Spread spectrum image steganography.

Science.gov (United States)

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.

Evaluation of an Acoustic Charge Transport (ACT) device for adaptive interference suppression in spread spectrum communications systems

Science.gov (United States)

Mills, Michael S.

1993-12-01

Analytical results have shown that adaptive filtering can be a powerful tool for the rejection of narrowband interference in a direct sequence spread spectrum receiver. However, the complexity of adaptive filtering hardware has hindered the experimental validation of these results. This thesis describes a unique adaptive filter architecture for implementing the Widrow-Hoff least mean square (LMS) algorithm using two state of the art acoustic charge transport (ACT) programmable transversal filters (PTF's). Signal to noise ratio improvement measurements demonstrate the effectiveness of the adaptive filter for suppressing single- and dual-tone jammers at jammer to signal ratios (JSR's) of up to 30 dB. It is shown that the ACT adaptive interference rejection system can consistently produce 55 dB notch depths with 3-dB bandwidths as low as 300 kHz with minimal degradation to the spread spectrum signal. It is also shown that the adaptive system can eliminate single tone jammers at any frequency within the spread spectrum bandwidth at any of 10, 20, or 30 dB JSRs within 10 to 15 iterations of the adaptive algorithm. The only drawback with the adaptive system as tested is the amount of time taken to perform an iteration because of the requirement to update the PTF tap weights sequentially. Suggestions are given as to how this particular parameter of the adaptive interference system could be optimized.

Spreading Sequence Design and Theoretical Limits for Quasisynchronous CDMA Systems

Directory of Open Access Journals (Sweden)

Fan Pingzhi

2004-01-01

Full Text Available For various quasisynchronous (QS CDMA systems such as LAS-CDMA system which emerged recently, in order to reduce or eliminate the multiple access interference and multipath interference, it is required to design a set of spreading sequences which are mutually orthogonal within a designed shift zone, called orthogonal zone. For traditional orthogonal sequences, such as Walsh sequences and orthogonal Gold sequences, the orthogonality can only be achieved at the inphase point; in other words, the orthogonality is destroyed whenever there is a relative shift between the sequences, that is, their orthogonal zone is 0. In this paper, new concepts of generalized orthogonality (GO and generalized quasiorthogonality (GQO for spreading sequence design in both direct sequence (DS QS-CDMA systems and time/frequency hopping (TH/FH QS-CDMA systems are presented. Besides, selected GO/GQO sequence designs and general theoretical periodic and aperiodic limits, together with several applications in QS-CDMA systems, are also reviewed and analyzed.

A STUDY ON DETERMINING THE REFERENCE SPREADING SEQUENCES FOR A DS/CDMACOMMUNICATION SYSTEM

Directory of Open Access Journals (Sweden)

Cebrail ÇİFTLİKLİ

2002-02-01

Full Text Available In a direct sequence/code division multiple access (DS/CDMA system, the role of the spreading sequences (codes is crucial since the multiple access interference (MAI is the main performance limitation. In this study, we propose an accurate criterion which enables the determination of the reference spreading codes which yield lower bit error rates (BER's in a given code set for a DS/CDMA system using despreading sequences weighted by stepping chip waveforms. The numerical results show that the spreading codes determined by the proposed criterion are the most suitable codes for using as references.

Spread-spectrum communication using binary spatiotemporal chaotic codes

International Nuclear Information System (INIS)

Wang Xingang; Zhan Meng; Gong Xiaofeng; Lai, C.H.; Lai, Y.-C.

2005-01-01

We propose a scheme to generate binary code for baseband spread-spectrum communication by using a chain of coupled chaotic maps. We compare the performances of this type of spatiotemporal chaotic code with those of a conventional code used frequently in digital communication, the Gold code, and demonstrate that our code is comparable or even superior to the Gold code in several key aspects: security, bit error rate, code generation speed, and the number of possible code sequences. As the field of communicating with chaos faces doubts in terms of performance comparison with conventional digital communication schemes, our work gives a clear message that communicating with chaos can be advantageous and it deserves further attention from the nonlinear science community

Estimation of wave directional spreading

Digital Repository Service at National Institute of Oceanography (India)

Deo, M.C.; Gondane, D.S.; SanilKumar, V.

One of the useful measures of waves directional spreading at a given location is the directional spreading parameter. This paper presents a new approach to arrive at its characteristic value using the computational technique of Artificial Neural...

Principles of spread-spectrum communication systems

CERN Document Server

Torrieri, Don

2015-01-01

This book provides a concise but lucid explanation of the fundamentals of spread-spectrum systems with an emphasis on theoretical principles. The choice of specific topics is tempered by the author’s judgment of their practical significance and interest to both researchers and system designers. The book contains many improved derivations of the classical theory and presents the latest research results that bring the reader to the frontier of the field. This third edition includes new coverage of topics such as CDMA networks, acquisition and synchronization in DS-CDMA cellular networks, hopsets for FH-CDMA ad hoc networks, implications of information theory, the central limit theorem, the power spectral density of FH/CPM complex envelopes, adaptive filters, and adaptive arrays.   ·         Focuses on the fundamentals of spread-spectrum communication systems and provides current examples of their applications ·         Includes problem sets at the end of each chapter to assist readers in co...

Improving performance of DS-CDMA systems using chaotic complex Bernoulli spreading codes

Science.gov (United States)

Farzan Sabahi, Mohammad; Dehghanfard, Ali

2014-12-01

The most important goal of spreading spectrum communication system is to protect communication signals against interference and exploitation of information by unintended listeners. In fact, low probability of detection and low probability of intercept are two important parameters to increase the performance of the system. In Direct Sequence Code Division Multiple Access (DS-CDMA) systems, these properties are achieved by multiplying the data information in spreading sequences. Chaotic sequences, with their particular properties, have numerous applications in constructing spreading codes. Using one-dimensional Bernoulli chaotic sequence as spreading code is proposed in literature previously. The main feature of this sequence is its negative auto-correlation at lag of 1, which with proper design, leads to increase in efficiency of the communication system based on these codes. On the other hand, employing the complex chaotic sequences as spreading sequence also has been discussed in several papers. In this paper, use of two-dimensional Bernoulli chaotic sequences is proposed as spreading codes. The performance of a multi-user synchronous and asynchronous DS-CDMA system will be evaluated by applying these sequences under Additive White Gaussian Noise (AWGN) and fading channel. Simulation results indicate improvement of the performance in comparison with conventional spreading codes like Gold codes as well as similar complex chaotic spreading sequences. Similar to one-dimensional Bernoulli chaotic sequences, the proposed sequences also have negative auto-correlation. Besides, construction of complex sequences with lower average cross-correlation is possible with the proposed method.

Generation of pseudo-random sequences for spread spectrum systems

Science.gov (United States)

Moser, R.; Stover, J.

1985-05-01

The characteristics of pseudo random radio signal sequences (PRS) are explored. The randomness of the PSR is a matter of artificially altering the sequence of binary digits broadcast. Autocorrelations of the two sequences shifted in time, if high, determine if the signals are the same and thus allow for position identification. Cross-correlation can also be calculated between sequences. Correlations closest to zero are obtained with large volume of prime numbers in the sequences. Techniques for selecting optimal and maximal lengths for the sequences are reviewed. If the correlations are near zero in the sequences, then signal channels can accommodate multiple users. Finally, Gold codes are discussed as a technique for maximizing the code lengths.

Wavelet versus DCT-based spread spectrum watermarking of image databases

Science.gov (United States)

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.

Epidemic spreading through direct and indirect interactions.

Science.gov (United States)

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.

Composite Binary Sequences with a Large Ensemble and Zero Correlation Zone

Directory of Open Access Journals (Sweden)

S. S. Yudachev

2015-01-01

Full Text Available The article considers a proposed class of derived signals such as composite binary sequences for application in advanced spread spectrum radio systems of various purposes, using signals based on spectrum spreading by direct sequence method. Considered composite sequences, having a representative set of lengths and unique correlation properties, compares favorably with the widely used at present large ensembles formed on a single algorithmic basis. To evaluate the properties of the composite sequences generated on the basis of two components - the Barker code and Kerdock sequences, expressions of periodic and aperiodic correlation functions are given.An algorithm for generating practical ensembles of composite sequences is presented. On the basis of the algorithm and its software implementation in C #, the samples of the sequence ensembles of various lengths were obtained and their periodic and aperiodic correlation functions and statistical characteristics were studied in detail. As an illustration, some of the most typical correlation functions are presented. The most remarkable characteristics allowing a ssessing the feasibility of using this type of sequences in the design of specific types of radio systems are considered.On the basis of the proposed program and the performed calculations the conclusions can be drawn about the possibility of using the sequences of these classes, with the aim of reducing intra-system disturbance in the projected spread spectrum CDMA.

Efficiently Synchronized Spread-Spectrum Audio Watermarking with Improved Psychoacoustic Model

Directory of Open Access Journals (Sweden)

Xing He

2008-01-01

Full Text Available This paper presents an audio watermarking scheme which is based on an efficiently synchronized spread-spectrum technique and a new psychoacoustic model computed using the discrete wavelet packet transform. The psychoacoustic model takes advantage of the multiresolution analysis of a wavelet transform, which closely approximates the standard critical band partition. The goal of this model is to include an accurate time-frequency analysis and to calculate both the frequency and temporal masking thresholds directly in the wavelet domain. Experimental results show that this watermarking scheme can successfully embed watermarks into digital audio without introducing audible distortion. Several common watermark attacks were applied and the results indicate that the method is very robust to those attacks.

Spreading Sequences Generated Using Asymmetrical Integer-Number Maps

Directory of Open Access Journals (Sweden)

V. Sebesta

2007-09-01

Full Text Available Chaotic sequences produced by piecewise linear maps can be transformed to binary sequences. The binary sequences are optimal for the asynchronous DS/CDMA systems in case of certain shapes of the maps. This paper is devoted to the one-to-one integer-number maps derived from the suitable asymmetrical piecewise linear maps. Such maps give periodic integer-number sequences, which can be transformed to the binary sequences. The binary sequences produced via proposed modified integer-number maps are perfectly balanced and embody good autocorrelation and crosscorrelation properties. The number of different binary sequences is sizable. The sequences are suitable as spreading sequences in DS/CDMA systems.

Spread Spectrum Techniques and their Applications to Wireless Communications

DEFF Research Database (Denmark)

Prasad, Ramjee; Cianca, E.

2005-01-01

Spread Spectrum (SS) radio communications is on the verge of potentially explosive commercial development An SS-based multiple access, such as CDMA, has been chosen for 3G wireless communications. Other current applications of SS techniues are in Wireless LANs and Satellite Navigation Systems...

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

Science.gov (United States)

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.

Upgrade of hybrid fibre coax networks towards bi-directional access

NARCIS (Netherlands)

Khoe, G.D.; Wolters, R.P.C.; Boom, van den H.P.A.; Prati, G.

1997-01-01

In this paper we describe an upgrade scenario for Hybrid Fibre Coax (HFC) CATV Networks towards hi-directional access. The communication system described has been newly designed, and is based on the use of Direct Sequence- Code Division Multiple-Access (DS-CDMA). Due to its spread-spectrum

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

Science.gov (United States)

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.

A Synchronisation Method For Informed Spread-Spectrum Audiowatermarking

OpenAIRE

Pierre-Yves Fulchiron; Barry O'Donovan; Guenole Silvestre; Neil Hurley

2003-01-01

Under perfect synchronisation conditions, watermarking schemes employing asymmetric spread-spectrum techniques are suitable for copy-protection of audio signals. This paper proposes to combine the use of a robust psychoacoustic projection for the extraction of a watermark feature vector along with non-linear detection functions optimised with side-information. The new proposed scheme benefits from an increased level of security through the use of asymmetric detectors. We apply this scheme to ...

Resource Allocation with Adaptive Spread Spectrum OFDM Using 2D Spreading for Power Line Communications

Science.gov (United States)

Baudais, Jean-Yves; Crussière, Matthieu

2007-12-01

Bit-loading techniques based on orthogonal frequency division mutiplexing (OFDM) are frequently used over wireline channels. In the power line context, channel state information can reasonably be obtained at both transmitter and receiver sides, and adaptive loading can advantageously be carried out. In this paper, we propose to apply loading principles to an spread spectrum OFDM (SS-OFDM) waveform which is a multicarrier system using 2D spreading in the time and frequency domains. The presented algorithm handles the subcarriers, spreading codes, bits and energies assignment in order to maximize the data rate and the range of the communication system. The optimization is realized at a target symbol error rate and under spectral mask constraint as usually imposed. The analytical study shows that the merging principle realized by the spreading code improves the rate and the range of the discrete multitone (DMT) system in single and multiuser contexts. Simulations have been run over measured power line communication (PLC) channel responses and highlight that the proposed system is all the more interesting than the received signal-to-noise ratio (SNR) is low.

HF band filter bank multi-carrier spread spectrum

Energy Technology Data Exchange (ETDEWEB)

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

2015-10-01

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. Simulation results using a wide band HF channel model demonstrate the robustness of this system over a wide range of delay and Doppler spreads.

