Petrescu, M.; Preteux, F.

2005-08-01

Nowadays, alongside with the traditional voice signal, music, video, and 3D characters tend to become common data to be run, stored and/or processed on mobile phones. Hence, to protect their related intellectual property rights also becomes a crucial issue. The video sequences involved in such applications are generally coded at very low bit rates. The present paper starts by presenting an accurate statistical investigation on such a video as well as on a very dangerous attack (the StirMark attack). The obtained results are turned into practice when adapting a spread spectrum watermarking method to such applications. The informed watermarking approach was also considered: an outstanding method belonging to this paradigm has been adapted and re evaluated under the low rate video constraint. The experimental results were conducted in collaboration with the SFR mobile services provider in France. They also allow a comparison between the spread spectrum and informed embedding techniques.

Multiple introductions and recombination in Cryphonectria hypovirus 1: perspective for a sustainable biological control of chestnut blight

PubMed Central

Feau, Nicolas; Dutech, Cyril; Brusini, Jérémie; Rigling, Daniel; Robin, Cécile

2014-01-01

Cryphonectria hypovirus 1 (CHV1) is a mycovirus which decreases the virulence of its fungal host Cryphonectria parasitica, the causal agent of chestnut blight recently introduced in Europe. The understanding of the evolutionary processes which have shaped CHV1 populations in Europe is required to develop a sustainable biocontrol strategy targeting chestnut blight and effective in European chestnut forests. To retrace the evolutionary history of CHV1, we analyzed sequences from two genomic regions on a collection of 55 CHV1 strains from France and northern Spain, two countries where multiple introductions of C. parasitica occurred. Several recombination events and variable selection pressures contributed to CHV1 evolution, agreeing with a non-clock-like diversification rate. These two mechanisms may be at the origin of CHV1 population diversity observed in western Europe. Considering the actual prevalence of CHV1 and its association with host genotypes, multiple introductions of CHV1 may have occurred in Europe, some of them directly from Asia and some of them through North America. Although some viral strains remained with low frequency in their introduction area, multiple infections might have allowed homologous recombination within parental sequences. Some of these recombinant lineages are associated with the spread of CHV1 in European regions. PMID:24944571

Robustness evaluation of transactional audio watermarking systems

NASA Astrophysics Data System (ADS)

Neubauer, Christian; Steinebach, Martin; Siebenhaar, Frank; Pickel, Joerg

2003-06-01

Distribution via Internet is of increasing importance. Easy access, transmission and consumption of digitally represented music is very attractive to the consumer but led also directly to an increasing problem of illegal copying. To cope with this problem watermarking is a promising concept since it provides a useful mechanism to track illicit copies by persistently attaching property rights information to the material. Especially for online music distribution the use of so-called transaction watermarking, also denoted with the term bitstream watermarking, is beneficial since it offers the opportunity to embed watermarks directly into perceptually encoded material without the need of full decompression/compression. Besides the concept of bitstream watermarking, former publications presented the complexity, the audio quality and the detection performance. These results are now extended by an assessment of the robustness of such schemes. The detection performance before and after applying selected attacks is presented for MPEG-1/2 Layer 3 (MP3) and MPEG-2/4 AAC bitstream watermarking, contrasted to the performance of PCM spread spectrum watermarking.

Multiple Scattering Effects on Pulse Propagation in Optically Turbid Media.

NASA Astrophysics Data System (ADS)

Joelson, Bradley David

The effects of multiple scattering in a optically turbid media is examined for an impulse solution to the radiative transfer equation for a variety of geometries and phase functions. In regions where the complexities of the phase function proved too cumbersome for analytic methods Monte Carlo techniques were developed to describe the entire scalar radiance distribution. The determination of a general spread function is strongly dependent on geometry and particular regions where limits can be placed on the variables of the problem. Hence, the general spread function is first simplified by considering optical regions which reduce the complexity of the variable dependence. First, in the small-angle limit we calculate some contracted spread functions along with their moments and then use Monte Carlo techniques to establish the limitations imposed by the small-angle approximation in planar geometry. The point spread function (PSF) for a spherical geometry is calculated for the full angular spread in the forward direction of ocean waters using Monte Carlo methods in the optically thin and moderate depths and analytic methods in the diffusion domain. The angular dependence of the PSF for various ocean waters is examined for a range of optical parameters. The analytic method used in the diffusion calculation is justified by examining the angular dependence of the radiance of a impulse solution in a planar geometry for a prolongated Henyey-Greenstein phase function of asymmetry factor approximately equal to that of the ocean phase functions. The Legendre moments of the radiance are examined in order to examine the viability of the diffusion approximation which assumes a linearly anisotropic angular distribution for the radiance. A realistic lidar calculation is performed for a variety of ocean waters to determine the effects of multiple scattering on the determination of the speed of sound by using the range gated frequency spectrum of the lidar signal. It is shown that the optical properties of the ocean help to ensure single scatter form for the frequency spectra of the lidar signal. This spectra can then be used to compute the speed of sound and backscatter probability.

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update

PubMed Central

Huynh, Tien; Rigoutsos, Isidore

2004-01-01

In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification—directly from sequence—of structural deviations from α-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/. PMID:15215340

A Random Access Algorithm for Frequency Hopped Spread Spectrum Packet Radio Networks

DTIC Science & Technology

1986-03-01

in section 4.3, the probability p is given by the following expression. N rj 1-p - N1 (NR7-1). f -• (20)~ j=o j. F,=ji < N We now present a...Algorithms," Univ. of Connecticut, EECS Dept. Technical Report UCT/ DEECS /TR-86-1, January 1986. Also, submitted for publication. 119] W. Peterson and E

Performance enhancement of optical code-division multiple-access systems using transposed modified Walsh code

NASA Astrophysics Data System (ADS)

Sikder, Somali; Ghosh, Shila

2018-02-01

This paper presents the construction of unipolar transposed modified Walsh code (TMWC) and analysis of its performance in optical code-division multiple-access (OCDMA) systems. Specifically, the signal-to-noise ratio, bit error rate (BER), cardinality, and spectral efficiency were investigated. The theoretical analysis demonstrated that the wavelength-hopping time-spreading system using TMWC was robust against multiple-access interference and more spectrally efficient than systems using other existing OCDMA codes. In particular, the spectral efficiency was calculated to be 1.0370 when TMWC of weight 3 was employed. The BER and eye pattern for the designed TMWC were also successfully obtained using OptiSystem simulation software. The results indicate that the proposed code design is promising for enhancing network capacity.

A Space-Time Signal Decomposition Algorithm for Downlink MIMO DS-CDMA Receivers

NASA Astrophysics Data System (ADS)

Wang, Yung-Yi; Fang, Wen-Hsien; Chen, Jiunn-Tsair

We propose a dimension reduction algorithm for the receiver of the downlink of direct-sequence code-division multiple access (DS-CDMA) systems in which both the transmitters and the receivers employ antenna arrays of multiple elements. To estimate the high order channel parameters, we develop a layered architecture using dimension-reduced parameter estimation algorithms to estimate the frequency-selective multipath channels. In the proposed architecture, to exploit the space-time geometric characteristics of multipath channels, spatial beamformers and constrained (or unconstrained) temporal filters are adopted for clustered-multipath grouping and path isolation. In conjunction with the multiple access interference (MAI) suppression techniques, the proposed architecture jointly estimates the direction of arrivals, propagation delays, and fading amplitudes of the downlink fading multipaths. With the outputs of the proposed architecture, the signals of interest can then be naturally detected by using path-wise maximum ratio combining. Compared to the traditional techniques, such as the Joint-Angle-and-Delay-Estimation (JADE) algorithm for DOA-delay joint estimation and the space-time minimum mean square error (ST-MMSE) algorithm for signal detection, computer simulations show that the proposed algorithm substantially mitigate the computational complexity at the expense of only slight performance degradation.

Enhanced science capability on the International Space Station

NASA Astrophysics Data System (ADS)

Felice, Ronald R.; Kienlen, Mike

2002-12-01

It is inevitable that the International Space Station (ISS) will play a significant role in the conduct of science in space. However, in order to provide this service to a wide and broad community and to perform it cost effectively, alternative concepts must be considered to complement NASA"s Institutional capability. Currently science payload forward and return data services must compete for higher priority ISS infrastructure support requirements. Furthermore, initial astronaut crews will be limited to a single shift. Much of their time and activities will be required to meet their physical needs (exercise, recreation, etc.), station maintenance, and station operations, leaving precious little time to actively conduct science payload operations. ISS construction plans include the provisioning of several truss mounted, space-hardened pallets, both zenith and nadir facing. The ISS pallets will provide a platform to conduct both earth and space sciences. Additionally, the same pallets can be used for life and material sciences, as astronauts could place and retrieve sealed canisters for long-term micro-gravity exposure. Thus the pallets provide great potential for enhancing ISS science return. This significant addition to ISS payload capacity has the potential to exacerbate priorities and service contention factors within the exiting institution. In order to have it all, i.e., more science and less contention, the pallets must be data smart and operate autonomously so that NASA institutional services are not additionally taxed. Specifically, the "Enhanced Science Capability on the International Space Station" concept involves placing data handling and spread spectrum X-band communications capabilities directly on ISS pallets. Spread spectrum techniques are considered as a means of discriminating between different pallets as well as to eliminate RFI. The data and RF systems, similar to that of "free flyers", include a fully functional command and data handling system, providing, in part, science solid state recorders and instrument command management sub-systems. This, together with just one direct-to-ground based X-Band station co-located with a science payload operations center provides for a direct data path to ground, bypassing NASA institutions. The science center exists to receive user service requests, perform required constraint checks necessary for safe instrument operations, and to disseminate user science data. Payload commands can be up-linked directly or, if required, relayed through the existing NASA institution. The concept is modular for the downlink Earth terminals; in that multiple downlink X-band ground stations can be utilized throughout the world. This has applications for Earth science data direct to regional centers similar to those services provided by the EOS Terra spacecraft. However, for the purposes of this concept, just one downlink site was selected in order to define the worst-case data acquisition scenario necessary to ascertain concept feasibility. The paper demonstrates that the concept is feasible and can lead to a design that significantly reduces operational dependency on the NASA institutions and astronauts while significantly increasing ISS science operational efficiency and access.

Method for determining shear direction using liquid crystal coatings

NASA Technical Reports Server (NTRS)

Reda, Daniel C.

1995-01-01

A method is provided for determining shear direction wherein a beam of white light is directed onto the surface of a liquid crystal coating to cause the white light to be dispersed (reflected) from the surface in a spectrum having bands of different colors in a fixed spatial 2 (angular) sequence. The system is calibrated by locating an observer, e.g., a video and movie camera, such that a particular color band (preferably at or near the center of the reflected spectrum) is observed to thereby provide a reference color band. Because the application of shear causes either clockwise or counterclockwise rotation of the reflected spectrum dependent on the direction of the shear, a determination is then made of the reflected color band observed by the observer when the surface of the liquid crystal is subjected to shear to thereby determine the direction of the shear based on the directional (rotation) relation of the observed color band with respect to the reference color band in the spatial sequence of color bands.

Research Trends in Military Communications: Proceedings of a Workshop Held at Wickenburg, Arizona on 1-4 May 1983.

DTIC Science & Technology

1983-12-17

weeks bensuygthsfrRd-omn:’-" been studying this for Reed- Solomon ago and they are doing more than lookingintoit.The remakng gros 95 codes where the...were formed in four basic areas: ’a) array signal processing in the spread spectrum environment, (b) spread spectrum communication in jamming, (c...research areas. Panels were formed in four basic areas: (a) array signal processing in the spread spectrum environment, (b) spread spectrum

A review of recommendations for sequencing receptive and expressive language instruction.

PubMed

Petursdottir, Anna Ingeborg; Carr, James E

2011-01-01

We review recommendations for sequencing instruction in receptive and expressive language objectives in early and intensive behavioral intervention (EIBI) programs. Several books recommend completing receptive protocols before introducing corresponding expressive protocols. However, this recommendation has little empirical support, and some evidence exists that the reverse sequence may be more efficient. Alternative recommendations include teaching receptive and expressive skills simultaneously (M. L. Sundberg & Partington, 1998) and building learning histories that lead to acquisition of receptive and expressive skills without direct instruction (Greer & Ross, 2008). Empirical support for these recommendations also is limited. Future research should assess the relative efficiency of receptive-before-expressive, expressive-before-receptive, and simultaneous training with children who have diagnoses of autism spectrum disorders. In addition, further evaluation is needed of the potential benefits of multiple-exemplar training and other variables that may influence the efficiency of receptive and expressive instruction.

A REVIEW OF RECOMMENDATIONS FOR SEQUENCING RECEPTIVE AND EXPRESSIVE LANGUAGE INSTRUCTION

PubMed Central

Petursdottir, Anna Ingeborg; Carr, James E

2011-01-01

We review recommendations for sequencing instruction in receptive and expressive language objectives in early and intensive behavioral intervention (EIBI) programs. Several books recommend completing receptive protocols before introducing corresponding expressive protocols. However, this recommendation has little empirical support, and some evidence exists that the reverse sequence may be more efficient. Alternative recommendations include teaching receptive and expressive skills simultaneously (M. L. Sundberg & Partington, 1998) and building learning histories that lead to acquisition of receptive and expressive skills without direct instruction (Greer & Ross, 2008). Empirical support for these recommendations also is limited. Future research should assess the relative efficiency of receptive-before-expressive, expressive-before-receptive, and simultaneous training with children who have diagnoses of autism spectrum disorders. In addition, further evaluation is needed of the potential benefits of multiple-exemplar training and other variables that may influence the efficiency of receptive and expressive instruction. PMID:22219535

Isolation and mapping of telomeric pentanucleotide (TAACC)n repeats of the Pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization.

PubMed

Alcivar-Warren, Acacia; Meehan-Meola, Dawn; Wang, Yongping; Guo, Ximing; Zhou, Linghua; Xiang, Jianhai; Moss, Shaun; Arce, Steve; Warren, William; Xu, Zhenkang; Bell, Kireina

2006-01-01

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)n repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective 1 showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA)n, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1>P2>P3>P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Adaptive digital beamforming for a CDMA mobile communications payload

NASA Technical Reports Server (NTRS)

Munoz-Garcia, Samuel G.; Ruiz, Javier Benedicto

1993-01-01

In recent years, Spread-Spectrum Code Division Multiple Access (CDMA) has become a very popular access scheme for mobile communications due to a variety of reasons: excellent performance in multipath environments, high scope for frequency reuse, graceful degradation near saturation, etc. In this way, a CDMA system can support simultaneous digital communication among a large community of relatively uncoordinated users sharing a given frequency band. Nevertheless, there are also important problems associated with the use of CDMA. First, in a conventional CDMA scheme, the signature sequences of asynchronous users are not orthogonal and, as the number of active users increases, the self-noise generated by the mutual interference between users considerably degrades the performance, particularly in the return link. Furthermore, when there is a large disparity in received powers - due to differences in slant range or atmospheric attenuation - the non-zero cross-correlation between the signals gives rise to the so-called near-far problem. This leads to an inefficient utilization of the satellite resources and, consequently, to a drastic reduction in capacity. Several techniques were proposed to overcome this problem, such as Synchronized CDMA - in which the signature sequences of the different users are quasi-orthogonal - and power control. At the expense of increased network complexity and user coordination, these techniques enable the system capacity to be restored by equitably sharing the satellite resources among the users. An alternative solution is presented based upon the use of time-reference adaptive digital beamforming on board the satellite. This technique enables a high number of independently steered beams to be generated from a single phased array antenna, which automatically track the desired user signal and null the unwanted interference source. In order to use a time-reference adaptive antenna in a communications system, the main challenge is to obtain a reference signal highly correlated with the desired user signal and uncorrelated with the interferences. CDMA lends itself very easily to the generation of such a reference signal, thanks to the a priori knowledge of the user's signature sequence. First, the integration of an adaptive antenna in an asynchronous CDMA system is analyzed. The adaptive antenna system can provide increased interference rejection - much higher than that afforded by the code alone - and, since CDMA is mainly interference limited, any reduction in interference converts directly and linearly into an increase in capacity. Analyses and computer simulations are presented that show how an asynchronous CDMA system incorporating adaptive beamforming can provide at least as much capacity as a synchronous system. More importantly, the proposed concept allows the near-far effect to be mitigated without requiring a tight coordination of the users in terms of transmitted power control or network synchronization. The system is extremely robust to the near-far effect because the signals reaching the satellite from directions other than that of the desired user - which are likely to have different power levels - are adaptively canceled by the antenna. Finally, a payload architecture is presented that illustrates the practical implementation of this concept. This digital payload architecture demonstrates that with the advent of high performance CMOS digital processing, the on-board implementation of complex DSP techniques - in particular Digital Beamforming - has become possible, being most attractive for Mobile Satellite Communications.

Adaptive digital beamforming for a CDMA mobile communications payload

NASA Astrophysics Data System (ADS)

Munoz-Garcia, Samuel G.; Ruiz, Javier Benedicto

In recent years, Spread-Spectrum Code Division Multiple Access (CDMA) has become a very popular access scheme for mobile communications due to a variety of reasons: excellent performance in multipath environments, high scope for frequency reuse, graceful degradation near saturation, etc. In this way, a CDMA system can support simultaneous digital communication among a large community of relatively uncoordinated users sharing a given frequency band. Nevertheless, there are also important problems associated with the use of CDMA. First, in a conventional CDMA scheme, the signature sequences of asynchronous users are not orthogonal and, as the number of active users increases, the self-noise generated by the mutual interference between users considerably degrades the performance, particularly in the return link. Furthermore, when there is a large disparity in received powers - due to differences in slant range or atmospheric attenuation - the non-zero cross-correlation between the signals gives rise to the so-called near-far problem. This leads to an inefficient utilization of the satellite resources and, consequently, to a drastic reduction in capacity. Several techniques were proposed to overcome this problem, such as Synchronized CDMA - in which the signature sequences of the different users are quasi-orthogonal - and power control. At the expense of increased network complexity and user coordination, these techniques enable the system capacity to be restored by equitably sharing the satellite resources among the users. An alternative solution is presented based upon the use of time-reference adaptive digital beamforming on board the satellite. This technique enables a high number of independently steered beams to be generated from a single phased array antenna, which automatically track the desired user signal and null the unwanted interference source. In order to use a time-reference adaptive antenna in a communications system, the main challenge is to obtain a reference signal highly correlated with the desired user signal and uncorrelated with the interferences. CDMA lends itself very easily to the generation of such a reference signal, thanks to the a priori knowledge of the user's signature sequence. First, the integration of an adaptive antenna in an asynchronous CDMA system is analyzed. The adaptive antenna system can provide increased interference rejection - much higher than that afforded by the code alone - and, since CDMA is mainly interference limited, any reduction in interference converts directly and linearly into an increase in capacity. Analyses and computer simulations are presented that show how an asynchronous CDMA system incorporating adaptive beamforming can provide at least as much capacity as a synchronous system. More importantly, the proposed concept allows the near-far effect to be mitigated without requiring a tight coordination of the users in terms of transmitted power control or network synchronization. The system is extremely robust to the near-far effect because the signals reaching the satellite from directions other than that of the desired user - which are likely to have different power levels - are adaptively canceled by the antenna. Finally, a payload architecture is presented that illustrates the practical implementation of this concept.

Wave directional spreading from point field measurements.

PubMed

McAllister, M L; Venugopal, V; Borthwick, A G L

2017-04-01

Ocean waves have multidirectional components. Most wave measurements are taken at a single point, and so fail to capture information about the relative directions of the wave components directly. Conventional means of directional estimation require a minimum of three concurrent time series of measurements at different spatial locations in order to derive information on local directional wave spreading. Here, the relationship between wave nonlinearity and directionality is utilized to estimate local spreading without the need for multiple concurrent measurements, following Adcock & Taylor (Adcock & Taylor 2009 Proc. R. Soc. A 465 , 3361-3381. (doi:10.1098/rspa.2009.0031)), with the assumption that directional spreading is frequency independent. The method is applied to measurements recorded at the North Alwyn platform in the northern North Sea, and the results compared against estimates of wave spreading by conventional measurement methods and hindcast data. Records containing freak waves were excluded. It is found that the method provides accurate estimates of wave spreading over a range of conditions experienced at North Alwyn, despite the noisy chaotic signals that characterize such ocean wave data. The results provide further confirmation that Adcock and Taylor's method is applicable to metocean data and has considerable future promise as a technique to recover estimates of wave spreading from single point wave measurement devices.

Wave directional spreading from point field measurements

PubMed Central

Venugopal, V.; Borthwick, A. G. L.

2017-01-01

Ocean waves have multidirectional components. Most wave measurements are taken at a single point, and so fail to capture information about the relative directions of the wave components directly. Conventional means of directional estimation require a minimum of three concurrent time series of measurements at different spatial locations in order to derive information on local directional wave spreading. Here, the relationship between wave nonlinearity and directionality is utilized to estimate local spreading without the need for multiple concurrent measurements, following Adcock & Taylor (Adcock & Taylor 2009 Proc. R. Soc. A 465, 3361–3381. (doi:10.1098/rspa.2009.0031)), with the assumption that directional spreading is frequency independent. The method is applied to measurements recorded at the North Alwyn platform in the northern North Sea, and the results compared against estimates of wave spreading by conventional measurement methods and hindcast data. Records containing freak waves were excluded. It is found that the method provides accurate estimates of wave spreading over a range of conditions experienced at North Alwyn, despite the noisy chaotic signals that characterize such ocean wave data. The results provide further confirmation that Adcock and Taylor's method is applicable to metocean data and has considerable future promise as a technique to recover estimates of wave spreading from single point wave measurement devices. PMID:28484326

PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.

PubMed

Caffrey, Daniel R; Dana, Paul H; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E; Somaroo, Shyamal; Caffrey, Brian E; Potluri, Shobha; Huang, Enoch S

2007-10-11

By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.

Evolution and spread of Ebola virus in Liberia, 2014–2015

PubMed Central

Ladner, Jason T.; Wiley, Michael R.; Mate, Suzanne; Dudas, Gytis; Prieto, Karla; Lovett, Sean; Nagle, Elyse R.; Beitzel, Brett; Gilbert, Merle L.; Fakoli, Lawrence; Diclaro, Joseph W.; Schoepp, Randal J.; Fair, Joseph; Kuhn, Jens H.; Hensley, Lisa E.; Park, Daniel J.; Sabeti, Pardis C.; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Bolay, Fatorma K.; Kugelman, Jeffrey R.; Palacios, Gustavo

2015-01-01

SUMMARY The 2013–present Western African Ebola virus disease (EVD) outbreak is the largest ever recorded with >28,000 reported cases. Ebola virus (EBOV) genome sequencing has played an important role throughout this outbreak; however, relatively few sequences have been determined from patients in Liberia, the second worst-affected country. Here, we report 140 EBOV genome sequences from the second wave of the Liberian outbreak and analyze them in combination with 782 previously published sequences from throughout the Western African outbreak. While multiple early introductions of EBOV to Liberia are evident, the majority of Liberian EVD cases are consistent with a single introduction, followed by spread and diversification within the country. Movement of the virus within Liberia was widespread and reintroductions from Liberia served as an important source for the continuation of the already ongoing EVD outbreak in Guinea. Overall, little evidence was found for incremental adaptation of EBOV to the human host. PMID:26651942

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Future of human mitochondrial DNA editing technologies.

PubMed

Verechshagina, N; Nikitchina, N; Yamada, Y; Harashima, Н; Tanaka, M; Orishchenko, K; Mazunin, I

2018-05-15

ATP and other metabolites, which are necessary for the development, maintenance, and functioning of bodily cells are all synthesized in the mitochondria. Multiple copies of the genome, present within the mitochondria, together with its maternal inheritance, determine the clinical manifestation and spreading of mutations in mitochondrial DNA (mtDNA). The main obstacle in the way of thorough understanding of mitochondrial biology and the development of gene therapy methods for mitochondrial diseases is the absence of systems that allow to directly change mtDNA sequence. Here, we discuss existing methods of manipulating the level of mtDNA heteroplasmy, as well as the latest systems, that could be used in the future as tools for human mitochondrial genome editing.

Comparative Large-Scale Analysis of Interactions between Several Crop Species and the Effector Repertoires from Multiple Pathovars of Pseudomonas and Ralstonia1[W][OA

PubMed Central

Wroblewski, Tadeusz; Caldwell, Katherine S.; Piskurewicz, Urszula; Cavanaugh, Keri A.; Xu, Huaqin; Kozik, Alexander; Ochoa, Oswaldo; McHale, Leah K.; Lahre, Kirsten; Jelenska, Joanna; Castillo, Jose A.; Blumenthal, Daniel; Vinatzer, Boris A.; Greenberg, Jean T.; Michelmore, Richard W.

2009-01-01

Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell. PMID:19571308

Coding for spread spectrum packet radios

NASA Technical Reports Server (NTRS)

Omura, J. K.

1980-01-01

Packet radios are often expected to operate in a radio communication network environment where there tends to be man made interference signals. To combat such interference, spread spectrum waveforms are being considered for some applications. The use of convolutional coding with Viterbi decoding to further improve the performance of spread spectrum packet radios is examined. At 0.00001 bit error rates, improvements in performance of 4 db to 5 db can easily be achieved with such coding without any change in data rate nor spread spectrum bandwidth. This coding gain is more dramatic in an interference environment.

Secure information transmission in filter bank multi-carrier spread spectrum systems

DOE PAGES

Majid, Arslan; Moradi, Hussein; Farhang-Boroujeny, Behrouz

2015-12-17

This report discusses the issue of secure information transmission for a spread-spectrum system, which in our case is Filter-Bank Multi-Carrier spread spectrum (FB-MC SS). We develop a novel method for generating a secret key to augment the security of the spread spectrum system. The proposed key generation takes advantage of the channel reciprocity exhibited between two communicating parties.We validate the key generation aspect of our system by using real-world measurements. It is found that our augmentation of strongest path cancellation (SPC) is shown to be highly effective in our measurement scenarios where the adversary’s key would otherwise be significantly correlatedmore » with the legitimate nodes. Our approach in using the proposed key generation method as a part of FB-MC SS allows for it to be fault tolerant and it is not necessarily limited to FB-MC SS or spread-spectrum system in general. However, the advantage that our approach has in the domain of spread-spectrum security is that it significantly decorrelates the adversary’s key from the authentic parties. This aspect is crucial because if the adversary’s key is similar to the legitamate parties, then the adversary obtains a sizable advantage due to the fault tolerance nature of the developed spread spectrum key.« less

Secure information transmission in filter bank multi-carrier spread spectrum systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majid, Arslan; Moradi, Hussein; Farhang-Boroujeny, Behrouz

This report discusses the issue of secure information transmission for a spread-spectrum system, which in our case is Filter-Bank Multi-Carrier spread spectrum (FB-MC SS). We develop a novel method for generating a secret key to augment the security of the spread spectrum system. The proposed key generation takes advantage of the channel reciprocity exhibited between two communicating parties.We validate the key generation aspect of our system by using real-world measurements. It is found that our augmentation of strongest path cancellation (SPC) is shown to be highly effective in our measurement scenarios where the adversary’s key would otherwise be significantly correlatedmore » with the legitimate nodes. Our approach in using the proposed key generation method as a part of FB-MC SS allows for it to be fault tolerant and it is not necessarily limited to FB-MC SS or spread-spectrum system in general. However, the advantage that our approach has in the domain of spread-spectrum security is that it significantly decorrelates the adversary’s key from the authentic parties. This aspect is crucial because if the adversary’s key is similar to the legitamate parties, then the adversary obtains a sizable advantage due to the fault tolerance nature of the developed spread spectrum key.« less

Analysis of Extreme Phenotype Bulk Copy Number Variation (XP-CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize.

PubMed

Hu, Ying; Ren, Jie; Peng, Zhao; Umana, Arnoldo A; Le, Ha; Danilova, Tatiana; Fu, Junjie; Wang, Haiyan; Robertson, Alison; Hulbert, Scot H; White, Frank F; Liu, Sanzhen

2018-01-01

Goss's wilt (GW) of maize is caused by the Gram-positive bacterium Clavibacter michiganensis subsp. nebraskensis (Cmn) and has spread in recent years throughout the Great Plains, posing a threat to production. The genetic basis of plant resistance is unknown. Here, a simple method for quantifying disease symptoms was developed and used to select cohorts of highly resistant and highly susceptible lines known as extreme phenotypes (XP). Copy number variation (CNV) analyses using whole genome sequences of bulked XP revealed 141 genes containing CNV between the two XP groups. The CNV genes include the previously identified common rust resistant locus rp1 . Multiple Rp1 accessions with distinct rp1 haplotypes in an otherwise susceptible accession exhibited hypersensitive responses upon inoculation. GW provides an excellent system for the genetic dissection of diseases caused by closely related subspecies of C. michiganesis . Further work will facilitate breeding strategies to control GW and provide needed insight into the resistance mechanism of important related diseases such as bacterial canker of tomato and bacterial ring rot of potato.

Optimized scheduling technique of null subcarriers for peak power control in 3GPP LTE downlink.

PubMed

Cho, Soobum; Park, Sang Kyu

2014-01-01

Orthogonal frequency division multiple access (OFDMA) is a key multiple access technique for the long term evolution (LTE) downlink. However, high peak-to-average power ratio (PAPR) can cause the degradation of power efficiency. The well-known PAPR reduction technique, dummy sequence insertion (DSI), can be a realistic solution because of its structural simplicity. However, the large usage of subcarriers for the dummy sequences may decrease the transmitted data rate in the DSI scheme. In this paper, a novel DSI scheme is applied to the LTE system. Firstly, we obtain the null subcarriers in single-input single-output (SISO) and multiple-input multiple-output (MIMO) systems, respectively; then, optimized dummy sequences are inserted into the obtained null subcarrier. Simulation results show that Walsh-Hadamard transform (WHT) sequence is the best for the dummy sequence and the ratio of 16 to 20 for the WHT and randomly generated sequences has the maximum PAPR reduction performance. The number of near optimal iteration is derived to prevent exhausted iterations. It is also shown that there is no bit error rate (BER) degradation with the proposed technique in LTE downlink system.

Optimized Scheduling Technique of Null Subcarriers for Peak Power Control in 3GPP LTE Downlink

PubMed Central

Park, Sang Kyu

2014-01-01

Orthogonal frequency division multiple access (OFDMA) is a key multiple access technique for the long term evolution (LTE) downlink. However, high peak-to-average power ratio (PAPR) can cause the degradation of power efficiency. The well-known PAPR reduction technique, dummy sequence insertion (DSI), can be a realistic solution because of its structural simplicity. However, the large usage of subcarriers for the dummy sequences may decrease the transmitted data rate in the DSI scheme. In this paper, a novel DSI scheme is applied to the LTE system. Firstly, we obtain the null subcarriers in single-input single-output (SISO) and multiple-input multiple-output (MIMO) systems, respectively; then, optimized dummy sequences are inserted into the obtained null subcarrier. Simulation results show that Walsh-Hadamard transform (WHT) sequence is the best for the dummy sequence and the ratio of 16 to 20 for the WHT and randomly generated sequences has the maximum PAPR reduction performance. The number of near optimal iteration is derived to prevent exhausted iterations. It is also shown that there is no bit error rate (BER) degradation with the proposed technique in LTE downlink system. PMID:24883376

Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer

PubMed Central

Murchison, Elizabeth P.; Schulz-Trieglaff, Ole B.; Ning, Zemin; Alexandrov, Ludmil B.; Bauer, Markus J.; Fu, Beiyuan; Hims, Matthew; Ding, Zhihao; Ivakhno, Sergii; Stewart, Caitlin; Ng, Bee Ling; Wong, Wendy; Aken, Bronwen; White, Simon; Alsop, Amber; Becq, Jennifer; Bignell, Graham R.; Cheetham, R. Keira; Cheng, William; Connor, Thomas R.; Cox, Anthony J.; Feng, Zhi-Ping; Gu, Yong; Grocock, Russell J.; Harris, Simon R.; Khrebtukova, Irina; Kingsbury, Zoya; Kowarsky, Mark; Kreiss, Alexandre; Luo, Shujun; Marshall, John; McBride, David J.; Murray, Lisa; Pearse, Anne-Maree; Raine, Keiran; Rasolonjatovo, Isabelle; Shaw, Richard; Tedder, Philip; Tregidgo, Carolyn; Vilella, Albert J.; Wedge, David C.; Woods, Gregory M.; Gormley, Niall; Humphray, Sean; Schroth, Gary; Smith, Geoffrey; Hall, Kevin; Searle, Stephen M.J.; Carter, Nigel P.; Papenfuss, Anthony T.; Futreal, P. Andrew; Campbell, Peter J.; Yang, Fengtang; Bentley, David R.; Evers, Dirk J.; Stratton, Michael R.

2012-01-01

Summary The Tasmanian devil (Sarcophilus harrisii), the largest marsupial carnivore, is endangered due to a transmissible facial cancer spread by direct transfer of living cancer cells through biting. Here we describe the sequencing, assembly, and annotation of the Tasmanian devil genome and whole-genome sequences for two geographically distant subclones of the cancer. Genomic analysis suggests that the cancer first arose from a female Tasmanian devil and that the clone has subsequently genetically diverged during its spread across Tasmania. The devil cancer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a distinct mutational process. Genotyping of somatic mutations in 104 geographically and temporally distributed Tasmanian devil tumors reveals the pattern of evolution and spread of this parasitic clonal lineage, with evidence of a selective sweep in one geographical area and persistence of parallel lineages in other populations. PaperClip PMID:22341448

Using time reversal to detect entanglement and spreading of quantum information

NASA Astrophysics Data System (ADS)

Gaerttner, Martin

2017-04-01

Characterizing and understanding the states of interacting quantum systems and their non-equilibrium dynamics is the goal of quantum simulation. For this it is crucial to find experimentally feasible means for quantifying how entanglement and correlation build up and spread. The ability of analog quantum simulators to reverse the unitary dynamics of quantum many-body systems provides new tools in this quest. One such tool is the multiple-quantum coherence (MQC) spectrum previously used in NMR spectroscopy which can now be studied in so far inaccessible parameter regimes near zero temperature in highly controllable environments. I present recent progress in relating the MQC spectrum to established entanglement witnesses such as quantum Fisher information. Recognizing the MQC as out-of-time-order correlation functions, which quantify the spreading, or scrambling, of quantum information, allows us to establish a connection between these quantities and multi-partite entanglement. I will show recent experimental results obtained with a trapped ion quantum simulator and a spinor BEC illustrating the power of time reversal protocols. Supported by: JILA-NSF-PFC-1125844, NSF-PHY-1521080, ARO, AFOSR, AFOSR-MURI, DARPA, NIST.

Distributed multiport memory architecture

NASA Technical Reports Server (NTRS)

Kohl, W. H. (Inventor)

1983-01-01

A multiport memory architecture is diclosed for each of a plurality of task centers connected to a command and data bus. Each task center, includes a memory and a plurality of devices which request direct memory access as needed. The memory includes an internal data bus and an internal address bus to which the devices are connected, and direct timing and control logic comprised of a 10-state ring counter for allocating memory devices by enabling AND gates connected to the request signal lines of the devices. The outputs of AND gates connected to the same device are combined by OR gates to form an acknowledgement signal that enables the devices to address the memory during the next clock period. The length of the ring counter may be effectively lengthened to any multiple of ten to allow for more direct memory access intervals in one repetitive sequence. One device is a network bus adapter which serially shifts onto the command and data bus, a data word (8 bits plus control and parity bits) during the next ten direct memory access intervals after it has been granted access. The NBA is therefore allocated only one access in every ten intervals, which is a predetermined interval for all centers. The ring counters of all centers are periodically synchronized by DMA SYNC signal to assure that all NBAs be able to function in synchronism for data transfer from one center to another.

Intentionally Short-Range Communications (ISRC)

NASA Astrophysics Data System (ADS)

Yen, J.; Poirier, P.; Obrien, M.

1994-02-01

The U.S. Marine Corps (USMC) desired to develop short-range communications links whose ranges are intentionally limited to very short distances. These links support tactical missions such as LAN Backbone, Wideband Data Link, and Company Radio. The short-range limitation arises from the need for low probability of detection and intercept (LPD/LPI). Since the detection of an undecipherable transmission would still provide an enemy with information regarding transmitter location and allow him to take countermeasures, the Marine Corps Systems Command (MARCORSYSCOM) is sponsoring the development of technologies that can be LPD by their very nature. The Intentionally Short-Range Communications (ISRC) project at the Naval Command, Control and Ocean Surveillance Center (NCCOSC) RDT&E Division (NRaD) is pursuing feasibility studies for these USMC missions based on such technologies as ultraviolet (LTV) lamps, UV lasers, infrared (IR) lasers, millimeter waves and direct sequence spread spectrum (DSSS) at radio frequencies.

Precise Ionosphere Monitoring via a DSFH Satellite TT&C Link

NASA Astrophysics Data System (ADS)

Chen, Xiao; Li, Guangxia; Li, Zhiqiang; Yue, Chao

2014-11-01

A phase-coherent and frequency-hopped PN ranging system was developed, originally for the purpose of anti-jamming TT&C (tracking, telemetry and telecommand) of military satellites of China, including the Beidou-2 navigation satellites. The key innovation in the synchronization of this system is the unambiguous phase recovery of direct sequence and frequency hopping (DSFH) spread spectrum signal and the correction of frequency-dependent phase rotation caused by ionosphere. With synchronization achieved, a TEC monitoring algorithm based on maximum likelihood (ML) principle is proposed and its measuring precision is analyzed through ground simulation, onboard confirmation tests will be performed when transionosphere DSFH links are established in 2014. The measuring precision of TEC exceeds that obtained from GPS receiver data because the measurement is derived from unambiguous carrier phase estimates, not pseudorange estimates. The observation results from TT&C stations can provide real time regional ionosphere TEC estimation.

User manual of the CATSS system (version 1.0) communication analysis tool for space station

NASA Technical Reports Server (NTRS)

Tsang, C. S.; Su, Y. T.; Lindsey, W. C.

1983-01-01

The Communication Analysis Tool for the Space Station (CATSS) is a FORTRAN language software package capable of predicting the communications links performance for the Space Station (SS) communication and tracking (C & T) system. An interactive software package was currently developed to run on the DEC/VAX computers. The CATSS models and evaluates the various C & T links of the SS, which includes the modulation schemes such as Binary-Phase-Shift-Keying (BPSK), BPSK with Direct Sequence Spread Spectrum (PN/BPSK), and M-ary Frequency-Shift-Keying with Frequency Hopping (FH/MFSK). Optical Space Communication link is also included. CATSS is a C & T system engineering tool used to predict and analyze the system performance for different link environment. Identification of system weaknesses is achieved through evaluation of performance with varying system parameters. System tradeoff for different values of system parameters are made based on the performance prediction.

Real-Time PCR Typing of Escherichia coli Based on Multiple Single Nucleotide Polymorphisms--a Convenient and Rapid Method.

PubMed

Lager, Malin; Mernelius, Sara; Löfgren, Sture; Söderman, Jan

2016-01-01

Healthcare-associated infections caused by Escherichia coli and antibiotic resistance due to extended-spectrum beta-lactamase (ESBL) production constitute a threat against patient safety. To identify, track, and control outbreaks and to detect emerging virulent clones, typing tools of sufficient discriminatory power that generate reproducible and unambiguous data are needed. A probe based real-time PCR method targeting multiple single nucleotide polymorphisms (SNP) was developed. The method was based on the multi locus sequence typing scheme of Institute Pasteur and by adaptation of previously described typing assays. An 8 SNP-panel that reached a Simpson's diversity index of 0.95 was established, based on analysis of sporadic E. coli cases (ESBL n = 27 and non-ESBL n = 53). This multi-SNP assay was used to identify the sequence type 131 (ST131) complex according to the Achtman's multi locus sequence typing scheme. However, it did not fully discriminate within the complex but provided a diagnostic signature that outperformed a previously described detection assay. Pulsed-field gel electrophoresis typing of isolates from a presumed outbreak (n = 22) identified two outbreaks (ST127 and ST131) and three different non-outbreak-related isolates. Multi-SNP typing generated congruent data except for one non-outbreak-related ST131 isolate. We consider multi-SNP real-time PCR typing an accessible primary generic E. coli typing tool for rapid and uniform type identification.

Multiple access techniques and spectrum utilization of the GLOBALSTAR mobile satellite system

NASA Astrophysics Data System (ADS)

Louie, Ming; Cohen, Michel; Rouffet, Denis; Gilhousen, Klein S.

The GLOBALSTAR System is a Low Earth Orbit (LEO) satellite-based mobile communications system that is interoperable with the current and future Public Land Mobile Network (PLMN). The GLOBALSTAR System concept is based upon technological advancement in two key areas: (1) the advancement in LEO satellite technology; (2) the advancement in cellular telephone technology, including the commercial applications of Code Division Multiple Access (CDMA) technologies, and of the most recent progress in Time Division Multiple Access technologies. The GLOBALSTAR System uses elements of CDMA, Frequency Division Multiple Access (FDMA), and Time Division Multiple Access (TDMA) technology, combining with satellite Multiple Beam Antenna (MBA) technology, to arrive at one of the most efficient modulation and multiple access system ever proposed for a satellite communications system. The technology used in GLOBALSTAR exploits the following techniques in obtaining high spectral efficiency and affordable cost per channel, with minimum coordination among different systems: power control, in open and closed loops, voice activation, spot beam satellite antenna for frequency reuse, weighted satellite antenna gain, multiple satellite coverage, and handoff between satellites. The GLOBALSTAR system design will use the following frequency bands: 1610-1626.5 MHz for up-link and 2483.5-2500 MHz for down-link.

The Sudden Dominance of bla CTX–M Harbouring Plasmids in Shigella spp. Circulating in Southern Vietnam

PubMed Central

Nhu, Nguyen Thi Khanh; Vinh, Ha; Nga, Tran Vu Thieu; Stabler, Richard; Duy, Pham Thanh; Thi Minh Vien, Le; van Doorn, H. Rogier; Cerdeño-Tárraga, Ana; Thomson, Nicholas; Campbell, James; Van Minh Hoang, Nguyen; Thi Thu Nga, Tran; Minh, Pham Van; Thuy, Cao Thu; Wren, Brendan; Farrar, Jeremy; Baker, Stephen

2010-01-01

Background Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem. The rise of CTX-M class extended spectrum beta lactamases (ESBLs) has been well documented in industrialized countries. Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges. Methodology We collected hospital admission data from the pediatric population attending the hospital for tropical diseases in Ho Chi Minh City with Shigella infections. Organisms were cultured from all enrolled patients and subjected to antimicrobial susceptibility testing. Those that were ESBL positive were subjected to further investigation. These investigations included PCR amplification for common ESBL genes, plasmid investigation, conjugation, microarray hybridization and DNA sequencing of a bla CTX–M encoding plasmid. Principal Findings We show that two different bla CTX-M genes are circulating in this bacterial population in this location. Sequence of one of the ESBL plasmids shows that rather than the gene being integrated into a preexisting MDR plasmid, the bla CTX-M gene is located on relatively simple conjugative plasmid. The sequenced plasmid (pEG356) carried the bla CTX-M-24 gene on an ISEcp1 element and demonstrated considerable sequence homology with other IncFI plasmids. Significance The rapid dissemination, spread of antimicrobial resistance and changing population of Shigella spp. concurrent with economic growth are pertinent to many other countries undergoing similar development. Third generation cephalosporins are commonly used empiric antibiotics in Ho Chi Minh City. We recommend that these agents should not be considered for therapy of dysentery in this setting. PMID:20544028

The first 100 feet: New options for Internet and broadband access. Final report, June 1, 1996--January 31, 1998

DOE Office of Scientific and Technical Information (OSTI.GOV)

Branscomb, L.; Hurley, D.; Keller, J.

