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

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.

Simulated Assessment of Interference Effects in Direct Sequence Spread Spectrum (DSSS) QPSK Receiver

DTIC Science & Technology

2014-03-27

bit error rate BPSK binary phase shift keying CDMA code division multiple access CSI comb spectrum interference CW continuous wave DPSK differential... CDMA ) and GPS systems which is a Gold code. This code is generated by a modulo-2 operation between two different preferred m-sequences. The preferred m...10 SNR Sim (dB) S N R O ut ( dB ) SNR RF SNR DS Figure 3.26: Comparison of input S NRS im and S NROut of the band-pass RF filter (S NRRF) and

Active Spread-Spectrum Steganalysis for Hidden Data Extraction

DTIC Science & Technology

2011-09-01

steganalysis. In particular, we aim to recover blindly se- cret data hidden in image hosts via (multi-signature) direct- sequence SS embedding [18]-[25...access (CDMA) communica- tion systems. Under the assumption that the embedded se- cret messages are independent identically distributed (i.i.d.) random

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.

Spectral shaping of spreading sequences as a mean to address the trade-off between narrowband and multi-access interferences in UWB systems

NASA Astrophysics Data System (ADS)

Mangia, Mauro; Pareschi, Fabio; Rovatti, Riccardo; Setti, Gianluca

This paper presents a way to cope with the need of simultaneously rejecting narrowband interference and multi-access interference in a UWB system based on direct-sequence CDMA. With this aim in mind, we rely on a closed-form expression of the system bit error probability in presence of both effects. By means of such a formula, we evaluate the effect of spectrum shaping techniques applied to the spreading sequences. The availability of a certain number of degrees of freedom in deciding the spectral profile allows us to cope with different configurations depending on the relative interfering power but also on the relative position of the signal center frequency and the narrowband interferer.

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.

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.

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

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.

A performance analysis of DS-CDMA and SCPC VSAT networks

NASA Technical Reports Server (NTRS)

Hayes, David P.; Ha, Tri T.

1990-01-01

Spread-spectrum and single-channel-per-carrier (SCPC) transmission techniques work well in very small aperture terminal (VSAT) networks for multiple-access purposes while allowing the earth station antennas to remain small. Direct-sequence code-division multiple-access (DS-CDMA) is the simplest spread-spectrum technique to use in a VSAT network since a frequency synthesizer is not required for each terminal. An examination is made of the DS-CDMA and SCPC Ku-band VSAT satellite systems for low-density (64-kb/s or less) communications. A method for improving the standardf link analysis of DS-CDMA satellite-switched networks by including certain losses is developed. The performance of 50-channel full mesh and star network architectures is analyzed. The selection of operating conditions producing optimum performance is demonstrated.

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

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.

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.

Performance of DS/SSMA (Direct-Sequence Spread-Spectrum Multiple-Access) Communications in Impulsive Channels.

DTIC Science & Technology

1986-11-01

mother and my brother. Their support and encouragement made this research exciting and enjoyable. I am grateful to my advisor, Professor H. Vincent Poor...the model. The m! M A variance of a random variable with density given by (A. 1) is a2 KmC 2 2A(I+l’)• (A.2) With the variance of the random variable

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

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.

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.

Asynchronous, Decentralized DS-CDMA Using Feedback-Controlled Spreading Sequences for Time-Dispersive Channels

NASA Astrophysics Data System (ADS)

Miyatake, Teruhiko; Chiba, Kazuki; Hamamura, Masanori; Tachikawa, Shin'ichi

We propose a novel asynchronous direct-sequence codedivision multiple access (DS-CDMA) using feedback-controlled spreading sequences (FCSSs) (FCSS/DS-CDMA). At the receiver of FCSS/DS-CDMA, the code-orthogonalizing filter (COF) produces a spreading sequence, and the receiver returns the spreading sequence to the transmitter. Then the transmitter uses the spreading sequence as its updated version. The performance of FCSS/DS-CDMA is evaluated over time-dispersive channels. The results indicate that FCSS/DS-CDMA greatly suppresses both the intersymbol interference (ISI) and multiple access interference (MAI) over time-invariant channels. FCSS/DS-CDMA is applicable to the decentralized multiple access.

A Code Division Multiple Access Communication System for the Low Frequency Band.

DTIC Science & Technology

1983-04-01

frequency channels spread-spectrum communication / complex sequences, orthogonal codes impulsive noise 20. ABSTRACT (Continue an reverse side It...their transmissions with signature sequences. Our LF/CDMA scheme is different in that each user’s signature sequence set consists of M orthogonal ...signature sequences. Our LF/CDMA scheme is different in that each user’s signature sequence set consists of M orthogonal sequences and thus log 2 M

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.

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.

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.

Multiuser signal detection using sequential decoding

NASA Astrophysics Data System (ADS)

Xie, Zhenhua; Rushforth, Craig K.; Short, Robert T.

1990-05-01

The application of sequential decoding to the detection of data transmitted over the additive white Gaussian noise channel by K asynchronous transmitters using direct-sequence spread-spectrum multiple access is considered. A modification of Fano's (1963) sequential-decoding metric, allowing the messages from a given user to be safely decoded if its Eb/N0 exceeds -1.6 dB, is presented. Computer simulation is used to evaluate the performance of a sequential decoder that uses this metric in conjunction with the stack algorithm. In many circumstances, the sequential decoder achieves results comparable to those obtained using the much more complicated optimal receiver.

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.

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.

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.

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.

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

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

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.

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

Binary Sequences for Spread-Spectrum Multiple-Access Communication

DTIC Science & Technology

1977-08-01

Massey, J. L., and Uhran, J. J., Jr., "Sub-baud coding," Proceedings of the Thirteenth Annual Allerton Conference on Circuit and System Theory, pp. 539...sequences in a multipl.e access environment," Proceedings of the Thirteenth Annual AIlerton Conference on Circuit and System Theory, pp. 21-27, October...34 Proceedings of the Thirteenth Annual Allertcn Conference on Circuit and System Theory, pp. 548-559, October 1975. Yao, K., *Performance bounds on

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

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).

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.

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.

Comparison of CDMA and FDMA for the MobileStar(sm) system

NASA Technical Reports Server (NTRS)

Jacobs, I. M.; Gilhousen, K. S.; Weaver, L. A.; Renshaw, K.; Murphy, T.

1988-01-01

Spread-spectrum code division multiple access (CDMA) and single channel per carrier frequency division multiple access (FDMA) systems are compared for spectrum efficiency. CDMA is shown to have greater maximum throughput than FDMA for the MobileStar(sm) system which uses digital voice activated carriers and directive circularly polarized satellite antennas.

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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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.

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.

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.

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

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

Study of spread spectrum multiple access systems for satellite communications with overlay on current services

NASA Technical Reports Server (NTRS)

Ha, Tri T.; Pratt, Timothy

1989-01-01

The feasibility of using spread spectrum techniques to provide a low-cost multiple access system for a very large number of low data terminals was investigated. Two applications of spread spectrum technology to very small aperture terminal (VSAT) satellite communication networks are presented. Two spread spectrum multiple access systems which use a form of noncoherent M-ary FSK (MFSK) as the primary modulation are described and the throughput analyzed. The analysis considers such factors as satellite power constraints and adjacent satellite interference. Also considered is the effect of on-board processing on the multiple access efficiency and the feasibility of overlaying low data rate spread spectrum signals on existing satellite traffic as a form of frequency reuse is investigated. The use of chirp is examined for spread spectrum communications. In a chirp communication system, each data bit is converted into one or more up or down sweeps of frequency, which spread the RF energy across a broad range of frequencies. Several different forms of chirp communication systems are considered, and a multiple-chirp coded system is proposed for overlay service. The mutual interference problem is examined in detail and a performance analysis undertaken for the case of a chirp data channel overlaid on a video channel.

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.

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.

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

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.

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.

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

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

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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...

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

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...

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

Spread-spectrum multiple access using wideband noncoherent MFSK

NASA Technical Reports Server (NTRS)

Ha, Tri T.; Pratt, Timothy; Maggenti, Mark A.

1987-01-01

Two spread-spectrum multiple access systems which use wideband M-ary frequency shift keying (FSK) (MFSK) as the primary modulation are presented. A bit error rate performance analysis is presented and system throughput is calculated for sample C band and Ku band satellite systems. Sample link analyses are included to illustrate power and adjacent satellite interference considerations in practical multiple access systems.

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.

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

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.

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.

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.

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/.

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.

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).

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.

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

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

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.

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.

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.

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.

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.

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.

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.

A ripple-spreading genetic algorithm for the aircraft sequencing problem.

PubMed

Hu, Xiao-Bing; Di Paolo, Ezequiel A

2011-01-01

When genetic algorithms (GAs) are applied to combinatorial problems, permutation representations are usually adopted. As a result, such GAs are often confronted with feasibility and memory-efficiency problems. With the aircraft sequencing problem (ASP) as a study case, this paper reports on a novel binary-representation-based GA scheme for combinatorial problems. Unlike existing GAs for the ASP, which typically use permutation representations based on aircraft landing order, the new GA introduces a novel ripple-spreading model which transforms the original landing-order-based ASP solutions into value-based ones. In the new scheme, arriving aircraft are projected as points into an artificial space. A deterministic method inspired by the natural phenomenon of ripple-spreading on liquid surfaces is developed, which uses a few parameters as input to connect points on this space to form a landing sequence. A traditional GA, free of feasibility and memory-efficiency problems, can then be used to evolve the ripple-spreading related parameters in order to find an optimal sequence. Since the ripple-spreading model is the centerpiece of the new algorithm, it is called the ripple-spreading GA (RSGA). The advantages of the proposed RSGA are illustrated by extensive comparative studies for the case of the ASP.

4D in vivo ultrafast ultrasound imaging using a row-column addressed matrix and coherently-compounded orthogonal plane waves

NASA Astrophysics Data System (ADS)

Flesch, M.; Pernot, M.; Provost, J.; Ferin, G.; Nguyen-Dinh, A.; Tanter, M.; Deffieux, T.

2017-06-01

4D ultrafast ultrasound imaging was recently shown using a 2D matrix (i.e. fully populated) connected to a 1024-channel ultrafast ultrasound scanner. In this study, we investigate the row-column addressing (RCA) matrix approach, which allows a reduction of independent channels from N  ×  N to N  +  N, with a dedicated beamforming strategy for ultrafast ultrasound imaging based on the coherent compounding of orthogonal plane wave (OPW). OPW is based on coherent compounding of plane wave transmissions in one direction with receive beamforming along the orthogonal direction and its orthogonal companion sequence. Such coherent recombination of complementary orthogonal sequences leads to the virtual transmit focusing in both directions which results into a final isotropic point spread function (PSF). In this study, a 32  ×  32 2D matrix array probe (1024 channels), centered at 5 MHz was considered. An RCA array, of same footprint with 32  +  32 elements (64 channels), was emulated by summing the elements either along a line or a column in software prior to beamforming. This approach allowed for the direct comparison of the 32  +  32 RCA scheme to the optimal fully sampled 32  ×  32 2D matrix configuration, which served as the gold standard. This approach was first studied through PSF simulations and then validated experimentally on a phantom consisting of anechoic cysts and echogenic wires. The contrast-to-noise ratio and the lateral resolution of the RCA approach were found to be approximately equal to half (in decibel) and twice the values, respectively, obtained when using the 2D matrix approach. Results in a Doppler phantom and the human humeral artery in vivo confirmed that ultrafast Doppler imaging can be achieved with reduced performances when compared against the equivalent 2D matrix. Volumetric anatomic Doppler rendering and voxel-based pulsed Doppler quantification are presented as well. OPW compound imaging using emulated RCA matrix can achieve a power Doppler with sufficient contrast to recover the vein shape and provides an accurate Doppler spectrum.

4D in vivo ultrafast ultrasound imaging using a row-column addressed matrix and coherently-compounded orthogonal plane waves.

PubMed

Flesch, M; Pernot, M; Provost, J; Ferin, G; Nguyen-Dinh, A; Tanter, M; Deffieux, T

2017-06-07

4D ultrafast ultrasound imaging was recently shown using a 2D matrix (i.e. fully populated) connected to a 1024-channel ultrafast ultrasound scanner. In this study, we investigate the row-column addressing (RCA) matrix approach, which allows a reduction of independent channels from N  ×  N to N  +  N, with a dedicated beamforming strategy for ultrafast ultrasound imaging based on the coherent compounding of orthogonal plane wave (OPW). OPW is based on coherent compounding of plane wave transmissions in one direction with receive beamforming along the orthogonal direction and its orthogonal companion sequence. Such coherent recombination of complementary orthogonal sequences leads to the virtual transmit focusing in both directions which results into a final isotropic point spread function (PSF). In this study, a 32  ×  32 2D matrix array probe (1024 channels), centered at 5 MHz was considered. An RCA array, of same footprint with 32  +  32 elements (64 channels), was emulated by summing the elements either along a line or a column in software prior to beamforming. This approach allowed for the direct comparison of the 32  +  32 RCA scheme to the optimal fully sampled 32  ×  32 2D matrix configuration, which served as the gold standard. This approach was first studied through PSF simulations and then validated experimentally on a phantom consisting of anechoic cysts and echogenic wires. The contrast-to-noise ratio and the lateral resolution of the RCA approach were found to be approximately equal to half (in decibel) and twice the values, respectively, obtained when using the 2D matrix approach. Results in a Doppler phantom and the human humeral artery in vivo confirmed that ultrafast Doppler imaging can be achieved with reduced performances when compared against the equivalent 2D matrix. Volumetric anatomic Doppler rendering and voxel-based pulsed Doppler quantification are presented as well. OPW compound imaging using emulated RCA matrix can achieve a power Doppler with sufficient contrast to recover the vein shape and provides an accurate Doppler spectrum.

Controlling laser driven protons acceleration using a deformable mirror at a high repetition rate

NASA Astrophysics Data System (ADS)

Noaman-ul-Haq, M.; Sokollik, T.; Ahmed, H.; Braenzel, J.; Ehrentraut, L.; Mirzaie, M.; Yu, L.-L.; Sheng, Z. M.; Chen, L. M.; Schnürer, M.; Zhang, J.

2018-03-01

We present results from a proof-of-principle experiment to optimize laser driven protons acceleration by directly feeding back its spectral information to a deformable mirror (DM) controlled by evolutionary algorithms (EAs). By irradiating a stable high-repetition rate tape driven target with ultra-intense pulses of intensities ∼1020 W/ cm2, we optimize the maximum energy of the accelerated protons with a stability of less than ∼5% fluctuations near optimum value. Moreover, due to spatio-temporal development of the sheath field, modulations in the spectrum are also observed. Particularly, a prominent narrow peak is observed with a spread of ∼15% (FWHM) at low energy part of the spectrum. These results are helpful to develop high repetition rate optimization techniques required for laser-driven ion accelerators.

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

Use of a priori statistics to minimize acquisition time for RFI immune spread spectrum systems

NASA Technical Reports Server (NTRS)

Holmes, J. K.; Woo, K. T.

1978-01-01

The optimum acquisition sweep strategy was determined for a PN code despreader when the a priori probability density function was not uniform. A psuedo noise spread spectrum system was considered which could be utilized in the DSN to combat radio frequency interference. In a sample case, when the a priori probability density function was Gaussian, the acquisition time was reduced by about 41% compared to a uniform sweep approach.

Defense Small Business Innovation Research Program (SBIR). Volume 4. Defense Agencies Abstracts of Phase 1 Awards 1992

DTIC Science & Technology

1992-01-01

perturbations and nonstationary interference effects so as to reduce decoding 13 DARPA SBIR PHASE I AWARDS errors for spread spectrum communications...potential applications - Utilization of spread spectrum techniques by DoD and others is increasing because ot robusines, to interference and fading...Mirror Devices ( DMD ) illuminated by a low power laser diode or led will be considered as a source. Commercial optical software in conjunction with in

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.

The phylogeography and spatiotemporal spread of south-central skunk rabies virus.

PubMed

Kuzmina, Natalia A; Lemey, Philippe; Kuzmin, Ivan V; Mayes, Bonny C; Ellison, James A; Orciari, Lillian A; Hightower, Dillon; Taylor, Steven T; Rupprecht, Charles E

2013-01-01

The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the present study we reconstructed spatiotemporal spread of SCSK in the whole territory of its circulation using a combination of Bayesian methods. The analysis based on 241 glycoprotein gene sequences demonstrated that SCSK is much more divergent phylogenetically than was appreciated previously. According to our analyses the SCSK originated in the territory of Texas ~170 years ago, and spread geographically during the following decades. The wavefront velocity in the northward direction was significantly greater than in the eastward and westward directions. Rivers (except the Mississippi River and Rio Grande River) did not constitute significant barriers for epizootic spread, in contrast to deserts and mountains. The mean dispersal rate of skunk rabies was lower than that of the raccoon and fox rabies. Viral lineages circulate in their areas with limited evidence of geographic spread during decades. However, spatiotemporal reconstruction shows that after a long period of stability the dispersal rate and wavefront velocity of SCSK are increasing. Our results indicate that there is a need to develop control measures for SCSK, and suggest how such measure can be implemented most efficiently. Our approach can be extrapolated to other rabies reservoirs and used as a tool for investigation of epizootic patterns and planning interventions towards disease elimination.

The Phylogeography and Spatiotemporal Spread of South-Central Skunk Rabies Virus

PubMed Central

Kuzmina, Natalia A.; Lemey, Philippe; Kuzmin, Ivan V.; Mayes, Bonny C.; Ellison, James A.; Orciari, Lillian A.; Hightower, Dillon; Taylor, Steven T.; Rupprecht, Charles E.

2013-01-01

The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the present study we reconstructed spatiotemporal spread of SCSK in the whole territory of its circulation using a combination of Bayesian methods. The analysis based on 241 glycoprotein gene sequences demonstrated that SCSK is much more divergent phylogenetically than was appreciated previously. According to our analyses the SCSK originated in the territory of Texas ~170 years ago, and spread geographically during the following decades. The wavefront velocity in the northward direction was significantly greater than in the eastward and westward directions. Rivers (except the Mississippi River and Rio Grande River) did not constitute significant barriers for epizootic spread, in contrast to deserts and mountains. The mean dispersal rate of skunk rabies was lower than that of the raccoon and fox rabies. Viral lineages circulate in their areas with limited evidence of geographic spread during decades. However, spatiotemporal reconstruction shows that after a long period of stability the dispersal rate and wavefront velocity of SCSK are increasing. Our results indicate that there is a need to develop control measures for SCSK, and suggest how such measure can be implemented most efficiently. Our approach can be extrapolated to other rabies reservoirs and used as a tool for investigation of epizootic patterns and planning interventions towards disease elimination. PMID:24312657

Accuracy of dynamical-decoupling-based spectroscopy of Gaussian noise

NASA Astrophysics Data System (ADS)

Szańkowski, Piotr; Cywiński, Łukasz

2018-03-01

The fundamental assumption of dynamical-decoupling-based noise spectroscopy is that the coherence decay rate of qubit (or qubits) driven with a sequence of many pulses, is well approximated by the environmental noise spectrum spanned on frequency comb defined by the sequence. Here we investigate the precise conditions under which this commonly used spectroscopic approach is quantitatively correct. To this end we focus on two representative examples of spectral densities: the long-tailed Lorentzian, and finite-ranged Gaussian—both expected to be encountered when using the qubit for nanoscale nuclear resonance imaging. We have found that, in contrast to Lorentz spectrum, for which the corrections to the standard spectroscopic formulas can easily be made negligible, the spectra with finite range are more challenging to reconstruct accurately. For Gaussian line shape of environmental spectral density, direct application of the standard dynamical-decoupling-based spectroscopy leads to erroneous attribution of long-tail behavior to the reconstructed spectrum. Fortunately, artifacts such as this, can be completely avoided with the simple extension to standard reconstruction method.

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.

Modular Multi-Function Multi-Band Airborne Radio System (MFBARS). Volume II. Detailed Report.

DTIC Science & Technology

1981-06-01

Three Platforms in a Field of Hyperbolic LOP’s.......................... 187 76 Comparison, MFBARS Versus Baseline .......... 190 77 Program Flow Chart...configure, from a set of common modules, a given total CNI capability on specific platforms for a given mission " the ability to take advantage of...X Comm/Nav GPS L-Band; Spread Spectrum Nay X X SEEK TALK UHF Spread; Spectrum Comm X X SINCGARS VHF; Freq. Hop Comm (some platforms ) AFSATCOM UHF

Marine asset security and tracking (MAST) system

DOEpatents

Hanson, Gregory Richard [Clinton, TN; Smith, Stephen Fulton [Loudon, TN; Moore, Michael Roy [Corryton, TN; Dobson, Eric Lesley [Charleston, SC; Blair, Jeffrey Scott [Charleston, SC; Duncan, Christopher Allen [Marietta, GA; Lenarduzzi, Roberto [Knoxville, TN

2008-07-01

Methods and apparatus are described for marine asset security and tracking (MAST). A method includes transmitting identification data, location data and environmental state sensor data from a radio frequency tag. An apparatus includes a radio frequency tag that transmits identification data, location data and environmental state sensor data. Another method includes transmitting identification data and location data from a radio frequency tag using hybrid spread-spectrum modulation. Another apparatus includes a radio frequency tag that transmits both identification data and location data using hybrid spread-spectrum modulation.

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.

Decay of S‐wave amplitudes with distance for earthquakes in the Charlevoix, Quebec, area: Effects of radiation pattern and directivity

USGS Publications Warehouse

Frankel, Arthur

2015-01-01

The decay of the Fourier spectral amplitudes of S waves over distances of 10–80 km near Charlevoix, Quebec, was determined using waveforms from seven earthquakes with MN 3.3–5.4. The S‐wave spectral amplitudes were corrected for site response and source amplitude by normalizing the coda‐wave spectrum at a fixed time after the origin time. The amplitude decay with distance was found to be less steep as the frequency increases from 1 to 14, contrary to what would be expected from anelastic and scattering attenuation for a point source with an isotropic radiation pattern. The decay at 14 Hz indicates that the geometrical spreading at distances less than 80 km is less steep than R−1.05. The steeper distance decay of the low‐frequency spectrum appears to be an artifact of the radiation pattern and rupture directivity, which affect the low‐frequency amplitude more than the high frequency. Synthetic seismograms were made for a horizontally layered crust for the Mw 4.6 Rivière du Loup earthquake and an Mw 3.3 event. The decay with distance of the 1 Hz spectral amplitudes of the synthetics is similar to that observed for the Rivière du Loup earthquake, indicating that radiation pattern and rupture directivity are important factors in determining the attenuation with distance at 1 Hz. For the Mw 3.3 earthquake, the distance decay of the 1 Hz spectral amplitudes was found to be sensitive to the focal mechanism. This study demonstrates that estimates of geometrical spreading made using 1 Hz amplitudes can be contaminated by radiation pattern and directivity effects and may not be applicable for constructing ground‐motion prediction equations for sources with other focal mechanisms and rupture behavior.

Spread spectrum image watermarking based on perceptual quality metric.

PubMed

Zhang, Fan; Liu, Wenyu; Lin, Weisi; Ngan, King Ngi

2011-11-01

Efficient image watermarking calls for full exploitation of the perceptual distortion constraint. Second-order statistics of visual stimuli are regarded as critical features for perception. This paper proposes a second-order statistics (SOS)-based image quality metric, which considers the texture masking effect and the contrast sensitivity in Karhunen-Loève transform domain. Compared with the state-of-the-art metrics, the quality prediction by SOS better correlates with several subjectively rated image databases, in which the images are impaired by the typical coding and watermarking artifacts. With the explicit metric definition, spread spectrum watermarking is posed as an optimization problem: we search for a watermark to minimize the distortion of the watermarked image and to maximize the correlation between the watermark pattern and the spread spectrum carrier. The simple metric guarantees the optimal watermark a closed-form solution and a fast implementation. The experiments show that the proposed watermarking scheme can take full advantage of the distortion constraint and improve the robustness in return.

Timing and frequency considerations in the worldwide testing of a spread spectrum communication system

NASA Technical Reports Server (NTRS)

Woodring, D. G.; Nichols, S. A.; Swanson, R.

1979-01-01

During 1978 and 1979, an Air Force C-135 test aircraft was flown to various locations in the North and South Atlantic and Pacific Oceans for satellite communications experiments. A part of the equipment tested on the aircraft was the SEACOM spread spectrum modem. The SEACOM modem operated at X band frequency from the aircraft via the DSCS II satellite to a ground station. For data to be phased successfully, it was necessary to maintain independent time and frequency accuracy over relatively long periods of time (up to two weeks) on the aircraft and at the ground station. To achieve this goal, two Efratom atomic frequency standards were used. The performance of these frequency standards as used in the spread spectrum modem is discussed, including the effects of high relative velocity, synchronization and the effects of the frequency standards on data performance is discussed. The aircraft environment, which includes extremes of temperature, as well as long periods of shutdown followed by rapid warmup requirements, is also discussed.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

PubMed

Quick, Joshua; 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 C; Black, Allison; Bedford, Trevor; Carroll, Miles W; Nunes, Marcio; Alcantara, Luiz Carlos; Sabino, Ester C; Baylis, Sally A; Faria, Nuno R; Loose, Matthew; Simpson, Jared T; Pybus, Oliver G; Andersen, Kristian G; Loman, Nicholas J

2017-06-01

Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which 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, optimized 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 in 1-2 d by starting with clinical samples and 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. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.

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.

47 CFR 87.479 - Harmful interference to radionavigation land stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... to establish wide-band systems using frequency-hopping spread spectrum techniques in the 960-1215 MHz... spectrum uniformly across the band; (2) The radiated pulse varies from the specified width of 6.4... peak of the JTIDS spectrum as measured in a 300 kHz bandwidth. The JTIDS will be prohibited from...

47 CFR 87.479 - Harmful interference to radionavigation land stations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... to establish wide-band systems using frequency-hopping spread spectrum techniques in the 960-1215 MHz... spectrum uniformly across the band; (2) The radiated pulse varies from the specified width of 6.4... peak of the JTIDS spectrum as measured in a 300 kHz bandwidth. The JTIDS will be prohibited from...

47 CFR 87.479 - Harmful interference to radionavigation land stations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... to establish wide-band systems using frequency-hopping spread spectrum techniques in the 960-1215 MHz... spectrum uniformly across the band; (2) The radiated pulse varies from the specified width of 6.4... peak of the JTIDS spectrum as measured in a 300 kHz bandwidth. The JTIDS will be prohibited from...

Characterization of OXA-48-like-producing Enterobacteriaceae isolated from river water in Algeria.

PubMed

Tafoukt, Rima; Touati, Abdelaziz; Leangapichart, Thongpan; Bakour, Sofiane; Rolain, Jean-Marc

2017-09-01

The spread of carbapenemase-producing Enterobacteriaceae (CPE) is a significant problem for healthcare worldwide. The prevalence of carbapenem-resistant Enterobacteriaceae (CPE) in water environments in Algeria are unknown. The aim of this study was to screen for the presence of CPE isolates in the Soummam River in Bejaia, Algeria. Isolates of Enterobacteriaceae recovered from twelve samples of river water and showing reduced susceptibility to carbapenems were included in this study. The isolates were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Isolates were subjected to antimicrobial susceptibility testing and the modified Carba NP test. Carbapenemase and extended-spectrum β-lactamase (ESBL) determinants were studied by PCR amplification and sequencing. The clonal relatedness between isolates was studied by Multilocus Sequence Typing (MLST) method. A total of 20 carbapenem-resistant Enterobacteriaceae strains were included in this study, identified as Escherichia coli (n = 12), Klebsiella pneumoniae (n = 3), Raoultella ornithinolytica (n = 3), Citrobacter freundii (n = 1) and Citrobacter braakii (n = 1). Carbapenemase genes identified in this study included bla OXA-48 , observed in 17 isolates (9 E. coli, 3 K. pneumoniae, 3 R. ornithinolytica, 1 C. freundii and 1 C. braakii), and bla OXA-244 , a variant of bla OXA-48 , was found in three E. coli isolates. MLST showed that 12 E. coli strains belonged to six different sequence types (ST559, ST38, ST212, ST3541, 1972 and ST2142), and we identified three different STs in K. pneumoniae isolates, including ST133, ST2055, and a new sequence type: ST2192. This study showed the presence of OXA-48-like-producing Enterobacteriaceae in water environments and highlighted the potential role of aquatic environments as reservoirs of clinically relevant antimicrobial-resistant bacteria, with the potential to spread throughout the community. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Spread spectrum phase modulation for coherent X-ray diffraction imaging.

PubMed

Zhang, Xuesong; Jiang, Jing; Xiangli, Bin; Arce, Gonzalo R

2015-09-21

High dynamic range, phase ambiguity and radiation limited resolution are three challenging issues in coherent X-ray diffraction imaging (CXDI), which limit the achievable imaging resolution. This paper proposes a spread spectrum phase modulation (SSPM) method to address the aforementioned problems in a single strobe. The requirements on phase modulator parameters are presented, and a practical implementation of SSPM is discussed via ray optics analysis. Numerical experiments demonstrate the performance of SSPM under the constraint of available X-ray optics fabrication accuracy, showing its potential to real CXDI applications.

Fluoroquinolone Resistance Mechanisms and population structure of Enterobacter cloacae non-susceptible to Ertapenem in North-Eastern France

PubMed Central

Guillard, Thomas; Cholley, Pascal; Limelette, Anne; Hocquet, Didier; Matton, Lucie; Guyeux, Christophe; Lebreil, Anne-Laure; Bajolet, Odile; Brasme, Lucien; Madoux, Janick; Vernet-Garnier, Véronique; Barbe, Coralie; Bertrand, Xavier; de Champs on behalf of CarbaFrEst Group, Christophe

2015-01-01

Fluoroquinolone (FQ) agents are a potential resort to treat infection due to Enterobacteriaceae producing extended spectrum β-lactamase and susceptible to FQ. In a context of increase of non-susceptibility to carbapenems among Enterobacteriaceae, we characterized FQ resistance mechanisms in 75 Enterobacter cloacae isolates non-susceptible to ertapenem in North-Eastern France in 2012 and describe the population structure by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Among them, 14.7% (12/75) carried a carbapenemase-encoding gene. Except one isolate producing VIM-1, the carbapenemase-producing isolates carried the well-known IncL/M pOXA48a plasmid. Most of the isolates (59/75) harbored at least a FQ-R determinant. qnr genes were predominant (40%, 30/75). The MLST study revealed that E. cloacae isolates’ clonality was wide [24 different sequence types (STs)]. The more widespread STs were ST74, ST101, ST110, ST114, and ST133. Carbapenem MICs were higher for E. cloacae ST74 than for other E. cloacae isolates. Plasmid-mediated quinolone resistance determinants were more often observed in E. cloacae ST74 isolates. These findings showed that (i) pOXA-48a is spreading in North-Eastern France, (ii) qnr is preponderant in E. cloacae, (iii) E. cloacae comprised a large amount of lineages spreading in North-Eastern France, and (iv) FQ as an alternative to β-lactams to treat ertapenem non-susceptible Enterobacteriaceae are compromised. PMID:26557115

Predicted sequence of cortical tau and amyloid-β deposition in Alzheimer disease spectrum.

PubMed

Cho, Hanna; Lee, Hye Sun; Choi, Jae Yong; Lee, Jae Hoon; Ryu, Young Hoon; Lee, Myung Sik; Lyoo, Chul Hyoung

2018-04-17

We investigated sequential order between tau and amyloid-β (Aβ) deposition in Alzheimer disease spectrum using a conditional probability method. Two hundred twenty participants underwent 18 F-flortaucipir and 18 F-florbetaben positron emission tomography scans and neuropsychological tests. The presence of tau and Aβ in each region and impairment in each cognitive domain were determined by Z-score cutoffs. By comparing pairs of conditional probabilities, the sequential order of tau and Aβ deposition were determined. Probability for the presence of tau in the entorhinal cortex was higher than that of Aβ in all cortical regions, and in the medial temporal cortices, probability for the presence of tau was higher than that of Aβ. Conversely, in the remaining neocortex above the inferior temporal cortex, probability for the presence of Aβ was always higher than that of tau. Tau pathology in the entorhinal cortex may appear earlier than neocortical Aβ and may spread in the absence of Aβ within the neighboring medial temporal regions. However, Aβ may be required for massive tau deposition in the distant cortical areas. Copyright © 2018 Elsevier Inc. All rights reserved.

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

HF band filter bank multi-carrier spread spectrum

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

Laraway, Stephen Andrew; Moradi, Hussein; Farhang-Boroujeny, Behrouz

Abstract—This paper describes modifications to the filter bank multicarrier spread spectrum (FB-MC-SS) system, that was presented in [1] and [2], to enable transmission of this waveform in the HF skywave channel. FB-MC-SS is well suited for the HF channel because it performs well in channels with frequency selective fading and interference. This paper describes new algorithms for packet detection, timing recovery and equalization that are suitable for the HF channel. Also, an algorithm for optimizing the peak to average power ratio (PAPR) of the FBMC- SS waveform is presented. Application of this algorithm results in a waveform with low PAPR.more » Simulation results using a wide band HF channel model demonstrate the robustness of this system over a wide range of delay and Doppler spreads.« less

Method for high resolution magnetic resonance analysis using magic angle technique

DOEpatents

Wind, Robert A.; Hu, Jian Zhi

2003-11-25

A method of performing a magnetic resonance analysis of a biological object that includes placing the biological object in a main magnetic field and in a radio frequency field, the main magnetic field having a static field direction; rotating the biological object at a rotational frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. According to another embodiment, the radio frequency is pulsed to provide a sequence capable of producing a spectrum that is substantially free of spinning sideband peaks.

Geologic maps of the Sacramento-San Joaquin Delta, California

USGS Publications Warehouse

Atwater, Brian F.

1982-01-01

The Sacramento-San Joaquin Delta, the arm of the San Francisco Bay estuary that reaches into the Central Valley of California, differs from typical coastal-plain deltas in three important respects.  First, rather than meeting the ocean individually and directly, all major waterways of this delta discharge via a single constricted outlet into a chain of estuarine bays and straits.  Second, in the most common vertical sequence of deposits, peat and mud deposited in tidal marshes and swamps (tidal wetlands) directly overlie alluvium or eolian sand, a sequence recording a landward spread of tidal environments rather than the seaward migration of fluvial environments that is typical of coastal-plain deltas (Cosby, 1941, p. 43; Thompson, 1957, p. 12; Shlemon and Begg, 1975, p. 259; Atwater and Belknap, 1980).  Finally, intensive human use has led to a peculiar set of conflicts involving rights to water and responsibilities for flood-control levees (Kockelman and other, 1982).

Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

DOEpatents

Weier, H.U.G.; Gray, J.W.

1995-06-27

A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

DOEpatents

Weier, Heinz-Ulrich G.; Gray, Joe W.

1995-01-01

A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

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.

Next-generation sequencing for typing and detection of resistance genes: performance of a new commercial method during an outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.

PubMed

Veenemans, J; Overdevest, I T; Snelders, E; Willemsen, I; Hendriks, Y; Adesokan, A; Doran, G; Bruso, S; Rolfe, A; Pettersson, A; Kluytmans, J A J W

2014-07-01

Next-generation sequencing (NGS) has the potential to provide typing results and detect resistance genes in a single assay, thus guiding timely treatment decisions and allowing rapid tracking of transmission of resistant clones. We evaluated the performance of a new NGS assay (Hospital Acquired Infection BioDetection System; Pathogenica) during an outbreak of sequence type 131 (ST131) Escherichia coli infections in a nursing home in The Netherlands. The assay was performed on 56 extended-spectrum-beta-lactamase (ESBL) E. coli isolates collected during 2 prevalence surveys (March and May 2013). Typing results were compared to those of amplified fragment length polymorphism (AFLP), whereby we visually assessed the agreement of the BioDetection phylogenetic tree with clusters defined by AFLP. A microarray was considered the gold standard for detection of resistance genes. AFLP identified a large cluster of 31 indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree showed that all isolates of this outbreak cluster were strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. The BioDetection assay detected ESBL genes in all but 1 isolate (sensitivity, 98%) but was unable to discriminate between ESBL and non-ESBL TEM and SHV beta-lactamases or to specify CTX-M genes by group. The performance of the hospital-acquired infection (HAI) BioDetection System for typing of E. coli isolates compared well with the results of AFLP. Its performance with larger collections from different locations, and for typing of other species, was not evaluated and needs further study. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Methods and apparatuses for self-generating fault-tolerant keys in spread-spectrum systems

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

Moradi, Hussein; Farhang, Behrouz; Subramanian, Vijayarangam

Self-generating fault-tolerant keys for use in spread-spectrum systems are disclosed. At a communication device, beacon signals are received from another communication device and impulse responses are determined from the beacon signals. The impulse responses are circularly shifted to place a largest sample at a predefined position. The impulse responses are converted to a set of frequency responses in a frequency domain. The frequency responses are shuffled with a predetermined shuffle scheme to develop a set of shuffled frequency responses. A set of phase differences is determined as a difference between an angle of the frequency response and an angle ofmore » the shuffled frequency response at each element of the corresponding sets. Each phase difference is quantized to develop a set of secret-key quantized phases and a set of spreading codes is developed wherein each spreading code includes a corresponding phase of the set of secret-key quantized phases.« less

Serendipity, Punctuated

NASA Astrophysics Data System (ADS)

Asmus, John F.

Laser divestment entered the field of art conservation through a nonlinear sequence of positive accidental events (serendipity) that involved the cinema industry, the invention of spread-spectrum and frequency-hopping communications, nuclear space propulsion, and oceanography. The unlikely chain of events began with the invention of a secure military communications system by a Viennese motion picture actress (1942). A first evaluation of the novel communications concept took place during a high-altitude nuclear test (TEAK) over the Pacific Ocean in 1958. The secure radio link proved to be a failure; however, analyses of the backscattered electromagnetic radiation contributed to the realization that nuclear-explosion plasmas need not be spherically symmetrical. Nobel Laureate Freeman Dyson exploited this nuclear option to guide in the design and prototype development of the ORION spaceship that was to rendezvous with the planet Saturn in 1970.

Discrete Ramanujan transform for distinguishing the protein coding regions from other regions.

PubMed

Hua, Wei; Wang, Jiasong; Zhao, Jian

2014-01-01

Based on the study of Ramanujan sum and Ramanujan coefficient, this paper suggests the concepts of discrete Ramanujan transform and spectrum. Using Voss numerical representation, one maps a symbolic DNA strand as a numerical DNA sequence, and deduces the discrete Ramanujan spectrum of the numerical DNA sequence. It is well known that of discrete Fourier power spectrum of protein coding sequence has an important feature of 3-base periodicity, which is widely used for DNA sequence analysis by the technique of discrete Fourier transform. It is performed by testing the signal-to-noise ratio at frequency N/3 as a criterion for the analysis, where N is the length of the sequence. The results presented in this paper show that the property of 3-base periodicity can be only identified as a prominent spike of the discrete Ramanujan spectrum at period 3 for the protein coding regions. The signal-to-noise ratio for discrete Ramanujan spectrum is defined for numerical measurement. Therefore, the discrete Ramanujan spectrum and the signal-to-noise ratio of a DNA sequence can be used for distinguishing the protein coding regions from the noncoding regions. All the exon and intron sequences in whole chromosomes 1, 2, 3 and 4 of Caenorhabditis elegans have been tested and the histograms and tables from the computational results illustrate the reliability of our method. In addition, we have analyzed theoretically and gotten the conclusion that the algorithm for calculating discrete Ramanujan spectrum owns the lower computational complexity and higher computational accuracy. The computational experiments show that the technique by using discrete Ramanujan spectrum for classifying different DNA sequences is a fast and effective method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Outcomes of Diagnostic Exome Sequencing in Patients With Diagnosed or Suspected Autism Spectrum Disorders.