Fault Detection of Aircraft Cable via Spread Spectrum Time Domain Reflectometry

Directory of Open Access Journals (Sweden)

Xudong SHI

2014-03-01

Full Text Available As the airplane cable fault detection based on TDR (time domain reflectometry is affected easily by various noise signals, which makes the reflected signal attenuate and distort heavily, failing to locate the fault. In order to solve these problems, a method of spread spectrum time domain reflectometry (SSTDR is introduced in this paper, taking the advantage of the sharp peak of correlation function. The test signal is generated from ML sequence (MLS modulated by sine wave in the same frequency. Theoretically, the test signal has the very high immunity of noise, which can be applied with excellent precision to fault location on the aircraft cable. In this paper, the method of SSTDR was normally simulated in MATLAB. Then, an experimental setup, based on LabVIEW, was organized to detect and locate the fault on the aircraft cable. It has been demonstrated that SSTDR has the high immunity of noise, reducing some detection errors effectively.

Resource Allocation with Adaptive Spread Spectrum OFDM Using 2D Spreading for Power Line Communications

Directory of Open Access Journals (Sweden)

Baudais Jean-Yves

2007-01-01

Full Text Available Bit-loading techniques based on orthogonal frequency division mutiplexing (OFDM are frequently used over wireline channels. In the power line context, channel state information can reasonably be obtained at both transmitter and receiver sides, and adaptive loading can advantageously be carried out. In this paper, we propose to apply loading principles to an spread spectrum OFDM (SS-OFDM waveform which is a multicarrier system using 2D spreading in the time and frequency domains. The presented algorithm handles the subcarriers, spreading codes, bits and energies assignment in order to maximize the data rate and the range of the communication system. The optimization is realized at a target symbol error rate and under spectral mask constraint as usually imposed. The analytical study shows that the merging principle realized by the spreading code improves the rate and the range of the discrete multitone (DMT system in single and multiuser contexts. Simulations have been run over measured power line communication (PLC channel responses and highlight that the proposed system is all the more interesting than the received signal-to-noise ratio (SNR is low.

Dielectric fluid directional spreading under the action of corona discharge

Science.gov (United States)

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.

Spreading Sequence System for Full Connectivity Relay Network

Science.gov (United States)

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

Wave directional spreading at shallow and intermediate depth

Digital Repository Service at National Institute of Oceanography (India)

SanilKumar, V.; Deo, M.C.; Anand, N.M.

. The spectrum computed from measured data shows that Scott spectrum approximates the observations in a fairly satisfactory way. A comparative study was carried out based on the directional spectrum estimated from Fourier coefficients and the model directional...

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

Science.gov (United States)

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.

Comparative study on spreading function for directional wave spectra

Digital Repository Service at National Institute of Oceanography (India)

Bhat, S.S.; Anand, N.M.; Nayak, B.U.

-dimensional wave energy S(f) and the directional spreading function D(f, theta). This paper reviews various spreading functions proposed in the past for estimating the directional wave energy and presents their application to the Indian wave condition. It is found...

Digital Watermarks Using Discrete Wavelet Transformation and Spectrum Spreading

Directory of Open Access Journals (Sweden)

Ryousuke Takai

2003-12-01

Full Text Available In recent tears, digital media makes rapid progress through the development of digital technology. Digital media normally assures fairly high quality, nevertheless can be easily reproduced in a perfect form. This perfect reproducibility takes and advantage from a certain point of view, while it produces an essential disadvantage, since digital media is frequently copied illegally. Thus the problem of the copyright protection becomes a very important issue. A solution of this problem is to embed digital watermarks that is not perceived clearly by usual people, but represents the proper right of original product. In our method, the images data in the frequency domain are transformed by the Discrete Wavelet Transform and analyzed by the multi resolution approximation, [1]. Further, the spectrum spreading is executed by using PN-sequences. Choi and Aizawa [7] embed watermarks by using block correlation of DCT coefficients. Thus, we apply Discrete Cosine Transformation, abbreviated to DCT, instead of the Fourier transformation in order to embed watermarks.If the value of this variance is high then we decide that the block has bigger magnitude for visual fluctuations. Henceforth, we may embed stronger watermarks, which gives resistance for images processing, such as attacks and/or compressions.

A Synchronisation Method For Informed Spread-Spectrum Audiowatermarking

Directory of Open Access Journals (Sweden)

Pierre-Yves Fulchiron

2003-12-01

Full Text Available Under perfect synchronisation conditions, watermarking schemes employing asymmetric spread-spectrum techniques are suitable for copy-protection of audio signals. This paper proposes to combine the use of a robust psychoacoustic projection for the extraction of a watermark feature vector along with non-linear detection functions optimised with side-information. The new proposed scheme benefits from an increased level of security through the use of asymmetric detectors. We apply this scheme to real audio signals and experimental results show an increased robustness to desynchronisation attacks such as random cropping.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Directionality and spread of shallow water waves along the eastern Arabian Sea

Digital Repository Service at National Institute of Oceanography (India)

SanilKumar, V.; Anoop, T.R.

, at http://www.cdc.noaa.gov/. 4 Results and discussions 4.1 Wave directional spreading For long-crested waves, the value of directional width is 0◦, and as the waves become short-crested, the value increases and the wave directional spreading increases...

PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

Directory of Open Access Journals (Sweden)

Sang Kyu Park

2005-03-01

Full Text Available An m-sequence (PN sequence preestimator scheme for direct-sequence spread spectrum (DS-SS signal acquisition by using block sequence estimation (BSE is proposed and analyzed. The proposed scheme consists of an estimator and a verifier which work according to the PN sequence chip clock, and provides not only the enhanced chip estimates with a threshold decision logic and one-chip error correction among the first m received chips, but also the reliability check of the estimates with additional decision logic. The probabilities of the estimator and verifier operations are calculated. With these results, the detection, the false alarm, and the missing probabilities of the proposed scheme are derived. In addition, using a signal flow graph, the average acquisition time is calculated. The proposed scheme can be used as a preestimator and easily implemented by changing the internal signal path of a generally used digital matched filter (DMF correlator or any other correlator that has a lot of sampling data memories for sampled PN sequence. The numerical results show rapid acquisition performance in a relatively good CNR.

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

Science.gov (United States)

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

Differential signaling spread-spectrum modulation of the LED visible light wireless communications using a mobile-phone camera

Science.gov (United States)

Chen, Shih-Hao; Chow, Chi-Wai

2015-02-01

Visible light communication (VLC) using spread spectrum modulation (SSM) and differential signaling (DS), detected by a mobile-phone camera is proposed and demonstrated for the first time to provide high immunity to background ambient light interference. The SSM signal provides the coding gain while the DS scheme enhances the clock recovery particular under high background ambient light. Experiment results confirm the feasibility of the proposed scheme, showing that the proposed system has 6-dB gain comparing with the traditional on-off keying (OOK) modulation under background ambient light of 3000 lux. The direct incident ambient light to the mobile-phone camera is 520 lux.

Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system.

Science.gov (United States)

Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

2007-02-01

We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

Source coherence impairments in a direct detection direct sequence optical code-division multiple-access system

Science.gov (United States)

Fsaifes, Ihsan; Lepers, Catherine; Lourdiane, Mounia; Gallion, Philippe; Beugin, Vincent; Guignard, Philippe

2007-02-01

We demonstrate that direct sequence optical code- division multiple-access (DS-OCDMA) encoders and decoders using sampled fiber Bragg gratings (S-FBGs) behave as multipath interferometers. In that case, chip pulses of the prime sequence codes generated by spreading in time-coherent data pulses can result from multiple reflections in the interferometers that can superimpose within a chip time duration. We show that the autocorrelation function has to be considered as the sum of complex amplitudes of the combined chip as the laser source coherence time is much greater than the integration time of the photodetector. To reduce the sensitivity of the DS-OCDMA system to the coherence time of the laser source, we analyze the use of sparse and nonperiodic quadratic congruence and extended quadratic congruence codes.

Spread Spectrum Based Energy Efficient Collaborative Communication in Wireless Sensor Networks.

Science.gov (United States)

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.

Well-spread sequences and edge-labellings with constant Hamilton-weight

Directory of Open Access Journals (Sweden)

P. Mark Kayll

2004-12-01

Full Text Available A sequence (a i of integers is well-spread if the sums a i +a j, for ispread sequence 0≤ a 1 <…

Directional spread parameter at intermediate water depth

Digital Repository Service at National Institute of Oceanography (India)

SanilKumar, V.; Deo, M.C.; Anand, N.M.; AshokKumar, K.

’ involves only the significant wave height, zero crossing wave period and water depth, the spreading function based on ‘s 3 ’ can be used for practical appli- cation. In the model based on ‘s 3 ’ the mean wave direction is an input and this has...-linearity parameter can be recommended for practical use as it provides an averaged distribution. Acknowledgements The authors would like to thank the Department of Science and Technology, New Delhi, for funding the project titled “Directional wave modelling...

CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

Directory of Open Access Journals (Sweden)

Charalambos Chrysostomou

2015-01-01

Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

Directional spectrum of ocean waves

Digital Repository Service at National Institute of Oceanography (India)

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

This paper describes a methodology for obtaining the directional spectrum of ocean waves from time series measurement of wave elevation at several gauges arranged in linear or polygonal arrays. Results of simulated studies using sinusoidal wave...

On the mass-spectrum relation for the main sequence stars

International Nuclear Information System (INIS)

Svechnikov, M.A.; Tajdakova, T.A.

1984-01-01

From 240 main-sequence stars with well-determined masses, a new mass-spectrum relation is obtained, which differs appreciably in certain intervals of spectral types from the mass-spectrum relations of Allen and Trimble. The accuracy of mass determination for the components of eclipsing binary systems of different types from their spectra given in the General Catalogue of Variable Stars (3rd edition) and in its supplements is evaluated

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

Science.gov (United States)

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

2000-09-01

.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.

Existing PON Infrastructure Supported Hybrid Fiber-Wireless Sensor Networks

DEFF Research Database (Denmark)

Yu, Xianbin; Zhao, Ying; Deng, Lei

2012-01-01

We propose a hybrid fiber wireless sensor network based on the existing PON infrastructure. The feasibility of remote sensing and PON convergence is experimentally proven by transmitting direct-sequence spread-spectrum wireless sensing and 2.5Gbps GPON signals.......We propose a hybrid fiber wireless sensor network based on the existing PON infrastructure. The feasibility of remote sensing and PON convergence is experimentally proven by transmitting direct-sequence spread-spectrum wireless sensing and 2.5Gbps GPON signals....

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

Science.gov (United States)

2014-03-27

1, then the product c(t − Td )c(t − T̂d) = 1 for optimum synchronization with Td = T̂d. For a synchronized signal, the correlator output is the...despread modulated signal (considering a random phase and delay Td .) Subsequently the signal is filtered in order to remove high frequency components and...wi + wM−i, wM/2 = wM/2, wi is the Hamming distance of bits assigned to symbol i and: Ai = F [ (2i + 1)π M ] − F [ (2i − 1)π M ] , (3.29) F(ψ

Iterative normalization technique for reference sequence generation for zero-tail discrete fourier transform spread orthogonal frequency division multiplexing

DEFF Research Database (Denmark)

2017-01-01

Systems, methods, apparatuses, and computer program products for generating sequences for zero-tail discrete fourier transform (DFT)-spread-orthogonal frequency division multiplexing (OFDM) (ZT DFT-s-OFDM) reference signals. One method includes adding a zero vector to an input sequence...... of each of the elements, converting the sequence to time domain, generating a zero-padded sequence by forcing a zero head and tail of the sequence, and repeating the steps until a final sequence with zero-tail and flat frequency response is obtained....

Direct, rapid RNA sequence analysis

International Nuclear Information System (INIS)

Peattie, D.A.

1987-01-01

The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks.

Directory of Open Access Journals (Sweden)

Gianluigi Rossi

2017-01-01

Full Text Available Animals' exchanges are considered the most effective route of between-farm infectious disease transmission. However, despite being often overlooked, the infection spread due to contaminated equipment, vehicles, or personnel proved to be important for several livestock epidemics. This study investigated the role of indirect contacts in a potential infection spread in the dairy farm network of the Province of Parma (Northern Italy. We built between-farm contact networks using data on cattle exchange (direct contacts, and on-farm visits by veterinarians (indirect contacts. We compared the features of the contact structures by using measures on static and temporal networks. We assessed the disease spreading potential of the direct and indirect network structures in the farm system by using data on the infection state of farms by paratuberculosis. Direct and indirect networks showed non-trivial differences with respect to connectivity, contact distribution, and super-spreaders identification. Furthermore, our analyses on paratuberculosis data suggested that the contributions of direct and indirect contacts on diseases spread are apparent at different spatial scales. Our results highlighted the potential role of indirect contacts in between-farm disease spread and underlined the need for a deeper understanding of these contacts to develop better strategies for prevention of livestock epidemics.