1998-04-01

This project was undertaken to explore new options for connecting homes and small businesses to high-speed communications networks, such as the Internet. Fundamental to this inquiry was an interest in looking at options which are newly enabled through changes in technology and regulation, and which go beyond the traditional topdown, centralized model for local access. In particular, the authors focused on opportunities for end-user and community-level investment. This project was intended to investigate the opportunities presented by the decreasing cost of computing and networking platforms, the unbundling of local exchange network elements, and the intelligent endpoints model of networking bestmore » exemplified by the Internet. Do these factors, along with communications technologies such as spread spectrum wireless, digital subscriber line services, and the ability to modulate a communications signal over the electric power line infrastructure, enable new models for end-user investment in intelligent infrastructure as a leverage point for accessing the broadband network? This question was first explored through a two-day conference held at the Freedom Forum in Arlington, Virginia, October 29 and 30, 1996. The workshop addressed issues in the consumer adoption of new communications technologies, use of the electric power line infrastructure, the role of municipalities, and the use of alternative technologies, such as XDSL, satellite, spread spectrum wireless, LMDS, and others. The best of these papers have been further developed, with editorial guidance provided by Harvard, and compiled in the form of a book (The First 100 Feet: New Options for Internet and Broadband Access, Deborah Hurley and James Keller, eds., MIT Press, 1998) to be published as part of the MIT Press Spring 1998 catalogue. A summary of topics covered by the book is given in this report.« less

Low Earth orbit communications satellite

NASA Technical Reports Server (NTRS)

Moroney, D.; Lashbrook, D.; Mckibben, B.; Gardener, N.; Rivers, T.; Nottingham, G.; Golden, B.; Barfield, B.; Bruening, J.; Wood, D.

1992-01-01

A current thrust in satellite communication systems considers a low-Earth orbiting constellations of satellites for continuous global coverage. Conceptual design studies have been done at the time of this design project by LORAL Aerospace Corporation under the program name GLOBALSTAR and by Motorola under their IRIDIUM program. This design project concentrates on the spacecraft design of the GLOBALSTAR low-Earth orbiting communication system. Overview information on the program was gained through the Federal Communications Commission licensing request. The GLOBALSTAR system consists of 48 operational satellites positioned in a Walker Delta pattern providing global coverage and redundancy. The operational orbit is 1389 km (750 nmi) altitude with eight planes of six satellites each. The orbital planes are spaced 45 deg., and the spacecraft are separated by 60 deg. within the plane. A Delta 2 launch vehicle is used to carry six spacecraft for orbit establishment. Once in orbit, the spacecraft will utilize code-division multiple access (spread spectrum modulation) for digital relay, voice, and radio determination satellite services (RDSS) yielding position determination with accuracy up to 200 meters.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

Design of a Transparent-Transponder System.

DTIC Science & Technology

1980-11-01

the slight advantage of re- ducing the number of frequencies needed. There are, however, some good reasons why a minimum CW tone capability should be...C. Link Computations In this section we evaluate the capacity quotient of three links: (1) the uplink, (2) the downlink reference or pilot signal...sequences of several lengths, we have some protection against this problem. However, as the code is shortened the spread-spectrum process- ing gai !L against

Ultra Wideband (UWB) communication vulnerability for security applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cooley, H. Timothy

2010-07-01

RF toxicity and Information Warfare (IW) are becoming omnipresent posing threats to the protection of nuclear assets, and within theatres of hostility or combat where tactical operation of wireless communication without detection and interception is important and sometimes critical for survival. As a result, a requirement for deployment of many security systems is a highly secure wireless technology manifesting stealth or covert operation suitable for either permanent or tactical deployment where operation without detection or interruption is important The possible use of ultra wideband (UWB) spectrum technology as an alternative physical medium for wireless network communication offers many advantages overmore » conventional narrowband and spread spectrum wireless communication. UWB also known as fast-frequency chirp is nonsinusoidal and sends information directly by transmitting sub-nanosecond pulses without the use of mixing baseband information upon a sinusoidal carrier. Thus UWB sends information using radar-like impulses by spreading its energy thinly over a vast spectrum and can operate at extremely low-power transmission within the noise floor where other forms of RF find it difficult or impossible to operate. As a result UWB offers low probability of detection (LPD), low probability of interception (LPI) as well as anti-jamming (AJ) properties in signal space. This paper analyzes and compares the vulnerability of UWB to narrowband and spread spectrum wireless network communication.« less

Draft genome sequence analysis of multidrug-resistant Escherichia coli strains isolated in 2013 from humans and chickens in Nigeria

USDA-ARS?s Scientific Manuscript database

Here, we present the draft genome sequences of nine multidrug-resistant Escherichia coli isolated from humans (n=6) and chicken carcass (n=3) from Lagos, Nigeria in 2013. Multiple extended-spectrum beta-lactamase (ESBL) genes were identified in these isolates. ...

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome.

PubMed

Lamm, Ayelet T; Stadler, Michael R; Zhang, Huibin; Gent, Jonathan I; Fire, Andrew Z

2011-02-01

We have used a combination of three high-throughput RNA capture and sequencing methods to refine and augment the transcriptome map of a well-studied genetic model, Caenorhabditis elegans. The three methods include a standard (non-directional) library preparation protocol relying on cDNA priming and foldback that has been used in several previous studies for transcriptome characterization in this species, and two directional protocols, one involving direct capture of single-stranded RNA fragments and one involving circular-template PCR (CircLigase). We find that each RNA-seq approach shows specific limitations and biases, with the application of multiple methods providing a more complete map than was obtained from any single method. Of particular note in the analysis were substantial advantages of CircLigase-based and ssRNA-based capture for defining sequences and structures of the precise 5' ends (which were lost using the double-strand cDNA capture method). Of the three methods, ssRNA capture was most effective in defining sequences to the poly(A) junction. Using data sets from a spectrum of C. elegans strains and stages and the UCSC Genome Browser, we provide a series of tools, which facilitate rapid visualization and assignment of gene structures.

Determination of dipole coupling constants using heteronuclear multiple quantum NMR

NASA Astrophysics Data System (ADS)

Weitekamp, D. P.; Garbow, J. R.; Pines, A.

1982-09-01

The problem of extracting dipole couplings from a system of N spins I = 1/2 and one spin S by NMR techniques is analyzed. The resolution attainable using a variety of single quantum methods is reviewed. The theory of heteronuclear multiple quantum (HMQ) NMR is developed, with particular emphasis being placed on the superior resolution available in HMQ spectra. Several novel pulse sequences are introduced, including a two-step method for the excitation of HMQ coherence. Experiments on partially oriented [1-13C] benzene demonstrate the excitation of the necessary HMQ coherence and illustrate the calculation of relative line intensities. Spectra of high order HMQ coherence under several different effective Hamiltonians achievable by multiple pulse sequences are discussed. A new effective Hamiltonian, scalar heteronuclear recoupled interactions by multiple pulse (SHRIMP), achieved by the simultaneous irradiation of both spin species with the same multiple pulse sequence, is introduced. Experiments are described which allow heteronuclear couplings to be correlated with an S-spin spreading parameter in spectra free of inhomogeneous broadening.

Effects of the distance among multiple spreaders on the spreading

NASA Astrophysics Data System (ADS)

Hu, Z.-L.; Liu, J.-G.; Yang, G.-Y.; Ren, Z.-M.

2014-04-01

It is very important to investigate the multiple spreaders' effects since the spreading phenomenon is ubiquitous in many complex systems. In this letter, we investigate the effects of the distance among the initial multiple spreaders for regular networks and WS (Watts-Strogatz) small-world networks based on the SIR (Susceptible-Infected-Recovered) model. Assuming the epidemics can spread over the network, the theoretical and experimental results show that for regular networks the larger the distance between spreaders is, the more effective the spreading is. For WS networks, the spreading efficiency will decrease when the distance exceeds a certain value, and a larger connection probability and average degree will result in a smaller distance of the most effective spreading. A better spreading strategy using n spreaders is to choose either the highest k or ks nodes with the condition that there are not any pairs of the n spreaders linked directly (Kitsak M. et al., Nat. Phys., 6 (2010) 888). However, we find that the spreading will be more effective when the distances among the largest-degree spreaders increase. All these results are independent of the network size for the two initial spreaders case. This work may give new insights to explore more effective methods to inhibit the epidemic spreading or increase the information diffusion.

78 FR 23952 - Notice of Temporary Closure on Public Lands in Elmore County, ID

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-23

...-grouse habitat. The closure will help to slow the spread of noxious weeds; allow planted shrub, forb, and... in the burned area to provide multiple age classes of shrubs in the burned area. Accessible areas of...

Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters.

PubMed

Jessen, Walter J; Hoose, Scott A; Kilgore, Jessica A; Kladde, Michael P

2006-03-01

Transcriptional activation is often associated with chromatin remodeling. However, little is known about the dynamics of remodeling of nucleosome arrays in vivo. Upon induction of Saccharomyces cerevisiae PHO5, a novel kinetic assay of DNA methyltransferase accessibility showed that nucleosomes adjacent to the histone-free upstream activating sequence (UASp1) are disrupted earlier and at higher frequency in the cell population than are those more distal. Individually cloned molecules, each representing the chromatin state of a full promoter from a single cell, revealed multiple promoter classes with either no remodeling or variable numbers of disrupted nucleosomes. Individual promoters in the remodeled fraction were highly enriched for contiguous blocks of disrupted nucleosomes, the majority of which overlapped the UAS region. These results support a probabilistic model in which chromatin remodeling at PHO5 spreads from sites of transactivator association with DNA and attenuates with distance.

Private and Efficient Query Processing on Outsourced Genomic Databases.

PubMed

Ghasemi, Reza; Al Aziz, Md Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian

2017-09-01

Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time consuming and expensive process. Second, it requires large-scale computation and storage systems to process genomic sequences. Third, genomic databases are often owned by different organizations, and thus, not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 Single Nucleotide Polymorphisms (SNPs) in a database of 20 000 records takes around 100 and 150 s, respectively.

Private and Efficient Query Processing on Outsourced Genomic Databases

PubMed Central

Ghasemi, Reza; Al Aziz, Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian

2017-01-01

Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time-consuming and expensive process. Second, it requires large-scale computation and storage systems to processes genomic sequences. Third, genomic databases are often owned by different organizations and thus not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 SNPs in a database of 20,000 records takes around 100 and 150 seconds, respectively. PMID:27834660

Occurrence of Stolbur Phytoplasma Disease in Spreading Type Petunia hybrida Cultivars in Korea

PubMed Central

Chung, Bong Nam; Jeong, Myeong Il; Choi, Seung Kook; Joa, Jae Ho; Choi, Kyeong San; Choi, In Myeong

2013-01-01

In January 2012, spreading type petunia cv. Wave Pink plants showing an abnormal growth habit of sprouting unusual multiple plantlets from the lateral buds were collected from a greenhouse in Gwacheon, Gyeonggi Province, Korea. The presence of phytoplasma was investigated using PCR with the primer pairs P1/P6, and R16F1/R1 for nested-PCR. In the nested PCR, 1,096 bp PCR products were obtained, and through sequencing 12 Pet-Stol isolates were identified. Comparison of the nucleotide sequences of 16S rRNA gene of the 12 Pet-Stol isolates with other phytoplasmas belonging to aster yellows or Stolbur showed that Pet-Stol isolates were members of Stolbur. The presence of phytoplasma in petunia was also confirmed by microscopic observation of the pathogens. In this study, Stolbur phytoplasma was identified from spreading type petunia cultivars by sequence analysis of 16S rRNA gene of phytoplasma and microscopic observation of phytoplasma bodies. This is the first report of Stolbur phytoplasma in commercial Petunia hybrida cultivars. PMID:25288978

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis.

PubMed

Ahmed, Ikhlak; Sarazin, Alexis; Bowler, Chris; Colot, Vincent; Quesneville, Hadi

2011-09-01

Transposable elements (TEs) and their relics play major roles in genome evolution. However, mobilization of TEs is usually deleterious and strongly repressed. In plants and mammals, this repression is typically associated with DNA methylation, but the relationship between this epigenetic mark and TE sequences has not been investigated systematically. Here, we present an improved annotation of TE sequences and use it to analyze genome-wide DNA methylation maps obtained at single-nucleotide resolution in Arabidopsis. We show that although the majority of TE sequences are methylated, ∼26% are not. Moreover, a significant fraction of TE sequences densely methylated at CG, CHG and CHH sites (where H = A, T or C) have no or few matching small interfering RNA (siRNAs) and are therefore unlikely to be targeted by the RNA-directed DNA methylation (RdDM) machinery. We provide evidence that these TE sequences acquire DNA methylation through spreading from adjacent siRNA-targeted regions. Further, we show that although both methylated and unmethylated TE sequences located in euchromatin tend to be more abundant closer to genes, this trend is least pronounced for methylated, siRNA-targeted TE sequences located 5' to genes. Based on these and other findings, we propose that spreading of DNA methylation through promoter regions explains at least in part the negative impact of siRNA-targeted TE sequences on neighboring gene expression.

An all-digital receiver for satellite audio broadcasting signals using trellis coded quasi-orthogonal code-division multiplexing

NASA Astrophysics Data System (ADS)

Braun, Walter; Eglin, Peter; Abello, Ricard

1993-02-01

Spread Spectrum Code Division Multiplex is an attractive scheme for the transmission of multiple signals over a satellite transponder. By using orthogonal or quasi-orthogonal spreading codes the interference between the users can be virtually eliminated. However, the acquisition and tracking of the spreading code phase can not take advantage of the code orthogonality since sequential acquisition and Delay-Locked loop tracking depend on correlation with code phases other than the optimal despreading phase. Hence, synchronization is a critical issue in such a system. A demonstration hardware for the verification of the orthogonal CDM synchronization and data transmission concept is being designed and implemented. The system concept, the synchronization scheme, and the implementation are described. The performance of the system is discussed based on computer simulations.

The influence of the directional energy distribution on the nonlinear dispersion relation in a random gravity wave field

NASA Technical Reports Server (NTRS)

Huang, N. E.; Tung, C.-C.

1977-01-01

The influence of the directional distribution of wave energy on the dispersion relation is calculated numerically using various directional wave spectrum models. The results indicate that the dispersion relation varies both as a function of the directional energy distribution and the direction of propagation of the wave component under consideration. Furthermore, both the mean deviation and the random scatter from the linear approximation increase as the energy spreading decreases. Limited observational data are compared with the theoretical results. The agreement is favorable.

Rotational spectroscopy with an optical centrifuge.

PubMed

Korobenko, Aleksey; Milner, Alexander A; Hepburn, John W; Milner, Valery

2014-03-07

We demonstrate a new spectroscopic method for studying electronic transitions in molecules with extremely broad range of angular momentum. We employ an optical centrifuge to create narrow rotational wave packets in the ground electronic state of (16)O2. Using the technique of resonance-enhanced multi-photon ionization, we record the spectrum of multiple ro-vibrational transitions between X(3)Σg(-) and C(3)Πg electronic manifolds of oxygen. Direct control of rotational excitation, extending to rotational quantum numbers as high as N ≳ 120, enables us to interpret the complex structure of rotational spectra of C(3)Πg beyond thermally accessible levels.

Estimation and Coordination of Sequence Patterns for Frequency Hopping Dynamic Spectrum Access Networks

DTIC Science & Technology

2014-03-27

Technology (AFIT). Research at AFIT investigates the use of DSA for both civilian and military applications while advancing technology in the area of radio...other military platforms is vital for successful operations. Twelve core functions comprise the US Air Force: Nuclear Deterrence Operations, Special...problems. This Air Force report discusses “Frequency Agile Spectrum Utilization”, a sub-topic of DSA, as a potential capability area [3]. Military

Evolution and Spread of Ebola Virus in Liberia, 2014-2015.

PubMed

Ladner, Jason T; Wiley, Michael R; Mate, Suzanne; Dudas, Gytis; Prieto, Karla; Lovett, Sean; Nagle, Elyse R; Beitzel, Brett; Gilbert, Merle L; Fakoli, Lawrence; Diclaro, Joseph W; Schoepp, Randal J; Fair, Joseph; Kuhn, Jens H; Hensley, Lisa E; Park, Daniel J; Sabeti, Pardis C; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Bolay, Fatorma K; Kugelman, Jeffrey R; Palacios, Gustavo

2015-12-09

The 2013-present Western African Ebola virus disease (EVD) outbreak is the largest ever recorded with >28,000 reported cases. Ebola virus (EBOV) genome sequencing has played an important role throughout this outbreak; however, relatively few sequences have been determined from patients in Liberia, the second worst-affected country. Here, we report 140 EBOV genome sequences from the second wave of the Liberian outbreak and analyze them in combination with 782 previously published sequences from throughout the Western African outbreak. While multiple early introductions of EBOV to Liberia are evident, the majority of Liberian EVD cases are consistent with a single introduction, followed by spread and diversification within the country. Movement of the virus within Liberia was widespread, and reintroductions from Liberia served as an important source for the continuation of the already ongoing EVD outbreak in Guinea. Overall, little evidence was found for incremental adaptation of EBOV to the human host. Copyright © 2015 Elsevier Inc. All rights reserved.

Phylogenetic Analysis of the Latvian HIV-1 Epidemic

PubMed Central

Balode, Dace; Skar, Helena; Mild, Mattias; Kolupajeva, Tatjana; Ferdats, Andris; Rozentale, Baiba; Leitner, Thomas

2012-01-01

Abstract The Latvian HIV-1 outbreak among intravenous drug users (IDUs) in 1997–1998 involved subtype A1. To obtain a more complete picture of the Latvian HIV-1 epidemic, 315 HIV-1-infected patients diagnosed in 1990–2005 representing different transmission groups and geographic regions were phylogenetically characterized using env V3 and gag p17 sequences. Subtypes A1 and B infections were found in 76% and 22% of the patients, respectively. The subtype A1 sequences formed one large cluster, which also included sequences from other parts of the former Soviet Union (FSU), whereas most subtype B sequences formed three distinct clusters. We estimated that subtype A1 was introduced from FSU around 1997 and initially spread explosively among IDUs in Riga. A recent increase of heterosexually infected persons did not form a separate subepidemic, but had multiple interactions with the IDU epidemic. Subtype B was introduced before the collapse of the Soviet Union and primarily has spread among men who have sex with men. PMID:22049908

Strategies for Disseminating Information on Biomedical Research on Autism to Hispanic Parents

ERIC Educational Resources Information Center

Lajonchere, Clara M.; Wheeler, Barbara Y.; Valente, Thomas W.; Kreutzer, Cary; Munson, Aron; Narayanan, Shrikanth; Kazemzadeh, Abe; Cruz, Roxana; Martinez, Irene; Schrager, Sheree M.; Schweitzer, Lisa; Chklovski, Tara; Hwang, Darryl

2016-01-01

Low income Hispanic families experience multiple barriers to accessing evidence-based information on Autism Spectrum Disorders (ASD). This study utilized a mixed-strategy intervention to create access to information in published bio-medical research articles on ASD by distilling the content into parent-friendly English- and Spanish-language ASD…

[Direct to consumer genetic testing: is it the moment?].

PubMed

Lamoril, Jérôme; Bogard, Marc

2016-01-01

Since the development of new human genome sequencing technologies at the beginning of the 2000, commercial companies have developped direct to consumer genomic services, which means without medical prescription. From 2007 to 2013, many companies have offered services assesing associated risk with human public health in the world especially in the United States. This kind of company is forbidden in France. From 2009 to 2013, in United States, under the pressure of national or state health administrations, these companies have been progressively forbidden. However, in certain parts of the world, companies are still offering such services. The latter raise many different questions such as ethical, juridical, medical, scientific, educative, professional one. Many studies and debates have demonstrated their limit and the lack of usefulness and advantage in the field of human health for the time being. The commercialization of this type of services has arrived all too soon et is not yet ripe. In our time of globalization, with the lack of international rules controlling direct access to genetic services in the field of human health, there is an urgent need to regulate. International administrations and politicians must act fast. Inevitably, under the pressure of lobbies and citizens, companies (multinational or not) will develop especially as 1) new sequencing technologies evolve rapidly, 2) are cheaper from year to year, 3) scientific and medical knowledges are progressing quickly, 4) services are spreading faster through the web and other networks.

Integrated databanks access and sequence/structure analysis services at the PBIL.

PubMed

Perrière, Guy; Combet, Christophe; Penel, Simon; Blanchet, Christophe; Thioulouse, Jean; Geourjon, Christophe; Grassot, Julien; Charavay, Céline; Gouy, Manolo; Duret, Laurent; Deléage, Gilbert

2003-07-01

The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.

Imaging System and Method for Biomedical Analysis

DTIC Science & Technology

2013-03-11

biological particles and items of interest. Broadly, Padmanabhan et al. utilize the diffraction of a laser light source in flow cytometry to count...spread of light from multiple LED devices over the entire sample surface. Preferably, light source 308 projects a full spectrum white light. Light...for example, red blood cells, white blood cells (which may include lymphocytes which are relatively large and easily detectable), T-helper cells

Consecutive analysis of mutation spectrum in the dystrophin gene of 507 Korean boys with Duchenne/Becker muscular dystrophy in a single center.

PubMed

Cho, Anna; Seong, Moon-Woo; Lim, Byung Chan; Lee, Hwa Jeen; Byeon, Jung Hye; Kim, Seung Soo; Kim, Soo Yeon; Choi, Sun Ah; Wong, Ai-Lynn; Lee, Jeongho; Kim, Jon Soo; Ryu, Hye Won; Lee, Jin Sook; Kim, Hunmin; Hwang, Hee; Choi, Ji Eun; Kim, Ki Joong; Hwang, Young Seung; Hong, Ki Ho; Park, Seungman; Cho, Sung Im; Lee, Seung Jun; Park, Hyunwoong; Seo, Soo Hyun; Park, Sung Sup; Chae, Jong Hee

2017-05-01

Duchenne and Becker muscular dystrophies (DMD and BMD) are allelic X-linked recessive muscle diseases caused by mutations in the large and complex dystrophin gene. We analyzed the dystrophin gene in 507 Korean DMD/BMD patients by multiple ligation-dependent probe amplification and direct sequencing. Overall, 117 different deletions, 48 duplications, and 90 pathogenic sequence variations, including 30 novel variations, were identified. Deletions and duplications accounted for 65.4% and 13.3% of Korean dystrophinopathy, respectively, suggesting that the incidence of large rearrangements in dystrophin is similar among different ethnic groups. We also detected sequence variations in >100 probands. The small variations were dispersed across the whole gene, and 12.3% were nonsense mutations. Precise genetic characterization in patients with DMD/BMD is timely and important for implementing nationwide registration systems and future molecular therapeutic trials in Korea and globally. Muscle Nerve 55: 727-734, 2017. © 2016 Wiley Periodicals, Inc.

The role of China in the global spread of the current cholera pandemic.

PubMed

Didelot, Xavier; Pang, Bo; Zhou, Zhemin; McCann, Angela; Ni, Peixiang; Li, Dongfang; Achtman, Mark; Kan, Biao

2015-03-01

Epidemics and pandemics of cholera, a severe diarrheal disease, have occurred since the early 19th century and waves of epidemic disease continue today. Cholera epidemics are caused by individual, genetically monomorphic lineages of Vibrio cholerae: the ongoing seventh pandemic, which has spread globally since 1961, is associated with lineage L2 of biotype El Tor. Previous genomic studies of the epidemiology of the seventh pandemic identified three successive sub-lineages within L2, designated waves 1 to 3, which spread globally from the Bay of Bengal on multiple occasions. However, these studies did not include samples from China, which also experienced multiple epidemics of cholera in recent decades. We sequenced the genomes of 71 strains isolated in China between 1961 and 2010, as well as eight from other sources, and compared them with 181 published genomes. The results indicated that outbreaks in China between 1960 and 1990 were associated with wave 1 whereas later outbreaks were associated with wave 2. However, the previously defined waves overlapped temporally, and are an inadequate representation of the shape of the global genealogy. We therefore suggest replacing them by a series of tightly delineated clades. Between 1960 and 1990 multiple such clades were imported into China, underwent further microevolution there and then spread to other countries. China was thus both a sink and source during the pandemic spread of V. cholerae, and needs to be included in reconstructions of the global patterns of spread of cholera.

Clinical and molecular characterization of KCNT1-related severe early-onset epilepsy

PubMed Central

Nair, Umesh; Malhotra, Sony; Meyer, Esther; Trump, Natalie; Gazina, Elena V.; Papandreou, Apostolos; Ngoh, Adeline; Ackermann, Sally; Ambegaonkar, Gautam; Appleton, Richard; Desurkar, Archana; Eltze, Christin; Kneen, Rachel; Kumar, Ajith V.; Lascelles, Karine; Montgomery, Tara; Ramesh, Venkateswaran; Samanta, Rajib; Scott, Richard H.; Tan, Jeen; Whitehouse, William; Poduri, Annapurna; Scheffer, Ingrid E.; Chong, W.K. “Kling”; Cross, J. Helen; Topf, Maya; Petrou, Steven

2018-01-01

Objective To characterize the phenotypic spectrum, molecular genetic findings, and functional consequences of pathogenic variants in early-onset KCNT1 epilepsy. Methods We identified a cohort of 31 patients with epilepsy of infancy with migrating focal seizures (EIMFS) and screened for variants in KCNT1 using direct Sanger sequencing, a multiple-gene next-generation sequencing panel, and whole-exome sequencing. Additional patients with non-EIMFS early-onset epilepsy in whom we identified KCNT1 variants on local diagnostic multiple gene panel testing were also included. When possible, we performed homology modeling to predict the putative effects of variants on protein structure and function. We undertook electrophysiologic assessment of mutant KCNT1 channels in a xenopus oocyte model system. Results We identified pathogenic variants in KCNT1 in 12 patients, 4 of which are novel. Most variants occurred de novo. Ten patients had a clinical diagnosis of EIMFS, and the other 2 presented with early-onset severe nocturnal frontal lobe seizures. Three patients had a trial of quinidine with good clinical response in 1 patient. Computational modeling analysis implicates abnormal pore function (F346L) and impaired tetramer formation (F502V) as putative disease mechanisms. All evaluated KCNT1 variants resulted in marked gain of function with significantly increased channel amplitude and variable blockade by quinidine. Conclusions Gain-of-function KCNT1 pathogenic variants cause a spectrum of severe focal epilepsies with onset in early infancy. Currently, genotype-phenotype correlations are unclear, although clinical outcome is poor for the majority of cases. Further elucidation of disease mechanisms may facilitate the development of targeted treatments, much needed for this pharmacoresistant genetic epilepsy. PMID:29196579

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

USDA-ARS?s Scientific Manuscript database

Reconstructing the phylogeny of Pyrus has been difficult due to the wide distribution of the genus and lack of informative data. In this study, we collected 110 accessions representing 25 Pyrus species and constructed both phylogenetic trees and phylogenetic networks based on multiple DNA sequence d...

Rapid high-resolution four-dimensional NMR spectroscopy using the filter diagonalization method and its advantages for detailed structural elucidation of oligosaccharides.

PubMed

Armstrong, Geoffrey S; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2005-03-01

Four-dimensional nuclear magnetic resonance spectroscopy with high resolution of signals in the indirect dimensions is reported as an implementation of the filter diagonalization method (FDM). Using an oligosaccharide derivatized with 13C-labeled acetyl isotags, a four-dimensional constant-time pulse sequence was tailored for conjoint use with the FDM. Results demonstrate that high resolution in all dimensions can be achieved using a relatively short experimental time period (19 h), even though the spectrum is highly congested in the direct and all three indirect dimensions. The combined use of isotags, constant-time pulse sequences, and FDM permits rapid isolation of sugar ring proton spin systems in multiple dimensions and enables all endocyclic J-couplings to be simply measured, the key goal to assigning sugar stereochemistry and anomeric configuration. A general method for rapid, unambiguous elucidation of spin systems in oligosaccharides has been a long-sought goal of carbohydrate NMR, and isotags combined with the FDM now enable this to be easily performed. Additional general advantages of the FDM program for generating high-resolution 2D slices in any dimension from a 4D spectrum are emphasized.

A new method to cluster genomes based on cumulative Fourier power spectrum.

PubMed

Dong, Rui; Zhu, Ziyue; Yin, Changchuan; He, Rong L; Yau, Stephen S-T

2018-06-20

Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum). Copyright © 2018. Published by Elsevier B.V.

Shuttle ku-band communications/radar technical concepts

NASA Technical Reports Server (NTRS)

Griffin, J. W.; Kelley, J. S.; Steiner, A. W.; Vang, H. A.; Zrubek, W. E.; Huth, G. K.

1985-01-01

Technical data on the Shuttle Orbiter K sub u-band communications/radar system are presented. The more challenging aspects of the system design and development are emphasized. The technical problems encountered and the advancements made in solving them are discussed. The radar functions are presented first. Requirements and design/implementation approaches are discussed. Advanced features are explained, including Doppler measurement, frequency diversity, multiple pulse repetition frequencies and pulse widths, and multiple modes. The communications functions that are presented include advances made because of the requirements for multiple communications modes. Spread spectrum, quadrature phase shift keying (QPSK), variable bit rates, and other advanced techniques are discussed. Performance results and conclusions reached are outlined.

Multiple-rotor-cycle 2D PASS experiments with applications to (207)Pb NMR spectroscopy.

PubMed

Vogt, F G; Gibson, J M; Aurentz, D J; Mueller, K T; Benesi, A J

2000-03-01

Thetwo-dimensional phase-adjusted spinning sidebands (2D PASS) experiment is a useful technique for simplifying magic-angle spinning (MAS) NMR spectra that contain overlapping or complicated spinning sideband manifolds. The pulse sequence separates spinning sidebands by their order in a two-dimensional experiment. The result is an isotropic/anisotropic correlation experiment, in which a sheared projection of the 2D spectrum effectively yields an isotropic spectrum with no sidebands. The original 2D PASS experiment works best at lower MAS speeds (1-5 kHz). At higher spinning speeds (8-12 kHz) the experiment requires higher RF power levels so that the pulses do not overlap. In the case of nuclei such as (207)Pb, a large chemical shift anisotropy often yields too many spinning sidebands to be handled by a reasonable 2D PASS experiment unless higher spinning speeds are used. Performing the experiment at these speeds requires fewer 2D rows and a correspondingly shorter experimental time. Therefore, we have implemented PASS pulse sequences that occupy multiple MAS rotor cycles, thereby avoiding pulse overlap. These multiple-rotor-cycle 2D PASS sequences are intended for use in high-speed MAS situations such as those required by (207)Pb. A version of the multiple-rotor-cycle 2D PASS sequence that uses composite pulses to suppress spectral artifacts is also presented. These sequences are demonstrated on (207)Pb test samples, including lead zirconate, a perovskite-phase compound that is representative of a large class of interesting materials. Copyright 2000 Academic Press.

A digital communications system for manned spaceflight applications.

NASA Technical Reports Server (NTRS)

Batson, B. H.; Moorehead, R. W.

1973-01-01

A highly efficient, all-digital communications signal design employing convolutional coding and PN spectrum spreading is described for two-way transmission of voice and data between a manned spacecraft and ground. Variable-slope delta modulation is selected for analog/digital conversion of the voice signal, and a convolutional decoder utilizing the Viterbi decoding algorithm is selected for use at each receiving terminal. A PN spread spectrum technique is implemented to protect against multipath effects and to reduce the energy density (per unit bandwidth) impinging on the earth's surface to a value within the guidelines adopted by international agreement. Performance predictions are presented for transmission via a TDRS (tracking and data relay satellite) system and for direct transmission between the spacecraft and earth. Hardware estimates are provided for a flight-qualified communications system employing the coded digital signal design.

A terrain based simulation system to predict the interference caused by networks of spread spectrum systems

NASA Astrophysics Data System (ADS)

Hagen, William E.; Holtzman, Julian C.

The Army Terrain Integrated Interference Prediction System (ATIIPS), a CAD terrain based simulation tool for determining the degradation effects on a network on nonspread spectrum radios caused by a network of spread spectrum radios is presented. A brief overview of the program is given, with typical graphics displays shown. Typical results for both a link simulation of interference and for a network simulation, using a slow hopped FM/FSK spread spectrum interfering radio network on a narrow band FM/FSK fixed frequency digital radio are presented.

Demographic History of European Populations of Arabidopsis thaliana

PubMed Central

François, Olivier; Blum, Michael G. B.; Jakobsson, Mattias; Rosenberg, Noah A.

2008-01-01

The model plant species Arabidopsis thaliana is successful at colonizing land that has recently undergone human-mediated disturbance. To investigate the prehistoric spread of A. thaliana, we applied approximate Bayesian computation and explicit spatial modeling to 76 European accessions sequenced at 876 nuclear loci. We find evidence that a major migration wave occurred from east to west, affecting most of the sampled individuals. The longitudinal gradient appears to result from the plant having spread in Europe from the east ∼10,000 years ago, with a rate of westward spread of ∼0.9 km/year. This wave-of-advance model is consistent with a natural colonization from an eastern glacial refugium that overwhelmed ancient western lineages. However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition. PMID:18483550

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

PubMed Central

Yuen, Ryan KC; Merico, Daniele; Bookman, Matt; Howe, Jennifer L; Thiruvahindrapuram, Bhooma; Patel, Rohan V; Whitney, Joe; Deflaux, Nicole; Bingham, Jonathan; Wang, Zhuozhi; Pellecchia, Giovanna; Buchanan, Janet A; Walker, Susan; Marshall, Christian R; Uddin, Mohammed; Zarrei, Mehdi; Deneault, Eric; D’Abate, Lia; Chan, Ada JS; Koyanagi, Stephanie; Paton, Tara; Pereira, Sergio L; Hoang, Ny; Engchuan, Worrawat; Higginbotham, Edward J; Ho, Karen; Lamoureux, Sylvia; Li, Weili; MacDonald, Jeffrey R; Nalpathamkalam, Thomas; Sung, Wilson WL; Tsoi, Fiona J; Wei, John; Xu, Lizhen; Tasse, Anne-Marie; Kirby, Emily; Van Etten, William; Twigger, Simon; Roberts, Wendy; Drmic, Irene; Jilderda, Sanne; Modi, Bonnie MacKinnon; Kellam, Barbara; Szego, Michael; Cytrynbaum, Cheryl; Weksberg, Rosanna; Zwaigenbaum, Lonnie; Woodbury-Smith, Marc; Brian, Jessica; Senman, Lili; Iaboni, Alana; Doyle-Thomas, Krissy; Thompson, Ann; Chrysler, Christina; Leef, Jonathan; Savion-Lemieux, Tal; Smith, Isabel M; Liu, Xudong; Nicolson, Rob; Seifer, Vicki; Fedele, Angie; Cook, Edwin H; Dager, Stephen; Estes, Annette; Gallagher, Louise; Malow, Beth A; Parr, Jeremy R; Spence, Sarah J; Vorstman, Jacob; Frey, Brendan J; Robinson, James T; Strug, Lisa J; Fernandez, Bridget A; Elsabbagh, Mayada; Carter, Melissa T; Hallmayer, Joachim; Knoppers, Bartha M; Anagnostou, Evdokia; Szatmari, Peter; Ring, Robert H; Glazer, David; Pletcher, Mathew T; Scherer, Stephen W

2017-01-01

We are performing whole genome sequencing (WGS) of families with Autism Spectrum Disorder (ASD) to build a resource, named MSSNG, to enable the sub-categorization of phenotypes and underlying genetic factors involved. Here, we report WGS of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible in a cloud platform, and through an internet portal with controlled access. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertion/deletions (indels) or copy number variations (CNVs) per ASD subject. We identified 18 new candidate ASD-risk genes such as MED13 and PHF3, and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (p=6×10−4). In 294/2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried CNV/chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. PMID:28263302

Transcription Factor Information System (TFIS): A Tool for Detection of Transcription Factor Binding Sites.

PubMed

Narad, Priyanka; Kumar, Abhishek; Chakraborty, Amlan; Patni, Pranav; Sengupta, Abhishek; Wadhwa, Gulshan; Upadhyaya, K C

2017-09-01

Transcription factors are trans-acting proteins that interact with specific nucleotide sequences known as transcription factor binding site (TFBS), and these interactions are implicated in regulation of the gene expression. Regulation of transcriptional activation of a gene often involves multiple interactions of transcription factors with various sequence elements. Identification of these sequence elements is the first step in understanding the underlying molecular mechanism(s) that regulate the gene expression. For in silico identification of these sequence elements, we have developed an online computational tool named transcription factor information system (TFIS) for detecting TFBS for the first time using a collection of JAVA programs and is mainly based on TFBS detection using position weight matrix (PWM). The database used for obtaining position frequency matrices (PFM) is JASPAR and HOCOMOCO, which is an open-access database of transcription factor binding profiles. Pseudo-counts are used while converting PFM to PWM, and TFBS detection is carried out on the basis of percent score taken as threshold value. TFIS is equipped with advanced features such as direct sequence retrieving from NCBI database using gene identification number and accession number, detecting binding site for common TF in a batch of gene sequences, and TFBS detection after generating PWM from known raw binding sequences in addition to general detection methods. TFIS can detect the presence of potential TFBSs in both the directions at the same time. This feature increases its efficiency. And the results for this dual detection are presented in different colors specific to the orientation of the binding site. Results obtained by the TFIS are more detailed and specific to the detected TFs as integration of more informative links from various related web servers are added in the result pages like Gene Ontology, PAZAR database and Transcription Factor Encyclopedia in addition to NCBI and UniProt. Common TFs like SP1, AP1 and NF-KB of the Amyloid beta precursor gene is easily detected using TFIS along with multiple binding sites. In another scenario of embryonic developmental process, TFs of the FOX family (FOXL1 and FOXC1) were also identified. TFIS is platform-independent which is publicly available along with its support and documentation at http://tfistool.appspot.com and http://www.bioinfoplus.com/tfis/ . TFIS is licensed under the GNU General Public License, version 3 (GPL-3.0).

Origin and Reticulate Evolutionary Process of Wheatgrass Elymus trachycaulus (Triticeae: Poaceae)

PubMed Central

Zuo, Hongwei; Wu, Panpan; Wu, Dexiang; Sun, Genlou

2015-01-01

To study origin and evolutionary dynamics of tetraploid Elymus trachycaulus that has been cytologically defined as containing StH genomes, thirteen accessions of E. trachycaulus were analyzed using two low-copy nuclear gene Pepc (phosphoenolpyruvate carboxylase) and Rpb2 (the second largest subunit of RNA polymerase II), and one chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Our chloroplast data indicated that Pseudoroegneria (St genome) was the maternal donor of E. trachycaulus. Rpb2 data indicated that the St genome in E. trachycaulus was originated from either P. strigosa, P. stipifolia, P. spicata or P. geniculate. The Hordeum (H genome)-like sequences of E. trachycaulus are polyphyletic in the Pepc tree, suggesting that the H genome in E. trachycaulus was contributed by multiple sources, whether due to multiple origins or introgression resulting from subsequent hybridization. Failure to recovering St copy of Pepc sequence in most accessions of E. trachycaulus might be caused by genome convergent evolution in allopolyploids. Multiple copies of H-like Pepc sequence from each accession with relative large deletions and insertions might be caused by either instability of Pepc sequence in H- genome or incomplete concerted evolution. Our results highlighted complex evolutionary history of E. trachycaulus. PMID:25946188

Combining results of multiple search engines in proteomics.

PubMed

Shteynberg, David; Nesvizhskii, Alexey I; Moritz, Robert L; Deutsch, Eric W

2013-09-01

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques.

Combining Results of Multiple Search Engines in Proteomics*

PubMed Central

Shteynberg, David; Nesvizhskii, Alexey I.; Moritz, Robert L.; Deutsch, Eric W.

2013-01-01

A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the parent molecular ion that produced each fragment ion spectrum in the dataset. There are many different search engines, both commercial and open source, each employing a somewhat different technique for spectrum identification. The set of high-scoring peptide-spectrum matches for a defined set of input spectra differs markedly among the various search engine results; individual engines each provide unique correct identifications among a core set of correlative identifications. This has led to the approach of combining the results from multiple search engines to achieve improved analysis of each dataset. Here we review the techniques and available software for combining the results of multiple search engines and briefly compare the relative performance of these techniques. PMID:23720762

Delayed P100-Like Latencies in Multiple Sclerosis: A Preliminary Investigation Using Visual Evoked Spread Spectrum Analysis

PubMed Central

Kiiski, Hanni S. M.; Ní Riada, Sinéad; Lalor, Edmund C.; Gonçalves, Nuno R.; Nolan, Hugh; Whelan, Robert; Lonergan, Róisín; Kelly, Siobhán; O'Brien, Marie Claire; Kinsella, Katie; Bramham, Jessica; Burke, Teresa; Ó Donnchadha, Seán; Hutchinson, Michael; Tubridy, Niall; Reilly, Richard B.

2016-01-01

Conduction along the optic nerve is often slowed in multiple sclerosis (MS). This is typically assessed by measuring the latency of the P100 component of the Visual Evoked Potential (VEP) using electroencephalography. The Visual Evoked Spread Spectrum Analysis (VESPA) method, which involves modulating the contrast of a continuous visual stimulus over time, can produce a visually evoked response analogous to the P100 but with a higher signal-to-noise ratio and potentially higher sensitivity to individual differences in comparison to the VEP. The main objective of the study was to conduct a preliminary investigation into the utility of the VESPA method for probing and monitoring visual dysfunction in multiple sclerosis. The latencies and amplitudes of the P100-like VESPA component were compared between healthy controls and multiple sclerosis patients, and multiple sclerosis subgroups. The P100-like VESPA component activations were examined at baseline and over a 3-year period. The study included 43 multiple sclerosis patients (23 relapsing-remitting MS, 20 secondary-progressive MS) and 42 healthy controls who completed the VESPA at baseline. The follow-up sessions were conducted 12 months after baseline with 24 MS patients (15 relapsing-remitting MS, 9 secondary-progressive MS) and 23 controls, and again at 24 months post-baseline with 19 MS patients (13 relapsing-remitting MS, 6 secondary-progressive MS) and 14 controls. The results showed P100-like VESPA latencies to be delayed in multiple sclerosis compared to healthy controls over the 24-month period. Secondary-progressive MS patients had most pronounced delay in P100-like VESPA latency relative to relapsing-remitting MS and controls. There were no longitudinal P100-like VESPA response differences. These findings suggest that the VESPA method is a reproducible electrophysiological method that may have potential utility in the assessment of visual dysfunction in multiple sclerosis. PMID:26726800

APPLaUD: access for patients and participants to individual level uninterpreted genomic data.