PubMed

Rossi, Mari; El-Khechen, Dima; Black, Mary Helen; Farwell Hagman, Kelly D; Tang, Sha; Powis, Zöe

2017-05-01

Exome sequencing has recently been proved to be a successful diagnostic method for complex neurodevelopmental disorders. However, the diagnostic yield of exome sequencing for autism spectrum disorders has not been extensively evaluated in large cohorts to date. We performed diagnostic exome sequencing in a cohort of 163 individuals with autism spectrum disorder (66.3%) or autistic features (33.7%). The diagnostic yield observed in patients in our cohort was 25.8% (42 of 163) for positive or likely positive findings in characterized disease genes, while a candidate genetic etiology was reported for an additional 3.3% (4 of 120) of patients. Among the positive findings in the patients with autism spectrum disorder or autistic features, 61.9% were the result of de novo mutations. Patients presenting with psychiatric conditions or ataxia or paraplegia in addition to autism spectrum disorder or autistic features were significantly more likely to receive positive results compared with patients without these clinical features (95.6% vs 27.1%, P < 0.0001; 83.3% vs 21.2%, P < 0.0001, respectively). The majority of the positive findings were in recently identified autism spectrum disorder genes, supporting the importance of diagnostic exome sequencing for patients with autism spectrum disorder or autistic features as the causative genes might evade traditional sequential or panel testing. These results suggest that diagnostic exome sequencing would be an efficient primary diagnostic method for patients with autism spectrum disorders or autistic features. Moreover, our data may aid clinicians to better determine which subset of patients with autism spectrum disorder with additional clinical features would benefit the most from diagnostic exome sequencing. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Familial Blau syndrome without uveitis caused by a novel mutation in the nucleotide-binding oligomerization domain-containing protein 2 gene with good response to infliximab.

PubMed

Toral-López, Jaime; González-Huerta, Luz M; Martín-Del Campo, Mónica; Messina-Baas, Olga; Cuevas-Covarrubias, Sergio A

2018-05-01

The proband in this study was a 4-year-old Mexican girl with Blau syndrome. She and her affected family members had skin rash and arthritis but no uveitis. Exome sequencing and DNA direct sequencing from blood samples revealed a novel nucleotide-binding oligomerization domain-containing protein 2 gene mutation in the affected family members. This study is the first report of a Mexican family with Blau syndrome showing good infliximab treatment response. The novel mutation in the nucleotide-binding oligomerization domain-containing protein 2 gene (c.1808A>G) enriches the mutation spectrum in Blau syndrome. This family represents one of the few cases of autosomal Blau syndrome with no uveitis; because of phenotype variability, it is important to recognize Blau syndrome's clinical spectrum and recommend genetic consultation. © 2018 Wiley Periodicals, Inc.

Implications for crustal accretion at fast spreading ridges from observations in Jurassic oceanic crust in the western Pacific

NASA Astrophysics Data System (ADS)

Pockalny, Robert A.; Larson, Roger L.

2003-01-01

Downhole logging data and basement stratigraphy interpretations are used to determine the spreading environment and crustal accretion history of the ocean basement cored at ODP Hole 801C located in the Jurassic Magnetic Quiet Zone of the western Pacific. High-resolution microresistivity data obtained with the Formation MicroScanner are used to measure the dip of the extrusive layers and indicate a 10°-30° increase in dip down the drill hole with lava flow contacts dipping back toward the original ridge axis. This structural pattern and the high proportion of massive flows relative to pillow units are consistent with prevailing crustal accretion models proposed for faster spreading ridges (e.g., >60 km/m.y., full-rate). A detailed analysis of the age data, basement lithology, related geochemistry, and structural attitudes suggest the shallowest 100 m of the drilled section (e.g., Sequences I-III) were emplaced just off the ridge (Sequence III) or significantly farther off-axis up to 5-15 m.y. later (Sequences I and II). The remainder of the drilled section (e.g., Sequences IV-VIII) has geochemical, lithological and physical trends that are assumed to be representative of crust created at faster spreading ridges. The pattern of dipping lava flow contacts from this deeper section of the drill hole suggests lava flows emanating from the ridge axis are limited to 1-2 km off-axis. Our results suggest ocean crust drilled at Hole 801C was created at faster spreading rates; however, caution should be used when incorporating Sequences I-III into geochemical reference sections for faster spreading ridges.

Implications of nonadventitious rhizome spread on reproduction, inbreeding, and conservation for a rare grassland legume.

PubMed

Severns, Paul M; Liston, Aaron; Wilson, Mark V

2011-01-01

Small population size, genetic diversity, and spatial patterns of vegetative spread are important aspects to consider when managing populations of rare clonal plant species. We used 5 variable nuclear simple sequence repeat nDNA loci to determine the extent of genet rhizome spread, examine the possibility of very small population sizes, and project how Bombus spp. (bumblebee) foraging may impact selfing (through geitonogamy) for a threatened lupine (Lupinus oreganus Heller) that sprawls through nonadventitious rhizomes. Genotyping identified 1 genet (27 × 13 m) that dominated about 30% of a study site, whereas 15 genets spread a maximum average distance of about 5.5 m (range 1.6 -27.1 m) and appeared to be well integrated with intervening genets. We found unexpectedly high genotype diversity, no evidence of a recent genetic bottleneck, and 5 of 6 patches had mean fixation index values that were near Hardy-Weinberg Equilibrium expectations. If the median maximum Bombus foraging distance observed in lupine patches (1.2 m) occurred within genotyped populations, a typical foraging flight would have >80% chance of occurring between different genets. Our study demonstrates that inferences associated with clonality, small population size, and inbreeding depression should be directly evaluated for rare vegetatively spreading plants.

Spectral dimension and dynamics for Harper's equation

NASA Astrophysics Data System (ADS)

Wilkinson, Michael; Austin, Elizabeth J.

1994-07-01

The spectrum of Harper's equation (a model for Bloch electrons in a magnetic field) is a fractal Cantor set if the ratio β of the area of a unit cell to that of a flux quantum is not a rational number. It has been conjectured that the second moment of an initially localized wave packet has a power-law growth of the form ~t2D0, where D0 is the box-counting dimension of the spectrum, and that D0=1/2. We present numerical results on the dimension of the spectrum and the spread of a wave packet indicating that these relationships are at best approximate. We also present heuristic arguments suggesting that there should be no general relationships between the dimension and the spread of a wave packet.

Autism Spectrum Conditions in Individuals with Mobius Sequence, CHARGE Syndrome and Oculo-Auriculo-Vertebral Spectrum: Diagnostic Aspects

ERIC Educational Resources Information Center

Johansson, Maria; Gillberg, Christopher; Rastam, Maria

2010-01-01

As part of multidisciplinary surveys of three Behavioural Phenotype Conditions (BPCs); Mobius sequence (Mobius), CHARGE syndrome (CHARGE) and oculo-auriculo-vertebral spectrum (OAV), autism spectrum conditions (ASCs) was diagnosed in 45%, 68% and 42% of the individuals, respectively. Diagnostic difficulties due to additional dysfunctions such as…

Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder.

PubMed

Steinberg, Karyn Meltz; Ramachandran, Dhanya; Patel, Viren C; Shetty, Amol C; Cutler, David J; Zwick, Michael E

2012-09-28

Autism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype. We surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility. We found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3' UTR variants did not show statistically significant effects on the expression of NLGN3 and NLGN4X. In addition, we identified two NLGN3 intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation. These data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects.

Identification of rare X-linked neuroligin variants by massively parallel sequencing in males with autism spectrum disorder

PubMed Central

2012-01-01

Background Autism spectrum disorder (ASD) is highly heritable, but the genetic risk factors for it remain largely unknown. Although structural variants with large effect sizes may explain up to 15% ASD, genome-wide association studies have failed to uncover common single nucleotide variants with large effects on phenotype. The focus within ASD genetics is now shifting to the examination of rare sequence variants of modest effect, which is most often achieved via exome selection and sequencing. This strategy has indeed identified some rare candidate variants; however, the approach does not capture the full spectrum of genetic variation that might contribute to the phenotype. Methods We surveyed two loci with known rare variants that contribute to ASD, the X-linked neuroligin genes by performing massively parallel Illumina sequencing of the coding and noncoding regions from these genes in males from families with multiplex autism. We annotated all variant sites and functionally tested a subset to identify other rare mutations contributing to ASD susceptibility. Results We found seven rare variants at evolutionary conserved sites in our study population. Functional analyses of the three 3’ UTR variants did not show statistically significant effects on the expression of NLGN3 and NLGN4X. In addition, we identified two NLGN3 intronic variants located within conserved transcription factor binding sites that could potentially affect gene regulation. Conclusions These data demonstrate the power of massively parallel, targeted sequencing studies of affected individuals for identifying rare, potentially disease-contributing variation. However, they also point out the challenges and limitations of current methods of direct functional testing of rare variants and the difficulties of identifying alleles with modest effects. PMID:23020841

Accurate estimation of motion blur parameters in noisy remote sensing image

NASA Astrophysics Data System (ADS)

Shi, Xueyan; Wang, Lin; Shao, Xiaopeng; Wang, Huilin; Tao, Zhong

2015-05-01

The relative motion between remote sensing satellite sensor and objects is one of the most common reasons for remote sensing image degradation. It seriously weakens image data interpretation and information extraction. In practice, point spread function (PSF) should be estimated firstly for image restoration. Identifying motion blur direction and length accurately is very crucial for PSF and restoring image with precision. In general, the regular light-and-dark stripes in the spectrum can be employed to obtain the parameters by using Radon transform. However, serious noise existing in actual remote sensing images often causes the stripes unobvious. The parameters would be difficult to calculate and the error of the result relatively big. In this paper, an improved motion blur parameter identification method to noisy remote sensing image is proposed to solve this problem. The spectrum characteristic of noisy remote sensing image is analyzed firstly. An interactive image segmentation method based on graph theory called GrabCut is adopted to effectively extract the edge of the light center in the spectrum. Motion blur direction is estimated by applying Radon transform on the segmentation result. In order to reduce random error, a method based on whole column statistics is used during calculating blur length. Finally, Lucy-Richardson algorithm is applied to restore the remote sensing images of the moon after estimating blur parameters. The experimental results verify the effectiveness and robustness of our algorithm.

Dielectric fluid directional spreading under the action of corona discharge

NASA Astrophysics Data System (ADS)

Zhou, Shangru; Liu, Jie; Hu, Qun; Jiang, Teng; Yang, Jinchu; Liu, Sheng; Zheng, Huai

2018-01-01

Liquid spreading is a very common nature phenomenon and of significant importance for a broad range of applications. In this study, a dielectric fluid directional spreading phenomenon is presented. Under the action of corona discharge, a dielectric fluid, here a typical silicone directionally spreads along conductive patterns on conductive/nonconductive substrates. Directional spreading behaviors of silicone were experimentally observed on different conductive patterns in detail. Spreading speeds were analyzed at different driving voltages, which induced the corona discharge. The presented phenomenon may be useful to inspire several techniques of manipulating liquid transportation and fabricating micropatterns.

Molecular and clinical characterization of plasmid-mediated AmpC β-lactamase-producing Escherichia coli bacteraemia: a comparison with extended-spectrum β-lactamase-producing and non-resistant E. coli bacteraemia.

PubMed

Matsumura, Y; Nagao, M; Iguchi, M; Yagi, T; Komori, T; Fujita, N; Yamamoto, M; Matsushima, A; Takakura, S; Ichiyama, S

2013-02-01

Plasmid-mediated AmpC β-lactamase-producing Escherichia coli (AmpC-E) bacteraemia was characterized by comparison with bacteraemia caused by extended-spectrum β-lactamase (ESBL)-producing E. coli (ESBL-E) and non-resistant E. coli (NR-E) in the era of the worldwide spread of the CTX-M-15-producing O25b-ST131-B2 clone. Of 706 bloodstream E. coli isolates collected between 2005 and 2010 in three Japanese university hospitals, 111 ESBL screening-positive isolates were analysed for AmpC and ESBL genes by PCR. A case-control study was performed in which the cases consisted of all of the patients with AmpC-E bacteraemia. Phylogenetic groups, sequence types and O25b serotype were determined. Twenty-seven AmpC-E isolates (26 of which were of the CMY-2 type) were identified, and 54 ESBL-E and 54 NR-E isolates were selected for the controls. Nineteen AmpC-E isolates were also positive for ESBL. CTX-M-14 was the most prevalent ESBL type among both the AmpC-E and ESBL-E isolates. The O25b-ST131-B2 clone was the most prevalent among the ESBL-E isolates (26%) and the second most prevalent among the NR-E isolates (13%), but only one O25b-ST131-B2 clone was found among the AmpC-E isolates. Twenty-three different sequence types were identified among the AmpC-E isolates. When compared with bacteraemia with ESBL-E, previous isolation of multidrug-resistant bacteria and intravascular catheterization were independently associated with a lower risk for AmpC-E. When compared with NR-E bacteraemia, prior use of antibiotics was the only significant risk factor for AmpC-E. Unlike the spread of the O25b-ST131-B2 clone between ESBL-E and NR-E, the AmpC-E isolates were not dominated by any specific clone. © 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.

A new modem for microwave time synchronisation via geosynchronous telecommunication satellites

NASA Astrophysics Data System (ADS)

Dienert, Michael

1992-06-01

A study illustrating the two way time transfer technique and describing the use of this technique with the MITREX (Microwave Time and Range Experiment) SATRE (Satellite Time and Range Experiment) modems is presented. The two way time transfer technique via geosynchronous telecom satellites is one of the most accurate methods for synchronization and comparison of remote clocks. Most of the unknown propagation delays can be eliminated by the two way principle. The use of a coherent spread spectrum technique with a truncated pseudonoise code offers a resolution better than 30 ps of the measured time interval. The receiver is built around a Delay Locked Loop (DLL), which correlates the received signal with the known PN sequence to derive the control signal of the loop. In the locked state both PN sequences are synchronous and tracking errors of less than 30 ps are possible. Results showing the accuracy of the modem depending on signal to noise ratio and variation of total input power levels are presented and show that the expected improvement of the jitter of the internal delay by an increase of the chip rate is possible.

Broad-Spectrum Inhibition of HIV-1 by a Monoclonal Antibody Directed against a gp120-Induced Epitope of CD4

PubMed Central

Burastero, Samuele E.; Frigerio, Barbara; Lopalco, Lucia; Sironi, Francesca; Breda, Daniela; Longhi, Renato; Scarlatti, Gabriella; Canevari, Silvana; Figini, Mariangela; Lusso, Paolo

2011-01-01

To penetrate susceptible cells, HIV-1 sequentially interacts with two highly conserved cellular receptors, CD4 and a chemokine receptor like CCR5 or CXCR4. Monoclonal antibodies (MAbs) directed against such receptors are currently under clinical investigation as potential preventive or therapeutic agents. We immunized Balb/c mice with molecular complexes of the native, trimeric HIV-1 envelope (Env) bound to a soluble form of the human CD4 receptor. Sera from immunized mice were found to contain gp120-CD4 complex-enhanced antibodies and showed broad-spectrum HIV-1-inhibitory activity. A proportion of MAbs derived from these mice preferentially recognized complex-enhanced epitopes. In particular, a CD4-specific MAb designated DB81 (IgG1Κ) was found to preferentially bind to a complex-enhanced epitope on the D2 domain of human CD4. MAb DB81 also recognized chimpanzee CD4, but not baboon or macaque CD4, which exhibit sequence divergence in the D2 domain. Functionally, MAb DB81 displayed broad HIV-1-inhibitory activity, but it did not exert suppressive effects on T-cell activation in vitro. The variable regions of the heavy and light chains of MAb DB81 were sequenced. Due to its broad-spectrum anti-HIV-1 activity and lack of immunosuppressive effects, a humanized derivative of MAb DB81 could provide a useful complement to current preventive or therapeutic strategies against HIV-1. PMID:21818294

Broad-spectrum inhibition of HIV-1 by a monoclonal antibody directed against a gp120-induced epitope of CD4.

PubMed

Burastero, Samuele E; Frigerio, Barbara; Lopalco, Lucia; Sironi, Francesca; Breda, Daniela; Longhi, Renato; Scarlatti, Gabriella; Canevari, Silvana; Figini, Mariangela; Lusso, Paolo

2011-01-01

To penetrate susceptible cells, HIV-1 sequentially interacts with two highly conserved cellular receptors, CD4 and a chemokine receptor like CCR5 or CXCR4. Monoclonal antibodies (MAbs) directed against such receptors are currently under clinical investigation as potential preventive or therapeutic agents. We immunized Balb/c mice with molecular complexes of the native, trimeric HIV-1 envelope (Env) bound to a soluble form of the human CD4 receptor. Sera from immunized mice were found to contain gp120-CD4 complex-enhanced antibodies and showed broad-spectrum HIV-1-inhibitory activity. A proportion of MAbs derived from these mice preferentially recognized complex-enhanced epitopes. In particular, a CD4-specific MAb designated DB81 (IgG1Κ) was found to preferentially bind to a complex-enhanced epitope on the D2 domain of human CD4. MAb DB81 also recognized chimpanzee CD4, but not baboon or macaque CD4, which exhibit sequence divergence in the D2 domain. Functionally, MAb DB81 displayed broad HIV-1-inhibitory activity, but it did not exert suppressive effects on T-cell activation in vitro. The variable regions of the heavy and light chains of MAb DB81 were sequenced. Due to its broad-spectrum anti-HIV-1 activity and lack of immunosuppressive effects, a humanized derivative of MAb DB81 could provide a useful complement to current preventive or therapeutic strategies against HIV-1.

A metasurface-based prism analogue for terahertz rainbow spectrum manipulation

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Spreading Sequence System for Full Connectivity Relay Network

NASA Technical Reports Server (NTRS)

Kwon, Hyuck M. (Inventor); Pham, Khanh D. (Inventor); Yang, Jie (Inventor)

2018-01-01

Fully connected uplink and downlink fully connected relay network systems using pseudo-noise spreading and despreading sequences subjected to maximizing the signal-to-interference-plus-noise ratio. The relay network systems comprise one or more transmitting units, relays, and receiving units connected via a communication network. The transmitting units, relays, and receiving units each may include a computer for performing the methods and steps described herein and transceivers for transmitting and/or receiving signals. The computer encodes and/or decodes communication signals via optimum adaptive PN sequences found by employing Cholesky decompositions and singular value decompositions (SVD). The PN sequences employ channel state information (CSI) to more effectively and more securely computing the optimal sequences.

GPS Radiosonde with Spread-Spectrum Transmitter for Aerial dE/dt Studies

NASA Astrophysics Data System (ADS)

Sonnenfeld, R.; John, B. D.; William, W. P.; Aulich, G.; Ken, E.

2003-12-01

Inexpensive, low-power and reliable telemetry is a continuous struggle for those engaged in developing balloon-borne instruments for atmospheric electric studies. Several custom designs, by NCAR and others, have enabled much useful work in radiosondes. Also, packet radio technology has been used with great success. Easily obtainable packet radios are currently limited to 9600 baud. In search of higher baud rates that integrate well with microprocessor-based data acquisition systems, we have tested a new commercial off-the-shelf spread-spectrum transmitter. The transmitter operates in the 900 MHz industrial, scientific and medical (ISM) band with a transmit power of 100 mW. The transmitter (a Maxstream XC09-019NST) is used with a dedicated receiver, such that the data to be transmitted is fed via RS-232C protocols to the transmitter, and received as a text string via a serial port on the receiver. We did tests at raw baud rates of 9600 and 19200 (roughly 1000-2000 characters/second). Initial range tests required integrating the transmitter with a GPS and sending the NMEA-position-string (National Marine Electronics Assoc.) to a ground-based receiver. In ground-based tests, we repeatedly saw that a clear line-of-sight between transmitter and receiver was required for successful telemetry. The maximum range obtained during ground tests was 15.3 km at 9600 baud. Initial balloon tests results were, as hoped, more encouraging than ground-based tests. The maximum range (ground distance and altitude) of any balloon transmission was 58.0 km in fair-weather with excellent line-of-sight visibility. Our highest altitude transmission was 28.6 km absolute altitude (25.3 km altitude relative to launch point). These numbers were determined from the GPS coordinates transmitted. Antenna alignment and acceptance angle effects were observed in our received data. For these reasons, the full data rate of 19200 baud was only obtained out to 10 km, and then again around 45-58 km. Performance of the system could be improved by spreading packets over a wider range of spectrum, improving the transmit antenna geometry, increasing power, using a more directional receive antenna; or all of the above.

Community-onset extended-spectrum-β-lactamase-producing Escherichia coli sequence type 131 at two Korean community hospitals: The spread of multidrug-resistant E. coli to the community via healthcare facilities.

PubMed

Kim, Young Ah; Kim, Jin Ju; Kim, Heejung; Lee, Kyungwon

2017-01-01

The recent molecular epidemiology of ESBL-producing Escherichia coli infection in two Korean community hospitals was evaluated in this prospective observational study. We collected non-duplicated E. coli isolates from consecutive, sequentially encountered patients with community-onset episodes between March and April 2016 in two community hospitals in Gyeonggi-do province, Korea. We studied the prevalence, clinical characteristics and molecular epidemiology of E. coli sequence type 131 (ST131) isolated from the community. From a total of 213 E. coli isolates collected from the community, 94 (44.1%) were community-onset healthcare-associated isolates and 119 (55.9%) were community-associated isolates, of which urinary tract infection was the majority. A total of 55 (25.8%) of the 213 E. coli isolates were confirmed to have ESBL genes, which were mainly CTX-M types such as CTX-M-14 and CTX-M-15. There was no difference in the proportion of globally epidemic ST131 clones or that of O25, O16, H30, or H30Rx subclones between community-associated and community-onset healthcare-associated isolates. In this study, considerable ST131 E. coli isolations in the community were observed and about half of them were related to the history of a visit to the healthcare facilities, indicating the spread of multidrug-resistant E. coli to the community via healthcare facilities. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Spread of imipenem-resistant Acinetobacter baumannii co-expressing OXA-23 and GES-11 carbapenemases in Lebanon.

PubMed

Hammoudi, D; Moubareck, C Ayoub; Hakime, N; Houmani, M; Barakat, A; Najjar, Z; Suleiman, M; Fayad, N; Sarraf, R; Sarkis, D Karam

2015-07-01

The acquisition of carbapenemases by Acinetobacter baumannii is reported increasingly worldwide, but data from Lebanon are limited. The aims of this study were to evaluate the prevalence of imipenem-resistant A. baumannii in Lebanon, identify resistance determinants, and detect clonal relatedness. Imipenem-resistant A. baumannii were collected from nine Lebanese hospitals during 2012. Antimicrobial susceptibility, the cloxacillin effect, and ethylenediaminetetraacetic acid (EDTA) synergy were determined. Genes encoding carbapenemases and insertion sequence ISAba1 were screened via PCR sequencing. ISAba1 position relative to genes encoding Acinetobacter-derived cephalosporinases (ADCs) and OXA-23 was studied by PCR mapping. Clonal linkage was examined by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Out of 724 A. baumannii isolated in 2012, 638 (88%) were imipenem-resistant. Of these, 142 were analyzed. Clavulanic acid-imipenem synergy suggested carbapenem-hydrolyzing extended-spectrum β-lactamase. A positive cloxacillin test indicated ADCs, while EDTA detection strips were negative. Genotyping indicated that 90% of isolates co-harbored blaOXA-23 and blaGES-11. The remaining strains had blaOXA-23, blaOXA-24, blaGES-11, or blaOXA-24 with blaGES-11. ISAba1 was located upstream of blaADC and blaOXA-23 in 97% and 100% of isolates, respectively. ERIC-PCR fingerprinting revealed 18 pulsotypes spread via horizontal gene transfer and clonal dissemination. This survey established baseline evidence of OXA-23 and GES-11-producing A. baumannii in Lebanon, indicating the need for further surveillance. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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.

Quantum centipedes: collective dynamics of interacting quantum walkers

NASA Astrophysics Data System (ADS)

Krapivsky, P. L.; Luck, J. M.; Mallick, K.

2016-08-01

We consider the quantum centipede made of N fermionic quantum walkers on the one-dimensional lattice interacting by means of the simplest of all hard-bound constraints: the distance between two consecutive fermions is either one or two lattice spacings. This composite quantum walker spreads ballistically, just as the simple quantum walk. However, because of the interactions between the internal degrees of freedom, the distribution of its center-of-mass velocity displays numerous ballistic fronts in the long-time limit, corresponding to singularities in the empirical velocity distribution. The spectrum of the centipede and the corresponding group velocities are analyzed by direct means for the first few values of N. Some analytical results are obtained for arbitrary N by exploiting an exact mapping of the problem onto a free-fermion system. We thus derive the maximal velocity describing the ballistic spreading of the two extremal fronts of the centipede wavefunction, including its non-trivial value in the large-N limit.

Spectral analysis of extinguished sunlight

NASA Astrophysics Data System (ADS)

Zagury, Frédéric; Goutail, Florence

2003-08-01

SAOZ (Système d'Analyse par Observation Zénitale) is a balloon-borne experiment which determines the column density of several molecular species from the visible spectrum of sunlight. We will use sequence of spectra collected during a sunset to discuss atmospheric extinction, and the nature of the radiation field in the atmosphere. The radiation field in the atmosphere is, from daylight to sunset, and with a clear sky, dominated by light coming from the direction of the sun. This light is composed of direct sunlight (extinguished by the gas), and of sunlight forward-scattered by aerosols. As the sun sets, aerosol scattering is first perceived towards the UV. It progressively replaces direct sunlight over all of the spectrum. Our analysis permits fixing the main parameters of each component of the radiation field at any time. The fits we find for the extinction of sunlight in the atmosphere must also apply to starlight. Thus, the present work can be used in astronomy to correct ground-based spectral observations for extinction in the atmosphere.

Emotional Feedback and the Viral Spread of Social Media Messages About Autism Spectrum Disorders

PubMed Central

2016-01-01

Objective. To determine whether exchanges of emotional language between health advocacy organizations and social media users predict the spread of posts about autism spectrum disorders (ASDs). Methods. I created a Facebook application that tracked views of ASD advocacy organizations' posts between July 19, 2011, and December 18, 2012. I evaluated the association between exchanges of emotional language and viral views of posts, controlling for additional characteristics of posts, the organizations that produced them, the social media users who viewed them, and the broader social environment. Results. Exchanges of emotional language between advocacy organizations and social media users are strongly associated with viral views of posts. Conclusions. Social media outreach may be more successful if organizations invite emotional dialogue instead of simply conveying information about ASDs. Yet exchanges of angry language may contribute to the viral spread of misinformation, such as the rumor that vaccines cause ASDs. PMID:27196641

Emotional Feedback and the Viral Spread of Social Media Messages About Autism Spectrum Disorders.

PubMed

Bail, Christopher A

2016-07-01

To determine whether exchanges of emotional language between health advocacy organizations and social media users predict the spread of posts about autism spectrum disorders (ASDs). I created a Facebook application that tracked views of ASD advocacy organizations' posts between July 19, 2011, and December 18, 2012. I evaluated the association between exchanges of emotional language and viral views of posts, controlling for additional characteristics of posts, the organizations that produced them, the social media users who viewed them, and the broader social environment. Exchanges of emotional language between advocacy organizations and social media users are strongly associated with viral views of posts. Social media outreach may be more successful if organizations invite emotional dialogue instead of simply conveying information about ASDs. Yet exchanges of angry language may contribute to the viral spread of misinformation, such as the rumor that vaccines cause ASDs.

Epidemic spreading through direct and indirect interactions.

PubMed

Ganguly, Niloy; Krueger, Tyll; Mukherjee, Animesh; Saha, Sudipta

2014-09-01

In this paper we study the susceptible-infected-susceptible epidemic dynamics, considering a specialized setting where popular places (termed passive entities) are visited by agents (termed active entities). We consider two types of spreading dynamics: direct spreading, where the active entities infect each other while visiting the passive entities, and indirect spreading, where the passive entities act as carriers and the infection is spread via them. We investigate in particular the effect of selection strategy, i.e., the way passive entities are chosen, in the spread of epidemics. We introduce a mathematical framework to study the effect of an arbitrary selection strategy and derive formulas for prevalence, extinction probabilities, and epidemic thresholds for both indirect and direct spreading. We also obtain a very simple relationship between the extinction probability and the prevalence. We pay special attention to preferential selection and derive exact formulas. The analysis reveals that an increase in the diversity in the selection process lowers the epidemic thresholds. Comparing the direct and indirect spreading, we identify regions in the parameter space where the prevalence of the indirect spreading is higher than the direct one.

Epidemic spreading through direct and indirect interactions

NASA Astrophysics Data System (ADS)

Ganguly, Niloy; Krueger, Tyll; Mukherjee, Animesh; Saha, Sudipta

2014-09-01

In this paper we study the susceptible-infected-susceptible epidemic dynamics, considering a specialized setting where popular places (termed passive entities) are visited by agents (termed active entities). We consider two types of spreading dynamics: direct spreading, where the active entities infect each other while visiting the passive entities, and indirect spreading, where the passive entities act as carriers and the infection is spread via them. We investigate in particular the effect of selection strategy, i.e., the way passive entities are chosen, in the spread of epidemics. We introduce a mathematical framework to study the effect of an arbitrary selection strategy and derive formulas for prevalence, extinction probabilities, and epidemic thresholds for both indirect and direct spreading. We also obtain a very simple relationship between the extinction probability and the prevalence. We pay special attention to preferential selection and derive exact formulas. The analysis reveals that an increase in the diversity in the selection process lowers the epidemic thresholds. Comparing the direct and indirect spreading, we identify regions in the parameter space where the prevalence of the indirect spreading is higher than the direct one.

Adaptively synchronous scalable spread spectrum (A4S) data-hiding strategy for three-dimensional visualization

NASA Astrophysics Data System (ADS)

Hayat, Khizar; Puech, William; Gesquière, Gilles

2010-04-01

We propose an adaptively synchronous scalable spread spectrum (A4S) data-hiding strategy to integrate disparate data, needed for a typical 3-D visualization, into a single JPEG2000 format file. JPEG2000 encoding provides a standard format on one hand and the needed multiresolution for scalability on the other. The method has the potential of being imperceptible and robust at the same time. While the spread spectrum (SS) methods are known for the high robustness they offer, our data-hiding strategy is removable at the same time, which ensures highest possible visualization quality. The SS embedding of the discrete wavelet transform (DWT)-domain depth map is carried out in transform domain YCrCb components from the JPEG2000 coding stream just after the DWT stage. To maintain synchronization, the embedding is carried out while taking into account the correspondence of subbands. Since security is not the immediate concern, we are at liberty with the strength of embedding. This permits us to increase the robustness and bring the reversibility of our method. To estimate the maximum tolerable error in the depth map according to a given viewpoint, a human visual system (HVS)-based psychovisual analysis is also presented.

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.

What caused the outbreak of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing

PubMed Central

Haller, Sebastian; Eller, Christoph; Hermes, Julia; Kaase, Martin; Steglich, Matthias; Radonić, Aleksandar; Dabrowski, Piotr Wojtek; Nitsche, Andreas; Pfeifer, Yvonne; Werner, Guido; Wunderle, Werner; Velasco, Edward; Abu Sin, Muna; Eckmanns, Tim; Nübel, Ulrich

2015-01-01

Objective We aimed to retrospectively reconstruct the timing of transmission events and pathways in order to understand why extensive preventive measures and investigations were not sufficient to prevent new cases. Methods We extracted available information from patient charts to describe cases and to compare them to the normal population of the ward. We conducted a cohort study to identify risk factors for pathogen acquisition. We sequenced the available isolates to determine the phylogenetic relatedness of Klebsiella pneumoniae isolates on the basis of their genome sequences. Results The investigation comprises 37 cases and the 10 cases with ESBL (extended-spectrum beta-lactamase)-producing K. pneumoniae bloodstream infection. Descriptive epidemiology indicated that a continuous transmission from person to person was most likely. Results from the cohort study showed that ‘frequent manipulation’ (a proxy for increased exposure to medical procedures) was significantly associated with being a case (RR 1.44, 95% CI 1.02 to 2.19). Genome sequences revealed that all 48 bacterial isolates available for sequencing from 31 cases were closely related (maximum genetic distance, 12 single nucleotide polymorphisms). Based on our calculation of evolutionary rate and sequence diversity, we estimate that the outbreak strain was endemic since 2008. Conclusions Epidemiological and phylogenetic analyses consistently indicated that there were additional, undiscovered cases prior to the onset of microbiological screening and that the spread of the pathogen remained undetected over several years, driven predominantly by person-to-person transmission. Whole-genome sequencing provided valuable information on the onset, course and size of the outbreak, and on possible ways of transmission. PMID:25967999

A single-chip event sequencer and related microcontroller instrumentation for atomic physics research.

PubMed

Eyler, E E

2011-01-01

A 16-bit digital event sequencer with 50 ns resolution and 50 ns trigger jitter is implemented by using an internal 32-bit timer on a dsPIC30F4013 microcontroller, controlled by an easily modified program written in standard C. It can accommodate hundreds of output events, and adjacent events can be spaced as closely as 1.5 μs. The microcontroller has robust 5 V inputs and outputs, allowing a direct interface to common laboratory equipment and other electronics. A USB computer interface and a pair of analog ramp outputs can be added with just two additional chips. An optional display/keypad unit allows direct interaction with the sequencer without requiring an external computer. Minor additions also allow simple realizations of other complex instruments, including a precision high-voltage ramp generator for driving spectrum analyzers or piezoelectric positioners, and a low-cost proportional integral differential controller and lock-in amplifier for laser frequency stabilization with about 100 kHz bandwidth.

Massive increase, spread, and exchange of extended spectrum β-lactamase-encoding genes among intestinal Enterobacteriaceae in hospitalized children with severe acute malnutrition in Niger.

PubMed

Woerther, Paul-Louis; Angebault, Cécile; Jacquier, Hervé; Hugede, Henri-Charles; Janssens, Ann-Carole; Sayadi, Sani; El Mniai, Assiya; Armand-Lefèvre, Laurence; Ruppé, Etienne; Barbier, François; Raskine, Laurent; Page, Anne-Laure; de Rekeneire, Nathalie; Andremont, Antoine

2011-10-01

From the time of CTX-M emergence, extended-spectrum β-lactamase-producing enterobacteria (ESBL-E) have spread worldwide in community settings as well as in hospitals, particularly in developing countries. Although their dissemination appears linked to Escherichia coli intestinal carriage, precise paths of this dynamic are largely unknown. Children from a pediatric renutrition center were prospectively enrolled in a fecal carriage study. Antibiotic exposure was recorded. ESBL-E strains were isolated using selective media from fecal samples obtained at admission and, when negative, also at discharge. ESBL-encoding genes were identified, their environments and plasmids were characterized, and clonality was assessed with polymerase chain reaction-based methods and pulsed-field gel electrophoresis for E. coli and Klebsiella pneumoniae. E. coli strains were subjected to multilocus sequence typing. The ESBL-E carriage rate was 31% at admission in the 55 children enrolled. All children enrolled received antibiotics during hospitalization. Among the ESBL-E-negative children, 16 were resampled at discharge, and the acquisition rate was 94%. The bla(CTX-M-15) gene was found in >90% of the carriers. Genetic environments and plasmid characterization evidenced the roles of a worldwide, previously described, multidrug-resistant region and of IncF plasmids in CTX-M-15 E. coli dissemination. Diversity of CTX-M-15-carrying genetic structures and clonality of acquired ESBL E. coli suggested horizontal genetic transfer and underlined the potential of some ST types for nosocomial cross-transmission. Cross-transmission and high selective pressure lead to very high acquisition of ESBL-E carriage, contributing to dissemination in the community. Strict hygiene measures as well as careful balancing of benefit-risk ratio of current antibiotic policies need to be reevaluated.

Prevalence and characterization of extended-spectrum beta-lactamase-producing Enterobacteriaceae in spring waters.

PubMed

Li, S; Zhu, Z C; Wang, L; Zhou, Y F; Tang, Y J; Miao, Z M

2015-12-01

The purpose of this study was to investigate the prevalence and characterization of extended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae from spring waters in Mountain Tai of China. ESBL-producing Enterobacteriaceae were found in four out of 50 sampled spring waters (4/50, 8·0%) and a total of 16 non-duplicate ESBL-producing Enterobacteriaceae were obtained, including 13 Escherichia coli (E. coli) and three Klebsiella pneumoniae (Kl. pneumoniae). All 16 nonduplicate ESBL-producing Enterobacteriaceae isolates harboured genes encoding CTX-M ESBLs, among which six expressed CTX-M-15, five produced CTX-M-14, three produced CTX-M-55 and two expressed CTX-M-27. Four multilocus sequence types (ST) were found and ST131 was the dominant type (8/16, 50·0%). Taken together, the contamination of ESBL-producing Enterobacteriaceae were present in spring waters of Mountain Tai. The results indicated that spring waters could become a reservoir of antibiotic resistant bacteria and contribute to the spread of antimicrobial-resistant bacteria via drinking water or food chain. In addition, wastewater discharge of restaurants or hotels may be an important contribution source of antibiotic resistant bacteria in spring waters. © 2015 The Society for Applied Microbiology.

IEEE 1988 International Symposium on Electromagnetic Compatibility, Seattle, WA, Aug. 2-4, 1988, Record

NASA Astrophysics Data System (ADS)

Various papers on electromagnetic compatibility are presented. Some of the optics considered include: field-to-wire coupling 1 to 18 GHz, SHF/EHF field-to-wire coupling model, numerical method for the analysis of coupling to thin wire structures, spread-spectrum system with an adaptive array for combating interference, technique to select the optimum modulation indices for suppression of undesired signals for simultaneous range and data operations, development of a MHz RF leak detector technique for aircraft harness surveillance, and performance of standard aperture shielding techniques at microwave frequncies. Also discussed are: spectrum efficiency of spread-spectrum systems, control of power supply ripple produced sidebands in microwave transistor amplifiers, an intership SATCOM versus radar electromagnetic interference prediction model, considerations in the design of a broadband E-field sensing system, unique bonding methods for spacecraft, and review of EMC practice for launch vehicle systems.