Different behaviors of epidemic spreading in scale-free networks with identical degree sequence

Energy Technology Data Exchange (ETDEWEB)

Chu Xiangwei; Guan Jihong [School of Electronics and Information, Tongji University, 4800 Cao' an Road, Shanghai 201804 (China); Zhang Zhongzhi; Zhou Shuigeng [School of Computer Science, Fudan University, Shanghai 200433 (China); Li Mo, E-mail: zhangzz@fudan.edu.c, E-mail: jhguan@tongj.edu.c, E-mail: sgzhou@fudan.edu.c [Software School, Fudan University, Shanghai 200433 (China)

2010-02-12

Recently, the study of dynamical behaviors of the susceptible-infected (SI) disease model in complex networks, especially in Barabasi-Albert (BA) scale-free networks, has attracted much attention. Although some interesting phenomena have been observed, the formative reasons for those particular dynamical behaviors are still not well understood, despite the speculation that topological properties (for example the degree distribution) have a strong impact on epidemic spreading. In this paper, we study the evolution behaviors of epidemic spreading on a class of scale-free networks sharing identical degree sequence, and observe significantly different evolution behaviors in the whole family of networks. We show that the power-law degree distribution does not suffice to characterize the dynamical behaviors of disease diffusion on scale-free networks.

Different behaviors of epidemic spreading in scale-free networks with identical degree sequence

International Nuclear Information System (INIS)

Chu Xiangwei; Guan Jihong; Zhang Zhongzhi; Zhou Shuigeng; Li Mo

2010-01-01

Recently, the study of dynamical behaviors of the susceptible-infected (SI) disease model in complex networks, especially in Barabasi-Albert (BA) scale-free networks, has attracted much attention. Although some interesting phenomena have been observed, the formative reasons for those particular dynamical behaviors are still not well understood, despite the speculation that topological properties (for example the degree distribution) have a strong impact on epidemic spreading. In this paper, we study the evolution behaviors of epidemic spreading on a class of scale-free networks sharing identical degree sequence, and observe significantly different evolution behaviors in the whole family of networks. We show that the power-law degree distribution does not suffice to characterize the dynamical behaviors of disease diffusion on scale-free networks.

Variation of wave directional spread parameters along the Indian coast

Digital Repository Service at National Institute of Oceanography (India)

SanilKumar, V.

through a directional wave spectrum, which represents distribution of wave energies over various wave frequencies and directions. Most widely practiced technique for directional data collection involves use of the floating buoys. The data analysis.... Estimation of directional spectra from the maximum entropy principle, Proceedings 5th International Conference on Offshore Mechanics and Arctic Engineering, Tokyo, Japan 1986; vol. I: 80-85. [6] Kuik AJ, Vledder G, Holthuijsen LH. A method for the routine...

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

Science.gov (United States)

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.

Pre-main sequence masses and the age spread in the Orion cluster

International Nuclear Information System (INIS)

McNamara, B.J.

1975-01-01

The spread in formation times for stars earlier than GO in the Orion cluster is investigated. The range of stellar ages in this cluster is found to extend from at least 10 6 years to about 10 7 years. On the basis of this evidence and the similarity of the color--magnitude diagrams of other young clusters to the Orion cluster, it is suggested that the current method of dating these clusters (from the point at which the most massive stars just reach the zero-age main sequence) might not be valid. The masses of forty-one pre-main sequence stars within the ranges 4.05 less than or equal to log(Te) less than or equal to 3.77 and 0.6 less than or equal to log (L/L/sub sun/) less than or equal to 2.1 are determined from observed effective temperatures, luminosities, and gravities. These masses were then compared with those expected from Iben's (1965) pre-main sequence evolutionary calculations. In most cases, the agreement between these values was found to be within the observational errors. Finally, the pre-main sequence stars possessing infrared excesses are found to be apparently among the most massive and youngest stars still contracting toward the zero-age main sequence

Direct RNA-based detection and differentiation of CTX-M-type extended-spectrum β-lactamases (ESBL.

Directory of Open Access Journals (Sweden)

Claudia Stein

Full Text Available 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.

Three-item Direct Observation Screen (TIDOS) for autism spectrum disorder.

Science.gov (United States)

Oner, Pinar; Oner, Ozgur; Munir, Kerim

2014-08-01

We compared ratings on the Three-Item Direct Observation Screen test for autism spectrum disorders completed by pediatric residents with the Social Communication Questionnaire parent reports as an augmentative tool for improving autism spectrum disorder screening performance. We examined three groups of children (18-60 months) comparable in age (18-24 month, 24-36 month, 36-60 preschool subgroups) and gender distribution: n = 86 with Diagnostic and Statistical Manual of Mental Disorders (4th ed., text rev.) autism spectrum disorders; n = 76 with developmental delay without autism spectrum disorders; and n = 97 with typical development. The Three-Item Direct Observation Screen test included the following (a) Joint Attention, (b) Eye Contact, and (c) Responsiveness to Name. The parent Social Communication Questionnaire ratings had a sensitivity of .73 and specificity of .70 for diagnosis of autism spectrum disorders. The Three-Item Direct Observation Screen test item Joint Attention had a sensitivity of .82 and specificity of .90, Eye Contact had a sensitivity of .89 and specificity of .91, and Responsiveness to Name had a sensitivity of .67 and specificity of .87. In the Three-Item Direct Observation Screen test, having at least one of the three items positive had a sensitivity of .95 and specificity of .85. Age, diagnosis of autism spectrum disorder, and developmental level were important factors affecting sensitivity and specificity. The results indicate that augmentation of autism spectrum disorder screening by observational items completed by trained pediatric-oriented professionals can be a highly effective tool in improving screening performance. If supported by future population studies, the results suggest that primary care practitioners will be able to be trained to use this direct procedure to augment screening for autism spectrum disorders in the community. © The Author(s) 2013.

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

NARCIS (Netherlands)

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

2017-01-01

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information,

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

DEFF Research Database (Denmark)

Taylor, Jenny C; Martin, Hilary C; Lise, Stefano

2015-01-01

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the numb...

抑制扩频系统中窄带干扰的新卡尔曼滤波算法%New Kalman Filtering Algorithm for Narrowband Interference Suppression in Spread Spectrum Systems

Institute of Scientific and Technical Information of China (English)

许光辉; 胡光锐

2005-01-01

A new Kalman filtering algorithm based on estimation of spread spectrum signal before suppression of narrowband interference (NBI) in spread spectrum systems, using the dependence of autoregressive (AR) interference, is presented compared with performance of the ACM nonlinear filtering algorithm, simulation results show that the proposed algorithm has preferable performance, there is about 5 dB SNR improvement in average.

Program Aplikasi Steganografi Menggunakan Metode Spread Spectrum pada Perangkat Mobile Berbasis Android

Directory of Open Access Journals (Sweden)

Rojali Rojali

2012-12-01

Full Text Available The exchange of traffic information in cyberspace grows fast. In all areas of life utilize technology to exchange information. One of the media owned by many people is mobile device such as mobile phone and tablet computer. In fact many people have been using mobile devices for information exchange function, and expect information to be transmitted quickly, accurately, and safely. The information security sent will be very important when the information is confidential. One way to secure information sent is the concealment of information into a media so that information hidden is beyond recognition by the human senses, which iscommonly referred to steganography. This research studied and implemented steganography using spread spectrum Method on Android-based mobile devices. The results showed that the inserted image before and after the message was inserted is not different with PSNR value of about 75.

Spreading Sequence Design for Multiple Cell Synchronous DS-CDMA Systems under Total Weighted Squared Correlation Criterion

Directory of Open Access Journals (Sweden)

Cotae Paul

2004-01-01

Full Text Available An algorithm for designing spreading sequences for an overloaded multicellular synchronous DS-CDMA system on uplink is introduced. The criterion used to measure the optimality of the design is the total weighted square correlation (TWSC assuming the channel state information known perfectly at both transmitter and receiver. By using this algorithm it is possible to obtain orthogonal generalized WBE sequences sets for any processing gain. The bandwidth of initial generalized WBE signals of each cell is preserved in the extended signal space associated to multicellular system. Mathematical formalism is illustrated by selected numerical examples.

Goal-directed action control in children with autism spectrum disorders

NARCIS (Netherlands)

Geurts, H.M.; de Wit, S.

2014-01-01

Repetitive behavior is a key characteristic of autism spectrum disorders. Our aim was to investigate the hypothesis that this abnormal behavioral repetition results from a tendency to over-rely on habits at the expense of flexible, goal-directed action. Twenty-four children with autism spectrum

Spread F bubbles - Nonlinear Rayleigh-Taylor mode in two dimensions

Science.gov (United States)

Hudson, M. K.

1978-01-01

The paper discusses long-wavelength developed bottomside spread F which has been attributed to the Rayleigh-Taylor instability. The nonlinear saturation amplitude and the k spectrum of the inertia-dominated Rayleigh-Taylor instability is found in two directions: east-west and vertical. As in the collisional case (Chaturvedi and Ossakow, 1977), the dominant nonlinearity is found to be two-dimensional. It is found that the linearly most unstable modes, which are primarily horizontal, saturate by the nonlinear generation of vertical spatial harmonics. The harmonics are damped by diffusion or recombination. The resulting amplitude spectrum indicates that bubbles are vertically elongated in both inertial and collisional regimes.

A New Images Hiding Scheme Based on Chaotic Sequences

Institute of Scientific and Technical Information of China (English)

LIU Nian-sheng; GUO Dong-hui; WU Bo-xi; Parr G

2005-01-01

We propose a data hidding technique in a still image. This technique is based on chaotic sequence in the transform domain of covert image. We use different chaotic random sequences multiplied by multiple sensitive images, respectively, to spread the spectrum of sensitive images. Multiple sensitive images are hidden in a covert image as a form of noise. The results of theoretical analysis and computer simulation show the new hiding technique have better properties with high security, imperceptibility and capacity for hidden information in comparison with the conventional scheme such as LSB (Least Significance Bit).

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

OpenAIRE

Taylor, Jenny C; Martin, Hilary C; Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A. Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David

2015-01-01

To assess factors influencing the success of whole genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases across a broad spectrum of disorders in whom prior screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritisation. We found that jointly calling variants across samples, filtering against both local and e...

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

Directory of Open Access Journals (Sweden)

Julia Neitzel

2018-01-01

Full Text Available 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.

Goal-Directed Action Control in Children with Autism Spectrum Disorders

Science.gov (United States)

Geurts, Hilde M; de Wit, Sanne

2014-01-01

Repetitive behavior is a key characteristic of autism spectrum disorders. Our aim was to investigate the hypothesis that this abnormal behavioral repetition results from a tendency to over-rely on habits at the expense of flexible, goal-directed action. Twenty-four children with autism spectrum disorders and 24 age- and gender-matched controls…

Epidemic spreading in annealed directed networks: susceptible-infected-susceptible model and contact process.

Science.gov (United States)

Kwon, Sungchul; Kim, Yup

2013-01-01

We investigate epidemic spreading in annealed directed scale-free networks with the in-degree (k) distribution P(in)(k)~k(-γ(in)) and the out-degree (ℓ) distribution, P(out)(ℓ)~ℓ(-γ(out)). The correlation of each node on the networks is controlled by the probability r(0≤r≤1) in two different algorithms, the so-called k and ℓ algorithms. For r=1, the k algorithm gives =, whereas the ℓ algorithm gives =. For r=0, = for both algorithms. As the prototype of epidemic spreading, the susceptible-infected-susceptible model and contact process on the networks are analyzed using the heterogeneous mean-field theory and Monte Carlo simulations. The directedness of links and the correlation of the network are found to play important roles in the spreading, so that critical behaviors of both models are distinct from those on undirected scale-free networks.

Demonstration of DFT-spread 256QAM-OFDM signal transmission with cost-effective directly modulated laser.

Science.gov (United States)

Li, Fan; Yu, Jianjun; Fang, Yuan; Dong, Ze; Li, Xinying; Chen, Lin

2014-04-07

We experimentally demonstrated a 256-ary quadrature amplitude modulation (256QAM) direct-detection optical orthogonal frequency division multiplexing (DDO-OFDM) transmission system utilizing a cost-effective directly modulated laser (DML). Intra-symbol frequency-domain averaging (ISFA) is applied to suppress in-band noise while the channel response estimation and Discrete Fourier Transform-spread (DFT-spread) is used to reduce the peak-to-average power ratio (PAPR) of the transmitted OFDM signal. The bit-error ratio (BER) of 15-Gbit/s 256QAM-OFDM signal has been measured after 20-km SSMF transmission that is less than 7% forward-error-correction (FEC) threshold of 3.8 × 10(-3) as the launch power into fiber is set at 6dBm. For 11.85-Gbit/s 256QAM-OFDM signal, with the aid of ISFA-based channel estimation and PAPR reduction enabled by DFT-spread, the BER after 20-km SSMF transmission can be improved from 6.4 × 10(-3) to 6.8 × 10(-4) when the received optical power is -6dBm.