PubMed

Thorogood, Adrian; Bobe, Jason; Prainsack, Barbara; Middleton, Anna; Scott, Erick; Nelson, Sarah; Corpas, Manuel; Bonhomme, Natasha; Rodriguez, Laura Lyman; Murtagh, Madeleine; Kleiderman, Erika

2018-02-17

There is a growing support for the stance that patients and research participants should have better and easier access to their raw (uninterpreted) genomic sequence data in both clinical and research contexts. We review legal frameworks and literature on the benefits, risks, and practical barriers of providing individuals access to their data. We also survey genomic sequencing initiatives that provide or plan to provide individual access. Many patients and research participants expect to be able to access their health and genomic data. Individuals have a legal right to access their genomic data in some countries and contexts. Moreover, increasing numbers of participatory research projects, direct-to-consumer genetic testing companies, and now major national sequencing initiatives grant individuals access to their genomic sequence data upon request. Drawing on current practice and regulatory analysis, we outline legal, ethical, and practical guidance for genomic sequencing initiatives seeking to offer interested patients and participants access to their raw genomic data.

Spread-Spectrum Random-Access Communications for HF Channels.

DTIC Science & Technology

1981-08-21

variables Zsm which are defined by (8) with cos[.] replaced by sin[-], have the same properties as Z . cm I. 9 IIII. PERFORMANCE OF FH/SSMA SYSTEM...patterns). An approximation which is valid under the same conditions is 18 P e,1 A PL + k (k+P 0 )(K-I)(1’_)K-2 ( 35 ) This approximation is very accurate...and approximation given in (32)-( 35 ) can be applied to any particular nonselective fading channel by substituting the appropriate expression for P0

SDIO (Strategic Defense Initiative Office) Technical Information Management Center Bibliography of Unclassified Documents: January - December 1988

DTIC Science & Technology

1988-12-01

Statistics to Studies of C3 and Spread Spectrum Communications Author(s): Pawula, R. F. * Date: 05/14/86 Pages:004 Report #: AFOSR-TR-87-0210 Corp. Author...1375 AD #: 0 TITLE: SPSS Statistical Algorithms Author(s): 0 Date: 01/01/85 Pages:230 Report #: CN83-60118 Corp. Author: SPSS Inc. 444 N. Michigan Ave...Assessment Mission Architecture Defense Battle Weapon Target Transitor Space Catastrophic Accession #: 1407 AD #: 0 TITLE: What price space-based interceptors

Genome Evolution and Plasticity of Serratia marcescens, an Important Multidrug-Resistant Nosocomial Pathogen

PubMed Central

Iguchi, Atsushi; Nagaya, Yutaka; Pradel, Elizabeth; Ooka, Tadasuke; Ogura, Yoshitoshi; Katsura, Keisuke; Kurokawa, Ken; Oshima, Kenshiro; Hattori, Masahira; Parkhill, Julian; Sebaihia, Mohamed; Coulthurst, Sarah J.; Gotoh, Naomasa; Thomson, Nicholas R.; Ewbank, Jonathan J.; Hayashi, Tetsuya

2014-01-01

Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents. PMID:25070509

Video Modeling and Observational Learning to Teach Gaming Access to Students with ASD

ERIC Educational Resources Information Center

Spriggs, Amy D.; Gast, David L.; Knight, Victoria F.

2016-01-01

The purpose of this study was to evaluate both video modeling and observational learning to teach age-appropriate recreation and leisure skills (i.e., accessing video games) to students with autism spectrum disorder. Effects of video modeling were evaluated via a multiple probe design across participants and criteria for mastery were based on…

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

PubMed Central

Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

2009-01-01

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method

PubMed Central

2014-01-01

Background Recent efforts in HIV-1 vaccine design have focused on immunogens that evoke potent neutralizing antibody responses to a broad spectrum of viruses circulating worldwide. However, the development of effective vaccines will depend on the identification and characterization of the neutralizing antibodies and their epitopes. We developed bioinformatics methods to predict epitope networks and antigenic determinants using structural information, as well as corresponding genotypes and phenotypes generated by a highly sensitive and reproducible neutralization assay. 282 clonal envelope sequences from a multiclade panel of HIV-1 viruses were tested in viral neutralization assays with an array of broadly neutralizing monoclonal antibodies (mAbs: b12, PG9,16, PGT121 - 128, PGT130 - 131, PGT135 - 137, PGT141 - 145, and PGV04). We correlated IC50 titers with the envelope sequences, and used this information to predict antibody epitope networks. Structural patches were defined as amino acid groups based on solvent-accessibility, radius, atomic depth, and interaction networks within 3D envelope models. We applied a boosted algorithm consisting of multiple machine-learning and statistical models to evaluate these patches as possible antibody epitope regions, evidenced by strong correlations with the neutralization response for each antibody. Results We identified patch clusters with significant correlation to IC50 titers as sites that impact neutralization sensitivity and therefore are potentially part of the antibody binding sites. Predicted epitope networks were mostly located within the variable loops of the envelope glycoprotein (gp120), particularly in V1/V2. Site-directed mutagenesis experiments involving residues identified as epitope networks across multiple mAbs confirmed association of these residues with loss or gain of neutralization sensitivity. Conclusions Computational methods were implemented to rapidly survey protein structures and predict epitope networks associated with response to individual monoclonal antibodies, which resulted in the identification and deeper understanding of immunological hotspots targeted by broadly neutralizing HIV-1 antibodies. PMID:24646213

Detection of Escherichia coli sequence type 131 by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: implications for infection control policies?

PubMed

Lafolie, J; Sauget, M; Cabrolier, N; Hocquet, D; Bertrand, X

2015-07-01

Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. The ST131 pandemic is mainly the result of clonal expansion of the single well-adapted subclone H30-Rx, which is acquired in hospitals more frequently than other ESBL-producing E. coli clones. To develop a rapid method using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify ST131 for infection control purposes. Peak biomarkers of ST131 were identified from the mass spectrum profiles of 109 E. coli isolates (including 50 ST131 isolates). The models accurately identified ST131 isolates from mass spectrum profiles obtained with and without protein extraction. The rapid identification of ST131 isolates with MALDI-TOF MS can be easily implemented in the laboratory, and could help to target infection control measures in patients carrying multi-drug-resistant E. coli that are more likely to spread. Copyright © 2015 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Molecular Characterization of Extended-Spectrum-β-Lactamase-Producing and Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli Isolated from Stray Dogs in South Korea

PubMed Central

Tamang, Migma Dorji; Nam, Hyang-Mi; Jang, Geum-Chan; Kim, Su-Ran; Chae, Myung Hwa; Jung, Suk-Chan; Byun, Jae-Won; Park, Yong Ho

2012-01-01

A total of 47 extended-spectrum-cephalosporin-resistant Escherichia coli strains isolated from stray dogs in 2006 and 2007 in the Republic of Korea were investigated using molecular methods. Extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase phenotypes were identified in 12 and 23 E. coli isolates, respectively. All 12 ESBL-producing isolates carried blaCTX-M genes. The most common CTX-M types were CTX-M-14 (n = 5) and CTX-M-24 (n = 3). Isolates producing CTX-M-3, CTX-M-55, CTX-M-27, and CTX-M-65 were also identified. Twenty-one of 23 AmpC β-lactamase-producing isolates were found to carry blaCMY-2 genes. TEM-1 was associated with CTX-M and CMY-2 β-lactamases in 4 and 15 isolates, respectively. In addition to blaTEM-1, two isolates carried blaDHA-1, and one of them cocarried blaCMY-2. Both CTX-M and CMY-2 genes were located on large (40 to 170 kb) conjugative plasmids that contained the insertion sequence ISEcp1 upstream of the bla genes. Only in the case of CTX-M genes was there an IS903 sequence downstream of the gene. The spread of ESBLs and AmpC β-lactamases occurred via both horizontal gene transfer, accounting for much of the CTX-M gene dissemination, and clonal spread, accounting for CMY-2 gene dissemination. The horizontal dissemination of blaCTX-M and blaCMY-2 genes was mediated by IncF and IncI1-Iγ plasmids, respectively. The clonal spread of blaCMY-2 was driven mainly by E. coli strains of virulent phylogroup D lineage ST648. To our knowledge, this is the first report of blaDHA-1 in E. coli strains isolated from companion animals. This study also represents the first report of CMY-2 β-lactamase-producing E. coli isolates from dogs in the Republic of Korea. PMID:22354297

Tracking the Origin and Deciphering the Phylogenetic Relationship of Porcine Epidemic Diarrhea Virus in Ecuador

PubMed Central

Barrera, Maritza; Garrido-Haro, Ana; Vaca, María S.; Granda, Danilo; Acosta-Batallas, Alfredo

2017-01-01

In 2010, new Chinese strains of porcine epidemic diarrhea virus (PEDV), clinically more severe than the classical strains, emerged. These strains were spread to United States in 2013 through an intercontinental transmission from China with further spreading across the world, evidencing the emergent nature of these strains. In the present study, an analysis of PEDV field sequences from Ecuador was conducted by comparing all the PEDV S gene sequences available in the GenBank database. Phylogenetic comparisons and Bayesian phylogeographic inference based on complete S gene sequences were also conducted to track the origin and putative route of PEDV. The sequence from the PED-outbreak in Ecuador was grouped into the clade II of PEDV genogroup 2a together with other sequences of isolates from Mexico, Canada, and United States. The phylogeographic study revealed the emergence of the Chinese PEDV strains, followed by spreading to US in 2013, from US to Korea, and later the introduction of PEDV to Canada, Mexico, and Ecuador directly from the US. The sources of imports of live swine in Ecuador in 2014 were mainly from Chile and US. Thus, this movement of pigs is suggested as the main way for introducing PEDV to Ecuador. PMID:29379796

Classification of Acousto-Optic Correlation Signatures of Spread Spectrum Signals Using Artificial Neural Networks

DTIC Science & Technology

1989-12-01

Ohio ’aPw iorlipuab muo i 0I2, AFIT/GE/ENG/89D-10 CLASSIFICATION OF ACOUSTO - OPTIC CORRELATION SIGNATURES OF SPREAD SPECTRUM SIGNALS USING ARTIFICIAL...ENG/89D- 10 CLASSIFICATION OF ACOUSTO - OPTIC CORRELATION SIGNATURES OF SPREAD SPECTRUM SIGNALS USING ARTIFICIAL NEURAL NETWORKS THESIS John W. DeBerry...Captain, USAF AFIT/GE/ENG/89D- 10 Approved for public release; distribution unlimited. AFIT/GE/ENG/89D-10 CLASSIFICATION OF ACOUSTO - OPTIC CORRELATION

Measuring the Non-Line-of-Sight Ultra-High-Frequency Channel in Mountainous Terrain: A Spread-Spectrum, Portable Channel Sounder

DTIC Science & Technology

2018-03-01

ER D C/ CR RE L TR -1 8- 3 ERDC 6.1 Basic Research Measuring the Non-Line-of-Sight Ultra- High - Frequency Channel in Mountainous Terrain... High - Frequency Channel in Mountainous Terrain A Spread-Spectrum, Portable Channel Sounder Samuel S. Streeter and Daniel J. Breton U.S. Army...spread-spectrum, portable channel sounder specifically designed to meas- ure the non-line-of-sight, ultra- high -frequency channel in mountainous terrain

Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

PubMed

Cho, Jin-Young; Lee, Hyoung-Joo; Jeong, Seul-Ki; Paik, Young-Ki

2017-12-01

Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modification options can increase processing time, false-positive errors in large and complicated MS data sets. Spectral library searching is an alternative solution, avoiding the limitations of sequence DB searching and allowing the detection of more peptides with high sensitivity. Unfortunately, this technique has less proteome coverage, resulting in limitations in the detection of novel and whole peptide sequences in biological samples. To solve these problems, we previously developed the "Combo-Spec Search" method, which uses manually multiple references and simulated spectral library searching to analyze whole proteomes in a biological sample. In this study, we have developed a new analytical interface tool called "Epsilon-Q" to enhance the functions of both the Combo-Spec Search method and label-free protein quantification. Epsilon-Q performs automatically multiple spectral library searching, class-specific false-discovery rate control, and result integration. It has a user-friendly graphical interface and demonstrates good performance in identifying and quantifying proteins by supporting standard MS data formats and spectrum-to-spectrum matching powered by SpectraST. Furthermore, when the Epsilon-Q interface is combined with the Combo-Spec search method, called the Epsilon-Q system, it shows a synergistic function by outperforming other sequence DB search engines for identifying and quantifying low-abundance proteins in biological samples. The Epsilon-Q system can be a versatile tool for comparative proteome analysis based on multiple spectral libraries and label-free quantification.

Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system

PubMed Central

Diener, Stephen E; Houfek, Thomas D; Kalat, Sam E; Windham, DE; Burke, Mark; Opperman, Charles; Dean, Ralph A

2005-01-01

Background - Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists. Results - Here we describe NuclearBLAST, a batch BLAST analysis, storage and management system designed for the biologist. It is a wrapper for NCBI BLAST which provides a user-friendly web interface which includes a request wizard and the ability to view and mine the results. All BLAST results are stored in a MySQL database which allows for more advanced data-mining through supplied command-line utilities or direct database access. NuclearBLAST can be installed on a single machine or clustered amongst a number of machines to improve analysis throughput. NuclearBLAST provides a platform which eases data-mining of multiple BLAST results. With the supplied scripts, the program can export data into a spreadsheet-friendly format, automatically assign Gene Ontology terms to sequences and provide bi-directional best hits between two datasets. Users with SQL experience can use the database to ask even more complex questions and extract any subset of data they require. Conclusion - This tool provides a user-friendly interface for requesting, viewing and mining of BLAST results which makes the management and data-mining of large sets of BLAST analyses tractable to biologists. PMID:15958161

Learning with Technology: Video Modeling with Concrete-Representational-Abstract Sequencing for Students with Autism Spectrum Disorder.

PubMed

Yakubova, Gulnoza; Hughes, Elizabeth M; Shinaberry, Megan

2016-07-01

The purpose of this study was to determine the effectiveness of a video modeling intervention with concrete-representational-abstract instructional sequence in teaching mathematics concepts to students with autism spectrum disorder (ASD). A multiple baseline across skills design of single-case experimental methodology was used to determine the effectiveness of the intervention on the acquisition and maintenance of addition, subtraction, and number comparison skills for four elementary school students with ASD. Findings supported the effectiveness of the intervention in improving skill acquisition and maintenance at a 3-week follow-up. Implications for practice and future research are discussed.

Support vector machine multiuser receiver for DS-CDMA signals in multipath channels.

PubMed

Chen, S; Samingan, A K; Hanzo, L

2001-01-01

The problem of constructing an adaptive multiuser detector (MUD) is considered for direct sequence code division multiple access (DS-CDMA) signals transmitted through multipath channels. The emerging learning technique, called support vector machines (SVM), is proposed as a method of obtaining a nonlinear MUD from a relatively small training data block. Computer simulation is used to study this SVM MUD, and the results show that it can closely match the performance of the optimal Bayesian one-shot detector. Comparisons with an adaptive radial basis function (RBF) MUD trained by an unsupervised clustering algorithm are discussed.

Iteration and superposition encryption scheme for image sequences based on multi-dimensional keys

NASA Astrophysics Data System (ADS)

Han, Chao; Shen, Yuzhen; Ma, Wenlin

2017-12-01

An iteration and superposition encryption scheme for image sequences based on multi-dimensional keys is proposed for high security, big capacity and low noise information transmission. Multiple images to be encrypted are transformed into phase-only images with the iterative algorithm and then are encrypted by different random phase, respectively. The encrypted phase-only images are performed by inverse Fourier transform, respectively, thus new object functions are generated. The new functions are located in different blocks and padded zero for a sparse distribution, then they propagate to a specific region at different distances by angular spectrum diffraction, respectively and are superposed in order to form a single image. The single image is multiplied with a random phase in the frequency domain and then the phase part of the frequency spectrums is truncated and the amplitude information is reserved. The random phase, propagation distances, truncated phase information in frequency domain are employed as multiple dimensional keys. The iteration processing and sparse distribution greatly reduce the crosstalk among the multiple encryption images. The superposition of image sequences greatly improves the capacity of encrypted information. Several numerical experiments based on a designed optical system demonstrate that the proposed scheme can enhance encrypted information capacity and make image transmission at a highly desired security level.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

PubMed Central

Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A. Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David; Bento, Celeste; Bignell, Patricia; Blair, Edward; Buckle, Veronica J; Bull, Katherine; Cais, Ondrej; Cario, Holger; Chapel, Helen; Copley, Richard R; Cornall, Richard; Craft, Jude; Dahan, Karin; Davenport, Emma E; Dendrou, Calliope; Devuyst, Olivier; Fenwick, Aimée L; Flint, Jonathan; Fugger, Lars; Gilbert, Rodney D; Goriely, Anne; Green, Angie; Greger, Ingo H.; Grocock, Russell; Gruszczyk, Anja V; Hastings, Robert; Hatton, Edouard; Higgs, Doug; Hill, Adrian; Holmes, Chris; Howard, Malcolm; Hughes, Linda; Humburg, Peter; Johnson, David; Karpe, Fredrik; Kingsbury, Zoya; Kini, Usha; Knight, Julian C; Krohn, Jonathan; Lamble, Sarah; Langman, Craig; Lonie, Lorne; Luck, Joshua; McCarthy, Davis; McGowan, Simon J; McMullin, Mary Frances; Miller, Kerry A; Murray, Lisa; Németh, Andrea H; Nesbit, M Andrew; Nutt, David; Ormondroyd, Elizabeth; Oturai, Annette Bang; Pagnamenta, Alistair; Patel, Smita Y; Percy, Melanie; Petousi, Nayia; Piazza, Paolo; Piret, Sian E; Polanco-Echeverry, Guadalupe; Popitsch, Niko; Powrie, Fiona; Pugh, Chris; Quek, Lynn; Robbins, Peter A; Robson, Kathryn; Russo, Alexandra; Sahgal, Natasha; van Schouwenburg, Pauline A; Schuh, Anna; Silverman, Earl; Simmons, Alison; Sørensen, Per Soelberg; Sweeney, Elizabeth; Taylor, John; Thakker, Rajesh V; Tomlinson, Ian; Trebes, Amy; Twigg, Stephen RF; Uhlig, Holm H; Vyas, Paresh; Vyse, Tim; Wall, Steven A; Watkins, Hugh; Whyte, Michael P; Witty, Lorna; Wright, Ben; Yau, Chris; Buck, David; Humphray, Sean; Ratcliffe, Peter J; Bell, John I; Wilkie, Andrew OM; Bentley, David; Donnelly, Peter; McVean, Gilean

2015-01-01

To assess factors influencing the success of whole genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases across a broad spectrum of disorders in whom prior screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritisation. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease causing variants in 21% of cases, rising to 34% (23/68) for Mendelian disorders and 57% (8/14) in trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, though only four were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis, but also highlight many outstanding challenges. PMID:25985138

Non-line-of-sight (NLOS), secure, low-probability of intercept (LPI), antijam (AJ), high frequency (HF), real time video communication system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lupinetti, F.

1988-01-01

This paper outlines a video communication system capable of non-line-of-sight (NLOS), secure, low-probability of intercept (LPI), antijam, real time transmission and reception of video information in a tactical enviroment. An introduction to a class of ternary PN sequences is presented to familiarize the reader with yet another avenue for spreading and despreading baseband information. The use of the high frequency (HF) band (1.5 to 30 MHz) for real time video transmission is suggested to allow NLOS communication. The spreading of the baseband information by means of multiple nontrivially different ternary pseudonoise (PN) sequence is used in order to assure encryptionmore » of the signal, enhanced security, a good degree of LPI, and good antijam features. 18 refs., 3 figs., 1 tab.« less

A multiple-scale turbulence model for incompressible flow

NASA Technical Reports Server (NTRS)

Duncan, B. S.; Liou, W. W.; Shih, T. H.

1993-01-01

A multiple-scale eddy viscosity model is described. This model splits the energy spectrum into a high wave number regime and a low wave number regime. Dividing the energy spectrum into multiple regimes simplistically emulates the cascade of energy through the turbulence spectrum. The constraints on the model coefficients are determined by examining decaying turbulence and homogeneous turbulence. A direct link between the partitioned energies and the energy transfer process is established through the coefficients. This new model was calibrated and tested for boundary-free turbulent shear flows. Calculations of mean and turbulent properties show good agreement with experimental data for two mixing layers, a plane jet and a round jet.

High order harmonics anomaly of jet screech

NASA Astrophysics Data System (ADS)

Chen, Zhe; Wu, Jiu Hui; Ren, A.-Dan; Chen, Xin

2018-05-01

Imperfectly expanded supersonic jets under strong screech could generate both fundamental screech tones and multiple tones at the harmonics of the fundamental frequency. The paper compares the fundamental frequency of jets from both AR = 3 (Aspect Ratio) and AR = 4 rectangular nozzles, and conducts analysis of harmonics on Sound Pressure Level (SPL) spectrums of jet noise. The research suggests that the fundamental frequency of the first two- or three-order harmonics increases when the Nozzle Pressure Ratio (NPR) decreases, whereas the highest order harmonic decreases when the NPR decreases. Besides, the paper also observes the differences between the highest order harmonics and other harmonics that have never been reported before. Further analysis on flow field schlieren of AR = 3 nozzle indicates that the highest order harmonic is the outcome of interaction between second shock-cell and nonlinear instable wave. The revolution of these high order harmonics can provide guidance for the prevention of small-scale structure fatigue damage. Moreover, the distribution test of the noises is also carried out to verify the high order harmonics anomaly, and indicate that the jet noise spreads mainly towards downstream while screech towards upstream. In addition, the broadband shock-associated noise spreads vertical to the jet flow and exhibits the feature of directivity.

Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study

PubMed Central

Cole, Kevin; Cole, Michelle J; Cresswell, Fiona; Dean, Gillian; Dave, Jayshree; Thomas, Daniel Rh; Foster, Kirsty; Waldram, Alison; Wilson, Daniel J; Didelot, Xavier; Grad, Yonatan H; Crook, Derrick W; Peto, Tim EA; Walker, A Sarah

2016-01-01

Background New approaches are urgently required to address increasing rates of gonorrhoea and the emergence and global spread of antibiotic-resistant Neisseria gonorrhoeae. Whole genome sequencing (WGS) can be applied to study transmission and track resistance. Methods We performed WGS on 1659 isolates from Brighton, UK, and 217 additional isolates from other UK locations. We included WGS data (n=196) from the USA. Estimated mutation rates, plus diversity observed within patients across anatomical sites and probable transmission pairs, were used to fit a coalescent model to determine the number of single nucleotide polymorphisms (SNPs) expected between sequences related by direct/indirect transmission, depending on the time between samples. Findings We detected extensive local transmission. 281/1061(26%) Brighton cases were indistinguishable (0 SNPs) to ≥1 previous case(s), and 786(74%) had evidence of a sampled direct or indirect Brighton source. There was evidence of sustained transmission of some lineages. We observed multiple related samples across geographic locations. Of 1273 infections in Brighton, 225(18%) were linked to another case from elsewhere in the UK, and 115(9%) to a case from the USA. Four lineages initially identified in Brighton could be linked to 70 USA sequences, including 61 from a lineage carrying the mosaic penA XXXIV associated with reduced cefixime susceptibility. Interpretation We present a WGS-based tool for genomic contact tracing of N. gonorrhoeae and demonstrate local, national and international transmission. WGS can be applied across geographical boundaries to investigate gonorrhoea transmission and to track antimicrobial resistance. Funding Oxford NIHR Health Protection Research Unit and Biomedical Research Centre. PMID:27427203

Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping

NASA Astrophysics Data System (ADS)

Müller, Vilhelm; Rajer, Fredrika; Frykholm, Karolin; Nyberg, Lena K.; Quaderi, Saair; Fritzsche, Joachim; Kristiansson, Erik; Ambjörnsson, Tobias; Sandegren, Linus; Westerlund, Fredrik

2016-12-01

Bacterial plasmids are extensively involved in the rapid global spread of antibiotic resistance. We here present an assay, based on optical DNA mapping of single plasmids in nanofluidic channels, which provides detailed information about the plasmids present in a bacterial isolate. In a single experiment, we obtain the number of different plasmids in the sample, the size of each plasmid, an optical barcode that can be used to identify and trace the plasmid of interest and information about which plasmid that carries a specific resistance gene. Gene identification is done using CRISPR/Cas9 loaded with a guide-RNA (gRNA) complementary to the gene of interest that linearizes the circular plasmids at a specific location that is identified using the optical DNA maps. We demonstrate the principle on clinically relevant extended spectrum beta-lactamase (ESBL) producing isolates. We discuss how the gRNA sequence can be varied to obtain the desired information. The gRNA can either be very specific to identify a homogeneous group of genes or general to detect several groups of genes at the same time. Finally, we demonstrate an example where we use a combination of two gRNA sequences to identify carbapenemase-encoding genes in two previously not characterized clinical bacterial samples.

Wireless sensor platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joshi, Pooran C.; Killough, Stephen M.; Kuruganti, Phani Teja

A wireless sensor platform and methods of manufacture are provided. The platform involves providing a plurality of wireless sensors, where each of the sensors is fabricated on flexible substrates using printing techniques and low temperature curing. Each of the sensors can include planar sensor elements and planar antennas defined using the printing and curing. Further, each of the sensors can include a communications system configured to encode the data from the sensors into a spread spectrum code sequence that is transmitted to a central computer(s) for use in monitoring an area associated with the sensors.

Towards Harmonious Coexistence in the Unlicensed Spectrum: Rational Cooperation of Operators

PubMed Central

2017-01-01

5G New Radio (NR) operating in the unlicensed spectrum is accelerating the Fourth Industrial Revolution by supporting Internet of Things (IoT) networks or Industrial IoT deployments. Specifically, LTE-Advanced (LTE-A) is looking to achieve spectrum integration through coexistence with multi-radio access technology (RAT) systems in the same unlicensed bands with both licensed-assisted and stand-alone access. The listen-before-talk (LBT) mechanism is mainly considered to enable an LTE operator to protect other incumbent unlicensed systems. In this article, we investigate the behaviors of multiple LTE operators along with the deployment of WiFi networks in the unlicensed spectrum from both short- and long-term points of view. In countries without mandatory LBT requirements, we show that an LTE operator is susceptible to collusion with another LTE operator, thus exploiting scarce spectrum resources by deceiving other wireless networks into thinking that channels are always busy; hence, mandatory usage of LTE with LBT is highly recommended at national level to achieve harmonious coexistence in the unlicensed spectrum. We discuss several possible coexistence scenarios to resolve the operator’s dilemmaas well as to improve unlicensed spectrum efficiency among multi-RAT systems, which is viable in the near future. PMID:29064434

Towards Harmonious Coexistence in the Unlicensed Spectrum: Rational Cooperation of Operators.

PubMed

Bae, Sunghwan; Kim, Hongseok

2017-10-24

5G New Radio (NR) operating in the unlicensed spectrum is accelerating the Fourth Industrial Revolution by supporting Internet of Things (IoT) networks or Industrial IoT deployments. Specifically, LTE-Advanced (LTE-A) is looking to achieve spectrum integration through coexistence with multi-radio access technology (RAT) systems in the same unlicensed bands with both licensed-assisted and stand-alone access. The listen-before-talk (LBT) mechanism is mainly considered to enable an LTE operator to protect other incumbent unlicensed systems. In this article, we investigate the behaviors of multiple LTE operators along with the deployment of WiFi networks in the unlicensed spectrum from both short- and long-term points of view. In countries without mandatory LBT requirements, we show that an LTE operator is susceptible to collusion with another LTE operator, thus exploiting scarce spectrum resources by deceiving other wireless networks into thinking that channels are always busy; hence, mandatory usage of LTE with LBT is highly recommended at national level to achieve harmonious coexistence in the unlicensed spectrum. We discuss several possible coexistence scenarios to resolve the operator's dilemmaas well as to improve unlicensed spectrum efficiency among multi-RAT systems, which is viable in the near future.

Research on Formation of Microsatellite Communication with Genetic Algorithm

PubMed Central

Wu, Guoqiang; Bai, Yuguang; Sun, Zhaowei

2013-01-01

For the formation of three microsatellites which fly in the same orbit and perform three-dimensional solid mapping for terra, this paper proposes an optimizing design method of space circular formation order based on improved generic algorithm and provides an intersatellite direct spread spectrum communication system. The calculating equation of LEO formation flying satellite intersatellite links is guided by the special requirements of formation-flying microsatellite intersatellite links, and the transmitter power is also confirmed throughout the simulation. The method of space circular formation order optimizing design based on improved generic algorithm is given, and it can keep formation order steady for a long time under various absorb impetus. The intersatellite direct spread spectrum communication system is also provided. It can be found that, when the distance is 1 km and the data rate is 1 Mbps, the input wave matches preferably with the output wave. And LDPC code can improve the communication performance. The correct capability of (512, 256) LDPC code is better than (2, 1, 7) convolution code, distinctively. The design system can satisfy the communication requirements of microsatellites. So, the presented method provides a significant theory foundation for formation-flying and intersatellite communication. PMID:24078796

Research on formation of microsatellite communication with genetic algorithm.

PubMed

Wu, Guoqiang; Bai, Yuguang; Sun, Zhaowei

2013-01-01

For the formation of three microsatellites which fly in the same orbit and perform three-dimensional solid mapping for terra, this paper proposes an optimizing design method of space circular formation order based on improved generic algorithm and provides an intersatellite direct spread spectrum communication system. The calculating equation of LEO formation flying satellite intersatellite links is guided by the special requirements of formation-flying microsatellite intersatellite links, and the transmitter power is also confirmed throughout the simulation. The method of space circular formation order optimizing design based on improved generic algorithm is given, and it can keep formation order steady for a long time under various absorb impetus. The intersatellite direct spread spectrum communication system is also provided. It can be found that, when the distance is 1 km and the data rate is 1 Mbps, the input wave matches preferably with the output wave. And LDPC code can improve the communication performance. The correct capability of (512, 256) LDPC code is better than (2, 1, 7) convolution code, distinctively. The design system can satisfy the communication requirements of microsatellites. So, the presented method provides a significant theory foundation for formation-flying and intersatellite communication.

Cooperative behavior cascades in human social networks.

PubMed

Fowler, James H; Christakis, Nicholas A

2010-03-23

Theoretical models suggest that social networks influence the evolution of cooperation, but to date there have been few experimental studies. Observational data suggest that a wide variety of behaviors may spread in human social networks, but subjects in such studies can choose to befriend people with similar behaviors, posing difficulty for causal inference. Here, we exploit a seminal set of laboratory experiments that originally showed that voluntary costly punishment can help sustain cooperation. In these experiments, subjects were randomly assigned to a sequence of different groups to play a series of single-shot public goods games with strangers; this feature allowed us to draw networks of interactions to explore how cooperative and uncooperative behaviors spread from person to person to person. We show that, in both an ordinary public goods game and in a public goods game with punishment, focal individuals are influenced by fellow group members' contribution behavior in future interactions with other individuals who were not a party to the initial interaction. Furthermore, this influence persists for multiple periods and spreads up to three degrees of separation (from person to person to person to person). The results suggest that each additional contribution a subject makes to the public good in the first period is tripled over the course of the experiment by other subjects who are directly or indirectly influenced to contribute more as a consequence. These results show experimentally that cooperative behavior cascades in human social networks.

Neisseria gonorrhoeae and extended-spectrum cephalosporins in California: surveillance and molecular detection of mosaic penA.

PubMed

Gose, Severin; Nguyen, Duylinh; Lowenberg, Daniella; Samuel, Michael; Bauer, Heidi; Pandori, Mark

2013-12-04

The spread of Neisseria gonorrhoeae strains with mosaic penA alleles and reduced susceptibility to extended-spectrum cephalosporins is a major public health problem. While much work has been performed internationally, little is known about the genetics or molecular epidemiology of N. gonorrhoeae isolates with reduced susceptibility to extended-spectrum cephalosporins in the United States. The majority of N. gonorrhoeae infections are diagnosed without a live culture. Molecular tools capable of detecting markers of extended-spectrum cephalosporin resistance are needed. Urethral N. gonorrhoeae isolates were collected from 684 men at public health clinics in California in 2011. Minimum inhibitory concentrations (MICs) to ceftriaxone, cefixime, cefpodoxime and azithromycin were determined by Etest and categorized according to the U.S. Centers for Disease Control 2010 alert value breakpoints. 684 isolates were screened for mosaic penA alleles using real-time PCR (RTPCR) and 59 reactive isolates were subjected to DNA sequencing of their penA alleles and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST). To increase the specificity of the screening RTPCR in detecting isolates with alert value extended-spectrum cephalosporin MICs, the primers were modified to selectively amplify the mosaic XXXIV penA allele. Three mosaic penA alleles were detected including two previously described alleles (XXXIV, XXXVIII) and one novel allele (LA-A). Of the 29 isolates with an alert value extended-spectrum cephalosporin MIC, all possessed the mosaic XXXIV penA allele and 18 were sequence type 1407, an internationally successful strain associated with multi-drug resistance. The modified RTPCR detected the mosaic XXXIV penA allele in urethral isolates and urine specimens and displayed no amplification of the other penA alleles detected in this study. N. gonorrhoeae isolates with mosaic penA alleles and reduced susceptibility to extended-spectrum cephalosporins are currently circulating in California. Isolates with the same NG-MAST ST, penA allele and extended-spectrum cephalosporin MICs have caused treatment failures elsewhere. The RTPCR assay presented here may be useful for the detection of N. gonorrheoae isolates and clinical specimens with reduced extended-spectrum cephalosporin MICs in settings where antimicrobial susceptibility testing is unavailable. In an era of increasing antimicrobial resistance and decreasing culture capacity, molecular assays capable of detecting extended-spectrum cephalosporin of resistance are essential to public health.

Neisseria gonorrhoeae and extended-spectrum cephalosporins in California: surveillance and molecular detection of mosaic penA

PubMed Central

2013-01-01

Background The spread of Neisseria gonorrhoeae strains with mosaic penA alleles and reduced susceptibility to extended-spectrum cephalosporins is a major public health problem. While much work has been performed internationally, little is known about the genetics or molecular epidemiology of N. gonorrhoeae isolates with reduced susceptibility to extended-spectrum cephalosporins in the United States. The majority of N. gonorrhoeae infections are diagnosed without a live culture. Molecular tools capable of detecting markers of extended-spectrum cephalosporin resistance are needed. Methods Urethral N. gonorrhoeae isolates were collected from 684 men at public health clinics in California in 2011. Minimum inhibitory concentrations (MICs) to ceftriaxone, cefixime, cefpodoxime and azithromycin were determined by Etest and categorized according to the U.S. Centers for Disease Control 2010 alert value breakpoints. 684 isolates were screened for mosaic penA alleles using real-time PCR (RTPCR) and 59 reactive isolates were subjected to DNA sequencing of their penA alleles and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST). To increase the specificity of the screening RTPCR in detecting isolates with alert value extended-spectrum cephalosporin MICs, the primers were modified to selectively amplify the mosaic XXXIV penA allele. Results Three mosaic penA alleles were detected including two previously described alleles (XXXIV, XXXVIII) and one novel allele (LA-A). Of the 29 isolates with an alert value extended-spectrum cephalosporin MIC, all possessed the mosaic XXXIV penA allele and 18 were sequence type 1407, an internationally successful strain associated with multi-drug resistance. The modified RTPCR detected the mosaic XXXIV penA allele in urethral isolates and urine specimens and displayed no amplification of the other penA alleles detected in this study. Conclusion N. gonorrhoeae isolates with mosaic penA alleles and reduced susceptibility to extended-spectrum cephalosporins are currently circulating in California. Isolates with the same NG-MAST ST, penA allele and extended-spectrum cephalosporin MICs have caused treatment failures elsewhere. The RTPCR assay presented here may be useful for the detection of N. gonorrheoae isolates and clinical specimens with reduced extended-spectrum cephalosporin MICs in settings where antimicrobial susceptibility testing is unavailable. In an era of increasing antimicrobial resistance and decreasing culture capacity, molecular assays capable of detecting extended-spectrum cephalosporin of resistance are essential to public health. PMID:24305088

Quantum game application to spectrum scarcity problems

NASA Astrophysics Data System (ADS)

Zabaleta, O. G.; Barrangú, J. P.; Arizmendi, C. M.

2017-01-01

Recent spectrum-sharing research has produced a strategy to address spectrum scarcity problems. This novel idea, named cognitive radio, considers that secondary users can opportunistically exploit spectrum holes left temporarily unused by primary users. This presents a competitive scenario among cognitive users, making it suitable for game theory treatment. In this work, we show that the spectrum-sharing benefits of cognitive radio can be increased by designing a medium access control based on quantum game theory. In this context, we propose a model to manage spectrum fairly and effectively, based on a multiple-users multiple-choice quantum minority game. By taking advantage of quantum entanglement and quantum interference, it is possible to reduce the probability of collision problems commonly associated with classic algorithms. Collision avoidance is an essential property for classic and quantum communications systems. In our model, two different scenarios are considered, to meet the requirements of different user strategies. The first considers sensor networks where the rational use of energy is a cornerstone; the second focuses on installations where the quality of service of the entire network is a priority.

Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.

PubMed

Iguchi, Atsushi; Nagaya, Yutaka; Pradel, Elizabeth; Ooka, Tadasuke; Ogura, Yoshitoshi; Katsura, Keisuke; Kurokawa, Ken; Oshima, Kenshiro; Hattori, Masahira; Parkhill, Julian; Sebaihia, Mohamed; Coulthurst, Sarah J; Gotoh, Naomasa; Thomson, Nicholas R; Ewbank, Jonathan J; Hayashi, Tetsuya

2014-08-01

Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Universal Frequency Domain Baseband Receiver Structure for Future Military Software Defined Radios

DTIC Science & Technology

2010-09-01

selective channels, i.e., it may have a poor performance at good conditions [4]. Military systems may require a direct sequence ( DS ) component for...frequency bins using a spreading code. This is called the MC- CDMA signal. Note that spreading does not need to cover all the subcarriers but just a few, like...preambles with appropriate frequency domain properties. A DS component can be added as usually. The FDP block then includes this code as a reference

International two-way satellite time transfers using INTELSAT space segment and small Earth stations

NASA Technical Reports Server (NTRS)

Veenstra, Lester B.

1990-01-01

The satellite operated by the International Telecommunications Satellite Organization (INTELSAT) provides new and unique capabilities for the coordinates of international time scales on a world wide basis using the two-way technique. A network of coordinated clocks using small earth stations collocated with the scales is possible. Antennas as small as 1.8 m at K-band and 3 m at C-band transmitting powers of less than 1 W will provide signals with time jitters of less than 1 ns existing spread spectrum modems. One way time broadcasting is also possible, under the INTELSAT INTELNET system, possibly using existing international data distribution (press and financial) systems that are already operating spread spectrum systems. The technical details of the satellite and requirements on satellite earth stations are given. The resources required for a regular operational international time transfer service are analyzed with respect to the existing international digital service offerings of the INTELSAT Business Service (IBS) and INTELNET. Coverage areas, typical link budgets, and a summary of previous domestic and international work using this technique are provided. Administrative procedures for gaining access to the space segment are outlined. Contact information for local INTELSAT signatories is listed.

Automatic segmentation of low-visibility moving objects through energy analyis of the local 3D spectrum

NASA Astrophysics Data System (ADS)

Nestares, Oscar; Miravet, Carlos; Santamaria, Javier; Fonolla Navarro, Rafael

1999-05-01

Automatic object segmentation in highly noisy image sequences, composed by a translating object over a background having a different motion, is achieved through joint motion-texture analysis. Local motion and/or texture is characterized by the energy of the local spatio-temporal spectrum, as different textures undergoing different translational motions display distinctive features in their 3D (x,y,t) spectra. Measurements of local spectrum energy are obtained using a bank of directional 3rd order Gaussian derivative filters in a multiresolution pyramid in space- time (10 directions, 3 resolution levels). These 30 energy measurements form a feature vector describing texture-motion for every pixel in the sequence. To improve discrimination capability and reduce computational cost, we automatically select those 4 features (channels) that best discriminate object from background, under the assumptions that the object is smaller than the background and has a different velocity or texture. In this way we reject features irrelevant or dominated by noise, that could yield wrong segmentation results. This method has been successfully applied to sequences with extremely low visibility and for objects that are even invisible for the eye in absence of motion.

Methodological considerations of acoustic playbacks to test the behavioral significance of call directionality in male northern elephant seals (Mirounga angustirostris)

NASA Astrophysics Data System (ADS)

Holt, Marla M.; Insley, Stephen J.; Southall, Brandon L.; Schusterman, Ronald J.

2005-09-01

While attempting to gain access to receptive females, male northern elephant seals form dominance hierarchies through multiple dyadic interactions involving visual and acoustic signals. These signals are both highly stereotyped and directional. Previous behavioral observations suggested that males attend to the directional cues of these signals. We used in situ vocal playbacks to test whether males attend to directional cues of the acoustic components of a competitors calls (i.e., variation in call spectra and source levels). Here, we will focus on playback methodology. Playback calls were multiple exemplars of a marked dominant male from an isolated area, recorded with a directional microphone and DAT recorder and edited into a natural sequence that controlled call amplitude. Control calls were recordings of ambient rookery sounds with the male calls removed. Subjects were 20 marked males (10 adults and 10 subadults) all located at An~o Nuevo, CA. Playback presentations, calibrated for sound-pressure level, were broadcast at a distance of 7 m from each subject. Most responses were classified into the following categories: visual orientation, postural change, calling, movement toward or away from the loudspeaker, and re-directed aggression. We also investigated developmental, hierarchical, and ambient noise variables that were thought to influence male behavior.

Characterization of Isolates of Salmonella enterica Serovar Stanley, a Serovar Endemic to Asia and Associated with Travel

PubMed Central

Le Hello, Simon; Bortolaia, Valeria; Pulsrikarn, Chaiwat; Nielsen, Eva Møller; Pornruangmong, Srirat; Chaichana, Phattharaporn; Svendsen, Christina Aaby; Weill, François-Xavier; Aarestrup, Frank M.

2012-01-01

Salmonella enterica serovar Stanley (S. Stanley) is a common serovar in Southeast Asia and was the second most common serovar implicated in human salmonellosis in Thailand in the years 2002 to 2007. In contrast, this serovar is relatively uncommon in Europe. The objective of this study was to characterize a collection of S. Stanley strains isolated from Thai (n = 62), Danish (n = 39), and French (n = 24) patients to gain a broader understanding of the genetic diversity, population dynamics, and susceptibility to antimicrobials. All isolates were characterized by pulsed-field gel electrophoresis and antimicrobial susceptibility testing. The molecular mechanisms of resistance to extended-spectrum cephalosporins and plasmid-mediated resistance to quinolones were characterized by PCR and sequencing. Plasmid profiling, replicon typing, and microarray analysis were used to characterize the genetic mechanisms of antimicrobial resistance in 10 extended-spectrum cephalosporinase-producing isolates. Considerable genetic diversity was observed among the isolates characterized with 91 unique XbaI pulsed-field gel electrophoresis (PFGE) patterns, including 17 distinct clusters consisting of two to seven indistinguishable isolates. We found some of the S. Stanley isolates isolated from patients in Europe were acquired during travel to Southeast Asia, including Thailand. The presence of multiple plasmid lineages carrying the extended-spectrum cephalosporinase-encoding blaCMY-2 gene in S. Stanley isolates from the central part of Thailand was confirmed. Our results emphasize that Thai authorities, as well as authorities in other countries lacking prudent use of antimicrobials, should improve the ongoing efforts to regulate antimicrobial use in agriculture and in clinical settings to limit the spread of multidrug-resistant Salmonella isolates and plasmids among humans and pigs in Thailand and abroad. PMID:22205822

Characterization of isolates of Salmonella enterica serovar Stanley, a serovar endemic to Asia and associated with travel.