Airborne spread of foot-and-mouth disease - model intercomparison

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

Gloster, J; Jones, A; Redington, A

2008-09-04

Foot-and-mouth disease is a highly infectious vesicular disease of cloven-hoofed animals caused by foot-and-mouth disease virus. It spreads by direct contact between animals, by animal products (milk, meat and semen), by mechanical transfer on people or fomites and by the airborne route - with the relative importance of each mechanism depending on the particular outbreak characteristics. Over the years a number of workers have developed or adapted atmospheric dispersion models to assess the risk of foot-and-mouth disease virus spread through the air. Six of these models were compared at a workshop hosted by the Institute for Animal Health/Met Office duringmore » 2008. A number of key issues emerged from the workshop and subsequent modelling work: (1) in general all of the models predicted similar directions for 'at risk' livestock with much of the remaining differences strongly related to differences in the meteorological data used; (2) determination of an accurate sequence of events is highly important, especially if the meteorological conditions vary substantially during the virus emission period; and (3) differences in assumptions made about virus release, environmental fate, and subsequent infection can substantially modify the size and location of the downwind risk area. Close relationships have now been established between participants, which in the event of an outbreak of disease could be readily activated to supply advice or modelling support.« less

Population structure of clinical Pseudomonas aeruginosa from West and Central African countries.

PubMed

Cholley, Pascal; Ka, Roughyatou; Guyeux, Christophe; Thouverez, Michelle; Guessennd, Nathalie; Ghebremedhin, Beniam; Frank, Thierry; Bertrand, Xavier; Hocquet, Didier

2014-01-01

Pseudomonas aeruginosa (PA) has a non-clonal, epidemic population with a few widely distributed and frequently encountered sequence types (STs) called 'high-risk clusters'. Clinical P. aeruginosa (clinPA) has been studied in all inhabited continents excepted in Africa, where a very few isolates have been analyzed. Here, we characterized a collection of clinPA isolates from four countries of West and Central Africa. 184 non-redundant isolates of clinPA from hospitals of Senegal, Ivory Coast, Nigeria, and Central African Republic were genotyped by MLST. We assessed their resistance level to antibiotics by agar diffusion and identified the extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) by sequencing. The population structure of the species was determined by a nucleotide-based analysis of the entire PA MLST database and further localized on the phylogenetic tree (i) the sequence types (STs) of the present collection, (ii) the STs by continents, (iii) ESBL- and MBL-producing STs from the MLST database. We found 80 distinct STs, of which 24 had no relationship with any known STs. 'High-risk' international clonal complexes (CC155, CC244, CC235) were frequently found in West and Central Africa. The five VIM-2-producing isolates belonged to CC233 and CC244. GES-1 and GES-9 enzymes were produced by one CC235 and one ST1469 isolate, respectively. We showed the spread of 'high-risk' international clonal complexes, often described as multidrug-resistant on other continents, with a fully susceptible phenotype. The MBL- and ESBL-producing STs were scattered throughout the phylogenetic tree and our data suggest a poor association between a continent and a specific phylogroup. ESBL- and MBL-encoding genes are borne by both successful international clonal complexes and distinct local STs in clinPA of West and Central Africa. Furthermore, our data suggest that the spread of a ST could be either due to its antibiotic resistance or to features independent from the resistance to antibiotics.

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

Large cohort screening of G6PD deficiency and the mutational spectrum in the Dongguan District in Southern China.

PubMed

Peng, Qi; Li, Siping; Ma, Keze; Li, Wenrui; Ma, Qiang; He, Xiaoguang; He, Yuejing; He, Ting; Lu, Xiaomei

2015-01-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common enzymatic disorder of the erythrocytes that affects 400 million people worldwide. We developed a PCR-reverse dot blot (RDB) assay to screen twenty genotypes of seventeen Chinese G6PD mutations and investigate the spectrum of G6PD deficiency mutations in Dongguan District, Guangdong Province, in southern China. The PCR-RDB assay consists of multiplex PCR amplification of seven fragments in the G6PD target sequence of wild-type and mutant genomic DNA samples followed by hybridization to a test strip containing allele-specific oligonucleotide probes. A total of 16,464 individuals were analyzed by a combination of phenotypic screening and genotypic detection using the PCR-RDB assay and DNA sequence analysis. The PCR-RDB assay had a detection rate of 98.1%, which was validated by direct sequencing in a blind study with 100% concordance. The G6PD deficiency incidence rate in Dongguan District is 4.08%. Thirty-two genotypes from 469 individuals were found. The two most common variants were c.1376G>T and c.1388G>A, followed by c.95A>G, c.871G>A, c.392G>T, and c.1024 C>T. In addition, two rare mutations (c.703C>A and c.406C>T) were detected by DNA sequencing analysis. In our study, 65 cases harbored the C1311T/IVS polymorphism and 67 cases were homozygote. The PCR-RDB assay we established is a reliable and effective method for screening G6PD mutations in the Chinese population. Data on the spectrum of mutations in the Dongguan District is beneficial to the clinical diagnosis and prevention of G6PD deficiency.

Large Cohort Screening of G6PD Deficiency and the Mutational Spectrum in the Dongguan District in Southern China

PubMed Central

Ma, Keze; Li, Wenrui; Ma, Qiang; He, Xiaoguang; He, Yuejing; He, Ting; Lu, Xiaomei

2015-01-01

Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common enzymatic disorder of the erythrocytes that affects 400 million people worldwide. We developed a PCR-reverse dot blot (RDB) assay to screen twenty genotypes of seventeen Chinese G6PD mutations and investigate the spectrum of G6PD deficiency mutations in Dongguan District, Guangdong Province, in southern China. Method The PCR-RDB assay consists of multiplex PCR amplification of seven fragments in the G6PD target sequence of wild-type and mutant genomic DNA samples followed by hybridization to a test strip containing allele-specific oligonucleotide probes. A total of 16,464 individuals were analyzed by a combination of phenotypic screening and genotypic detection using the PCR-RDB assay and DNA sequence analysis. Results The PCR-RDB assay had a detection rate of 98.1%, which was validated by direct sequencing in a blind study with 100% concordance. The G6PD deficiency incidence rate in Dongguan District is 4.08%. Thirty-two genotypes from 469 individuals were found. The two most common variants were c.1376G>T and c.1388G>A, followed by c.95A>G, c.871G>A, c.392G>T, and c.1024 C>T. In addition, two rare mutations (c.703C>A and c.406C>T) were detected by DNA sequencing analysis. In our study, 65 cases harbored the C1311T/IVS polymorphism and 67 cases were homozygote. Conclusion The PCR-RDB assay we established is a reliable and effective method for screening G6PD mutations in the Chinese population. Data on the spectrum of mutations in the Dongguan District is beneficial to the clinical diagnosis and prevention of G6PD deficiency. PMID:25775246

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

Fecal Carriage of Extended-Spectrum β-Lactamases in Healthy Humans, Poultry, and Wild Birds in León, Nicaragua-A Shared Pool of blaCTX-M Genes and Possible Interspecies Clonal Spread of Extended-Spectrum β-Lactamases-Producing Escherichia coli.

PubMed

Hasan, Badrul; Laurell, Karl; Rakib, Mufti Mahmud; Ahlstedt, Erik; Hernandez, Jorge; Caceres, Mercedes; Järhult, Josef D

2016-12-01

Antibiotic-resistant bacteria are a major concern in the healthcare of today, especially the increasing number of gram-negative bacteria producing β-lactamases such as extended-spectrum β-lactamases (ESBLs). However, little is known about the relationship of ESBL producers in humans and domestic and wild birds, especially in a low-income setting. Therefore, we studied the fecal carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae in healthy humans, poultry, and wild birds in the vicinity of León, Nicaragua. Three hundred fecal samples were collected during December 2012 from humans (n = 100), poultry (n = 100) and wild birds (n = 100). The samples were examined for ESBL-producing E. coli and K. pneumoniae, revealing the prevalence of 27% in humans, 13% in poultry, and 8% in wild birds. Further characterization of the ESBL-producing isolates was performed through polymerase chain reaction (PCR) (NDM, CTX-M), epidemiological typing (ERIC2-PCR), multilocus sequence typing, and sequencing. ESBL producers harbored bla CTX-M-2 , bla CTX-M-15 , bla CTX-M-22 , and bla CTX-M-3 genotypes. The bla CTX-M-15 constituted the absolute majority of ESBL genes among all samples. ERIC-PCR demonstrated highly related E. coli clones among humans, poultry, and wild birds. Clinically relevant E. coli clone ST648 was found in humans and poultry. There is a shared pool of bla CTX-M genes between humans and domesticated and wild birds in Nicaragua, and the results suggest shared clones of ESBL-producing E. coli. The study adds to the notion that wild birds and poultry can pick up antibiotic-resistant bacteria of human origin and function as a melting pot of resistance. Structured surveillance programs of antimicrobial resistance and a more regulated prescription of antibiotics are warranted in Nicaragua.

A Spread-Spectrum SQUID Multiplexer

NASA Astrophysics Data System (ADS)

Irwin, K. D.; Chaudhuri, S.; Cho, H.-M.; Dawson, C.; Kuenstner, S.; Li, D.; Titus, C. J.; Young, B. A.

2018-06-01

The transition-edge sensor (TES) is a mature, high-resolution x-ray spectrometer technology that provides a much higher efficiency than dispersive spectrometers such as gratings and crystal spectrometers. As larger arrays are developed, time-division multiplexing schemes operating at MHz frequencies are being replaced by microwave SQUID multiplexers using frequency-division multiplexing at GHz frequencies. However, the multiplexing factor achievable with microwave SQUIDs is limited by the high slew rate on the leading edge of x-ray pulses. In this paper, we propose a new multiplexing scheme for high-slew-rate TES x-ray calorimeters: the spread-spectrum SQUID multiplexer, which has the potential to enable higher multiplexing factors, especially in applications with lower photon-arrival rates.

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.

Performance Analysis of HF Band FB-MC-SS

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

Hussein Moradi; Stephen Andrew Laraway; Behrouz Farhang-Boroujeny

Abstract—In a recent paper [1] the filter bank multicarrier spread spectrum (FB-MC-SS) waveform was proposed for wideband spread spectrum HF communications. A significant benefit of this waveform is robustness against narrow and partial band interference. Simulation results in [1] demonstrated good performance in a wideband HF channel over a wide range of conditions. In this paper we present a theoretical analysis of the bit error probably for this system. Our analysis tailors the results from [2] where BER performance was analyzed for maximum ration combining systems that accounted for correlation between subcarriers and channel estimation error. Equations are give formore » BER that closely match the simulated performance in most situations.« less

Characterization of epidemic IncI1-Iγ plasmids harboring ambler class A and C genes in Escherichia coli and Salmonella enterica from animals and humans.

PubMed

Smith, Hilde; Bossers, Alex; Harders, Frank; Wu, Guanghui; Woodford, Neil; Schwarz, Stefan; Guerra, Beatriz; Rodríguez, Irene; van Essen-Zandbergen, Alieda; Brouwer, Michael; Mevius, Dik

2015-09-01

The aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-Iγ plasmids obtained from Escherichia coli and Salmonella enterica isolates from animal and human reservoirs. For this, 251 IncI1-Iγ plasmids carrying various extended-spectrum β-lactamase (ESBL) or AmpC β-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-Iγ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation in traY and excA genes found in IncI1-Iγ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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.

Needle Tip Position and Bevel Direction Have No Effect in the Fluoroscopic Epidural Spreading Pattern in Caudal Epidural Injections: A Randomized Trial

PubMed Central

Kwon, Won Kyoung; Kim, Ah Na; Lee, Pil Moo; Park, Cheol Hwan; Kim, Jae Hun

2016-01-01

Background. Caudal epidural steroid injections (CESIs) are an effective treatment for pain. If the injection spreads in a specific pattern depending on the needle position or bevel direction, it would be possible to inject the agent into a specific and desired area. Objectives. We conducted a prospective randomized trial to determine if the needle position and bevel direction have any effect on the epidural spreading pattern in CESI. Methods. Demographic data of the patient were collected. During CESI, the needle position (middle or lateral) and direction (ventral or dorsal) were randomly allocated. Following fluoroscope-guided injection of 4 mL contrast media and 10 mL of injectates, the epidural spreading patterns (ventral or dorsal, bilateral or lateral) were imaged. Results. In the 210 CESIs performed, the needle tip position and bevel direction did not influence the epidural spreading patterns at L4-5 and L5-S1 disc levels. A history of Lumbar spine surgery was associated with a significantly limited spread to each disc level. A midline needle tip position was more effective than the lateral position in spreading to the distant disc levels. Conclusions. Neither the needle tip position nor the bevel direction affected the epidural drug spreading pattern during CESI. PMID:27445609

Spectral evolution of weakly nonlinear random waves: kinetic description vs direct numerical simulations

NASA Astrophysics Data System (ADS)

Annenkov, Sergei; Shrira, Victor

2016-04-01

We study numerically the long-term evolution of water wave spectra without wind forcing, using three different models, aiming at understanding the role of different sets of assumptions. The first model is the classical Hasselmann kinetic equation (KE). We employ the WRT code kindly provided by G. van Vledder. Two other models are new. As the second model, we use the generalised kinetic equation (gKE), derived without the assumption of quasi-stationarity. Thus, unlike the KE, the gKE is valid in the cases when a wave spectrum is changing rapidly (e.g. at the initial stage of evolution of a narrow spectrum). However, the gKE employs the same statistical closure as the KE. The third model is based on the Zakharov integrodifferential equation for water waves and does not depend on any statistical assumptions. Since the Zakharov equation plays the role of the primitive equation of the theory of wave turbulence, we refer to this model as direct numerical simulation of spectral evolution (DNS-ZE). For initial conditions, we choose two narrow-banded spectra with the same frequency distribution (a JONSWAP spectrum with high peakedness γ = 6) and different degrees of directionality. These spectra are from the set of observations collected in a directional wave tank by Onorato et al (2009). Spectrum A is very narrow in angle (corresponding to N = 840 in the cosN directional model). Spectrum B is initially wider in angle (corresponds to N = 24). Short-term evolution of both spectra (O(102) wave periods) has been studied numerically by Xiao et al (2013) using two other approaches (broad-band modified nonlinear Schrödinger equation and direct numerical simulation based on the high-order spectral method). We use these results to verify the initial stage of our DNS-ZE simulations. However, the advantage of the DNS-ZE method is that it allows to study long-term spectral evolution (up to O(104) periods), which was previously possible only with the KE. In the short-term evolution, we find a good agreement between our DNS-ZE results and simulations by Xiao et al (2013), both for the evolution of frequency spectra and for the directional spreading. In the long term, all three approaches demonstrate very close evolution of integral characteristics of spectra, approaching for large time the theoretical asymptotes of the self-similar stage of evolution. However, the detailed comparison of the spectral evolution shows certain notable differences. Both kinetic equations give virtually identical evolution of spectrum B, but in the case of initially nearly one-dimensional spectrum A the KE overestimates the amplitude of the spectral peak. Meanwhile, the DNS-ZE results show considerably wider spectra with less pronounced peak. There is a striking difference for the rate of spectral broadening, which is much larger for the gKE and especially for the KE, than for the DNS-ZE. We show that the rates of change of the spectra obtained with the DNS-ZE are proportional to the fourth power of nonlinearity, corresponding to the dynamical timescale of evolution, rather than the statistical timescale of both kinetic equations.

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.

Molecular genealogy tools for white-tailed deer with chronic wasting disease

PubMed Central

Ernest, Holly B.; Hoar, Bruce R.; Well, Jay A.; O’Rourke, Katherine I.

2010-01-01

Molecular genetic data provide powerful tools for genealogy reconstruction to reveal mechanisms underlying disease ecology. White-tailed deer (Odocoileus virginianus) congregate in matriarchal groups; kin-related close social spacing may be a factor in the spread of infectious diseases. Spread of chronic wasting disease (CWD), a prion disorder of deer and their cervid relatives, is presumed to be associated with direct contact between individuals and by exposure to shared food and water sources contaminated with prions shed by infected deer. Key aspects of disease ecology are yet unknown. DNA tools for pedigree reconstruction were developed to fill knowledge gaps in disease dynamics in prion-infected wild animals. Kinship indices using data from microsatellite loci and sequence haplotypes of mitochondrial DNA were employed to assemble genealogies. Molecular genealogy tools will be useful for landscape-level population genetic research and monitoring, in addition to epidemiologic studies examining transmission of CWD in captive and free-ranging cervids. PMID:20592847

Delay Tracking of Spread-Spectrum Signals for Indoor Optical Ranging

PubMed Central

Salido-Monzú, David; Martín-Gorostiza, Ernesto; Lázaro-Galilea, José Luis; Martos-Naya, Eduardo; Wieser, Andreas

2014-01-01

Delay tracking of spread-spectrum signals is widely used for ranging in radio frequency based navigation. Its use in non-coherent optical ranging, however, has not been extensively studied since optical channels are less subject to narrowband interference situations where these techniques become more useful. In this work, an early-late delay-locked loop adapted to indoor optical ranging is presented and analyzed. The specific constraints of free-space infrared channels in this context substantially differ from those typically considered in radio frequency applications. The tracking stage is part of an infrared differential range measuring system with application to mobile target indoor localization. Spread-spectrum signals are used in this context to provide accurate ranging while reducing the effect of multipath interferences. The performance of the stage regarding noise and dynamic errors is analyzed and validated, providing expressions that allow an adequate selection of the design parameters depending on the expected input signal characteristics. The behavior of the stage in a general multipath scenario is also addressed to estimate the multipath error bounds. The results, evaluated under realistic conditions corresponding to an 870 nm link with 25 MHz chip-rate, built with low-cost up-to-date devices, show that an overall error below 6% of a chip time can be achieved. PMID:25490585

A virus spreading model for cognitive radio networks

NASA Astrophysics Data System (ADS)

Hou, L.; Yeung, K. H.; Wong, K. Y.

2012-12-01

Since cognitive radio (CR) networks could solve the spectrum scarcity problem, they have drawn much research in recent years. Artificial intelligence(AI) is introduced into CRs to learn from and adapt to their environment. Nonetheless, AI brings in a new kind of attacks specific to CR networks. The most powerful one is a self-propagating AI virus. And no spreading properties specific to this virus have been reported in the literature. To fill this research gap, we propose a virus spreading model of an AI virus by considering the characteristics of CR networks and the behavior of CR users. Several important observations are made from the simulation results based on the model. Firstly, the time taken to infect the whole network increases exponentially with the network size. Based on this result, CR network designers could calculate the optimal network size to slow down AI virus propagation rate. Secondly, the anti-virus performance of static networks to an AI virus is better than dynamic networks. Thirdly, if the CR devices with the highest degree are initially infected, the AI virus propagation rate will be increased substantially. Finally, it is also found that in the area with abundant spectrum resource, the AI virus propagation speed increases notably but the variability of the spectrum does not affect the propagation speed much.

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].

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.

Progression of cutaneous melanoma: implications for treatment

PubMed Central

Leong, Stanley P. L.; Mihm, Martin C.; Murphy, George F.; Hoon, Dave S. B.; Kashani-Sabet, Mohammed; Agarwala, Sanjiv S.; Zager, Jonathan S.; Hauschild, Axel; Sondak, Vernon K.; Guild, Valerie; Kirkwood, John M.

2015-01-01

The survival rates of melanoma, like any type of cancer, become worse with advancing stage. Spectrum theory is most consistent with the progression of melanoma from the primary site to the in-transit locations, regional or sentinel lymph nodes and beyond to the distant sites. Therefore, early diagnosis and surgical treatment before its spread is the most effective treatment. Recently, new approaches have revolutionized the diagnosis and treatment of melanoma. Genomic profiling and sequencing will form the basis for molecular taxonomy for more accurate subgrouping of melanoma patients in the future. New insights of molecular mechanisms of metastasis are summarized in this review article. Sentinel lymph node biopsy has become a standard of care for staging primary melanoma without the need for a more morbid complete regional lymph node dissection. With recent developments in molecular biology and genomics, novel molecular targeted therapy is being developed through clinical trials. PMID:22892755

Diversity of chromosomal karyotypes in maize and its relatives.

PubMed

Albert, P S; Gao, Z; Danilova, T V; Birchler, J A

2010-07-01

Maize is a highly diverse species on the gene sequence level. With the recent development of methods to distinguish each of the 10 pairs of homologues in somatic root tip spreads, a wide collection of maize lines was subjected to karyotype analysis to serve as a reference for the community and to examine the spectrum of chromosomal features in the species. The core nested association mapping progenitor collection and additional selections of diversity lines were examined. Commonly used inbred lines were included in the analysis. The centromere 4 specific repeat and ribosomal RNA loci were invariant. The CentC centromere repeat exhibited extensive differences in quantity on any particular chromosome across lines. Knob heterochromatin was highly variable with locations at many sites in the genome. Lastly, representative examples from other species in the genus Zea (teosintes) were examined, which provide information on the evolution of chromosomal features. Copyright 2010 S. Karger AG, Basel.

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.

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

A viral histone H4 encoded by Cotesia plutellae bracovirus inhibits haemocyte-spreading behaviour of the diamondback moth, Plutella xylostella.

PubMed

Gad, Wael; Kim, Yonggyun

2008-04-01

Histone H4 is highly conserved and forms a central-core nucleosome with H3 in eukaryotic chromatin. Its covalent modification at the protruding N-terminal region from the nucleosomal core can change the chromatin conformation in order to regulate gene expression. A viral H4 was found in the genome of Cotesia plutellae bracovirus (CpBV). The obligate host of the virus is an endoparasitoid wasp, C. plutellae, which parasitizes the diamondback moth, Plutella xylostella, and interrupts host development and immune reactions. CpBV has been regarded as a major source for interrupting the physiological processes during parasitization. CpBV H4 shows high sequence identity with the amino acid sequence of P. xylostella H4 except for an extended N-terminal region (38 aa). This extended N-terminal CpBV H4 contains nine lysine residues. CpBV H4 was expressed in P. xylostella parasitized by C. plutellae. Western blot analysis using a wide-spectrum H4 antibody showed two H4s in parasitized P. xylostella. In parasitized haemocytes, CpBV H4 was detected predominantly in the nucleus and was highly acetylated. The effect of CpBV H4 on haemocytes was analysed by transient expression using a eukaryotic expression vector, which was injected into non-parasitized P. xylostella. Expression of CpBV H4 was confirmed in the transfected P. xylostella by RT-PCR and immunofluorescence assays. Haemocytes of the transfected larvae lost their spreading ability on an extracellular matrix. Inhibition of the cellular immune response by transient expression was reversed by RNA interference using dsRNA of CpBV H4. These results suggest that CpBV H4 plays a critical role in suppressing host immune responses during parasitization.

Anthropogenic antibiotic resistance genes mobilization to the polar regions.

PubMed

Hernández, Jorge; González-Acuña, Daniel

2016-01-01

Anthropogenic influences in the southern polar region have been rare, but lately microorganisms associated with humans have reached Antarctica, possibly from military bases, fishing boats, scientific expeditions, and/or ship-borne tourism. Studies of seawater in areas of human intervention and proximal to fresh penguin feces revealed the presence of Escherichia coli strains least resistant to antibiotics in penguins, whereas E. coli from seawater elsewhere showed resistance to one or more of the following antibiotics: ampicillin, tetracycline, streptomycin, and trim-sulfa. In seawater samples, bacteria were found carrying extended-spectrum β-lactamase (ESBL)-type CTX-M genes in which multilocus sequencing typing (MLST) showed different sequence types (STs), previously reported in humans. In the Arctic, on the contrary, people have been present for a long time, and the presence of antibiotic resistance genes (ARGs) appears to be much more wide-spread than was previously reported. Studies of E coli from Arctic birds (Bering Strait) revealed reduced susceptibility to antibiotics, but one globally spreading clone of E. coli genotype O25b-ST131, carrying genes of ESBL-type CTX-M, was identified. In the few years between sample collections in the same area, differences in resistance pattern were observed, with E. coli from birds showing resistance to a maximum of five different antibiotics. Presence of resistance-type ESBLs (TEM, SHV, and CTX-M) in E. coli and Klebsiella pneumoniae was also confirmed by specified PCR methods. MLST revealed that those bacteria carried STs that connect them to previously described strains in humans. In conclusion, bacteria previously related to humans could be found in relatively pristine environments, and presently human-associated, antibiotic-resistant bacteria have reached a high global level of distribution that they are now found even in the polar regions.

Mutations in the newly identified RAX regulatory sequence are not a frequent cause of micro/anophthalmia.

PubMed

Chassaing, Nicolas; Vigouroux, Adeline; Calvas, Patrick

2009-06-01

Microphthalmia and anophthalmia are at the severe end of the spectrum of abnormalities in ocular development. A few genes (SOX2, OTX2, RAX, and CHX10) have been implicated in isolated micro/anophthalmia, but causative mutations of these genes explain less than a quarter of these developmental defects. A specifically conserved SOX2/OTX2-mediated RAX expression regulatory sequence has recently been identified. We postulated that mutations in this sequence could lead to micro/anophthalmia, and thus we performed molecular screening of this regulatory element in patients suffering from micro/anophthalmia. Fifty-one patients suffering from nonsyndromic microphthalmia (n = 40) or anophthalmia (n = 11) were included in this study after negative molecular screening for SOX2, OTX2, RAX, and CHX10 mutations. Mutation screening of the RAX regulatory sequence was performed by direct sequencing for these patients. No mutations were identified in the highly conserved RAX regulatory sequence in any of the 51 patients. Mutations in the newly identified RAX regulatory sequence do not represent a frequent cause of nonsyndromic micro/anophthalmia.

Revisions to some parameters used in stochastic-method simulations of ground motion

USGS Publications Warehouse

Boore, David; Thompson, Eric M.

2015-01-01

The stochastic method of ground‐motion simulation specifies the amplitude spectrum as a function of magnitude (M) and distance (R). The manner in which the amplitude spectrum varies with M and R depends on physical‐based parameters that are often constrained by recorded motions for a particular region (e.g., stress parameter, geometrical spreading, quality factor, and crustal amplifications), which we refer to as the seismological model. The remaining ingredient for the stochastic method is the ground‐motion duration. Although the duration obviously affects the character of the ground motion in the time domain, it also significantly affects the response of a single‐degree‐of‐freedom oscillator. Recently published updates to the stochastic method include a new generalized double‐corner‐frequency source model, a new finite‐fault correction, a new parameterization of duration, and a new duration model for active crustal regions. In this article, we augment these updates with a new crustal amplification model and a new duration model for stable continental regions. Random‐vibration theory (RVT) provides a computationally efficient method to compute the peak oscillator response directly from the ground‐motion amplitude spectrum and duration. Because the correction factor used to account for the nonstationarity of the ground motion depends on the ground‐motion amplitude spectrum and duration, we also present new RVT correction factors for both active and stable regions.

Fingerprint multicast in secure video streaming.

PubMed

Zhao, H Vicky; Liu, K J Ray

2006-01-01

Digital fingerprinting is an emerging technology to protect multimedia content from illegal redistribution, where each distributed copy is labeled with unique identification information. In video streaming, huge amount of data have to be transmitted to a large number of users under stringent latency constraints, so the bandwidth-efficient distribution of uniquely fingerprinted copies is crucial. This paper investigates the secure multicast of anticollusion fingerprinted video in streaming applications and analyzes their performance. We first propose a general fingerprint multicast scheme that can be used with most spread spectrum embedding-based multimedia fingerprinting systems. To further improve the bandwidth efficiency, we explore the special structure of the fingerprint design and propose a joint fingerprint design and distribution scheme. From our simulations, the two proposed schemes can reduce the bandwidth requirement by 48% to 87%, depending on the number of users, the characteristics of video sequences, and the network and computation constraints. We also show that under the constraint that all colluders have the same probability of detection, the embedded fingerprints in the two schemes have approximately the same collusion resistance. Finally, we propose a fingerprint drift compensation scheme to improve the quality of the reconstructed sequences at the decoder's side without introducing extra communication overhead.

Moebius Sequence and Autism Spectrum Disorders--Less Frequently Associated than Formerly Thought

ERIC Educational Resources Information Center

Briegel, Wolfgang; Schimek, Martina; Kamp-Becker, Inge

2010-01-01

Moebius sequence is a rare congenital disorder usually defined as a combination of facial weakness with impairment of ocular abduction. It is questionable, whether there is a strong association of the sequence with autism spectrum disorders (ASDs) as suggested in some earlier case reports and studies. Twenty-two participants with Moebius sequence…

A Robust Definition for the Turbulent Langmuir Number

NASA Astrophysics Data System (ADS)

Christensen, K. H.; Breivik, O.; Sutherland, G.; Belcher, S. E.; Gargett, A.

2016-02-01

The turbulent Langmuir number combines the water side friction velocity and the surface value of the Stokes drift, and is central to parameterizations of mixing by Langmuir turbulence. Making a direct comparison between such parameterizations and observations is difficult since the surface Stokes drift is sensitive to both the spectral tail and the directional spread of the waves. We propose a new definition for the turbulent Langmuir number based on low order moments of the one-dimensional frequency spectrum, hence eliminating most of the uncertainties associated with the diagnostic spectral tail. Comparison is made between the old and the new definitions using both observed and modeled wave spectra. The new definition has a higher variation around the mean and is better at resolving typical oceanic conditions. In addition, it is backwards compatible with the old definition for monochromatic waves, which means that scalings based on large eddy simulations with monochromatic wave forcing are still valid.

Detection and tracking of a low energy swell system off the U.S. East Coast with the Seasat SAR

NASA Technical Reports Server (NTRS)

Beal, R. C.

1980-01-01

It is noted that on the morning of September 28, 1978, at 1520 GMT, Seasat approached the East Coast of the U.S. with the 100 km swath of its synthetic aperture radar (SAR) running approximately parallel to the coast but displayed eastward by about 20 km. This pass is analyzed and the following conclusions are drawn: (1) the SAR can successfully detect low-energy swell systems with wave heights under 1 m (actually 0.65 + or - 0.25 m); (2) the refraction of low-energy but well-organized swells deriving from changes in the local depth of the ocean is clearly detectable in both wavelength and direction; and (3) the complexity of the ocean spectrum (whether composed of more than one system or spread in direction and wave number) appears to have little bearing on the threshold detection limits.

The rapidly emerging ESBL-producing Escherichia coli O25-ST131 clone carries LPS core synthesis genes of the K-12 type.

PubMed

Szijártó, Valéria; Pal, Tibor; Nagy, Gabor; Nagy, Eszter; Ghazawi, Akela; al-Haj, Mohammed; El Kurdi, Sylvia; Sonnevend, Agnes

2012-07-01

The clone Escherichia coli O25 ST131, typically producing extended-spectrum beta-lactamases (ESBLs), has spread globally and became the dominant type among extraintestinal isolates at many parts of the world. However, the reasons behind the emergence and success of this clone are only partially understood. We compared the core type genes by PCR of ESBL-producing and ESBL-nonproducing strains isolated from urinary tract infections in the United Arab Emirates and found a surprisingly high frequency of the K-12 core type (44.6%) among members of the former group, while in the latter one, it was as low (3.7%), as reported earlier. The high figure was almost entirely attributable to the presence of members of the clone O25 ST131 among ESBL producers. Strains from the same clone isolated in Europe also carried the K-12 core type genes. Sequencing the entire core operon of an O25 ST131 isolate revealed a high level of similarity to known K-12 core gene sequences and an almost complete identity with a recently sequenced non-O25 ST131 fecal isolate. The exact chemical structure and whether and how this unusual core type contributed to the sudden emergence of ST131 require further investigations. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

PubMed Central

Jühling, Frank; Pütz, Joern; Bernt, Matthias; Donath, Alexander; Middendorf, Martin; Florentz, Catherine; Stadler, Peter F.

2012-01-01

Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit ‘bizarre’ secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading ‘pseudogenes’, even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders. PMID:22139921

An analysis of the role of drift waves in equatorial spread F

NASA Technical Reports Server (NTRS)

Labelle, J.; Kelley, M. C.; Seyler, C. E.

1986-01-01

An account is given of results of rocket measurements of the wave number spectrum of equatorial spread F irregularities, with emphasis on wavelengths less than 100 m. The measurements were made from two sounding rockets launched from Peru as part of Project Condor. The Condor density fluctuation spectra display a break at a wavelength near 100 m, identical to that found in the PLUMEX experiment (Kelley et al., 1982). The Condor data also confirm a subrange in which the density and the wave potential obey the Boltzmann relation - a strong indication of the presence of low-frequency electrostatic waves with finite wavelength parallel to the magnetic field, perhaps low-frequency drift waves as proposed by Kelley et al. The Condor data are also consistent with the previous conjecture that drift waves only exist above 300 km altitude. To investigate the difference in spectra observed over two altitude ranges, the data must be fitted to a form for the power spectrum taken from Keskinen and Ossakow (1981). The fitted spectrum, along with empirically determined growth and dissipation rates, is used to calculate the energy pumped into the spectrum at long wavelengths as well as the energy dissipated at shorter wavelengths. It is found that the energy is balanced by classical collisional effects in the low-altitude case, but energy balance in the high-altitude case requires an enhanced dissipation of about 500 times that due to classical diffusion. The model is consistent with, but does not uniquely imply, an inverse cascade of drift wave turbulence in equatorial spread F.

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.

The Age Related Properties of Solar Type Stars

NASA Technical Reports Server (NTRS)

Soderblom, David

1999-01-01

The studies of lithium in solar-type stars in clusters of a wide range of ages has provided critical information on a tracer of convective processes, especially among very young stars. Our most recent work has been on a pre-main sequence cluster (NGC 2264) that took place after this grant expired, but was founded on it. The spread seen in Li in Zero-Age Main Sequence clusters like the Pleiades is huge and possibly related to rotation. No clear spread in seen in NGC 2264, so it does not have its origins in the conditions of formation but is instead a result of processes occurring during PMS evolution. Our observations of M67 were particularly interesting because this cluster is the same age as the Sun, i.e.,very old. Clear evidence was seen for a spread in Li there too, indicating that the spread seen in very young stars perpetuates itself into old age.

[Molecular characterization of resistance mechanisms: methicillin resistance Staphylococcus aureus, extended spectrum β-lactamases and carbapenemases].

PubMed

Oteo, Jesús; Belén Aracil, María

2015-07-01

Multi-drug resistance in bacterial pathogens increases morbidity and mortality in infected patients and it is a threat to public health concern by their high capacity to spread. For both reasons, the rapid detection of multi-drug resistant bacteria is critical. Standard microbiological procedures require 48-72 h to provide the antimicrobial susceptibility results, thus there is emerging interest in the development of rapid detection techniques. In recent years, the use of selective and differential culture-based methods has widely spread. However, the capacity for detecting antibiotic resistance genes and their low turnaround times has made molecular methods a reference for diagnosis of multidrug resistance. This review focusses on the molecular methods for detecting some mechanisms of antibiotic resistance with a high clinical and epidemiological impact: a) Enzymatic resistance to broad spectrum β-lactam antibiotics in Enterobacteriaceae, mainly extended spectrum β-lactamases (ESBL) and carbapenemases; and b) methicillin resistance in Staphylococcus aureus. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

Discovery of Extended Main-sequence Turnoffs in Four Young Massive Clusters in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Li, Chengyuan; de Grijs, Richard; Deng, Licai; Milone, Antonino P.

2017-08-01

An increasing number of young massive clusters (YMCs) in the Magellanic Clouds have been found to exhibit bimodal or extended main sequences (MSs) in their color-magnitude diagrams (CMDs). These features are usually interpreted in terms of a coeval stellar population with different stellar rotational rates, where the blue and red MS stars are populated by non- (or slowly) and rapidly rotating stellar populations, respectively. However, some studies have shown that an age spread of several million years is required to reproduce the observed wide turnoff regions in some YMCs. Here we present the ultraviolet-visual CMDs of four Large and Small Magellanic Cloud YMCs, NGC 330, NGC 1805, NGC 1818, and NGC 2164, based on high-precision Hubble Space Telescope photometry. We show that they all exhibit extended main-sequence turnoffs (MSTOs). The importance of age spreads and stellar rotation in reproducing the observations is investigated. The observed extended MSTOs cannot be explained by stellar rotation alone. Adopting an age spread of 35-50 Myr can alleviate this difficulty. We conclude that stars in these clusters are characterized by ranges in both their ages and rotation properties, but the origin of the age spread in these clusters remains unknown.

Sequence-dependent modelling of local DNA bending phenomena: curvature prediction and vibrational analysis.

PubMed

Vlahovicek, K; Munteanu, M G; Pongor, S

1999-01-01

Bending is a local conformational micropolymorphism of DNA in which the original B-DNA structure is only distorted but not extensively modified. Bending can be predicted by simple static geometry models as well as by a recently developed elastic model that incorporate sequence dependent anisotropic bendability (SDAB). The SDAB model qualitatively explains phenomena including affinity of protein binding, kinking, as well as sequence-dependent vibrational properties of DNA. The vibrational properties of DNA segments can be studied by finite element analysis of a model subjected to an initial bending moment. The frequency spectrum is obtained by applying Fourier analysis to the displacement values in the time domain. This analysis shows that the spectrum of the bending vibrations quite sensitively depends on the sequence, for example the spectrum of a curved sequence is characteristically different from the spectrum of straight sequence motifs of identical basepair composition. Curvature distributions are genome-specific, and pronounced differences are found between protein-coding and regulatory regions, respectively, that is, sites of extreme curvature and/or bendability are less frequent in protein-coding regions. A WWW server is set up for the prediction of curvature and generation of 3D models from DNA sequences (http:@www.icgeb.trieste.it/dna).

Effect of target composition on proton acceleration in ultraintense laser-thin foil interaction

NASA Astrophysics Data System (ADS)

Liu, Qingcao; Liu, Meng; Yu, Tongpu; Ding, Pengji; Liu, Zuoye; Sun, Shaohua; Liu, Xiaoliang; Lu, Xing; Guo, Zeqin; Hu, Bitao

2012-09-01

The interactions of ultraintense circularly polarized laser pulses with a mixed solid target and a double-layer target are studied by two-dimensional particle-in-cell simulations. Different carbon and proton compositions in the targets are used in the simulations. It is shown that the proton acceleration mechanisms in both targets are very sensitive to the ion density ratios between protons and carbon ions. For a mixed solid target, a relatively low proton density gives rise to monoenergetic peaks in the proton energy spectrum while a high proton density leads to a large cut-off energy and wide energy spread. With the increase of the ratio, the so-called directed-Coulomb-explosion becomes dominated over the radiation pressure. Surprisingly, for a double-layer target with a front proton layer and an ultrathin rear carbon layer, a highly monoenergetic proton beam with a peak energy of 1.7 GeV/u, an energy spread of ˜4%, and a divergency angle of 2° can be obtained, which might have diverse applications in medical therepy and proton imaging in future.