Spread spectrum image data hiding in the encrypted discrete cosine transform coefficients

Science.gov (United States)

Zhang, Xiaoqiang; Wang, Z. Jane

2013-10-01

Digital watermarking and data hiding are important tools for digital rights protection of media data. Spread spectrum (SS)-based watermarking and data-hiding approaches are popular due to their outstanding robustness, but their security might not be sufficient. To improve the security of SS, a SS-based image data-hiding approach is proposed by encrypting the discrete cosine transform coefficients of the host image with the piecewise linear chaotic map, before the operation of watermark embedding. To evaluate the performance of the proposed approach, simulations and analyses of its robustness and security are carried out. The average bit-error-rate values on 100 real images from the Berkeley segmentation dataset under the JPEG compression, additive Gaussian noise, salt and pepper noise, and cropping attacks are reported. Experimental results show that the proposed approach can maintain the high robustness of traditional SS schemes and, meanwhile, also improve the security. The proposed approach can extend the key space of traditional SS schemes from 10 to 10 and thus can resist brute-force attack and unauthorized detection watermark attack.

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

Directory of Open Access Journals (Sweden)

Sergio I Nemirovsky

Full Text Available 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.

Spreading convulsions, spreading depolarization and epileptogenesis in human cerebral cortex

DEFF Research Database (Denmark)

Dreier, Jens P; Major, Sebastian; Pannek, Heinz-Wolfgang

2012-01-01

Spreading depolarization of cells in cerebral grey matter is characterized by massive ion translocation, neuronal swelling and large changes in direct current-coupled voltage recording. The near-complete sustained depolarization above the inactivation threshold for action potential generating...... stimulations. Eventually, epileptic field potentials were recorded during the period that had originally seen spreading depression of activity. Such spreading convulsions are characterized by epileptic field potentials on the final shoulder of the large slow potential change of spreading depolarization. We...

Double random phase spread spectrum spread space technique for secure parallel optical multiplexing with individual encryption key

Science.gov (United States)

Hennelly, B. M.; Javidi, B.; Sheridan, J. T.

2005-09-01

A number of methods have been recently proposed in the literature for the encryption of 2-D information using linear optical systems. In particular the double random phase encoding system has received widespread attention. This system uses two Random Phase Keys (RPK) positioned in the input spatial domain and the spatial frequency domain and if these random phases are described by statistically independent white noises then the encrypted image can be shown to be a white noise. Decryption only requires knowledge of the RPK in the frequency domain. The RPK may be implemented using a Spatial Light Modulators (SLM). In this paper we propose and investigate the use of SLMs for secure optical multiplexing. We show that in this case it is possible to encrypt multiple images in parallel and multiplex them for transmission or storage. The signal energy is effectively spread in the spatial frequency domain. As expected the number of images that can be multiplexed together and recovered without loss is proportional to the ratio of the input image and the SLM resolution. Many more images may be multiplexed with some loss in recovery. Furthermore each individual encryption is more robust than traditional double random phase encoding since decryption requires knowledge of both RPK and a lowpass filter in order to despread the spectrum and decrypt the image. Numerical simulations are presented and discussed.

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

Science.gov (United States)

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.

Spreading depolarizations have prolonged direct current shifts and are associated with poor outcome in brain trauma

DEFF Research Database (Denmark)

Hartings, Jed A; Watanabe, Tomas; Bullock, M Ross

2011-01-01

, although prolonged events have not been observed in animal models. To determine whether detrimental penumbral-type depolarizations occur in human brain trauma, we analysed electrocorticographic recordings obtained by subdural electrode-strip monitoring during intensive care. Of 53 patients studied, 10......Cortical spreading depolarizations occur spontaneously after ischaemic, haemorrhagic and traumatic brain injury. Their effects vary spatially and temporally as graded phenomena, from infarction to complete recovery, and are reflected in the duration of depolarization measured by the negative direct...... current shift of electrocorticographic recordings. In the focal ischaemic penumbra, peri-infarct depolarizations have prolonged direct current shifts and cause progressive recruitment of the penumbra into the core infarct. In traumatic brain injury, the effects of spreading depolarizations are unknown...

Cardiac tumors: optimal cardiac MR sequences and spectrum of imaging appearances.

LENUS (Irish Health Repository)

O'Donnell, David H

2012-02-01

OBJECTIVE: This article reviews the optimal cardiac MRI sequences for and the spectrum of imaging appearances of cardiac tumors. CONCLUSION: Recent technologic advances in cardiac MRI have resulted in the rapid acquisition of images of the heart with high spatial and temporal resolution and excellent myocardial tissue characterization. Cardiac MRI provides optimal assessment of the location, functional characteristics, and soft-tissue features of cardiac tumors, allowing accurate differentiation of benign and malignant lesions.

Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins.

Science.gov (United States)

Gupta, Radhey S

2012-11-01

The origin of photosynthesis and how this capability has spread to other bacterial phyla remain important unresolved questions. I describe here a number of conserved signature indels (CSIs) in key proteins involved in bacteriochlorophyll (Bchl) biosynthesis that provide important insights in these regards. The proteins BchL and BchX, which are essential for Bchl biosynthesis, are derived by gene duplication in a common ancestor of all phototrophs. More ancient gene duplication gave rise to the BchX-BchL proteins and the NifH protein of the nitrogenase complex. The sequence alignment of NifH-BchX-BchL proteins contain two CSIs that are uniquely shared by all NifH and BchX homologs, but not by any BchL homologs. These CSIs and phylogenetic analysis of NifH-BchX-BchL protein sequences strongly suggest that the BchX homologs are ancestral to BchL and that the Bchl-based anoxygenic photosynthesis originated prior to the chlorophyll (Chl)-based photosynthesis in cyanobacteria. Another CSI in the BchX-BchL sequence alignment that is uniquely shared by all BchX homologs and the BchL sequences from Heliobacteriaceae, but absent in all other BchL homologs, suggests that the BchL homologs from Heliobacteriaceae are primitive in comparison to all other photosynthetic lineages. Several other identified CSIs in the BchN homologs are commonly shared by all proteobacterial homologs and a clade consisting of the marine unicellular Cyanobacteria (Clade C). These CSIs in conjunction with the results of phylogenetic analyses and pair-wise sequence similarity on the BchL, BchN, and BchB proteins, where the homologs from Clade C Cyanobacteria and Proteobacteria exhibited close relationship, provide strong evidence that these two groups have incurred lateral gene transfers. Additionally, phylogenetic analyses and several CSIs in the BchL-N-B proteins that are uniquely shared by all Chlorobi and Chloroflexi homologs provide evidence that the genes for these proteins have also been

Semi-Blind Error Resilient SLM for PAPR Reduction in OFDM Using Spread Spectrum Codes

Science.gov (United States)

Elhelw, Amr M.; Badran, Ehab F.

2015-01-01

High peak to average power ratio (PAPR) is one of the major problems of OFDM systems. Selected mapping (SLM) is a promising choice that can elegantly tackle this problem. Nevertheless, side information (SI) index is required to be transmitted which reduces the overall throughput. This paper proposes a semi-blind error resilient SLM system that utilizes spread spectrum codes for embedding the SI index in the transmitted symbols. The codes are embedded in an innovative manner which does not increase the average energy per symbol. The use of such codes allows the correction of probable errors in the SI index detection. A new receiver, which does not require perfect channel state information (CSI) for the detection of the SI index and has relatively low computational complexity, is proposed. Simulations results show that the proposed system performs well both in terms SI index detection error and bit error rate. PMID:26018504

Semi-Blind Error Resilient SLM for PAPR Reduction in OFDM Using Spread Spectrum Codes.

Directory of Open Access Journals (Sweden)

Amr M Elhelw

Full Text Available High peak to average power ratio (PAPR is one of the major problems of OFDM systems. Selected mapping (SLM is a promising choice that can elegantly tackle this problem. Nevertheless, side information (SI index is required to be transmitted which reduces the overall throughput. This paper proposes a semi-blind error resilient SLM system that utilizes spread spectrum codes for embedding the SI index in the transmitted symbols. The codes are embedded in an innovative manner which does not increase the average energy per symbol. The use of such codes allows the correction of probable errors in the SI index detection. A new receiver, which does not require perfect channel state information (CSI for the detection of the SI index and has relatively low computational complexity, is proposed. Simulations results show that the proposed system performs well both in terms SI index detection error and bit error rate.

Directional wave spectra off southeast coast of Tamil Nadu

Digital Repository Service at National Institute of Oceanography (India)

SanilKumar, V.; Deo, M.C.; Anand, N.M.; Gowthaman, R.

directional spreading. A well established way to describe the energy content in an irregular wind generated surface wave assumes superposition of linear waves and the two dimensional energy spectrum can be conveniently expressed as a product of the one...

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

Science.gov (United States)

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…

Collateral damage: Spread of repeat-induced point mutation from a ...

Indian Academy of Sciences (India)

Unknown

of the erg-3 gene, present in single copy, to the spread of RIP from duplications of adjoining sequences. Ge- ... RIP can spread across as much as 1 kb of unduplicated DNA. ... sequences that are > 500 bp and share > 80% similarity.

Three-item Direct Observation Screen (TIDOS) for autism spectrum disorder

OpenAIRE

Oner, Pinar; Oner, Ozgur; Munir, Kerim

2013-01-01

We compared ratings on the Three-Item Direct Observation Screen test for autism spectrum disorders completed by pediatric residents with the Social Communication Questionnaire parent reports as an augmentative tool for improving autism spectrum disorder screening performance. We examined three groups of children (18–60 months) comparable in age (18–24 month, 24–36 month, 36–60 preschool subgroups) and gender distribution: n = 86 with Diagnostic and Statistical Manual of Mental Disorders (4th ...

Optimizing Hybrid Spreading in Metapopulations.

OpenAIRE

Zhang, C.; Zhou, S.; Miller, J. C.; Cox, I. J.; Chain, B. M.

2015-01-01

Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemic...

Optimizing Hybrid Spreading in Metapopulations

OpenAIRE

Zhang, Changwang; Zhou, Shi; Miller, Joel C.; Cox, Ingemar J.; Chain, Benjamin M.

2014-01-01

Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemic...

Combinatorics of spreads and parallelisms

CERN Document Server

Johnson, Norman

2010-01-01

Partitions of Vector Spaces Quasi-Subgeometry Partitions Finite Focal-SpreadsGeneralizing André SpreadsThe Going Up Construction for Focal-SpreadsSubgeometry Partitions Subgeometry and Quasi-Subgeometry Partitions Subgeometries from Focal-SpreadsExtended André SubgeometriesKantor's Flag-Transitive DesignsMaximal Additive Partial SpreadsSubplane Covered Nets and Baer Groups Partial Desarguesian t-Parallelisms Direct Products of Affine PlanesJha-Johnson SL(2,

Tracking Small Satellites using Translated GPS

OpenAIRE

Lefevre, Don; Mulally, Daniel

1991-01-01

This paper discusses using translated GPS for tracking small satellites, the technical trade-offs involved, and the position and timing accuracies which are achievable using translated GPS. The Global Positioning System (GPS) uses the relative times-of-arrival of multiple spread-spectrum signals at an antenna to determine the position of the antenna. The system can also determine the time the antenna was at that position. The direct sequence spread spectrum signals are transmitted from GPS sa...

Energy efficiency in wireless communication systems

Science.gov (United States)

Caffrey, Michael Paul; Palmer, Joseph McRae

2012-12-11

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

Estimations of On-site Directional Wave Spectra from Measured Ship Responses

DEFF Research Database (Denmark)

Nielsen, Ulrik Dam

2006-01-01

include an quivalence of energy in the governing equations and, as regards the parametric concept, a frequency dependent spreading of the waves is introduced. The paper includes an extensive analysis of full-scale measurements for which the directional wave spectra are estimated by the two ship response......In general, two main concepts can be applied to estimate the on-site directional wave spectrum on the basis of ship response measurements: 1) a parametric method which assumes the wave spectrum to be composed by parameterised wave spectra, or 2) a non-parametric method where the directional wave...

How Is Mono Spread?

Science.gov (United States)

... 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 ...

Fidelity and Mutational Spectrum of Pfu DNA Polymerase on a Human Mitochondrial DNA Sequence

Science.gov (United States)

André, Paulo; Kim, Andrea; Khrapko, Konstantin; Thilly, William G.