PubMed

Hendriksen, Rene S; Le Hello, Simon; Bortolaia, Valeria; Pulsrikarn, Chaiwat; Nielsen, Eva Møller; Pornruangmong, Srirat; Chaichana, Phattharaporn; Svendsen, Christina Aaby; Weill, François-Xavier; Aarestrup, Frank M

2012-03-01

Salmonella enterica serovar Stanley (S. Stanley) is a common serovar in Southeast Asia and was the second most common serovar implicated in human salmonellosis in Thailand in the years 2002 to 2007. In contrast, this serovar is relatively uncommon in Europe. The objective of this study was to characterize a collection of S. Stanley strains isolated from Thai (n = 62), Danish (n = 39), and French (n = 24) patients to gain a broader understanding of the genetic diversity, population dynamics, and susceptibility to antimicrobials. All isolates were characterized by pulsed-field gel electrophoresis and antimicrobial susceptibility testing. The molecular mechanisms of resistance to extended-spectrum cephalosporins and plasmid-mediated resistance to quinolones were characterized by PCR and sequencing. Plasmid profiling, replicon typing, and microarray analysis were used to characterize the genetic mechanisms of antimicrobial resistance in 10 extended-spectrum cephalosporinase-producing isolates. Considerable genetic diversity was observed among the isolates characterized with 91 unique XbaI pulsed-field gel electrophoresis (PFGE) patterns, including 17 distinct clusters consisting of two to seven indistinguishable isolates. We found some of the S. Stanley isolates isolated from patients in Europe were acquired during travel to Southeast Asia, including Thailand. The presence of multiple plasmid lineages carrying the extended-spectrum cephalosporinase-encoding bla(CMY-2) gene in S. Stanley isolates from the central part of Thailand was confirmed. Our results emphasize that Thai authorities, as well as authorities in other countries lacking prudent use of antimicrobials, should improve the ongoing efforts to regulate antimicrobial use in agriculture and in clinical settings to limit the spread of multidrug-resistant Salmonella isolates and plasmids among humans and pigs in Thailand and abroad.

D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs

PubMed Central

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-01-01

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D­MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co­regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos­box cis­regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D­MATRIX tool is accessible through the CIMAP domain network. Availability http://203.190.147.116/dmatrix/ PMID:19759861

D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.

PubMed

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-07-27

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network. http://203.190.147.116/dmatrix/

SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes.

PubMed

Bielejec, Filip; Baele, Guy; Vrancken, Bram; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2016-08-01

Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST (http://beast.bio.ed.ac.uk, last accessed 9 May 2016). The integration of JavaScript D3 libraries (www.d3.org, last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest. © The Author 2016. 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.

Feedback power control strategies in wireless sensor networks with joint channel decoding.

PubMed

Abrardo, Andrea; Ferrari, Gianluigi; Martalò, Marco; Perna, Fabio

2009-01-01

In this paper, we derive feedback power control strategies for block-faded multiple access schemes with correlated sources and joint channel decoding (JCD). In particular, upon the derivation of the feasible signal-to-noise ratio (SNR) region for the considered multiple access schemes, i.e., the multidimensional SNR region where error-free communications are, in principle, possible, two feedback power control strategies are proposed: (i) a classical feedback power control strategy, which aims at equalizing all link SNRs at the access point (AP), and (ii) an innovative optimized feedback power control strategy, which tries to make the network operational point fall in the feasible SNR region at the lowest overall transmit energy consumption. These strategies will be referred to as "balanced SNR" and "unbalanced SNR," respectively. While they require, in principle, an unlimited power control range at the sources, we also propose practical versions with a limited power control range. We preliminary consider a scenario with orthogonal links and ideal feedback. Then, we analyze the robustness of the proposed power control strategies to possible non-idealities, in terms of residual multiple access interference and noisy feedback channels. Finally, we successfully apply the proposed feedback power control strategies to a limiting case of the class of considered multiple access schemes, namely a central estimating officer (CEO) scenario, where the sensors observe noisy versions of a common binary information sequence and the AP's goal is to estimate this sequence by properly fusing the soft-output information output by the JCD algorithm.

A multiple-scale turbulence model for incompressible flow

NASA Technical Reports Server (NTRS)

Duncan, B. S.; Liou, W. W.; Shih, T. H.

1993-01-01

A multiple-scale eddy viscosity model is described in this paper. This model splits the energy spectrum into a high wave number regime and a low wave number regime. Dividing the energy spectrum into multiple regimes simplistically emulates the cascade of energy through the turbulence spectrum. The constraints on the model coefficients are determined by examining decaying turbulence and homogeneous turbulence. A direct link between the partitioned energies and the energy transfer process is established through the coefficients. This new model has been calibrated and tested for boundary-free turbulent shear flows. Calculations of mean and turbulent properties show good agreement with experimental data for two mixing layers, a plane jet and a round jet.

Rising Expectations: Access to Biomedical Information

PubMed Central

Lindberg, D. A. B.; Humphreys, B. L.

2008-01-01

Summary Objective To provide an overview of the expansion in public access to electronic biomedical information over the past two decades, with an emphasis on developments to which the U.S. National Library of Medicine contributed. Methods Review of the increasingly broad spectrum of web-accessible genomic data, biomedical literature, consumer health information, clinical trials data, and images. Results The amount of publicly available electronic biomedical information has increased dramatically over the past twenty years. Rising expectations regarding access to biomedical information were stimulated by the spread of the Internet, the World Wide Web, advanced searching and linking techniques. These informatics advances simplified and improved access to electronic information and reduced costs, which enabled inter-organizational collaborations to build and maintain large international information resources and also aided outreach and education efforts The demonstrated benefits of free access to electronic biomedical information encouraged the development of public policies that further increase the amount of information available. Conclusions Continuing rapid growth of publicly accessible electronic biomedical information presents tremendous opportunities and challenges, including the need to ensure uninterrupted access during disasters or emergencies and to manage digital resources so they remain available for future generations. PMID:18587496

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.

PubMed

Alcantara, Luiz Carlos Junior; Cassol, Sharon; Libin, Pieter; Deforche, Koen; Pybus, Oliver G; Van Ranst, Marc; Galvão-Castro, Bernardo; Vandamme, Anne-Mieke; de Oliveira, Tulio

2009-07-01

Human immunodeficiency virus type-1 (HIV-1), hepatitis B and C and other rapidly evolving viruses are characterized by extremely high levels of genetic diversity. To facilitate diagnosis and the development of prevention and treatment strategies that efficiently target the diversity of these viruses, and other pathogens such as human T-lymphotropic virus type-1 (HTLV-1), human herpes virus type-8 (HHV8) and human papillomavirus (HPV), we developed a rapid high-throughput-genotyping system. The method involves the alignment of a query sequence with a carefully selected set of pre-defined reference strains, followed by phylogenetic analysis of multiple overlapping segments of the alignment using a sliding window. Each segment of the query sequence is assigned the genotype and sub-genotype of the reference strain with the highest bootstrap (>70%) and bootscanning (>90%) scores. Results from all windows are combined and displayed graphically using color-coded genotypes. The new Virus-Genotyping Tools provide accurate classification of recombinant and non-recombinant viruses and are currently being assessed for their diagnostic utility. They have incorporated into several HIV drug resistance algorithms including the Stanford (http://hivdb.stanford.edu) and two European databases (http://www.umcutrecht.nl/subsite/spread-programme/ and http://www.hivrdb.org.uk/) and have been successfully used to genotype a large number of sequences in these and other databases. The tools are a PHP/JAVA web application and are freely accessible on a number of servers including: http://bioafrica.mrc.ac.za/rega-genotype/html/, http://lasp.cpqgm.fiocruz.br/virus-genotype/html/, http://jose.med.kuleuven.be/genotypetool/html/.

Emergence and Spread of Neisseria gonorrhoeae Isolates With Decreased Susceptibility to Extended-Spectrum Cephalosporins in Argentina, 2009 to 2013.

PubMed

Gianecini, Ricardo; Romero, Maria de Las Mercedes; Oviedo, Claudia; Vacchino, Martin; Galarza, Patricia

2017-06-01

The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins represents a major concern globally. The aim of this study was to examine the phenotypic and molecular characteristics of N. gonorrhoeae isolates with decreased susceptibility to ceftriaxone and cefixime in Argentina. A total of 1987 isolates were collected during 2009 and 2013. The susceptibility to penicillin G, tetracycline, ciprofloxacin, cefixime, ceftriaxone, and azithromycin was determined using the agar dilution method. The major extended-spectrum cephalosporin resistance determinants (penA, mtrR, and porB1b) were sequenced in 42 N. gonorrhoeae isolates that showed decreased susceptibility to ceftriaxone (minimum inhibitory concentration [MIC], 0.06-0.125 mg/L) and cefixime (MIC, 0.125-0.25 mg/L). Genotyping by N. gonorrhoeae multiantigen sequence typing (NG-MAST) was performed. Between 2009 and 2013, there was a shift in the modal MICs for ceftriaxone. Among the 42 isolates exhibiting decreased susceptibility to ceftriaxone and cefixime, 95.2% were resistant to penicillin G, 95.2% to tetracycline, 97.6% to ciprofloxacin, and 33.3% to azithromycin. Thirty-five (83.3%) of the 42 isolates had a mosaic penA allele XXXIV, which has been previously associated with resistance to ceftriaxone and cefixime as well as treatment failures. The isolates that contained the mosaic penicillin-binding protein 2 (PBP2) XXXIV were associated with NG-MAST ST1407 or closely related genotypes. In Argentina, N. gonorrhoeae isolates with decreased susceptibility to cefixime and ceftriaxone have now emerged, mostly due to the introduction of the internationally spread multidrug-resistant NG-MAST ST1407.

Ultra-wideband communication system prototype using orthogonal frequency coded SAW correlators.

PubMed

Gallagher, Daniel R; Kozlovski, Nikolai Y; Malocha, Donald C

2013-03-01

This paper presents preliminary ultra-wideband (UWB) communication system results utilizing orthogonal frequency coded SAW correlators. Orthogonal frequency coding (OFC) and pseudo-noise (PN) coding provides a means for spread-spectrum UWB. The use of OFC spectrally spreads a PN sequence beyond that of CDMA; allowing for improved correlation gain. The transceiver approach is still very similar to that of the CDMA approach, but provides greater code diversity. Use of SAW correlators eliminates many of the costly components that are typically needed in the intermediate frequency (IF) section in the transmitter and receiver, and greatly reduces the signal processing requirements. Development and results of an experimental prototype system with center frequency of 250 MHz are presented. The prototype system is configured using modular RF components and benchtop pulse generator and frequency source. The SAW correlation filters used in the test setup were designed using 7 chip frequencies within the transducer. The fractional bandwidth of approximately 29% was implemented to exceed the defined UWB specification. Discussion of the filter design and results are presented and are compared with packaged device measurements. A prototype UWB system using OFC SAW correlators is demonstrated in wired and wireless configurations. OFC-coded SAW filters are used for generation of a transmitted spread-spectrum UWB and matched filter correlated reception. Autocorrelation and cross-correlation system outputs are compared. The results demonstrate the feasibility of UWB SAW correlators for use in UWB communication transceivers.

A New Integrative Conjugative Element Occurs in Mycoplasma agalactiae as Chromosomal and Free Circular Forms

PubMed Central

Marenda, Marc; Barbe, Valérie; Gourgues, Géraldine; Mangenot, Sophie; Sagne, Evelyne; Citti, Christine

2006-01-01

An integrative conjugative element, ICEA, was characterized in Mycoplasma agalactiae strain 5632, in which it occurs as multiple chromosomal copies and as a free circular form. The distribution of ICEA sequences in M. agalactiae strains and their occurrence in Mycoplasma bovis suggest the spreading of the element within or between species. PMID:16707706

Measuring landscape-scale spread and persistence of an invaded submerged plant community from airborne remote sensing.

PubMed

Santos, Maria J; Khanna, Shruti; Hestir, Erin L; Greenberg, Jonathan A; Ustin, Susan L

2016-09-01

Processes of spread and patterns of persistence of invasive species affect species and communities in the new environment. Predicting future rates of spread is of great interest for timely management decisions, but this depends on models that rely on understanding the processes of invasion and historic observations of spread and persistence. Unfortunately, the rates of spread and patterns of persistence are difficult to model or directly observe, especially when multiple rates of spread and diverse persistence patterns may be co-occurring over the geographic distribution of the invaded ecosystem. Remote sensing systematically acquires data over large areas at fine spatial and spectral resolutions over multiple time periods that can be used to quantify spread processes and persistence patterns. We used airborne imaging spectroscopy data acquired once a year for 5 years from 2004 to 2008 to map an invaded submerged aquatic vegetation (SAV) community across 2220 km 2 of waterways in the Sacramento-San Joaquin River Delta, California, USA, and measured its spread rate and its persistence. Submerged aquatic vegetation covered 13-23 km 2 of the waterways (6-11%) every year. Yearly new growth accounted for 40-60% of the SAV area, ~50% of which survived to following year. Spread rates were overall negative and persistence decreased with time. From this dataset, we were able to identify both radial and saltatorial spread of the invaded SAV in the entire extent of the Delta over time. With both decreasing spread rate and persistence, it is possible that over time the invasion of this SAV community could decrease its ecological impact. A landscape-scale approach allows measurements of all invasion fronts and the spatial anisotropies associated with spread processes and persistence patterns, without spatial interpolation, at locations both proximate and distant to the focus of invasion at multiple points in time. © 2016 by the Ecological Society of America.

Mobile Practices in Everyday Life: Popular Digital Technologies and Schooling Revisited

ERIC Educational Resources Information Center

Merchant, Guy

2012-01-01

Mobile phones have rapidly been absorbed into the fabric of our day-to-day lives. They are now a key consumer item, a symbol of social capital and they connect their users to a mobile web with multiple applications. As ownership and access to smartphones has spread into the teenage years, their place in institutions of formal education has been…

Wavelet based mobile video watermarking: spread spectrum vs. informed embedding

NASA Astrophysics Data System (ADS)

Mitrea, M.; Prêteux, F.; Duţă, S.; Petrescu, M.

2005-11-01

The cell phone expansion provides an additional direction for digital video content distribution: music clips, news, sport events are more and more transmitted toward mobile users. Consequently, from the watermarking point of view, a new challenge should be taken: very low bitrate contents (e.g. as low as 64 kbit/s) are now to be protected. Within this framework, the paper approaches for the first time the mathematical models for two random processes, namely the original video to be protected and a very harmful attack any watermarking method should face the StirMark attack. By applying an advanced statistical investigation (combining the Chi square, Ro, Fisher and Student tests) in the discrete wavelet domain, it is established that the popular Gaussian assumption can be very restrictively used when describing the former process and has nothing to do with the latter. As these results can a priori determine the performances of several watermarking methods, both of spread spectrum and informed embedding types, they should be considered in the design stage.

The search for multiple populations in Magellanic Cloud Clusters IV: Coeval multiple stellar populations in the young star cluster NGC 1978

NASA Astrophysics Data System (ADS)

Martocchia, S.; Niederhofer, F.; Dalessandro, E.; Bastian, N.; Kacharov, N.; Usher, C.; Cabrera-Ziri, I.; Lardo, C.; Cassisi, S.; Geisler, D.; Hilker, M.; Hollyhead, K.; Kozhurina-Platais, V.; Larsen, S.; Mackey, D.; Mucciarelli, A.; Platais, I.; Salaris, M.

2018-04-01

We have recently shown that the ˜2 Gyr old Large Magellanic Cloud star cluster NGC 1978 hosts multiple populations in terms of star-to-star abundance variations in [N/Fe]. These can be seen as a splitting or spread in the sub-giant and red giant branches (SGB and RGB) when certain photometric filter combinations are used. Due to its relative youth, NGC 1978 can be used to place stringent limits on whether multiple bursts of star-formation have taken place within the cluster, as predicted by some models for the origin of multiple populations. We carry out two distinct analyses to test whether multiple star-formation epochs have occurred within NGC 1978. First, we use UV CMDs to select stars from the first and second population along the SGB, and then compare their positions in optical CMDs, where the morphology is dominantly controlled by age as opposed to multiple population effects. We find that the two populations are indistinguishable, with age differences of 1 ± 20 Myr between them. This is in tension with predictions from the AGB scenario for the origin of multiple populations. Second, we estimate the broadness of the main sequence turnoff (MSTO) of NGC 1978 and we report that it is consistent with the observational errors. We find an upper limit of ˜65 Myr on the age spread in the MSTO of NGC 1978. This finding is in conflict with the age spread scenario as origin of the extendend MSTO in intermediate age clusters, while it fully supports predictions from the stellar rotation model.

The search for multiple populations in Magellanic Cloud clusters - IV. Coeval multiple stellar populations in the young star cluster NGC 1978

NASA Astrophysics Data System (ADS)

Martocchia, S.; Niederhofer, F.; Dalessandro, E.; Bastian, N.; Kacharov, N.; Usher, C.; Cabrera-Ziri, I.; Lardo, C.; Cassisi, S.; Geisler, D.; Hilker, M.; Hollyhead, K.; Kozhurina-Platais, V.; Larsen, S.; Mackey, D.; Mucciarelli, A.; Platais, I.; Salaris, M.

2018-07-01

We have recently shown that the ˜2 Gyr old Large Magellanic Cloud star cluster NGC 1978 hosts multiple populations in terms of star-to-star abundance variations in [N/Fe]. These can be seen as a splitting or spread in the subgiant and red giant branches (SGB and RGB) when certain photometric filter combinations are used. Because of its relative youth, NGC 1978 can be used to place stringent limits on whether multiple bursts of star formation have taken place within the cluster, as predicted by some models for the origin of multiple populations. We carry out two distinct analyses to test whether multiple star formation epochs have occurred within NGC 1978. First, we use ultraviolet colour-magnitude diagrams (CMDs) to select stars from the first and second population along the SGB, and then compare their positions in optical CMDs, where the morphology is dominantly controlled by age as opposed to multiple population effects. We find that the two populations are indistinguishable, with age differences of 1 ± 20 Myr between them. This is in tension with predictions from the asymptotic giant branch scenario for the origin of multiple populations. Second, we estimate the broadness of the main-sequence turn-off (MSTO) of NGC 1978 and we report that it is consistent with the observational errors. We find an upper limit of ˜65 Myr on the age spread in the MSTO of NGC 1978. This finding is in conflict with the age spread scenario as origin of the extended MSTO in intermediate-age clusters, while it fully supports predictions from the stellar rotation model.

Performance Evaluation of High Speed Multicarrier System for Optical Wireless Communication

NASA Astrophysics Data System (ADS)

Mathur, Harshita; Deepa, T.; Bartalwar, Sophiya

2018-04-01

Optical wireless communication (OWC) in the infrared and visible range is quite impressive solution, especially where radio communication face challenges. Visible light communication (VLC) uses visible light over a range of 400 and 800 THz and is a subdivision of OWC technologies. With an increasing demand for use of wireless communications, wireless access via Wi-Fi is facing many challenges especially in terms of capacity, availability, security and efficiency. VLC uses intensity modulation and direct detection (IM/DD) techniques and hence they require the signals to certainly be real valued positive sequences. These constraints pose limitation on digital modulation techniques. These limitations result in spectrum-efficiency or power-efficiency losses. In this paper, we investigate an amplitude shift keying (ASK) based orthogonal frequency division multiplexing (OFDM) signal transmission scheme using LabVIEW for VLC technology.

Object-directed imitation in autism spectrum disorder is differentially influenced by motoric task complexity, but not social contextual cues.

PubMed

Chetcuti, Lacey; Hudry, Kristelle; Grant, Megan; Vivanti, Giacomo

2017-11-01

We examined the role of social motivation and motor execution factors in object-directed imitation difficulties in autism spectrum disorder. A series of to-be-imitated actions was presented to 35 children with autism spectrum disorder and 20 typically developing children on an Apple ® iPad ® by a socially responsive or aloof model, under conditions of low and high motor demand. There were no differences in imitation performance (i.e. the number of actions reproduced within a fixed sequence), for either group, in response to a model who acted socially responsive or aloof. Children with autism spectrum disorder imitated the high motor demand task more poorly than the low motor demand task, while imitation performance for typically developing children was equivalent across the low and high motor demand conditions. Furthermore, imitative performance in the autism spectrum disorder group was unrelated to social reciprocity, though positively associated with fine motor coordination. These results suggest that difficulties in object-directed imitation in autism spectrum disorder are the result of motor execution difficulties, not reduced social motivation.

Microwave Comb Generator

NASA Technical Reports Server (NTRS)

Sigman, E. H.

1989-01-01

Stable reference tones aid testing and calibration of microwave receivers. Signal generator puts out stable tones in frequency range of 2 to 10 GHz at all multiples of reference input frequency, at any frequency up to 1 MHz. Called "comb generator" because spectral plot resembles comb. DC reverse-bias current switched on and off at 1 MHz to generate sharp pulses in step-recovery diode. Microwave components mounted on back of special connector containing built-in attenuator. Used in testing microwave and spread-spectrum wide-band receivers.

Single-cell genomic sequencing using Multiple Displacement Amplification.

PubMed

Lasken, Roger S

2007-10-01

Single microbial cells can now be sequenced using DNA amplified by the Multiple Displacement Amplification (MDA) reaction. The few femtograms of DNA in a bacterium are amplified into micrograms of high molecular weight DNA suitable for DNA library construction and Sanger sequencing. The MDA-generated DNA also performs well when used directly as template for pyrosequencing by the 454 Life Sciences method. While MDA from single cells loses some of the genomic sequence, this approach will greatly accelerate the pace of sequencing from uncultured microbes. The genetically linked sequences from single cells are also a powerful tool to be used in guiding genomic assembly of shotgun sequences of multiple organisms from environmental DNA extracts (metagenomic sequences).

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

PubMed

Werling, Donna M; Brand, Harrison; An, Joon-Yong; Stone, Matthew R; Zhu, Lingxue; Glessner, Joseph T; Collins, Ryan L; Dong, Shan; Layer, Ryan M; Markenscoff-Papadimitriou, Eirene; Farrell, Andrew; Schwartz, Grace B; Wang, Harold Z; Currall, Benjamin B; Zhao, Xuefang; Dea, Jeanselle; Duhn, Clif; Erdman, Carolyn A; Gilson, Michael C; Yadav, Rachita; Handsaker, Robert E; Kashin, Seva; Klei, Lambertus; Mandell, Jeffrey D; Nowakowski, Tomasz J; Liu, Yuwen; Pochareddy, Sirisha; Smith, Louw; Walker, Michael F; Waterman, Matthew J; He, Xin; Kriegstein, Arnold R; Rubenstein, John L; Sestan, Nenad; McCarroll, Steven A; Neale, Benjamin M; Coon, Hilary; Willsey, A Jeremy; Buxbaum, Joseph D; Daly, Mark J; State, Matthew W; Quinlan, Aaron R; Marth, Gabor T; Roeder, Kathryn; Devlin, Bernie; Talkowski, Michael E; Sanders, Stephan J

2018-05-01

Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we present a comparable framework to evaluate rare and de novo noncoding single-nucleotide variants, insertion/deletions, and all classes of structural variation from whole-genome sequencing (WGS). Integrating genomic annotations at the level of nucleotides, genes, and regulatory regions, we define 51,801 annotation categories. Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests. Without appropriate correction, biologically plausible associations are observed in both cases and controls. Despite excluding previously identified gene-disrupting mutations, coding regions still exhibited the strongest associations. Thus, in autism, the contribution of de novo noncoding variation is probably modest in comparison to that of de novo coding variants. Robust results from future WGS studies will require large cohorts and comprehensive analytical strategies that consider the substantial multiple-testing burden.

Genetic Local Search for Optimum Multiuser Detection Problem in DS-CDMA Systems

NASA Astrophysics Data System (ADS)

Wang, Shaowei; Ji, Xiaoyong

Optimum multiuser detection (OMD) in direct-sequence code-division multiple access (DS-CDMA) systems is an NP-complete problem. In this paper, we present a genetic local search algorithm, which consists of an evolution strategy framework and a local improvement procedure. The evolution strategy searches the space of feasible, locally optimal solutions only. A fast iterated local search algorithm, which employs the proprietary characteristics of the OMD problem, produces local optima with great efficiency. Computer simulations show the bit error rate (BER) performance of the GLS outperforms other multiuser detectors in all cases discussed. The computation time is polynomial complexity in the number of users.

Molecular epidemiology over an 11-year period (2000 to 2010) of extended-spectrum β-lactamase-producing Escherichia coli causing bacteremia in a centralized Canadian region.

PubMed

Peirano, Gisele; van der Bij, Akke K; Gregson, Daniel B; Pitout, Johann D D

2012-02-01

A study was designed to assess the importance of sequence types among extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates causing bacteremia over an 11-year period (2000 to 2010) in a centralized Canadian region. A total of 197 patients with incident infections were identified; the majority presented with community-onset urosepsis, with a significant increase in the prevalence of ESBL-producing E. coli during the later part of the study. The majority of E. coli isolates produced either CTX-M-15 or CTX-M-14. We identified 7 different major sequence types among 91% of isolates (i.e., the ST10 clonal complex, ST38, ST131, ST315, ST393, ST405, and ST648) and provided insight into their clinical and molecular characteristics. ST38 was the most antimicrobial-susceptible sequence type and predominated during 2000 to 2004 but disappeared after 2008. ST131 was the most antimicrobial-resistant sequence type, and the influx of a single pulsotype of this sequence type was responsible for the significant increase of ESBL-producing E. coli strains since 2007. During 2010, 49/63 (78%) of the ESBL-producing E. coli isolates belonged to ST131, and this sequence type had established itself as a major drug-resistant pathogen in Calgary, Alberta, Canada, posing an important new public health threat within our region. We urgently need well-designed epidemiological and molecular studies to understand the dynamics of transmission, risk factors, and reservoirs for E. coli ST131. This will provide insight into the emergence and spread of this multiresistant sequence type.

Prototype Parts of a Digital Beam-Forming Wide-Band Receiver

NASA Technical Reports Server (NTRS)

Kaplan, Steven B.; Pylov, Sergey V.; Pambianchi, Michael

2003-01-01

Some prototype parts of a digital beamforming (DBF) receiver that would operate at multigigahertz carrier frequencies have been developed. The beam-forming algorithm in a DBF receiver processes signals from multiple antenna elements with appropriate time delays and weighting factors chosen to enhance the reception of signals from a specific direction while suppressing signals from other directions. Such a receiver would be used in the directional reception of weak wideband signals -- for example, spread-spectrum signals from a low-power transmitter on an Earth-orbiting spacecraft or other distant source. The prototype parts include superconducting components on integrated-circuit chips, and a multichip module (MCM), within which the chips are to be packaged and connected via special inter-chip-communication circuits. The design and the underlying principle of operation are based on the use of the rapid single-flux quantum (RSFQ) family of logic circuits to obtain the required processing speed and signal-to-noise ratio. RSFQ circuits are superconducting circuits that exploit the Josephson effect. They are well suited for this application, having been proven to perform well in some circuits at frequencies above 100 GHz. In order to maintain the superconductivity needed for proper functioning of the RSFQ circuits, the MCM must be kept in a cryogenic environment during operation.

Spreading of triboelectrically charged granular matter

NASA Astrophysics Data System (ADS)

Kumar, Deepak; Sane, A.; Gohil, Smita.; Bandaru, P. R.; Bhattacharya, S.; Ghosh, Shankar

2014-06-01

We report on the spreading of triboelectrically charged glass particles on an oppositely charged surface of a plastic cylindrical container in the presence of a constant mechanical agitation. The particles spread via sticking, as a monolayer on the cylinder's surface. Continued agitation initiates a sequence of instabilities of this monolayer, which first forms periodic wavy-stripe-shaped transverse density modulation in the monolayer and then ejects narrow and long particle-jets from the tips of these stripes. These jets finally coalesce laterally to form a homogeneous spreading front that is layered along the spreading direction. These remarkable growth patterns are related to a time evolving frictional drag between the moving charged glass particles and the countercharges on the plastic container. The results provide insight into the multiscale time-dependent tribolelectric processes and motivates further investigation into the microscopic causes of these macroscopic dynamical instabilities and spatial structures.

Image compression-encryption algorithms by combining hyper-chaotic system with discrete fractional random transform

NASA Astrophysics Data System (ADS)

Gong, Lihua; Deng, Chengzhi; Pan, Shumin; Zhou, Nanrun

2018-07-01

Based on hyper-chaotic system and discrete fractional random transform, an image compression-encryption algorithm is designed. The original image is first transformed into a spectrum by the discrete cosine transform and the resulting spectrum is compressed according to the method of spectrum cutting. The random matrix of the discrete fractional random transform is controlled by a chaotic sequence originated from the high dimensional hyper-chaotic system. Then the compressed spectrum is encrypted by the discrete fractional random transform. The order of DFrRT and the parameters of the hyper-chaotic system are the main keys of this image compression and encryption algorithm. The proposed algorithm can compress and encrypt image signal, especially can encrypt multiple images once. To achieve the compression of multiple images, the images are transformed into spectra by the discrete cosine transform, and then the spectra are incised and spliced into a composite spectrum by Zigzag scanning. Simulation results demonstrate that the proposed image compression and encryption algorithm is of high security and good compression performance.

Zadoff-Chu sequence-based hitless ranging scheme for OFDMA-PON configured 5G fronthaul uplinks

NASA Astrophysics Data System (ADS)

Reza, Ahmed Galib; Rhee, June-Koo Kevin

2017-05-01

A Zadoff-Chu (ZC) sequence-based low-complexity hitless upstream time synchronization scheme is proposed for an orthogonal frequency division multiple access passive optical network configured cloud radio access network fronthaul. The algorithm is based on gradual loading of the ZC sequences, where the phase discontinuity due to the cyclic prefix is alleviated by a frequency domain phase precoder, eliminating the requirements of guard bands to mitigate intersymbol interference and inter-carrier interference. Simulation results for uncontrolled-wavelength asynchronous transmissions from four concurrent transmitting optical network units are presented to demonstrate the effectiveness of the proposed scheme.

Los Angeles FOT spread spectrum radio traffic signal interconnect evaluation task : final report on full deployment

DOT National Transportation Integrated Search

1998-10-01

The use of a spread spectrum radio network (SSRN) as an alternative to hard-wired communications between field equipment and the City of Los Angeless Automated Traffic Surveillance and Control (ATSAC) system has been investigated. The aim of using...

The Facilitators, Obstacles and Needs of Individuals with Autism Spectrum Conditions Accessing Further and Higher Education: A Systematic Review

ERIC Educational Resources Information Center

Toor, Nicky; Hanley, Terry; Hebron, Judith

2016-01-01

Many young adults diagnosed with autism spectrum conditions (ASC) intend to go to college and/or university, yet research suggests that these individuals find aspects of college and university life challenging. To explore the views of individuals directly affected by these challenges, a systematic review of the existing qualitative literature in…

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

PubMed Central

Cannone, Jamie J.; Sweeney, Blake A.; Petrov, Anton I.; Gutell, Robin R.; Zirbel, Craig L.; Leontis, Neocles

2015-01-01

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. PMID:26048960

The Multiple Stellar Populations in the Ancient LMC Globular Clusters Hodge 11 and NGC 2210

NASA Astrophysics Data System (ADS)

Chaboyer, Brian; Gilligan, Christina; Wagner-Kaiser, Rachel; Mackey, Dougal; Sarajedini, Ata; Cummings, Jeffrey; Grocholski, Aaron; Geisler, Doug; Cohen, Roger; Villanova, Sandro; Yang, Soung-Chul; Parisi, Celeste

2018-01-01

Hubble Space telescope images of the ancient LMC globular clusters Hodge 11 and NGC 2210 in the F336W, F606W and F814W filters were obtained between June 2016 and April 2017. These deep images has been analyzed with the Dolphot software package. High quality photometry has been obtained from three magnitudes brighter than the horizontal branch, to about four magnitudes fainter than the main sequence turn-off. Both clusters show an excess of red main sequence stars in the F336W filter, indicating that multiple stellar populations exist in both clusters. Hodge 11 shows irregularities in its horizontal branch morphology, which is indicative of the presence of an approximately 0.1 dex internal helium abundance spread.

Language Barriers Impact Access to Services for Children with Autism Spectrum Disorders.

PubMed

St Amant, Helaine G; Schrager, Sheree M; Peña-Ricardo, Carolina; Williams, Marian E; Vanderbilt, Douglas L

2018-02-01

Racial and ethnic disparities in accessing health care have been described in children with autism spectrum disorder (ASD). In a retrospective chart review of 152 children with ASD, children of parents whose primary language was English were significantly more likely to have both social skills and communication goals within their individualized education plan (IEP) compared to children of parents whose primary language was not English. Additionally, children of primary English speakers received significantly more hours of direct services from their state disability program. After controlling for demographic covariates, findings suggest that language barriers may negatively affect parents' abilities to access health care services for their child with ASD. Acculturation factors must therefore be considered when analyzing disparities in autism.

ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer.

PubMed

Michael, Geovana Brenner; Kadlec, Kristina; Sweeney, Michael T; Brzuszkiewicz, Elzbieta; Liesegang, Heiko; Daniel, Rolf; Murray, Robert W; Watts, Jeffrey L; Schwarz, Stefan

2012-01-01

Integrative and conjugative elements (ICEs) have not been detected in Pasteurella multocida. In this study the multiresistance ICEPmu1 from bovine P. multocida was analysed for its core genes and its ability to conjugatively transfer into strains of the same and different genera. ICEPmu1 was identified during whole genome sequencing. Coding sequences were predicted by bioinformatic tools and manually curated using the annotation software ERGO. Conjugation into P. multocida, Mannheimia haemolytica and Escherichia coli recipients was performed by mating assays. The presence of ICEPmu1 and its circular intermediate in the recipient strains was confirmed by PCR and sequence analysis. Integration sites were sequenced. Susceptibility testing of the ICEPmu1-carrying recipients was conducted by broth microdilution. The 82 214 bp ICEPmu1 harbours 88 genes. The core genes of ICEPmu1, which are involved in excision/integration and conjugative transfer, resemble those found in a 66 641 bp ICE from Histophilus somni. ICEPmu1 integrates into a tRNA(Leu) and is flanked by 13 bp direct repeats. It is able to conjugatively transfer to P. multocida, M. haemolytica and E. coli, where it also uses a tRNA(Leu) for integration and produces closely related 13 bp direct repeats. PCR assays and susceptibility testing confirmed the presence and the functional activity of the ICEPmu1-associated resistance genes in the recipient strains. The observation that the multiresistance ICEPmu1 is present in a bovine P. multocida and can easily spread across strain and genus boundaries underlines the risk of a rapid dissemination of multiple resistance genes, which will distinctly decrease the therapeutic options.

Interconexión de la Estación Astrofísica de Bosque Alegre y la red local de datos del Observatorio Astronómico de Córdoba

NASA Astrophysics Data System (ADS)

Nicotra, M. A.; Anun, S.; Montes, M.; Goldes, G.; Carranza, G.

We describe the outlines of a project for the interconnection between the Astrophysical Station of Bosque Alegre and the wide area network of the University of Córdoba. The Astrophysical Station is located 38.55 km (23.96 milles) from the Observatory of Córdoba. This location is suitable for radio links in the range of centimeters wavelenghts. In the last years, Spread-Spectrum technology equipments has become popular. Spread-Spectrum signals, contrary to narrow band radio signals, operates within a widthband 20 to 200 times broader than the widthband of the modulated information. Signals are modulated by special spreading codes, in such a way that emulates noisy signals. These codes are known under the generic designation of pseudo-random or pseudo-noise. In addition, the wide band is correlated with a low power density in the emitted signals. Spread-Spectrum equipment links are stable, exhibits low interferences with conventional radio transmitters, and their commercial prices are remarkably lower than those for the conventional microwave devices. Data links are compliant with Ethernet protocol networks and operates with data tramsmition rates up to 4 Mbits per second. The described equipment will enable the access to full-Internet services for visitor astronomers in Bosque Alegre. Also, it will be possible fast transfer for the observational data from telescope to computers in the local area network at Córdoba. This project must be considered as the second stage of another wide purpose project, which has the main purpose in transforming the Bosque Alegre Station as a fully robotic station controlled from the computational center at the Observatory in Cordoba. The advantages of robotic telescopes has recently been the subject of several discussions. However, it is now widely accepted that an automatic station enables some important options in the use of the astronomical instruments, such us the possibility of performing parallel programs, one of which is selected accordingly to environmental conditions in the instant of the observation.

Medhost: An encyclopedic bibliography of the host plants of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), version 3.0

USDA-ARS?s Scientific Manuscript database

The Mediterranean fruit fly (Medfly), Ceratitis capitata (Wiedemann), causes direct damage to fruits and vegetables through oviposition and larval feeding. Rigorous quarantine procedures are currently enforced to prevent domestic and transnational spread of Medfly. Accessible and reliable informatio...

Full-Length Venom Protein cDNA Sequences from Venom-Derived mRNA: Exploring Compositional Variation and Adaptive Multigene Evolution

PubMed Central

Modahl, Cassandra M.; Mackessy, Stephen P.

2016-01-01

Envenomation of humans by snakes is a complex and continuously evolving medical emergency, and treatment is made that much more difficult by the diverse biochemical composition of many venoms. Venomous snakes and their venoms also provide models for the study of molecular evolutionary processes leading to adaptation and genotype-phenotype relationships. To compare venom complexity and protein sequences, venom gland transcriptomes are assembled, which usually requires the sacrifice of snakes for tissue. However, toxin transcripts are also present in venoms, offering the possibility of obtaining cDNA sequences directly from venom. This study provides evidence that unknown full-length venom protein transcripts can be obtained from the venoms of multiple species from all major venomous snake families. These unknown venom protein cDNAs are obtained by the use of primers designed from conserved signal peptide sequences within each venom protein superfamily. This technique was used to assemble a partial venom gland transcriptome for the Middle American Rattlesnake (Crotalus simus tzabcan) by amplifying sequences for phospholipases A2, serine proteases, C-lectins, and metalloproteinases from within venom. Phospholipase A2 sequences were also recovered from the venoms of several rattlesnakes and an elapid snake (Pseudechis porphyriacus), and three-finger toxin sequences were recovered from multiple rear-fanged snake species, demonstrating that the three major clades of advanced snakes (Elapidae, Viperidae, Colubridae) have stable mRNA present in their venoms. These cDNA sequences from venom were then used to explore potential activities derived from protein sequence similarities and evolutionary histories within these large multigene superfamilies. Venom-derived sequences can also be used to aid in characterizing venoms that lack proteomic profiles and identify sequence characteristics indicating specific envenomation profiles. This approach, requiring only venom, provides access to cDNA sequences in the absence of living specimens, even from commercial venom sources, to evaluate important regional differences in venom composition and to study snake venom protein evolution. PMID:27280639

Analysis of Ribosome Inactivating Protein (RIP): A Bioinformatics Approach

NASA Astrophysics Data System (ADS)

Jothi, G. Edward Gnana; Majilla, G. Sahaya Jose; Subhashini, D.; Deivasigamani, B.

2012-10-01

In spite of the medical advances in recent years, the world is in need of different sources to encounter certain health issues.Ribosome Inactivating Proteins (RIPs) were found to be one among them. In order to get easy access about RIPs, there is a need to analyse RIPs towards constructing a database on RIPs. Also, multiple sequence alignment was done towards screening for homologues of significant RIPs from rare sources against RIPs from easily available sources in terms of similarity. Protein sequences were retrieved from SWISS-PROT and are further analysed using pair wise and multiple sequence alignment.Analysis shows that, 151 RIPs have been characterized to date. Amongst them, there are 87 type I, 37 type II, 1 type III and 25 unknown RIPs. The sequence length information of various RIPs about the availability of full or partial sequence was also found. The multiple sequence alignment of 37 type I RIP using the online server Multalin, indicates the presence of 20 conserved residues. Pairwise alignment and multiple sequence alignment of certain selected RIPs in two groups namely Group I and Group II were carried out and the consensus level was found to be 98%, 98% and 90% respectively.

Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients.

PubMed

Ssengooba, Willy; de Jong, Bouke C; Joloba, Moses L; Cobelens, Frank G; Meehan, Conor J

2016-08-05

In the context of advanced immunosuppression, M. tuberculosis is known to cause detectable mycobacteremia. However, little is known about the intra-patient mycobacterial microevolution and the direction of seeding between the sputum and blood compartments. From a diagnostic study of HIV-infected TB patients, 51 pairs of concurrent blood and sputum M. tuberculosis isolates from the same patient were available. In a previous analysis, we identified a subset with genotypic concordance, based on spoligotyping and 24 locus MIRU-VNTR. These paired isolates with identical genotypes were analyzed by whole genome sequencing and phylogenetic analysis. Of the 25 concordant pairs (49 % of the 51 paired isolates), 15 (60 %) remained viable for extraction of high quality DNA for whole genome sequencing. Two patient pairs were excluded due to poor quality sequence reads. The median CD4 cell count was 32 (IQR; 16-101)/mm(3) and ten (77 %) patients were on ART. No drug resistance mutations were identified in any of the sequences analyzed. Three (23.1 %) of 13 patients had SNPs separating paired isolates from blood and sputum compartments, indicating evidence of microevolution. Using a phylogenetic approach to identify the ancestral compartment, in two (15 %) patients the blood isolate was ancestral to the sputum isolate, in one (8 %) it was the opposite, and ten (77 %) of the pairs were identical. Among HIV-infected patients with poor cellular immunity, infection with multiple strains of M. tuberculosis was found in half of the patients. In those patients with identical strains, whole genome sequencing indicated that M. tuberculosis intra-patient microevolution does occur in a few patients, yet did not reveal a consistent direction of spread between sputum and blood. This suggests that these compartments are highly connected and potentially seed each other repeatedly.