CT Image Sequence Restoration Based on Sparse and Low-Rank Decomposition

PubMed Central

Gou, Shuiping; Wang, Yueyue; Wang, Zhilong; Peng, Yong; Zhang, Xiaopeng; Jiao, Licheng; Wu, Jianshe

2013-01-01

Blurry organ boundaries and soft tissue structures present a major challenge in biomedical image restoration. In this paper, we propose a low-rank decomposition-based method for computed tomography (CT) image sequence restoration, where the CT image sequence is decomposed into a sparse component and a low-rank component. A new point spread function of Weiner filter is employed to efficiently remove blur in the sparse component; a wiener filtering with the Gaussian PSF is used to recover the average image of the low-rank component. And then we get the recovered CT image sequence by combining the recovery low-rank image with all recovery sparse image sequence. Our method achieves restoration results with higher contrast, sharper organ boundaries and richer soft tissue structure information, compared with existing CT image restoration methods. The robustness of our method was assessed with numerical experiments using three different low-rank models: Robust Principle Component Analysis (RPCA), Linearized Alternating Direction Method with Adaptive Penalty (LADMAP) and Go Decomposition (GoDec). Experimental results demonstrated that the RPCA model was the most suitable for the small noise CT images whereas the GoDec model was the best for the large noisy CT images. PMID:24023764

The TANAMI Multiwavelength Program: Dynamic spectral energy distributions of southern blazars

DOE PAGES

Krauß, F.; Wilms, J.; Kadler, M.; ...

2016-06-28

Simultaneous broadband spectral and temporal studies of blazars are an important tool for investigating active galactic nuclei (AGN) jet physics. Aims. Here, we study the spectral evolution between quiescent and flaring periods of 22 radio-loud AGN through multiepoch, quasi-simultaneous broadband spectra. For many of these sources these are the first broadband studies. We also use a Bayesian block analysis of Fermi/LAT light curves to determine time ranges of constant flux for constructing quasi-simultaneous spectral energy distributions (SEDs). The shapes of the resulting 81 SEDs are described by two logarithmic parabolas and a blackbody spectrum where needed. The peak frequencies andmore » luminosities agree well with the blazar sequence for low states with higher luminosity implying lower peak frequencies. This is not true for sources in high states. The γ-ray photon index in Fermi/LAT correlates with the synchrotron peak frequency in low and intermediate states. No correlation is present in high states. The black hole mass cannot be determined from the SEDs. Surprisingly, the thermal excess often found in FSRQs at optical/UV wavelengths can be described by blackbody emission and not an accretion disk spectrum. The so-called harder-when-brighter trend, typically seen in X-ray spectra of flaring blazars, is visible in the blazar sequence. Furthermore, our results for low and intermediate states, as well as the Compton dominance, are in agreement with previous results. Black hole mass estimates using recently published parameters are in agreement with some of the more direct measurements. For two sources, estimates disagree by more than four orders of magnitude, possibly owing to boosting effects. The shapes of the thermal excess seen predominantly in flat spectrum radio quasars are inconsistent with a direct accretion disk origin.« less

Determining geographical spread pattern of MERS-CoV by distance method using Kimura model

NASA Astrophysics Data System (ADS)

Amiroch, Siti; Rohmatullah, Arif

2017-03-01

MERS-CoV or generally called as Middle East Respiratory Syndrome Coronavirus, a respiratory disease syndrome caused by a corona virus that attacks the respiratory tract ranging from mild to severe acute indication of fever, cough and shortness of breath. The cases happened relate to the countries in the Arabian Peninsula (Middle East) and there were 356 deaths have been reported due to the spread of the epidemic MERS. The data used in the case of MERS are the data DNA sequences taken from Genbank, the online database of the United States that stores the results of molecular biological experiments from all over the world (http://www.ncbi.nlm.nih.gov). In this case, bioinformatics plays an important role of reading sequences of DNA and genetic information by using the main device in the form of software that is supported by the availability of the Internet, while the analysis there in made and proven with mathematical methods. In similar research conducted by molecular biologists and physicians, the process of DNA sequencing is done with software that is already available like BLAST. In order to determine the MERS geographical distribution patterns in the Arabian Peninsula is done with program Clustal W, Bayesian, Phylip, etc. In this study, the writer use the Matlab simulation for all processes starting sequence alignment, counting the number of transitions and transversion substitutions for each sequence and its location up to the process of forming a phylogenetic tree that figures out the pattern of spread of the epidemic MERS. Mathematical analysis performed on a decline in the formula is to find Kimura evolutionary models and the process of forming a phylogenetic tree (the pattern of the epidemic MERS distribution) with neighbor joining algorithm. Finally it was obtained the pattern of geographical spread with 6 groups epidemic of MERS which ultimately turns out that all the MERS viruses that were spread in the Arabian Peninsula everything are almost the same as the virus sequence found in al-Hasa.

Effects of channel tap spacing on delay-lock tracking

NASA Astrophysics Data System (ADS)

Dana, Roger A.; Milner, Brian R.; Bogusch, Robert L.

1995-12-01

High fidelity simulations of communication links operating through frequency selective fading channels require both accurate channel models and faithful reproduction of the received signal. In modern radio receivers, processing beyond the analog-to-digital converter (A/D) is done digitally, so a high fidelity simulation is actually an emulation of this digital signal processing. The 'simulation' occurs in constructing the output of the A/D. One approach to constructing the A/D output is to convolve the channel impulse response function with the combined impulse response of the transmitted modulation and the A/D. For both link simulations and hardware channel simulators, the channel impulse response function is then generated with a finite number of samples per chip, and the convolution is implemented in a tapped delay line. In this paper we discuss the effects of the channel model tap spacing on the performance of delay locked loops (DLLs) in both direct sequence and frequency hopped spread spectrum systems. A frequency selective fading channel is considered, and the channel impulse response function is constructed with an integer number of taps per modulation symbol or chip. The tracking loop time delay is computed theoretically for this tapped delay line channel model and is compared to the results of high fidelity simulations of actual DLLs. A surprising result is obtained. The performance of the DLL depends strongly on the number of taps per chip. As this number increases the DLL delay approaches the theoretical limit.

On the Stellar Population and Star-Forming History of the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Hillenbrand, Lynne A.

1997-05-01

We report on the first phase of a study of the stellar population comprising the Orion Nebula Cluster (ONC). Approximately 50% of the ~ 3500 stars identified to date within ~ 2.5 pc of the namesake Trapezium stars are optically visible, and in this paper we focus on that sample with I < 17.5 mag. The large number and number density (npeak > 10(4) pc(-3) ) of stars, the wide range in stellar mass ( ~ 0.1-50 M_⊙), and the extreme youth (< 1-2 Myr) of the stellar population, make the ONC the best site for investigating: 1) the detailed shape of a truly ``initial'' mass spectrum; 2) the apparent age spread in a region thought to have undergone triggered star formation; 3) the time sequence of star formation as a function of stellar mass; and 4) trends of all of the above with cluster radius. Nearly 60% of the ~ 1600 optical stars have sufficient data (spectroscopy and photometry) for placement on a theoretical HR diagram; this subsample is unbiased with respect to apparent brightness or cluster radius, complete down to ~ 1 M_⊙, and representative of the total optical sample below ~ 1 M_⊙ for the age and extinction ranges characteristic of the cluster. Comparison of the derived HR diagram with traditional pre-main sequence evolutionary calculations shows a trend of increasing stellar age with increasing stellar mass. To avoid the implication of earlier characteristic formation times for higher-mass stars than for lower-mass stars, refinement of early evolutionary theory in a manner similar to the birthline hypothesis of Palla & Stahler (1993), is required. Subject to uncertainties in the tracks and isochrones, we can still investigate stellar mass and age distributions in the ONC. We find the ONC as a whole to be characterized by a mass spectrum which is not grossly inconsistent with ``standard'' stellar mass spectra. In particular, although there are structural differences between the detailed ONC mass spectrum and various models constructed from solar neighborhood data, the observed mass spectrum appears to a peak at ~ 0.2 M_⊙ and to fall off rapidly towards lower masses; several substellar objects are present. The abundance of low-mass stars relative to high-mass stars suggests that there is no bi-modal star formation mode; somewhat ironically, the ONC probably contains fractionally more low-mass stars than the solar neighborhood since the population not yet located on the HR diagram is dominated by sub-solar-mass stars. Nonetheless, the ONC mass spectrum is biased towards higher-mass stars within the innermost cluster radii (rprojected < 0.3 pc). We find the ONC as a whole to be characterized by a mean age of < 1 Myr and an age spread which is probably less than 2 Myr, but also by a bias towards younger stars at smaller projected cluster radii. Although the most massive stars and the youngest stars are found preferentially towards the center of the ONC it does not follow that the most massive stars are the youngest stars. A lower limit to the total cluster mass in stars is Mstars ~ 900 M_⊙ (probably a factor of < 2 underestimate). A lower limit to the recent star formation rate is ~ 10(-4) M_⊙ yr(-1) . All observational data in this study as well as stellar parameters derived from them are available in electronic format.

Candida auris

MedlinePlus

... auris infection spread globally? CDC conducted whole genome sequencing of C. auris specimens from countries in the ... Asia, southern Africa, and South America. Whole genome sequencing produces detailed DNA fingerprints of organisms. CDC found ...

Extended-spectrum beta-lactamase-producing Escherichia coli in common vampire bats Desmodus rotundus and livestock in Peru.

PubMed

Benavides, J A; Shiva, C; Virhuez, M; Tello, C; Appelgren, A; Vendrell, J; Solassol, J; Godreuil, S; Streicker, D G

2018-06-01

Antibiotic resistance mediated by bacterial production of extended-spectrum beta-lactamase (ESBL) is a global threat to public health. ESBL resistance is most commonly hospital-acquired; however, infections acquired outside of hospital settings have raised concerns over the role of livestock and wildlife in the zoonotic spread of ESBL-producing bacteria. Only limited data are available on the circulation of ESBL-producing bacteria in animals. Here, we report ESBL-producing Escherichia coli in wild common vampire bats Desmodus rotundus and livestock near Lima, Peru. Molecular analyses revealed that most of this resistance resulted from the expression of bla CTX-M-15 genes carried by plasmids, which are disseminating worldwide in hospital settings and have also been observed in healthy children of Peru. Multilocus sequence typing showed a diverse pool of E. coli strains carrying this resistance that were not always host species-specific, suggesting sharing of strains between species or infection from a common source. This study shows widespread ESBL resistance in wild and domestic animals, supporting animal communities as a potential source of resistance. Future work is needed to elucidate the role of bats in the dissemination of antibiotic-resistant strains of public health importance and to understand the origin of the observed resistance. © 2018 Blackwell Verlag GmbH.

Golay sequences coded coherent optical OFDM for long-haul transmission

NASA Astrophysics Data System (ADS)

Qin, Cui; Ma, Xiangrong; Hua, Tao; Zhao, Jing; Yu, Huilong; Zhang, Jian

2017-09-01

We propose to use binary Golay sequences in coherent optical orthogonal frequency division multiplexing (CO-OFDM) to improve the long-haul transmission performance. The Golay sequences are generated by binary Reed-Muller codes, which have low peak-to-average power ratio and certain error correction capability. A low-complexity decoding algorithm for the Golay sequences is then proposed to recover the signal. Under same spectral efficiency, the QPSK modulated OFDM with binary Golay sequences coding with and without discrete Fourier transform (DFT) spreading (DFTS-QPSK-GOFDM and QPSK-GOFDM) are compared with the normal BPSK modulated OFDM with and without DFT spreading (DFTS-BPSK-OFDM and BPSK-OFDM) after long-haul transmission. At a 7% forward error correction code threshold (Q2 factor of 8.5 dB), it is shown that DFTS-QPSK-GOFDM outperforms DFTS-BPSK-OFDM by extending the transmission distance by 29% and 18%, in non-dispersion managed and dispersion managed links, respectively.

Sequence Learning with Stochastic Feedback in a Cross-Cultural Sample of Boys in the Autistic Spectrum

ERIC Educational Resources Information Center

Hentschel, Maren; Lange-Kuttner, Christiane; Averbeck, Bruno B.

2016-01-01

The study investigated sequence learning from stochastic feedback in boys with Autistic Spectrum Disorder (ASD) and typically developed (TD) boys. We asked boys with ASD from Nigeria and the UK as well as age- and gender-matched controls (also males only) to deduce a sequence of four left and right button presses, LLRR, RRLL, LRLR, RLRL, LRRL and…

A study of flame spread in engineered cardboard fuelbeds: Part I: Correlations and observations

Treesearch

Mark A. Finney; Jason Forthofer; Isaac C. Grenfell; Brittany A. Adam; Nelson K. Akafuah; Kozo Saito

2013-01-01

Wind tunnel laboratory fires spreading through laser-cut cardboard fuel beds were instrumented and analyzed for physical processes associated with spread. Flames in the span-wise direction appeared as a regular series of peaks-and-troughs that scaled directly with flame length. Flame structure in the stream-wise direction fluctuated with the forward advection of...

Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

PubMed Central

Kinloch, Natalie N.; MacMillan, Daniel R.; Le, Anh Q.; Cotton, Laura A.; Bangsberg, David R.; Buchbinder, Susan; Carrington, Mary; Fuchs, Jonathan; Harrigan, P. Richard; Koblin, Beryl; Kushel, Margot; Markowitz, Martin; Mayer, Kenneth; Milloy, M. J.; Schechter, Martin T.; Wagner, Theresa; Walker, Bruce D.; Carlson, Jonathan M.; Poon, Art F. Y.

2015-01-01

ABSTRACT Human leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989; n = 338) and modern (2001 to 2011; n = 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era. IMPORTANCE HLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may accumulate in circulation over time, potentially undermining host antiviral immunity to the transmitted viral strain. We studied >600 experimentally collected HIV-1 polymerase sequences linked to host HLA information dating back to 1979, along with phylogenetically reconstructed HIV-1 sequences dating back to the virus' introduction into North America. Overall, our results support the gradual spread of many—though not all—HIV-1 polymerase immune escape mutations in circulation over time. This is consistent with recent observations from other global regions, though the extent of polymorphism accumulation in North America appears to be lower than in populations with high seroprevalence, older epidemics, and/or limited HLA diversity. Importantly, the risk of acquiring an HIV-1 polymerase sequence at transmission that is substantially preadapted to one's HLA profile remains relatively low in North America, even in the present era. PMID:26559841

Inventory of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae in France as Assessed by a Multicenter Study.

PubMed

Robin, F; Beyrouthy, R; Bonacorsi, S; Aissa, N; Bret, L; Brieu, N; Cattoir, V; Chapuis, A; Chardon, H; Degand, N; Doucet-Populaire, F; Dubois, V; Fortineau, N; Grillon, A; Lanotte, P; Leyssene, D; Patry, I; Podglajen, I; Recule, C; Ros, A; Colomb-Cotinat, M; Ponties, V; Ploy, M C; Bonnet, R

2017-03-01

The objective of this study was to perform an inventory of the extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae isolates responsible for infections in French hospitals and to assess the mechanisms associated with ESBL diffusion. A total of 200 nonredundant ESBL-producing Enterobacteriaceae strains isolated from clinical samples were collected during a multicenter study performed in 18 representative French hospitals. Antibiotic resistance genes were identified by PCR and sequencing experiments. The clonal relatedness between isolates was investigated by the use of the DiversiLab system. ESBL-encoding plasmids were compared by PCR-based replicon typing and plasmid multilocus sequence typing. CTX-M-15, CTX-M-1, CTX-M-14, and SHV-12 were the most prevalent ESBLs (8% to 46.5%). The three CTX-M-type EBSLs were significantly observed in Escherichia coli (37.1%, 24.2%, and 21.8%, respectively), and CTX-M-15 was the predominant ESBL in Klebsiella pneumoniae (81.1%). SHV-12 was associated with ESBL-encoding Enterobacter cloacae strains (37.9%). qnrB , aac(6 ' )-Ib-cr , and aac(3)-II genes were the main plasmid-mediated resistance genes, with prevalences ranging between 19.5% and 45% according to the ESBL results. Molecular typing did not identify wide clonal diffusion. Plasmid analysis suggested the diffusion of low numbers of ESBL-encoding plasmids, especially in K. pneumoniae and E. cloacae However, the ESBL-encoding genes were observed in different plasmid replicons according to the bacterial species. The prevalences of ESBL subtypes differ according to the Enterobacteriaceae species. Plasmid spread is a key determinant of this epidemiology, and the link observed between the ESBL-encoding plasmids and the bacterial host explains the differences observed in the Enterobacteriaceae species. Copyright © 2017 American Society for Microbiology.

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.

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.

A New Observation Technique Applied to Early/Fast VLF Scattering Events

NASA Astrophysics Data System (ADS)

Kotovsky, D. A.; Moore, R. C.

2012-12-01

Early/fast very low frequency (VLF, 3-30 kHz) events are understood to result from ionospheric conductivity changes associated with lightning. Early/fast amplitude and phase perturbations have been observed coincidentally with various optical observations of transient luminous events (TLEs), including elves, sprites, and sprite halos, each of which can have temporal characteristics consistent with those of early/fast VLF events. It is yet unresolved, however, whether a specific type of TLE is directly related to the ionospheric conductivity changes responsible for the typical early/fast event. In this paper, we present spread spectrum VLF scattering observations of early/fast events. The spread spectrum analysis technique determines the amplitude and phase of a subionospherically propagating VLF signal as a function of time during the early/fast event and as a function of frequency across the 200 Hz bandwidth of the VLF transmission. VLF scattering observations, each identified with causative lightning logged by the National Lightning Detection Network (NLDN), are compared with the predictions of the Long-Wave Propagation Capability (LWPC) code, a three-dimensional earth-ionosphere waveguide propagation and scattering model. Theoretical predictions for VLF scattering from ionization changes associated with elves are compared with those associated with sprite halos, and each are compared with experimental observations. Results indicate that the observed frequency dependence of VLF scattering during early/fast events results from the combination of scattering source properties and Earth-ionosphere waveguide propagation effects. Observations are more consistent with the modeled amplitude perturbations associated with sprite halos than those with elves.

Study on the spectral efficiency of SFH-GMSK in land mobile telephone communication by direct simulation

NASA Technical Reports Server (NTRS)

Bao, H.; Kwatra, S. C.; Kim, Junghwan; Stevens, G. H.

1990-01-01

A spread spectrum system, slow frequency hopping with GMSK (Gaussian minimum shift keying) modulation (SFH-GMSK), is proposed for mobile telephone communications. The system performance is evaluated using computer simulation and is compared with an unspread system. Results show that under multipath fading conditions, when the signal-to-noise ratio (SNR) is greater than 15 dB, slow frequency hopping gives some bit error rate improvement over the unspread system. Theoretical predictions indicate that a system efficiency of 20-65 users per cell can be achieved in the cellular configuration. Joint use of SFH-GMSK and FM is also investigated. It is shown that FM interference can cause serious degradation to the SFH-GMSK performance.

Manifestations of Dynamical Localization in the Disordered XXZ Spin Chain

NASA Astrophysics Data System (ADS)

Elgart, Alexander; Klein, Abel; Stolz, Günter

2018-04-01

We study disordered XXZ spin chains in the Ising phase exhibiting droplet localization, a single cluster localization property we previously proved for random XXZ spin chains. It holds in an energy interval I near the bottom of the spectrum, known as the droplet spectrum. We establish dynamical manifestations of localization in the energy window I, including non-spreading of information, zero-velocity Lieb-Robinson bounds, and general dynamical clustering. Our results do not rely on knowledge of the dynamical characteristics of the model outside the droplet spectrum. A byproduct of our analysis is that for random XXZ spin chains this droplet localization can happen only inside the droplet spectrum.

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.

Limited Dissemination of Extended-Spectrum β-Lactamase- and Plasmid-Encoded AmpC-Producing Escherichia coli from Food and Farm Animals, Sweden.

PubMed

Börjesson, Stefan; Ny, Sofia; Egervärn, Maria; Bergström, Jakob; Rosengren, Åsa; Englund, Stina; Löfmark, Sonja; Byfors, Sara

2016-04-01

Extended-spectrum β-lactamase (ESBL)- and plasmid-encoded ampC (pAmpC)-producing Enterobacteriaceae might spread from farm animals to humans through food. However, most studies have been limited in number of isolates tested and areas studied. We examined genetic relatedness of 716 isolates from 4,854 samples collected from humans, farm animals, and foods in Sweden to determine whether foods and farm animals might act as reservoirs and dissemination routes for ESBL/pAmpC-producing Escherichia coli. Results showed that clonal spread to humans appears unlikely. However, we found limited dissemination of genes encoding ESBL/pAmpC and plasmids carrying these genes from foods and farm animals to healthy humans and patients. Poultry and chicken meat might be a reservoir and dissemination route to humans. Although we found no evidence of clonal spread of ESBL/pAmpC-producing E. coli from farm animals or foods to humans, ESBL/pAmpC-producing E. coli with identical genes and plasmids were present in farm animals, foods, and humans.

A label-free ultrasensitive fluorescence detection of viable Salmonella enteritidis using enzyme-induced cascade two-stage toehold strand-displacement-driven assembly of G-quadruplex DNA.

PubMed

Zhang, Peng; Liu, Hui; Ma, Suzhen; Men, Shuai; Li, Qingzhou; Yang, Xin; Wang, Hongning; Zhang, Anyun

2016-06-15

The harm of Salmonella enteritidis (S. enteritidis ) to public health mainly by contaminating fresh food and water emphasizes the urgent need for rapid detection techniques to help control the spread of the pathogen. In this assay, an newly designed capture probe complex that contained specific S. enteritidis-aptamer and hybridized signal target sequence was used for viable S. enteritidis recognition directly. In the presence of the target S. enteritidis, single-stranded target sequences were liberated and initiated the replication-cleavage reaction, producing numerous G-quadruplex structures with a linker on the 3'-end. And then, the sensing system took innovative advantage of quadratic linker-induced strand-displacement for the first time to release target sequence in succession, leading to the cyclic reuse of the target sequences and cascade signal amplification, thereby achieving the successive production of G-quadruplex structures. The fluorescent dye, N-Methyl mesoporphyrin IX, binded to these G-quadruplex structures and generated significantly enhanced fluorescent signals to achieve highly sensitive detection of S. enteritidis down to 60 CFU/mL with a linear range from 10(2) to 10(7)CFU/mL. By coupling the cascade two-stage target sequences-recyclable toehold strand-displacement with aptamer-based target recognition successfully, it is the first report on a novel non-label, modification-free and DNA extraction-free ultrasensitive fluorescence biosensor for detecting viable S. enteritidis directly, which can discriminate from dead S. enteritidis. Copyright © 2016 Elsevier B.V. All rights reserved.

A label-free fluorescent direct detection of live Salmonella typhimurium using cascade triple trigger sequences-regenerated strand displacement amplification and hairpin template-generated-scaffolded silver nanoclusters.

PubMed

Zhang, Peng; Liu, Hui; Li, Xiaocheng; Ma, Suzhen; Men, Shuai; Wei, Heng; Cui, Jingjing; Wang, Hongning

2017-01-15

The harm of Salmonella typhimurium (S. typhimurium) to public health mainly by the consumption of contaminated agricultural products or water stresses an urgent need for rapid detection methods to help control the spread of S. typhimurium. In this work, an intelligently designed sensor system took creative advantage of triple trigger sequences-regenerated strand displacement amplification and self-protective hairpin template-generated-scaffolded silver nanoclusters (AgNCs) for the first time. In the presence of live S. typhimurium, single-stranded trigger sequences were released from aptamer-trigger sequences complex, initiating a branch migration to open the hairpin template I containing complementary scaffolds of AgNCs. Then the first strand displacement amplification was induced to produce numerous scaffolds of AgNCs and reporter strands which initiated a branch migration to open the hairpin template II containing complementary scaffolds of AgNCs. Then the second strand displacement amplification was induced to generate numerous scaffolds of AgNCs and trigger sequences which initiated the third branch migration and strand displacement amplification to produce numerous scaffolds of AgNCs and reporter strands in succession. Cyclically, the reproduction of the trigger sequences and cascade successive production of scaffolds were achieved successfully, forming highly fluorescent AgNCs, thus providing significantly enhanced fluorescent signals to achieve ultrasensitive detection of live S. typhimurium down to 50 CFU/mL with a linear range from 10 2 to 10 7 CFU/mL. It is the first report on a fluorescent biosensor for detecting viable S. typhimurium directly, which can distinguish from heat denatured S. typhimurium. And it develops a new strategy to generate the DNA-scaffolds for forming AgNCs. Copyright © 2016 Elsevier B.V. All rights reserved.

Migration pattern of hepatitis A virus genotype IA in North-Central Tunisia.

PubMed

Beji-Hamza, Abir; Taffon, Stefania; Mhalla, Salma; Lo Presti, Alessandra; Equestre, Michele; Chionne, Paola; Madonna, Elisabetta; Cella, Eleonora; Bruni, Roberto; Ciccozzi, Massimo; Aouni, Mahjoub; Ciccaglione, Anna Rita

2015-02-08

Hepatitis A virus (HAV) epidemiology in Tunisia has changed from high to intermediate endemicity in the last decades. However, several outbreaks continue to occur. The last reported sequences from Tunisian HAV strains date back to 2006. In order to provide an updated overview of the strains currently circulating in Tunisia, a large-scale molecular analysis of samples from hepatitis A cases was performed, the first in Tunisia. Biological samples were collected from patients with laboratory confirmed hepatitis A: 145 sera samples in Tunis, Monastir, Sousse and Kairouan from 2008 to 2013 and 45 stool samples in Mahdia in 2009. HAV isolates were characterised by nested RT-PCR (VP1/2A region) and sequencing. The sequences finally obtained from 81 samples showed 78 genotype IA and 3 genotype IB isolates. A Tunisian genotype IA sequence dataset, including both the 78 newly obtained IA sequences and 51 sequences retrieved from GenBank, was used for phylogenetic investigation, including analysis of migration pattern among six towns. Virus gene flow from Sfax and Monastir was directed to all other towns; in contrast, the gene flows from Sousse, Tunis, Mahdia and Kairouan were directed to three, two, one and no towns, respectively. Several different HAV strains co-circulate in Tunisia, but the predominant genotype still continues to be IA (78/81, 96% isolates). A complex gene flow (migration) of HAV genotype IA was observed, with Sfax and Monastir showing gene flows to all other investigated towns. This approach coupled to a wider sampling can prove useful to investigate the factors underlying the spread of HAV in Tunisia and, thus, to implement appropriate preventing measures.

A note on the revised galactic neutron spectrum of the Ames collaborative study

NASA Technical Reports Server (NTRS)

Schaefer, H. J.

1980-01-01

Energy distributions of the neutron dose equivalents in the 0.1 to 300 Mev interval for the Ames and Hess spectra are compared. The Ames spectrum shows no evaporation peak, moves the bulk of the flux away from the region of elastic collision and spreads it more evenly over higher energies. The neutron spectrum in space does not seem to hear out the Ames model. Emulsion findings on all manned missions of the past consistently indicate that evaporation events are a prolific source of neutrons in space.

Continuous Spectrum of Crustal Structures and Spreading Processes from Volcanic Rifted Margins to Mid-Ocean Ridges

NASA Astrophysics Data System (ADS)

Karson, J. A.

2016-12-01

Structures generated by seafloor spreading in oceanic crust (and ophiolites) and thick oceanic crust of Iceland show a continuous spectrum of features that formed by similar mechanisms but at different scales. A high magma budget near the Iceland hotspot generates thick (40-25 km) mafic crust in a plate boundary zone about 50 km wide. The upper crust ( 10 km thick) is constructed by the subaxial subsidence and thickening of lavas fed by dense dike swarms over a hot, weak lower crust to produce structures analogous to seaward-dipping reflectors of volcanic rifted margins. Segmented rift zones propagate away from the hotspot creating migrating transform fault zones, microplate-like crustal blocks and rift-parallel strike-slip faults. These structures are decoupled from the underlying lower crustal gabbroic rocks that thin by along-axis flow that reduces the overall crustal thickness and smooths-out local crustal thickness variations. Spreading on mid-ocean ridges with high magma budgets have much thinner crust (10-5 km) generated at a much narrower (few km) plate boundary zone. Subaxial subsidence accommodates the thickening of the upper crust of inward-dipping lavas and outward-dipping dikes about 1-2 km thick over a hot weak lower crust. Along-axis (high-temperature ductile and magmatic) flow of lower crustal material may help account for the relatively uniform seismic thickness of oceanic crust worldwide. Spreading along even slow-spreading mid-ocean ridges near hotspots (e.g., the Reykjanes Ridge) probably have similar features that are transitional between these extremes. In all of these settings, upper crustal and lower crustal structures are decoupled near the plate boundary but eventually welded together as the crust ages and cools. Similar processes are likely to occur along volcanic rifted margins as spreading begins.

Reviewing the history of HIV-1: spread of subtype B in the Americas.

PubMed

Junqueira, Dennis Maletich; de Medeiros, Rúbia Marília; Matte, Maria Cristina Cotta; Araújo, Leonardo Augusto Luvison; Chies, Jose Artur Bogo; Ashton-Prolla, Patricia; Almeida, Sabrina Esteves de Matos

2011-01-01

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950-1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion.

Reviewing the History of HIV-1: Spread of Subtype B in the Americas

PubMed Central

Junqueira, Dennis Maletich; de Medeiros, Rúbia Marília; Matte, Maria Cristina Cotta; Araújo, Leonardo Augusto Luvison; Chies, Jose Artur Bogo; Ashton-Prolla, Patricia; Almeida, Sabrina Esteves de Matos

2011-01-01

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and Bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950–1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion. PMID:22132104

Phylodynamic Analysis Revealed That Epidemic of CRF07_BC Strain in Men Who Have Sex with Men Drove Its Second Spreading Wave in China.

PubMed

Zhang, Min; Jia, Dijing; Li, Hanping; Gui, Tao; Jia, Lei; Wang, Xiaolin; Li, Tianyi; Liu, Yongjian; Bao, Zuoyi; Liu, Siyang; Zhuang, Daomin; Li, Jingyun; Li, Lin

2017-10-01

CRF07_BC was originally formed in Yunnan province of China in 1980s and spread quickly in injecting drug users (IDUs). In recent years, it has been introduced into men who have sex with men (MSM) and become the most dominant strain in China. In this study, we performed a comprehensively phylodynamic analysis of CRF07_BC sequences from China. All CRF07_BC sequences identified in China were retrieved from database. More sequences obtained in our laboratory were added to make the dataset more representative. A maximum-likelihood (ML) tree was constructed with PhyML3.0. Maximum clade credibility (MCC) tree and effective population size were predicted by using Markov Chains Monte Carlo sampling method with Beast software. A total of 610 CRF07_BC sequences coving 1,473 bp of the gag gene (from 817 to 2,289 according to HXB2 calculator) were included into the dataset. Three epidemic clusters were identified; two clusters comprised sequences from IDUs, while one cluster mainly contained sequences from MSMs. The time of the most recent common ancestor of clusters that composed of sequences from MSMs was estimated to be in 2000. Two rapid spreading waves of effective population size of CRF07_BC infections were identified in the skyline plot. The second wave coincided with the expanding of MSM cluster. The results indicated that the control of CRF07_BC infections in MSMs would help to decrease its epidemic in China.

The Port Isabel Fold Belt: Salt enhanced Neogene Gravitational Spreading in the East Breaks, Western Gulf of Mexico

NASA Astrophysics Data System (ADS)

Lebit, Hermann; Clavaud, Marie; Whitehead, Sam; Opdyke, Scott; Luneburg, Catalina

2017-04-01

The Port Isabel fold belt is situated at the northwestern corner of the deep water Gulf of Mexico where the regional E-W trending Texas-Louisiana shelf bends into the NNE-SSW trend of the East Mexico Shelf. The fold belt forms an allochthonous wedge that ramps up from West to East with its front occupied by shallow salt complexes (local canopies). It is assumed that the belt predominantly comprises Oligocene siliciclastic sequences which reveal eastward facing folds and thrusts with a NE-SW regional trend. The structural architecture of the fold belt is very well imaged on recently processed 3D seismic volumes. Crystal III is a wide-azimuth survey acquired in 2011 and reprocessed in 2016 leveraging newly developed state-of-the-art technology. 3D deghosting, directional designature and multi-model 3D SRME resulted in broader frequency spectrum. The new image benefits from unique implementation of FWI, combined with classic tomographic updates. Seismically transparent zones indicating over-pressured shales are limited to the core of anticlines or to the footwall of internal thrust. Mobile shales associated with diapirs are absent in the study area. In contrast, salt is mobile and apparently forms the major decollement of the PIFB as indicated by remnant salt preferentially located in triangles along the major thrusts and fault intersections or at the core of anticlines. Shallow salt diapirs seam to root in the fold belt, while lacking evidence for salt feeders being connected to the deep salt underlying the Mesozoic to Paleogene substratum of the fold belt. Towards the WNW the fold belt is transient into a extensional regime, characterized by roll-over structures associated with deep reaching normal faults which form ultra-deep mini basins filled with Neogene deposits. Kinematic restorations confirm the simultaneous evolution of the deep mini basins and the outboard fold belt. This resembles a gravitational spreading system with the extensional tectonics of the deep Neogene mini basin balanced by the outboard compressional domains of the displaced Paleogene sediment sequence. In this context the role of salt is enigmatic, as the system's concave, deep reaching major detachment conflicts with the interpretation of a destabilized former salt canopy. It rather indicates syn-kinematic salt extrusion from a deeper source along the major frontal thrust ramp. A syn-kinematic (Poiseuille) salt flow along the major decollement (channel flow) is required to feed the salt accumulations at the frontal section of the fold belt and the shallow salt diapirs.

Earthquake source parameters for the 2010 western Gulf of Aden rifting episode

NASA Astrophysics Data System (ADS)

Shuler, Ashley; Nettles, Meredith

2012-08-01

On 2010 November 14, an intense swarm of earthquakes began in the western Gulf of Aden. Within a 48-hr period, 82 earthquakes with magnitudes between 4.5 and 5.5 were reported along an ˜80-km-long segment of the east-west trending Aden Ridge, making this swarm one of the largest ever observed in an extensional oceanic setting. In this study, we calculate centroid-moment-tensor solutions for 110 earthquakes that occurred between 2010 November and 2011 April. Over 80 per cent of the cumulative seismic moment results from earthquakes that occurred within 1 week of the onset of the swarm. We find that this sequence has a b-value of ˜1.6 and is dominated by normal-faulting earthquakes that, early in the swarm, migrate westwards with time. These earthquakes are located in rhombic basins along a section of the ridge that was previously characterized by low levels of seismicity and a lack of recent volcanism on the seafloor. Body-wave modelling demonstrates that the events occur in the top 2-3 km of the crust. Nodal planes of the normal-faulting earthquakes are consistent with previously mapped faults in the axial valley. A small number of strike-slip earthquakes observed between two basins near 44°E, where the axial valley changes orientation, depth and width, likely indicate the presence of an incipient transform fault and the early stages of ridge-transform segmentation. The direction of extension accommodated by the earthquakes is intermediate between the rift orthogonal and the direction of relative motion between the Arabian and Somalian plates, consistent with the oblique style of rifting occurring along the slow-spreading Aden Ridge. The 2010 swarm shares many characteristics with dyke-induced rifting episodes from both oceanic and continental settings. We conclude that the 2010 swarm represents the seismic component of an undersea magmatic rifting episode along the nascent Aden Ridge, and attribute the large size of the earthquakes to the combined effects of the slow spreading rate, relatively thick crust and recent quiescence. We estimate that the rifting episode was caused by dyke intrusions that propagated laterally for 12-18 hr, accommodating ˜1-14 m of opening or ˜85-800 yr of spreading along this section of the ridge. Our findings demonstrate the westward propagation of active seafloor spreading into this section of the western Gulf of Aden and illustrate that deformation at the onset of seafloor spreading may be accommodated by discrete episodes of faulting and magmatism. A comparison with similar sequences on land suggests that the 2010 episode may be only the first of several dyke-induced rifting episodes to occur in the western Gulf of Aden.

Discovery of Extended Main-sequence Turnoffs in Four Young Massive Clusters in the Magellanic Clouds

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

Li, Chengyuan; De Grijs, Richard; Deng, Licai

An increasing number of young massive clusters (YMCs) in the Magellanic Clouds have been found to exhibit bimodal or extended main sequences (MSs) in their color–magnitude diagrams (CMDs). These features are usually interpreted in terms of a coeval stellar population with different stellar rotational rates, where the blue and red MS stars are populated by non- (or slowly) and rapidly rotating stellar populations, respectively. However, some studies have shown that an age spread of several million years is required to reproduce the observed wide turnoff regions in some YMCs. Here we present the ultraviolet–visual CMDs of four Large and Smallmore » Magellanic Cloud YMCs, NGC 330, NGC 1805, NGC 1818, and NGC 2164, based on high-precision Hubble Space Telescope photometry. We show that they all exhibit extended main-sequence turnoffs (MSTOs). The importance of age spreads and stellar rotation in reproducing the observations is investigated. The observed extended MSTOs cannot be explained by stellar rotation alone. Adopting an age spread of 35–50 Myr can alleviate this difficulty. We conclude that stars in these clusters are characterized by ranges in both their ages and rotation properties, but the origin of the age spread in these clusters remains unknown.« less

Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods.

PubMed

Meinel, Dominik M; Heinzinger, Susanne; Eberle, Ute; Ackermann, Nikolaus; Schönberger, Katharina; Sing, Andreas

2018-02-01

Influenza with its annual epidemic waves is a major cause of morbidity and mortality worldwide. However, only little whole genome data are available regarding the molecular epidemiology promoting our understanding of viral spread in human populations. We implemented a RT-PCR strategy starting from patient material to generate influenza A whole genome sequences for molecular epidemiological surveillance. Samples were obtained within the Bavarian Influenza Sentinel. The complete influenza virus genome was amplified by a one-tube multiplex RT-PCR and sequenced on an Illumina MiSeq. We report whole genomic sequences for 50 influenza A H3N2 viruses, which was the predominating virus in the season 2014/15, directly from patient specimens. The dataset included random samples from Bavaria (Germany) throughout the influenza season and samples from three suspected transmission clusters. We identified the outbreak samples based on sequence identity. Whole genome sequencing (WGS) was superior in resolution compared to analysis of single segments or partial segment analysis. Additionally, we detected manifestation of substantial amounts of viral quasispecies in several patients, carrying mutations varying from the dominant virus in each patient. Our rapid whole genome sequencing approach for influenza A virus shows that WGS can effectively be used to detect and understand outbreaks in large communities. Additionally, the genomic data provide in-depth details about the circulating virus within one season.

Regional outbreak of CTX-M-2 β-lactamase-producing Proteus mirabilis in Japan.