1997-01-01

The study of rare genetic changes in human tissues requires specialized techniques. Point mutations at fractions at or below 10−6 must be observed to discover even the most prominent features of the point mutational spectrum. PCR permits the increase in number of mutant copies but does so at the expense of creating many additional mutations or “PCR noise”. Thus, each DNA sequence studied must be characterized with regard to the DNA polymerase and conditions used to avoid interpreting a PCR-generated mutation as one arising in human tissue. The thermostable DNA polymerase derived from Pyrococcus furiosus designated Pfu has the highest fidelity of any DNA thermostable polymerase studied to date, and this property recommends it for analyses of tissue mutational spectra. Here, we apply constant denaturant capillary electrophoresis (CDCE) to separate and isolate the products of DNA amplification. This new strategy permitted direct enumeration and identification of point mutations created by Pfu DNA polymerase in a 96-bp low melting domain of a human mitochondrial sequence despite the very low mutant fractions generated in the PCR process. This sequence, containing part of the tRNA glycine and NADH dehydrogenase subunit 3 genes, is the target of our studies of mitochondrial mutagenesis in human cells and tissues. Incorrectly synthesized sequences were separated from the wild type as mutant/wild-type heteroduplexes by sequential enrichment on CDCE. An artificially constructed mutant was used as an internal standard to permit calculation of the mutant fraction. Our study found that the average error rate (mutations per base pair duplication) of Pfu was 6.5 × 10−7, and five of its more frequent mutations (hot spots) consisted of three transversions (GC → TA, AT → TA, and AT → CG), one transition (AT → GC), and one 1-bp deletion (in an AAAAAA sequence). To achieve an even higher sensitivity, the amount of Pfu-induced mutants must be

Fidelity and mutational spectrum of Pfu DNA polymerase on a human mitochondrial DNA sequence.

Science.gov (United States)

André, P; Kim, A; Khrapko, K; Thilly, W G

1997-08-01

The study of rare genetic changes in human tissues requires specialized techniques. Point mutations at fractions at or below 10(-6) must be observed to discover even the most prominent features of the point mutational spectrum. PCR permits the increase in number of mutant copies but does so at the expense of creating many additional mutations or "PCR noise". Thus, each DNA sequence studied must be characterized with regard to the DNA polymerase and conditions used to avoid interpreting a PCR-generated mutation as one arising in human tissue. The thermostable DNA polymerase derived from Pyrococcus furiosus designated Pfu has the highest fidelity of any DNA thermostable polymerase studied to date, and this property recommends it for analyses of tissue mutational spectra. Here, we apply constant denaturant capillary electrophoresis (CDCE) to separate and isolate the products of DNA amplification. This new strategy permitted direct enumeration and identification of point mutations created by Pfu DNA polymerase in a 96-bp low melting domain of a human mitochondrial sequence despite the very low mutant fractions generated in the PCR process. This sequence, containing part of the tRNA glycine and NADH dehydrogenase subunit 3 genes, is the target of our studies of mitochondrial mutagenesis in human cells and tissues. Incorrectly synthesized sequences were separated from the wild type as mutant/wild-type heteroduplexes by sequential enrichment on CDCE. An artificially constructed mutant was used as an internal standard to permit calculation of the mutant fraction. Our study found that the average error rate (mutations per base pair duplication) of Pfu was 6.5 x 10(-7), and five of its more frequent mutations (hot spots) consisted of three transversions (GC-->TA, AT-->TA, and AT-->CG), one transition (AT-->GC), and one 1-bp deletion (in an AAAAAA sequence). To achieve an even higher sensitivity, the amount of Pfu-induced mutants must be reduced.

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

Directory of Open Access Journals (Sweden)

Marta Brozynska

Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

Linear theory of equatorial spread F

International Nuclear Information System (INIS)

Hudson, M.K.; Kennel, C.F.

1975-01-01

A fluid dispersion relation for the drift and interchange (Rayleigh-Taylor) modes in a collisional plasma forms the basis for a linear theory of equatorial spread F. The collisional drift mode growth rate will exceed the growth rate of the Rayleigh-Taylor mode at short perpendicular wavelengths and density gradient scale lengths, and the drift mode can grow on top side as well as on bottom side density gradients. However, below the F peak, where spread F predominates, it is concluded that both the drift and the Rayleigh-Taylor modes contribute to the total spread F spectrum, the Rayleigh-Taylor mode dominating at long and the drift mode at short perpendicular wavelengths above the ion Larmor radius

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

Science.gov (United States)

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

2015-01-01

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

Optimizing hybrid spreading in metapopulations.

Science.gov (United States)

Zhang, Changwang; Zhou, Shi; Miller, Joel C; Cox, Ingemar J; Chain, Benjamin M

2015-04-29

Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by local spreading, where infected nodes can only infect a limited set of direct target nodes and global spreading, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemics, and examine the optimum balance between spreading mechanisms in terms of achieving the maximum outbreak size. We show the existence of critically hybrid epidemics where neither spreading mechanism alone can cause a noticeable spread but a combination of the two spreading mechanisms would produce an enormous outbreak. Our results provide new strategies for maximising beneficial epidemics and estimating the worst outcome of damaging hybrid epidemics.

(D,A)∞-modules over (D,A)∞-algebras and spectral sequences

International Nuclear Information System (INIS)

Lapin, S V

2002-01-01

We introduce the construction of a (D,A) ∞ -(co)module over a (D,A) ∞ -(co) algebra and study its main homotopy properties. We establish a connection between (D,A) ∞ -(co)modules over (D,A) ∞ -(co)algebras and spectral sequences, and thus obtain the structure of an A ∞ -comodule over the Milnor A ∞ -coalgebra on the homology of any spectrum directly from the differentials of the Adams spectral sequence of this spectrum

Consistency of the directionality of partially coherent beams in turbulence expressed in terms of the angular spread and the far-field average intensity

International Nuclear Information System (INIS)

Xiao-Wen, Chen; Xiao-Ling, Ji

2010-01-01

Under the quadratic approximation of the Rytov's phase structure function, this paper derives the general closed-form expressions for the mean-squared width and the angular spread of partially coherent beams in turbulence. It finds that under a certain condition different types of partially coherent beams may have the same directionality as a fully coherent Gaussian beam in free space and also in atmospheric turbulence if the angular spread is chosen as the characteristic parameter of beam directionality. On the other hand, it shows that generally, the directionality of partially coherent beams expressed in terms of the angular spread is not consistent with that in terms of the normalized far-field average intensity distribution in free space, but the consistency can be achieved due to turbulence. (classical areas of phenomenology)

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

Science.gov (United States)

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…

Constructing and sampling directed graphs with given degree sequences

International Nuclear Information System (INIS)

Kim, H; Del Genio, C I; Bassler, K E; Toroczkai, Z

2012-01-01

The interactions between the components of complex networks are often directed. Proper modeling of such systems frequently requires the construction of ensembles of digraphs with a given sequence of in- and out-degrees. As the number of simple labeled graphs with a given degree sequence is typically very large even for short sequences, sampling methods are needed for statistical studies. Currently, there are two main classes of methods that generate samples. One of the existing methods first generates a restricted class of graphs and then uses a Markov chain Monte-Carlo algorithm based on edge swaps to generate other realizations. As the mixing time of this process is still unknown, the independence of the samples is not well controlled. The other class of methods is based on the configuration model that may lead to unacceptably many sample rejections due to self-loops and multiple edges. Here we present an algorithm that can directly construct all possible realizations of a given bi-degree sequence by simple digraphs. Our method is rejection-free, guarantees the independence of the constructed samples and provides their weight. The weights can then be used to compute statistical averages of network observables as if they were obtained from uniformly distributed sampling or from any other chosen distribution. (paper)

Direct chromosome-length haplotyping by single-cell sequencing

NARCIS (Netherlands)

Porubský, David; Sanders, Ashley D; van Wietmarschen, Niek; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Bevova, Marianna R; Guryev, Victor; Lansdorp, Peter Michael

Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid

Does Gaze Direction Modulate Facial Expression Processing in Children with Autism Spectrum Disorder?

Science.gov (United States)

Akechi, Hironori; Senju, Atsushi; Kikuchi, Yukiko; Tojo, Yoshikuni; Osanai, Hiroo; Hasegawa, Toshikazu

2009-01-01

Two experiments investigated whether children with autism spectrum disorder (ASD) integrate relevant communicative signals, such as gaze direction, when decoding a facial expression. In Experiment 1, typically developing children (9-14 years old; n = 14) were faster at detecting a facial expression accompanying a gaze direction with a congruent…

Analysis of wave directional spreading using neural networks

Digital Repository Service at National Institute of Oceanography (India)

Deo, M.C.; Gondane, D.S.; SanilKumar, V.

describes how a representative spreading parameter could be arrived at from easily available wave parameters such as significant wave height and average zero-cross wave period, using the technique of neural networks. It is shown that training of the network...

Energy spectrum control for modulated proton beams

International Nuclear Information System (INIS)

Hsi, Wen C.; Moyers, Michael F.; Nichiporov, Dmitri; Anferov, Vladimir; Wolanski, Mark; Allgower, Chris E.; Farr, Jonathan B.; Mascia, Anthony E.; Schreuder, Andries N.

2009-01-01

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.

Hybrid PAPR reduction scheme with Huffman coding and DFT-spread technique for direct-detection optical OFDM systems

Science.gov (United States)

Peng, Miao; Chen, Ming; Zhou, Hui; Wan, Qiuzhen; Jiang, LeYong; Yang, Lin; Zheng, Zhiwei; Chen, Lin

2018-01-01

High peak-to-average power ratio (PAPR) of the transmit signal is a major drawback in optical orthogonal frequency division multiplexing (OOFDM) system. In this paper, we propose and experimentally demonstrate a novel hybrid scheme, combined the Huffman coding and Discrete Fourier Transmission-Spread (DFT-spread), in order to reduce high PAPR in a 16-QAM short-reach intensity-modulated and direct-detection OOFDM (IMDD-OOFDM) system. The experimental results demonstrated that the hybrid scheme can reduce the PAPR by about 1.5, 2, 3 and 6 dB, and achieve 1.5, 1, 2.5 and 3 dB receiver sensitivity improvement compared to clipping, DFT-spread and Huffman coding and original OFDM signals, respectively, at an error vector magnitude (EVM) of -10 dB after transmission over 20 km standard single-mode fiber (SSMF). Furthermore, the throughput gain can be of the order of 30% by using the hybrid scheme compared with the cases of without applying the Huffman coding.

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

Directory of Open Access Journals (Sweden)

Natalia A Kuzmina

Full Text Available 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.

Ultra-fast evaluation of protein energies directly from sequence.

Directory of Open Access Journals (Sweden)

Gevorg Grigoryan

2006-06-01

Full Text Available The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7 compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0. Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages

Directed PCR-free engineering of highly repetitive DNA sequences

Directory of Open Access Journals (Sweden)

Preissler Steffen

2011-09-01

Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Samuele E Burastero

Full Text Available 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.

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

Science.gov (United States)

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.

Spread Spectrum Modulation by Using Asymmetric-Carrier Random PWM

DEFF Research Database (Denmark)

Mathe, Laszlo; Lungeanu, Florin; Sera, Dezso

2012-01-01

is very effective and is independent from the modulation index. The flat motor current spectrum generates an acoustical noise close to the white noise, which improves the acoustical performance of the drive. The new carrier wave is easy to implement digitally, without employing any external circuits...

Engineering of a DNA Polymerase for Direct m6 A Sequencing.

Science.gov (United States)

Aschenbrenner, Joos; Werner, Stephan; Marchand, Virginie; Adam, Martina; Motorin, Yuri; Helm, Mark; Marx, Andreas

2018-01-08

Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N 6 -methyladenosine (m 6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m 6 A-containing RNA prior to sequencing, since m 6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m 6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N 6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m 6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m 6 A sites directly from the sequencing data of untreated RNA samples. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Estimation of directional wave spreading

Digital Repository Service at National Institute of Oceanography (India)

Mandal, S.; Bhat, S.S.; Anand, N.M.; Nayak, B.U.

Directional properties of ocean waves are of great economic interest. The knowledge of wave directionality is important for the design of maritime structures and offshore operations. Two main aspects are considered for this study for the data...