Progression of regional grey matter atrophy in multiple sclerosis

PubMed Central

Marinescu, Razvan V; Young, Alexandra L; Firth, Nicholas C; Jorge Cardoso, M; Tur, Carmen; De Angelis, Floriana; Cawley, Niamh; Brownlee, Wallace J; De Stefano, Nicola; Laura Stromillo, M; Battaglini, Marco; Ruggieri, Serena; Gasperini, Claudio; Filippi, Massimo; Rocca, Maria A; Rovira, Alex; Sastre-Garriga, Jaume; Geurts, Jeroen J G; Vrenken, Hugo; Wottschel, Viktor; Leurs, Cyra E; Uitdehaag, Bernard; Pirpamer, Lukas; Enzinger, Christian; Ourselin, Sebastien; Gandini Wheeler-Kingshott, Claudia A; Chard, Declan; Thompson, Alan J; Barkhof, Frederik; Alexander, Daniel C; Ciccarelli, Olga

2018-01-01

Abstract See Stankoff and Louapre (doi:10.1093/brain/awy114) for a scientific commentary on this article. Grey matter atrophy is present from the earliest stages of multiple sclerosis, but its temporal ordering is poorly understood. We aimed to determine the sequence in which grey matter regions become atrophic in multiple sclerosis and its association with disability accumulation. In this longitudinal study, we included 1417 subjects: 253 with clinically isolated syndrome, 708 with relapsing-remitting multiple sclerosis, 128 with secondary-progressive multiple sclerosis, 125 with primary-progressive multiple sclerosis, and 203 healthy control subjects from seven European centres. Subjects underwent repeated MRI (total number of scans 3604); the mean follow-up for patients was 2.41 years (standard deviation = 1.97). Disability was scored using the Expanded Disability Status Scale. We calculated the volume of brain grey matter regions and brainstem using an unbiased within-subject template and used an established data-driven event-based model to determine the sequence of occurrence of atrophy and its uncertainty. We assigned each subject to a specific event-based model stage, based on the number of their atrophic regions. Linear mixed-effects models were used to explore associations between the rate of increase in event-based model stages, and T2 lesion load, disease-modifying treatments, comorbidity, disease duration and disability accumulation. The first regions to become atrophic in patients with clinically isolated syndrome and relapse-onset multiple sclerosis were the posterior cingulate cortex and precuneus, followed by the middle cingulate cortex, brainstem and thalamus. A similar sequence of atrophy was detected in primary-progressive multiple sclerosis with the involvement of the thalamus, cuneus, precuneus, and pallidum, followed by the brainstem and posterior cingulate cortex. The cerebellum, caudate and putamen showed early atrophy in relapse-onset multiple sclerosis and late atrophy in primary-progressive multiple sclerosis. Patients with secondary-progressive multiple sclerosis showed the highest event-based model stage (the highest number of atrophic regions, P < 0.001) at the study entry. All multiple sclerosis phenotypes, but clinically isolated syndrome, showed a faster rate of increase in the event-based model stage than healthy controls. T2 lesion load and disease duration in all patients were associated with increased event-based model stage, but no effects of disease-modifying treatments and comorbidity on event-based model stage were observed. The annualized rate of event-based model stage was associated with the disability accumulation in relapsing-remitting multiple sclerosis, independent of disease duration (P < 0.0001). The data-driven staging of atrophy progression in a large multiple sclerosis sample demonstrates that grey matter atrophy spreads to involve more regions over time. The sequence in which regions become atrophic is reasonably consistent across multiple sclerosis phenotypes. The spread of atrophy was associated with disease duration and with disability accumulation over time in relapsing-remitting multiple sclerosis. PMID:29741648

Progression of regional grey matter atrophy in multiple sclerosis.

PubMed

Eshaghi, Arman; Marinescu, Razvan V; Young, Alexandra L; Firth, Nicholas C; Prados, Ferran; Jorge Cardoso, M; Tur, Carmen; De Angelis, Floriana; Cawley, Niamh; Brownlee, Wallace J; De Stefano, Nicola; Laura Stromillo, M; Battaglini, Marco; Ruggieri, Serena; Gasperini, Claudio; Filippi, Massimo; Rocca, Maria A; Rovira, Alex; Sastre-Garriga, Jaume; Geurts, Jeroen J G; Vrenken, Hugo; Wottschel, Viktor; Leurs, Cyra E; Uitdehaag, Bernard; Pirpamer, Lukas; Enzinger, Christian; Ourselin, Sebastien; Gandini Wheeler-Kingshott, Claudia A; Chard, Declan; Thompson, Alan J; Barkhof, Frederik; Alexander, Daniel C; Ciccarelli, Olga

2018-06-01

See Stankoff and Louapre (doi:10.1093/brain/awy114) for a scientific commentary on this article.Grey matter atrophy is present from the earliest stages of multiple sclerosis, but its temporal ordering is poorly understood. We aimed to determine the sequence in which grey matter regions become atrophic in multiple sclerosis and its association with disability accumulation. In this longitudinal study, we included 1417 subjects: 253 with clinically isolated syndrome, 708 with relapsing-remitting multiple sclerosis, 128 with secondary-progressive multiple sclerosis, 125 with primary-progressive multiple sclerosis, and 203 healthy control subjects from seven European centres. Subjects underwent repeated MRI (total number of scans 3604); the mean follow-up for patients was 2.41 years (standard deviation = 1.97). Disability was scored using the Expanded Disability Status Scale. We calculated the volume of brain grey matter regions and brainstem using an unbiased within-subject template and used an established data-driven event-based model to determine the sequence of occurrence of atrophy and its uncertainty. We assigned each subject to a specific event-based model stage, based on the number of their atrophic regions. Linear mixed-effects models were used to explore associations between the rate of increase in event-based model stages, and T2 lesion load, disease-modifying treatments, comorbidity, disease duration and disability accumulation. The first regions to become atrophic in patients with clinically isolated syndrome and relapse-onset multiple sclerosis were the posterior cingulate cortex and precuneus, followed by the middle cingulate cortex, brainstem and thalamus. A similar sequence of atrophy was detected in primary-progressive multiple sclerosis with the involvement of the thalamus, cuneus, precuneus, and pallidum, followed by the brainstem and posterior cingulate cortex. The cerebellum, caudate and putamen showed early atrophy in relapse-onset multiple sclerosis and late atrophy in primary-progressive multiple sclerosis. Patients with secondary-progressive multiple sclerosis showed the highest event-based model stage (the highest number of atrophic regions, P < 0.001) at the study entry. All multiple sclerosis phenotypes, but clinically isolated syndrome, showed a faster rate of increase in the event-based model stage than healthy controls. T2 lesion load and disease duration in all patients were associated with increased event-based model stage, but no effects of disease-modifying treatments and comorbidity on event-based model stage were observed. The annualized rate of event-based model stage was associated with the disability accumulation in relapsing-remitting multiple sclerosis, independent of disease duration (P < 0.0001). The data-driven staging of atrophy progression in a large multiple sclerosis sample demonstrates that grey matter atrophy spreads to involve more regions over time. The sequence in which regions become atrophic is reasonably consistent across multiple sclerosis phenotypes. The spread of atrophy was associated with disease duration and with disability accumulation over time in relapsing-remitting multiple sclerosis.

76 FR 44324 - Information Collection Being Reviewed by the Federal Communications Commission for Extension...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-25

.../WTB-1, and ``Wireless Services Licensing Records.'' Needs and Uses: The Commission is seeking Office... spread spectrum (ss) transmissions by amateur radio operators. This requirement is necessary so that... inability to quickly obtain vital information used to demodulate spread spectrum transmissions. OMB Control...

Feedback Power Control Strategies in Wireless Sensor Networks with Joint Channel Decoding

PubMed Central

Abrardo, Andrea; Ferrari, Gianluigi; Martalò, Marco; Perna, Fabio

2009-01-01

In this paper, we derive feedback power control strategies for block-faded multiple access schemes with correlated sources and joint channel decoding (JCD). In particular, upon the derivation of the feasible signal-to-noise ratio (SNR) region for the considered multiple access schemes, i.e., the multidimensional SNR region where error-free communications are, in principle, possible, two feedback power control strategies are proposed: (i) a classical feedback power control strategy, which aims at equalizing all link SNRs at the access point (AP), and (ii) an innovative optimized feedback power control strategy, which tries to make the network operational point fall in the feasible SNR region at the lowest overall transmit energy consumption. These strategies will be referred to as “balanced SNR” and “unbalanced SNR,” respectively. While they require, in principle, an unlimited power control range at the sources, we also propose practical versions with a limited power control range. We preliminary consider a scenario with orthogonal links and ideal feedback. Then, we analyze the robustness of the proposed power control strategies to possible non-idealities, in terms of residual multiple access interference and noisy feedback channels. Finally, we successfully apply the proposed feedback power control strategies to a limiting case of the class of considered multiple access schemes, namely a central estimating officer (CEO) scenario, where the sensors observe noisy versions of a common binary information sequence and the AP's goal is to estimate this sequence by properly fusing the soft-output information output by the JCD algorithm. PMID:22291536

A bioeconomic analysis of an emerald ash borer invasion of an urban forest with multiple jurisdictions

Treesearch

Kent F. Kovacs; Robert G. Haight; Rodrigo J. Mercader; Deborah G. McCullough

2014-01-01

Bio-invasions occur in management mosaics where local control affects spread and damage across political boundaries. We address two obstacles to local implementation of optimal regional control of a bio-invasion that damages public and private resources across jurisdictions: lack of local funds to protect the public resource and lack of access to protect the private...

Interference Canceller Based on Cycle-and-Add Property for Single User Detection in DS-CDMA

NASA Astrophysics Data System (ADS)

Hettiarachchi, Ranga; Yokoyama, Mitsuo; Uehara, Hideyuki; Ohira, Takashi

In this paper, performance of a novel interference cancellation technique for the single user detection in a direct-sequence code-division multiple access (DS-CDMA) system has been investigated. This new algorithm is based on the Cycle-and-Add property of PN (Pseudorandom Noise) sequences and can be applied for both synchronous and asynchronous systems. The proposed strategy provides a simple method that can delete interference signals one by one in spite of the power levels of interferences. Therefore, it is possible to overcome the near-far problem (NFP) in a successive manner without using transmit power control (TPC) techniques. The validity of the proposed procedure is corroborated by computer simulations in additive white Gaussian noise (AWGN) and frequency-nonselective fading channels. Performance results indicate that the proposed receiver outperforms the conventional receiver and, in many cases, it does so with a considerable gain.

NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads.

PubMed

Kulsum, Umay; Kapil, Arti; Singh, Harpreet; Kaur, Punit

2018-01-01

Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species. It can also assist in identifying drug targets and proposing vaccine candidates. The effective analysis of these large genome datasets necessitates the development of robust tools. Current methods to develop pan-genome do not support direct input of raw reads from the sequencer machine but require preprocessing of reads as an assembled protein/gene sequence file or the binary matrix of orthologous genes/proteins. We have designed an easy-to-use integrated pipeline, NGSPanPipe, which can directly identify the pan-genome from short reads. The output from the pipeline is compatible with other pan-genome analysis tools. We evaluated our pipeline with other methods for developing pan-genome, i.e. reference-based assembly and de novo assembly using simulated reads of Mycobacterium tuberculosis. The single script pipeline (pipeline.pl) is applicable for all bacterial strains. It integrates multiple in-house Perl scripts and is freely accessible from https://github.com/Biomedinformatics/NGSPanPipe .

Role for migratory wild birds in the global spread of avian influenza H5N8

USGS Publications Warehouse

,; Ip, Hon S.

2016-01-01

Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014–2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses. Further, we found that the hemagglutinin of clade 2.3.4.4 virus was remarkably promiscuous, creating reassortants with multiple neuraminidase subtypes. Improving our understanding of the circumpolar circulation of avian influenza viruses in migratory waterfowl will help to provide early warning of threats from avian influenza to poultry, and potentially human, health.

Cooperative behavior cascades in human social networks

PubMed Central

Fowler, James H.; Christakis, Nicholas A.

2010-01-01

Theoretical models suggest that social networks influence the evolution of cooperation, but to date there have been few experimental studies. Observational data suggest that a wide variety of behaviors may spread in human social networks, but subjects in such studies can choose to befriend people with similar behaviors, posing difficulty for causal inference. Here, we exploit a seminal set of laboratory experiments that originally showed that voluntary costly punishment can help sustain cooperation. In these experiments, subjects were randomly assigned to a sequence of different groups to play a series of single-shot public goods games with strangers; this feature allowed us to draw networks of interactions to explore how cooperative and uncooperative behaviors spread from person to person to person. We show that, in both an ordinary public goods game and in a public goods game with punishment, focal individuals are influenced by fellow group members’ contribution behavior in future interactions with other individuals who were not a party to the initial interaction. Furthermore, this influence persists for multiple periods and spreads up to three degrees of separation (from person to person to person to person). The results suggest that each additional contribution a subject makes to the public good in the first period is tripled over the course of the experiment by other subjects who are directly or indirectly influenced to contribute more as a consequence. These results show experimentally that cooperative behavior cascades in human social networks. PMID:20212120

The Carriage Of Multiresistant Bacteria After Travel (COMBAT) prospective cohort study: methodology and design.

PubMed

Arcilla, Maris S; van Hattem, Jarne M; Bootsma, Martin C J; van Genderen, Perry J; Goorhuis, Abraham; Schultsz, Constance; Stobberingh, Ellen E; Verbrugh, Henri A; de Jong, Menno D; Melles, Damian C; Penders, John

2014-04-28

Antimicrobial resistance (AMR) is one of the major threats to public health around the world. Besides the intense use and misuse of antimicrobial agents as the major force behind the increase in antimicrobial resistance, the exponential increase of international travel may also substantially contribute to the emergence and spread of AMR. However, knowledge on the extent to which international travel contributes to this is still limited. The Carriage Of Multiresistant Bacteria After Travel (COMBAT) study aims to 1. determine the acquisition rate of multiresistant Enterobacteriaceae during foreign travel 2. ascertain the duration of carriage of these micro-organisms 3. determine the transmission rate within households 4. identify risk factors for acquisition, persistence of carriage and transmission of multiresistant Enterobacteriaceae. The COMBAT-study is a large-scale multicenter longitudinal cohort study among travellers (n = 2001) and their non-travelling household members (n = 215). Faecal samples are collected before and immediately after travel and 1 month after return from all participants. Follow-up faecal samples are collected 3, 6 and 12 months after return from travellers (and their non-travelling household members) who acquired multiresistant Enterobacteriaceae. Questionnaires are collected from all participants at each time-point. Faecal samples are screened phenotypically for the presence of extended-spectrum beta-lactamase (ESBL) or carbapenemase-producing Enterobacteriaceae. Positive post-travel isolates from travellers with negative pre-travel samples are genotypically analysed for ESBL and carbapenemase genes with microarray and gene sequencing. The design and scale of the COMBAT-study will enable us to provide much needed detailed insights into the risks and dynamics of introduction and spread of ESBL- and carbapenemase-producing Enterobacteriaceae by healthy travellers and the potential need and measures to monitor or manage these risks. The study is registered at clinicaltrials.gov under accession number NCT01676974.

Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity

PubMed Central

Swarnkar, Mohit Kumar; Vyas, Pratibha; Rahi, Praveen; Thakur, Rishu; Thakur, Namika; Singh, Anil Kumar

2015-01-01

The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-3-acetic acid (IAA) production, and stress response. PMID:26337878

Multiple, novel biologically active endophytic actinomycetes isolated from upper Amazonian rainforests.

PubMed

Bascom-Slack, Carol A; Ma, Cong; Moore, Emily; Babbs, Beatrice; Fenn, Kathleen; Greene, Joshua S; Hann, Bradley D; Keehner, Jocelyn; Kelley-Swift, Elizabeth G; Kembaiyan, Vivek; Lee, Sun Jin; Li, Puyao; Light, David Y; Lin, Emily H; Schorn, Michelle A; Vekhter, Daniel; Boulanger, Lori-Ann; Hess, W M; Vargas, Percy Núñez; Strobel, Gary A; Strobel, Scott A

2009-08-01

Microbial biodiversity provides an increasingly important source of medically and industrially useful compounds. We have isolated 14 actinomycete species from a collection of approximately 300 plant stem samples from the upper Amazonian rainforest in Peru. All of the cultured isolates produce substances with inhibitory activity directed at a range of potential fungal and bacterial pathogens. For some organisms, this activity is very broad in spectrum while other organisms show specific activity against a limited number of organisms. Two of these organisms preferentially inhibit bacterial test organisms over eukaryotic organisms. rDNA sequence analysis indicates that these organisms are not equivalent to any other cultured deposits in GenBank. Our results provide evidence of the untapped biodiversity in the form of biologically active microbes present within the tissues of higher plants.

Protospacer Adjacent Motif (PAM)-Distal Sequences Engage CRISPR Cas9 DNA Target Cleavage

PubMed Central

Ethier, Sylvain; Schmeing, T. Martin; Dostie, Josée; Pelletier, Jerry

2014-01-01

The clustered regularly interspaced short palindromic repeat (CRISPR)-associated enzyme Cas9 is an RNA-guided nuclease that has been widely adapted for genome editing in eukaryotic cells. However, the in vivo target specificity of Cas9 is poorly understood and most studies rely on in silico predictions to define the potential off-target editing spectrum. Using chromatin immunoprecipitation followed by sequencing (ChIP-seq), we delineate the genome-wide binding panorama of catalytically inactive Cas9 directed by two different single guide (sg) RNAs targeting the Trp53 locus. Cas9:sgRNA complexes are able to load onto multiple sites with short seed regions adjacent to 5′NGG3′ protospacer adjacent motifs (PAM). Yet among 43 ChIP-seq sites harboring seed regions analyzed for mutational status, we find editing only at the intended on-target locus and one off-target site. In vitro analysis of target site recognition revealed that interactions between the 5′ end of the guide and PAM-distal target sequences are necessary to efficiently engage Cas9 nucleolytic activity, providing an explanation for why off-target editing is significantly lower than expected from ChIP-seq data. PMID:25275497

Typing Clostridium difficile strains based on tandem repeat sequences

PubMed Central

2009-01-01

Background Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies. Results This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. Conclusion We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. PMID:19133124

Channel fading for mobile satellite communications using spread spectrum signaling and TDRSS

NASA Technical Reports Server (NTRS)

Jenkins, Jeffrey D.; Fan, Yiping; Osborne, William P.

1995-01-01

This paper will present some preliminary results from a propagation experiment which employed NASA's TDRSS and an 8 MHz chip rate spread spectrum signal. Channel fade statistics were measured and analyzed in 21 representative geographical locations covering urban/suburban, open plain, and forested areas. Cumulative distribution Functions (CDF's) of 12 individual locations are presented and classified based on location. Representative CDF's from each of these three types of terrain are summarized. These results are discussed, and the fade depths exceeded 10 percent of the time in three types of environments are tabulated. The spread spectrum fade statistics for tree-lined roads are compared with the Empirical Roadside Shadowing Model.

Spread spectrum communication link using surface wave devices

NASA Technical Reports Server (NTRS)

Hunsinger, B. J.; Fugit, B. B.

1971-01-01

A fast lock-up, 8-MHz bandwidth 8,000 bit per second data rate spread spectrum communication link breadboard is described that is implemented using surface wave devices as the primary signal generators and signal processing elements. It uses surface wave tapped delay lines in the transmitter to generate the signals and in the receiver to detect them. The breadboard provides a measured processing gain for Gaussian noise of 31.5 dB which is within one dB of the theoretical optimum. This development demonstrates that spread spectrum receivers implemented with surface wave devices have sensitivities and complexities comparable to those of serial correlation receivers, but synchronization search times which are two to three orders of magnitude smaller.

Draft Genome Sequence of Streptomyces sp. Strain Wb2n-11, a Desert Isolate with Broad-Spectrum Antagonism against Soilborne Phytopathogens

DOE PAGES

Köberl, Martina; White, Richard A.; Erschen, Sabine; ...

2015-08-06

Streptomyces sp. strain Wb2n-11, isolated from native desert soil, exhibited broad-spectrum antagonism against plant pathogenic fungi, bacteria, and nematodes. The 8.2-Mb draft genome reveals genes putatively responsible for its promising biocontrol activity and genes which enable the soil bacterium to directly interact beneficially with plants.

Multiple Evolutionary Events Involved in Maintaining Homologs of Resistance to Powdery Mildew 8 in Brassica napus.

PubMed

Li, Qin; Li, Jing; Sun, Jin-Long; Ma, Xian-Feng; Wang, Ting-Ting; Berkey, Robert; Yang, Hui; Niu, Ying-Ze; Fan, Jing; Li, Yan; Xiao, Shunyuan; Wang, Wen-Ming

2016-01-01

The Resistance to Powdery Mildew 8 (RPW8) locus confers broad-spectrum resistance to powdery mildew in Arabidopsis thaliana. There are four Homologous to RPW8s (BrHRs) in Brassica rapa and three in Brassica oleracea (BoHRs). Brassica napus (Bn) is derived from diploidization of a hybrid between B. rapa and B. oleracea, thus should have seven homologs of RPW8 (BnHRs). It is unclear whether these genes are still maintained or lost in B. napus after diploidization and how they might have been evolved. Here, we reported the identification and sequence polymorphisms of BnHRs from a set of B. napus accessions. Our data indicated that while the BoHR copy from B. oleracea is highly conserved, the BrHR copy from B. rapa is relatively variable in the B. napus genome owing to multiple evolutionary events, such as gene loss, point mutation, insertion, deletion, and intragenic recombination. Given the overall high sequence homology of BnHR genes, it is not surprising that both intragenic recombination between two orthologs and two paralogs were detected in B. napus, which may explain the loss of BoHR genes in some B. napus accessions. When ectopically expressed in Arabidopsis, a C-terminally truncated version of BnHRa and BnHRb, as well as the full length BnHRd fused with YFP at their C-termini could trigger cell death in the absence of pathogens and enhanced resistance to powdery mildew disease. Moreover, subcellular localization analysis showed that both BnHRa-YFP and BnHRb-YFP were mainly localized to the extra-haustorial membrane encasing the haustorium of powdery mildew. Taken together, our data suggest that the duplicated BnHR genes might have been subjected to differential selection and at least some may play a role in defense and could serve as resistance resource in engineering disease-resistant plants.

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

DOE PAGES

Hong, Matthew K. H.; Macintyre, Geoff; Wedge, David C.; ...

2015-04-01

Tumour heterogeneity in primary prostate cancer is a well-established phenomenon. However, how the subclonal diversity of tumours changes during metastasis and progression to lethality is poorly understood. Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic tumours. We find one case of metastatic spread to the surgical bed causing local recurrence, and another case of cross-metastatic site seeding combining with dynamic remoulding of subclonal mixtures in response to therapy. By ultra-deep sequencing end-stage blood, we detect both metastatic and primary tumour clones,more » even years after removal of the prostate. As a result, analysis of mutations associated with metastasis reveals an enrichment of TP53 mutations, and additional sequencing of metastases from 19 patients demonstrates that acquisition of TP53 mutations is linked with the expansion of subclones with metastatic potential which we can detect in the blood.« less

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer.

PubMed

Hong, Matthew K H; Macintyre, Geoff; Wedge, David C; Van Loo, Peter; Patel, Keval; Lunke, Sebastian; Alexandrov, Ludmil B; Sloggett, Clare; Cmero, Marek; Marass, Francesco; Tsui, Dana; Mangiola, Stefano; Lonie, Andrew; Naeem, Haroon; Sapre, Nikhil; Phal, Pramit M; Kurganovs, Natalie; Chin, Xiaowen; Kerger, Michael; Warren, Anne Y; Neal, David; Gnanapragasam, Vincent; Rosenfeld, Nitzan; Pedersen, John S; Ryan, Andrew; Haviv, Izhak; Costello, Anthony J; Corcoran, Niall M; Hovens, Christopher M

2015-04-01

Tumour heterogeneity in primary prostate cancer is a well-established phenomenon. However, how the subclonal diversity of tumours changes during metastasis and progression to lethality is poorly understood. Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic tumours. We find one case of metastatic spread to the surgical bed causing local recurrence, and another case of cross-metastatic site seeding combining with dynamic remoulding of subclonal mixtures in response to therapy. By ultra-deep sequencing end-stage blood, we detect both metastatic and primary tumour clones, even years after removal of the prostate. Analysis of mutations associated with metastasis reveals an enrichment of TP53 mutations, and additional sequencing of metastases from 19 patients demonstrates that acquisition of TP53 mutations is linked with the expansion of subclones with metastatic potential which we can detect in the blood.

Adaptive receiver structures for asynchronous CDMA systems

NASA Astrophysics Data System (ADS)

Rapajic, Predrag B.; Vucetic, Branka S.

1994-05-01

Adaptive linear and decision feedback receiver structures for coherent demodulation in asynchronous code division multiple access (CDMA) systems are considered. It is assumed that the adaptive receiver has no knowledge of the signature waveforms and timing of other users. The receiver is trained by a known training sequence prior to data transmission and continuously adjusted by an adaptive algorithm during data transmission. The proposed linear receiver is as simple as a standard single-user detector receiver consisting of a matched filter with constant coefficients, but achieves essential advantages with respect to timing recovery, multiple access interference elimination, near/far effect, narrowband and frequency-selective fading interference suppression, and user privacy. An adaptive centralized decision feedback receiver has the same advantages of the linear receiver but, in addition, achieves a further improvement in multiple access interference cancellation at the expense of higher complexity. The proposed receiver structures are tested by simulation over a channel with multipath propagation, multiple access interference, narrowband interference, and additive white Gaussian noise.

Looking for Photometric Signatures of Fast Rotation in Intermediate-Age Star Clusters in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Goudfrooij, Paul

2017-08-01

Recently, deep color-magnitude diagrams from HST data revealed that several massive intermediate-age star clusters in the Magellanic Clouds exhibit extended main-sequence turn-offs (eMSTOs). This discovery posed serious questions regarding the mechanisms responsible for the formation of massive globular clusters and their well-known multiple stellar populations. The nature of eMSTOs is a hotly debated topic of study. Several studies argued that the eMSTOs are caused by an age range of up to a few hundred Myr, while other studies indicate that eMSTOs can instead be caused by a coeval population in which the stars span a range of rotation velocities. Formal evidence to (dis-)prove either scenario still remains at large, in part because stellar tracks that incorporate the effects of rotation have so far only been available for masses > 1.7 Msun whereas the stars in the known eMSTOs of intermediate-age star clusters are less massive. In this proposal we aim to look for photometric signatures of fast rotators in eMSTO clusters that have been observed by HST in three passbands including (at least) F336W and F814W. We will study spreads in different stellar colors, testing against those predicted with the aid of von Zeipel's geometric study for a population of rotating stars with a significant spread in their inclination. Importantly, this spread due to the presence of rotation is predicted to occur along well-defined lines in color-color diagrams, in directions that are distinct from those in color-magnitude diagrams and distinct from the spread predicted for the age range scenario.

LAMB1 polymorphism is associated with autism symptom severity in Korean autism spectrum disorder patients.

PubMed

Kim, Young Jong; Park, Jin Kyung; Kang, Won Sub; Kim, Su Kang; Park, Hae Jeong; Nam, Min; Kim, Jong Woo

2015-01-01

LAMB1 encodes laminin beta-1, which is expressed during early development of the human nervous system, and could be involved in the pathogenesis of neurodevelopmental disorders. In our study, we aimed to investigate whether single nucleotide polymorphisms (SNPs) in LAMB1 were associated with autism spectrum disorder (ASD) and with related clinical severities of ASD. Two coding SNPs (rs20556 and rs25659) and two intronic SNPs (rs2158836 and rs2237659) were compared between 180 patients with ASD and 147 healthy control subjects using direct sequencing. The Korean version of the Childhood Autism Rating Scale (K-CARS) was used to assess clinical severities. Multiple logistic regression models were employed to analyze genetic data, and associations with symptom severity were tested with the Kruskal-Wallis and the Mann-Whitney U tests. None of the four examined SNPs was associated with ASD risk. However, the GG genotype of rs2158836 was associated with more severe symptoms for the "object use" and "non-verbal communication" measures. The results of our study suggest the association between rs2158836 polymorphisms and symptom severity in ASD.

Claustrum of the short-tailed fruit bat, Carollia perspicillata: Alignment of cellular orientation and functional connectivity.

PubMed

Orman, Rena; Kollmar, Richard; Stewart, Mark

2017-04-15

The claustrum is a gray-matter structure that underlies neocortex and reciprocates connections with cortical and subcortical targets. In lower mammals, the claustrum is directly adjacent to neocortex, making the definition of claustral boundaries challenging. Latexin, an endogenous inhibitor of metallocarboxypeptidases, localizes to claustral cells, enabling a clear delineation of claustrum. Given its proportionately large claustrum, we hypothesized that the short-tailed fruit bat, Carollia perspicillata, can be a useful model for claustral structure-function relations. We used latexin immunohistochemistry to identify claustral boundaries and intrinsic structure and multielectrode recordings from brain slices to explore intrinsic excitatory connectivity of the claustrum. Carollia's claustrum contains cells whose intrinsic connectivity and alignment permit the generation of spontaneous, synchronous population events and mirror their pattern of spread in disinhibited brain slices over millimeters. Carollia shows cellular alignment and spontaneous population-activity spread along both horizontal and dorsoventral axes. Carollia claustrum possesses intrinsic excitatory connectivity sufficient to: 1) generate single, spontaneous, synchronized burst discharges, 2) support activity spread along axes where claustral cells are aligned, and 3), because of multiple axes for cell alignment, support activity spread along both rostrocaudal and dorsoventral axes. The smaller event sizes in bat claustrum compared with rat claustrum are consistent with events occurring in population subsets rather than the full claustral cell population. The overall size of claustrum, its pronounced vascularity, and its more complex intrinsic connectivity than rat suggest that the bat is an animal model for claustral structure and function that will permit unique access to claustrum's processing capabilities. J. Comp. Neurol. 525:1459-1474, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Instructive Feedback Embedded within Group Instruction for Children Diagnosed with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Leaf, Justin B.; Cihon, Joseph H.; Alcalay, Aditt; Mitchell, Erin; Townley-Cochran, Donna; Miller, Kevin; Leaf, Ronald; Taubman, Mitchell; McEachin, John

2017-01-01

The present study evaluated the effects of instructive feedback embedded within a group discrete trial teaching to teach tact relations to nine children diagnosed with autism spectrum disorder using a nonconcurrent multiple-baseline design. Dependent variables included correct responses for: primary targets (directly taught), secondary targets…

MARSnet: Mission-aware Autonomous Radar Sensor Network for Future Combat Systems

DTIC Science & Technology

2009-03-23

15 , , L x(s)x*(s) ds WdB = lOlog Jo Y ; ; (19) In addition, the sidelobe structure is changed because of the Dop])ler shift...Synchro- nous CDMA Systems.’’ IEICE Trans.Fundamentals. E832A(11): 1 16, 2000. 24 [10] P. Z. Fan. "New Direction in Spreading Sequence Design and the...Suehiro , N Kuroyanagi and P Z Fan. "Two types of polyphase sequence set. for approximately synchronized CDMA systems." IEICE Trans. Fundamentals. E862A

Paleomagnetic constraints on deformation of superfast-spread oceanic crust exposed at Pito Deep Rift

NASA Astrophysics Data System (ADS)

Horst, A. J.; Varga, R. J.; Gee, J. S.; Karson, J. A.

2011-12-01

The uppermost oceanic crust produced at the superfast spreading (˜142 km Ma-1, full-spreading rate) southern East Pacific Rise (EPR) during the Gauss Chron is exposed in a tectonic window along the northeastern wall of the Pito Deep Rift. Paleomagnetic analysis of fully oriented dike (62) and gabbro (5) samples from two adjacent study areas yield bootstrapped mean remanence directions of 38.9° ± 8.1°, -16.7° ± 15.6°, n = 23 (Area A) and 30.4° ± 8.0°, -25.1° ± 12.9°, n = 44 (Area B), both are significantly distinct from the Geocentric Axial Dipole expected direction at 23° S. Regional tectonics and outcrop-scale structural data combined with bootstrapped remanence directions constrain models that involve a sequence of three rotations that result in dikes restored to subvertical orientations related to (1) inward-tilting of crustal blocks during spreading (Area A = 11°, Area B = 22°), (2) clockwise, vertical-axis rotation of the Easter Microplate (A = 46°, B = 44°), and (3) block tilting at Pito Deep Rift (A = 21°, B = 10°). These data support a structural model for accretion at the southern EPR in which outcrop-scale faulting and block rotation accommodates spreading-related subaxial subsidence that is generally less than that observed in crust generated at a fast spreading rate exposed at Hess Deep Rift. These data also support previous estimates for the clockwise rotation of crust adjacent to the Easter Microplate. Dike sample natural remanent magnetization (NRM) has an arithmetic mean of 5.96 A/m ± 3.76, which suggests that they significantly contribute to observed magnetic anomalies from fast- to superfast-spread crust.

Bispectral analysis of equatorial spread F density irregularities

NASA Technical Reports Server (NTRS)

Labelle, J.; Lund, E. J.

1992-01-01

Bispectral analysis has been applied to density irregularities at frequencies 5-30 Hz observed with a sounding rocket launched from Peru in March 1983. Unlike the power spectrum, the bispectrum contains statistical information about the phase relations between the Fourier components which make up the waveform. In the case of spread F data from 475 km the 5-30 Hz portion of the spectrum displays overall enhanced bicoherence relative to that of the background instrumental noise and to that expected due to statistical considerations, implying that the observed f exp -2.5 power law spectrum has a significant non-Gaussian component. This is consistent with previous qualitative analyses. The bicoherence has also been calculated for simulated equatorial spread F density irregularities in approximately the same wavelength regime, and the resulting bispectrum has some features in common with that of the rocket data. The implications of this analysis for equatorial spread F are discussed, and some future investigations are suggested.

Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley.

PubMed

Dai, Fei; Chen, Zhong-Hua; Wang, Xiaolei; Li, Zefeng; Jin, Gulei; Wu, Dezhi; Cai, Shengguan; Wang, Ning; Wu, Feibo; Nevo, Eviatar; Zhang, Guoping

2014-09-16

The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accessions were generated. We reported 12,530 de novo assembled transcripts in all of the 21 samples. Population structure analysis showed that Tibetan hulless barley (qingke) might have existed in the early stage of domestication. Based on the large number of unique genomic regions showing the similarity between cultivated and wild-barley groups, we propose that the genomic origin of modern cultivated barley is derived from wild-barley genotypes in the Fertile Crescent (mainly in chromosomes 1H, 2H, and 3H) and Tibet (mainly in chromosomes 4H, 5H, 6H, and 7H). This study indicates that the domestication of barley may have occurred over time in geographically distinct regions.

Extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in local and imported poultry meat in Ghana.

PubMed

Eibach, Daniel; Dekker, Denise; Gyau Boahen, Kennedy; Wiafe Akenten, Charity; Sarpong, Nimako; Belmar Campos, Cristina; Berneking, Laura; Aepfelbacher, Martin; Krumkamp, Ralf; Owusu-Dabo, Ellis; May, Jürgen

2018-04-01

Antibiotic use in animal husbandry has raised concerns on the spread of resistant bacteria. Currently animal products are traded globally with unprecedented ease, which has been challenging the control of antimicrobial resistance. This study aims to detect and characterize extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae from imported and locally produced poultry products sold in Ghana. Local and imported chicken meat was collected from 94 stores and markets throughout Kumasi (Ghana) and cultured on selective ESBL screening agar. Phenotypic ESBL-producing E. coli and K. pneumoniae isolates were confirmed by combined disc test and further characterized by antibiotic susceptibility testing, amplification of the bla CTX-M , bla TEM and bla SHV genes as well as multilocus sequence typing (MLST) and linked to the country of origin. Out of 200 meat samples, 71 (36%) samples revealed 81 ESBL-producing isolates (46 E. coli and 35 K. pneumoniae), with 44% (30/68) of local poultry and 31% (41/132) of imported products being contaminated. Most ESBL-producing isolates harboured the bla CTX-M-15 gene (61/81, 75%) and the dominant Sequence Types (ST) were ST2570 (7/35, 20%) among K. pneumoniae and ST10 (5/46, 11%) among E. coli. High numbers of ESBL-producing bacteria, particularly on local but also imported poultry meat, represent a potential source for human colonization and infection as well as spread within the community. Surveillance along the poultry production-food-consumer chain would be a valuable tool to identify sources of emerging multidrug resistant pathogens in Ghana. Copyright © 2018 Elsevier B.V. All rights reserved.

Shuttle spectrum despreader

NASA Technical Reports Server (NTRS)

1976-01-01

The results of the spread spectrum despreader project are reported and three principal products are designed and tested. The products are, (1) a spread spectrum despreader breadboard, (2) associated test equipment consisting of a spectrum spreader and bit reconstruction/error counter and (3) paper design of a Ku-band receiver which would incorporate the despreader as a principal subsystem. The despreader and test set are designed for maximum flexibility. A choice of unbalanced quadriphase or biphase shift keyed data modulation is available. Selectable integration time and threshold voltages on the despreader further lend true usefulness as laboratory test equipment to the delivered hardware.

Antibiotic Susceptibilities and Genetic Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Stools of Pediatric Diarrhea Patients in Surabaya, Indonesia.

PubMed

Bagus Wasito, Eddy; Shigemura, Katsumi; Osawa, Kayo; Fardah, Alpha; Kanaida, Akiho; Raharjo, Dadik; Kuntaman, K; Hadi, Usman; Harijono, Sugeng; Marto Sudarmo, Subijanto; Nakamura, Tatsuya; Shibayama, Keigo; Fujisawa, Masato; Shirakawa, Toshiro

2017-07-24

The purpose of this study was to investigate extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates from pediatric (aged 0 to 3 years) diarrhea patients in Surabaya, Indonesia, where this kind of survey is rare; our study included assessment of their antibiotic susceptibilities, as well as ESBL typing, multilocus sequence typing (MLST), and diarrheagenic E. coli (DEC)-typing. ESBL-producing E. coli were detected in 18.8% of all the samples. Many ESBL-producing E. coli had significantly lower susceptibility to gentamicin (p ＜ 0.0001) and the quinolones nalidixic acid (p＝0.004) and ciprofloxacin (p ＜ 0.0001) than non-producers. In ESBL-producing E. coli, 84.0% of strains expressed CTX-M-15 alone or in combination with other ESBL types. MLST revealed that 24.0% of ESBL-producers had sequence type 617, all of which expressed the CTX-M-15 gene; we also detected expression of 3 DEC-related genes: 2 enteroaggregative E. coli genes and 1 enteropathogenic E. coli gene. In conclusion, CTX-M-15-type ESBL-producing E. coli ST617 appear to have spread to Indonesia.

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

PubMed

Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej

2017-05-15

Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

PubMed

Cannone, Jamie J; Sweeney, Blake A; Petrov, Anton I; Gutell, Robin R; Zirbel, Craig L; Leontis, Neocles

2015-07-01

The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to curated, representative ribosomal RNA sequence alignments from bacterial, archaeal, eukaryal and organellar ribosomes, using nucleotide numbers from representative atomic-resolution 3D structures. A web-based front end is available for manual entry and an Application Program Interface for programmatic access. Users can specify up to five ranges of nucleotides and 50 nucleotide positions per range. The R3D-2-MSA server maps these ranges to the appropriate columns of the corresponding MSA and returns the contents of the columns, either for display in a web browser or in JSON format for subsequent programmatic use. The browser output page provides a 3D interactive display of the query, a full list of sequence variants with taxonomic information and a statistical summary of distinct sequence variants found. The output can be filtered and sorted in the browser. Previous user queries can be viewed at any time by resubmitting the output URL, which encodes the search and re-generates the results. The service is freely available with no login requirement at http://rna.bgsu.edu/r3d-2-msa. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative Sequence and X-Inactivation Analyses of a Domain of Escape in Human Xp11.2 and the Conserved Segment in Mouse

PubMed Central

Tsuchiya, Karen D.; Greally, John M.; Yi, Yajun; Noel, Kevin P.; Truong, Jean-Pierre; Disteche, Christine M.

2004-01-01

We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared this region with the region of conserved synteny in mouse. We identified several new transcripts from this region in human and in mouse, which defined the full extent of the domain escaping X inactivation in both species. In human, escape from X inactivation involves an uninterrupted 235-kb domain of multiple genes. Despite highly conserved gene content and order between the two species, Smcx is the only mouse gene from the conserved segment that escapes inactivation. As repetitive sequences are believed to facilitate spreading of X inactivation along the chromosome, we compared the repetitive sequence composition of this region between the two species. We found that long terminal repeats (LTRs) were decreased in the human domain of escape, but not in the majority of the conserved mouse region adjacent to Smcx in which genes were subject to X inactivation, suggesting that these repeats might be excluded from escape domains to prevent spreading of silencing. Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome. PMID:15197169

Complete Sequence and Molecular Epidemiology of IncK Epidemic Plasmid Encoding blaCTX-M-14

PubMed Central

Cottell, Jennifer L.; Webber, Mark A.; Coldham, Nick G.; Taylor, Dafydd L.; Cerdeño-Tárraga, Anna M.; Hauser, Heidi; Thomson, Nicholas R.; Woodward, Martin J.

2011-01-01

Antimicrobial drug resistance is a global challenge for the 21st century with the emergence of resistant bacterial strains worldwide. Transferable resistance to β-lactam antimicrobial drugs, mediated by production of extended-spectrum β-lactamases (ESBLs), is of particular concern. In 2004, an ESBL-carrying IncK plasmid (pCT) was isolated from cattle in the United Kingdom. The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, blaCTX-M-14. From this information, PCRs identifying novel features of pCT were designed and applied to isolates from several countries, showing that the plasmid has disseminated worldwide in bacteria from humans and animals. Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals. PMID:21470454

Demonstration of an SOA-assisted open metro-access infrastructure for heterogeneous services.

PubMed

Schmuck, H; Bonk, R; Poehlmann, W; Haslach, C; Kuebart, W; Karnick, D; Meyer, J; Fritzsche, D; Weis, E; Becker, J; Freude, W; Pfeiffer, T

2014-01-13

An open converged metro-access network approach allows for sharing optical layer resources like fibers and optical spectrum among different services and operators. We demonstrated experimentally the feasibility of such a concept by the simultaneous operation of multiple services showing different modulation formats and multiplexing techniques. Flexible access nodes are implemented including semiconductor optical amplifiers to create a transparent and reconfigurable optical ring network. The impact of cascaded optical amplifiers on the signal quality is studied along the ring. In addition, the influence of high power rival signals in the same waveband and in the same fiber is analyzed.

The Effects of Rotation on the Main-sequence Turnoff of Intermediate-age Massive Star Clusters

NASA Astrophysics Data System (ADS)

Yang, Wuming; Bi, Shaolan; Meng, Xiangcun; Liu, Zhie

2013-10-01

The double or extended main-sequence turnoffs (MSTOs) in the color-magnitude diagram (CMD) of intermediate-age massive star clusters in the Large Magellanic Cloud are generally interpreted as age spreads of a few hundred Myr. However, such age spreads do not exist in younger clusters (i.e., 40-300 Myr), which challenges this interpretation. The effects of rotation on the MSTOs of star clusters have been studied in previous works, but the results obtained are conflicting. Compared with previous works, we consider the effects of rotation on the main-sequence lifetime of stars. Our calculations show that rotating models have a fainter and redder MSTO with respect to non-rotating counterparts with ages between about 0.8 and 2.2 Gyr, but have a brighter and bluer MSTO when age is larger than 2.4 Gyr. The spread of the MSTO caused by a typical rotation rate is equivalent to the effect of an age spread of about 200 Myr. Rotation could lead to the double or extended MSTOs in the CMD of the star clusters with ages between about 0.8 and 2.2 Gyr. However, the extension is not significant, and it does not even exist in younger clusters. If the efficiency of the mixing were high enough, the effects of the mixing would counteract the effect of the centrifugal support in the late stage of evolution, and the rotationally induced extension would disappear in the old intermediate-age star clusters, but younger clusters would have an extended MSTO. Moreover, the effects of rotation might aid in understanding the formation of some "multiple populations" in globular clusters.

Orthogonal Polynomials on the Unit Circle with Fibonacci Verblunsky Coefficients, II. Applications

NASA Astrophysics Data System (ADS)

Damanik, David; Munger, Paul; Yessen, William N.