PubMed

Nakano, Ryuichi; Nakano, Akiyo; Abe, Michiko; Inoue, Matsuhisa; Okamoto, Ryoichi

2012-12-01

Proteus mirabilis is a common cause of urinary tract infection. Wild-type P. mirabilis strains are usually susceptible to penicillins and cephalosporins, but occurrences of P. mirabilis producing extended-spectrum β-lactamases (ESBLs) have been recently reported. Here, we surveyed the prevalence of cefotaxime resistance among P. mirabilis strains at seven different hospitals in Kanagawa Prefecture, Japan, and investigated their molecular epidemiology to explain the mechanism of their spread. The prevalence of cefotaxime resistance among P. mirabilis increased annually, from 10.1 % in 1998 to 23.1 % in 2003, and increased drastically in 2004, exceeding 40 %. We collected 105 consecutive and non-duplicate cefotaxime-resistant P. mirabilis isolates (MIC 16 to >256 µg ml(-1)) from these hospitals from June 2004 to May 2005 and characterized their profile. PCR and sequence analysis revealed that all resistant strains produced exclusively CTX-M-2 β-lactamase. PFGE analysis identified 47 banding patterns with 83 % or greater similarity. These results indicated that a regional outbreak of P. mirabilis producing CTX-M-2 β-lactamase has occurred in Japan and suggest that the epidemic spread occurred within and across hospitals and communities by extended clonal strains. Plasmid analysis revealed that 44.8 % of plasmids harboured by bla(CTX-M-2) isolates had common profiles, encoding ISEcp1, IS26 and Int1, and belonged to incompatibility group T. Spread of the resistant isolates in Japan resulted from dissemination of narrow-host-range plasmids of the IncT group encoding bla(CTX-M-2). These findings indicate the rapidly developing problem of treating the species to prevent dissemination of ESBL producers.

Myxobolus cerebralis internal transcribed spacer 1 (ITS-1) sequences support recent spread of the parasite to North America and within Europe

USGS Publications Warehouse

Whipps, Christopher M.; El-Matbouli, M.; Hedrick, R.P.; Blazer, V.; Kent, M.L.

2004-01-01

Molecular approaches for resolving relationships among the Myxozoa have relied mainly on small subunit (SSU) ribosomal DNA (rDNA) sequence analysis. This region of the gene is generally used for higher phylogenetic studies, and the conservative nature of this gene may make it inadequate for intraspecific comparisons. Previous intraspecific studies of Myxobolus cerebralis based on molecular analyses reported that the sequence of SSU rDNA and the internal transcribed spacer (ITS) were highly conserved in representatives of the parasite from North America and Europe. Considering that the ITS is usually a more variable region than the SSU, we reanalyzed available sequences on GenBank and obtained sequences from other M. cerebralis representatives from the states of California and West Virginia in the USA and from Germany and Russia. With the exception of 7 base pairs, most of the sequence designated as ITS-1 in GenBank was a highly conserved portion of the rDNA near the 3-prime end of the SSU region. Nonetheless, the additional ITS-1 sequences obtained from the available geographic representatives were well conserved. It is unlikely that we would have observed virtually identical ITS-1 sequences between European and American M. cerebralis samples had it spread naturally over time, particularly when compared to the variation seen between isolates of another myxozoan (Kudoa thyrsites) that has most likely spread naturally. These data further support the hypothesis that the current distribution of M. cerebralis in North America is a result of recent introductions followed by dispersal via anthropogenic means, largely through the stocking of infected trout for sport fishing.

Numerical simulations and observations of surface wave fields under an extreme tropical cyclone

USGS Publications Warehouse

Fan, Y.; Ginis, I.; Hara, T.; Wright, C.W.; Walsh, E.J.

2009-01-01

The performance of the wave model WAVEWATCH III under a very strong, category 5, tropical cyclone wind forcing is investigated with different drag coefficient parameterizations and ocean current inputs. The model results are compared with field observations of the surface wave spectra from an airborne scanning radar altimeter, National Data Buoy Center (NDBC) time series, and satellite altimeter measurements in Hurricane Ivan (2004). The results suggest that the model with the original drag coefficient parameterization tends to overestimate the significant wave height and the dominant wavelength and produces a wave spectrum with narrower directional spreading. When an improved drag parameterization is introduced and the wave-current interaction is included, the model yields an improved forecast of significant wave height, but underestimates the dominant wavelength. When the hurricane moves over a preexisting mesoscale ocean feature, such as the Loop Current in the Gulf of Mexico or a warm-and cold-core ring, the current associated with the feature can accelerate or decelerate the wave propagation and significantly modulate the wave spectrum. ?? 2009 American Meteorological Society.

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

Population Structure of Clinical Pseudomonas aeruginosa from West and Central African Countries

PubMed Central

Cholley, Pascal; Ka, Roughyatou; Guyeux, Christophe; Thouverez, Michelle; Guessennd, Nathalie; Ghebremedhin, Beniam; Frank, Thierry; Bertrand, Xavier; Hocquet, Didier

2014-01-01

Background Pseudomonas aeruginosa (PA) has a non-clonal, epidemic population with a few widely distributed and frequently encountered sequence types (STs) called ‘high-risk clusters’. Clinical P. aeruginosa (clinPA) has been studied in all inhabited continents excepted in Africa, where a very few isolates have been analyzed. Here, we characterized a collection of clinPA isolates from four countries of West and Central Africa. Methodology 184 non-redundant isolates of clinPA from hospitals of Senegal, Ivory Coast, Nigeria, and Central African Republic were genotyped by MLST. We assessed their resistance level to antibiotics by agar diffusion and identified the extended-spectrum β-lactamases (ESBLs) and metallo-β-lactamases (MBLs) by sequencing. The population structure of the species was determined by a nucleotide-based analysis of the entire PA MLST database and further localized on the phylogenetic tree (i) the sequence types (STs) of the present collection, (ii) the STs by continents, (iii) ESBL- and MBL-producing STs from the MLST database. Principal Findings We found 80 distinct STs, of which 24 had no relationship with any known STs. ‘High-risk’ international clonal complexes (CC155, CC244, CC235) were frequently found in West and Central Africa. The five VIM-2-producing isolates belonged to CC233 and CC244. GES-1 and GES-9 enzymes were produced by one CC235 and one ST1469 isolate, respectively. We showed the spread of ‘high-risk’ international clonal complexes, often described as multidrug-resistant on other continents, with a fully susceptible phenotype. The MBL- and ESBL-producing STs were scattered throughout the phylogenetic tree and our data suggest a poor association between a continent and a specific phylogroup. Conclusions ESBL- and MBL-encoding genes are borne by both successful international clonal complexes and distinct local STs in clinPA of West and Central Africa. Furthermore, our data suggest that the spread of a ST could be either due to its antibiotic resistance or to features independent from the resistance to antibiotics. PMID:25187957

Mapping Challenging Mutations by Whole-Genome Sequencing

PubMed Central

Smith, Harold E.; Fabritius, Amy S.; Jaramillo-Lambert, Aimee; Golden, Andy

2016-01-01

Whole-genome sequencing provides a rapid and powerful method for identifying mutations on a global scale, and has spurred a renewed enthusiasm for classical genetic screens in model organisms. The most commonly characterized category of mutation consists of monogenic, recessive traits, due to their genetic tractability. Therefore, most of the mapping methods for mutation identification by whole-genome sequencing are directed toward alleles that fulfill those criteria (i.e., single-gene, homozygous variants). However, such approaches are not entirely suitable for the characterization of a variety of more challenging mutations, such as dominant and semidominant alleles or multigenic traits. Therefore, we have developed strategies for the identification of those classes of mutations, using polymorphism mapping in Caenorhabditis elegans as our model for validation. We also report an alternative approach for mutation identification from traditional recombinant crosses, and a solution to the technical challenge of sequencing sterile or terminally arrested strains where population size is limiting. The methods described herein extend the applicability of whole-genome sequencing to a broader spectrum of mutations, including classes that are difficult to map by traditional means. PMID:26945029

Genomic Epidemiology of Vibrio cholerae O1 Associated with Floods, Pakistan, 2010

PubMed Central

Shah, Muhammad Ali; Mutreja, Ankur; Thomson, Nicholas; Baker, Stephen; Parkhill, Julian; Dougan, Gordon; Bokhari, Habib

2014-01-01

In August 2010, Pakistan experienced major floods and a subsequent cholera epidemic. To clarify the population dynamics and transmission of Vibrio cholerae in Pakistan, we sequenced the genomes of all V. cholerae O1 El Tor isolates and compared the sequences to a global collection of 146 V. cholerae strains. Within the global phylogeny, all isolates from Pakistan formed 2 new subclades (PSC-1 and PSC-2), lying in the third transmission wave of the seventh-pandemic lineage that could be distinguished by signature deletions and their antimicrobial susceptibilities. Geographically, PSC-1 isolates originated from the coast, whereas PSC-2 isolates originated from inland areas flooded by the Indus River. Single-nucleotide polymorphism accumulation analysis correlated river flow direction with the spread of PSC-2. We found at least 2 sources of cholera in Pakistan during the 2010 epidemic and illustrate the value of a global genomic data bank in contextualizing cholera outbreaks. PMID:24378019

Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

PubMed

Shah, Muhammad Ali; Mutreja, Ankur; Thomson, Nicholas; Baker, Stephen; Parkhill, Julian; Dougan, Gordon; Bokhari, Habib; Wren, Brendan W

2014-01-01

In August 2010, Pakistan experienced major floods and a subsequent cholera epidemic. To clarify the population dynamics and transmission of Vibrio cholerae in Pakistan, we sequenced the genomes of all V. cholerae O1 El Tor isolates and compared the sequences to a global collection of 146 V. cholerae strains. Within the global phylogeny, all isolates from Pakistan formed 2 new subclades (PSC-1 and PSC-2), lying in the third transmission wave of the seventh-pandemic lineage that could be distinguished by signature deletions and their antimicrobial susceptibilities. Geographically, PSC-1 isolates originated from the coast, whereas PSC-2 isolates originated from inland areas flooded by the Indus River. Single-nucleotide polymorphism accumulation analysis correlated river flow direction with the spread of PSC-2. We found at least 2 sources of cholera in Pakistan during the 2010 epidemic and illustrate the value of a global genomic data bank in contextualizing cholera outbreaks.

Asymptotic convertibility of entanglement: An information-spectrum approach to entanglement concentration and dilution

NASA Astrophysics Data System (ADS)

Jiao, Yong; Wakakuwa, Eyuri; Ogawa, Tomohiro

2018-02-01

We consider asymptotic convertibility of an arbitrary sequence of bipartite pure states into another by local operations and classical communication (LOCC). We adopt an information-spectrum approach to address cases where each element of the sequences is not necessarily a tensor power of a bipartite pure state. We derive necessary and sufficient conditions for the LOCC convertibility of one sequence to another in terms of spectral entropy rates of entanglement of the sequences. Based on these results, we also provide simple proofs for previously known results on the optimal rates of entanglement concentration and dilution of general sequences of bipartite pure states.

Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae.

PubMed

Zhou, Kai; Lokate, Mariette; Deurenberg, Ruud H; Tepper, Marga; Arends, Jan P; Raangs, Erwin G C; Lo-Ten-Foe, Jerome; Grundmann, Hajo; Rossen, John W A; Friedrich, Alexander W

2016-02-11

The study describes the transmission of a CTX-M-15-producing ST15 Klebsiella pneumoniae between patients treated in a single center and the subsequent inter-institutional spread by patient referral occurring between May 2012 and September 2013. A suspected epidemiological link between clinical K. pneumoniae isolates was supported by patient contact tracing and genomic phylogenetic analysis from May to November 2012. By May 2013, a patient treated in three institutions in two cities was involved in an expanding cluster caused by this high-risk clone (HiRiC) (local expansion, CTX-M-15 producing, and containing hypervirulence factors). A clone-specific multiplex PCR was developed for patient screening by which another patient was identified in September 2013. Genomic phylogenetic analysis including published ST15 genomes revealed a close homology with isolates previously found in the USA. Environmental contamination and lack of consistent patient screening were identified as being responsible for the clone dissemination. The investigation addresses the advantages of whole-genome sequencing in the early detection of HiRiC with a high propensity of nosocomial transmission and prolonged circulation in the regional patient population. Our study suggests the necessity for inter-institutional/regional collaboration for infection/outbreak management of K. pneumoniae HiRiCs.

Whole Genome Sequence Analysis of the First Australian OXA-48-Producing Outbreak-Associated Klebsiella pneumoniae Isolates: The Resistome and In Vivo Evolution

PubMed Central

Espedido, Björn A.; Steen, Jason A.; Ziochos, Helen; Grimmond, Sean M.; Cooper, Matthew A.; Gosbell, Iain B.; van Hal, Sebastiaan J.; Jensen, Slade O.

2013-01-01

Whole genome sequencing was used to characterize the resistome of intensive care unit (ICU) outbreak-associated carbapenem-resistant K. pneumoniae isolates. Importantly, and of particular concern, the carbapenem-hydrolyzing β-lactamase gene bla OXA-48 and the extended-spectrum β-lactamase gene bla CTX-M-14, were identified on a single broad host-range conjugative plasmid. This represents the first report of bla OXA-48 in Australia and highlights the importance of resistance gene surveillance, as such plasmids can silently spread amongst enterobacterial populations and have the potential to drastically limit treatment options. Furthermore, the in vivo evolution of these isolates was also examined after 18 months of intra-abdominal carriage in a patient that transited through the ICU during the outbreak period. Reflecting the clonality of K. pneumoniae, only 11 single nucleotide polymorphisms (SNPs) were accumulated during this time-period and many of these were associated with genes involved in tolerance/resistance to antibiotics, metals or organic solvents, and transcriptional regulation. Collectively, these SNPs are likely to be associated with changes in virulence (at least to some extent) that have refined the in vivo colonization capacity of the original outbreak isolate. PMID:23555831

How to Pluck a Spectrum from a Planet

NASA Image and Video Library

2007-02-21

This diagram illustrates how astronomers using NASA Spitzer Space Telescope can capture the elusive spectra of hot-Jupiter planets. Spectra are an object light spread apart into its basic components, or wavelengths.

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

Flexible digital signal processing architecture for narrowband and spread-spectrum lock-in detection in multiphoton microscopy and time-resolved spectroscopy

PubMed Central

Wilson, Jesse W.; Park, Jong Kang; Warren, Warren S.

2015-01-01

The lock-in amplifier is a critical component in many different types of experiments, because of its ability to reduce spurious or environmental noise components by restricting detection to a single frequency and phase. One example application is pump-probe microscopy, a multiphoton technique that leverages excited-state dynamics for imaging contrast. With this application in mind, we present here the design and implementation of a high-speed lock-in amplifier on the field-programmable gate array (FPGA) coprocessor of a data acquisition board. The most important advantage is the inherent ability to filter signals based on more complex modulation patterns. As an example, we use the flexibility of the FPGA approach to enable a novel pump-probe detection scheme based on spread-spectrum communications techniques. PMID:25832238

Flexible digital signal processing architecture for narrowband and spread-spectrum lock-in detection in multiphoton microscopy and time-resolved spectroscopy.

PubMed

Wilson, Jesse W; Park, Jong Kang; Warren, Warren S; Fischer, Martin C

2015-03-01

The lock-in amplifier is a critical component in many different types of experiments, because of its ability to reduce spurious or environmental noise components by restricting detection to a single frequency and phase. One example application is pump-probe microscopy, a multiphoton technique that leverages excited-state dynamics for imaging contrast. With this application in mind, we present here the design and implementation of a high-speed lock-in amplifier on the field-programmable gate array (FPGA) coprocessor of a data acquisition board. The most important advantage is the inherent ability to filter signals based on more complex modulation patterns. As an example, we use the flexibility of the FPGA approach to enable a novel pump-probe detection scheme based on spread-spectrum communications techniques.

Unimodular sequence design under frequency hopping communication compatibility requirements

NASA Astrophysics Data System (ADS)

Ge, Peng; Cui, Guolong; Kong, Lingjiang; Yang, Jianyu

2016-12-01

The integrated design for both radar and anonymous communication has drawn more attention recently since wireless communication system appeals to enhance security and reliability. Given the frequency hopping (FH) communication system, an effective way to realize integrated design is to meet the spectrum compatibility between these two systems. The paper deals with a unimodular sequence design technique which considers optimizing both the spectrum compatibility and peak sidelobes levels (PSL) of auto-correlation function (ACF). The spectrum compatibility requirement realizes anonymous communication for the FH system and provides this system lower probability of intercept (LPI) since the spectrum of the FH system is hidden in that of the radar system. The proposed algorithm, named generalized fitting template (GFT) technique, converts the sequence optimization design problem to a iterative fitting process. In this process, the power spectrum density (PSD) and PSL behaviors of the generated sequences fit both PSD and PSL templates progressively. Two templates are established based on the spectrum compatibility requirement and the expected PSL. As noted, in order to ensure the communication security and reliability, spectrum compatibility requirement is given a higher priority to achieve in the GFT algorithm. This algorithm realizes this point by adjusting the weight adaptively between these two terms during the iteration process. The simulation results are analyzed in terms of bit error rate (BER), PSD, PSL, and signal-interference rate (SIR) for both the radar and FH systems. The performance of GFT is compared with SCAN, CAN, FRE, CYC, and MAT algorithms in the above aspects, which shows its good effectiveness.

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…

Disruption of Neurexin 1 Associated with Autism Spectrum Disorder

PubMed Central

Kim, Hyung-Goo; Kishikawa, Shotaro; Higgins, Anne W.; Seong, Ihn-Sik; Donovan, Diana J.; Shen, Yiping; Lally, Eric; Weiss, Lauren A.; Najm, Juliane; Kutsche, Kerstin; Descartes, Maria; Holt, Lynn; Braddock, Stephen; Troxell, Robin; Kaplan, Lee; Volkmar, Fred; Klin, Ami; Tsatsanis, Katherine; Harris, David J.; Noens, Ilse; Pauls, David L.; Daly, Mark J.; MacDonald, Marcy E.; Morton, Cynthia C.; Quade, Bradley J.; Gusella, James F.

2008-01-01

Autism is a neurodevelopmental disorder of complex etiology in which genetic factors play a major role. We have implicated the neurexin 1 (NRXN1) gene in two independent subjects who display an autism spectrum disorder (ASD) in association with a balanced chromosomal abnormality involving 2p16.3. In the first, with karyotype 46,XX,ins(16;2)(q22.1;p16.1p16.3)pat, NRXN1 is directly disrupted within intron 5. Importantly, the father possesses the same chromosomal abnormality in the absence of ASD, indicating that the interruption of α-NRXN1 is not fully penetrant and must interact with other factors to produce ASD. The breakpoint in the second subject, with 46,XY,t(1;2)(q31.3;p16.3)dn, occurs ∼750 kb 5′ to NRXN1 within a 2.6 Mb genomic segment that harbors no currently annotated genes. A scan of the NRXN1 coding sequence in a cohort of ASD subjects, relative to non-ASD controls, revealed that amino acid alterations in neurexin 1 are not present at high frequency in ASD. However, a number of rare sequence variants in the coding region, including two missense changes in conserved residues of the α-neurexin 1 leader sequence and of an epidermal growth factor (EGF)-like domain, respectively, suggest that even subtle changes in NRXN1 might contribute to susceptibility to ASD. PMID:18179900

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.

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

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.

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

Low Statistics Reconstruction of the Compton Camera Point Spread Function in 3D Prompt-γ Imaging of Ion Beam Therapy

NASA Astrophysics Data System (ADS)

Lojacono, Xavier; Richard, Marie-Hélène; Ley, Jean-Luc; Testa, Etienne; Ray, Cédric; Freud, Nicolas; Létang, Jean Michel; Dauvergne, Denis; Maxim, Voichiţa; Prost, Rémy

2013-10-01

The Compton camera is a relevant imaging device for the detection of prompt photons produced by nuclear fragmentation in hadrontherapy. It may allow an improvement in detection efficiency compared to a standard gamma-camera but requires more sophisticated image reconstruction techniques. In this work, we simulate low statistics acquisitions from a point source having a broad energy spectrum compatible with hadrontherapy. We then reconstruct the image of the source with a recently developed filtered backprojection algorithm, a line-cone approach and an iterative List Mode Maximum Likelihood Expectation Maximization algorithm. Simulated data come from a Compton camera prototype designed for hadrontherapy online monitoring. Results indicate that the achievable resolution in directions parallel to the detector, that may include the beam direction, is compatible with the quality control requirements. With the prototype under study, the reconstructed image is elongated in the direction orthogonal to the detector. However this direction is of less interest in hadrontherapy where the first requirement is to determine the penetration depth of the beam in the patient. Additionally, the resolution may be recovered using a second camera.

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.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

PubMed

Liu, Siyang; Huang, Shujia; Rao, Junhua; Ye, Weijian; Krogh, Anders; Wang, Jun

2015-01-01

Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure.

Parametric instability, inverse cascade and the range of solar-wind turbulence

NASA Astrophysics Data System (ADS)

Chandran, Benjamin D. G.

2018-02-01

In this paper, weak-turbulence theory is used to investigate the nonlinear evolution of the parametric instability in three-dimensional low- plasmas at wavelengths much greater than the ion inertial length under the assumption that slow magnetosonic waves are strongly damped. It is shown analytically that the parametric instability leads to an inverse cascade of Alfvén wave quanta, and several exact solutions to the wave kinetic equations are presented. The main results of the paper concern the parametric decay of Alfvén waves that initially satisfy +\\gg e-$ , where +$ and -$ are the frequency ( ) spectra of Alfvén waves propagating in opposite directions along the magnetic field lines. If +$ initially has a peak frequency 0$ (at which +$ is maximized) and an `infrared' scaling p$ at smaller with , then +$ acquires an -1$ scaling throughout a range of frequencies that spreads out in both directions from 0$ . At the same time, -$ acquires an -2$ scaling within this same frequency range. If the plasma parameters and infrared +$ spectrum are chosen to match conditions in the fast solar wind at a heliocentric distance of 0.3 astronomical units (AU), then the nonlinear evolution of the parametric instability leads to an +$ spectrum that matches fast-wind measurements from the Helios spacecraft at 0.3 AU, including the observed -1$ scaling at -4~\\text{Hz}$ . The results of this paper suggest that the -1$ spectrum seen by Helios in the fast solar wind at -4~\\text{Hz}$ is produced in situ by parametric decay and that the -1$ range of +$ extends over an increasingly narrow range of frequencies as decreases below 0.3 AU. This prediction will be tested by measurements from the Parker Solar Probe.

Assessment of area spread of porcine reproductive and respiratory syndrome (PRRS) virus in three clusters of swine farms.

PubMed

Arruda, A G; Sanhueza, J; Corzo, C; Vilalta, C

2018-04-14

Despite decades of porcine reproductive and respiratory syndrome (PRRS) research, outbreaks with emerging and re-emerging PRRS virus (PRRSV) strains are not uncommon in North America. The role of area spread, commonly referred but not limited to airborne transmission, in originating such outbreaks is currently unknown. The main objective of this study was to explore the role of area spread on the occurrence of new PRRSV cases by combining information on genetic similarity among recovered PRRSV isolate's open-reading frame (ORF) 5 sequences and publicly available weather data. Three small regions were enrolled in the study for which high farm-level participation rate was achieved, and swine sites within those regions were readily sampled after reporting of an outbreak in a sow farm. Oral fluid PCR testing was used to determine PRRSV status of farms, and wind roses were generated for assessment of prevailing wind directions during 2-14 days preceding the outbreak. Under the conditions of this study, the data did not support the area spread theory as the main cause for these outbreaks. We suggest that for future studies, analysis of animal movement and other links between farms such as personnel, equipment and sharing of service providers should be incorporated for better insights on source of the virus. Furthermore, the development of rapid and easy diagnostic methods for ruling out resident PRRSV is urgently needed. © 2018 Blackwell Verlag GmbH.

Molecular Phylogeny of Heme Peroxidases

NASA Astrophysics Data System (ADS)

Zámocký, Marcel; Obinger, Christian

All currently available gene sequences of heme peroxidases can be phylogenetically divided in two superfamilies and three families. In this chapter, the phylogenetics and genomic distribution of each group are presented. Within the peroxidase-cyclooxygenase superfamily, the main evolutionary direction developed peroxidatic heme proteins involved in the innate immune defense system and in biosynthesis of (iodinated) hormones. The peroxidase-catalase superfamily is widely spread mainly among bacteria, fungi, and plants, and particularly in Class I led to the evolution of bifunctional catalase-peroxidases. Its numerous fungal representatives of Class II are involved in carbon recycling via lignin degradation, whereas Class III secretory peroxidases from algae and plants are included in various forms of secondary metabolism. The family of di-heme peroxidases are predominantly bacteria-inducible enzymes; however, a few corresponding genes were also detected in archaeal genomes. Four subfamilies of dyp-type peroxidases capable of degradation of various xenobiotics are abundant mainly among bacteria and fungi. Heme-haloperoxidase genes are widely spread among sac and club fungi, but corresponding genes were recently found also among oomycetes. All described families herein represent heme peroxidases of broad diversity in structure and function. Our accumulating knowledge about the evolution of various enzymatic functions and physiological roles can be exploited in future directed evolution approaches for engineering peroxidase genes de novo for various demands.

Frequency Spectrum for New Aviation Data Links: Initial Study Results

NASA Technical Reports Server (NTRS)

Matolak, David W.; Branstetter, James R.

2004-01-01

We describe results from an initial study to assess the suitability of various spectral bands for supporting the deployment of new aviation data links (ADL). The study focused on systems and spectral bands that can deliver VHF data link (VDL)-or-higher data rates in a two-way communication setting, including air-ground, ground-air, and air-air modes of operation. In the first part of our paper, we briefly discuss the current situation regarding communications, navigation, and surveillance (CNS) links and existing spectrum, and the well-known need for new aviation data links. We next provide an overview of related systems, and discuss key factors involved in the use of spectrum in various bands for any future integrated CNS data link, addressing primarily the lower few layers of the communications protocol stack. Desired attributes of a new ADL system are discussed, and the beneficial aspects of a particular transmission technique spread spectrum are summarized. We also provide a short list of several example potential spectral regions, and note that while none of the existing systems will likely meet the full range of desired features of a new ADL, several systems and spectral regions offer promise in terms of one or more characteristics. A detailed discussion and evaluation of these spectral regions is proposed as future work. We include a few brief examples to illustrate initial technical results regarding spread spectrum overlay, also a subject for future work.

Mutational spectrum of Xeroderma pigmentosum group A in Egyptian patients.

PubMed

Amr, Khalda; Messaoud, Olfa; El Darouti, Mohamad; Abdelhak, Sonia; El-Kamah, Ghada

2014-01-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive hereditary disease characterized by hyperphotosensitivity, DNA repair defects and a predisposition to skin cancers. The most frequently occurring type worldwide is the XP group A (XPA). There is a close relationship between the clinical features that ranged from severe to mild form and the mutational site in XPA gene. The aim of this study is to carry out the mutational analysis in Egyptian patients with XP-A. This study was carried out on four unrelated Egyptian XP-A families. Clinical features were examined and direct sequencing of the coding region of XPA gene was performed in patients and their parents. Direct sequencing of the whole coding region of the XPA gene revealed the identification of two homozygous nonsense mutations: (c.553C >T; p.(Gln185)) and (c.331G>T; p.(Glu111)), which create premature, stop codon and a homodeletion (c.374delC: p.Thr125Ilefs 15) that leads to frameshift and premature translation termination. We report the identification of one novel XPA gene mutation and two known mutations in four unrelated Egyptian families with Xermoderma pigmentosum. All explored patients presented severe neurological abnormalities and have mutations located in the DNA binding domain. This report gives insight on the mutation spectrum of XP-A in Egypt. This would provide a valuable tool for early diagnosis of this severe disease. © 2013 Elsevier B.V. All rights reserved.

Whole-Genome Sequences of Listeria monocytogenes Sequence Type 6 Isolates Associated with a Large Foodborne Outbreak in South Africa, 2017 to 2018

PubMed Central

Tau, Nomsa; Smouse, Shannon L.; Mtshali, Phillip S.; Mnyameni, Florah; Khumalo, Zamantungwa T. H.; Ismail, Arshad; Govender, Nevashan; Thomas, Juno

2018-01-01

ABSTRACT We report whole-genome sequences for 10 Listeria monocytogenes sequence type 6 isolates associated with a large listeriosis outbreak in South Africa, which occurred over the period of 2017 to 2018. The possibility of listeriosis spreading beyond South Africa’s borders as a result of exported contaminated food products prompted us to make the genome sequences publicly available. PMID:29930052

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.

Travel Time Data Collection Field Tests - Lessons Learned

DOT National Transportation Integrated Search

1999-06-28

The Los Angeles Spread Spectrum Radio (SSR) Traffic Signal Interconnect Field Operational Test (FOT) investigated the feasibility of using wireless communications as an alternative to traditional hard-wire interconnection, to extend the coverage of c...

47 CFR 87.479 - Harmful interference to radionavigation land stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... to establish wide-band systems using frequency-hopping spread spectrum techniques in the 960-1215 MHz.... Transmissions will be automatically prevented if: (1) The frequency-hopping mode fails to distribute the JTIDS...

Nomographs for estimating surface fire behavior characteristics

Treesearch

Joe H. Scott

2007-01-01

A complete set of nomographs for estimating surface fire rate of spread and flame length for the original 13 and new 40 fire behavior fuel models is presented. The nomographs allow calculation of spread rate and flame length for wind in any direction with respect to slope and allow for nonheading spread directions. Basic instructions for use are included.

Strain Anomalies during an Earthquake Sequence in the South Iceland Seismic Zone

NASA Astrophysics Data System (ADS)

Arnadottir, T.; Haines, A. J.; Geirsson, H.; Hreinsdottir, S.

2017-12-01

The South Iceland Seismic Zone (SISZ) accommodates E-W translation due to oblique spreading between the North American/Hreppar microplate and Eurasian plate, in South Iceland. Strain is released in the SISZ during earthquake sequences that last days to years, at average intervals of 80-100 years. The SISZ is currently in the midst of an earthquake sequence that started with two M6.5 earthquakes in June 2000, and continued with two M6 earthquakes in May 2008. Estimates of geometric strain accumulation, and seismic strain release in these events indicate that they released at most only half of the strain accumulated since the last earthquake cycle in 1896-1912. Annual GPS campaigns and continuous measurements during 2001-2015 were used to calculate station velocities and strain rates from a new method using the vertical derivatives of horizontal stress (VDoHS). This new method allows higher resolution of strain rates than other (older) approaches, as the strain rates are estimated by integrating VDoHS rates obtained by inversion rather than differentiating interpolated GPS velocities. Estimating the strain rates for eight 1-2 year intervals indicates temporal and spatial variation of strain rates in the SISZ. In addition to earthquake faulting, the strain rates in the SISZ are influenced by anthropogenic signals due to geothermal exploitation, and magma movements in neighboring volcanoes - Hekla and Eyjafjallajökull. Subtle signals of post-seismic strain rate changes are seen following the June 2000 M6.5 main shocks, but interestingly, much larger strain rate variations are observed after the two May 2008 M6 main shocks. A prominent strain anomaly is evident in the epicentral area prior to the May 2008 earthquake sequence. The strain signal persists over at least 4 years in the epicentral area, leading up to the M6 main shocks. The strain is primarily extension in ESE-WNW direction (sub-parallel to the direction of plate spreading), but overall shear across the N-S faults that subsequently ruptured, increases with time. The pre-2008 strain anomaly and large post-2008 strain variations are enigmatic, but may signify crustal fluids and/or differences in rheology and crustal thickness between the 2000 and 2008 epicentral areas.

Mutational spectrum in breast cancer associated BRCA1 and BRCA2 genes in Colombia

PubMed Central

Gómez-Gutiérrez, Alberto; Díaz-Dussán, Natalia Andrea; Noguera-Santamaría, María Claudia; Díaz-Rincón, Diego; Casas-Gómez, María Consuelo

2017-01-01

Abstract Introduction: The risk of developing breast and ovarian cancer is higher in families that carry mutations in BRCA1 or BRCA2 genes, and timely mutation detection is critical. Objective: To identify the presence of mutations in the Colombian population and evaluate two testing strategies. Methods: From a total universe of 853 individual blood samples referred for BRCA1 and BRCA2 typing, 256 cases were analyzed by complete direct sequencing of both genes in Myriad Genetics, and the remaining 597 cases were studied by partial sequencing based on founder mutations in a PCR test designed by ourselves ("Profile Colombia"). Results: We found 107 patients carrying deleterious mutations in this group of patients, 69 (64.5%) located in BRCA1, and 38 (35.5%) in BRCA2. Overall, we detected 39 previously unreported mutations in Colombia (22 in BRCA1 and 17 in BRCA2) and only 4 out of the 6 previously reported founder mutations. Sixty four out of 597 patients (10.7%) studied by "Profile Colombia" showed mutations in BRCA1 or BRCA2, and 41/256 patients (16%) showed mutations by complete BRCA1-BRCA2 sequencing. Conclusions: The spectrum of 44 different mutations in Colombia as detected in our study is broader than the one previously reported for this country. "Profile Colombia" is a useful screening test to establish both founder and new mutations (detection rate of 10.7%) in cases with family history of breast cancer. Complete sequencing shows a detection rate of 16.0%, and should complement the study of the genetic basis of this disease. PMID:29021639

Temperature Regulation of Shigella Virulence: Identification of Temperature-Regulated Shigella Invasion Genes by the Isolation of inv::lacZ Operon Fusions and the Characterization of the Virulence Gene Regulator virR

DTIC Science & Technology

1991-04-10

Partial nucleotide sequence of viri? clone pAEH122 102 14. Effects of VirR’ activity on Ipa expression 106 15. Sequencing strategy for the 2.3 kb EcoRl...Confluent monolayers of mammalian cells are challenged with virulent organisms and invasion and intercellular spread result in a cytopathic effect ...destruction of the mucosal surface and an inflammatory response ensues which mimics the effects of invasion and intercellular spread in the mucosa of the

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.

Exome sequencing is an efficient tool for variant late-infantile neuronal ceroid lipofuscinosis molecular diagnosis.

PubMed

Patiño, Liliana Catherine; Battu, Rajani; Ortega-Recalde, Oscar; Nallathambi, Jeyabalan; Anandula, Venkata Ramana; Renukaradhya, Umashankar; Laissue, Paul

2014-01-01

The neuronal ceroid-lipofuscinoses (NCL) is a group of neurodegenerative disorders characterized by epilepsy, visual failure, progressive mental and motor deterioration, myoclonus, dementia and reduced life expectancy. Classically, NCL-affected individuals have been classified into six categories, which have been mainly defined regarding the clinical onset of symptoms. However, some patients cannot be easily included in a specific group because of significant variation in the age of onset and disease progression. Molecular genetics has emerged in recent years as a useful tool for enhancing NCL subtype classification. Fourteen NCL genetic forms (CLN1 to CLN14) have been described to date. The variant late-infantile form of the disease has been linked to CLN5, CLN6, CLN7 (MFSD8) and CLN8 mutations. Despite advances in the diagnosis of neurodegenerative disorders mutations in these genes may cause similar phenotypes, which rends difficult accurate candidate gene selection for direct sequencing. Three siblings who were affected by variant late-infantile NCL are reported in the present study. We used whole-exome sequencing, direct sequencing and in silico approaches to identify the molecular basis of the disease. We identified the novel c.1219T>C (p.Trp407Arg) and c.1361T>C (p.Met454Thr) MFSD8 pathogenic mutations. Our results highlighted next generation sequencing as a novel and powerful methodological approach for the rapid determination of the molecular diagnosis of NCL. They also provide information regarding the phenotypic and molecular spectrum of CLN7 disease.

Low-cost TDRSS communications for NASA's long duration balloon project

NASA Technical Reports Server (NTRS)

Israel, David J.

1993-01-01

A new transponder and RF ground support equipment for the NASA Tracking and Data Relay Satellite System (TDRSS) intended to support long duration scientific balloon flights in Antarctica are described. The new balloon class transponder features a highly integrated spread spectrum receiver design based on programmable charge coupled device (CCD) correlators and digital signal processing chips. The correlator chip is a Lincoln Labs 4ABC with four CCD channels. The balloon transponder is capable of reporting an estimate of its input bit error rate using digital signal processing. The TDRSS user RF test set is based on a set of RF ground support equipment capable of providing both the RF communications and direct control and monitoring necessary for transponder testing and a two-way RF link for preflight testing.

Satellite sound broadcasting system study: Mobile considerations

NASA Technical Reports Server (NTRS)

Golshan, Nasser

1990-01-01

Discussed here is the mobile reception part of a study to investigate a satellite sound broadcast system in the UHF or L bands. Existing propagation and reception measurements are used with proper interpretation to evaluate the signaling, coding, and diversity alternatives suitable for the system. Signal attenuation in streets shadowed by buildings appear to be around 29 db, considerably higher than the 10 db adopted by CCIR. With the marriage of proper technologies, an LMSS class satellite can provide substantial direct satellite audio broadcast capability in UHF or L bands for high quality mobile and portable indoor reception by low cost radio receivers. This scheme requires terrestrial repeaters for satisfactory mobile reception in urban areas. A specialized bandwidth efficient spread spectrum signalling technique is particularly suitable for the terrestrial repeaters.

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…

Universal Sequence Replication, Reversible Polymerization and Early Functional Biopolymers: A Model for the Initiation of Prebiotic Sequence Evolution

PubMed Central

Walker, Sara Imari; Grover, Martha A.; Hud, Nicholas V.

2012-01-01

Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer/polymer diffusivities. PMID:22493682

Rabies in the arctic fox population, Svalbard, Norway.

PubMed

Mørk, Torill; Bohlin, Jon; Fuglei, Eva; Åsbakk, Kjetil; Tryland, Morten

2011-10-01

Arctic foxes, 620 that were trapped and 22 found dead on Svalbard, Norway (1996-2004), as well as 10 foxes trapped in Nenets, North-West Russia (1999), were tested for rabies virus antigen in brain tissue by standard direct fluorescent antibody test. Rabies antigen was found in two foxes from Svalbard and in three from Russia. Blood samples from 515 of the fox carcasses were screened for rabies antibodies with negative result. Our results, together with a previous screening (1980-1989, n=817) indicate that the prevalence of rabies in Svalbard has remained low or that the virus has not been enzootic in the arctic fox population since the first reported outbreak in 1980. Brain tissues from four arctic foxes (one from Svalbard, three from Russia) in which rabies virus antigen was detected were further analyzed by reverse-transcriptase polymerase chain reaction direct amplicon sequencing and phylogenetic analysis. Sequences were compared to corresponding sequences from rabies virus isolates from other arctic regions. The Svalbard isolate and two of the Russian isolates were identical (310 nucleotides), whereas the third Russian isolate differed in six nucleotide positions. However, when translated into amino acid sequences, none of these substitutions produced changes in the amino acid sequence. These findings suggest that the spread of rabies virus to Svalbard was likely due to migration of arctic foxes over sea ice from Russia to Svalbard. Furthermore, when compared to other Arctic rabies virus isolates, a high degree of homology was found, suggesting a high contact rate between arctic fox populations from different arctic regions. The high degree of homology also indicates that other, and more variable, regions of the genome than this part of the nucleoprotein gene should be used to distinguish Arctic rabies virus isolates for epidemiologic purposes.