Direct detection of a break in the teraelectronvolt cosmic-ray spectrum of electrons and positrons

Science.gov (United States)

DAMPE Collaboration; Ambrosi, G.; An, Q.; Asfandiyarov, R.; Azzarello, P.; Bernardini, P.; Bertucci, B.; Cai, M. S.; Chang, J.; Chen, D. Y.; Chen, H. F.; Chen, J. L.; Chen, W.; Cui, M. Y.; Cui, T. S.; D'Amone, A.; de Benedittis, A.; De Mitri, I.; di Santo, M.; Dong, J. N.; Dong, T. K.; Dong, Y. F.; Dong, Z. X.; Donvito, G.; Droz, D.; Duan, K. K.; Duan, J. L.; Duranti, M.; D'Urso, D.; Fan, R. R.; Fan, Y. Z.; Fang, F.; Feng, C. Q.; Feng, L.; Fusco, P.; Gallo, V.; Gan, F. J.; Gao, M.; Gao, S. S.; Gargano, F.; Garrappa, S.; Gong, K.; Gong, Y. Z.; Guo, D. Y.; Guo, J. H.; Hu, Y. M.; Huang, G. S.; Huang, Y. Y.; Ionica, M.; Jiang, D.; Jiang, W.; Jin, X.; Kong, J.; Lei, S. J.; Li, S.; Li, X.; Li, W. L.; Li, Y.; Liang, Y. F.; Liang, Y. M.; Liao, N. H.; Liu, H.; Liu, J.; Liu, S. B.; Liu, W. Q.; Liu, Y.; Loparco, F.; Ma, M.; Ma, P. X.; Ma, S. Y.; Ma, T.; Ma, X. Q.; Ma, X. Y.; Marsella, G.; Mazziotta, M. N.; Mo, D.; Niu, X. Y.; Peng, X. Y.; Peng, W. X.; Qiao, R.; Rao, J. N.; Salinas, M. M.; Shang, G. Z.; H. Shen, W.; Shen, Z. Q.; Shen, Z. T.; Song, J. X.; Su, H.; Su, M.; Sun, Z. Y.; Surdo, A.; Teng, X. J.; Tian, X. B.; Tykhonov, A.; Vagelli, V.; Vitillo, S.; Wang, C.; Wang, H.; Wang, H. Y.; Wang, J. Z.; Wang, L. G.; Wang, Q.; Wang, S.; Wang, X. H.; Wang, X. L.; Wang, Y. F.; Wang, Y. P.; Wang, Y. Z.; Wen, S. C.; Wang, Z. M.; Wei, D. M.; Wei, J. J.; Wei, Y. F.; Wu, D.; Wu, J.; Wu, L. B.; Wu, S. S.; Wu, X.; Xi, K.; Xia, Z. Q.; Xin, Y. L.; Xu, H. T.; Xu, Z. L.; Xu, Z. Z.; Xue, G. F.; Yang, H. B.; Yang, P.; Yang, Y. Q.; Yang, Z. L.; Yao, H. J.; Yu, Y. H.; Yuan, Q.; Yue, C.; Zang, J. J.; Zhang, C.; Zhang, D. L.; Zhang, F.; Zhang, J. B.; Zhang, J. Y.; Zhang, J. Z.; Zhang, L.; Zhang, P. F.; Zhang, S. X.; Zhang, W. Z.; Zhang, Y.; Zhang, Y. J.; Zhang, Y. Q.; Zhang, Y. L.; Zhang, Y. P.; Zhang, Z.; Zhang, Z. Y.; Zhao, H.; Zhao, H. Y.; Zhao, X. F.; Zhou, C. Y.; Zhou, Y.; Zhu, X.; Zhu, Y.; Zimmer, S.

2017-12-01

High-energy cosmic-ray electrons and positrons (CREs), which lose energy quickly during their propagation, provide a probe of Galactic high-energy processes and may enable the observation of phenomena such as dark-matter particle annihilation or decay. The CRE spectrum has been measured directly up to approximately 2 teraelectronvolts in previous balloon- or space-borne experiments, and indirectly up to approximately 5 teraelectronvolts using ground-based Cherenkov γ-ray telescope arrays. Evidence for a spectral break in the teraelectronvolt energy range has been provided by indirect measurements, although the results were qualified by sizeable systematic uncertainties. Here we report a direct measurement of CREs in the energy range 25 gigaelectronvolts to 4.6 teraelectronvolts by the Dark Matter Particle Explorer (DAMPE) with unprecedentedly high energy resolution and low background. The largest part of the spectrum can be well fitted by a ‘smoothly broken power-law’ model rather than a single power-law model. The direct detection of a spectral break at about 0.9 teraelectronvolts confirms the evidence found by previous indirect measurements, clarifies the behaviour of the CRE spectrum at energies above 1 teraelectronvolt and sheds light on the physical origin of the sub-teraelectronvolt CREs.

MIMO Based Multimedia Communication System

OpenAIRE

Kandar, D.; Dhar, Sourav; Bera, Rabindranath; Sarkar, C. K.

2009-01-01

High data rate is required for multimedia communication. But the communication at high data rate is always challenging. In this work we have successfully performed data chatting, Voice chatting and high quality video transmission between two distant units using MIMO adapter, Direct sequence spread spectrum system and MATLAB/SIMULINK platform.

A Study on the Security Levels of Spread-Spectrum Embedding Schemes in the WOA Framework.

Science.gov (United States)

Wang, Yuan-Gen; Zhu, Guopu; Kwong, Sam; Shi, Yun-Qing

2017-08-23

Security analysis is a very important issue for digital watermarking. Several years ago, according to Kerckhoffs' principle, the famous four security levels, namely insecurity, key security, subspace security, and stego-security, were defined for spread-spectrum (SS) embedding schemes in the framework of watermarked-only attack. However, up to now there has been little application of the definition of these security levels to the theoretical analysis of the security of SS embedding schemes, due to the difficulty of the theoretical analysis. In this paper, based on the security definition, we present a theoretical analysis to evaluate the security levels of five typical SS embedding schemes, which are the classical SS, the improved SS (ISS), the circular extension of ISS, the nonrobust and robust natural watermarking, respectively. The theoretical analysis of these typical SS schemes are successfully performed by taking advantage of the convolution of probability distributions to derive the probabilistic models of watermarked signals. Moreover, simulations are conducted to illustrate and validate our theoretical analysis. We believe that the theoretical and practical analysis presented in this paper can bridge the gap between the definition of the four security levels and its application to the theoretical analysis of SS embedding schemes.

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

Energy Technology Data Exchange (ETDEWEB)

Gloster, J; Jones, A; Redington, A; Burgin, L; Sorensen, J H; Turner, R; Dillon, M; Hullinger, P; Simpson, M; Astrup, P; Garner, G; Stewart, P; D' Amours, R; Sellers, R; Paton, D

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 during 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.

Physics Implications of Flat Directions in Free Fermionic Superstring Models; 1, Mass Spectrum and Couplings

CERN Document Server

Cleaver, G; Espinosa, J R; Everett, L; Langacker, P G; Wang, J

1999-01-01

From the "top-down" approach we investigate physics implications of the class of D- and F- flat directions formed from non-Abelian singlets which are proven flat to all orders in the nonrenormalizable superpotential, for a prototype quasi-realistic free fermionic string model with the standard model gauge group and three families (CHL5). These flat directions have at least an additional U(1)' unbroken at the string scale. For each flat direction, the complete set of effective mass terms and effective trilinear superpotential terms in the observable sector are computed to all orders in the VEV's of the fields in the flat direction. The "string selection-rules" disallow a large number of couplings allowed by gauge invariance, resulting in a massless spectrum with a large number of exotics, in most cases excluded by experiment, thus signifying a generic flaw of these models. Nevertheless, the resulting trilinear couplings of the massless spectrum possess a number of interesting features which we analyse for two ...

A wave parameters and directional spectrum analysis for extreme winds

OpenAIRE

Montoya Ramírez, Rubén Darío; Osorio Arias, Andres Fernando; Ortiz Royero, Juan Carlos; Ocampo-Torres, Francisco Javier

2013-01-01

In this research a comparison between two of the most popular ocean wave models, WAVEWATCH III™ and SWAN, was performed using data from hurricane Katrina in the Gulf of Mexico. The numerical simulation of sea surface directional wave spectrum and other wave parameters for several parameter- izations and its relation with the drag coefficient was carried out. The simulated data were compared with in-situ NOAA buoy data. For most of the buoys, WAVEWATCH III™ presented the best statistical compar...

On the calculation of the water particle kinematics arising in a directionally spread wavefield

CERN Document Server

Bateman, W J D; Taylor, P H

2003-01-01

This paper concerns the calculation of the water particle kinematics generated by the propagation of surface gravity waves. The motivation for this work lies in recent advances in the description of the water surface elevation associated with extreme waves that are highly nonlinear and involve a spread of wave energy in both frequency and direction. To provide these exact numerical descriptions the nonlinear free-surface boundary conditions are time-marched, with the most efficient solutions simply based upon the water surface elevation, eta, and the velocity potential, phi, on that surface. In many broad-banded problems, computational efficiency is not merely desirable but absolutely essential to resolve the complex interactions between wave components with widely varying length-scales and different directions of propagation. Although such models have recently been developed, the calculation of the underlying water particle kinematics, based on the surface properties alone, remains a significant obstacle to ...

Extended Main-sequence Turn-offs in Intermediate-age Star Clusters: Stellar Rotation Diminishes, but Does Not Eliminate, Age Spreads

Energy Technology Data Exchange (ETDEWEB)

Goudfrooij, Paul; Correnti, Matteo [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Girardi, Léo, E-mail: goudfroo@stsci.edu [Osservatorio Astronomico di Padova—INAF, Vicolo dell’Osservatorio 5, I-35122 Padova (Italy)

2017-09-01

Extended main-sequence turn-off (eMSTO) regions are a common feature in color–magnitude diagrams of young- and intermediate-age star clusters in the Magellanic Clouds. The nature of eMSTOs remains debated in the literature. The currently most popular scenarios are extended star formation activity and ranges of stellar rotation rates. Here we study details of differences in main-sequence turn-off (MSTO) morphology expected from spreads in age versus spreads in rotation rates, using Monte Carlo simulations with the Geneva syclist isochrone models that include the effects of stellar rotation. We confirm a recent finding of Niederhofer et al. that a distribution of stellar rotation velocities yields an MSTO extent that is proportional to the cluster age, as observed. However, we find that stellar rotation yields MSTO crosscut widths that are generally smaller than observed ones at a given age. We compare the simulations with high-quality Hubble Space Telescope data of NGC 1987 and NGC 2249, which are the two only relatively massive star clusters with an age of ∼1 Gyr for which such data is available. We find that the distribution of stars across the eMSTOs of these clusters cannot be explained solely by a distribution of stellar rotation velocities, unless the orientations of rapidly rotating stars are heavily biased toward an equator-on configuration. Under the assumption of random viewing angles, stellar rotation can account for ∼60% and ∼40% of the observed FWHM widths of the eMSTOs of NGC 1987 and NGC 2249, respectively. In contrast, a combination of distributions of stellar rotation velocities and stellar ages fits the observed eMSTO morphologies very well.

Conflict adaptation and congruency sequence effects to social-emotional stimuli in individuals with autism spectrum disorders.

Science.gov (United States)

Worsham, Whitney; Gray, Whitney E; Larson, Michael J; South, Mikle

2015-11-01

The modification of performance following conflict can be measured using conflict adaptation tasks thought to measure the change in the allocation of cognitive resources in order to reduce conflict interference and improve performance. While previous studies have suggested atypical processing during nonsocial cognitive control tasks, conflict adaptation (i.e. congruency sequence effects) for social-emotional stimuli have not been previously studied in autism spectrum disorder. A total of 32 participants diagnosed with autism spectrum disorder and 27 typically developing matched controls completed an emotional Stroop conflict task that required the classification of facial affect while simultaneously ignoring an overlaid affective word. Both groups showed behavioral evidence for emotional conflict adaptation based on response times and accuracy rates. However, the autism spectrum disorder group demonstrated a speed-accuracy trade-off manifested through significantly faster response times and decreased accuracy rates on trials containing conflict between the emotional face and the overlaid emotional word. Reduced selective attention toward socially relevant information may bias individuals with autism spectrum disorder toward more rapid processing and decision making even when conflict is present. Nonetheless, the loss of important information from the social stimuli reduces decision-making accuracy, negatively affecting the ability to adapt both cognitively and emotionally when conflict arises. © The Author(s) 2014.

Application of swine manure on agricultural fields contributes to extended-spectrum β-lactamase-producing Escherichia coli spread in Tai’an, China

Directory of Open Access Journals (Sweden)

Lili eGao

2015-04-01

Full Text Available The prevalence of extended-spectrum beta-lactamase (ESBL-producing Escherichia coli (E. coli is increasing rapidly in both hospital environments and animal farms. A lot of animal manure has been directly applied into arable fields in the developing countries. But the impact of ESBL-positive bacteria from animal manure on the agricultural fields is sparse, especially in the rural regions of Tai’an, China. Here, we collected 29, 3, and 10 ESBL-producing E. coli from pig manure, compost, and soil samples, respectively. To track ESBL-harboring E. coli from agricultural soil, these isolates of different sources were analyzed with regard to antibiotic resistance profiles, ESBL genes, plasmid replicons, and enterobacterial repetitive intergenic consensus (ERIC-polymerase chain reaction (PCR typing. The results showed that all the isolates exhibited multi-drug resistance. CTX-M gene was the predominant ESBL gene in the isolates from pig farm samples (30/32, 93.8% and soil samples (7/10, 70.0%, but no SHV gene was detected. 25 isolates contained the IncF-type replicon of plasmid, including 18 strains (18/32, 56.3% from the pig farm and 7 (7/10, 70.0% from the soil samples. ERIC-PCR demonstrated that 3 isolates from the soil had above 90% genetic similarity with strains from pig farm samples. In conclusion, application of animal manure carrying drug-resistant bacteria on agricultural fields is a likely contributor to antibiotic resistance gene spread.

A comparison of response spectrum and direct integration analysis methods as applied to a nuclear component support structure

International Nuclear Information System (INIS)

Bryan, B.J.; Flanders, H.E. Jr.