2013-10-01

We consider CMV matrices with Verblunsky coefficients determined in an appropriate way by the Fibonacci sequence and present two applications of the spectral theory of such matrices to problems in mathematical physics. In our first application we estimate the spreading rates of quantum walks on the line with time-independent coins following the Fibonacci sequence. The estimates we obtain are explicit in terms of the parameters of the system. In our second application, we establish a connection between the classical nearest neighbor Ising model on the one-dimensional lattice in the complex magnetic field regime, and CMV operators. In particular, given a sequence of nearest-neighbor interaction couplings, we construct a sequence of Verblunsky coefficients, such that the support of the Lee-Yang zeros of the partition function for the Ising model in the thermodynamic limit coincides with the essential spectrum of the CMV matrix with the constructed Verblunsky coefficients. Under certain technical conditions, we also show that the zeros distribution measure coincides with the density of states measure for the CMV matrix.

Average Likelihood Methods for Code Division Multiple Access (CDMA)

DTIC Science & Technology

2014-05-01

lengths in the range of 22 to 213 and possibly higher. Keywords: DS / CDMA signals, classification, balanced CDMA load, synchronous CDMA , decision...likelihood ratio test (ALRT). We begin this classification problem by finding the size of the spreading matrix that generated the DS - CDMA signal. As...Theoretical Background The classification of DS / CDMA signals should not be confused with the problem of multiuser detection. The multiuser detection deals

Pulse transmission transceiver architecture for low power communications

DOEpatents

Dress, Jr., William B.; Smith, Stephen F.

2003-08-05

Systems and methods for pulse-transmission low-power communication modes are disclosed. A method of pulse transmission communications includes: generating a modulated pulse signal waveform; transforming said modulated pulse signal waveform into at least one higher-order derivative waveform; and transmitting said at least one higher-order derivative waveform as an emitted pulse. The systems and methods significantly reduce lower-frequency emissions from pulse transmission spread-spectrum communication modes, which reduces potentially harmful interference to existing radio frequency services and users and also simultaneously permit transmission of multiple data bits by utilizing specific pulse shapes.

Complete Genome Sequence of the Rhizobacterium Pseudomonas trivialis Strain IHBB745 with Multiple Plant Growth-Promoting Activities and Tolerance to Desiccation and Alkalinity.

PubMed

Gulati, Arvind; Swarnkar, Mohit Kumar; Vyas, Pratibha; Rahi, Praveen; Thakur, Rishu; Thakur, Namika; Singh, Anil Kumar

2015-09-03

The complete genome sequence of 6.45 Mb is reported here for Pseudomonas trivialis strain IHBB745 (MTCC 5336), which is an efficient, stress-tolerant, and broad-spectrum plant growth-promoting rhizobacterium. The gene-coding clusters predicted the genes for phosphate solubilization, siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-3-acetic acid (IAA) production, and stress response. Copyright © 2015 Gulati et al.

A DS-UWB Cognitive Radio System Based on Bridge Function Smart Codes

NASA Astrophysics Data System (ADS)

Xu, Yafei; Hong, Sheng; Zhao, Guodong; Zhang, Fengyuan; di, Jinshan; Zhang, Qishan

This paper proposes a direct-sequence UWB Gaussian pulse of cognitive radio systems based on bridge function smart sequence matrix and the Gaussian pulse. As the system uses the spreading sequence code, that is the bridge function smart code sequence, the zero correlation zones (ZCZs) which the bridge function sequences' auto-correlation functions had, could reduce multipath fading of the pulse interference. The Modulated channel signal was sent into the IEEE 802.15.3a UWB channel. We analysis the ZCZs's inhibition to the interference multipath interference (MPI), as one of the main system sources interferences. The simulation in SIMULINK/MATLAB is described in detail. The result shows the system has better performance by comparison with that employing Walsh sequence square matrix, and it was verified by the formula in principle.

Wireless spread-spectrum telesensor chip with synchronous digital architecture

DOEpatents

Smith, Stephen F.; Turner, Gary W.; Wintenberg, Alan L.; Emery, Michael Steven

2005-03-08

A fully integrated wireless spread-spectrum sensor incorporating all elements of an "intelligent" sensor on a single circuit chip is capable of telemetering data to a receiver. Synchronous control of all elements of the chip provides low-cost, low-noise, and highly robust data transmission, in turn enabling the use of low-cost monolithic receivers.

Examination of Wildland Fire Spread at Small Scales Using Direct Numerical Simulations and High-Speed Laser Diagnostics

NASA Astrophysics Data System (ADS)

Wimer, N. T.; Mackoweicki, A. S.; Poludnenko, A. Y.; Hoffman, C.; Daily, J. W.; Rieker, G. B.; Hamlington, P.

2017-12-01

Results are presented from a joint computational and experimental research effort focused on understanding and characterizing wildland fire spread at small scales (roughly 1m-1mm) using direct numerical simulations (DNS) with chemical kinetics mechanisms that have been calibrated using data from high-speed laser diagnostics. The simulations are intended to directly resolve, with high physical accuracy, all small-scale fluid dynamic and chemical processes relevant to wildland fire spread. The high fidelity of the simulations is enabled by the calibration and validation of DNS sub-models using data from high-speed laser diagnostics. These diagnostics have the capability to measure temperature and chemical species concentrations, and are used here to characterize evaporation and pyrolysis processes in wildland fuels subjected to an external radiation source. The chemical kinetics code CHEMKIN-PRO is used to study and reduce complex reaction mechanisms for water removal, pyrolysis, and gas phase combustion during solid biomass burning. Simulations are then presented for a gaseous pool fire coupled with the resulting multi-step chemical reaction mechanisms, and the results are connected to the fundamental structure and spread of wildland fires. It is anticipated that the combined computational and experimental approach of this research effort will provide unprecedented access to information about chemical species, temperature, and turbulence during the entire pyrolysis, evaporation, ignition, and combustion process, thereby permitting more complete understanding of the physics that must be represented by coarse-scale numerical models of wildland fire spread.

Algorithms and semantic infrastructure for mutation impact extraction and grounding.

PubMed

Laurila, Jonas B; Naderi, Nona; Witte, René; Riazanov, Alexandre; Kouznetsov, Alexandre; Baker, Christopher J O

2010-12-02

Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases. We present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework. We address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.

Role for migratory wild birds in the global spread of avian influenza H5N8.

PubMed

2016-10-14

Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014-2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses. Further, we found that the hemagglutinin of clade 2.3.4.4 virus was remarkably promiscuous, creating reassortants with multiple neuraminidase subtypes. Improving our understanding of the circumpolar circulation of avian influenza viruses in migratory waterfowl will help to provide early warning of threats from avian influenza to poultry, and potentially human, health. Copyright © 2016, American Association for the Advancement of Science.

Toward Meaningful Outcomes in Teaching Conversation and Greeting Skills with Individuals with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Hood, Stephanie A.; Luczynski, Kevin C.; Mitteer, Daniel R.

2017-01-01

We identified greeting and conversation deficits based on a parent interview and semistructured direct assessment for one child and two adolescents with autism spectrum disorder. We taught the greeting and conversation skills using behavioral skills training and within-session corrective feedback. A multiple baseline across conversation and…

Informant Discrepancies in Externalizing and Internalizing Symptoms and Adaptive Skills of High-Functioning Children with Autism Spectrum Disorder

ERIC Educational Resources Information Center

McDonald, Christin A.; Lopata, Christopher; Donnelly, James P.; Thomeer, Marcus L.; Rodgers, Jonathan D.; Jordan, Allyson K.

2016-01-01

Assessment of clinical symptoms requires information from multiple informants. Discrepancies between informants' ratings can have significant implications in school settings (e.g., access to services, treatment planning, progress monitoring). This study examined parent-teacher discrepancies for ratings of internalizing and externalizing symptoms,…

A Review on Spectral Amplitude Coding Optical Code Division Multiple Access

NASA Astrophysics Data System (ADS)

Kaur, Navpreet; Goyal, Rakesh; Rani, Monika

2017-06-01

This manuscript deals with analysis of Spectral Amplitude Coding Optical Code Division Multiple Access (SACOCDMA) system. The major noise source in optical CDMA is co-channel interference from other users known as multiple access interference (MAI). The system performance in terms of bit error rate (BER) degrades as a result of increased MAI. It is perceived that number of users and type of codes used for optical system directly decide the performance of system. MAI can be restricted by efficient designing of optical codes and implementing them with unique architecture to accommodate more number of users. Hence, it is a necessity to design a technique like spectral direct detection (SDD) technique with modified double weight code, which can provide better cardinality and good correlation property.

Genomic Footprints of Selective Sweeps from Metabolic Resistance to Pyrethroids in African Malaria Vectors Are Driven by Scale up of Insecticide-Based Vector Control.

PubMed

Barnes, Kayla G; Weedall, Gareth D; Ndula, Miranda; Irving, Helen; Mzihalowa, Themba; Hemingway, Janet; Wondji, Charles S

2017-02-01

Insecticide resistance in mosquito populations threatens recent successes in malaria prevention. Elucidating patterns of genetic structure in malaria vectors to predict the speed and direction of the spread of resistance is essential to get ahead of the 'resistance curve' and to avert a public health catastrophe. Here, applying a combination of microsatellite analysis, whole genome sequencing and targeted sequencing of a resistance locus, we elucidated the continent-wide population structure of a major African malaria vector, Anopheles funestus. We identified a major selective sweep in a genomic region controlling cytochrome P450-based metabolic resistance conferring high resistance to pyrethroids. This selective sweep occurred since 2002, likely as a direct consequence of scaled up vector control as revealed by whole genome and fine-scale sequencing of pre- and post-intervention populations. Fine-scaled analysis of the pyrethroid resistance locus revealed that a resistance-associated allele of the cytochrome P450 monooxygenase CYP6P9a has swept through southern Africa to near fixation, in contrast to high polymorphism levels before interventions, conferring high levels of pyrethroid resistance linked to control failure. Population structure analysis revealed a barrier to gene flow between southern Africa and other areas, which may prevent or slow the spread of the southern mechanism of pyrethroid resistance to other regions. By identifying a genetic signature of pyrethroid-based interventions, we have demonstrated the intense selective pressure that control interventions exert on mosquito populations. If this level of selection and spread of resistance continues unabated, our ability to control malaria with current interventions will be compromised.

Energy spectrum control for modulated proton beams.

PubMed

Hsi, Wen C; Moyers, Michael F; Nichiporov, Dmitri; Anferov, Vladimir; Wolanski, Mark; Allgower, Chris E; Farr, Jonathan B; Mascia, Anthony E; Schreuder, Andries N

2009-06-01

In proton therapy delivered with range modulated beams, the energy spectrum of protons entering the delivery nozzle can affect the dose uniformity within the target region and the dose gradient around its periphery. For a cyclotron with a fixed extraction energy, a rangeshifter is used to change the energy but this produces increasing energy spreads for decreasing energies. This study investigated the magnitude of the effects of different energy spreads on dose uniformity and distal edge dose gradient and determined the limits for controlling the incident spectrum. A multilayer Faraday cup (MLFC) was calibrated against depth dose curves measured in water for nonmodulated beams with various incident spectra. Depth dose curves were measured in a water phantom and in a multilayer ionization chamber detector for modulated beams using different incident energy spreads. Some nozzle entrance energy spectra can produce unacceptable dose nonuniformities of up to +/-21% over the modulated region. For modulated beams and small beam ranges, the width of the distal penumbra can vary by a factor of 2.5. When the energy spread was controlled within the defined limits, the dose nonuniformity was less than +/-3%. To facilitate understanding of the results, the data were compared to the measured and Monte Carlo calculated data from a variable extraction energy synchrotron which has a narrow spectrum for all energies. Dose uniformity is only maintained within prescription limits when the energy spread is controlled. At low energies, a large spread can be beneficial for extending the energy range at which a single range modulator device can be used. An MLFC can be used as part of a feedback to provide specified energy spreads for different energies.

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins.

PubMed

Klemm, Elizabeth J; Shakoor, Sadia; Page, Andrew J; Qamar, Farah Naz; Judge, Kim; Saeed, Dania K; Wong, Vanessa K; Dallman, Timothy J; Nair, Satheesh; Baker, Stephen; Shaheen, Ghazala; Qureshi, Shahida; Yousafzai, Mohammad Tahir; Saleem, Muhammad Khalid; Hasan, Zahra; Dougan, Gordon; Hasan, Rumina

2018-02-20

Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi, the causative agent of typhoid. Multidrug-resistant (MDR) isolates are prevalent in parts of Asia and Africa and are often associated with the dominant H58 haplotype. Reduced susceptibility to fluoroquinolones is also widespread, and sporadic cases of resistance to third-generation cephalosporins or azithromycin have also been reported. Here, we report the first large-scale emergence and spread of a novel S  Typhi clone harboring resistance to three first-line drugs (chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) as well as fluoroquinolones and third-generation cephalosporins in Sindh, Pakistan, which we classify as extensively drug resistant (XDR). Over 300 XDR typhoid cases have emerged in Sindh, Pakistan, since November 2016. Additionally, a single case of travel-associated XDR typhoid has recently been identified in the United Kingdom. Whole-genome sequencing of over 80 of the XDR isolates revealed remarkable genetic clonality and sequence conservation, identified a large number of resistance determinants, and showed that these isolates were of haplotype H58. The XDR S  Typhi clone encodes a chromosomally located resistance region and harbors a plasmid encoding additional resistance elements, including the bla CTX-M-15 extended-spectrum β-lactamase, and carrying the qnrS fluoroquinolone resistance gene. This antibiotic resistance-associated IncY plasmid exhibited high sequence identity to plasmids found in other enteric bacteria isolated from widely distributed geographic locations. This study highlights three concerning problems: the receding antibiotic arsenal for typhoid treatment, the ability of S  Typhi to transform from MDR to XDR in a single step by acquisition of a plasmid, and the ability of XDR clones to spread globally. IMPORTANCE Typhoid fever is a severe disease caused by the Gram-negative bacterium Salmonella enterica serovar Typhi. Antibiotic-resistant S  Typhi strains have become increasingly common. Here, we report the first large-scale emergence and spread of a novel extensively drug-resistant (XDR) S  Typhi clone in Sindh, Pakistan. The XDR S  Typhi is resistant to the majority of drugs available for the treatment of typhoid fever. This study highlights the evolving threat of antibiotic resistance in S  Typhi and the value of antibiotic susceptibility testing and whole-genome sequencing in understanding emerging infectious diseases. We genetically characterized the XDR S  Typhi to investigate the phylogenetic relationship between these isolates and a global collection of S  Typhi isolates and to identify multiple genes linked to antibiotic resistance. This S  Typhi clone harbored a promiscuous antibiotic resistance plasmid previously identified in other enteric bacteria. The increasing antibiotic resistance in S  Typhi observed here adds urgency to the need for typhoid prevention measures. Copyright © 2018 Klemm et al.

Energy spectrum of cosmic-ray electrons at TeV energies.

PubMed

Aharonian, F; Akhperjanian, A G; Barres de Almeida, U; Bazer-Bachi, A R; Becherini, Y; Behera, B; Benbow, W; Bernlöhr, K; Boisson, C; Bochow, A; Borrel, V; Braun, I; Brion, E; Brucker, J; Brun, P; Brucker, R; Bulik, T; Büsching, I; Boutelier, T; Carrigan, S; Chadwick, P M; Charbonnier, A; Chaves, R C G; Cheesebrough, A; Chounet, L M; Clapson, A C; Coignet, G; Costamante, L; Dalton, M; Degrange, B; Deil, C; Dickinson, H J; Djannati-Ataï, A; Domainko, W; Drury, L O'C; Dubois, F; Dubus, G; Dyks, J; Dyrda, M; Egberts, K; Emmanoulopoulos, D; Espigat, P; Farnier, C; Feinstein, F; Fiasson, A; Fontaine, G; Füsling, M; Gabici, S; Gallant, Y A; Gérard, L; Giebels, B; Glicenstein, J F; Glück, B; Goret, P; Hadjichristidis, C; Hauser, D; Hauser, M; Heinz, S; Heinzelmann, G; Henri, G; Hermann, G; Hinton, J A; Hoffmann, A; Hofmann, W; Holleran, M; Hoppe, S; Horns, D; Jacholkowska, A; de Jager, O C; Jung, I; Katarzyński, K; Kaufmann, S; Kendziorra, E; Kerschhaggl, M; Khangulyan, D; Khélifi, B; Keogh, D; Komin, Nu; Kosack, K; Lamanna, G; Lenain, J P; Lohse, T; Marandon, V; Martin, J M; Martineau-Huynh, O; Marcowith, A; Maurin, D; McComb, T J L; Medina, C; Moderski, R; Moulin, E; Naumann-Godo, M; de Naurois, M; Nedbal, D; Nekrassov, D; Niemiec, J; Nolan, S J; Ohm, S; Olive, J F; de Oña Wilhelmi, E; Orford, K J; Osborne, J L; Ostrowski, M; Panter, M; Pedaletti, G; Pelletier, G; Petrucci, P O; Pita, S; Pühlhofer, G; Punch, M; Quirrenbach, A; Raubenheimer, B C; Raue, M; Rayner, S M; Renaud, M; Rieger, F; Ripken, J; Rob, L; Rosier-Lees, S; Rowell, G; Rudak, B; Rulten, C B; Ruppel, J; Sahakian, V; Santangelo, A; Schlickeiser, R; Schöck, F M; Schröder, R; Schwanke, U; Schwarzburg, S; Schwemmer, S; Shalchi, A; Skilton, J L; Sol, H; Spangler, D; Stawarz, Ł; Steenkamp, R; Stegmann, C; Superina, G; Tam, P H; Tavernet, J P; Terrier, R; Tibolla, O; van Eldik, C; Vasileiadis, G; Venter, C; Vialle, J P; Vincent, P; Vivier, M; Völk, H J; Volpe, F; Wagner, S J; Ward, M; Zdziarski, A A; Zech, A

2008-12-31

The very large collection area of ground-based gamma-ray telescopes gives them a substantial advantage over balloon or satellite based instruments in the detection of very-high-energy (>600 GeV) cosmic-ray electrons. Here we present the electron spectrum derived from data taken with the High Energy Stereoscopic System (H.E.S.S.) of imaging atmospheric Cherenkov telescopes. In this measurement, the first of this type, we are able to extend the measurement of the electron spectrum beyond the range accessible to direct measurements. We find evidence for a substantial steepening in the energy spectrum above 600 GeV compared to lower energies.

New directions for psychiatric rehabilitation in the USA.

PubMed

Bond, G R; Drake, R E

2017-06-01

American researchers have led the world in developing, evaluating, and disseminating evidence-based psychiatric rehabilitation practices for people with serious mental illness. Paradoxically, however, the USA lags behind most industrialized nations in providing access to high-quality mental health and psychiatric services. This essay examines several evidence-based practices developed in the USA, the spread of these practices, the barriers to ensuring availability to people who could benefit from these services, and some promising directions for overcoming the barriers. Factors influencing the growth and sustainment of effective client-centred practices include the availability of adequate and stable funding, committed leadership, and the influence of vested interests. Two strategies for promoting the spread and sustainment of well-implemented evidence-based practices are the adoption of fidelity scales and learning communities.

A Novel Agonist of the TRIF Pathway Induces a Cellular State Refractory to Replication of Zika, Chikungunya, and Dengue Viruses

PubMed Central

Pryke, Kara M.; Abraham, Jinu; Sali, Tina M.; Gall, Bryan J.; Archer, Iris; Liu, Andrew; Bambina, Shelly; Baird, Jason; Gough, Michael; Chakhtoura, Marita; Haddad, Elias K.; Kirby, Ilsa T.; Nilsen, Aaron; Streblow, Daniel N.; Hirsch, Alec J.; Smith, Jessica L.

2017-01-01

ABSTRACT The ongoing concurrent outbreaks of Zika, Chikungunya, and dengue viruses in Latin America and the Caribbean highlight the need for development of broad-spectrum antiviral treatments. The type I interferon (IFN) system has evolved in vertebrates to generate tissue responses that actively block replication of multiple known and potentially zoonotic viruses. As such, its control and activation through pharmacological agents may represent a novel therapeutic strategy for simultaneously impairing growth of multiple virus types and rendering host populations resistant to virus spread. In light of this strategy’s potential, we undertook a screen to identify novel interferon-activating small molecules. Here, we describe 1-(2-fluorophenyl)-2-(5-isopropyl-1,3,4-thiadiazol-2-yl)-1,2-dihydrochromeno[2,3-c]pyrrole-3,9-dione, which we termed AV-C. Treatment of human cells with AV-C activates innate and interferon-associated responses that strongly inhibit replication of Zika, Chikungunya, and dengue viruses. By utilizing genome editing, we investigated the host proteins essential to AV-C-induced cellular states. This showed that the compound requires a TRIF-dependent signaling cascade that culminates in IFN regulatory factor 3 (IRF3)-dependent expression and secretion of type I interferon to elicit antiviral responses. The other canonical IRF3-terminal adaptor proteins STING and IPS-1/MAVS were dispensable for AV-C-induced phenotypes. However, our work revealed an important inhibitory role for IPS-1/MAVS, but not TRIF, in flavivirus replication, implying that TRIF-directed viral evasion may not occur. Additionally, we show that in response to AV-C, primary human peripheral blood mononuclear cells secrete proinflammatory cytokines that are linked with establishment of adaptive immunity to viral pathogens. Ultimately, synthetic innate immune activators such as AV-C may serve multiple therapeutic purposes, including direct antimicrobial responses and facilitation of pathogen-directed adaptive immunity. PMID:28465426

GenomeGems: evaluation of genetic variability from deep sequencing data

PubMed Central

2012-01-01

Background Detection of disease-causing mutations using Deep Sequencing technologies possesses great challenges. In particular, organizing the great amount of sequences generated so that mutations, which might possibly be biologically relevant, are easily identified is a difficult task. Yet, for this assignment only limited automatic accessible tools exist. Findings We developed GenomeGems to gap this need by enabling the user to view and compare Single Nucleotide Polymorphisms (SNPs) from multiple datasets and to load the data onto the UCSC Genome Browser for an expanded and familiar visualization. As such, via automatic, clear and accessible presentation of processed Deep Sequencing data, our tool aims to facilitate ranking of genomic SNP calling. GenomeGems runs on a local Personal Computer (PC) and is freely available at http://www.tau.ac.il/~nshomron/GenomeGems. Conclusions GenomeGems enables researchers to identify potential disease-causing SNPs in an efficient manner. This enables rapid turnover of information and leads to further experimental SNP validation. The tool allows the user to compare and visualize SNPs from multiple experiments and to easily load SNP data onto the UCSC Genome browser for further detailed information. PMID:22748151

Spatial and spectral characteristics of the distribution post-filamentation zone of femtosecond laser pulses

NASA Astrophysics Data System (ADS)

Apeksimov, D. V.; Zemlyanov, A. A.; Iglakova, A. N.; Kabanov, A. M.; Kuchinskaya, O. I.; Matvienko, G. G.; Oshlakov, V. K.; Petrov, A. V.

2017-11-01

The transverse structure formation processes of a laser beam after multiple filamentation were investigated. It is shown that the spectra of post-filamentation light channels (PFC), rings and beam differ substantially. The spectrum of PFC has a significant and symmetrical spectral broadening and covers a range of 600-1100 nm. The broadening of the spectrum of the rings is asymmetric and is directed mainly to the short-wavelength region of the spectrum. The broadening data are stable and do not change when moving away from the multiple filamentation zone. The annular structure of radiation in the cross section of the beam is formed around individual filaments within the region of multiple filamentation, and at a distance of tens of meters from it begins to form a common ring structure surrounding postfilamentation channels.

Performance Comparison of Bench-Top Next Generation Sequencers Using Microdroplet PCR-Based Enrichment for Targeted Sequencing in Patients with Autism Spectrum Disorder

PubMed Central

Okamoto, Nobuhiko; Nakashima, Mitsuko; Tsurusaki, Yoshinori; Miyake, Noriko; Saitsu, Hirotomo; Matsumoto, Naomichi

2013-01-01

Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum disorder (ASD). We assessed the performance of the bench-top Ion Torrent PGM and Illumina MiSeq platforms as optimized solutions for mutation detection, using microdroplet PCR-based enrichment of 62 ASD associated genes. Ten patients with known mutations were sequenced using NGS to validate the sensitivity of our method. The overall read quality was better with MiSeq, largely because of the increased indel-related error associated with PGM. The sensitivity of SNV detection was similar between the two platforms, suggesting they are both suitable for SNV detection in the human genome. Next, we used these methods to analyze 28 patients with ASD, and identified 22 novel variants in genes associated with ASD, with one mutation detected by MiSeq only. Thus, our results support the combination of target gene enrichment and NGS as a valuable molecular method for investigating rare variants in ASD. PMID:24066114

A Direct TeX-to-Braille Transcribing Method

ERIC Educational Resources Information Center

Papasalouros, Andreas; Tsolomitis, Antonis

2017-01-01

The TeX/LaTeX typesetting system is the most wide-spread system for creating documents in Mathematics and Science. However, no reliable tool exists to this day for automatically transcribing documents from the above formats into Braille/Nemeth code. Thus, visually impaired students of related fields do not have access to the bulk of study material…

Research on synchronization technology of frequency hopping communication system

NASA Astrophysics Data System (ADS)

Zhao, Xiangwu; Quan, Houde; Cui, Peizhang

2018-05-01

Frequency Hopping (FH) communication is a technology of spread spectrum communication. It has strong anti-interference, anti-interception and security capabilities, and has been widely applied in the field of communications. Synchronization technology is one of the most crucial technologies in frequency hopping communication. The speed of synchronization establishment and the reliability of synchronous system directly affect the performance of frequency hopping communication system. Therefore, the research of synchronization technology in frequency hopping communication has important value.

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

PubMed Central

Sugathan, Aarathi; Biagioli, Marta; Golzio, Christelle; Erdin, Serkan; Blumenthal, Ian; Manavalan, Poornima; Ragavendran, Ashok; Brand, Harrison; Lucente, Diane; Miles, Judith; Sheridan, Steven D.; Stortchevoi, Alexei; Kellis, Manolis; Haggarty, Stephen J.; Katsanis, Nicholas; Gusella, James F.; Talkowski, Michael E.

2014-01-01

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P < 10−8) and CHD8-bound genes (P = 0.0043), which align with previously identified coexpression modules during fetal development. We also find an intriguing enrichment of cancer-related gene sets among CHD8-bound genes (P < 10−10). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene-expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis. PMID:25294932

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

PubMed Central

Quick, Josh; Grubaugh, Nathan D; Pullan, Steven T; Claro, Ingra M; Smith, Andrew D; Gangavarapu, Karthik; Oliveira, Glenn; Robles-Sikisaka, Refugio; Rogers, Thomas F; Beutler, Nathan A; Burton, Dennis R; Lewis-Ximenez, Lia Laura; de Jesus, Jaqueline Goes; Giovanetti, Marta; Hill, Sarah; Black, Allison; Bedford, Trevor; Carroll, Miles W; Nunes, Marcio; Alcantara, Luiz Carlos; Sabino, Ester C; Baylis, Sally A; Faria, Nuno; Loose, Matthew; Simpson, Jared T; Pybus, Oliver G; Andersen, Kristian G; Loman, Nicholas J

2018-01-01

Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples without isolation remains challenging for viruses such as Zika, where metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence complete genomes comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimised library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved starting with clinical samples in 1-2 days following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. PMID:28538739

Telehealth delivery of cognitive-behavioral intervention to youth with autism spectrum disorder and anxiety: A pilot study

PubMed Central

Hepburn, Susan L; Blakeley-Smith, Audrey; Wolff, Brian; Reaven, Judy A

2015-01-01

Youth with autism spectrum disorders frequently experience significant symptoms of anxiety. Empirically supported psychosocial interventions exist, yet access is limited, especially for families in rural areas. Telehealth (i.e. videoconferencing) has potential to reduce barriers to access to care; however, little is known about the feasibility or efficacy of directly intervening with youth with autism spectrum disorders through this modality. This study details the pilot testing of a telehealth version of an empirically supported intervention targeting anxiety in youth with autism spectrum disorders. The primary focus of this study is on feasibility, with evaluation of outcomes as a starting point for future randomized trials. In all, 33 families of youth with autism spectrum disorders and significant anxiety symptoms participated in this study (Telehealth Facing Your Fears (FYF) Intervention: n = 17; Wait-list control: n = 16). Youth of all functioning levels were included. Acceptability was strong; however, the usability of the technology was problematic for some families and impeded some sessions significantly. Fidelity of the telehealth version to the critical elements of the original, in vivo version was excellent. More work is needed to improve delivery of exposure practices and parent coaching. Preliminary efficacy analyses are promising, with improvements observed in youth anxiety over time (relative to a comparison group waiting for live intervention) and parent sense of competence (within group). Clearly, stronger designs are necessary to evaluate efficacy sufficiently; however, this study does provide support for further investigation of clinic-to-home videoconferencing as a direct intervention tool for youth with autism spectrum disorders and their parents. PMID:25896267

Telehealth delivery of cognitive-behavioral intervention to youth with autism spectrum disorder and anxiety: A pilot study.

PubMed

Hepburn, Susan L; Blakeley-Smith, Audrey; Wolff, Brian; Reaven, Judy A

2016-02-01

Youth with autism spectrum disorders frequently experience significant symptoms of anxiety. Empirically supported psychosocial interventions exist, yet access is limited, especially for families in rural areas. Telehealth (i.e. videoconferencing) has potential to reduce barriers to access to care; however, little is known about the feasibility or efficacy of directly intervening with youth with autism spectrum disorders through this modality. This study details the pilot testing of a telehealth version of an empirically supported intervention targeting anxiety in youth with autism spectrum disorders. The primary focus of this study is on feasibility, with evaluation of outcomes as a starting point for future randomized trials. In all, 33 families of youth with autism spectrum disorders and significant anxiety symptoms participated in this study (Telehealth Facing Your Fears (FYF) Intervention: n = 17; Wait-list control: n = 16). Youth of all functioning levels were included. Acceptability was strong; however, the usability of the technology was problematic for some families and impeded some sessions significantly. Fidelity of the telehealth version to the critical elements of the original, in vivo version was excellent. More work is needed to improve delivery of exposure practices and parent coaching. Preliminary efficacy analyses are promising, with improvements observed in youth anxiety over time (relative to a comparison group waiting for live intervention) and parent sense of competence (within group). Clearly, stronger designs are necessary to evaluate efficacy sufficiently; however, this study does provide support for further investigation of clinic-to-home videoconferencing as a direct intervention tool for youth with autism spectrum disorders and their parents. © The Author(s) 2015.

MILCOM '85 - Military Communications Conference, Boston, MA, October 20-23, 1985, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

The present conference on the development status of communications systems in the context of electronic warfare gives attention to topics in spread spectrum code acquisition, digital speech technology, fiber-optics communications, free space optical communications, the networking of HF systems, and applications and evaluation methods for digital speech. Also treated are issues in local area network system design, coding techniques and applications, technology applications for HF systems, receiver technologies, software development status, channel simultion/prediction methods, C3 networking spread spectrum networks, the improvement of communication efficiency and reliability through technical control methods, mobile radio systems, and adaptive antenna arrays. Finally, communications system cost analyses, spread spectrum performance, voice and image coding, switched networks, and microwave GaAs ICs, are considered.

Spectrum Efficiency Through Dynamic Spectrum Access Techniques (Briefing Charts)

DTIC Science & Technology

2014-06-01

Telemetry Data Sources IP BASED TELEMETRY STATION Flow control • Volume- based • Credit- based • Rate- based Signaling using custom protocols or standards...Responsible for all T&E infrastructure assessment within the Major Range and Test Facility Base (MRTFB) DoD Directive 3200.11 • Administer three...Memorandum Unleashing of the Wireless Broadband Revolution THE WHY: Based on the view that “we are now beginning the next transformation in

Hot-spot evolution and the global tectonics of Venus

NASA Astrophysics Data System (ADS)

Phillips, R. J.; Grimm, R. E.; Malin, M. C.

1991-05-01

The global tectonics of Venus may be dominated by plumes rising from the mantle and impinging on the lithosphere, giving rise to hot spots. Global sea-floor spreading does not take place, but direct convective coupling of mantle flow fields to the lithosphere leads to regional-scale deformation and may allow lithospheric transport on a limited scale. A hot-spot evolutionary sequence comprises (1) a broad domal uplift resulting from a rising mantle plume, (2) massive partial melting in the plume head and generation of a thickened crust or crustal plateau, (3) collapse of dynamic topography, and (4) creep spreading of the crustal plateau. Crust on Venus is produced by gradual vertical differentiation with little recycling rather than by the rapid horizontal creation and consumption characteristic of terrestrial sea-floor spreading.

Hot-spot evolution and the global tectonics of Venus

NASA Technical Reports Server (NTRS)

Phillips, Roger J.; Grimm, Robert E.; Malin, Michael C.

1991-01-01

The global tectonics of Venus may be dominated by plumes rising from the mantle and impinging on the lithosphere, giving rise to hot spots. Global sea-floor spreading does not take place, but direct convective coupling of mantle flow fields to the lithosphere leads to regional-scale deformation and may allow lithospheric transport on a limited scale. A hot-spot evolutionary sequence comprises (1) a broad domal uplift resulting from a rising mantle plume, (2) massive partial melting in the plume head and generation of a thickened crust or crustal plateau, (3) collapse of dynamic topography, and (4) creep spreading of the crustal plateau. Crust on Venus is produced by gradual vertical differentiation with little recycling rather than by the rapid horizontal creation and consumption characteristic of terrestrial sea-floor spreading.

Hot-spot evolution and the global tectonics of venus.

PubMed

Phillips, R J; Grimm, R E; Malin, M C

1991-05-03

The global tectonics of Venus may be dominated by plumes rising from the mantle and impinging on the lithosphere, giving rise to hot spots. Global sea-floor spreading does not take place, but direct convective coupling of mantle flow fields to the lithosphere leads to regional-scale deformation and may allow lithospheric transport on a limited scale. A hot-spot evolutionary sequence comprises (i) a broad domal uplift resulting from a rising mantle plume, (ii) massive partial melting in the plume head and generation of a thickened crust or crustal plateau, (iii) collapse of dynamic topography, and (iv) creep spreading of the crustal plateau. Crust on Venus is produced by gradual vertical differentiation with little recycling rather than by the rapid horizontal creation and consumption characteristic of terrestrial sea-floor spreading.

High Prevalence of Escherichia coli-Producing CTX-M-15 Extended-Spectrum Beta-Lactamases in Poultry and Human Clinical Isolates in Romania.

PubMed

Maciuca, Iuliana E; Williams, Nicola J; Tuchilus, Cristina; Dorneanu, Olivia; Guguianu, Eleonora; Carp-Carare, Catalin; Rimbu, Cristina; Timofte, Dorina

2015-12-01

Use of antibiotics in food animals may contribute to development and spread of resistant organisms, particularly so in some countries. The aim of this study was two-fold; first, to establish the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in chicken production in a region within Romania. Second, to study the relatedness of ESBL-producing E. coli isolates recovered from broilers, abattoir workers where the chickens were slaughtered and from the human clinical specimens from two regional hospitals. The results indicated a very high (69%) rate of carriage of ESBL and AmpC-producing E. coli in chickens with 36% CTX-M producers. Sequencing showed that chickens in Romania have the highest worldwide prevalence (53%) of blaCTX-M-15 reported in poultry E. coli isolates. The majority (53%) of the extended-spectrum cephalosporin-resistant E. coli carried plasmid-mediated blaampC genes, mostly blaCMY-2 type, one of the highest prevalences reported in Europe. The predominant CTX-M type found in the human clinical E. coli isolates was blaCTX-M-15 and most isolates coharbored blaOXA-1, blaTEM, and aac(6')-ib-cr. The majority (60%) of the human clinical isolates belonged to the pandemic virulent clone B2-ST131. The clonal relationship between broiler and the human CTX-M-producing E. coli isolates was assessed by macrorestriction pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), which indicated strain diversity with no common STs found between human and poultry isolates. Moreover, IncI1 was the most prevalent replicon found in broiler ESBL-producing E. coli isolates and also in transconjugants, indicating that plasmids and not clonal spread may play a role in the transfer of blaCTX-M genes. This study identifies a high prevalence of ESBL-producing E. coli from broiler chickens in Romania with a high occurrence incidence of blaCTX-M-15, which reflects the main ESBL type found in human E. coli infections in this country.

Development and evaluation of clicker methodology for introductory physics courses

NASA Astrophysics Data System (ADS)

Lee, Albert H.

Many educators understand that lectures are cost effective but not learning efficient, so continue to search for ways to increase active student participation in this traditionally passive learning environment. In-class polling systems, or "clickers", are inexpensive and reliable tools allowing students to actively participate in lectures by answering multiple-choice questions. Students assess their learning in real time by observing instant polling summaries displayed in front of them. This in turn motivates additional discussions which increase the opportunity for active learning. We wanted to develop a comprehensive clicker methodology that creates an active lecture environment for a broad spectrum of students taking introductory physics courses. We wanted our methodology to incorporate many findings of contemporary learning science. It is recognized that learning requires active construction; students need to be actively involved in their own learning process. Learning also depends on preexisting knowledge; students construct new knowledge and understandings based on what they already know and believe. Learning is context dependent; students who have learned to apply a concept in one context may not be able to recognize and apply the same concept in a different context, even when both contexts are considered to be isomorphic by experts. On this basis, we developed question sequences, each involving the same concept but having different contexts. Answer choices are designed to address students preexisting knowledge. These sequences are used with the clickers to promote active discussions and multiple assessments. We have created, validated, and evaluated sequences sufficient in number to populate all of introductory physics courses. Our research has found that using clickers with our question sequences significantly improved student conceptual understanding. Our research has also found how to best measure student conceptual gain using research-based instruments. Finally, we discovered that students need to have full access to the question sequences after lectures to reap the maximum benefit. Chapter 1 provides an introduction to our research. Chapter 2 provides a literature review relevant for our research. Chapter 3 discusses the creation of the clicker question sequences. Chapter 4 provides a picture of the validation process involving both physics experts and the introductory physics students. Chapter 5 describes how the sequences have been used with clickers in lectures. Chapter 6 provides the evaluation of the effectiveness of the clicker methodology. Chapter 7 contains a brief summary of research results and conclusions.

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico.

PubMed

Thézé, Julien; Li, Tony; du Plessis, Louis; Bouquet, Jerome; Kraemer, Moritz U G; Somasekar, Sneha; Yu, Guixia; de Cesare, Mariateresa; Balmaseda, Angel; Kuan, Guillermina; Harris, Eva; Wu, Chieh-Hsi; Ansari, M Azim; Bowden, Rory; Faria, Nuno R; Yagi, Shigeo; Messenger, Sharon; Brooks, Trevor; Stone, Mars; Bloch, Evan M; Busch, Michael; Muñoz-Medina, José E; González-Bonilla, Cesar R; Wolinsky, Steven; López, Susana; Arias, Carlos F; Bonsall, David; Chiu, Charles Y; Pybus, Oliver G

2018-06-13

The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Psychiatric rehabilitation education for physicians.

PubMed

Rudnick, Abraham; Eastwood, Diane

2013-06-01

As part of a rapidly spreading reform toward recovery-oriented services, mental health care systems are adopting Psychiatric/Psychosocial Rehabilitation (PSR). Accordingly, PSR education and training programs are now available and accessible. Although psychiatrists and sometimes other physicians (such as family physicians) provide important services to people with serious mental illnesses and may, therefore, need knowledge and skill in PSR, it seems that the medical profession has been slow to participate in PSR education. Based on our experience working in Canada as academic psychiatrists who are also Certified Psychiatric Rehabilitation Practitioners (CPRPs), we offer descriptions of several Canadian initiatives that involve physicians in PSR education. Multiple frameworks guide PSR education for physicians. First, guidance is provided by published PSR principles, such as the importance of self-determination (www.psrrpscanada.ca). Second, guidance is provided by adult education (andragogy) principles, emphasizing the importance of addressing attitudes in addition to knowledge and skills (Knowles, Holton, & Swanson, 2011). Third, guidance in Canada is provided by Canadian Medical Education Directives for Specialists (CanMEDS) principles, which delineate the multiple roles of physicians beyond that of medical expert (Frank, 2005) and have recently been adopted in Australia (Boyce, Spratt, Davies, & McEvoy, 2011). (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Multiple Sclerosis in Malaysia: Demographics, Clinical Features, and Neuroimaging Characteristics

PubMed Central

Viswanathan, S.; Rose, N.; Masita, A.; Dhaliwal, J. S.; Puvanarajah, S. D.; Rafia, M. H.; Muda, S.

2013-01-01

Background. Multiple sclerosis (MS) is an uncommon disease in multiracial Malaysia. Diagnosing patients with idiopathic inflammatory demyelinating diseases has been greatly aided by the evolution in diagnostic criterion, the identification of new biomarkers, and improved accessibility to neuroimaging in the country. Objectives. To investigate the spectrum of multiple sclerosis in Malaysia. Methods. Retrospective analysis with longitudinal follow-up of patients referred to a single tertiary medical center with neurology services in Malaysia. Results. Out of 245 patients with idiopathic inflammatory demyelinating disease, 104 patients had multiple sclerosis. Female to male ratio was 5 : 1. Mean age at onset was 28.6 ± 9.9 years. The Malays were the predominant racial group affected followed by the Chinese, Indians, and other indigenous groups. Subgroup analysis revealed more Chinese having neuromyelitis optica and its spectrum disorders rather than multiple sclerosis. Positive family history was reported in 5%. Optic neuritis and myelitis were the commonest presentations at onset of disease, and relapsing remitting course was the commonest disease pattern observed. Oligoclonal band positivity was 57.6%. At disease onset, 61.5% and 66.4% fulfilled the 2005 and 2010 McDonald's criteria for dissemination in space. Mean cord lesion length was 1.86 ± 1.65 vertebral segments in the relapsing remitting group as opposed to 6.25 ± 5.18 vertebral segments in patients with neuromyelitis optica and its spectrum disorders. Conclusion. The spectrum of multiple sclerosis in Malaysia has changed over the years. Further advancement in diagnostic criteria will no doubt continue to contribute to the evolution of this disease here. PMID:24455266

Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences.

PubMed

Guo, Guo-Ye; Chen, Fang; Shi, Xiao-Dong; Tian, Yin-Shuai; Yu, Mao-Qun; Han, Xue-Qin; Yuan, Li-Chun; Zhang, Ying

2016-01-01

Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Iterative pass optimization of sequence data

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

A spread-spectrum modem using constant envelope BPSK for a mobile satellite communications terminal

NASA Technical Reports Server (NTRS)

Iizuka, N.; Yamashita, A.; Takenaka, S.; Morikawa, E.; Ikegami, T.

1990-01-01

This paper describes a 5-kilobit/s spread spectrum modem with a 1.275 mega-Hz chip rate for mobile satellite communications. We used a Viterbi decoder with a coding gain of 7.8 dB at a BER of 10(exp -5) to decrease the required receiver power. This reduces the cost of communication services. The spread spectrum technique makes the modem immune to terrestrial radio signals and keeps it from causing interference in terrestrial radio systems. A class C power amplifier reduces the modem's power consumption. To avoid nonlinear distortion caused by the amplifier, the envelope of the input signal is kept constant by adding quadrature channel signal to the BPSK signal. To simulate the worst case, we measured the modem's output spectrum using a limiting amplifier instead of the class C amplifier, and found that 99 percent of the spectral power was confined to the specified 2.55 mega-Hz bandwidth.

Procedure to Measure Effect of Excess Body Mass on Musculoskeleture: I. Foundation

NASA Astrophysics Data System (ADS)

Shaibani, Saami J.