Three-dimensional tracking for efficient fire fighting in complex situations

NASA Astrophysics Data System (ADS)

Akhloufi, Moulay; Rossi, Lucile

2009-05-01

Each year, hundred millions hectares of forests burn causing human and economic losses. For efficient fire fighting, the personnel in the ground need tools permitting the prediction of fire front propagation. In this work, we present a new technique for automatically tracking fire spread in three-dimensional space. The proposed approach uses a stereo system to extract a 3D shape from fire images. A new segmentation technique is proposed and permits the extraction of fire regions in complex unstructured scenes. It works in the visible spectrum and combines information extracted from YUV and RGB color spaces. Unlike other techniques, our algorithm does not require previous knowledge about the scene. The resulting fire regions are classified into different homogenous zones using clustering techniques. Contours are then extracted and a feature detection algorithm is used to detect interest points like local maxima and corners. Extracted points from stereo images are then used to compute the 3D shape of the fire front. The resulting data permits to build the fire volume. The final model is used to compute important spatial and temporal fire characteristics like: spread dynamics, local orientation, heading direction, etc. Tests conducted on the ground show the efficiency of the proposed scheme. This scheme is being integrated with a fire spread mathematical model in order to predict and anticipate the fire behaviour during fire fighting. Also of interest to fire-fighters, is the proposed automatic segmentation technique that can be used in early detection of fire in complex scenes.

Predicting spatial spread of rabies in skunk populations using surveillance data reported by the public

PubMed Central

Streicker, Daniel G.; Fischer, Justin W.; VerCauteren, Kurt C.; Gilbert, Amy T.

2017-01-01

Background Prevention and control of wildlife disease invasions relies on the ability to predict spatio-temporal dynamics and understand the role of factors driving spread rates, such as seasonality and transmission distance. Passive disease surveillance (i.e., case reports by public) is a common method of monitoring emergence of wildlife diseases, but can be challenging to interpret due to spatial biases and limitations in data quantity and quality. Methodology/Principal findings We obtained passive rabies surveillance data from dead striped skunks (Mephitis mephitis) in an epizootic in northern Colorado, USA. We developed a dynamic patch-occupancy model which predicts spatio-temporal spreading while accounting for heterogeneous sampling. We estimated the distance travelled per transmission event, direction of invasion, rate of spatial spread, and effects of infection density and season. We also estimated mean transmission distance and rates of spatial spread using a phylogeographic approach on a subsample of viral sequences from the same epizootic. Both the occupancy and phylogeographic approaches predicted similar rates of spatio-temporal spread. Estimated mean transmission distances were 2.3 km (95% Highest Posterior Density (HPD95): 0.02, 11.9; phylogeographic) and 3.9 km (95% credible intervals (CI95): 1.4, 11.3; occupancy). Estimated rates of spatial spread in km/year were: 29.8 (HPD95: 20.8, 39.8; phylogeographic, branch velocity, homogenous model), 22.6 (HPD95: 15.3, 29.7; phylogeographic, diffusion rate, homogenous model) and 21.1 (CI95: 16.7, 25.5; occupancy). Initial colonization probability was twice as high in spring relative to fall. Conclusions/Significance Skunk-to-skunk transmission was primarily local (< 4 km) suggesting that if interventions were needed, they could be applied at the wave front. Slower viral invasions of skunk rabies in western USA compared to a similar epizootic in raccoons in the eastern USA implies host species or landscape factors underlie the dynamics of rabies invasions. Our framework provides a straightforward method for estimating rates of spatial spread of wildlife diseases. PMID:28759576

Chemical environments of submarine hydrothermal systems

NASA Technical Reports Server (NTRS)

Shock, Everett L.

1992-01-01

Perhaps because black-smoker chimneys make tremendous subjects for magazine covers, the proposal that submarine hydrothermal systems were involved in the origin of life has caused many investigators to focus on the eye-catching hydrothermal vents. In much the same way that tourists rush to watch the spectacular eruptions of Old Faithful geyser with little regard for the hydrology of the Yellowstone basin, attention is focused on the spectacular, high-temperature hydrothermal vents to the near exclusion of the enormous underlying hydrothermal systems. Nevertheless, the magnitude and complexity of geologic structures, heat flow, and hydrologic parameters which characterize the geyser basins at Yellowstone also characterize submarine hydrothermal systems. However, in the submarine systems the scale can be considerably more vast. Like Old Faithful, submarine hydrothermal vents have a spectacular quality, but they are only one fascinating aspect of enormous geologic systems operating at seafloor spreading centers throughout all of the ocean basins. A critical study of the possible role of hydrothermal processes in the origin of life should include the full spectrum of probable environments. The goals of this chapter are to synthesize diverse information about the inorganic geochemistry of submarine hydrothermal systems, assemble a description of the fundamental physical and chemical attributes of these systems, and consider the implications of high-temperature, fluid-driven processes for organic synthesis. Information about submarine hydrothermal systems comes from many directions. Measurements made directly on venting fluids provide useful, but remarkably limited, clues about processes operating at depth. The oceanic crust has been drilled to approximately 2.0 km depth providing many other pieces of information, but drilling technology has not allowed the bore holes and core samples to reach the maximum depths to which aqueous fluids circulate in oceanic crust. Such determinations rely on studies of pieces of deep oceanic crust uplifted by tectonic forces such as along the Southwest Indian Ridge, or more complete sections of oceanic crust called ophiolite sequences which are presently exposed on continents owing to tectonic emplacement. Much of what is thought to happen in submarine hydrothermal systems is inferred from studies of ophiolite sequences, and especially from the better-exposed ophiolites in Oman, Cyprus and North America. The focus of much that follows is on a few general features: pressure, temperature, oxidation states, fluid composition and mineral alteration, because these features will control whether organic synthesis can occur in hydrothermal systems.

Strain-specific transmission in an outbreak of ESBL-producing Enterobacteriaceae in the hemato-oncology care unit: a cohort study.

PubMed

Uemura, Makiko; Imataki, Osamu; Uchida, Shumpei; Nakayama-Imaohji, Haruyuki; Ohue, Yukiko; Matsuka, Harumi; Mori, Hatsune; Dobashi, Hiroaki; Kuwahara, Tomomi; Kadowaki, Norimitsu

2017-01-05

Extended-spectrum β-lactamase (ESBL)-producing bacteria are resistant to several types of antibiotics excluding carbapenems. A transmissibility of ESBL-producing Enterobacteriaceae would be depending on each bacterial property, however, that has not been elucidated in clinical setting. In this study, we attempted to identify the source of an outbreak of ESBL-producing bacteria in a medical oncology and immunology care unit. An ESBL-producing Enterobacteriaceae (ESBL-E) outbreak observed between July 2012 and August 2012 in Kagawa University Hospital was surveyed using various molecular microbiology techniques. We used Pulsed-field gel electrophoresis (PFGE), PCR-based ESBL gene typing, and direct sequence of ESBL gene as molecular microbiology typing method to distinguish each strain. The typical prevalence of ESBL-E isolation in the unit was 7.0 per month (1.7 per week). The prevalence of ESBL-E isolation during the target research period was 20.0 per month (5.0 per week). In total, 19 isolates (11 K. pneumoniae and 8 E. coli) were obtained from clinical samples, including four control strains (two each of both bacteria), that were physically different from those obtained from other inpatient units in our hospital. Pulsed-field gel electrophoresis (PFGE) for K. pneumoniae (digested by XbaI) produced similar patterns excluding one control strain. PCR classification of the ESBL gene for K. pneumoniae revealed that all strains other than the control strain carried SHV and CTX-M-9. This result was reconfirmed by direct DNA sequencing. Although the outbreak of K. pneumoniae was considered to be "clonal," PFGE and PCR classification of the ESBL genes for E. coli uncovered at least six different "non-clonal" strains possessing individual ESBL gene patterns. According to the result of an antibiogram, the pattern of antimicrobial susceptibility was more variable for K. pneumoniae than for E. coli. Typing by PFGE and ESBL gene PCR analysis is practical for discriminating various organisms. In our cohort, two outbreaks were concomitantly spread with different transmission strategies, namely clonal and non-clonal, in the same unit. This might represent clinical evidence that transmissibility differs according to the type of strain. We speculated that patient-to-patient transmission of ESBL-E occurred according to the properties of each individual strain.

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.

EVIDENCE OF SPREADING LAYER EMISSION IN A THERMONUCLEAR SUPERBURST

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

Koljonen, K. I. I.; Kajava, J. J. E.; Kuulkers, E., E-mail: karri.koljonen@nyu.edu

2016-10-01

When a neutron star (NS) accretes matter from a companion star in a low-mass X-ray binary, the accreted gas settles onto the stellar surface through a boundary/spreading layer. On rare occasions the accumulated gas undergoes a powerful thermonuclear superburst powered by carbon burning deep below the NS atmosphere. In this paper, we apply the non-negative matrix factorization spectral decomposition technique to show that the spectral variations during a superburst from 4U 1636–536 can be explained by two distinct components: (1) the superburst emission characterized by a variable temperature blackbody radiation component and (2) a quasi-Planckian component with a constant, ∼2.5more » keV, temperature varying by a factor of ∼15 in flux. The spectrum of the quasi-Planckian component is identical in shape and characteristics to the frequency-resolved spectra observed in the accretion/persistent spectrum of NS low-mass X-ray binaries and agrees well with the predictions of the spreading layer model by Inogamov and Sunyaev. Our results provide yet more observational evidence that superbursts—and possibly also normal X-ray bursts—induce changes in the disc–star boundary.« less

Isolation and characterisation of lytic bacteriophages of Klebsiella pneumoniae and Klebsiella oxytoca.

PubMed

Karumidze, Natia; Kusradze, Ia; Rigvava, Sophio; Goderdzishvili, Marine; Rajakumar, Kumar; Alavidze, Zemphira

2013-03-01

Klebsiella bacteria have emerged as an increasingly important cause of community-acquired nosocomial infections. Extensive use of broad-spectrum antibiotics in hospitalised patients has led to both increased carriage of Klebsiella and the development of multidrug-resistant strains that frequently produce extended-spectrum β-lactamases and/or other defences against antibiotics. Many of these strains are highly virulent and exhibit a strong propensity to spread. In this study, six lytic Klebsiella bacteriophages were isolated from sewage-contaminated river water in Georgia and characterised as phage therapy candidates. Two of the phages were investigated in greater detail. Biological properties, including phage morphology, nucleic acid composition, host range, growth phenotype, and thermal and pH stability were studied for all six phages. Limited sample sequencing was performed to define the phylogeny of the K. pneumoniae- and K. oxytoca-specific bacteriophages vB_Klp_5 and vB_Klox_2, respectively. Both of the latter phages had large burst sizes, efficient rates of adsorption and were stable under different adverse conditions. Phages reported in this study are double-stranded DNA bacterial viruses belonging to the families Podoviridae and Siphoviridae. One or more of the six phages was capable of efficiently lysing ~63 % of Klebsiella strains comprising a collection of 123 clinical isolates from Georgia and the United Kingdom. These phages exhibit a number of properties indicative of potential utility in phage therapy cocktails.

Extended-Spectrum Beta-Lactamases Producing E. coli in Wildlife, yet Another Form of Environmental Pollution?

PubMed Central

Guenther, Sebastian; Ewers, Christa; Wieler, Lothar H.

2011-01-01

Wildlife is normally not exposed to clinically used antimicrobial agents but can acquire antimicrobial resistant bacteria through contact with humans, domesticated animals and the environment, where water polluted with feces seems to be the most important vector. Escherichia coli, an ubiquitous commensal bacterial species colonizing the intestinal tract of mammals and birds, is also found in the environment. Extended-spectrum beta-lactamases producing E. coli (ESBL-E. coli) represent a major problem in human and veterinary medicine, particular in nosocomial infections. Additionally an onset of community-acquired ESBL-E. coli infections and an emergence in livestock farming has been observed in recent years, suggesting a successful transmission as well as persistence of ESBL-E. coli strains outside clinical settings. Another parallel worldwide phenomenon is the spread of ESBL-E. coli into the environment beyond human and domesticated animal populations, and this seems to be directly influenced by antibiotic practice. This might be a collateral consequence of the community-onset of ESBL-E. coli infections but can result (a) in a subsequent colonization of wild animal populations which can turn into an infectious source or even a reservoir of ESBL-E. coli, (b) in a contribution of wildlife to the spread and transmission of ESBL-E. coli into fragile environmental niches, (c) in new putative infection cycles between wildlife, domesticated animals and humans, and (d) in problems in the medical treatment of wildlife. This review aims to summarize the current knowledge on ESBL-E. coli in wildlife, in turn underlining the need for more large scale investigations, in particular sentinel studies to monitor the impact of multiresistant bacteria on wildlife. PMID:22203818

Identification of defective illegitimate recombinational repair of oxidatively-induced DNA double-strand breaks in ataxia-telangiectasia cells

NASA Technical Reports Server (NTRS)

Dar, M. E.; Winters, T. A.; Jorgensen, T. J.

1997-01-01

Ataxia-telangiectasia (A-T) is an autosomal-recessive lethal human disease. Homozygotes suffer from a number of neurological disorders, as well as very high cancer incidence. Heterozygotes may also have a higher than normal risk of cancer, particularly for the breast. The gene responsible for the disease (ATM) has been cloned, but its role in mechanisms of the disease remain unknown. Cellular A-T phenotypes, such as radiosensitivity and genomic instability, suggest that a deficiency in the repair of DNA double-strand breaks (DSBs) may be the primary defect; however, overall levels of DSB rejoining appear normal. We used the shuttle vector, pZ189, containing an oxidatively-induced DSB, to compare the integrity of DSB rejoining in one normal and two A-T fibroblast cells lines. Mutation frequencies were two-fold higher in A-T cells, and the mutational spectrum was different. The majority of the mutations found in all three cell lines were deletions (44-63%). The DNA sequence analysis indicated that 17 of the 17 plasmids with deletion mutations in normal cells occurred between short direct-repeat sequences (removing one of the repeats plus the intervening sequences), implicating illegitimate recombination in DSB rejoining. The combined data from both A-T cell lines showed that 21 of 24 deletions did not involve direct-repeats sequences, implicating a defect in the illegitimate recombination pathway. These findings suggest that the A-T gene product may either directly participate in illegitimate recombination or modulate the pathway. Regardless, this defect is likely to be important to a mechanistic understanding of this lethal disease.

Accurate simulation of backscattering spectra in the presence of sharp resonances

NASA Astrophysics Data System (ADS)

Barradas, N. P.; Alves, E.; Jeynes, C.; Tosaki, M.

2006-06-01

In elastic backscattering spectrometry, the shape of the observed spectrum due to resonances in the nuclear scattering cross-section is influenced by many factors. If the energy spread of the beam before interaction is larger than the resonance width, then a simple convolution with the energy spread on exit and with the detection system resolution will lead to a calculated spectrum with a resonance much sharper than the observed signal. Also, the yield from a thin layer will not be calculated accurately. We have developed an algorithm for the accurate simulation of backscattering spectra in the presence of sharp resonances. Albeit approximate, the algorithm leads to dramatic improvements in the quality and accuracy of the simulations. It is simple to implement and leads to only small increases of the calculation time, being thus suitable for routine data analysis. We show different experimental examples, including samples with roughness and porosity.

Efficient monoenergetic proton beam from ultra-fast laser interaction with nanostructured targets

NASA Astrophysics Data System (ADS)

Fazeli, R.

2018-03-01

The broad energy spectrum of laser-accelerated proton beams is the most important difficulty associated with such particle sources on the way to future applications such as medical therapy, proton imaging, inertial fusion, and high-energy physics. The generation of proton beams with enhanced monoenergetic features through an ultra-intense laser interaction with optimized nanostructured targets is reported. Targets were irradiated by 40 fs laser pulses of intensity 5.5 ×1020 W c m -2 and wavelength 1 μm. The results of multi-parametric Particle-in-Cell calculations showed that proton beams with considerably reduced energy spread can be obtained by using the proposed nanostructured target. At optimized target dimensions, the proton spectrum was found to exhibit a narrow peak at about 63 MeV with a relative energy spread of ΔE /Epeak˜ 5 % which is efficiently lower than what is expected for unstructured double layer targets (˜70%).

Whole-Genome Sequences of Listeria monocytogenes Sequence Type 6 Isolates Associated with a Large Foodborne Outbreak in South Africa, 2017 to 2018.

PubMed

Allam, Mushal; Tau, Nomsa; Smouse, Shannon L; Mtshali, Phillip S; Mnyameni, Florah; Khumalo, Zamantungwa T H; Ismail, Arshad; Govender, Nevashan; Thomas, Juno; Smith, Anthony M

2018-06-21

We report whole-genome sequences for 10 Listeria monocytogenes sequence type 6 isolates associated with a large listeriosis outbreak in South Africa, which occurred over the period of 2017 to 2018. The possibility of listeriosis spreading beyond South Africa's borders as a result of exported contaminated food products prompted us to make the genome sequences publicly available. Copyright © 2018 Allam et al.

Prevalence and risk factors for CTX-M gram-negative bacteria in hospitalized patients at a tertiary care hospital in Kilimanjaro, Tanzania.

PubMed

Sonda, Tolbert; Kumburu, Happiness; van Zwetselaar, Marco; Alifrangis, Michael; Mmbaga, Blandina T; Lund, Ole; Aarestrup, Frank M; Kibiki, Gibson

2018-05-01

Emergence and spread of extended spectrum beta-lactamase (ESBL)-producing gram-negative bacteria, mainly due to CTX-M, is a major global public health problem. Patients infected with ESBL-producing gram-negative bacteria have an increased risk of treatment failure and death. We investigated the prevalence and risk factors for CTX-M gram-negative bacteria isolated from clinical specimens of patients hospitalized at a tertiary care hospital in Kilimanjaro, Tanzania. Isolated gram-negative bacteria from inpatients admitted at Kilimanjaro Christian Medical Centre (KCMC) between August 2013 and August 2015 were fully genome sequenced. The prevalence of ESBL-producing gram-negative bacteria was determined based on the presence of bla CTX-M . The odds ratio (OR) and risk factors for ESBL-producing gram-negative bacteria due to CTX-M were assessed using logistic regression models. The overall CTX-M prevalence (95% CI) was 13.6% (10.1-18.1). Adjusted for other factors, the OR of CTX-M gram-negative bacteria for patients previously hospitalized was 0.26 (0.08-0.88), p = 0.031; the OR for patients currently on antibiotics was 4.02 (1.29-12.58), p = 0.017; the OR for patients currently on ceftriaxone was 0.14 (0.04-0.46), p = 0.001; and the OR for patients with wound infections was 0.24 (0.09-0.61), p = 0.003. The prevalence of ESBL-producing gram-negative bacteria due to CTX-M in this setting is relatively low compared to other previous reports in similar settings. However, to properly stop further spread in the hospital, we recommend setting up a hospital surveillance system that takes full advantage of the available next-generation sequencing facility to routinely screen for all types of bacterial resistance genes.

Robust High Data Rate MIMO Underwater Acoustic Communications

DTIC Science & Technology

2010-12-31

algorithm is referred to as periodic CAN ( PeCAN ). Unlike most existing sequence construction methods which are algebraic and deterministic in nature, we...start the iteration of PeCAN from random phase initializations and then proceed to cyclically minimize the desired metric. In this way, through...by the foe and hence are especially useful as training sequences or as spreading sequences for UAC applications. We will use PeCAN sequences for

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.

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region

PubMed Central

Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J.

2013-01-01

Background Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Methodology/Principal Findings Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. Conclusions/Significance To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide. PMID:23805195

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region.

PubMed

Alfonso-Morales, Abdulahi; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Majó, Natàlia; Ganges, Llilianne; Pérez, Lester J

2013-01-01

Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains. Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection. To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.

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

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.

A Summary of the Naval Postgraduate School Research Program and Recent Publications

DTIC Science & Technology

1990-09-01

principles to divide the spectrum of MATLAB computer program on a 386-type a wide-band spread-spectrum signal into sub- computer. Because of the high rf...original in time and a large data sample was required. An signal. Effects due the fiber optic pickup array extended version of MATLAB that allows and...application, such as orbital mechanics and weather prediction. Professor Gragg has also developed numerous MATLAB programs for linear programming problems

Coordination sequences and information spreading in small-world networks

NASA Astrophysics Data System (ADS)

Herrero, Carlos P.

2002-10-01

We study the spread of information in small-world networks generated from different d-dimensional regular lattices, with d=1, 2, and 3. With this purpose, we analyze by numerical simulations the behavior of the coordination sequence, e.g., the average number of sites C(n) that can be reached from a given node of the network in n steps along its bonds. For sufficiently large networks, we find an asymptotic behavior C(n)~ρn, with a constant ρ that depends on the network dimension d and on the rewiring probability p (which measures the disorder strength of a given network). A simple model of information spreading in these networks is studied, assuming that only a fraction q of the network sites are active. The number of active nodes reached in n steps has an asymptotic form λn, λ being a constant that depends on p and q, as well as on the dimension d of the underlying lattice. The information spreading presents two different regimes depending on the value of λ: For λ>1 the information propagates along the whole system, and for λ<1 the spreading is damped and the information remains confined in a limited region of the network. We discuss the connection of these results with site percolation in small-world networks.

How to Pluck a Spectrum from a Planet

NASA Technical Reports Server (NTRS)

2007-01-01

This diagram illustrates how astronomers using NASA's Spitzer Space Telescope can capture the elusive spectra of hot-Jupiter planets. Spectra are an object's light spread apart into its basic components, or wavelengths. By dissecting light in this way, scientists can sort through it and uncover clues about the composition of the object giving off the light.

To obtain a spectrum for an object, one first needs to capture its light. Hot-Jupiter planets are so close to their stars that even the most powerful telescopes can't distinguish their light from the light of their much brighter stars.

But, there are a few planetary systems that allow astronomers to measure the light from just the planet by using a clever technique. Such 'transiting' systems are oriented in such a way that, from our vantage point, the planets' orbits are seen edge-on and cross directly in front of and behind their stars.

In this technique, known as the secondary eclipse method, changes in the total infrared light from a star system are measured as its planet transits behind the star, vanishing from our Earthly point of view. The dip in observed light can then be attributed to the planet alone.

To capture a spectrum of the planet, Spitzer must observe the system twice. It takes a spectrum of the star together with the planet (first panel), then, as the planet disappears from view, a spectrum of just the star (second panel). By subtracting the star's spectrum from the combined spectrum of the star plus the planet, it is able to get the spectrum for just the planet (third panel).

This ground-breaking technique was used by Spitzer to obtain the first-ever spectra of two planets beyond our solar system, HD 209458b and HD 189733b. The results suggest that the hot planets are socked in with dry clouds high up in the planet's stratospheres. In addition, HD 209458b showed hints of silicates, indicating those high clouds might be made of very fine sand-like particles.

Enhanced photon indistinguishability in pulse-driven quantum emitters

NASA Astrophysics Data System (ADS)

Fotso, Herbert F.

2017-04-01

Photon indistinguishability is an essential ingredient for the realization of scalable quantum networks. For quantum bits in the solid state, this is hindered by spectral diffusion, the uncontrolled random drift of the emission/absorption spectrum as a result of fluctuations in the emitter's environment. We study optical properties of a quantum emitter in the solid state when it is driven by a periodic sequence of optical pulses with finite detuning with respect to the emitter. We find that a pulse sequence can effectively mitigate spectral diffusion and enhance photon indistinguishability. The bulk of the emission occurs at a set target frequency; Photon indistinguishability is enhanced and is restored to its optimal value after every even pulse. Also, for moderate values of the sequence period and of the detuning, both the emission spectrum and the absorption spectrum have lineshapes with little dependence on the detuning. We describe the solution and the evolution of the emission/absorption spectrum as a function time.

Properties of the Magnitude Terms of Orthogonal Scaling Functions.

PubMed

Tay, Peter C; Havlicek, Joseph P; Acton, Scott T; Hossack, John A

2010-09-01

The spectrum of the convolution of two continuous functions can be determined as the continuous Fourier transform of the cross-correlation function. The same can be said about the spectrum of the convolution of two infinite discrete sequences, which can be determined as the discrete time Fourier transform of the cross-correlation function of the two sequences. In current digital signal processing, the spectrum of the contiuous Fourier transform and the discrete time Fourier transform are approximately determined by numerical integration or by densely taking the discrete Fourier transform. It has been shown that all three transforms share many analogous properties. In this paper we will show another useful property of determining the spectrum terms of the convolution of two finite length sequences by determining the discrete Fourier transform of the modified cross-correlation function. In addition, two properties of the magnitude terms of orthogonal wavelet scaling functions are developed. These properties are used as constraints for an exhaustive search to determine an robust lower bound on conjoint localization of orthogonal scaling functions.

Computer program for calculating and plotting fire direction and rate of spread.

Treesearch

James E. Eenigenburg

1987-01-01

Presents an analytical procedure that uses a FORTRAN 77 program to estimate fire direction and rate of spread. The program also calculates the variability of these parameters, both for subsections of the fire and for the fires as a whole. An option in the program allows users with a CALCOMP plotter to obtain a map of the fire with spread vectors.

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.

PubMed

Di Giallonardo, Francesca; Geoghegan, Jemma L; Docherty, Douglas E; McLean, Robert G; Zody, Michael C; Qu, James; Yang, Xiao; Birren, Bruce W; Malboeuf, Christine M; Newman, Ruchi M; Ip, Hon S; Holmes, Edward C

2016-01-15

The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers. How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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.

Separability of spatiotemporal spectra of image sequences. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Eckert, Michael P.; Buchsbaum, Gershon; Watson, Andrew B.

1992-01-01

The spatiotemporal power spectrum was calculated of 14 image sequences in order to determine the degree to which the spectra are separable in space and time, and to assess the validity of the commonly used exponential correlation model found in the literature. The spectrum was expanded by a Singular Value Decomposition into a sum of separable terms and an index was defined of spatiotemporal separability as the fraction of the signal energy that can be represented by the first (largest) separable term. All spectra were found to be highly separable with an index of separability above 0.98. The power spectra of the sequences were well fit by a separable model. The power spectrum model corresponds to a product of exponential autocorrelation functions separable in space and time.

An Underlay Communication Channel for 5G Cognitive Mesh Networks: Packet Design, Implementation, Analysis, and Experimental Results

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

Tarek Haddadin; Stephen Andrew Laraway; Arslan Majid

This paper proposes and presents the design and implementation of an underlay communication channel (UCC) for 5G cognitive mesh networks. The UCC builds its waveform based on filter bank multicarrier spread spectrum (FB-MCSS) signaling. The use of this novel spread spectrum signaling allows the device-to-device (D2D) user equipments (UEs) to communicate at a level well below noise temperature and hence, minimize taxation on macro-cell/small-cell base stations and their UEs in 5G wireless systems. Moreover, the use of filter banks allows us to avoid those portions of the spectrum that are in use by macro-cell and small-cell users. Hence, both D2D-to-cellularmore » and cellular-to-D2D interference will be very close to none. We propose a specific packet for UCC and develop algorithms for packet detection, timing acquisition and tracking, as well as channel estimation and equalization. We also present the detail of an implementation of the proposed transceiver on a software radio platform and compare our experimental results with those from a theoretical analysis of our packet detection algorithm.« less

Broad-spectrum antiviral activity of chebulagic acid and punicalagin against viruses that use glycosaminoglycans for entry

PubMed Central

2013-01-01

Background We previously identified two hydrolyzable tannins, chebulagic acid (CHLA) and punicalagin (PUG) that blocked herpes simplex virus type 1 (HSV-1) entry and spread. These compounds inhibited viral glycoprotein interactions with cell surface glycosaminoglycans (GAGs). Based on this property, we evaluated their antiviral efficacy against several different viruses known to employ GAGs for host cell entry. Results Extensive analysis of the tannins’ mechanism of action was performed on a panel of viruses during the attachment and entry steps of infection. Virus-specific binding assays and the analysis of viral spread during treatment with these compounds were also conducted. CHLA and PUG were effective in abrogating infection by human cytomegalovirus (HCMV), hepatitis C virus (HCV), dengue virus (DENV), measles virus (MV), and respiratory syncytial virus (RSV), at μM concentrations and in dose-dependent manners without significant cytotoxicity. Moreover, the natural compounds inhibited viral attachment, penetration, and spread, to different degrees for each virus. Specifically, the tannins blocked all these steps of infection for HCMV, HCV, and MV, but had little effect on the post-fusion spread of DENV and RSV, which could suggest intriguing differences in the roles of GAG-interactions for these viruses. Conclusions CHLA and PUG may be of value as broad-spectrum antivirals for limiting emerging/recurring viruses known to engage host cell GAGs for entry. Further studies testing the efficacy of these tannins in vivo against certain viruses are justified. PMID:23924316

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

PubMed Central

Robins-Browne, Roy M.; Holt, Kathryn E.; Ingle, Danielle J.; Hocking, Dianna M.; Yang, Ji; Tauschek, Marija

2016-01-01

The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods. PMID:27917373

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

PubMed

Robins-Browne, Roy M; Holt, Kathryn E; Ingle, Danielle J; Hocking, Dianna M; Yang, Ji; Tauschek, Marija

2016-01-01

The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E .coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli . Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli , which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods.

The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae

PubMed Central

Mathers, Amy J.; Peirano, Gisele

2015-01-01

SUMMARY Escherichia coli sequence type 131 (ST131) and Klebsiella pneumoniae ST258 emerged in the 2000s as important human pathogens, have spread extensively throughout the world, and are responsible for the rapid increase in antimicrobial resistance among E. coli and K. pneumoniae strains, respectively. E. coli ST131 causes extraintestinal infections and is often fluoroquinolone resistant and associated with extended-spectrum β-lactamase production, especially CTX-M-15. K. pneumoniae ST258 causes urinary and respiratory tract infections and is associated with carbapenemases, most often KPC-2 and KPC-3. The most prevalent lineage within ST131 is named fimH30 because it contains the H30 variant of the type 1 fimbrial adhesin gene, and recent molecular studies have demonstrated that this lineage emerged in the early 2000s and was then followed by the rapid expansion of its sublineages H30-R and H30-Rx. K. pneumoniae ST258 comprises 2 distinct lineages, namely clade I and clade II. Moreover, it seems that ST258 is a hybrid clone that was created by a large recombination event between ST11 and ST442. Epidemic plasmids with blaCTX-M and blaKPC belonging to incompatibility group F have contributed significantly to the success of these clones. E. coli ST131 and K. pneumoniae ST258 are the quintessential examples of international multidrug-resistant high-risk clones. PMID:25926236

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs.

PubMed

Chen-Harris, Haiyin; Borucki, Monica K; Torres, Clinton; Slezak, Tom R; Allen, Jonathan E

2013-02-12

High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution, thus enabling the close examination of viral mutational dynamics both within- and between-hosts. The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors. We demonstrate that overlapping read pairs (ORP) -- generated by combining short fragment sequencing libraries and longer sequencing reads -- significantly reduce sequencing error rates and improve rare variant detection accuracy. Using this sequencing protocol and an error model optimized for variant detection, we are able to capture a large number of genetic mutations present within a viral population at ultra-low frequency levels (<0.05%). Our rare variant detection strategies have important implications beyond viral evolution and can be applied to any basic and clinical research area that requires the identification of rare mutations.

Third-Generation-Cephalosporin-Resistant Klebsiella pneumoniae Isolates from Humans and Companion Animals in Switzerland: Spread of a DHA-Producing Sequence Type 11 Clone in a Veterinary Setting

PubMed Central

Wohlwend, Nadia; Francey, Thierry

2015-01-01

Characterization of third-generation-cephalosporin-resistant Klebsiella pneumoniae isolates originating mainly from one human hospital (n = 22) and one companion animal hospital (n = 25) in Bern (Switzerland) revealed the absence of epidemiological links between human and animal isolates. Human infections were not associated with the spread of any specific clone, while the majority of animal infections were due to K. pneumoniae sequence type 11 isolates producing plasmidic DHA AmpC. This clonal dissemination within the veterinary hospital emphasizes the need for effective infection control practices. PMID:25733505

Droplet impact on regular micro-grooved surfaces

NASA Astrophysics Data System (ADS)

Hu, Hai-Bao; Huang, Su-He; Chen, Li-Bin

2013-08-01

We have investigated experimentally the process of a droplet impact on a regular micro-grooved surface. The target surfaces are patterned such that micro-scale spokes radiate from the center, concentric circles, and parallel lines on the polishing copper plate, using Quasi-LIGA molding technology. The dynamic behavior of water droplets impacting on these structured surfaces is examined using a high-speed camera, including the drop impact processes, the maximum spreading diameters, and the lengths and numbers of fingers at different values of Weber number. Experimental results validate that the spreading processes are arrested on all target surfaces at low velocity. Also, the experimental results at higher impact velocity demonstrate that the spreading process is conducted on the surface parallel to the micro-grooves, but is arrested in the direction perpendicular to the micro-grooves. Besides, the lengths of fingers increase observably, even when they are ejected out as tiny droplets along the groove direction, at the same time the drop recoil velocity is reduced by micro-grooves which are parallel to the spreading direction, but not by micro-grooves which are vertical to the spreading direction.

Refining rates and treatment sequences for cogongrass (Imperata Cylindrica) control with imazapyr and glyphosate

Treesearch

James H. Miller

2001-01-01

Cogongrass (Imperata cylindrica (L.) Palisot) is an aggressive invasive plant on all continents and has been spreading northward in the Southeast's Gulf Coastal Plain and into Florida for 80 years. It spreads by prolific windblown seeds and with movement of infested soils while infestations increase in size and become more dense by rhizome...

[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.

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

Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated 'subtype I', reveals a unique complex A/G/H/K/? mosaic pattern.

PubMed

Paraskevis, D; Magiorkinis, M; Vandamme, A M; Kostrikis, L G; Hatzakis, A

2001-03-01

Human immunodeficiency virus type 1 (HIV-1) has been classified into three main groups and 11 distinct subtypes. Moreover, several circulating recombinant forms (CRFs) of HIV-1 have been recently documented to have spread widely causing extensive HIV-1 epidemics. A subtype, initially designated I (CRF04_cpx), was documented in Cyprus and Greece and was found to comprise regions of sequence derived from subtypes A and G as well as regions of unclassified sequence. Re-analysis of the three full-length CRF04_cpx sequences that were available revealed a mosaic genomic organization of unique complexity comprising regions of sequence from at least five distinct subtypes, A, G, H, K and unclassified regions. These strains account for approximately 2% of the total HIV-1-infected population in Greece, thus providing evidence of the great capability of HIV-1 to recombine and produce highly divergent strains which can be spread successfully through different infection routes.

Common cold outbreaks: A network theory approach

NASA Astrophysics Data System (ADS)

Vishkaie, Faranak Rajabi; Bakouie, Fatemeh; Gharibzadeh, Shahriar

2014-11-01

In this study, at first we evaluated the network structure in social encounters by which respiratory diseases can spread. We considered common-cold and recorded a sample of human population and actual encounters between them. Our results show that the database structure presents a great value of clustering. In the second step, we evaluated dynamics of disease spread with SIR model by assigning a function to each node of the structural network. The rate of disease spread in networks was observed to be inversely correlated with characteristic path length. Therefore, the shortcuts have a significant role in increasing spread rate. We conclude that the dynamics of social encounters' network stands between the random and the lattice in network spectrum. Although in this study we considered the period of common-cold disease for network dynamics, it seems that similar approaches may be useful for other airborne diseases such as SARS.

Improvement of energy efficiency via spectrum optimization of excitation sequence for multichannel simultaneously triggered airborne sonar system

NASA Astrophysics Data System (ADS)

Meng, Qing-Hao; Yao, Zhen-Jing; Peng, Han-Yang

2009-12-01

Both the energy efficiency and correlation characteristics are important in airborne sonar systems to realize multichannel ultrasonic transducers working together. High energy efficiency can increase echo energy and measurement range, and sharp autocorrelation and flat cross correlation can help eliminate cross-talk among multichannel transducers. This paper addresses energy efficiency optimization under the premise that cross-talk between different sonar transducers can be avoided. The nondominated sorting genetic algorithm-II is applied to optimize both the spectrum and correlation characteristics of the excitation sequence. The central idea of the spectrum optimization is to distribute most of the energy of the excitation sequence within the frequency band of the sonar transducer; thus, less energy is filtered out by the transducers. Real experiments show that a sonar system consisting of eight-channel Polaroid 600 series electrostatic transducers excited with 2 ms optimized pulse-position-modulation sequences can work together without cross-talk and can measure distances up to 650 cm with maximal 1% relative error.

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.

High-Level Cefixime- and Ceftriaxone-Resistant Neisseria gonorrhoeae in France: Novel penA Mosaic Allele in a Successful International Clone Causes Treatment Failure

PubMed Central

Golparian, Daniel; Nicholas, Robert; Ohnishi, Makoto; Gallay, Anne; Sednaoui, Patrice

2012-01-01

Recently, the first Neisseria gonorrhoeae strain (H041) highly resistant to the expanded-spectrum cephalosporins (ESCs) ceftriaxone and cefixime, which are the last remaining options for first-line gonorrhea treatment, was isolated in Japan. Here, we confirm and characterize a second strain (F89) with high-level cefixime and ceftriaxone resistance which was isolated in France and most likely caused a treatment failure with cefixime. F89 was examined using six species-confirmatory tests, antibiograms (33 antimicrobials), porB sequencing, N. gonorrhoeae multiantigen sequence typing (NG-MAST), multilocus sequence typing (MLST), and sequencing of known gonococcal resistance determinants (penA, mtrR, penB, ponA, and pilQ). F89 was assigned to MLST sequence type 1901 (ST1901) and NG-MAST ST1407, which is a successful gonococcal clone that has spread globally. F89 has high-level resistance to cefixime (MIC = 4 μg/ml) and ceftriaxone (MIC = 1 to 2 μg/ml) and resistance to most other antimicrobials examined. A novel penA mosaic allele (penA-CI), which was penA-XXXIV with an additional A501P alteration in penicillin-binding protein 2, was the primary determinant for high-level ESC resistance, as determined by transformation into a set of recipient strains. N. gonorrhoeae appears to be emerging as a superbug, and in certain circumstances and settings, gonorrhea may become untreatable. Investigations of the biological fitness and enhanced understanding and monitoring of the ESC-resistant clones and their international transmission are required. Enhanced disease control activities, antimicrobial resistance control and surveillance worldwide, and public health response plans for global (and national) perspectives are also crucial. Nevertheless, new treatment strategies and/or drugs and, ideally, a vaccine are essential to develop for efficacious gonorrhea management. PMID:22155830

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.

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.

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

Optimum constrained image restoration filters

NASA Technical Reports Server (NTRS)

Riemer, T. E.; Mcgillem, C. D.

1974-01-01

The filter was developed in Hilbert space by minimizing the radius of gyration of the overall or composite system point-spread function subject to constraints on the radius of gyration of the restoration filter point-spread function, the total noise power in the restored image, and the shape of the composite system frequency spectrum. An iterative technique is introduced which alters the shape of the optimum composite system point-spread function, producing a suboptimal restoration filter which suppresses undesirable secondary oscillations. Finally this technique is applied to multispectral scanner data obtained from the Earth Resources Technology Satellite to provide resolution enhancement. An experimental approach to the problems involving estimation of the effective scanner aperture and matching the ERTS data to available restoration functions is presented.

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.