1992-01-01

Seismic qualification of Class I nuclear components is accomplished using a variety of analytical methods. This paper compares the results of time history dynamic analyses of a heat exchanger support structure using response spectrum and time history direct integration analysis methods. Dynamic analysis is performed on the detailed component models using the two methods. A nonlinear elastic model is used for both the response spectrum and direct integration methods. A nonlinear model which includes friction and nonlinear springs, is analyzed using time history input by direct integration. The loads from the three cases are compared

The potential role of microbiota for controlling the spread of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE in neonatal population [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Thibaud Delerue

2017-07-01

Full Text Available The spread of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE in the hospital and also the community is worrisome. Neonates particularly are exposed to the risk of ESBL-PE acquisition and, owing to the immaturity of their immune system, to a higher secondary risk of ESBL-PE-related infection. Reducing the risk of acquisition in the hospital is usually based on a bundle of measures, including screening policies at admission, improving hand hygiene compliance, and decreasing antibiotic consumption. However, recent scientific data suggest new prevention opportunities based on microbiota modifications.

Inoculation effects on root-colonizing arbuscular mycorrhizal fungal communities spread beyond directly inoculated plants

Science.gov (United States)

Krak, Karol; Vosátka, Miroslav; Püschel, David; Štorchová, Helena

2017-01-01

Inoculation with arbuscular mycorrhizal fungi (AMF) may improve plant performance at disturbed sites, but inoculation may also suppress root colonization by native AMF and decrease the diversity of the root-colonizing AMF community. This has been shown for the roots of directly inoculated plants, but little is known about the stability of inoculation effects, and to which degree the inoculant and the inoculation-induced changes in AMF community composition spread into newly emerging seedlings that were not in direct contact with the introduced propagules. We addressed this topic in a greenhouse experiment based on the soil and native AMF community of a post-mining site. Plants were cultivated in compartmented pots with substrate containing the native AMF community, where AMF extraradical mycelium radiating from directly inoculated plants was allowed to inoculate neighboring plants. The abundances of the inoculated isolate and of native AMF taxa were monitored in the roots of the directly inoculated plants and the neighboring plants by quantitative real-time PCR. As expected, inoculation suppressed root colonization of the directly inoculated plants by other AMF taxa of the native AMF community and also by native genotypes of the same species as used for inoculation. In the neighboring plants, high abundance of the inoculant and the suppression of native AMF were maintained. Thus, we demonstrate that inoculation effects on native AMF propagate into plants that were not in direct contact with the introduced inoculum, and are therefore likely to persist at the site of inoculation. PMID:28738069

Inoculation effects on root-colonizing arbuscular mycorrhizal fungal communities spread beyond directly inoculated plants.

Directory of Open Access Journals (Sweden)

Martina Janoušková

Full Text Available Inoculation with arbuscular mycorrhizal fungi (AMF may improve plant performance at disturbed sites, but inoculation may also suppress root colonization by native AMF and decrease the diversity of the root-colonizing AMF community. This has been shown for the roots of directly inoculated plants, but little is known about the stability of inoculation effects, and to which degree the inoculant and the inoculation-induced changes in AMF community composition spread into newly emerging seedlings that were not in direct contact with the introduced propagules. We addressed this topic in a greenhouse experiment based on the soil and native AMF community of a post-mining site. Plants were cultivated in compartmented pots with substrate containing the native AMF community, where AMF extraradical mycelium radiating from directly inoculated plants was allowed to inoculate neighboring plants. The abundances of the inoculated isolate and of native AMF taxa were monitored in the roots of the directly inoculated plants and the neighboring plants by quantitative real-time PCR. As expected, inoculation suppressed root colonization of the directly inoculated plants by other AMF taxa of the native AMF community and also by native genotypes of the same species as used for inoculation. In the neighboring plants, high abundance of the inoculant and the suppression of native AMF were maintained. Thus, we demonstrate that inoculation effects on native AMF propagate into plants that were not in direct contact with the introduced inoculum, and are therefore likely to persist at the site of inoculation.

Multicarrier Block-Spread CDMA for Broadband Cellular Downlink

Directory of Open Access Journals (Sweden)

Leus Geert

2004-01-01

Full Text Available Effective suppression of multiuser interference (MUI and mitigation of frequency-selective fading effects within the complexity constraints of the mobile constitute major challenges for broadband cellular downlink transceiver design. Existing wideband direct-sequence (DS code division multiple access (CDMA transceivers suppress MUI statistically by restoring the orthogonality among users at the receiver. However, they call for receive diversity and multichannel equalization to improve the fading effects caused by deep channel fades. Relying on redundant block spreading and linear precoding, we design a so-called multicarrier block-spread- (MCBS-CDMA transceiver that preserves the orthogonality among users and guarantees symbol detection, regardless of the underlying frequency-selective fading channels. These properties allow for deterministic MUI elimination through low-complexity block despreading and enable full diversity gains, irrespective of the system load. Different options to perform equalization and decoding, either jointly or separately, strike the trade-off between performance and complexity. To improve the performance over multi-input multi-output (MIMO multipath fading channels, our MCBS-CDMA transceiver combines well with space-time block-coding (STBC techniques, to exploit both multiantenna and multipath diversity gains, irrespective of the system load. Simulation results demonstrate the superior performance of MCBS-CDMA compared to competing alternatives.

Wave-like spread of Ebola Zaire.

Directory of Open Access Journals (Sweden)

2005-11-01

Full Text Available In the past decade the Zaire strain of Ebola virus (ZEBOV has emerged repeatedly into human populations in central Africa and caused massive die-offs of gorillas and chimpanzees. We tested the view that emergence events are independent and caused by ZEBOV variants that have been long resident at each locality. Phylogenetic analyses place the earliest known outbreak at Yambuku, Democratic Republic of Congo, very near to the root of the ZEBOV tree, suggesting that viruses causing all other known outbreaks evolved from a Yambuku-like virus after 1976. The tendency for earlier outbreaks to be directly ancestral to later outbreaks suggests that outbreaks are epidemiologically linked and may have occurred at the front of an advancing wave. While the ladder-like phylogenetic structure could also bear the signature of positive selection, our statistical power is too weak to reach a conclusion in this regard. Distances among outbreaks indicate a spread rate of about 50 km per year that remains consistent across spatial scales. Viral evolution is clocklike, and sequences show a high level of small-scale spatial structure. Genetic similarity decays with distance at roughly the same rate at all spatial scales. Our analyses suggest that ZEBOV has recently spread across the region rather than being long persistent at each outbreak locality. Controlling the impact of Ebola on wild apes and human populations may be more feasible than previously recognized.

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

Science.gov (United States)

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.

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

KAUST Repository

Teng, Haotian; Cao, Minh Duc; Hall, Michael B; Duarte, Tania; Wang, Sheng; Coin, Lachlan J M

2018-01-01

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

KAUST Repository

Teng, Haotian

2018-04-10

Sequencing by translocating DNA fragments through an array of nanopores is a rapidly maturing technology that offers faster and cheaper sequencing than other approaches. However, accurately deciphering the DNA sequence from the noisy and complex electrical signal is challenging. Here, we report Chiron, the first deep learning model to achieve end-to-end basecalling and directly translate the raw signal to DNA sequence without the error-prone segmentation step. Trained with only a small set of 4,000 reads, we show that our model provides state-of-the-art basecalling accuracy, even on previously unseen species. Chiron achieves basecalling speeds of more than 2,000 bases per second using desktop computer graphics processing units.

Interference Suppression Performance of Automotive UWB Radars Using Pseudo Random Sequences

Directory of Open Access Journals (Sweden)

I. Pasya

2015-12-01

Full Text Available Ultra wideband (UWB automotive radars have attracted attention from the viewpoint of reducing traffic accidents. The performance of automotive radars may be degraded by interference from nearby radars using the same frequency. In this study, a scenario where two cars pass each other on a road was considered. Considering the utilization of cross-polarization, the desired-to-undesired signal power ratio (DUR was found to vary approximately from -10 to 30 dB. Different pseudo random sequences were employed for spectrum spreading the different radar signals to mitigate the interference effects. This paper evaluates the interference suppression provided by maximum length sequence (MLS and Gold sequence (GS through numerical simulations of the radar’s performance in terms of probability of false alarm and probability of detection. It was found that MLS and GS yielded nearly the same performance when the DUR is -10 dB (worst case; for example when fixing the probability of false alarm to 0.0001, the probabilities of detection were 0.964 and 0.946 respectively. The GS are more advantageous than MLS due to larger number of different sequences having the same length in GS than in MLS.

Epidemic spreading on random surfer networks with infected avoidance strategy

International Nuclear Information System (INIS)

Feng Yun; Ding Li; Huang Yun-Han; Guan Zhi-Hong

2016-01-01

In this paper, we study epidemic spreading on random surfer networks with infected avoidance (IA) strategy. In particular, we consider that susceptible individuals’ moving direction angles are affected by the current location information received from infected individuals through a directed information network. The model is mainly analyzed by discrete-time numerical simulations. The results indicate that the IA strategy can restrain epidemic spreading effectively. However, when long-distance jumps of individuals exist, the IA strategy’s effectiveness on restraining epidemic spreading is heavily reduced. Finally, it is found that the influence of the noises from information transferring process on epidemic spreading is indistinctive. (paper)

The role of the temporal sequences in the Augmentative and Alternative Communication Systems for the Autism Spectrum Disorders

Directory of Open Access Journals (Sweden)

Saverio Fontani

2014-12-01

Full Text Available The Augmentative and Alternative Communication systems (AAC represent a promising integration for more effective models of special education specifically developed for the special educational needs of children with Autism Spectrum Disorders. In this paper the historical foundations of the approach are presented, and its implications on the promotion of functional spontaneous communication skills based on the temporal sequences approach are discussed.  

Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing.

Science.gov (United States)

Lalonde, Emilie; Albrecht, Steffen; Ha, Kevin C H; Jacob, Karine; Bolduc, Nathalie; Polychronakos, Constantin; Dechelotte, Pierre; Majewski, Jacek; Jabado, Nada

2010-08-01

Protein coding genes constitute approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., "whole exome") have the potential to contribute our understanding of human diseases. We used a method for whole-exome sequencing coupling Agilent whole-exome capture to the Illumina DNA-sequencing platform, and investigated two unrelated fetuses from nonconsanguineous families with Fowler Syndrome (FS), a stereotyped phenotype lethal disease. We report novel germline mutations in feline leukemia virus subgroup C cellular-receptor-family member 2, FLVCR2, which has recently been shown to cause FS. Using this technology, we identified three types of genetic abnormalities: point-mutations, insertions-deletions, and intronic splice-site changes (first pathogenic report using this technology), in the fetuses who both were compound heterozygotes for the disease. Although revealing a high level of allelic heterogeneity and mutational spectrum in FS, this study further illustrates the successful application of whole-exome sequencing to uncover genetic defects in rare Mendelian disorders. Of importance, we show that we can identify genes underlying rare, monogenic and recessive diseases using a limited number of patients (n=2), in the absence of shared genetic heritage and in the presence of allelic heterogeneity.

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

DEFF Research Database (Denmark)

Joensen, Katrine Grimstrup; Engsbro, A L Ø; Lukjancenko, Oksana

2017-01-01

The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study...... was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included...

Infants learn better from left to right: a directional bias in infants' sequence learning.

Science.gov (United States)

Bulf, Hermann; de Hevia, Maria Dolores; Gariboldi, Valeria; Macchi Cassia, Viola

2017-05-26

A wealth of studies show that human adults map ordered information onto a directional spatial continuum. We asked whether mapping ordinal information into a directional space constitutes an early predisposition, already functional prior to the acquisition of symbolic knowledge and language. While it is known that preverbal infants represent numerical order along a left-to-right spatial continuum, no studies have investigated yet whether infants, like adults, organize any kind of ordinal information onto a directional space. We investigated whether 7-month-olds' ability to learn high-order rule-like patterns from visual sequences of geometric shapes was affected by the spatial orientation of the sequences (left-to-right vs. right-to-left). Results showed that infants readily learn rule-like patterns when visual sequences were presented from left to right, but not when presented from right to left. This result provides evidence that spatial orientation critically determines preverbal infants' ability to perceive and learn ordered information in visual sequences, opening to the idea that a left-to-right spatially organized mental representation of ordered dimensions might be rooted in biologically-determined constraints on human brain development.

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

Science.gov (United States)

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

Brief Report: Imitation of Object-Directed Acts in Young Children with Autism Spectrum Disorders

Science.gov (United States)

Gonsiorowski, Anna; Williamson, Rebecca A.; Robins, Diana L.

2016-01-01

Children with autism spectrum disorders (ASD) imitate less than typically developing (TD) children; however, the specific features and causes of this deficit are still unclear. The current study investigates the role of joint engagement, specifically children's visual attention to demonstrations, in an object-directed imitation task. This sample…

Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

Science.gov (United States)

V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

2016-12-01

Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

Stability of the spreading in small-world network with predictive controller

International Nuclear Information System (INIS)

Bao, Z.J.; Jiang, Q.Y.; Yan, W.J.; Cao, Y.J.