2008-03-01

Increasing levels of obesity are having an increasingly adverse impact on individual and societal health. While much effort is directed to the harmful consequences of excess body mass on the cardiovascular system, there is relatively little research on how obesity compromises the response of the musculoskeletal system across the complete range of body types. This shortfall is addressed here by a comprehensive physics-based approach to produce a wide spectrum of representative adults, who are carefully chosen to cover both sexes, a full spread of percentiles for stature, and multiple weight levels. The latter encompass healthy, overweight and obese conditions defined by the standard parameter, body mass index (BMI). The distribution of body mass is computed for female and male subjects at all height percentiles and values of BMI to generate a detailed description of a diverse population. This cohort can then be examined for more advanced aspects of musculoskeleture, an important precursor for which is included here by calculating the extent of excess body mass at each body part as a function of BMI.

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

PubMed

Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian

2013-05-03

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

rrndb: the Ribosomal RNA Operon Copy Number Database

PubMed Central

Klappenbach, Joel A.; Saxman, Paul R.; Cole, James R.; Schmidt, Thomas M.

2001-01-01

The Ribosomal RNA Operon Copy Number Database (rrndb) is an Internet-accessible database containing annotated information on rRNA operon copy number among prokaryotes. Gene redundancy is uncommon in prokaryotic genomes, yet the rRNA genes can vary from one to as many as 15 copies. Despite the widespread use of 16S rRNA gene sequences for identification of prokaryotes, information on the number and sequence of individual rRNA genes in a genome is not readily accessible. In an attempt to understand the evolutionary implications of rRNA operon redundancy, we have created a phylogenetically arranged report on rRNA gene copy number for a diverse collection of prokaryotic microorganisms. Each entry (organism) in the rrndb contains detailed information linked directly to external websites including the Ribosomal Database Project, GenBank, PubMed and several culture collections. Data contained in the rrndb will be valuable to researchers investigating microbial ecology and evolution using 16S rRNA gene sequences. The rrndb web site is directly accessible on the WWW at http://rrndb.cme.msu.edu. PMID:11125085

USMC ISR: Preparing for the A2AD Threat

DTIC Science & Technology

2014-06-13

millimeter waves, high - power microwaves, lasers or electromagnetic pulses (Brimley 2013, 15). Replacing modern day munitions, directed- energy ...space and cyber capabilities” (JCS, 26). The precept further states the need to protect access to the electromagnetic spectrum. Given the high cost...is the “division of electronic warfare involving the use of electromagnetic , directed energy , or antiradiation weapons to attack personnel, facilities

Outbreak of vancomycin-resistant enterococcus colonization among pediatric oncology patients.

PubMed

Nolan, Sheila M; Gerber, Jeffrey S; Zaoutis, Theoklis; Prasad, Priya; Rettig, Susan; Gross, Kimberly; McGowan, Karin L; Reilly, Anne F; Coffin, Susan E

2009-04-01

To detect the burden of vancomycin-resistant Enterococcus (VRE) colonization among pediatric oncology patients and to determine risk factors for VRE acquisition. Retrospective case-control study. The Children's Hospital of Philadelphia. Pediatric oncology patients hospitalized from June 2006 through December 2007. Prevalence surveys revealed an increased VRE burden among pediatric oncology patients. For the case-control study, the 16 case patients were pediatric oncology patients who had 1 stool sample negative for VRE at screening before having a stool sample positive for VRE at screening; the 62 control patients had 2 consecutive screenings in which stool samples were negative for VRE. Case and control patients were matched on the duration of the interval between screens. Analyses were performed to determine the association between multiple exposures and VRE acquisition. The prevalence survey revealed that 5 (9.6%) of 52 patients had unsuspected VRE colonization at the time of hospitalization. Multivariate analysis identified a lack of empirical contact precautions (odds ratio [OR], 17.16 [95% confidence interval {CI}, 1.49-198.21]; P= .02) and the presence of a gastrointestinal device (OR, 4.03 [95% CI, 1.04-15.56]; P= .04) as significant risk factors for acquisition of VRE. Observations in the interventional radiology department revealed that staff could not access the portions of the electronic medical record in which isolation precautions were documented. Simple interventions that granted access and that trained interventional radiology staff to review the need for precautions, coupled with enhanced infection control practices, interrupted ongoing transmission and reduced the proportion of VRE screens that were positive to 15 (1.2%) of 1,270. Inadequate communication with regard to infection control precautions can increase the risk of transmission of epidemiologically important organisms, particularly when patients receive care at multiple clinic locations. Adherence to infection control practices across the spectrum of care may limit the spread of resistant organisms.

Outbreak of Vancomycin-Resistant Enterococcus Colonization Among Pediatric Oncology Patients

PubMed Central

Nolan, Sheila M.; Gerber, Jeffrey S.; Zaoutis, Theoklis; Prasad, Priya; Rettig, Susan; Gross, Kimberly; McGowan, Karin L.; Reilly, Anne F.; Coffin, Susan E.

2010-01-01

OBJECTIVE To detect the burden of vancomycin-resistant Enterococcus (VRE) colonization among pediatric oncology patients and to determine risk factors for VRE acquisition. DESIGN Retrospective case-control study. SETTING The Children’s Hospital of Philadelphia. PATIENTS Pediatric oncology patients hospitalized from June 2006 through December 2007. METHODS Prevalence surveys revealed an increased VRE burden among pediatric oncology patients. For the case-control study, the 16 case patients were pediatric oncology patients who had 1 stool sample negative for VRE at screening before having a stool sample positive for VRE at screening; the 62 control patients had 2 consecutive screenings in which stool samples were negative for VRE. Case and control patients were matched on the duration of the interval between screens. Analyses were performed to determine the association between multiple exposures and VRE acquisition. RESULTS The prevalence survey revealed that 5 (9.6%) of 52 patients had unsuspected VRE colonization at the time of hospitalization. Multivariate analysis identified a lack of empirical contact precautions (odds ratio [OR], 17.16 [95% confidence interval {CI}, 1.49–198.21]; P = .02) and the presence of a gastrointestinal device (OR, 4.03 [95% CI, 1.04–15.56]; P = .04) as significant risk factors for acquisition of VRE. Observations in the interventional radiology department revealed that staff could not access the portions of the electronic medical record in which isolation precautions were documented. Simple interventions that granted access and that trained interventional radiology staff to review the need for precautions, coupled with enhanced infection control practices, interrupted ongoing transmission and reduced the proportion of VRE screens that were positive to 15 (1.2%) of 1,270. CONCLUSIONS Inadequate communication with regard to infection control precautions can increase the risk of transmission of epidemiologically important organisms, particularly when patients receive care at multiple clinic locations. Adherence to infection control practices across the spectrum of care may limit the spread of resistant organisms. PMID:19239375

Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110.

PubMed

Fomukong, N G; Tang, T H; al-Maamary, S; Ibrahim, W A; Ramayah, S; Yates, M; Zainuddin, Z F; Dale, J W

1994-12-01

DNA fingerprinting with the insertion sequence IS6110 (also known as IS986) has become established as a major tool for investigating the spread of tuberculosis. Most strains of Mycobacterium tuberculosis have multiple copies of IS6110, but a small minority carry a single copy only. We have examined selected strains from Malaysia, Tanzania and Oman, in comparison with M. bovis isolates and BCG strains carrying one or two copies of IS6110. The insertion sequence appears to be present in the same position in all these strains, which suggests that in these organisms the element is defective in transposition and that the loss of transposability may have occurred at an early stage in the evolution of the M. tuberculosis complex.

Agile waveforms for joint SAR-GMTI processing

NASA Astrophysics Data System (ADS)

Jaroszewski, Steven; Corbeil, Allan; McMurray, Stephen; Majumder, Uttam; Bell, Mark R.; Corbeil, Jeffrey; Minardi, Michael

2016-05-01

Wideband radar waveforms that employ spread-spectrum techniques were investigated and experimentally tested. The waveforms combine bi-phase coding with a traditional LFM chirp and are applicable to joint SAR-GMTI processing. After de-spreading, the received signals can be processed to support simultaneous GMTI and high resolution SAR imaging missions by airborne radars. The spread spectrum coding techniques can provide nearly orthogonal waveforms and offer enhanced operations in some environments by distributing the transmitted energy over a large instantaneous bandwidth. The LFM component offers the desired Doppler tolerance. In this paper, the waveforms are formulated and a shift-register approach for de-spreading the received signals is described. Hardware loop-back testing has shown the feasibility of using these waveforms in experimental radar test bed.

Genetic evolution and clinical impact in extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae.

PubMed

Chong, Yong; Ito, Yoshikiyo; Kamimura, Tomohiko

2011-10-01

The emergence of extended-spectrum β-lactamase (ESBL)-producing bacteria, particularly Escherichia coli and Klebsiella pneumoniae, is now a critical concern for the development of therapies against bacterial infection. ESBLs consist of three major genetic groups: TEM, SHV, and CTX-M types. Nosocomial infections due to TEM and SHV-producing K. pneumoniae strains were frequently documented until the late 1990s. The number of reports on community-acquired infections caused by CTX-M-producing E. coli strains have dramatically increased over the last decade; however, K. pneumoniae strains, of either the TEM or SHV types, are persistent and important ESBL producers. The spread of ESBL genes is associated with various mobile genetic elements, such as transposons, insertion sequences, and integrons. The rapid dissemination of ESBL genes of the CTX-M type may be related to highly complicated genetic structures. These structures harboring ESBL genes and mobile elements are found in a variety of plasmids, which often carry many other antibiotic resistance genes. Multidrug-resistant CTX-M-15-producing E. coli strains disseminate worldwide. Efficient mobile elements and plasmids may have accelerated the genetic diversity and the rapid spread of ESBL genes, and their genetic evolution has caused an emerging threat to the bacteria for which few effective drugs have been identified. Copyright © 2011 Elsevier B.V. All rights reserved.

MIPS: a database for genomes and protein sequences.

PubMed Central

Mewes, H W; Heumann, K; Kaps, A; Mayer, K; Pfeiffer, F; Stocker, S; Frishman, D

1999-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database. PMID:9847138

Ease of Access to List Items in Short-Term Memory Depends on the Order of the Recognition Probes

ERIC Educational Resources Information Center

Lange, Elke B.; Cerella, John; Verhaeghen, Paul

2011-01-01

We report data from 4 experiments using a recognition design with multiple probes to be matched to specific study positions. Items could be accessed rapidly, independent of set size, when the test order matched the study order (forward condition). When the order of testing was random, backward, or in a prelearned irregular sequence (reordered…

How do long-offset oceanic transforms adapt to plate motion changes? The example of the Western Pacific-Antarctic plate boundary

NASA Astrophysics Data System (ADS)

Lodolo, Emanuele; Coren, Franco; Ben-Avraham, Zvi

2013-03-01

Oceanic transform faults respond to changes in the direction of relative plate motion. Studies have shown that short-offset transforms generally adjust with slight bends near the ridge axis, while long-offset ones have a remarkably different behavior. The western Pacific-Antarctic plate boundary highlights these differences. A set of previously unpublished seismic profiles, in combination with magnetic anomaly identifications, shows how across a former, ~1250 km long transform (the Emerald Fracture Zone), plate motion changes have produced a complex geometric readjustment. Three distinct sections are recognized along this plate boundary: an eastern section, characterized by parallel, multiple fault strand lineaments; a central section, shallower than the rest of the ridge system, overprinted by a mantle plume track; and a western section, organized in a cascade of short spreading axes/transform lineaments. This configuration was produced by changes that occurred since 30 Ma in the Australia-Pacific relative plate motion, combined with a gradual clockwise change in Pacific-Antarctic plate motion. These events caused extension along the former Emerald Fracture Zone, originally linking the Pacific-Antarctic spreading ridge system with the Southeast Indian ridge. Then an intra-transform propagating ridge started to develop in response to a ~6 Ma change in the Pacific-Antarctic spreading direction. The close proximity of the Euler poles of rotation amplified the effects of the geometric readjustments that occurred along the transform system. This analysis shows that when a long-offset transform older than 20 Ma is pulled apart by changes in spreading velocity vectors, it responds with the development of multiple discrete, parallel fault strands, whereas in younger lithosphere, locally modified by thermal anisotropies, tensional stresses generate an array of spreading axes offset by closely spaced transforms.

A novel approach to tracking antigen-experienced CD4 T cells into functional compartments via tandem deep and shallow TCR clonotyping.

PubMed

Estorninho, Megan; Gibson, Vivienne B; Kronenberg-Versteeg, Deborah; Liu, Yuk-Fun; Ni, Chester; Cerosaletti, Karen; Peakman, Mark

2013-12-01

Extensive diversity in the human repertoire of TCRs for Ag is both a cornerstone of effective adaptive immunity that enables host protection against a multiplicity of pathogens and a weakness that gives rise to potential pathological self-reactivity. The complexity arising from diversity makes detection and tracking of single Ag-specific CD4 T cells (ASTs) involved in these immune responses challenging. We report a tandem, multistep process to quantify rare TCRβ-chain variable sequences of ASTs in large polyclonal populations. The approach combines deep high-throughput sequencing (HTS) within functional CD4 T cell compartments, such as naive/memory cells, with shallow, multiple identifier-based HTS of ASTs identified by activation marker upregulation after short-term Ag stimulation in vitro. We find that clonotypes recognizing HLA class II-restricted epitopes of both pathogen-derived Ags and self-Ags are oligoclonal and typically private. Clonotype tracking within an individual reveals private AST clonotypes resident in the memory population, as would be expected, representing clonal expansions (identical nucleotide sequence; "ultraprivate"). Other AST clonotypes share CDR3β amino acid sequences through convergent recombination and are found in memory populations of multiple individuals. Tandem HTS-based clonotyping will facilitate studying AST dynamics, epitope spreading, and repertoire changes that arise postvaccination and following Ag-specific immunotherapies for cancer and autoimmune disease.

Epidemic spreading with activity-driven awareness diffusion on multiplex network.

PubMed

Guo, Quantong; Lei, Yanjun; Jiang, Xin; Ma, Yifang; Huo, Guanying; Zheng, Zhiming

2016-04-01

There has been growing interest in exploring the interplay between epidemic spreading with human response, since it is natural for people to take various measures when they become aware of epidemics. As a proper way to describe the multiple connections among people in reality, multiplex network, a set of nodes interacting through multiple sets of edges, has attracted much attention. In this paper, to explore the coupled dynamical processes, a multiplex network with two layers is built. Specifically, the information spreading layer is a time varying network generated by the activity driven model, while the contagion layer is a static network. We extend the microscopic Markov chain approach to derive the epidemic threshold of the model. Compared with extensive Monte Carlo simulations, the method shows high accuracy for the prediction of the epidemic threshold. Besides, taking different spreading models of awareness into consideration, we explored the interplay between epidemic spreading with awareness spreading. The results show that the awareness spreading can not only enhance the epidemic threshold but also reduce the prevalence of epidemics. When the spreading of awareness is defined as susceptible-infected-susceptible model, there exists a critical value where the dynamical process on the awareness layer can control the onset of epidemics; while if it is a threshold model, the epidemic threshold emerges an abrupt transition with the local awareness ratio α approximating 0.5. Moreover, we also find that temporal changes in the topology hinder the spread of awareness which directly affect the epidemic threshold, especially when the awareness layer is threshold model. Given that the threshold model is a widely used model for social contagion, this is an important and meaningful result. Our results could also lead to interesting future research about the different time-scales of structural changes in multiplex networks.

Epidemic spreading with activity-driven awareness diffusion on multiplex network

NASA Astrophysics Data System (ADS)

Guo, Quantong; Lei, Yanjun; Jiang, Xin; Ma, Yifang; Huo, Guanying; Zheng, Zhiming

2016-04-01

There has been growing interest in exploring the interplay between epidemic spreading with human response, since it is natural for people to take various measures when they become aware of epidemics. As a proper way to describe the multiple connections among people in reality, multiplex network, a set of nodes interacting through multiple sets of edges, has attracted much attention. In this paper, to explore the coupled dynamical processes, a multiplex network with two layers is built. Specifically, the information spreading layer is a time varying network generated by the activity driven model, while the contagion layer is a static network. We extend the microscopic Markov chain approach to derive the epidemic threshold of the model. Compared with extensive Monte Carlo simulations, the method shows high accuracy for the prediction of the epidemic threshold. Besides, taking different spreading models of awareness into consideration, we explored the interplay between epidemic spreading with awareness spreading. The results show that the awareness spreading can not only enhance the epidemic threshold but also reduce the prevalence of epidemics. When the spreading of awareness is defined as susceptible-infected-susceptible model, there exists a critical value where the dynamical process on the awareness layer can control the onset of epidemics; while if it is a threshold model, the epidemic threshold emerges an abrupt transition with the local awareness ratio α approximating 0.5. Moreover, we also find that temporal changes in the topology hinder the spread of awareness which directly affect the epidemic threshold, especially when the awareness layer is threshold model. Given that the threshold model is a widely used model for social contagion, this is an important and meaningful result. Our results could also lead to interesting future research about the different time-scales of structural changes in multiplex networks.

UWB radar technique for arc detection in coaxial cables and waveguides

NASA Astrophysics Data System (ADS)

Maggiora, R.; Salvador, S.

2009-11-01

As spread spectrum technology has revolutionized the communications industry, Ultra Wide Band (UWB) technology is dramatically improving radar performances. These advanced signal processing techniques have been adapted to coaxial cables and waveguides to provide new features and enhanced performance on arc detection. UWB signals constituted by a sequence of chips (properly chosen to reduce side lobes and to improve detection accuracy) are transmitted along the transmission lines at a specified Pulse Repetition Frequency (PRF) and their echoes are received by means of directional couplers. The core of the receiver is an ultra high-speed correlator implemented in a Digital Signal Processor (DSP). When a target (arc) is detected, its position and its "radar cross section" are calculated to be able to provide the arc position along the transmission line and to be able to classify the type of detected arc. The "background scattering" is routinely extracted from the received signal at any pulse. This permits to be resilient to the background structure of transmission lines (bends, junctions, windows, etc.). Thanks to the localization feature, segmentation is also possible for creating sensed and non-sensed zones (for example, to be insensitive to antenna load variations).

Micro-miniature radio frequency transmitter for communication and tracking applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crutcher, R.I.; Emery, M.S.; Falter, K.G.

1996-12-31

A micro-miniature radio frequency (rf) transmitter has been developed and demonstrated by the Oak Ridge National Laboratory. The objective of the rf transmitter development was to maximize the transmission distance while drastically shrinking the overall transmitter size, including antenna. Based on analysis and testing, an application-specific integrated circuit (ASIC) with a 16-GHz gallium arsenide (GaAs) oscillator and integrated on-chip antenna was designed and fabricated using microwave monolithic integrated circuit (MMIC) technology. Details of the development and the results of various field tests will be discussed. The rf transmitter is applicable to covert surveillance and tracking scenarios due to its smallmore » size of 2.2 x 2.2 mm, including the antenna. Additionally, the 16-GHz frequency is well above the operational range of consumer-grade radio scanners, providing a degree of protection from unauthorized interception. Variations of the transmitter design have been demonstrated for tracking and tagging beacons, transmission of digital data, and transmission of real-time analog video from a surveillance camera. Preliminary laboratory measurements indicate adaptability to direct-sequence spread-spectrum transmission, providing a low probability of intercept and/or detection. Concepts related to law enforcement applications will be presented.« less

Method and apparatus for controlling multiple motors

DOEpatents

Jones, Rollin G.; Kortegaard, Bert L.; Jones, David F.

1987-01-01

A method and apparatus are provided for simultaneously controlling a plurality of stepper motors. Addressing circuitry generates address data for each motor in a periodic address sequence. Memory circuits respond to the address data for each motor by accessing a corresponding memory location containing a first operational data set functionally related to a direction for moving the motor, speed data, and rate of speed change. First logic circuits respond to the first data set to generate a motor step command. Second logic circuits respond to the command from the first logic circuits to generate a third data set for replacing the first data set in memory with a current operational motor status, which becomes the first data set when the motor is next addressed.

2-Step Maximum Likelihood Channel Estimation for Multicode DS-CDMA with Frequency-Domain Equalization

NASA Astrophysics Data System (ADS)

Kojima, Yohei; Takeda, Kazuaki; Adachi, Fumiyuki

Frequency-domain equalization (FDE) based on the minimum mean square error (MMSE) criterion can provide better downlink bit error rate (BER) performance of direct sequence code division multiple access (DS-CDMA) than the conventional rake combining in a frequency-selective fading channel. FDE requires accurate channel estimation. In this paper, we propose a new 2-step maximum likelihood channel estimation (MLCE) for DS-CDMA with FDE in a very slow frequency-selective fading environment. The 1st step uses the conventional pilot-assisted MMSE-CE and the 2nd step carries out the MLCE using decision feedback from the 1st step. The BER performance improvement achieved by 2-step MLCE over pilot assisted MMSE-CE is confirmed by computer simulation.

Performance Analysis of Blind Subspace-Based Signature Estimation Algorithms for DS-CDMA Systems with Unknown Correlated Noise

NASA Astrophysics Data System (ADS)

Zarifi, Keyvan; Gershman, Alex B.

2006-12-01

We analyze the performance of two popular blind subspace-based signature waveform estimation techniques proposed by Wang and Poor and Buzzi and Poor for direct-sequence code division multiple-access (DS-CDMA) systems with unknown correlated noise. Using the first-order perturbation theory, analytical expressions for the mean-square error (MSE) of these algorithms are derived. We also obtain simple high SNR approximations of the MSE expressions which explicitly clarify how the performance of these techniques depends on the environmental parameters and how it is related to that of the conventional techniques that are based on the standard white noise assumption. Numerical examples further verify the consistency of the obtained analytical results with simulation results.

Stars caught in the braking stage in young Magellanic Cloud clusters

NASA Astrophysics Data System (ADS)

D'Antona, Francesca; Milone, Antonino P.; Tailo, Marco; Ventura, Paolo; Vesperini, Enrico; di Criscienzo, Marcella

2017-08-01

The colour-magnitude diagrams of many Magellanic Cloud clusters (with ages up to 2 billion years) display extended turnoff regions where the stars leave the main sequence, suggesting the presence of multiple stellar populations with ages that may differ even by hundreds of millions of years 1,2,3 . A strongly debated question is whether such an extended turnoff is instead due to populations with different stellar rotations3,4,5,6 . The recent discovery of a 'split' main sequence in some younger clusters (~80-400 Myr) added another piece to this puzzle. The blue side of the main sequence is consistent with slowly rotating stellar models, and the red side consistent with rapidly rotating models7,8,9,10. However, a complete theoretical characterization of the observed colour-magnitude diagram also seemed to require an age spread9. We show here that, in the three clusters so far analysed, if the blue main-sequence stars are interpreted with models in which the stars have always been slowly rotating, they must be ~30% younger than the rest of the cluster. If they are instead interpreted as stars that were initially rapidly rotating but have later slowed down, the age difference disappears, and this 'braking' also helps to explain the apparent age differences of the extended turnoff. The age spreads in Magellanic Cloud clusters are thus a manifestation of rotational stellar evolution. Observational tests are suggested.

Dissemination of Novel Antimicrobial Resistance Mechanisms through the Insertion Sequence Mediated Spread of Metabolic Genes

PubMed Central

Furi, Leonardo; Haigh, Richard; Al Jabri, Zaaima J. H.; Morrissey, Ian; Ou, Hong-Yu; León-Sampedro, Ricardo; Martinez, Jose L.; Coque, Teresa M.; Oggioni, Marco R.

2016-01-01

The widely used biocide triclosan selectively targets FabI, the NADH-dependent trans-2-enoyl-acyl carrier protein (ACP) reductase, which is also an important target for the development of narrow spectrum antibiotics. The analysis of triclosan resistant Staphylococcus aureus isolates had previously shown that in about half of the strains, the mechanism of triclosan resistance consists on the heterologous duplication of the triclosan target gene due to the acquisition of an additional fabI allele derived from Staphylococcus haemolyticus (sh-fabI). In the current work, the genomic sequencing of 10 of these strains allowed the characterization of two novel composite transposons TnSha1 and TnSha2 involved in the spread of sh-fabI. TnSha1 harbors one copy of IS1272, whereas TnSha2 is a 11.7 kb plasmid carrying TnSha1 present either as plasmid or in an integrated form generally flanked by two IS1272 elements. The target and mechanism of integration for IS1272 and TnSha1 are novel and include targeting of DNA secondary structures, generation of blunt-end deletions of the stem-loop and absence of target duplication. Database analyses showed widespread occurrence of these two elements in chromosomes and plasmids, with TnSha1 mainly in S. aureus and with TnSha2 mainly in S. haemolyticus and S. epidermidis. The acquisition of resistance by means of an insertion sequence-based mobilization and consequent duplication of drug-target metabolic genes, as observed here for sh-fabI, is highly reminiscent of the situation with the ileS2 gene conferring mupirocin resistance, and the dfrA and dfrG genes conferring trimethoprim resistance both of which are mobilized by IS257. These three examples, which show similar mechanisms and levels of spread of metabolic genes linked to IS elements, highlight the importance of this genetic strategy for recruitment and rapid distribution of novel resistance mechanisms in staphylococci. PMID:27446047

Measuring Time-of-Flight in an Ultrasonic LPS System Using Generalized Cross-Correlation

PubMed Central

Villladangos, José Manuel; Ureña, Jesús; García, Juan Jesús; Mazo, Manuel; Hernández, Álvaro; Jiménez, Ana; Ruíz, Daniel; De Marziani, Carlos

2011-01-01

In this article, a time-of-flight detection technique in the frequency domain is described for an ultrasonic Local Positioning System (LPS) based on encoded beacons. Beacon transmissions have been synchronized and become simultaneous by means of the DS-CDMA (Direct-Sequence Code Division Multiple Access) technique. Every beacon has been associated to a 255-bit Kasami code. The detection of signal arrival instant at the receiver, from which the distance to each beacon can be obtained, is based on the application of the Generalized Cross-Correlation (GCC), by using the cross-spectral density between the received signal and the sequence to be detected. Prior filtering to enhance the frequency components around the carrier frequency (40 kHz) has improved estimations when obtaining the correlation function maximum, which implies an improvement in distance measurement precision. Positioning has been achieved by using hyperbolic trilateration, based on the Time Differences of Arrival (TDOA) between a reference beacon and the others. PMID:22346645

Measuring time-of-flight in an ultrasonic LPS system using generalized cross-correlation.

PubMed

Villladangos, José Manuel; Ureña, Jesús; García, Juan Jesús; Mazo, Manuel; Hernández, Alvaro; Jiménez, Ana; Ruíz, Daniel; De Marziani, Carlos

2011-01-01

In this article, a time-of-flight detection technique in the frequency domain is described for an ultrasonic local positioning system (LPS) based on encoded beacons. Beacon transmissions have been synchronized and become simultaneous by means of the DS-CDMA (direct-sequence code Division multiple access) technique. Every beacon has been associated to a 255-bit Kasami code. The detection of signal arrival instant at the receiver, from which the distance to each beacon can be obtained, is based on the application of the generalized cross-correlation (GCC), by using the cross-spectral density between the received signal and the sequence to be detected. Prior filtering to enhance the frequency components around the carrier frequency (40 kHz) has improved estimations when obtaining the correlation function maximum, which implies an improvement in distance measurement precision. Positioning has been achieved by using hyperbolic trilateration, based on the time differences of arrival (TDOA) between a reference beacon and the others.

Multiuser receiver for DS-CDMA signals in multipath channels: an enhanced multisurface method.

PubMed

Mahendra, Chetan; Puthusserypady, Sadasivan

2006-11-01

This paper deals with the problem of multiuser detection in direct-sequence code-division multiple-access (DS-CDMA) systems in multipath environments. The existing multiuser detectors can be divided into two categories: (1) low-complexity poor-performance linear detectors and (2) high-complexity good-performance nonlinear detectors. In particular, in channels where the orthogonality of the code sequences is destroyed by multipath, detectors with linear complexity perform much worse than the nonlinear detectors. In this paper, we propose an enhanced multisurface method (EMSM) for multiuser detection in multipath channels. EMSM is an intermediate piecewise linear detection scheme with a run-time complexity linear in the number of users. Its bit error rate performance is compared with existing linear detectors, a nonlinear radial basis function detector trained by the new support vector learning algorithm, and Verdu's optimal detector. Simulations in multipath channels, for both synchronous and asynchronous cases, indicate that it always outperforms all other linear detectors, performing nearly as well as nonlinear detectors.

A Continental-Wide Perspective: The Genepool of Nuclear Encoded Ribosomal DNA and Single-Copy Gene Sequences in North American Boechera (Brassicaceae)

PubMed Central

Kiefer, Christiane; Koch, Marcus A.

2012-01-01

74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data. PMID:22606266

Effect of Pointing Error on the BER Performance of an Optical CDMA FSO Link with SIK Receiver

NASA Astrophysics Data System (ADS)

Nazrul Islam, A. K. M.; Majumder, S. P.

2017-12-01

An analytical approach is presented for an optical code division multiple access (OCDMA) system over free space optical (FSO) channel considering the effect of pointing error between the transmitter and the receiver. Analysis is carried out with an optical sequence inverse keying (SIK) correlator receiver with intensity modulation and direct detection (IM/DD) to find the bit error rate (BER) with pointing error. The results are evaluated numerically in terms of signal-to-noise plus multi-access interference (MAI) ratio, BER and power penalty due to pointing error. It is noticed that the OCDMA FSO system is highly affected by pointing error with significant power penalty at a BER of 10-6 and 10-9. For example, penalty at BER 10-9 is found to be 9 dB corresponding to normalized pointing error of 1.4 for 16 users with processing gain of 256 and is reduced to 6.9 dB when the processing gain is increased to 1,024.

Relaxation of Distributed Data Aggregation for Underwater Acoustic Sensor Networks

DTIC Science & Technology

2014-03-31

2 3.1 Gossip algorithms for distributed averaging . . . . . . . . . . . . . . . . . 3 3.2 Distributed particle filtering...algorithm that had direct access to all of the measurements. We use gossip algorithms (discussed in Section 3.1) to diffuse information across the...2 3.1 Gossip algorithms for distributed averaging We begin by discussing gossip algorithms, which we use to synchronize and spread infor- mation

Resolution enhancement using a new multiple-pulse decoupling sequence for quadrupolar nuclei.

PubMed

Delevoye, L; Trébosc, J; Gan, Z; Montagne, L; Amoureux, J-P

2007-05-01

A new decoupling composite pulse sequence is proposed to remove the broadening on spin S=1/2 magic-angle spinning (MAS) spectra arising from the scalar coupling with a quadrupolar nucleus I. It is illustrated on the (31)P spectrum of an aluminophosphate, AlPO(4)-14, which is broadened by the presence of (27)Al/(31)P scalar couplings. The multiple-pulse (MP) sequence has the advantage over the continuous wave (CW) irradiation to efficiently annul the scalar dephasing without reintroducing the dipolar interaction. The MP decoupling sequence is first described in a rotor-synchronised version (RS-MP) where one parameter only needs to be adjusted. It clearly avoids the dipolar recoupling in order to achieve a better resolution than using the CW sequence. In a second improved version, the MP sequence is experimentally studied in the vicinity of the perfect rotor-synchronised conditions. The linewidth at half maximum (FWHM) of 65 Hz using (27)Al CW decoupling decreases to 48 Hz with RS-MP decoupling and to 30 Hz with rotor-asynchronised MP (RA-MP) decoupling. The main phenomena are explained using both experimental results and numerical simulations.

High Diversity of CTX-M Extended-Spectrum β-Lactamases in Municipal Wastewater and Urban Wetlands

PubMed Central

Borgogna, Timothy R.; Borgogna, Joanna-Lynn; Mielke, Jenna A.; Brown, Celeste J.; Top, Eva M.; Botts, Ryan T.

2016-01-01

The CTX-M-type extended-spectrum β-lactamases (ESBLs) present a serious public health threat as they have become nearly ubiquitous among clinical gram-negative pathogens, particularly the enterobacteria. To aid in the understanding and eventual control of the spread of such resistance genes, we sought to determine the diversity of CTX-M ESBLs not among clinical isolates, but in the environment, where weaker and more diverse selective pressures may allow greater enzyme diversification. This was done by examining the CTX-M diversity in municipal wastewater and urban coastal wetlands in southern California, United States, by Sanger sequencing of polymerase chain reaction amplicons. Of the five known CTX-M phylogroups (1, 2, 8, 9, and 25), only genes from groups 1 and 2 were detected in both wastewater treatment plants (WWTPs), and group 1 genes were also detected in one of the two wetlands after a winter rain. The highest relative abundance of blaCTX-M group 1 genes was in the sludge of one WWTP (2.1 × 10−4 blaCTX-M copies/16S rRNA gene copy). Gene libraries revealed surprisingly high nucleotide sequence diversity, with 157 new variants not found in GenBank, representing 99 novel amino acid sequences. Our results indicate that the resistomes of WWTPs and urban wetlands contain diverse blaCTX-M ESBLs, which may constitute a mobile reservoir of clinically relevant resistance genes. PMID:26670020

Infrared maritime target detection using a probabilistic single Gaussian model of sea clutter in Fourier domain

NASA Astrophysics Data System (ADS)

Zhou, Anran; Xie, Weixin; Pei, Jihong; Chen, Yapei

2018-02-01

For ship targets detection in cluttered infrared image sequences, a robust detection method, based on the probabilistic single Gaussian model of sea background in Fourier domain, is put forward. The amplitude spectrum sequences at each frequency point of the pure seawater images in Fourier domain, being more stable than the gray value sequences of each background pixel in the spatial domain, are regarded as a Gaussian model. Next, a probability weighted matrix is built based on the stability of the pure seawater's total energy spectrum in the row direction, to make the Gaussian model more accurate. Then, the foreground frequency points are separated from the background frequency points by the model. Finally, the false-alarm points are removed utilizing ships' shape features. The performance of the proposed method is tested by visual and quantitative comparisons with others.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

PubMed

Bolleman, Jerven T; Mungall, Christopher J; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J P; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; Cock, Peter J A

2016-06-13

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

DOE PAGES

Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco; ...

2016-06-13

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. In this paper, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data formatmore » to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Finally, data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. In this paper, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data formatmore » to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Finally, data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

Measuring distance through dense weighted networks: The case of hospital-associated pathogens

PubMed Central

Smieszek, Timo; Henderson, Katherine L.; Johnson, Alan P.

2017-01-01

Hospital networks, formed by patients visiting multiple hospitals, affect the spread of hospital-associated infections, resulting in differences in risks for hospitals depending on their network position. These networks are increasingly used to inform strategies to prevent and control the spread of hospital-associated pathogens. However, many studies only consider patients that are received directly from the initial hospital, without considering the effect of indirect trajectories through the network. We determine the optimal way to measure the distance between hospitals within the network, by reconstructing the English hospital network based on shared patients in 2014–2015, and simulating the spread of a hospital-associated pathogen between hospitals, taking into consideration that each intermediate hospital conveys a delay in the further spread of the pathogen. While the risk of transferring a hospital-associated pathogen between directly neighbouring hospitals is a direct reflection of the number of shared patients, the distance between two hospitals far-away in the network is determined largely by the number of intermediate hospitals in the network. Because the network is dense, most long distance transmission chains in fact involve only few intermediate steps, spreading along the many weak links. The dense connectivity of hospital networks, together with a strong regional structure, causes hospital-associated pathogens to spread from the initial outbreak in a two-step process: first, the directly surrounding hospitals are affected through the strong connections, second all other hospitals receive introductions through the multitude of weaker links. Although the strong connections matter for local spread, weak links in the network can offer ideal routes for hospital-associated pathogens to travel further faster. This hold important implications for infection prevention and control efforts: if a local outbreak is not controlled in time, colonised patients will appear in other regions, irrespective of the distance to the initial outbreak, making import screening ever more difficult. PMID:28771581

Impact of PACS On The Organization Of Radiology Departments

NASA Astrophysics Data System (ADS)

Zielonka, Jason S.

1983-05-01

The radiologist serves as a consultant to other physicians in the practice of clinical medicine; the image obtained and the reported interpretation of that image represent the service rendered and are therefore of major importance (medically, legally and economically) to the radiologist. Because many radiology departments are organized along subspecialty lines or (in the case of a single department serving several institutions) along combined institutional and subspecialty lines, many patients may undergo diagnostic evaluation sequences in which several studies are performed and multiple simultaneous consultations may result. In the past, the lack of availability of multiple copies of the study (for multiple interested parties) has prevented the effective tailoring of subsequent examinations until the prior exam results were available; the advent of digital networks for PACS may result in a significant change in this procedure and, accordingly, in the pattern of interpretation, internal referral and organization of radiology departments. In addition, since clinicians may have access to studies directly and, possibly, prior to official interpretation, the nature of the relationship between the clinician and the radiologist may be altered by PACS.

Information resources at the National Center for Biotechnology Information.

PubMed Central

Woodsmall, R M; Benson, D A

1993-01-01

The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, was established in 1988 to perform basic research in the field of computational molecular biology as well as build and distribute molecular biology databases. The basic research has led to new algorithms and analysis tools for interpreting genomic data and has been instrumental in the discovery of human disease genes for neurofibromatosis and Kallmann syndrome. The principal database responsibility is the National Institutes of Health (NIH) genetic sequence database, GenBank. NCBI, in collaboration with international partners, builds, distributes, and provides online and CD-ROM access to over 112,000 DNA sequences. Another major program is the integration of multiple sequences databases and related bibliographic information and the development of network-based retrieval systems for Internet access. PMID:8374583

Pulse patterning effect in optical pulse division multiplexing for flexible single wavelength multiple access optical network

NASA Astrophysics Data System (ADS)

Jung, Sun-Young; Kim, Chang-Hun; Han, Sang-Kook

2018-05-01

A demand for high spectral efficiency requires multiple access within a single wavelength, but the uplink signals are significantly degraded because of optical beat interference (OBI) in intensity modulation/direct detection system. An optical pulse division multiplexing (OPDM) technique was proposed that could effectively reduce the OBI via a simple method as long as near-orthogonality is satisfied, but the condition was strict, and thus, the number of multiplexing units was very limited. We propose pulse pattern enhanced OPDM (e-OPDM) to reduce the OBI and improve the flexibility in multiple access within a single wavelength. The performance of the e-OPDM and patterning effect are experimentally verified after 23-km single mode fiber transmission. By employing pulse patterning in OPDM, the tight requirement was relaxed by extending the optical delay dynamic range. This could support more number of access with reduced OBI, which could eventually enhance a multiple access function.

Multi-Hadron Observables from Lattice Quantum Chromodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hansen, Maxwell

2014-01-01

We describe formal work that relates the nite-volume spectrum in a quantum eld theory to scattering and decay amplitudes. This is of particular relevance to numerical calculations performed using Lattice Quantum Chromodynamics (LQCD). Correlators calculated using LQCD can only be determined on the Euclidean time axis. For this reason the standard method of determining scattering amplitudes via the Lehmann-Symanzik-Zimmermann reduction formula cannot be employed. By contrast, the nite-volume spectrum is directly accessible in LQCD calculations. Formalism for relating the spectrum to physical scattering observables is thus highly desirable. In this thesis we develop tools for extracting physical information from LQCDmore » for four types of observables. First we analyze systems with multiple, strongly-coupled two-scalar channels. Here we accommodate both identical and nonidentical scalars, and in the latter case allow for degenerate as well as nondegenerate particle masses. Using relativistic eld theory, and summing to all orders in perturbation theory, we derive a result relating the nite-volume spectrum to the two-to-two scattering amplitudes of the coupled-channel theory. This generalizes the formalism of Martin L uscher for the case of single-channel scattering. Second we consider the weak decay of a single particle into multiple, coupled two-scalar channels. We show how the nite-volume matrix element extracted in LQCD is related to matrix elements of asymptotic two-particle states, and thus to decay amplitudes. This generalizes work by Laurent Lellouch and Martin L uscher. Third we extend the method for extracting matrix elements by considering currents which insert energy, momentum and angular momentum. This allows one to extract transition matrix elements and form factors from LQCD. Finally we look beyond two-particle systems to those with three-particles in asymptotic states. Working again to all orders in relativistic eld theory, we derive a relation between the spectrum and an in nite-volume three-to-three scattering quantity. This nal analysis is the most complicated of the four, because the all-orders summation is more di cult for this system, and also because a number of new technical issues arise in analyzing the contributing diagrams.« less

Molecular and Cytogenetic Characterization of Wild Musa Species

PubMed Central

Čížková, Jana; Hřibová, Eva; Christelová, Pavla; Van den Houwe, Ines; Häkkinen, Markku; Roux, Nicolas; Swennen, Rony; Doležel, Jaroslav

2015-01-01

The production of bananas is threatened by rapid spreading of various diseases and adverse environmental conditions. The preservation and characterization of banana diversity is essential for the purposes of crop improvement. The world's largest banana germplasm collection maintained at the Bioversity International Transit Centre (ITC) in Belgium is continuously expanded by new accessions of edible cultivars and wild species. Detailed morphological and molecular characterization of the accessions is necessary for efficient management of the collection and utilization of banana diversity. In this work, nuclear DNA content and genomic distribution of 45S and 5S rDNA were examined in 21 diploid accessions recently added to ITC collection, representing both sections of the genus Musa. 2C DNA content in the section Musa ranged from 1.217 to 1.315 pg. Species belonging to section Callimusa had 2C DNA contents ranging from 1.390 to 1.772 pg. While the number of 45S rDNA loci was conserved in the section Musa, it was highly variable in Callimusa species. 5S rRNA gene clusters were found on two to eight chromosomes per diploid cell. The accessions were genotyped using a set of 19 microsatellite markers to establish their relationships with the remaining accessions held at ITC. Genetic diversity done by SSR genotyping platform was extended by phylogenetic analysis of ITS region. ITS sequence data supported the clustering obtained by SSR analysis for most of the accessions. High level of nucleotide diversity and presence of more than two types of ITS sequences in eight wild diploids pointed to their origin by hybridization of different genotypes. This study significantly expands the number of wild Musa species where nuclear genome size and genomic distribution of rDNA loci is known. SSR genotyping identified Musa species that are closely related to the previously characterized accessions and provided data to aid in their classification. Sequence analysis of ITS region provided further information about evolutionary relationships between individual accessions and suggested that some of analyzed accessions were interspecific hybrids and/or backcross progeny. PMID:26252482

Extended-spectrum β-lactamases, transferable quinolone resistance, and virulotyping in extra-intestinal E. coli in Uruguay.

PubMed

Vignoli, Rafael; García-Fulgueiras, Virginia; Cordeiro, Nicolás F; Bado, Inés; Seija, Verónica; Aguerrebere, Paula; Laguna, Gabriel; Araújo, Lucía; Bazet, Cristina; Gutkind, Gabriel; Chabalgoity, José

2016-01-31

To characterize extended-spectrum β-lactamases (ESBLs) and plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli isolates obtained from extra-intestinal samples in three Uruguayan hospitals. Fifty-five ESBL-producing E. coli isolates were studied. Virulence genes, ESBLs, and PMQR genes were detected by polymerase chain reaction. ESBL-producing isolates were compared by pulsed-field gel electrophoresis. Multi-locus sequence typing was also performed on 13 selected isolates. Thirty-seven isolates harbored blaCTX-M-15 (67.3%), eight blaCTX-M-2 (14.6%), five blaCTX-M-14 (9.1%), three carried both blaCTX-M-2 and blaCTX-M-14, one blaCTX-M-9, and one blaCTX-M-8. Among the CTX-M-15 producers, 92% belonged to sequence types ST131 and ST405, and carried aac(6')Ib-cr as well. Isolates harboring blaCTX-M-2, blaCTX-M-14, blaCTX-M-9, or blaCTX-M-8 were found to be genetically unrelated. The successful dissemination of CTX-M-15-producing E.coli isolates seems to be linked to the spreading of high-risk clones and horizontal gene transfer. A trade-off between carrying more antibiotic resistance and less virulence-related genes could partially account for the evolutionary advantages featured by successful clones.