Toward direct pore-scale modeling of three-phase displacements

NASA Astrophysics Data System (ADS)

Mohammadmoradi, Peyman; Kantzas, Apostolos

2017-12-01

A stable spreading film between water and gas can extract a significant amount of bypassed non-aqueous phase liquid (NAPL) through immiscible three-phase gas/water injection cycles. In this study, the pore-scale displacement mechanisms by which NAPL is mobilized are incorporated into a three-dimensional pore morphology-based model under water-wet and capillary equilibrium conditions. The approach is pixel-based and the sequence of invasions is determined by the fluids' connectivity and the threshold capillary pressure of the advancing interfaces. In addition to the determination of three-phase spatial saturation profiles, residuals, and capillary pressure curves, dynamic finite element simulations are utilized to predict the effective permeabilities of the rock microtomographic images as reasonable representations of the geological formations under study. All the influential features during immiscible fluid flow in pore-level domains including wetting and spreading films, saturation hysteresis, capillary trapping, connectivity, and interface development strategies are taken into account. The capabilities of the model are demonstrated by the successful prediction of saturation functions for Berea sandstone and the accurate reconstruction of three-phase fluid occupancies through a micromodel.

How Is Mono Spread?

MedlinePlus

... How Is Mono Spread? Print My sister has mononucleosis. I drank out of her drink before we ... that I have mono now? – Kyle* Mono, or mononucleosis, is spread through direct contact with saliva. This ...

Extended-spectrum β-lactamase/AmpC- and carbapenemase-producing Enterobacteriaceae in animals: a threat for humans?

PubMed

Madec, J-Y; Haenni, M; Nordmann, P; Poirel, L

2017-11-01

There has been a great and long-term concern that extended-spectrum β-lactamase (ESBL)/AmpC- and carbapenemase-producing Enterobacteriaceae occurring in animals may constitute a public-health issue. A large number of factors with complex interrelations contribute to the spread of those bacteria among animals and humans. ESBL/AmpC- or carbapenemase-encoding genes are most often located on mobile genetic elements favouring their dissemination. Some shared reservoirs of ESBL/AmpC or carbapenemase genes, plasmids or clones have been identified and suggest cross-transmissions. Even though exposure to animals is regarded as a risk factor, evidence for a direct transfer of ESBL/AmpC-producing bacteria from animals to humans through close contacts is limited. Nonetheless, the size of the commensal ESBL/AmpC reservoir in non-human sources is dramatically rising. This may constitute an indirect risk to public health by increasing the gene pool from which pathogenic bacteria can pick up ESBL/AmpC/carbapenemase genes. The extent to which food contributes to potential transmission of ESBL/AmpC producers to humans is also not well established. Overall, events leading to the occurrence of ESBL/AmpC- and carbapenemase-encoding genes in animals seem very much multifactorial. The impact of animal reservoirs on human health still remains debatable and unclear; nonetheless, there are some examples of direct links that have been identified. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Genotype-phenotype correlation of xeroderma pigmentosum in a Chinese Han population.

PubMed

Sun, Z; Zhang, J; Guo, Y; Ni, C; Liang, J; Cheng, R; Li, M; Yao, Z

2015-04-01

Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder characterized by extreme sensitivity to sunlight, freckle-like pigmentation and a greatly increased incidence of skin cancers. Genetic mutation detection and genotype-phenotype analysis of XP are rarely reported in the Chinese Han population. To investigate the mutational spectrum of XP in a Chinese Han population, to discover any genotype-phenotype correlation and, consequently, to propose a simple and effective tool for the molecular diagnosis of XP. This study was carried out on 12 unrelated Chinese families that included 13 patients with clinically suspected XP. Genomic DNA was extracted from peripheral blood samples. Mutation screening was performed by direct sequencing of exons and flanking intron-exon boundaries for the entire coding region of eight XP genes. In 12 patients, direct sequencing of the whole coding region of eight XP genes revealed pathogenic mutations, including seven compound heterozygous mutations, three homozygous mutations and a Japanese founder mutation. Thirteen mutations have not been previously identified. This cohort was composed of four patients with XP-C (XPC), two with XP-G (ERCC5), three with XP-A (XPA) and three with XP-V (POLH). This study identified 13 novel mutations and extended the mutation spectrum of XP in the Chinese Han population. In this cohort, we found that patients with XP-G have no neurological symptoms, and patients with XP-A and XP-V have a high incidence of malignancy. Furthermore, lack of stringent protection against sunlight, late diagnosis and long duration of disease play an important role. © 2014 British Association of Dermatologists.

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

PubMed

Hia, Fabian; Chionh, Yok Hian; Pang, Yan Ling Joy; DeMott, Michael S; McBee, Megan E; Dedon, Peter C

2015-03-11

A major challenge in the study of mycobacterial RNA biology is the lack of a comprehensive RNA isolation method that overcomes the unusual cell wall to faithfully yield the full spectrum of non-coding RNA (ncRNA) species. Here, we describe a simple and robust procedure optimized for the isolation of total ncRNA, including 5S, 16S and 23S ribosomal RNA (rRNA) and tRNA, from mycobacteria, using Mycobacterium bovis BCG to illustrate the method. Based on a combination of mechanical disruption and liquid and solid-phase technologies, the method produces all major species of ncRNA in high yield and with high integrity, enabling direct chemical and sequence analysis of the ncRNA species. The reproducibility of the method with BCG was evident in bioanalyzer electrophoretic analysis of isolated RNA, which revealed quantitatively significant differences in the ncRNA profiles of exponentially growing and non-replicating hypoxic bacilli. The method also overcame an historical inconsistency in 5S rRNA isolation, with direct sequencing revealing a novel post-transcriptional processing of 5S rRNA to its functional form and with chemical analysis revealing seven post-transcriptional ribonucleoside modifications in the 5S rRNA. This optimized RNA isolation procedure thus provides a means to more rigorously explore the biology of ncRNA species in mycobacteria. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Anti-jamming Technology in Small Satellite Communication

NASA Astrophysics Data System (ADS)

Jia, Zixiang

2018-01-01

Small satellite communication has an increasingly important position among the wireless communications due to the advantages of low cost and high technology. However, in view of the case that its relay station stays outside the earth, its uplink may face interference from malicious signal frequently. Here this paper classified enumerates existing interferences, and proposes channel signals as main interference by comparison. Based on a basic digital communication process, then this paper discusses the possible anti - jamming techniques that commonly be realized at all stages in diverse processes, and comes to the conclusion that regarding the spread spectrum technology and antenna anti-jamming technology as fundamental direction of future development. This work provides possible thought for the design of new small satellite communication system with the coexistence of multi - technologies. This basic popular science can be consulted for people interested in small satellite communication.

COSMIC SHEAR MEASUREMENT USING AUTO-CONVOLVED IMAGES

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

Li, Xiangchong; Zhang, Jun, E-mail: betajzhang@sjtu.edu.cn

2016-10-20

We study the possibility of using quadrupole moments of auto-convolved galaxy images to measure cosmic shear. The autoconvolution of an image corresponds to the inverse Fourier transformation of its power spectrum. The new method has the following advantages: the smearing effect due to the point-spread function (PSF) can be corrected by subtracting the quadrupole moments of the auto-convolved PSF; the centroid of the auto-convolved image is trivially identified; the systematic error due to noise can be directly removed in Fourier space; the PSF image can also contain noise, the effect of which can be similarly removed. With a large ensemblemore » of simulated galaxy images, we show that the new method can reach a sub-percent level accuracy under general conditions, albeit with increasingly large stamp size for galaxies of less compact profiles.« less

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

Ikegami, M.; Iwashita, Y.; Shirai, T.

MeV quasi-mono-energetic proton beam is produced by a combination of a synchronous radio frequency (rf) electric field and laser-plasma ion acceleration. The experiment was carried out at the Kansai Photon Science Institute, JAEA, using the Ti:Sapphire laser system called J-KAREN. The proton beam is emitted normal to the rear surface of the thin polyimide target of the thickness 7.5 {mu}m irradiated at peak intensity of 4x10{sup 18} W/cm{sup 2}. The energy spread is compressed from 100% to less than 11% at FWHM by the rf field. The focusing and defocusing effect of the transverse direction is also observed. These aremore » also studied by a Monte Carlo simulation. The relation between the transverse focusing and the energy spectrum of the phase-rotated beam is systematically shown by the simulation.« less

Exome Sequencing Is an Efficient Tool for Variant Late-Infantile Neuronal Ceroid Lipofuscinosis Molecular Diagnosis

PubMed Central

Ortega-Recalde, Oscar; Nallathambi, Jeyabalan; Anandula, Venkata Ramana; Renukaradhya, Umashankar; Laissue, Paul

2014-01-01

The neuronal ceroid-lipofuscinoses (NCL) is a group of neurodegenerative disorders characterized by epilepsy, visual failure, progressive mental and motor deterioration, myoclonus, dementia and reduced life expectancy. Classically, NCL-affected individuals have been classified into six categories, which have been mainly defined regarding the clinical onset of symptoms. However, some patients cannot be easily included in a specific group because of significant variation in the age of onset and disease progression. Molecular genetics has emerged in recent years as a useful tool for enhancing NCL subtype classification. Fourteen NCL genetic forms (CLN1 to CLN14) have been described to date. The variant late-infantile form of the disease has been linked to CLN5, CLN6, CLN7 (MFSD8) and CLN8 mutations. Despite advances in the diagnosis of neurodegenerative disorders mutations in these genes may cause similar phenotypes, which rends difficult accurate candidate gene selection for direct sequencing. Three siblings who were affected by variant late-infantile NCL are reported in the present study. We used whole-exome sequencing, direct sequencing and in silico approaches to identify the molecular basis of the disease. We identified the novel c.1219T>C (p.Trp407Arg) and c.1361T>C (p.Met454Thr) MFSD8 pathogenic mutations. Our results highlighted next generation sequencing as a novel and powerful methodological approach for the rapid determination of the molecular diagnosis of NCL. They also provide information regarding the phenotypic and molecular spectrum of CLN7 disease. PMID:25333361

Molecular typing of enteroviruses associated with viral meningitis in Cyprus, 2000-2002.

PubMed

Richter, Jan; Koptides, Dana; Tryfonos, Christina; Christodoulou, Christina

2006-08-01

Human enteroviruses are responsible for a wide spectrum of clinical diseases affecting many different organ systems. Although infection is usually asymptomatic, infections of the central nervous system manifested as meningitis or encephalitis can pose a serious public health problem, especially during outbreaks. In this study, samples from 218 patients diagnosed with enteroviral meningitis between January 2000 and December 2002 were analysed in order to assess the epidemiology of human enteroviruses as a cause of viral meningitis in Cyprus. A new typing strategy, based on partial sequencing of the 5' non-coding region (5'NCR), prediction of type, and selection of type-specific primers for sensitive VP1 PCR amplification, was developed. As clustering in the 5'NCR was concordant with clustering in the VP1 region, quick and reliable typing by VP1 sequencing was achieved without virus isolation in cell culture. The most frequent enterovirus serotypes identified were Human echovirus 30 (55.5%), Human echovirus 13 (15.1%), Human echovirus 6 (13.8%) and Human echovirus 9 (8.3%). Human coxsackieviruses B2, B1 and B5, Human echovirus 4, Human enterovirus 71 and Human coxsackievirus A6 represented rather rare serotypes. This is the first molecular epidemiological study of enterovirus meningitis in Cyprus. Serotype distribution corresponded basically with observations in other European countries, suggesting the spread of enteroviruses by tourism.

Genome Sequences of Multidrug-Resistant Salmonella enterica subsp. enterica Serovar Infantis Strains from Broiler Chicks in Hungary

PubMed Central

Wilk, Tímea; Szabó, Móni; Szmolka, Ama; Kiss, János; Barta, Endre; Nagy, Tibor

2016-01-01

Three strains of Salmonella enterica serovar Infantis isolated from healthy broiler chickens from 2012 to 2013 have been sequenced. Comparison of these and previously published S. Infantis genome sequences of broiler origin in 1996 and 2004 will provide new insight into the genome evolution and recent spread of S. Infantis in poultry. PMID:27979950

Clonal Spread of 16S rRNA Methyltransferase-Producing Klebsiella pneumoniae ST37 with High Prevalence of ESBLs from Companion Animals in China

PubMed Central

Xia, Jing; Fang, Liang-Xing; Cheng, Ke; Xu, Guo-Hao; Wang, Xi-Ran; Liao, Xiao-Ping; Liu, Ya-Hong; Sun, Jian

2017-01-01

We screened 30 Klebsiella pneumoniae isolates from dogs and cats at a single animal hospital in Guangdong Province, China. Among them, 12 K. pneumoniae strains possessed high-level resistance to amikacin and gentamicin and these were screened for 16S rRNA methyltransferase (16S-RMTase) genes. And then the genes positive isolates were detected for ESBLs (extended spectrum β-lactamases) and analyzed by pulsed-field gel electrophoresis, multilocus sequence typing, PCR-based replicon typing and plasmid analysis. The genetic profiles of rmtB were also determined by PCR mapping. The twelve 16S-RMTase gene-positive isolates were rmtB (11/30) and armA (2/30) with one isolate carrying both genes. Extended spectrum β-lactamases genes were represented by blaCTX-M-55 (9/12), blaCTX-M-27 (2/12) and blaCTX-M-14 (1/12). The twelve 16S-RMTase containing strains were grouped into five clonal patterns and ST37 was the most prevalent sequence type. Ten rmtB-bearing plasmids conjugated successfully and all belonged to IncN and IncF (F33:A-:B-) incompatibility groups. Nine of the transconjugants carried a 97 kb plasmid and the other harbored both ∼60 and ∼200 kb plasmids. rmtB and blaCTX-M-55 were present on the same plasmid and indicated the co-transfer of these two genes, with the rmtB gene showing highly relevant relationships with IS26 and Tn3. Our findings suggested a high prevalence of 16S-RMTase genes in K. pneumonia ST37 from dogs and cats. Additional studies are needed to trace the evolutionary path of this type of resistance among the K. pneumonia isolates, and to determine whether they have been transferred to humans. PMID:28446899

High prevalence of extended-spectrum ß-lactamase producing enterobacteriaceae among clinical isolates in Burkina Faso.

PubMed

Ouedraogo, Abdoul-Salam; Sanou, Mahamadou; Kissou, Aimée; Sanou, Soufiane; Solaré, Hermann; Kaboré, Firmin; Poda, Armel; Aberkane, Salim; Bouzinbi, Nicolas; Sano, Idrissa; Nacro, Boubacar; Sangaré, Lassana; Carrière, Christian; Decré, Dominique; Ouégraogo, Rasmata; Jean-Pierre, Hélène; Godreuil, Sylvain

2016-07-11

Nothing is known about the epidemiology and resistance mechanisms of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-PE) in Burkina Faso. The objective of this study was to determine ESBL-PE prevalence and to characterize ESBL genes in Burkina Faso. During 2 months (June-July 2014), 1602 clinical samples were sent for bacteriologic investigations to the microbiology laboratories of the tree main hospitals of Burkina Faso. Isolates were identified by mass spectrometry using a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) BioTyper. Antibiotic susceptibility was tested using the disk diffusion method on Müller-Hinton agar. The different ESBL genes in potential ESBL-producing isolates were detected by PCR and double stranded DNA sequencing. Escherichia coli phylogenetic groups were determined using a PCR-based method. ESBL-PE frequency was 58 % (179 strains among the 308 Enterobacteriaceae isolates identified in the collected samples; 45 % in outpatients and 70 % in hospitalized patients). The CTX-M-1 group was dominant (94 %, CTX-M-15 enzyme), followed by the CTX-M-9 group (4 %). ESBL producers were more often found in E. coli (67.5 %) and Klebsiella pneumoniae (26 %) isolates. E. coli isolates (n = 202; 60 % of all Enterobacteriaceae samples) were distributed in eight phylogenetic groups (A = 49, B1 = 15, B2 = 43, C = 22, Clade I = 7, D = 37, F = 13 and 16 unknown); 22 strains belonged to the sequence type ST131. No association between a specific strain and ESBL production was detected. This report shows the alarming spread of ESBL genes in Burkina Faso. Public health efforts should focus on education (population and healthcare professionals), surveillance and promotion of correct and restricted antibiotic use to limit their dissemination.

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products.

PubMed

Johnston, Chad W; Skinnider, Michael A; Wyatt, Morgan A; Li, Xiang; Ranieri, Michael R M; Yang, Lian; Zechel, David L; Ma, Bin; Magarvey, Nathan A

2015-09-28

Bacterial natural products are a diverse and valuable group of small molecules, and genome sequencing indicates that the vast majority remain undiscovered. The prediction of natural product structures from biosynthetic assembly lines can facilitate their discovery, but highly automated, accurate, and integrated systems are required to mine the broad spectrum of sequenced bacterial genomes. Here we present a genome-guided natural products discovery tool to automatically predict, combinatorialize and identify polyketides and nonribosomal peptides from biosynthetic assembly lines using LC-MS/MS data of crude extracts in a high-throughput manner. We detail the directed identification and isolation of six genetically predicted polyketides and nonribosomal peptides using our Genome-to-Natural Products platform. This highly automated, user-friendly programme provides a means of realizing the potential of genetically encoded natural products.

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.

Physiological recordings and RNA sequencing of the gustatory appendages of the yellow-fever mosquito Aedes aegypti.

PubMed

Sparks, Jackson T; Dickens, Joseph C

2014-12-30

Electrophysiological recording of action potentials from sensory neurons of mosquitoes provides investigators a glimpse into the chemical perception of these disease vectors. We have recently identified a bitter sensing neuron in the labellum of female Aedes aegypti that responds to DEET and other repellents, as well as bitter quinine, through direct electrophysiological investigation. These gustatory receptor neuron responses prompted our sequencing of total mRNA from both male and female labella and tarsi samples to elucidate the putative chemoreception genes expressed in these contact chemoreception tissues. Samples of tarsi were divided into pro-, meso- and metathoracic subtypes for both sexes. We then validated our dataset by conducting qRT-PCR on the same tissue samples and used statistical methods to compare results between the two methods. Studies addressing molecular function may now target specific genes to determine those involved in repellent perception by mosquitoes. These receptor pathways may be used to screen novel repellents towards disruption of host-seeking behavior to curb the spread of harmful viruses.

A Directed Molecular Evolution Approach to Improved Immunogenicity of the HIV-1 Envelope Glycoprotein

PubMed Central

Du, Sean X.; Xu, Li; Zhang, Wenge; Tang, Susan; Boenig, Rebecca I.; Chen, Helen; Mariano, Ellaine B.; Zwick, Michael B.; Parren, Paul W. H. I.; Burton, Dennis R.; Wrin, Terri; Petropoulos, Christos J.; Ballantyne, John A.; Chambers, Michael; Whalen, Robert G.

2011-01-01

A prophylactic vaccine is needed to slow the spread of HIV-1 infection. Optimization of the wild-type envelope glycoproteins to create immunogens that can elicit effective neutralizing antibodies is a high priority. Starting with ten genes encoding subtype B HIV-1 gp120 envelope glycoproteins and using in vitro homologous DNA recombination, we created chimeric gp120 variants that were screened for their ability to bind neutralizing monoclonal antibodies. Hundreds of variants were identified with novel antigenic phenotypes that exhibit considerable sequence diversity. Immunization of rabbits with these gp120 variants demonstrated that the majority can induce neutralizing antibodies to HIV-1. One novel variant, called ST-008, induced significantly improved neutralizing antibody responses when assayed against a large panel of primary HIV-1 isolates. Further study of various deletion constructs of ST-008 showed that the enhanced immunogenicity results from a combination of effective DNA priming, an enhanced V3-based response, and an improved response to the constant backbone sequences. PMID:21738594

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

PubMed Central

Welker, Frido; Hajdinjak, Mateja; Talamo, Sahra; Jaouen, Klervia; Dannemann, Michael; David, Francine; Julien, Michèle; Meyer, Matthias; Barnes, Ian; Brace, Selina; Kamminga, Pepijn; Fischer, Roman; Kessler, Benedikt M.; Stewart, John R.; Pääbo, Svante; Collins, Matthew J.; Hublin, Jean-Jacques

2016-01-01

In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this “transitional” assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal–Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne. PMID:27638212

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne.

PubMed

Welker, Frido; Hajdinjak, Mateja; Talamo, Sahra; Jaouen, Klervia; Dannemann, Michael; David, Francine; Julien, Michèle; Meyer, Matthias; Kelso, Janet; Barnes, Ian; Brace, Selina; Kamminga, Pepijn; Fischer, Roman; Kessler, Benedikt M; Stewart, John R; Pääbo, Svante; Collins, Matthew J; Hublin, Jean-Jacques

2016-10-04

In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.

Whole Genome Sequencing Reveals a De Novo SHANK3 Mutation in Familial Autism Spectrum Disorder

PubMed Central

Nemirovsky, Sergio I.; Córdoba, Marta; Zaiat, Jonathan J.; Completa, Sabrina P.; Vega, Patricia A.; González-Morón, Dolores; Medina, Nancy M.; Fabbro, Mónica; Romero, Soledad; Brun, Bianca; Revale, Santiago; Ogara, María Florencia; Pecci, Adali; Marti, Marcelo; Vazquez, Martin; Turjanski, Adrián; Kauffman, Marcelo A.

2015-01-01

Introduction Clinical genomics promise to be especially suitable for the study of etiologically heterogeneous conditions such as Autism Spectrum Disorder (ASD). Here we present three siblings with ASD where we evaluated the usefulness of Whole Genome Sequencing (WGS) for the diagnostic approach to ASD. Methods We identified a family segregating ASD in three siblings with an unidentified cause. We performed WGS in the three probands and used a state-of-the-art comprehensive bioinformatic analysis pipeline and prioritized the identified variants located in genes likely to be related to ASD. We validated the finding by Sanger sequencing in the probands and their parents. Results Three male siblings presented a syndrome characterized by severe intellectual disability, absence of language, autism spectrum symptoms and epilepsy with negative family history for mental retardation, language disorders, ASD or other psychiatric disorders. We found germline mosaicism for a heterozygous deletion of a cytosine in the exon 21 of the SHANK3 gene, resulting in a missense sequence of 5 codons followed by a premature stop codon (NM_033517:c.3259_3259delC, p.Ser1088Profs*6). Conclusions We reported an infrequent form of familial ASD where WGS proved useful in the clinic. We identified a mutation in SHANK3 that underscores its relevance in Autism Spectrum Disorder. PMID:25646853

Whole genome sequencing reveals a de novo SHANK3 mutation in familial autism spectrum disorder.

PubMed

Nemirovsky, Sergio I; Córdoba, Marta; Zaiat, Jonathan J; Completa, Sabrina P; Vega, Patricia A; González-Morón, Dolores; Medina, Nancy M; Fabbro, Mónica; Romero, Soledad; Brun, Bianca; Revale, Santiago; Ogara, María Florencia; Pecci, Adali; Marti, Marcelo; Vazquez, Martin; Turjanski, Adrián; Kauffman, Marcelo A

2015-01-01

Clinical genomics promise to be especially suitable for the study of etiologically heterogeneous conditions such as Autism Spectrum Disorder (ASD). Here we present three siblings with ASD where we evaluated the usefulness of Whole Genome Sequencing (WGS) for the diagnostic approach to ASD. We identified a family segregating ASD in three siblings with an unidentified cause. We performed WGS in the three probands and used a state-of-the-art comprehensive bioinformatic analysis pipeline and prioritized the identified variants located in genes likely to be related to ASD. We validated the finding by Sanger sequencing in the probands and their parents. Three male siblings presented a syndrome characterized by severe intellectual disability, absence of language, autism spectrum symptoms and epilepsy with negative family history for mental retardation, language disorders, ASD or other psychiatric disorders. We found germline mosaicism for a heterozygous deletion of a cytosine in the exon 21 of the SHANK3 gene, resulting in a missense sequence of 5 codons followed by a premature stop codon (NM_033517:c.3259_3259delC, p.Ser1088Profs*6). We reported an infrequent form of familial ASD where WGS proved useful in the clinic. We identified a mutation in SHANK3 that underscores its relevance in Autism Spectrum Disorder.

Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans

PubMed Central

Kihara, Terue C.; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

2016-01-01

Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima’s D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings. PMID:27732624

Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.

PubMed

Gollner, Sabine; Stuckas, Heiko; Kihara, Terue C; Laurent, Stefan; Kodami, Sahar; Martinez Arbizu, Pedro

2016-01-01

Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings.

Jamming Signal Reduction in Spread Spectrum Systems.

DTIC Science & Technology

1979-04-26

the addition of an appropriate equalizer netowrk . The original signal and the estimate of the jamming signal are matched and added by a resistor...ADDRESS(SI different from Controllln~ OWce) IS. SECURITY CLASS. (of this report) Unclassified IS.. OECLASSIFICATION /DOWNGRAD IHO SCHEDULE $6. DISTRIB

The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders.

PubMed

Buxbaum, Joseph D; Daly, Mark J; Devlin, Bernie; Lehner, Thomas; Roeder, Kathryn; State, Matthew W

2012-12-20

Research during the past decade has seen significant progress in the understanding of the genetic architecture of autism spectrum disorders (ASDs), with gene discovery accelerating as the characterization of genomic variation has become increasingly comprehensive. At the same time, this research has highlighted ongoing challenges. Here we address the enormous impact of high-throughput sequencing (HTS) on ASD gene discovery, outline a consensus view for leveraging this technology, and describe a large multisite collaboration developed to accomplish these goals. Similar approaches could prove effective for severe neurodevelopmental disorders more broadly. Copyright © 2012 Elsevier Inc. All rights reserved.

Strategies for efficient resolution analysis in full-waveform inversion

NASA Astrophysics Data System (ADS)

Fichtner, A.; van Leeuwen, T.; Trampert, J.

2016-12-01

Full-waveform inversion is developing into a standard method in the seismological toolbox. It combines numerical wave propagation for heterogeneous media with adjoint techniques in order to improve tomographic resolution. However, resolution becomes increasingly difficult to quantify because of the enormous computational requirements. Here we present two families of methods that can be used for efficient resolution analysis in full-waveform inversion. They are based on the targeted extraction of resolution proxies from the Hessian matrix, which is too large to store and to compute explicitly. Fourier methods rest on the application of the Hessian to Earth models with harmonic oscillations. This yields the Fourier spectrum of the Hessian for few selected wave numbers, from which we can extract properties of the tomographic point-spread function for any point in space. Random probing methods use uncorrelated, random test models instead of harmonic oscillations. Auto-correlating the Hessian-model applications for sufficiently many test models also characterises the point-spread function. Both Fourier and random probing methods provide a rich collection of resolution proxies. These include position- and direction-dependent resolution lengths, and the volume of point-spread functions as indicator of amplitude recovery and inter-parameter trade-offs. The computational requirements of these methods are equivalent to approximately 7 conjugate-gradient iterations in full-waveform inversion. This is significantly less than the optimisation itself, which may require tens to hundreds of iterations to reach convergence. In addition to the theoretical foundations of the Fourier and random probing methods, we show various illustrative examples from real-data full-waveform inversion for crustal and mantle structure.

Autism Spectrum Disorder

MedlinePlus

... person’s cells, recent research has also shown that de novo , or spontaneous, gene mutations can influence the risk of developing autism spectrum disorder. De novo mutations are changes in sequences of deoxyribonucleic ...

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.

Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa.

PubMed

Khaledi, Ariane; Schniederjans, Monika; Pohl, Sarah; Rainer, Roman; Bodenhofer, Ulrich; Xia, Boyang; Klawonn, Frank; Bruchmann, Sebastian; Preusse, Matthias; Eckweiler, Denitsa; Dötsch, Andreas; Häussler, Susanne

2016-08-01

Emerging resistance to antimicrobials and the lack of new antibiotic drug candidates underscore the need for optimization of current diagnostics and therapies to diminish the evolution and spread of multidrug resistance. As the antibiotic resistance status of a bacterial pathogen is defined by its genome, resistance profiling by applying next-generation sequencing (NGS) technologies may in the future accomplish pathogen identification, prompt initiation of targeted individualized treatment, and the implementation of optimized infection control measures. In this study, qualitative RNA sequencing was used to identify key genetic determinants of antibiotic resistance in 135 clinical Pseudomonas aeruginosa isolates from diverse geographic and infection site origins. By applying transcriptome-wide association studies, adaptive variations associated with resistance to the antibiotic classes fluoroquinolones, aminoglycosides, and β-lactams were identified. Besides potential novel biomarkers with a direct correlation to resistance, global patterns of phenotype-associated gene expression and sequence variations were identified by predictive machine learning approaches. Our research serves to establish genotype-based molecular diagnostic tools for the identification of the current resistance profiles of bacterial pathogens and paves the way for faster diagnostics for more efficient, targeted treatment strategies to also mitigate the future potential for resistance evolution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Transcriptome Profiling of Antimicrobial Resistance in Pseudomonas aeruginosa

PubMed Central

Khaledi, Ariane; Schniederjans, Monika; Pohl, Sarah; Rainer, Roman; Bodenhofer, Ulrich; Xia, Boyang; Klawonn, Frank; Bruchmann, Sebastian; Preusse, Matthias; Eckweiler, Denitsa; Dötsch, Andreas

2016-01-01

Emerging resistance to antimicrobials and the lack of new antibiotic drug candidates underscore the need for optimization of current diagnostics and therapies to diminish the evolution and spread of multidrug resistance. As the antibiotic resistance status of a bacterial pathogen is defined by its genome, resistance profiling by applying next-generation sequencing (NGS) technologies may in the future accomplish pathogen identification, prompt initiation of targeted individualized treatment, and the implementation of optimized infection control measures. In this study, qualitative RNA sequencing was used to identify key genetic determinants of antibiotic resistance in 135 clinical Pseudomonas aeruginosa isolates from diverse geographic and infection site origins. By applying transcriptome-wide association studies, adaptive variations associated with resistance to the antibiotic classes fluoroquinolones, aminoglycosides, and β-lactams were identified. Besides potential novel biomarkers with a direct correlation to resistance, global patterns of phenotype-associated gene expression and sequence variations were identified by predictive machine learning approaches. Our research serves to establish genotype-based molecular diagnostic tools for the identification of the current resistance profiles of bacterial pathogens and paves the way for faster diagnostics for more efficient, targeted treatment strategies to also mitigate the future potential for resistance evolution. PMID:27216077

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.

A growing global network’s role in outbreak response: AFHSC-GEIS 2008-2009

PubMed Central

2011-01-01

A cornerstone of effective disease surveillance programs comprises the early identification of infectious threats and the subsequent rapid response to prevent further spread. Effectively identifying, tracking and responding to these threats is often difficult and requires international cooperation due to the rapidity with which diseases cross national borders and spread throughout the global community as a result of travel and migration by humans and animals. From Oct.1, 2008 to Sept. 30, 2009, the United States Department of Defense’s (DoD) Armed Forces Health Surveillance Center Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) identified 76 outbreaks in 53 countries. Emerging infectious disease outbreaks were identified by the global network and included a wide spectrum of support activities in collaboration with host country partners, several of which were in direct support of the World Health Organization’s (WHO) International Health Regulations (IHR) (2005). The network also supported military forces around the world affected by the novel influenza A/H1N1 pandemic of 2009. With IHR (2005) as the guiding framework for action, the AFHSC-GEIS network of international partners and overseas research laboratories continues to develop into a far-reaching system for identifying, analyzing and responding to emerging disease threats. PMID:21388563

Motor and cognitive stereotypies in the BTBR T+tf/J mouse model of autism

PubMed Central

Pearson, BL; Pobbe, RLH; Defensor, EB; Oasay, L; Bolivar, VJ; Blanchard, DC; Blanchard, RJ

2010-01-01

The BTBR T+tf/J inbred mouse strain displays a variety of persistent phenotypic alterations similar to those exhibited in autism spectrum disorders. The unique genetic background of the BTBR strain is thought to underlie its lack of reciprocal social interactions, elevated repetitive self-directed grooming and restricted exploratory behaviors. In order to clarify the existence, range and mechanisms of abnormal repetitive behaviors within BTBR mice, we performed detailed analyses of the microstructure of self-grooming patterns and noted increased overall grooming, higher percentages of interruptions in grooming bouts and a concomitant decrease in the proportion of incorrect sequence transitions compared to C57BL/6J inbred mice. Analyses of active phase home cage behavior also revealed an increase in stereotypic bar-biting behavior in the BTBR strain relative to B6 mice. Finally, in a novel object investigation task, BTBR mice exhibited greater baseline preference for specific unfamiliar objects as well as more patterned sequences of sequential investigations of those items. These results suggest that the repetitive, stereotyped behavior patterns of BTBR mice are relatively pervasive and reflect both motor and cognitive mechanisms. Furthermore, other pre-clinical mouse models of autism spectrum disorders may benefit from these more detailed analyses of stereotypic behavior. PMID:21040460

47 CFR 90.903 - Competitive bidding mechanisms.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Bureau will establish and may vary the sequence in which 800 MHz SMR licenses for Spectrum Blocks A through V will be auctioned. (b) Grouping. (1) All EA licenses for Spectrum Blocks A through V will be... the auction, an alternative method of grouping these licenses for auction. (2) Spectrum blocks D...

47 CFR 90.903 - Competitive bidding mechanisms.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Bureau will establish and may vary the sequence in which 800 MHz SMR licenses for Spectrum Blocks A through V will be auctioned. (b) Grouping. (1) All EA licenses for Spectrum Blocks A through V will be... the auction, an alternative method of grouping these licenses for auction. (2) Spectrum blocks D...

47 CFR 90.903 - Competitive bidding mechanisms.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Bureau will establish and may vary the sequence in which 800 MHz SMR licenses for Spectrum Blocks A through V will be auctioned. (b) Grouping. (1) All EA licenses for Spectrum Blocks A through V will be... the auction, an alternative method of grouping these licenses for auction. (2) Spectrum blocks D...

47 CFR 90.903 - Competitive bidding mechanisms.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Bureau will establish and may vary the sequence in which 800 MHz SMR licenses for Spectrum Blocks A through V will be auctioned. (b) Grouping. (1) All EA licenses for Spectrum Blocks A through V will be... the auction, an alternative method of grouping these licenses for auction. (2) Spectrum blocks D...

Space-time properties of wind-waves: a new look at directional wave distributions

NASA Astrophysics Data System (ADS)

Leckler, Fabien; Ardhuin, Fabrice; Benetazzo, Alvise; Fedele, Francesco; Bergamasco, Filippo; Dulov, Vladimir

2014-05-01

Few accurate observed directional wave spectra are available in the literature at spatial scales ranging between 0.5 and 5.0 m. These intermediate wave scales, relevant for air-sea fluxes and remote sensing are also expected to feed back on the dominant wave properties through wave generation. These wave scales can be prolifically investigated using the well-known optical stereo methods that provides, from a couple of synchronized images, instantaneous representation of wave elevations over a given sea surface. Thus, two stereo systems (the so-called Wave Acquisition Stereo Systems, WASS) were deployed on top of the deep-water platform at Katsiveli, in the Black Sea, in September 2011 and 2013. From image pairs taken by the couple of synchronized high-resolution cameras, ocean surfaces have been reconstructed by stereo-triangulation. Here we analyze sea states corresponding to mean wind speeds of 11 to 14 m/s, and young wave ages of 0.35 to 0.42, associated to significant wave heights of 0.3 to 0.55m. As a result, four 12 Hz time evolutions of sea surface elevation maps with areas about 10 x 10 m2 have been obtained for sequence durations ranging between 15 and 30 minutes, and carefully validated with nearby capacitance wave gauges. The evolving free surfaces elevations were processed into frequency-wavenumber-direction 3D spectra. We found that wave energy chiefly follows the dispersion relation up to frequency of 1.6Hz and wavenumber of 10 rad/m, corresponding to wavelength of about 0.5 m. These spectra also depict well the energy contribution from non-linear waves, which is quantified and compared to theory. A strong bi-modality of the linear spectra was also observed, with the angle of the two maxima separated by about 160 degrees. Furthermore, spectra also exhibit the bimodality of the non-linear part. Integrated over positive frequencies to obtain wavenumber spectra unambiguous in direction, the bimodality of the spectra is partially hidden by the energy from second order waves, in particular from wave harmonics of the peak waves. However, the obtained spreading functions and integrals question the isotropy of the spectrum at high frequencies, generally assumed to explain deep water pressure measurement.

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.

Ocular manifestations of branchio-oculo-facial syndrome: Report of a novel mutation and review of the literature

PubMed Central

Al-Dosari, M.S.; Almazyad, M.; Al-Ebdi, L.; Mohamed, J.Y.; Al-Dahmash, Saad; Al-Dhibi, Hassan; Al-Kahtani, Eman; Al-Turkmani, Shahira; Hall, B.D.

2010-01-01

Purpose To report unusual ocular manifestations of branchio-oculo-facial syndrome (BOFS) caused by a novel mutation in activating enhancer binding protein 2 alpha (TFAP2A). Methods Full ophthalmological evaluation and direct sequencing of TFAP2A. Results A 10-year-old girl with unusual ocular manifestations of BOFS such as elliptical shaped microcornea and a novel de novo TFAP2A mutation was identified. Conclusions This report expands the ocular phenotypic spectrum of BOFS and adds to the small number of reported TFAP2A mutations. PMID:20461149

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.

Lymphogranuloma venereum rates increased and Chlamydia trachomatis genotypes changed among men who have sex with men in Sweden 2004-2016.

PubMed

Isaksson, Jenny; Carlsson, Ola; Airell, Åsa; Strömdahl, Susanne; Bratt, Göran; Herrmann, Björn

2017-11-01

This study aimed to determine the incidence of lymphogranuloma venereum (LGV) in Sweden since 2004 and to study in detail a consecutive number of Chlamydia trachomatis cases in men who have sex with men (MSM) during a 10 month period (September 2014 to July 2015). LGV increased from sporadic import cases in 2004 to comprise a spread within Sweden in 2016. Initially, only the L2b ompA genotype was detected, but in 2015 half of the genotyped LGV cases were L2 genotype. The changing genotype distribution in Sweden is linked to increased LGV spread in Europe. High-resolution multilocus sequence typing of 168 C. trachomatis cases from MSM in 2015 resulted in 29 sequence types, of which 3 accounted for 49 % of cases. The increased rates and different genotypes of LGV indicate that more concern for high-risk taking MSM is needed to avoid further spread of this invasive infection.

Modelling indirect interactions during failure spreading in a project activity network.

PubMed

Ellinas, Christos

2018-03-12

Spreading broadly refers to the notion of an entity propagating throughout a networked system via its interacting components. Evidence of its ubiquity and severity can be seen in a range of phenomena, from disease epidemics to financial systemic risk. In order to understand the dynamics of these critical phenomena, computational models map the probability of propagation as a function of direct exposure, typically in the form of pairwise interactions between components. By doing so, the important role of indirect interactions remains unexplored. In response, we develop a simple model that accounts for the effect of both direct and subsequent exposure, which we deploy in the novel context of failure propagation within a real-world engineering project. We show that subsequent exposure has a significant effect in key aspects, including the: (a) final spreading event size, (b) propagation rate, and (c) spreading event structure. In addition, we demonstrate the existence of 'hidden influentials' in large-scale spreading events, and evaluate the role of direct and subsequent exposure in their emergence. Given the evidence of the importance of subsequent exposure, our findings offer new insight on particular aspects that need to be included when modelling network dynamics in general, and spreading processes specifically.