Wireless visual sensor network resource allocation using cross-layer optimization

NASA Astrophysics Data System (ADS)

Bentley, Elizabeth S.; Matyjas, John D.; Medley, Michael J.; Kondi, Lisimachos P.

2009-01-01

In this paper, we propose an approach to manage network resources for a Direct Sequence Code Division Multiple Access (DS-CDMA) visual sensor network where nodes monitor scenes with varying levels of motion. It uses cross-layer optimization across the physical layer, the link layer and the application layer. Our technique simultaneously assigns a source coding rate, a channel coding rate, and a power level to all nodes in the network based on one of two criteria that maximize the quality of video of the entire network as a whole, subject to a constraint on the total chip rate. One criterion results in the minimal average end-to-end distortion amongst all nodes, while the other criterion minimizes the maximum distortion of the network. Our approach allows one to determine the capacity of the visual sensor network based on the number of nodes and the quality of video that must be transmitted. For bandwidth-limited applications, one can also determine the minimum bandwidth needed to accommodate a number of nodes with a specific target chip rate. Video captured by a sensor node camera is encoded and decoded using the H.264 video codec by a centralized control unit at the network layer. To reduce the computational complexity of the solution, Universal Rate-Distortion Characteristics (URDCs) are obtained experimentally to relate bit error probabilities to the distortion of corrupted video. Bit error rates are found first by using Viterbi's upper bounds on the bit error probability and second, by simulating nodes transmitting data spread by Total Square Correlation (TSC) codes over a Rayleigh-faded DS-CDMA channel and receiving that data using Auxiliary Vector (AV) filtering.

Phylogeographic characteristics of vesicular stomatitis New Jersey viruses circulating in Mexico from 2005 to 2011 and their relationship to epidemics in the United States.

PubMed

Velazquez-Salinas, Lauro; Pauszek, Steven J; Zarate, Selene; Basurto-Alcantara, Francisco J; Verdugo-Rodriguez, Antonio; Perez, Andres M; Rodriguez, Luis L

2014-01-20

We analyzed the phylogenetic and time-space relationships (phylodynamics) of 181 isolates of vesicular stomatitis New Jersey virus (VSNJV) causing disease in Mexico and the United States (US) from 2005 through 2012. We detail the emergence of a genetic lineage in southern Mexico causing outbreaks in central Mexico spreading into northern Mexico and eventually into the US. That emerging lineage showed higher nucleotide sequence identity (99.5%) than that observed for multiple lineages circulating concurrently in southern Mexico (96.8%). Additionally, we identified 58 isolates from Mexico that, unlike previous isolates from Mexico, grouped with northern Central America clade II viruses. This study provides the first direct evidence for the emergence and northward migration of a specific VSNJV genetic lineage from endemic areas in Mexico causing VS outbreaks in the US. In addition we document the emergence of a Central American VSNJV genetic lineage moving northward and causing outbreaks in central Mexico. © 2013 Published by Elsevier Inc.

Phenotypic spectrum associated with mutations of the mitochondrial polymerase gamma gene.

PubMed

Horvath, Rita; Hudson, Gavin; Ferrari, Gianfrancesco; Fütterer, Nancy; Ahola, Sofia; Lamantea, Eleonora; Prokisch, Holger; Lochmüller, Hanns; McFarland, Robert; Ramesh, V; Klopstock, Thomas; Freisinger, Peter; Salvi, Fabrizio; Mayr, Johannes A; Santer, Rene; Tesarova, Marketa; Zeman, Jiri; Udd, Bjarne; Taylor, Robert W; Turnbull, Douglass; Hanna, Michael; Fialho, Doreen; Suomalainen, Anu; Zeviani, Massimo; Chinnery, Patrick F

2006-07-01

Mutations in the gene coding for the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase gamma (POLG1) have recently been described in patients with diverse clinical presentations, revealing a complex relationship between genotype and phenotype in patients and their families. POLG1 was sequenced in patients from different European diagnostic and research centres to define the phenotypic spectrum and advance understanding of the recurrence risks. Mutations were identified in 38 cases, with the majority being sporadic compound heterozygotes. Eighty-nine DNA sequence changes were identified, including 2 predicted to alter a splice site, 1 predicted to cause a premature stop codon and 13 predicted to cause novel amino acid substitutions. The majority of children had a mutation in the linker region, often 1399G-->A (A467T), and a mutation affecting the polymerase domain. Others had mutations throughout the gene, and 11 had 3 or more substitutions. The clinical presentation ranged from the neonatal period to late adult life, with an overlapping phenotypic spectrum from severe encephalopathy and liver failure to late-onset external ophthalmoplegia, ataxia, myopathy and isolated muscle pain or epilepsy. There was a strong gender bias in children, with evidence of an environmental interaction with sodium valproate. POLG1 mutations cause an overlapping clinical spectrum of disease with both dominant and recessive modes of inheritance. 1399G-->A (A467T) is common in children, but complete POLG1 sequencing is required to identify multiple mutations that can have complex implications for genetic counselling.

Collective Influence of Multiple Spreaders Evaluated by Tracing Real Information Flow in Large-Scale Social Networks.

PubMed

Teng, Xian; Pei, Sen; Morone, Flaviano; Makse, Hernán A

2016-10-26

Identifying the most influential spreaders that maximize information flow is a central question in network theory. Recently, a scalable method called "Collective Influence (CI)" has been put forward through collective influence maximization. In contrast to heuristic methods evaluating nodes' significance separately, CI method inspects the collective influence of multiple spreaders. Despite that CI applies to the influence maximization problem in percolation model, it is still important to examine its efficacy in realistic information spreading. Here, we examine real-world information flow in various social and scientific platforms including American Physical Society, Facebook, Twitter and LiveJournal. Since empirical data cannot be directly mapped to ideal multi-source spreading, we leverage the behavioral patterns of users extracted from data to construct "virtual" information spreading processes. Our results demonstrate that the set of spreaders selected by CI can induce larger scale of information propagation. Moreover, local measures as the number of connections or citations are not necessarily the deterministic factors of nodes' importance in realistic information spreading. This result has significance for rankings scientists in scientific networks like the APS, where the commonly used number of citations can be a poor indicator of the collective influence of authors in the community.

Batrachochytrium dendrobatidis prevalence and haplotypes in domestic and imported pet amphibians in Japan.

PubMed

Tamukai, Kenichi; Une, Yumi; Tominaga, Atsushi; Suzuki, Kazutaka; Goka, Koichi

2014-05-13

The international trade in amphibians is believed to have increased the spread of Batrachochytrium dendrobatidis (Bd), the fungal pathogen responsible for chytridiomycosis, which has caused a rapid decline in amphibian populations worldwide. We surveyed amphibians imported into Japan and those held in captivity for a long period or bred in Japan to clarify the Bd infection status. Samples were taken from 820 individuals of 109 amphibian species between 2008 and 2011 and were analyzed by a nested-PCR assay. Bd prevalence in imported amphibians was 10.3% (58/561), while it was 6.9% (18/259) in those in private collections and commercially bred amphibians in Japan. We identified the genotypes of this fungus using partial DNA sequences of the internal transcribed spacer (ITS) region. Sequencing of PCR products of all 76 Bd-positive samples revealed 11 haplotypes of the Bd ITS region. Haplotype A (DNA Data Bank of Japan accession number AB435211) was found in 90% (52/58) of imported amphibians. The results show that Bd is currently entering Japan via the international trade in exotic amphibians as pets, suggesting that the trade has indeed played a major role in the spread of Bd.

Challenges of coverage policy development for next-generation tumor sequencing panels: experts and payers weigh in.

PubMed

Trosman, Julia R; Weldon, Christine B; Kelley, R Kate; Phillips, Kathryn A

2015-03-01

Next-generation tumor sequencing (NGTS) panels, which include multiple established and novel targets across cancers, are emerging in oncology practice, but lack formal positive coverage by US payers. Lack of coverage may impact access and adoption. This study identified challenges of NGTS coverage by private payers. We conducted semi-structured interviews with 14 NGTS experts on potential NGTS benefits, and with 10 major payers, representing more than 125,000,000 enrollees, on NGTS coverage considerations. We used the framework approach of qualitative research for study design and thematic analyses and simple frequencies to further describe findings. All interviewed payers see potential NGTS benefits, but all noted challenges to formal coverage: 80% state that inherent features of NGTS do not fit the medical necessity definition required for coverage, 70% view NGTS as a bundle of targets versus comprehensive tumor characterization and may evaluate each target individually, and 70% express skepticism regarding new evidence methods proposed for NGTS. Fifty percent of payers expressed sufficient concerns about NGTS adoption and implementation that will preclude their ability to issue positive coverage policies. Payers perceive that NGTS holds significant promise but, in its current form, poses disruptive challenges to coverage policy frameworks. Proactive multidisciplinary efforts to define the direction for NGTS development, evidence generation, and incorporation into coverage policy are necessary to realize its promise and provide patient access. This study contributes to current literature, as possibly the first study to directly interview US payers on NGTS coverage and reimbursement. Copyright © 2015 by the National Comprehensive Cancer Network.

Challenges of Coverage Policy Development for Next-Generation Tumor Sequencing Panels: Experts and Payers Weigh In

PubMed Central

Trosman, Julia R.; Weldon, Christine B.; Kate Kelley, R.; Phillips, Kathryn A.

2015-01-01

Background Next-generation tumor sequencing (NGTS) panels, which include multiple established and novel targets across cancers, are emerging in oncology practice, but lack formal positive coverage by US payers. Lack of coverage may impact access and adoption. This study identified challenges of NGTS coverage by private payers. Methods We conducted semi-structured interviews with 14 NGTS experts on potential NGTS benefits, and with 10 major payers, representing more than 125,000,000 enrollees, on NGTS coverage considerations. We used the framework approach of qualitative research for study design and thematic analyses and simple frequencies to further describe findings. Results All interviewed payers see potential NGTS benefits, but all noted challenges to formal coverage: 80% state that inherent features of NGTS do not fit the medical necessity definition required for coverage, 70% view NGTS as a bundle of targets versus comprehensive tumor characterization and may evaluate each target individually, and 70% express skepticism regarding new evidence methods proposed for NGTS. Fifty percent of payers expressed sufficient concerns about NGTS adoption and implementation that will preclude their ability to issue positive coverage policies. Conclusions Payers perceive that NGTS holds significant promise but, in its current form, poses disruptive challenges to coverage policy frameworks. Proactive multidisciplinary efforts to define the direction for NGTS development, evidence generation, and incorporation into coverage policy are necessary to realize its promise and provide patient access. This study contributes to current literature, as possibly the first study to directly interview US payers on NGTS coverage and reimbursement. PMID:25736008

The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts

NASA Astrophysics Data System (ADS)

Rinaldi, Arlie J.; Lund, Paul E.; Blanco, Mario R.; Walter, Nils G.

2016-01-01

In response to intracellular signals in Gram-negative bacteria, translational riboswitches--commonly embedded in messenger RNAs (mRNAs)--regulate gene expression through inhibition of translation initiation. It is generally thought that this regulation originates from occlusion of the Shine-Dalgarno (SD) sequence upon ligand binding; however, little direct evidence exists. Here we develop Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to investigate the ligand-dependent accessibility of the SD sequence of an mRNA hosting the 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch. Spike train analysis reveals that individual mRNA molecules alternate between two conformational states, distinguished by `bursts' of probe binding associated with increased SD sequence accessibility. Addition of preQ1 decreases the lifetime of the SD's high-accessibility (bursting) state and prolongs the time between bursts. In addition, ligand-jump experiments reveal imperfect riboswitching of single mRNA molecules. Such complex ligand sensing by individual mRNA molecules rationalizes the nuanced ligand response observed during bulk mRNA translation.

Energy landscape of LeuT from molecular simulations

NASA Astrophysics Data System (ADS)

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-12-01

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ˜40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

Energy landscape of LeuT from molecular simulations.

PubMed

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-12-28

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

Energy landscape of LeuT from molecular simulations

PubMed Central

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

2015-01-01

The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates. PMID:26723619

Molecular Diagnosis of Orthopedic-Device-Related Infection Directly from Sonication Fluid by Metagenomic Sequencing

PubMed Central

Sanderson, Nicholas D.; Atkins, Bridget L.; Brent, Andrew J.; Cole, Kevin; Foster, Dona; McNally, Martin A.; Oakley, Sarah; Peto, Leon; Taylor, Adrian; Peto, Tim E. A.; Crook, Derrick W.; Eyre, David W.

2017-01-01

ABSTRACT Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI. PMID:28490492

Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach.

PubMed

Klimochkin, Yuri N; Shiryaev, Vadim A; Petrov, Pavel V; Radchenko, Eugene V; Palyulin, Vladimir A; Zefirov, Nikolay S

2016-01-01

The influenza A virus M2 proton channel plays a critical role in its life cycle. However, known M2 inhibitors have lost their clinical efficacy due to the spread of resistant mutant channels. Thus, the search for broad-spectrum M2 channel inhibitors is of great importance. The goal of the present work was to develop a general approach supporting the design of ligands interacting with multiple labile targets and to propose on its basis the potential broad-spectrum inhibitors of the M2 proton channel. The dynamic dimer-of-dimers structures of the three primary M2 target variants, wild-type, S31N and V27A, were modeled by molecular dynamics and thoroughly analyzed in order to define the inhibitor binding sites. The potential inhibitor structures were identified by molecular docking and their binding was verified by molecular dynamics simulation. The binding sites of the M2 proton channel inhibitors were analyzed, a number of potential broad-spectrum inhibitors were identified and the binding modes and probable mechanisms of action of one promising compound were clarified. Using the molecular dynamics and molecular docking techniques, we have refined the dynamic dimer-ofdimers structures of the WT, S31N and V27A variants of the M2 proton channel of the influenza A virus, analyzed the inhibitor binding sites, identified a number of potential broad-spectrum inhibitor structures targeting them, and clarified the binding modes and probable mechanisms of action of one promising compound. The proposed approach is also suitable for the design of ligands interacting with other multiple labile targets.

Extrapulmonary localization of gallium in sarcoidosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rohatgi, P.K.; Singh, R.; Vieras, F.

1987-01-01

This paper describes the spectrum of extrapulmonary localization of gallium in patients with sarcoidosis. The usefulness of Ga-67 scintiscans in detecting clinically occult lesions, in directing clinicians to accessible sites for biopsy, and in following the course of extrapulmonary sites of involvement with therapy is emphasized.

Direct memory access transfer completion notification

DOEpatents

Chen, Dong; Giampapa, Mark E.; Heidelberger, Philip; Kumar, Sameer; Parker, Jeffrey J.; Steinmacher-Burow, Burkhard D.; Vranas, Pavlos

2010-07-27

Methods, compute nodes, and computer program products are provided for direct memory access (`DMA`) transfer completion notification. Embodiments include determining, by an origin DMA engine on an origin compute node, whether a data descriptor for an application message to be sent to a target compute node is currently in an injection first-in-first-out (`FIFO`) buffer in dependence upon a sequence number previously associated with the data descriptor, the total number of descriptors currently in the injection FIFO buffer, and the current sequence number for the newest data descriptor stored in the injection FIFO buffer; and notifying a processor core on the origin DMA engine that the message has been sent if the data descriptor for the message is not currently in the injection FIFO buffer.

Identifying Stimuli that Alter Immediate and Subsequent Levels of Vocal Stereotypy: A Further Analysis of Functionally Matched Stimulation

ERIC Educational Resources Information Center

Lanovaz, Marc J.; Fletcher, Sarah E.; Rapp, John T.

2009-01-01

We used a three-component multiple-schedule with a brief reversal design to evaluate the effects of structurally unmatched and matched stimuli on immediate and subsequent vocal stereotypy that was displayed by three children with autism spectrum disorders. For 2 of the 3 participants, access to matched stimuli, unmatched stimuli, and music…

Genetic analysis of PAX3 for diagnosis of Waardenburg syndrome type I.

PubMed

Matsunaga, Tatsuo; Mutai, Hideki; Namba, Kazunori; Morita, Noriko; Masuda, Sawako

2013-04-01

PAX3 genetic analysis increased the diagnostic accuracy for Waardenburg syndrome type I (WS1). Analysis of the three-dimensional (3D) structure of PAX3 helped verify the pathogenicity of a missense mutation, and multiple ligation-dependent probe amplification (MLPA) analysis of PAX3 increased the sensitivity of genetic diagnosis in patients with WS1. Clinical diagnosis of WS1 is often difficult in individual patients with isolated, mild, or non-specific symptoms. The objective of the present study was to facilitate the accurate diagnosis of WS1 through genetic analysis of PAX3 and to expand the spectrum of known PAX3 mutations. In two Japanese families with WS1, we conducted a clinical evaluation of symptoms and genetic analysis, which involved direct sequencing, MLPA analysis, quantitative PCR of PAX3, and analysis of the predicted 3D structure of PAX3. The normal-hearing control group comprised 92 subjects who had normal hearing according to pure tone audiometry. In one family, direct sequencing of PAX3 identified a heterozygous mutation, p.I59F. Analysis of PAX3 3D structures indicated that this mutation distorted the DNA-binding site of PAX3. In the other family, MLPA analysis and subsequent quantitative PCR detected a large, heterozygous deletion spanning 1759-2554 kb that eliminated 12-18 genes including a whole PAX3 gene.

Three patients with Schaaf-Yang syndrome exhibiting arthrogryposis and endocrinological abnormalities.

PubMed

Enya, Takuji; Okamoto, Nobuhiko; Iba, Yoshinori; Miyazawa, Tomoki; Okada, Mitsuru; Ida, Shinobu; Naruto, Takuya; Imoto, Issei; Fujita, Atsushi; Miyake, Noriko; Matsumoto, Naomichi; Sugimoto, Keisuke; Takemura, Tsukasa

2018-03-01

MAGEL2 is the paternally expressed gene within Prader-Willi syndrome critical region at 15q11.2. We encountered three individuals in whom truncating mutations of MAGEL2 were identified. Patients 1 and 2, siblings born to healthy, non-consanguineous Japanese parents, showed generalized hypotonia, lethargy, severe respiratory difficulty, poor feeding, and multiple anomalies including arthrogryposis soon after birth. We carried out whole-exome sequencing, which detected a MAGEL2 mutation (c.1912C>T, p.Gln638*, heterozygous). The patients' father was heterozygous for the mutation. Patient 3 was a female infant, showed respiratory difficulty reflecting pulmonary hypoplasia, generalized hypotonia, feeding difficulty and multiple anomalies soon after birth. Targeted next-generation sequencing detected a novel heterozygous mutation in MAGEL2 (c.3131C>A, p.Ser1044*). This mutation was not found in the parents. MAGEL2 mutations, first reported to be the cause of the Prader-Willi like syndrome with autism by Schaaf et al. (2013) Nature Genetics, 45: 1405-1408 show the wide range of phenotypic spectrum from lethal arthrogryposis multiplex congenital to autism spectrum disorder (ASD) and mild intellectual disability (ID). Our results indicate that MAGEL2 mutations cause multiple congenital anomalies and intellectual disability accompanied by arthrogryposis multiplex congenita and various endocrinologic abnormalities, supporting that the view that clinical phenotypes of MAGEL2 mutations are variable. © 2018 Wiley Periodicals, Inc.

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

PubMed

Chen, Xingqi; Shen, Ying; Draper, Will; Buenrostro, Jason D; Litzenburger, Ulrike; Cho, Seung Woo; Satpathy, Ansuman T; Carter, Ava C; Ghosh, Rajarshi P; East-Seletsky, Alexandra; Doudna, Jennifer A; Greenleaf, William J; Liphardt, Jan T; Chang, Howard Y

2016-12-01

Spatial organization of the genome plays a central role in gene expression, DNA replication, and repair. But current epigenomic approaches largely map DNA regulatory elements outside of the native context of the nucleus. Here we report assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that employs direct imaging of the accessible genome in situ, cell sorting, and deep sequencing to reveal the identity of the imaged elements. ATAC-see revealed the cell-type-specific spatial organization of the accessible genome and the coordinated process of neutrophil chromatin extrusion, termed NETosis. Integration of ATAC-see with flow cytometry enables automated quantitation and prospective cell isolation as a function of chromatin accessibility, and it reveals a cell-cycle dependence of chromatin accessibility that is especially dynamic in G1 phase. The integration of imaging and epigenomics provides a general and scalable approach for deciphering the spatiotemporal architecture of gene control.

Mining sequence variations in representative polyploid sugarcane germplasm accessions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiping; Song, Jian; You, Qian

Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes.more » To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.« less

Mining sequence variations in representative polyploid sugarcane germplasm accessions

DOE PAGES

Yang, Xiping; Song, Jian; You, Qian; ...

2017-08-09

Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes.more » To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species.« less

Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays▿ †

PubMed Central

Lin, Baochuan; Malanoski, Anthony P.; Wang, Zheng; Blaney, Kate M.; Long, Nina C.; Meador, Carolyn E.; Metzgar, David; Myers, Christopher A.; Yingst, Samuel L.; Monteville, Marshall R.; Saad, Magdi D.; Schnur, Joel M.; Tibbetts, Clark; Stenger, David A.

2009-01-01

Zoonotic microbes have historically been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the appearance of some human infections have increased the concern of a possible new influenza pandemic, which highlights the need for broad-spectrum detection methods for rapidly identifying the spread or outbreak of all variants of avian influenza virus. In this study, we demonstrate that high-density resequencing pathogen microarrays (RPM) can be such a tool. The results from 37 influenza virus isolates show that the RPM platform is an effective means for detecting and subtyping influenza virus, while simultaneously providing sequence information for strain resolution, pathogenicity, and drug resistance without additional analysis. This study establishes that the RPM platform is a broad-spectrum pathogen detection and surveillance tool for monitoring the circulation of prevalent influenza viruses in the poultry industry and in wild birds or incidental exposures and infections in humans. PMID:19279171

Direct synthesis of antimicrobial coatings based on tailored bi-elemental nanoparticles

NASA Astrophysics Data System (ADS)

Benetti, Giulio; Cavaliere, Emanuele; Canteri, Adalberto; Landini, Giulia; Rossolini, Gian Maria; Pallecchi, Lucia; Chiodi, Mirco; Van Bael, Margriet J.; Winckelmans, Naomi; Bals, Sara; Gavioli, Luca

2017-03-01

Ultrathin coatings based on bi-elemental nanoparticles (NPs) are very promising to limit the surface-related spread of bacterial pathogens, particularly in nosocomial environments. However, tailoring the synthesis, composition, adhesion to substrate, and antimicrobial spectrum of the coating is an open challenge. Herein, we report on a radically new nanostructured coating, obtained by a one-step gas-phase deposition technique, and composed of bi-elemental Janus type Ag/Ti NPs. The NPs are characterized by a cluster-in-cluster mixing phase with metallic Ag nano-crystals embedded in amorphous TiO2 and present a promising antimicrobial activity including also multidrug resistant strains. We demonstrate the flexibility of the method to tune the embedded Ag nano-crystals dimension, the total relative composition of the coating, and the substrate type, opening the possibility of tailoring the dimension, composition, antimicrobial spectrum, and other physical/chemical properties of such multi-elemental systems. This work is expected to significantly spread the range of applications of NPs coatings, not only as an effective tool in the prevention of healthcare-associated infections but also in other technologically relevant fields like sensors or nano-/micro joining.

Spread Spectrum Based Energy Efficient Collaborative Communication in Wireless Sensor Networks.

PubMed

Ghani, Anwar; Naqvi, Husnain; Sher, Muhammad; Khan, Muazzam Ali; Khan, Imran; Irshad, Azeem

2016-01-01

Wireless sensor networks consist of resource limited devices. Most crucial of these resources is battery life, as in most applications like battle field or volcanic area monitoring, it is often impossible to replace or recharge the power source. This article presents an energy efficient collaborative communication system based on spread spectrum to achieve energy efficiency as well as immunity against jamming, natural interference, noise suppression and universal frequency reuse. Performance of the proposed system is evaluated using the received signal power, bit error rate (BER) and energy consumption. The results show a direct proportionality between the power gain and the number of collaborative nodes as well as BER and signal-to-noise ratio (Eb/N0). The analytical and simulation results of the proposed system are compared with SISO system. The comparison reveals that SISO perform better than collaborative communication in case of small distances whereas collaborative communication performs better than SISO in case of long distances. On the basis of these results it is safe to conclude that collaborative communication in wireless sensor networks using wideband systems improves the life time of nodes in the networks thereby prolonging the network's life time.

On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing.

PubMed

Grissa, Ibtissem; Bouchon, Patrick; Pourcel, Christine; Vergnaud, Gilles

2008-04-01

The control of bacterial pathogens requires the development of tools allowing the precise identification of strains at the subspecies level. It is now widely accepted that these tools will need to be DNA-based assays (in contrast to identification at the species level, where biochemical based assays are still widely used, even though very powerful 16S DNA sequence databases exist). Typing assays need to be cheap and amenable to the designing of international databases. The success of such subspecies typing tools will eventually be measured by the size of the associated reference databases accessible over the internet. Three methods have shown some potential in this direction, the so-called spoligotyping assay (Mycobacterium tuberculosis, 40,000 entries database), Multiple Loci Sequence Typing (MLST; up to a few thousands entries for the more than 20 bacterial species), and more recently Multiple Loci VNTR Analysis (MLVA; up to a few hundred entries, assays available for more than 20 pathogens). In the present report we will review the current status of the tools and resources we have developed along the past seven years to help in the setting-up or the use of MLVA assays or lately for analysing Clustered Regularly Interspaced Short Palindromic Repeats called CRISPRs which are the basis for spoligotyping assays.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Performance Analysis of a De-correlated Modified Code Tracking Loop for Synchronous DS-CDMA System under Multiuser Environment

NASA Astrophysics Data System (ADS)

Wu, Ya-Ting; Wong, Wai-Ki; Leung, Shu-Hung; Zhu, Yue-Sheng

This paper presents the performance analysis of a De-correlated Modified Code Tracking Loop (D-MCTL) for synchronous direct-sequence code-division multiple-access (DS-CDMA) systems under multiuser environment. Previous studies have shown that the imbalance of multiple access interference (MAI) in the time lead and time lag portions of the signal causes tracking bias or instability problem in the traditional correlating tracking loop like delay lock loop (DLL) or modified code tracking loop (MCTL). In this paper, we exploit the de-correlating technique to combat the MAI at the on-time code position of the MCTL. Unlike applying the same technique to DLL which requires an extensive search algorithm to compensate the noise imbalance which may introduce small tracking bias under low signal-to-noise ratio (SNR), the proposed D-MCTL has much lower computational complexity and exhibits zero tracking bias for the whole range of SNR, regardless of the number of interfering users. Furthermore, performance analysis and simulations based on Gold codes show that the proposed scheme has better mean square tracking error, mean-time-to-lose-lock and near-far resistance than the other tracking schemes, including traditional DLL (T-DLL), traditional MCTL (T-MCTL) and modified de-correlated DLL (MD-DLL).

Sequencing of cDNA Clones from the Genetic Map of Tomato (Lycopersicon esculentum)

PubMed Central

Ganal, Martin W.; Czihal, Rosemarie; Hannappel, Ulrich; Kloos, Dorothee-U.; Polley, Andreas; Ling, Hong-Qing

1998-01-01

The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes was found. The information will permit the conversion of those markers to STS markers and allow their use in PCR-based mapping experiments. Furthermore, it will facilitate the comparative mapping of genes across distantly related plant species by direct comparison of DNA sequences and map positions. [cDNA sequence data reported in this paper have been submitted to the EMBL database under accession nos. AA824695–AA825005 and the dbEST_Id database under accession nos. 1546519–1546862.] PMID:9724330

Identification of Broad-Spectrum Dengue/Zika Virus Replication Inhibitors by Functionalization of Quinoline and 2,6-Diaminopurine Scaffolds.

PubMed

Kaptein, Suzanne J F; Vincetti, Paolo; Crespan, Emmanuele; Rivera, Jorge I Armijos; Costantino, Gabriele; Maga, Giovanni; Neyts, Johan; Radi, Marco

2018-05-09

Social and demographic changes across the world over the past 50 years have resulted in significant outbreaks of arboviruses such as dengue virus (DENV) and Zika virus (ZIKV). Despite the increased threat of infection, no approved drugs or fully protective vaccines are available to counteract the spread of DENV and ZIKV. The development of "broad-spectrum" antivirals (BSAs) that target common components of multiple viruses can be a more effective strategy to limit the rapid emergence of viral pathogens than the classic "one-bug/one-drug" approach. Starting from previously identified multitarget DENV inhibitors, herein we report the identification of novel 2,6-diaminopurine derivatives that are able to block the replication of both Zika virus and all serotypes of dengue virus (DENV 1-4) in infected cells. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulating the epidemiological and economic effects of an African swine fever epidemic in industrialized swine populations.

PubMed

Halasa, Tariq; Bøtner, Anette; Mortensen, Sten; Christensen, Hanne; Toft, Nils; Boklund, Anette

2016-09-25

African swine fever (ASF) is a notifiable infectious disease with a considerable impact on animal health and is currently one of the most important emerging diseases of domestic pigs. ASF was introduced into Georgia in 2007 and subsequently spread to the Russian Federation and several Eastern European countries. Consequently, there is a non-negligible risk of ASF spread towards Western Europe. Therefore it is important to develop tools to improve our understanding of the spread and control of ASF for contingency planning. A stochastic and dynamic spatial spread model (DTU-DADS) was adjusted to simulate the spread of ASF virus between domestic swine herds exemplified by the Danish swine population. ASF was simulated to spread via animal movement, low- or medium-risk contacts and local spread. Each epidemic was initiated in a randomly selected herd - either in a nucleus herd, a sow herd, a randomly selected herd or in multiple herds simultaneously. A sensitivity analysis was conducted on input parameters. Given the inputs and assumptions of the model, epidemics of ASF in Denmark are predicted to be small, affecting about 14 herds in the worst-case scenario. The duration of an epidemic is predicted to vary from 1 to 76days. Substantial economic damages are predicted, with median direct costs and export losses of €12 and €349 million, respectively, when epidemics were initiated in multiple herds. Each infectious herd resulted in 0 to 2 new infected herds varying from 0 to 5 new infected herds, depending on the index herd type. Copyright © 2016 Elsevier B.V. All rights reserved.

Physically Protected Spread Spectrum Communications

DTIC Science & Technology

2016-04-14

Kirtland AFB, NM 87117-5776 NUMBER(S) AFRL -RV-PS-TR-2016-0046 12. DISTRIBUTION / AVAILABILITY STATEMENT Approved for public release; distribution... AFRL /RVIL Kirtland AFB, NM 87117-5776 2 cys Official Record Copy AFRL /RVSW/Khanh Pham 1 cy 38 Approved for public release; distribution is unlimited. (This page intentionally left blank) ... AFRL -RV-PS- AFRL -RV-PS- TR-2016-0046 TR-2016-0046 PHYSICALLY PROTECTED SPREAD SPECTRUM COMMUNICATIONS Hyuck M. Kwon Wichita State

Self-registering spread-spectrum barcode method

DOEpatents

Cummings, Eric B.; Even Jr., William R.

2004-11-09

A novel spread spectrum barcode methodology is disclosed that allows a barcode to be read in its entirety even when a significant fraction or majority of the barcode is obscured. The barcode methodology makes use of registration or clocking information that is distributed along with the encoded user data across the barcode image. This registration information allows for the barcode image to be corrected for imaging distortion such as zoom, rotation, tilt, curvature, and perspective.

Spread spectrum image steganography.

PubMed

Marvel, L M; Boncelet, C R; Retter, C T

1999-01-01

In this paper, we present a new method of digital steganography, entitled spread spectrum image steganography (SSIS). Steganography, which means "covered writing" in Greek, is the science of communicating in a hidden manner. Following a discussion of steganographic communication theory and review of existing techniques, the new method, SSIS, is introduced. This system hides and recovers a message of substantial length within digital imagery while maintaining the original image size and dynamic range. The hidden message can be recovered using appropriate keys without any knowledge of the original image. Image restoration, error-control coding, and techniques similar to spread spectrum are described, and the performance of the system is illustrated. A message embedded by this method can be in the form of text, imagery, or any other digital signal. Applications for such a data-hiding scheme include in-band captioning, covert communication, image tamperproofing, authentication, embedded control, and revision tracking.

Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an RNA virus.

PubMed

Cabanillas, Laura; Arribas, María; Lázaro, Ester

2013-01-16

When beneficial mutations present in different genomes spread simultaneously in an asexual population, their fixation can be delayed due to competition among them. This interference among mutations is mainly determined by the rate of beneficial mutations, which in turn depends on the population size, the total error rate, and the degree of adaptation of the population. RNA viruses, with their large population sizes and high error rates, are good candidates to present a great extent of interference. To test this hypothesis, in the current study we have investigated whether competition among beneficial mutations was responsible for the prolonged presence of polymorphisms in the mutant spectrum of an RNA virus, the bacteriophage Qβ, evolved during a large number of generations in the presence of the mutagenic nucleoside analogue 5-azacytidine. The analysis of the mutant spectra of bacteriophage Qβ populations evolved at artificially increased error rate shows a large number of polymorphic mutations, some of them with demonstrated selective value. Polymorphisms distributed into several evolutionary lines that can compete among them, making it difficult the emergence of a defined consensus sequence. The presence of accompanying deleterious mutations, the high degree of recurrence of the polymorphic mutations, and the occurrence of epistatic interactions generate a highly complex interference dynamics. Interference among beneficial mutations in bacteriophage Qβ evolved at increased error rate permits the coexistence of multiple adaptive pathways that can provide selective advantages by different molecular mechanisms. In this way, interference can be seen as a positive factor that allows the exploration of the different local maxima that exist in rugged fitness landscapes.

Targets of small interfering RNA restriction during human immunodeficiency virus type 1 replication.

PubMed

Gao, Yong; Lobritz, Michael A; Roth, Justin; Abreha, Measho; Nelson, Kenneth N; Nankya, Immaculate; Moore-Dudley, Dawn M; Abraha, Awet; Gerson, Stanton L; Arts, Eric J

2008-03-01

Small interfering RNAs (siRNAs) have been shown to effectively inhibit human immunodeficiency virus type 1 (HIV-1) replication in vitro. The mechanism(s) for this inhibition is poorly understood, as siRNAs may interact with multiple HIV-1 RNA species during different steps of the retroviral life cycle. To define susceptible HIV-1 RNA species, siRNAs were first designed to specifically inhibit two divergent primary HIV-1 isolates via env and gag gene targets. A self-inactivating lentiviral vector harboring these target sequences confirmed that siRNA cannot degrade incoming genomic RNA. Disruption of the incoming core structure by rhesus macaque TRIM5alpha did, however, provide siRNA-RNA-induced silencing complex access to HIV-1 genomic RNA and promoted degradation. In the absence of accelerated core disruption, only newly transcribed HIV-1 mRNA in the cytoplasm is sensitive to siRNA degradation. Inhibitors of HIV-1 mRNA nuclear export, such as leptomycin B and camptothecin, blocked siRNA restriction. All HIV-1 RNA regions and transcripts found 5' of the target sequence, including multiply spliced HIV-1 RNA, were degraded by unidirectional 3'-to-5' siRNA amplification and spreading. In contrast, HIV-1 RNA 3' of the target sequence was not susceptible to siRNA. Even in the presence of siRNA, full-length HIV-1 RNA is still encapsidated into newly assembled viruses. These findings suggest that siRNA can target only a relatively "naked" cytoplasmic HIV-1 RNA despite the involvement of viral RNA at nearly every step in the retroviral life cycle. Protection of HIV-1 RNA within the core following virus entry, during encapsidation/virus assembly, or within the nucleus may reflect virus evolution in response to siRNA, TRIM5alpha, or other host restriction factors.

Phylogenetic analysis of a transfusion-transmitted hepatitis A outbreak.

PubMed

Hettmann, Andrea; Juhász, Gabriella; Dencs, Ágnes; Tresó, Bálint; Rusvai, Erzsébet; Barabás, Éva; Takács, Mária

2017-02-01

A transfusion-associated hepatitis A outbreak was found in the first time in Hungary. The outbreak involved five cases. Parenteral transmission of hepatitis A is rare, but may occur during viraemia. Direct sequencing of nested PCR products was performed, and all the examined samples were identical in the VP1/2A region of the hepatitis A virus genome. HAV sequences found in recent years were compared and phylogenetic analysis showed that the strain which caused these cases is the same as that had spread in Hungary recently causing several hepatitis A outbreaks throughout the country.

Molecular epidemiology of Pseudomonas aeruginosa clinical isolates from Korea producing β-lactamases with extended-spectrum activity.

PubMed

Bae, Il Kwon; Suh, Borum; Jeong, Seok Hoon; Wang, Kang-Kyun; Kim, Yong-Rok; Yong, Dongeun; Lee, Kyungwon

2014-07-01

This study was performed to investigate the prevalence and molecular epidemiology of Pseudomonas aeruginosa isolates from Korea that produce enzymes with extended-spectrum (ES) activity to β-lactams. A total of 205 non-duplicate P. aeruginosa clinical isolates were collected from 18 university hospitals in Korea. PCR and sequencing experiments were performed to identify genes encoding β-lactamases. PCR mapping and sequencing of the regions surrounding the β-lactamase genes were performed. Multilocus sequence typing experiments were performed. The most common sequence type (ST) was ST235 (n = 96), and 2 single-locus variants of ST235, ST1015 (n = 1) and ST1162 (n = 1), were also identified. These 3 STs were grouped as a clonal complex (CC), CC235. The remaining 107 isolates were identified as 59 different STs. Isolates belonging to CC235 showed higher rates of non-susceptibility to imipenem (85.4% versus 47.7%) and meropenem (92.7% versus 52.3%) compared to non-CC235 isolates. All the metallo-β-lactamase (MBL)-producing isolates were identified as CC235, except for 1 ST591. Genes encoding OXA-17 and OXA-142 were detected in 1 isolate and 4 isolates of CC235, respectively; while the bla(SHV-12) gene was detected in 4 non-CC235 isolates. Class A and D β-lactamases with ES activity play a role in acquiring ceftazidime resistance in P. aeruginosa in Korea. Production of IMP-6 and VIM-2 MBLs is the main mechanisms in acquiring resistance to ceftazidime and carbapenems in P. aeruginosa isolates in Korea. Clonal spread of P. aeruginosa CC235 may be an important conduit for the dissemination of MBL genes in Korea. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecular characterisation of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates from hospital and ambulatory patients in Germany.

PubMed

Pietsch, Michael; Eller, Christoph; Wendt, Constanze; Holfelder, Martin; Falgenhauer, Linda; Fruth, Angelika; Grössl, Tobias; Leistner, Rasmus; Valenza, Giuseppe; Werner, Guido; Pfeifer, Yvonne

2017-02-01

The increase of Escherichia coli producing extended-spectrum β-lactamases (ESBL) in hospitals and their emergence as intestinal colonisers of healthy humans is of concern. Transmission ways and the extent of spread of distinct E. coli clones or ESBL genes among humans and animals via the food chain or the environment is a matter of debate. In this study we determined ESBL genotypes in E. coli isolates (n=233) resistant to 3rd generation cephalosporins from hospitals and medical practices using PCR and sequencing. Bacterial strain typing was performed by PCR-based phylogrouping, multilocus sequence typing (MLST) and a ST131-specific PCR. Results showed that CTX-M-15 (50.4%), CTX-M-1 (28.4%) and CTX-M-14 (5.6%) were the most common ESBL types. Especially, CTX-M-15 was associated with E. coli ST131 of phylogenetic group B2, which was the dominant sequence type among our isolates (35.8%). MLST typing revealed 40 different sequence types (STs), with ST131, ST410, ST10 and ST38 as the most prevalent ones. Our findings give an overview of the current distribution of ESBL-producing E. coli isolates from humans in Germany. E. coli O25b:H4-ST131 was confirmed to be the most common clone, which is known for its successful dissemination worldwide. Although heterogeneity among the isolates was found, several successful clones previously described in animals (ST410, ST10) also occurred in our isolate collection. Further detailed investigations of ESBL-producing isolates from different habitats are needed to evaluate possible transfer ways. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiple origins and incursions of the Atlantic barnacle Chthamalus proteus in the Pacific.

PubMed

Zardus, John D; Hadfield, Michael G

2005-10-01

Chthamalus proteus, a barnacle native to the Caribbean and western Atlantic, was introduced to the Pacific within the last few decades. Using direct sequencing of mitochondrial DNA (COI), we characterized genetic variation in native and introduced populations and searched for genetic matches between regions to determine if there were multiple geographical sources and introduction points for this barnacle. In the native range, we found great genetic differences among populations (max. F(ST) = 0.613) encompassing four lineages: one endemic to Panama, one endemic to Brazil, and two occurring Caribbean-wide. All four lineages were represented in the Pacific, but not equally; the Brazilian lineage was most prevalent and the Panamanian least common. Twenty-one individuals spread among nearly every island from where the barnacle is known in the Pacific, exactly matched six haplotypes scattered among Curaçao, the Netherlands Antilles; St John, US Virgin Islands; Puerto Rico; and Brazil, confirming a multigeographical origin for the Pacific populations. Significant genetic differences were also found in introduced populations from the Hawaiian Islands (F(CT) = 0.043, P < 0.001), indicating introduction events have occurred at more than one locality. However, the sequence, timing and number of arrival events remains unknown. Possible reasons for limited transport of this barnacle through the Panama Canal are discussed. This and a preponderance of Brazilian-type individuals in the Pacific suggest an unexpected route of entry from around Cape Horn, South America. Unification in the Pacific of historically divergent lineages of this barnacle raises the possibility for selection of 'hybrids' with novel ecological adaptations in its new environment.

Sequencing of the large dsDNA genome of Oryctes rhinoceros nudivirus using multiple displacement amplification of nanogram amounts of virus DNA.

PubMed

Wang, Yongjie; Kleespies, Regina G; Ramle, Moslim B; Jehle, Johannes A

2008-09-01

The genomic sequence analysis of many large dsDNA viruses is hampered by the lack of enough sample materials. Here, we report a whole genome amplification of the Oryctes rhinoceros nudivirus (OrNV) isolate Ma07 starting from as few as about 10 ng of purified viral DNA by application of phi29 DNA polymerase- and exonuclease-resistant random hexamer-based multiple displacement amplification (MDA) method. About 60 microg of high molecular weight DNA with fragment sizes of up to 25 kbp was amplified. A genomic DNA clone library was generated using the product DNA. After 8-fold sequencing coverage, the 127,615 bp of OrNV whole genome was sequenced successfully. The results demonstrate that the MDA-based whole genome amplification enables rapid access to genomic information from exiguous virus samples.