Conceptual development of a ground-based radio-beacon navigation system for use on the surface of the moon

NASA Technical Reports Server (NTRS)

Beggins, Andrew J.; Canney, Lora M.; Dolezal, Anna Belle

1988-01-01

A spread-spectrum radio-beacon navigation system for use on the lunar surface is described. The subjects discussed are principle of operation and specifications to include power requirements, operating frequencies, weight, size, and range.

Methodology of Spread-Spectrum Image Steganography

DTIC Science & Technology

1998-06-01

the message was literally uncovered. Modern times have yielded more advanced techniques, such as the use of invisible inks, where certain chemical ...MILITARY ACADEMY MATH SCI CTR OF EXCELLENCE DEPT OF MATHEMATICAL SCI MDN A MAJ DON ENGEN THAYERHALL WEST POINT NY 10996-1786 1 DIRECTOR

High community faecal carriage rates of CTX-M ESBL-producing Escherichia coli in a specific population group in Birmingham, UK.

PubMed

Wickramasinghe, Nimal H; Xu, Li; Eustace, Andrew; Shabir, Sahida; Saluja, Tranprit; Hawkey, Peter M

2012-05-01

To determine the proportion of E. coli carrying specific CTX-M extended-spectrum β-lactamase (ESBL) genotypes in a community population of East and North Birmingham. General practice and outpatient stool samples from 732 individuals submitted for examination for faecal pathogens in 2010 were screened for ESBL-producing E. coli using chromogenic agar. Multiplex PCR, denaturing HPLC, DNA sequencing and PFGE were used to determine the CTX-M genotype and clonal subtype. Isolates from people were assigned to 'Europe', 'Middle East/South Asia' (MESA) or 'uncategorized' groups using software to determine probable global origin based on the subject's full name. Prevalence of CTX-M carriage in the sample population was 11.3%. There was a statistically significant difference (P < 0.001) between carriage in the Europe group (8.1%) and the MESA group (22.8%). There was also a higher rate of carriage of CTX-M-15-producing E. coli (P < 0.001) in MESA subjects. The high community carriage rate and the significant difference in carriage between the Europe and MESA subjects may have important consequences for therapy. If the rising trend in carriage of bacteria producing ESBLs continues, guidelines for empirical therapy for patients presenting from the community may need to be modified. The findings also raise the concern that the pattern and routes of spread of CTX-M-15 may be replicated in the future by broader-spectrum β-lactamases, such as New Delhi metallo-β-lactamase ('NDM-1').

Comparison between variable and fixed dwell-time PN acquisition algorithms. [for synchronization in pseudonoise spread spectrum systems

NASA Technical Reports Server (NTRS)

Braun, W. R.

1981-01-01

Pseudo noise (PN) spread spectrum systems require a very accurate alignment between the PN code epochs at the transmitter and receiver. This synchronism is typically established through a two-step algorithm, including a coarse synchronization procedure and a fine synchronization procedure. A standard approach for the coarse synchronization is a sequential search over all code phases. The measurement of the power in the filtered signal is used to either accept or reject the code phase under test as the phase of the received PN code. This acquisition strategy, called a single dwell-time system, has been analyzed by Holmes and Chen (1977). A synopsis of the field of sequential analysis as it applies to the PN acquisition problem is provided. From this, the implementation of the variable dwell time algorithm as a sequential probability ratio test is developed. The performance of this algorithm is compared to the optimum detection algorithm and to the fixed dwell-time system.

OXA-48 and CTX-M-15 extended-spectrum beta-lactamases in raw milk in Lebanon: epidemic spread of dominant Klebsiella pneumoniae clones.

PubMed

Diab, Mohamad; Hamze, Monzer; Bonnet, Richard; Saras, Estelle; Madec, Jean-Yves; Haenni, Marisa

2017-11-01

Raw milk has recently been reported as a source of extended-spectrum beta-lactamase (ESBL) and carbapenemase genes. We thus investigated the prevalence of ESBL- and carbapenemase-producing Enterobacteriaceae in raw milk in Lebanon in order to assess the risk of transfer of these bacteria to humans. A high prevalence (30.2 %) of CTX-M-15-producing K. pneumoniae was detected in raw bovine milk. Three main K. pneumoniae clones were identified by PFGE and MLST typing. Southern blot experiments revealed that one of these clones carried the blaCTX-M-15 gene chromosomally. Moreover, one OXA-48-producing K. pneumoniae ST530 and seven CTX-M-15-producing Escherichia coli sharing the same ST were also detected. These findings highlight the spread of dominant CTX-M-15-producing K. pneumoniae clones and OXA-48-producing isolates in the food chain. Milk, which is mostly consumed raw in Lebanon, may be a source of human exposure to ESBLs and carbapenemases.

A new orange emitting luciferase from the Southern-Amazon Pyrophorus angustus (Coleoptera: Elateridae) click-beetle: structure and bioluminescence color relationship, evolutional and ecological considerations.

PubMed

Amaral, Danilo T; Oliveira, Gabriela; Silva, Jaqueline R; Viviani, Vadim R

2016-08-31

Bioluminescent click-beetles display a wide variation of bioluminescence colors ranging from green to orange, including an unusual intra-specific color variation in the Jamaican Pyrophorus plagiophthalamus. Recently, we collected individuals of the Pyrophorus angustus species from the Southern Amazon forest, in Brazil, which displays an orange light emitting abdominal lantern. This species was also previously described from Central America, but displaying a bioluminescence spectrum from 536 nm (dorsal) to 578 nm (ventral). The biogeographic variation of the bioluminescence color in this species could be an adaptation to environmental reflectance and inter/intraspecific sexual competition. Here, we cloned, sequenced, characterized and performed site-direct mutagenesis of this new orange emitting luciferase. The in vitro luciferase spectrum displayed a peak at 594 nm, KM values for ATP and d-luciferin of 160 μM and 17 μM, respectively, and an optimum pH of approximately 8.5. Comparative multialignment and site-directed mutagenesis using different color emitting click-beetle luciferases from P. angustus, Fulgeochlizus bruchi and Pyrearinus termitilluminans luciferases cloned by our group showed an integral role of residue 247 in bioluminescence color modulation.

Droplet impact dynamics for two liquids impinging on anisotropic superhydrophobic surfaces

NASA Astrophysics Data System (ADS)

Pearson, John T.; Maynes, Daniel; Webb, Brent W.

2012-09-01

Droplet impingement experiments were performed on grooved hydrophobic surfaces with cavity fractions of 0, 80, and 93 % using droplets of water and a 50 %/50 % water/glycerol mixture. The influence of liquid viscosity, cavity fraction, and spreading direction, relative to the surface grooves, is explored qualitatively and quantitatively. The maximum droplet spread diameter, velocity of the rebounding jet, and the time delay between droplet impact and jet emission were characterized for Weber numbers, We, based on droplet impact speed and diameter, up to 500. The unequal shear stresses and contact angles influence the maximum spread diameters in the two primary spread directions. At We > 100, the ratio of the spread diameter along the direction of the grooves to the spread diameter perpendicular to the grooves increases above unity with increasing We. The maximum droplet spread diameter is compared to recent predictive models, and the data reveal differing behavior for the two fluids considered. The results also reveal the existence of very high relative jet velocities in the range 5 ≤ We ≤ 15 for water droplets, while such jets were not observed for the more viscous mixture. Further, in the range 115 ≤ We ≤ 265, the water/glycerol jet formation dynamics are radically different from the water behavior. Most evident is the existence of two-pronged jets, which arise from the anisotropy of the surface and the unequal shear stresses and contact angles that prevail on the surfaces. It is these influences that give rise to differences in the maximum spread diameters in the two primary spread directions. Similar two-pronged jet emission was observed for water over the very narrow range of We from 91 to 96. The issuing jet velocities were also observed to increase with increasing cavity fraction for both fluids and over the entire range of We explored. Lastly, the elapsed time between droplet impact and jet emission decreased with increasing cavity fraction.

Fluid spatial dynamics of West Nile virus in the USA: Rapid spread in a permissive host environment

USGS Publications Warehouse

Di Giallonardo , Francesca; Geoghegan, Jemma L.; Docherty, Douglas E.; McLean, Robert G.; Zody, Michael C.; Qu, James; Yang, Xiao; Birren, Bruce W.; Malboeuf, Christine M.; Newman, R.; Ip, Hon S.; Holmes, Edward C.

2016-01-01

The introduction of West Nile virus (WNV) into North America in 1999 is a classical example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology we sequenced the complete genomes of approximately 300 avian isolates sampled across the USA between 2001-2012. Phylogenetic analysis revealed a relatively ‘star-like' tree structure, indicative of explosive viral spread in US, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well sampled avian species. The genome sequence data analysed here also contain relatively little evidence for adaptive evolution, particularly on structural proteins, suggesting that most viral lineages are of similar fitness, and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the USA. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers.

Simultaneous observation of glutamate, gamma-aminobutyric acid, and glutamine in human brain at 4.7 T using localized two-dimensional constant-time correlation spectroscopy.

PubMed

Watanabe, H; Takaya, N; Mitsumori, F

2008-06-01

Localized two-dimensional constant-time correlation spectroscopy (CT-COSY) was used to resolve glutamate (Glu), gamma-aminobutyric acid (GABA), and glutamine (Gln) in the human brain at 4.7 T. In this method, three-dimensional localization was achieved using three radio frequency pulses of the CT-COSY module for slice selection. As this sequence could decouple JHH along the F1 direction, peak resolution of metabolites was improved even on a magnitude-mode display. In experiments on a phantom containing N-acetylaspartate, creatine, Glu, Gln, and GABA with a constant time delay (Tct) of 110 ms, cross peaks of Glu, Gln, and GABA were obtained on a spectrum processed with standard sine-bell windows, which emphasize sine-dependent signals along the t2 direction. In contrast, diagonal peaks of Glu C4H at 2.35 ppm, GABA C2H at 2.28 ppm, and Gln C4H at 2.44 ppm were resolved on a spectrum processed with Gaussian windows, which emphasize cosine-dependent signals along t2. Human brain spectra were obtained from a 27 mL voxel within the parieto-occipital region using a volume transverse electromagnetic (TEM) coil for both transmission and reception. Tct was 110 ms; the total scan time was 30 min. Diagonal peaks of Glu C4H, GABA C2H, and Gln C4H were also resolved on the spectrum processed with Gaussian windows. These results show that the localized two-dimensional CT-COSY method featuring 1H decoupling along the F1 direction could resolve Glu, GABA, and Gln signals in the human brain. Copyright (c) 2008 John Wiley & Sons, Ltd.

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.

Application of high-throughput sequencing to whole rabies viral genome characterisation and its use for phylogenetic re-evaluation of a raccoon strain incursion into the province of Ontario.

PubMed

Nadin-Davis, Susan A; Colville, Adam; Trewby, Hannah; Biek, Roman; Real, Leslie

2017-03-15

Raccoon rabies remains a serious public health problem throughout much of the eastern seaboard of North America due to the urban nature of the reservoir host and the many challenges inherent in multi-jurisdictional efforts to administer co-ordinated and comprehensive wildlife rabies control programmes. Better understanding of the mechanisms of spread of rabies virus can play a significant role in guiding such control efforts. To facilitate a detailed molecular epidemiological study of raccoon rabies virus movements across eastern North America, we developed a methodology to efficiently determine whole genome sequences of hundreds of viral samples. The workflow combines the generation of a limited number of overlapping amplicons covering the complete viral genome and use of high throughput sequencing technology. The value of this approach is demonstrated through a retrospective phylogenetic analysis of an outbreak of raccoon rabies which occurred in the province of Ontario between 1999 and 2005. As demonstrated by the number of single nucleotide polymorphisms detected, whole genome sequence data were far more effective than single gene sequences in discriminating between samples and this facilitated the generation of more robust and informative phylogenies that yielded insights into the spatio-temporal pattern of viral spread. With minor modification this approach could be applied to other rabies virus variants thereby facilitating greatly improved phylogenetic inference and thus better understanding of the spread of this serious zoonotic disease. Such information will inform the most appropriate strategies for rabies control in wildlife reservoirs. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction.

PubMed

Matamoros, Sébastien; van Hattem, Jarne M; Arcilla, Maris S; Willemse, Niels; Melles, Damian C; Penders, John; Vinh, Trung Nguyen; Thi Hoa, Ngo; de Jong, Menno D; Schultsz, Constance

2017-11-10

To understand the dynamics behind the worldwide spread of the mcr-1 gene, we determined the population structure of Escherichia coli and of mobile genetic elements (MGEs) carrying the mcr-1 gene. After a systematic review of the literature we included 65 E. coli whole genome sequences (WGS), adding 6 recently sequenced travel related isolates, and 312 MLST profiles. We included 219 MGEs described in 7 Enterobacteriaceae species isolated from human, animal and environmental samples. Despite a high overall diversity, 2 lineages were observed in the E. coli population that may function as reservoirs of the mcr-1 gene, the largest of which was linked to ST10, a sequence type known for its ubiquity in human faecal samples and in food samples. No genotypic clustering by geographical origin or isolation source was observed. Amongst a total of 13 plasmid incompatibility types, the IncI2, IncX4 and IncHI2 plasmids accounted for more than 90% of MGEs carrying the mcr-1 gene. We observed significant geographical clustering with regional spread of IncHI2 plasmids in Europe and IncI2 in Asia. These findings point towards promiscuous spread of the mcr-1 gene by efficient horizontal gene transfer dominated by a limited number of plasmid incompatibility types.

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane

PubMed Central

Benevenuto, Juliana; Peters, Leila P.; Carvalho, Giselle; Palhares, Alessandra; Quecine, Maria C.; Nunes, Filipe R. S.; Kmit, Maria C. P.; Wai, Alvan; Hausner, Georg; Aitken, Karen S.; Berkman, Paul J.; Fraser, James A.; Moolhuijzen, Paula M.; Coutinho, Luiz L.; Creste, Silvana; Vieira, Maria L. C.; Kitajima, João P.; Monteiro-Vitorello, Claudia B.

2015-01-01

Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions. PMID:26065709

Seizure semiology reflects spread from frontal to temporal lobe: evolution of hyperkinetic to automotor seizures as documented by invasive EEG video recordings.

PubMed

Tezer, Fadime Irsel; Agan, Kadriye; Borggraefe, Ingo; Noachtar, Soheyl

2013-09-01

This patient report demonstrates the importance of seizure evolution in the localising value of seizure semiology. Spread of epileptic activity from frontal to temporal lobe, as demonstrated by invasive recordings, was reflected by change from hyperkinetic movements to arrest of activity with mild oral and manual automatisms. [Published with video sequences].

Parallel evolution or purifying selection, not introgression, explain similarity in the pyrethroid detoxification linked GSTE4 of Anopheles gambiae and An. arabiensis

PubMed Central

Wilding, C.S.; Weetman, D.; Rippon, E.J.; Steen, K.; Mawejje, H.D.; Barsukov, I.; Donnelly, M.J.

2014-01-01

Insecticide resistance is a major impediment to the control of vectors and pests of public health importance and is a strongly selected trait capable of rapid spread, sometimes even between closely-related species. Elucidating the mechanisms generating insecticide resistance in mosquito vectors of disease, and understanding the spread of resistance within and between populations and species are vital for the development of robust resistance management strategies. Here we studied the mechanisms of resistance in two sympatric members of the Anopheles gambiae species complex – the major vector of malaria in sub-Saharan Africa – in order to understand how resistance has developed and spread in eastern Uganda, a region with some of the highest levels of malaria. In eastern Uganda, where the mosquitoes Anopheles arabiensis and An. gambiae can be found sympatrically, low levels of hybrids (0.4%) occur, offering a route for introgression of adaptively important variants between species. In independent microarray studies of insecticide resistance, Gste4, an insect-specific glutathione S-transferase, was among the most significantly up-regulated genes in both species. To test the hypothesis of interspecific introgression, we sequenced 2.3kbp encompassing Gste4. Whilst this detailed sequencing ruled out introgression, we detected strong positive selection acting on Gste4. However, these sequences, followed by haplotype-specific qPCR, showed that the apparent up-regulation in An. arabiensis is a result of allelic variation across the microarray probe binding sites which artefactually elevates the gene expression signal. Thus, face-value acceptance of microarray data can be misleading and it is advisable to conduct a more detailed investigation of the causes and nature of such signal. The identification of positive selection acting on this locus led us to functionally express and characterise allelic variants of GSTE4. Although the in vitro data do not support a direct role for GSTE4 in metabolism, they do support a role for this enzyme in insecticide sequestration. Thus, the demonstration of a role for an up-regulated gene in metabolic resistance to insecticides should not be limited to simply whether it can metabolise insecticide; such a strict criterion would argue against the involvement of GSTE4 despite the weight of evidence to the contrary. PMID:25213601

Numerical Calculation of the Spectrum of the Severe (1%) Lighting Current and Its First Derivative

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

Brown, C G; Ong, M M; Perkins, M P

2010-02-12

Recently, the direct-strike lighting environment for the stockpile-to-target sequence was updated [1]. In [1], the severe (1%) lightning current waveforms for first and subsequent return strokes are defined based on Heidler's waveform. This report presents numerical calculations of the spectra of those 1% lightning current waveforms and their first derivatives. First, the 1% lightning current models are repeated here for convenience. Then, the numerical method for calculating the spectra is presented and tested. The test uses a double-exponential waveform and its first derivative, which we fit to the previous 1% direct-strike lighting environment from [2]. Finally, the resulting spectra aremore » given and are compared with those of the double-exponential waveform and its first derivative.« less

Determination of a mutational spectrum

DOEpatents

Thilly, William G.; Keohavong, Phouthone

1991-01-01

A method of resolving (physically separating) mutant DNA from nonmutant DNA and a method of defining or establishing a mutational spectrum or profile of alterations present in nucleic acid sequences from a sample to be analyzed, such as a tissue or body fluid. The present method is based on the fact that it is possible, through the use of DGGE, to separate nucleic acid sequences which differ by only a single base change and on the ability to detect the separate mutant molecules. The present invention, in another aspect, relates to a method for determining a mutational spectrum in a DNA sequence of interest present in a population of cells. The method of the present invention is useful as a diagnostic or analytical tool in forensic science in assessing environmental and/or occupational exposures to potentially genetically toxic materials (also referred to as potential mutagens); in biotechnology, particularly in the study of the relationship between the amino acid sequence of enzymes and other biologically-active proteins or protein-containing substances and their respective functions; and in determining the effects of drugs, cosmetics and other chemicals for which toxicity data must be obtained.

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.

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.

Perspectives on How Human Simultaneous Multi-Modal Imaging Adds Directionality to Spread Models of Alzheimer’s Disease

PubMed Central

Neitzel, Julia; Nuttall, Rachel; Sorg, Christian

2018-01-01

Previous animal research suggests that the spread of pathological agents in Alzheimer’s disease (AD) follows the direction of signaling pathways. Specifically, tau pathology has been suggested to propagate in an infection-like mode along axons, from transentorhinal cortices to medial temporal lobe cortices and consequently to other cortical regions, while amyloid-beta (Aβ) pathology seems to spread in an activity-dependent manner among and from isocortical regions into limbic and then subcortical regions. These directed connectivity-based spread models, however, have not been tested directly in AD patients due to the lack of an in vivo method to identify directed connectivity in humans. Recently, a new method—metabolic connectivity mapping (MCM)—has been developed and validated in healthy participants that uses simultaneous FDG-PET and resting-state fMRI data acquisition to identify directed intrinsic effective connectivity (EC). To this end, postsynaptic energy consumption (FDG-PET) is used to identify regions with afferent input from other functionally connected brain regions (resting-state fMRI). Here, we discuss how this multi-modal imaging approach allows quantitative, whole-brain mapping of signaling direction in AD patients, thereby pointing out some of the advantages it offers compared to other EC methods (i.e., Granger causality, dynamic causal modeling, Bayesian networks). Most importantly, MCM provides the basis on which models of pathology spread, derived from animal studies, can be tested in AD patients. In particular, future work should investigate whether tau and Aβ in humans propagate along the trajectories of directed connectivity in order to advance our understanding of the neuropathological mechanisms causing disease progression. PMID:29434570

The spread of hepatitis C virus genotype 1a in North America: a retrospective phylogenetic study.

PubMed

Joy, Jeffrey B; McCloskey, Rosemary M; Nguyen, Thuy; Liang, Richard H; Khudyakov, Yury; Olmstead, Andrea; Krajden, Mel; Ward, John W; Harrigan, P Richard; Montaner, Julio S G; Poon, Art F Y

2016-06-01

The timing of the initial spread of hepatitis C virus genotype 1a in North America is controversial. In particular, how and when hepatitis C virus reached extraordinary prevalence in specific demographic groups remains unclear. We quantified, using all available hepatitis C virus sequence data and phylodynamic methods, the timing of the spread of hepatitis C virus genotype 1a in North America. We screened 45 316 publicly available sequences of hepatitis C virus genotype 1a for location and genotype, and then did phylogenetic analyses of available North American sequences from five hepatitis C virus genes (E1, E2, NS2, NS4B, NS5B), with an emphasis on including as many sequences with early collection dates as possible. We inferred the historical population dynamics of this epidemic for all five gene regions using Bayesian skyline plots. Most of the spread of genotype 1a in North America occurred before 1965, and the hepatitis C virus epidemic has undergone relatively little expansion since then. The effective population size of the North American epidemic stabilised around 1960. These results were robust across all five gene regions analysed, although analyses of each gene separately show substantial variation in estimates of the timing of the early exponential growth, ranging roughly from 1940 for NS2, to 1965 for NS4B. The expansion of genotype 1a before 1965 suggests that nosocomial or iatrogenic factors rather than past sporadic behavioural risk (ie, experimentation with injection drug use, unsafe tattooing, high risk sex, travel to high endemic areas) were key contributors to the hepatitis C virus epidemic in North America. Our results might reduce stigmatisation around screening and diagnosis, potentially increasing rates of screening and treatment for hepatitis C virus. The Canadian Institutes of Health Research, Michael Smith Foundation for Health Research, and BC Centre for Excellence in HIV/AIDS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome Sequences of Multidrug-Resistant, Colistin-Susceptible and -Resistant Klebsiella pneumoniae Clinical Isolates from Pakistan

PubMed Central

Crawford, Matthew A.; Timme, Ruth; Lomonaco, Sara; Lascols, Christine; Fisher, Debra J.; Sharma, Shashi K.; Strain, Errol; Allard, Marc W.; Brown, Eric W.; McFarland, Melinda A.; Croley, Tim; Hammack, Thomas S.; Weigel, Linda M.; Anderson, Kevin; Hodge, David R.; Pillai, Segaran P.; Morse, Stephen A.; Khan, Erum

2016-01-01

The emergence and spread of colistin resistance among multidrug-resistant (MDR) Klebsiella pneumoniae represent a critical threat to global health. Here, we report the complete genome sequences of 10 MDR, colistin-susceptible and -resistant K. pneumoniae clinical isolates obtained in Pakistan between 2010 and 2013. PMID:27979956

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

Jamming protection of spread spectrum RFID system

NASA Astrophysics Data System (ADS)

Mazurek, Gustaw

2006-10-01

This paper presents a new transform-domain processing algorithm for rejection of narrowband interferences in RFID/DS-CDMA systems. The performance of the proposed algorithm has been verified via computer simulations. Implementation issues have been discussed. The algorithm can be implemented in the FPGA or DSP technology.

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.

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.

Parametric Instability, Inverse Cascade, and the 1/f Range of Solar-Wind Turbulence.

PubMed

Chandran, Benjamin D G

2018-02-01

In this paper, weak turbulence theory is used to investigate the nonlinear evolution of the parametric instability in 3D low- β plasmas at wavelengths much greater than the ion inertial length under the assumption that slow magnetosonic waves are strongly damped. It is shown analytically that the parametric instability leads to an inverse cascade of Alfvén wave quanta, and several exact solutions to the wave kinetic equations are presented. The main results of the paper concern the parametric decay of Alfvén waves that initially satisfy e + ≫ e - , where e + and e - are the frequency ( f ) spectra of Alfvén waves propagating in opposite directions along the magnetic field lines. If e + initially has a peak frequency f 0 (at which fe + is maximized) and an "infrared" scaling f p at smaller f with -1 < p < 1, then e + acquires an f -1 scaling throughout a range of frequencies that spreads out in both directions from f 0 . At the same time, e - acquires an f -2 scaling within this same frequency range. If the plasma parameters and infrared e + spectrum are chosen to match conditions in the fast solar wind at a heliocentric distance of 0.3 astronomical units (AU), then the nonlinear evolution of the parametric instability leads to an e + spectrum that matches fast-wind measurements from the Helios spacecraft at 0.3 AU, including the observed f -1 scaling at f ≳ 3 × 10 -4 Hz. The results of this paper suggest that the f -1 spectrum seen by Helios in the fast solar wind at f ≳ 3 × 10 -4 Hz is produced in situ by parametric decay and that the f -1 range of e + extends over an increasingly narrow range of frequencies as r decreases below 0.3 AU. This prediction will be tested by measurements from the Parker Solar Probe .

A Simple Model to Rank Shellfish Farming Areas Based on the Risk of Disease Introduction and Spread.

PubMed

Thrush, M A; Pearce, F M; Gubbins, M J; Oidtmann, B C; Peeler, E J

2017-08-01

The European Union Council Directive 2006/88/EC requires that risk-based surveillance (RBS) for listed aquatic animal diseases is applied to all aquaculture production businesses. The principle behind this is the efficient use of resources directed towards high-risk farm categories, animal types and geographic areas. To achieve this requirement, fish and shellfish farms must be ranked according to their risk of disease introduction and spread. We present a method to risk rank shellfish farming areas based on the risk of disease introduction and spread and demonstrate how the approach was applied in 45 shellfish farming areas in England and Wales. Ten parameters were used to inform the risk model, which were grouped into four risk themes based on related pathways for transmission of pathogens: (i) live animal movement, (ii) transmission via water, (iii) short distance mechanical spread (birds) and (iv) long distance mechanical spread (vessels). Weights (informed by expert knowledge) were applied both to individual parameters and to risk themes for introduction and spread to reflect their relative importance. A spreadsheet model was developed to determine quantitative scores for the risk of pathogen introduction and risk of pathogen spread for each shellfish farming area. These scores were used to independently rank areas for risk of introduction and for risk of spread. Thresholds were set to establish risk categories (low, medium and high) for introduction and spread based on risk scores. Risk categories for introduction and spread for each area were combined to provide overall risk categories to inform a risk-based surveillance programme directed at the area level. Applying the combined risk category designation framework for risk of introduction and spread suggested by European Commission guidance for risk-based surveillance, 4, 10 and 31 areas were classified as high, medium and low risk, respectively. © 2016 Crown copyright.

Genomic Investigation of a Legionellosis Outbreak in a Persistently Colonized Hotel.

PubMed

Sánchez-Busó, Leonor; Guiral, Silvia; Crespi, Sebastián; Moya, Víctor; Camaró, María L; Olmos, María P; Adrián, Francisco; Morera, Vicente; González-Morán, Francisco; Vanaclocha, Hermelinda; González-Candelas, Fernando

2015-01-01

A long-lasting legionellosis outbreak was reported between November 2011 and July 2012 in a hotel in Calpe (Spain) affecting 44 patients including six deaths. Intensive epidemiological and microbiological investigations were performed in order to detect the reservoirs. Clinical and environmental samples were tested for the presence and genetic characterization of Legionella pneumophila. Six of the isolates were subjected to whole-genome sequencing. Sequencing of 14 clinical and 260 environmental samples revealed sequence type (ST) 23 as the main responsible strain for the infections. This ST was found in the spa pool, from where it spread to other hotel public spaces, explaining the ST23 clinical cases, including guests who had not visited the spa. Uncultured clinical specimens showed profiles compatible with ST23, ST578, and mixed patterns. Profiles compatible with ST578 were obtained by direct sequencing from biofilm samples collected from the domestic water system, which provided evidence for the source of infection for non ST23 patients. Whole genome data from five ST23 strains and the identification of different STs and Legionella species showed that different hotel premises were likely colonized since the hotel opening thus explaining how different patients had been infected by distinct STs. Both epidemiological and molecular data are essential in the investigation of legionellosis outbreaks. Whole-genome sequencing data revealed significant intra-ST variability and allowed to make further inference on the short-term evolution of a local colonization of L. pneumophila.

Genomic Investigation of a Legionellosis Outbreak in a Persistently Colonized Hotel

PubMed Central

Sánchez-Busó, Leonor; Guiral, Silvia; Crespi, Sebastián; Moya, Víctor; Camaró, María L.; Olmos, María P.; Adrián, Francisco; Morera, Vicente; González-Morán, Francisco; Vanaclocha, Hermelinda; González-Candelas, Fernando

2016-01-01

Objectives: A long-lasting legionellosis outbreak was reported between November 2011 and July 2012 in a hotel in Calpe (Spain) affecting 44 patients including six deaths. Intensive epidemiological and microbiological investigations were performed in order to detect the reservoirs. Methods: Clinical and environmental samples were tested for the presence and genetic characterization of Legionella pneumophila. Six of the isolates were subjected to whole-genome sequencing. Results: Sequencing of 14 clinical and 260 environmental samples revealed sequence type (ST) 23 as the main responsible strain for the infections. This ST was found in the spa pool, from where it spread to other hotel public spaces, explaining the ST23 clinical cases, including guests who had not visited the spa. Uncultured clinical specimens showed profiles compatible with ST23, ST578, and mixed patterns. Profiles compatible with ST578 were obtained by direct sequencing from biofilm samples collected from the domestic water system, which provided evidence for the source of infection for non ST23 patients. Whole genome data from five ST23 strains and the identification of different STs and Legionella species showed that different hotel premises were likely colonized since the hotel opening thus explaining how different patients had been infected by distinct STs. Conclusions: Both epidemiological and molecular data are essential in the investigation of legionellosis outbreaks. Whole-genome sequencing data revealed significant intra-ST variability and allowed to make further inference on the short-term evolution of a local colonization of L. pneumophila. PMID:26834713

Spectral and cross-spectral analysis of uneven time series with the smoothed Lomb-Scargle periodogram and Monte Carlo evaluation of statistical significance

NASA Astrophysics Data System (ADS)

Pardo-Igúzquiza, Eulogio; Rodríguez-Tovar, Francisco J.

2012-12-01

Many spectral analysis techniques have been designed assuming sequences taken with a constant sampling interval. However, there are empirical time series in the geosciences (sediment cores, fossil abundance data, isotope analysis, …) that do not follow regular sampling because of missing data, gapped data, random sampling or incomplete sequences, among other reasons. In general, interpolating an uneven series in order to obtain a succession with a constant sampling interval alters the spectral content of the series. In such cases it is preferable to follow an approach that works with the uneven data directly, avoiding the need for an explicit interpolation step. The Lomb-Scargle periodogram is a popular choice in such circumstances, as there are programs available in the public domain for its computation. One new computer program for spectral analysis improves the standard Lomb-Scargle periodogram approach in two ways: (1) It explicitly adjusts the statistical significance to any bias introduced by variance reduction smoothing, and (2) it uses a permutation test to evaluate confidence levels, which is better suited than parametric methods when neighbouring frequencies are highly correlated. Another novel program for cross-spectral analysis offers the advantage of estimating the Lomb-Scargle cross-periodogram of two uneven time series defined on the same interval, and it evaluates the confidence levels of the estimated cross-spectra by a non-parametric computer intensive permutation test. Thus, the cross-spectrum, the squared coherence spectrum, the phase spectrum, and the Monte Carlo statistical significance of the cross-spectrum and the squared-coherence spectrum can be obtained. Both of the programs are written in ANSI Fortran 77, in view of its simplicity and compatibility. The program code is of public domain, provided on the website of the journal (http://www.iamg.org/index.php/publisher/articleview/frmArticleID/112/). Different examples (with simulated and real data) are described in this paper to corroborate the methodology and the implementation of these two new programs.

Bioinspired second harmonic generation

NASA Astrophysics Data System (ADS)

Sonay, Ali Y.; Pantazis, Periklis

2017-07-01

Second harmonic generation (SHG) is a microscopic technique applicable to a broad spectrum of biological and medical imaging due to its excellent photostability, high signal-to-noise ratio (SNR) and narrow emission profile. Current SHG microscopy techniques rely on two main contrast modalities. These are endogenous SHG generated by tissue structures, which is clinically relevant but cannot be targeted to another location, or SHG nanoprobes, inorganic nanocrystals that can be directed to proteins and cells of interest, but cannot be applied for clinical imaging due to their chemical composition. Here we analyzed SHG signal generated by large-scale peptide assemblies. Our results show the sequence of peptides play an important role on both the morphology and SHG signal of the peptide assemblies. Changing peptide sequence allows confinement of large number of peptides to smaller voxels, generating intense SHG signal. With miniaturization of these peptides and their proper functionalization strategies, such bioinspired nanoparticles would emerge as valuable tools for clinical imaging.

Noncoherent Tracking of a Source of a Data-Modulated Signal

NASA Technical Reports Server (NTRS)

Arndt, G. Dickey; Ngo, Phong; Chen, Henry; Phan, Chau T.; Hill, Brent; Bourgeois, Brian; Dusl, John

2003-01-01

A proposed tracking receiver system containing three suitably positioned antenna elements and special signal-processing equipment would determine the direction of incidence of a microwave signal containing spread-spectrum digital data modulation. If the system were to contain two sets of antenna elements separated by a known baseline, it could determine the location of the transmitter as the intersection of the lines of incidence on the two antennas. Such systems could be used for diverse purposes in outer space and on Earth, including tracking astronauts and small robotic spacecraft working outside a spacecraft or space station, and locating cellular telephones from which distress calls have been made. The principle of operation does not require the transmission of a special identifying or distress signal by the cellular telephone or other transmitter to be tracked; instead, the system could utilize the data signal routinely sent by the transmitter, provided that the signal had the characteristics needed for processing.

HIV-2 and its neurological manifestations.

PubMed

Rolfe, M

1994-08-01

The human immunodeficiency virus type 2 (HIV-2) produces a similar spectrum of illness as HIV-1, including AIDS, and is clinically indistinguishable. There is evidence that it is less pathogenic, with a longer natural history. HIV-2 infection is endemic in West Africa, especially in the former Portuguese and French colonies. Trade, migration, war and tourism have been important factors in the spread of the virus through the subregion and beyond. Diagnostic facilities necessary for the accurate diagnosis of neurological disease are not available in most of Africa and autopsy reports have been few. These constraints have restricted the information available on the pattern of neuropathology induced by HIV-2. However, it possesses neurotropic properties similar to those of HIV-1 and produces disease by means of direct action of the virus on the nervous system, and immunosuppression which allows opportunistic infections and tumours to occur.

Tracking Characteristics of a Triangular-Aperture Mounted Optical Head Slider to Which a Polarized Violet Laser Source Is Applied

NASA Astrophysics Data System (ADS)

Ohkubo, Toshifumi; Park, Majung; Hirata, Masakazu; Oumi, Manabu; Nakajima, Kunio

In near-field optical recording, the combination of a triangular aperture and a polarized illuminating light is thought to be one of the most promising breakthroughs for improving both spatial resolution and signal-to-noise ratio. In light of this, we have already fabricated a triangular-aperture mounted optical head slider and demonstrated its superior performance while clarifying the influence of the polarization direction on the spatial resolution in the circumferential direction. When the polarization direction was perpendicular to the bottom side (which is parallel to the slider trailing edge) of the aperture, the highest spatial resolution and signal contrast were obtained, in spite of the usage of a fairly large aperture, indicating the presence of clear readout signal waveforms corresponding down to 100 nm line-and-space (L/S) patterns. In this study, we tried to experimentally clarify the influence of the polarization direction of the illuminating light on an aperture's field spread in the radial direction. In order to concretely evaluate the field spread, we prepared 1-mm-long linearly arranged (in the circumferential direction) L/S patterns on a metal-layered medium, and a piezo-electric actuator combined positioner. Intersecting the aperture at two portions of the tracks, directly acquired signal waveforms could be successfully transformed into the waveforms that would be obtained if the aperture had crossed the track at right angles. The field spreads in the radial direction were estimated to be approximately 250 nm when the polarization direction was perpendicular to the bottom side. In contrast, when the polarization direction was 45 degrees, the stationary field spread in the radial direction was estimated to be approximately 350 - 370 nm. It could be confirmed experimentally that both the highest spatial resolution in the circumferential direction and the smallest field spread in the radial direction were realized with the combination of the triangular aperture and the illuminating polarized light whose direction was perpendicular to the bottom side. Based on these results, the signal-to-noise ratio will be evaluated and discussed in the future with respect to the above-mentioned optimum aperture structure and conditions.

Novel microsatellite DNA markers indicate strict parthenogenesis and few genotypes in the invasive willow sawfly Nematus oligospilus.

PubMed

Caron, V; Norgate, M; Ede, F J; Nyman, T; Sunnucks, P

2013-02-01

Invasive organisms can have major impacts on the environment. Some invasive organisms are parthenogenetic in their invasive range and, therefore, exist as a number of asexual lineages (=clones). Determining the reproductive mode of invasive species has important implications for understanding the evolutionary genetics of such species, more especially, for management-relevant traits. The willow sawfly Nematus oligospilus Förster (Hymenoptera: Tenthredinidae) has been introduced unintentionally into several countries in the Southern Hemisphere where it has subsequently become invasive. To assess the population expansion, reproductive mode and host-plant relationships of this insect, microsatellite markers were developed and applied to natural populations sampled from the native and expanded range, along with sequencing of the cytochrome-oxidase I mitochondrial DNA (mtDNA) region. Other tenthredinids across a spectrum of taxonomic similarity to N. oligospilus and having a range of life strategies were also tested. Strict parthenogenesis was apparent within invasive N. oligospilus populations throughout the Southern Hemisphere, which comprised only a small number of genotypes. Sequences of mtDNA were identical for all individuals tested in the invasive range. The microsatellite markers were used successfully in several sawfly species, especially Nematus spp. and other genera of the Nematini tribe, with the degree of success inversely related to genetic divergence as estimated from COI sequences. The confirmation of parthenogenetic reproduction in N. oligospilus and the fact that it has a very limited pool of genotypes have important implications for understanding and managing this species and its biology, including in terms of phenotypic diversity, host relationships, implications for spread and future adaptive change. It would appear to be an excellent model study system for understanding evolution of invasive parthenogens that diverge without sexual reproduction and genetic recombination.

Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

PubMed Central

Marquez-Ortiz, Ricaurte Alejandro; Haggerty, Leanne; Olarte, Narda; Duarte, Carolina; Garza-Ramos, Ulises; Silva-Sanchez, Jesus; Castro, Betsy E.; Sim, Eby M.; Beltran, Mauricio; Moncada, María V.; Valderrama, Alberto; Castellanos, Jaime E.; Charles, Ian G.; Vanegas, Natasha

2017-01-01

Abstract Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes. PMID:28854628