2010-01-01

In this Letter, we apply the predictive control strategy to suppress the propagation of diseases or viruses in small-world network. The stability of small-world spreading model with predictive controller is investigated. The sufficient and necessary stability condition is given, which is closely related to the controller parameters and small-world rewiring probability p. Our simulations discover a phenomenon that, with the fixed predictive controller parameters, the spreading dynamics become more and more stable when p decreases from a larger value to a smaller one, and the suitable controller parameters can effectively suppress the spreading behaviors even when p varies within the whole spectrum, and the unsuitable controller parameters can lead to oscillation when p lies within a certain range.

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

Science.gov (United States)

Currin, Andrew; Swainston, Neil; Day, Philip J.

2015-01-01

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole

Fluorescent visualization of a spreading surfactant

Energy Technology Data Exchange (ETDEWEB)

Fallest, David W; Lichtenberger, Adele M; Fox, Christopher J; Daniels, Karen E, E-mail: kdaniel@ncsu.ed [Department of Physics, North Carolina State University, Raleigh, NC 27695 (United States)

2010-07-15

The spreading of surfactants on thin films is an industrially and medically important phenomenon, but the dynamics are highly nonlinear and visualization of the surfactant dynamics has been a long-standing experimental challenge. We perform the first quantitative, spatiotemporally resolved measurements of the spreading of an insoluble surfactant on a thin fluid layer. During the spreading process, we directly observe both the radial height profile of the spreading droplet and the spatial distribution of the fluorescently tagged surfactant. We find that the leading edge of a spreading circular layer of surfactant forms a Marangoni ridge in the underlying fluid, with a trough trailing the ridge as expected. However, several novel features are observed using the fluorescence technique, including a peak in the surfactant concentration that trails the leading edge, and a flat, monolayer-scale spreading film that differs from concentration profiles predicted by current models. Both the Marangoni ridge and the surfactant leading edge can be described to spread as R{approx}t{sup {delta}}. We find spreading exponents {delta}{sub H}{approx}0.30 and {delta}{sub {Gamma}}{approx}0.22 for the ridge peak and surfactant leading edge, respectively, which are in good agreement with theoretical predictions of {delta}=1/4. In addition, we observe that the surfactant leading edge initially leads the peak of the Marangoni ridge, with the peak later catching up to the leading edge.

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

Science.gov (United States)

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.

A comparison of EGFR mutation testing methods in lung carcinoma: direct sequencing, real-time PCR and immunohistochemistry.

Directory of Open Access Journals (Sweden)

Bárbara Angulo

Full Text Available The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry, with direct sequencing and to investigate the limit of detection (LOD of both PCR-based methods. We identified EGFR mutations in 21 (16% of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%, which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%. Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+ yielded similar results. Immunohistochemistry (IHC staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity.

Design of a TDOA location engine and development of a location system based on chirp spread spectrum.

Science.gov (United States)

Wang, Rui-Rong; Yu, Xiao-Qing; Zheng, Shu-Wang; Ye, Yang

2016-01-01

Location based services (LBS) provided by wireless sensor networks have garnered a great deal of attention from researchers and developers in recent years. Chirp spread spectrum (CSS) signaling formatting with time difference of arrival (TDOA) ranging technology is an effective LBS technique in regards to positioning accuracy, cost, and power consumption. The design and implementation of the location engine and location management based on TDOA location algorithms were the focus of this study; as the core of the system, the location engine was designed as a series of location algorithms and smoothing algorithms. To enhance the location accuracy, a Kalman filter algorithm and moving weighted average technique were respectively applied to smooth the TDOA range measurements and location results, which are calculated by the cooperation of a Kalman TDOA algorithm and a Taylor TDOA algorithm. The location management server, the information center of the system, was designed with Data Server and Mclient. To evaluate the performance of the location algorithms and the stability of the system software, we used a Nanotron nanoLOC Development Kit 3.0 to conduct indoor and outdoor location experiments. The results indicated that the location system runs stably with high accuracy at absolute error below 0.6 m.

A Model of Path Arrival Rate for In-Room Radio Channels with Directive Antennas

DEFF Research Database (Denmark)

Pedersen, Troels

and orientation are picked uniformly at random we derive an exact expression of the mean arrival rate for a rectangular room predicted by the mirror source theory. The rate is quadratic in delay, inversely proportional to the room volume, and proportional to the product of beam coverage fractions...... that the power-delay spectrum is unaffected by the antenna directivity. However, Monte Carlo simulations show that antenna directivity does indeed play an important role for the distribution of instantaneous mean delay and rms delay spread....

On the fine spectrum of the generalized difference operator B(r,s over the sequence spaces c0 and c

Directory of Open Access Journals (Sweden)

Bilâl Altay

2005-01-01

Full Text Available We determine the fine spectrum of the generalized difference operator B(r,s defined by a band matrix over the sequence spaces c0 and c, and derive a Mercerian theorem. This generalizes our earlier work (2004 for the difference operator Δ, and includes as other special cases the right shift and the Zweier matrices.

A novel neural-net-based nonlinear adaptive control and application to the cross-direction deviations control of a polymer film spread line

International Nuclear Information System (INIS)

Chen Zengqiang; Li Xiang; Liu Zhongxin; Yuan Zhuzhi

2008-01-01

A novel neural adaptive controller is presented to effectively control multivariable nonlinear systems. The proposed neural controller has been successfully applied to the cross-direction deviation control system of a polymer film spread line, whose good performance has been verified with real-time running results

Spectrum-to-Spectrum Searching Using a Proteome-wide Spectral Library*

Science.gov (United States)

Yen, Chia-Yu; Houel, Stephane; Ahn, Natalie G.; Old, William M.

2011-01-01

The unambiguous assignment of tandem mass spectra (MS/MS) to peptide sequences remains a key unsolved problem in proteomics. Spectral library search strategies have emerged as a promising alternative for peptide identification, in which MS/MS spectra are directly compared against a reference library of confidently assigned spectra. Two problems relate to library size. First, reference spectral libraries are limited to rediscovery of previously identified peptides and are not applicable to new peptides, because of their incomplete coverage of the human proteome. Second, problems arise when searching a spectral library the size of the entire human proteome. We observed that traditional dot product scoring methods do not scale well with spectral library size, showing reduction in sensitivity when library size is increased. We show that this problem can be addressed by optimizing scoring metrics for spectrum-to-spectrum searches with large spectral libraries. MS/MS spectra for the 1.3 million predicted tryptic peptides in the human proteome are simulated using a kinetic fragmentation model (MassAnalyzer version2.1) to create a proteome-wide simulated spectral library. Searches of the simulated library increase MS/MS assignments by 24% compared with Mascot, when using probabilistic and rank based scoring methods. The proteome-wide coverage of the simulated library leads to 11% increase in unique peptide assignments, compared with parallel searches of a reference spectral library. Further improvement is attained when reference spectra and simulated spectra are combined into a hybrid spectral library, yielding 52% increased MS/MS assignments compared with Mascot searches. Our study demonstrates the advantages of using probabilistic and rank based scores to improve performance of spectrum-to-spectrum search strategies. PMID:21532008

Development and application of network virtual instrument for emission spectrum of pulsed high-voltage direct current discharge

Science.gov (United States)

Gong, X.; Wu, Q.

2017-12-01

Network virtual instrument (VI) is a new development direction in current automated test. Based on LabVIEW, the software and hardware system of VI used for emission spectrum of pulsed high-voltage direct current (DC) discharge is developed and applied to investigate pulsed high-voltage DC discharge of nitrogen. By doing so, various functions are realized including real time collection of emission spectrum of nitrogen, monitoring operation state of instruments and real time analysis and processing of data. By using shared variables and DataSocket technology in LabVIEW, the network VI system based on field VI is established. The system can acquire the emission spectrum of nitrogen in the test site, monitor operation states of field instruments, realize real time face-to-face interchange of two sites, and analyze data in the far-end from the network terminal. By employing the network VI system, the staff in the two sites acquired the same emission spectrum of nitrogen and conducted the real time communication. By comparing with the previous results, it can be seen that the experimental data obtained by using the system are highly precise. This implies that the system shows reliable network stability and safety and satisfies the requirements for studying the emission spectrum of pulsed high-voltage discharge in high-precision fields or network terminals. The proposed architecture system is described and the target group gets the useful enlightenment in many fields including engineering remote users, specifically in control- and automation-related tasks.

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing

DEFF Research Database (Denmark)

Wu, Jia Qian; Shteynberg, David; Arumugam, Manimozhiyan

2004-01-01

an alternative approach: reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing based on dual-genome de novo predictions from TWINSCAN. We tested 444 TWINSCAN-predicted rat genes that showed significant homology to known human genes implicated in disease but that were partially...... in the single-intron experiment. Spliced sequences were amplified in 46 cases (34%). We conclude that this procedure for elucidating gene structures with native cDNA sequences is cost-effective and will become even more so as it is further optimized.......The publication of a draft sequence of a third mammalian genome--that of the rat--suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive annotation efforts that are currently being devoted to human. In this paper, we demonstrate...

Impact of Different Spreading Codes Using FEC on DWT Based MC-CDMA System

OpenAIRE

Masum, Saleh; Kabir, M. Hasnat; Islam, Md. Matiqul; Shams, Rifat Ara; Ullah, Shaikh Enayet

2012-01-01

The effect of different spreading codes in DWT based MC-CDMA wireless communication system is investigated. In this paper, we present the Bit Error Rate (BER) performance of different spreading codes (Walsh-Hadamard code, Orthogonal gold code and Golay complementary sequences) using Forward Error Correction (FEC) of the proposed system. The data is analyzed and is compared among different spreading codes in both coded and uncoded cases. It is found via computer simulation that the performance...

Modelling unidirectional liquid spreading on slanted microposts

DEFF Research Database (Denmark)

Cavalli, Andrea; Blow, Matthew L.; Yeomans, Julia M.

2013-01-01

A lattice Boltzmann algorithm is used to simulate the slow spreading of drops on a surface patterned with slanted micro-posts. Gibb's pinning of the interface on the sides or top of the posts leads to unidirectional spreading over a wide range of contact angles and inclination angles of the posts....... Regimes for spreading in no, one or two directions are identified, and shown to agree well with a two-dimensional theory proposed in Chu, Xiao and Wang. A more detailed numerical analysis of the contact line shapes allows us to understand deviations from the two dimensional model, and to identify...

A Study on Spreading Direction of Coal-fire Based with TIR Remote Sensing in Wuda Coalfield from 2000 to 2006, Northern China

International Nuclear Information System (INIS)

Huo, H-Y; Jiang, X-G; Song, X-F; Liu, L; Ni, Z-Y; Gao, C-X; Zhang, Y-Z

2014-01-01

Coal fires are a common and serious problem in most coal producing countries. Coal fires could not only lead to a huge loss of non-renewable energy resources, but it also can cause many environmental problems such as GHG emission, land subsidence and increment of surface temperature. So it is very important to monitor the dynamic changes of coal fires. As far as large scale coal field, remote sensing provided researchers with a new and useful technique for coal fire detection. This paper developed a research over coal fire spreading direction using a multi-temporal TIR remote sensing approach. The results successfully showed that the direction of coal fire spreading and predicted the coal fire direction of development on a regional scale or on a whole coal field scale, and a quantitative analysis of coal fires was made in the research. The results showed that the coal fires had an average annual increase of 0.5 million square meters from 1999 to 2006, and the TIR remote sensing proved to be an available tool for coal fire mapping and prediction of coal fire development

Reconstruction of a direction-dependent primordial power spectrum from Planck CMB data

Science.gov (United States)

Durakovic, Amel; Hunt, Paul; Mukherjee, Suvodip; Sarkar, Subir; Souradeep, Tarun

2018-02-01

We consider the possibility that the primordial curvature perturbation is direction-dependent. To first order this is parameterised by a quadrupolar modulation of the power spectrum and results in statistical anisotropy of the CMB, which can be quantified using `bipolar spherical harmonics'. We compute these for the Planck DR2-2015 SMICA map and estimate the noise covariance from Planck Full Focal Plane 9 simulations. A constant quadrupolar modulation is detected with 2.2 σ significance, dropping to 2σ when the primordial power is assumed to scale with wave number k as a power law. Going beyond previous work we now allow the spectrum to have arbitrary scale-dependence. Our non-parametric reconstruction then suggests several spectral features, the most prominent at k ~ 0.006 Mpc‑1. When a constant quadrupolar modulation is fitted to data in the range 0.005 <= k/Mpc‑1 <= 0.008, its preferred directions are found to be related to the cosmic hemispherical asymmetry and the CMB dipole. To determine the significance we apply two test statistics to our reconstructions of the quadrupolar modulation from data, against reconstructions of realisations of noise only. With a test statistic sensitive only to the amplitude of the modulation, the reconstructions from the multipole range 30 <= l <= 1200 are unusual with 2.1σ significance. With the second test statistic, sensitive also to the direction, the significance rises to 6.9σ. Our approach is easily generalised to include other data sets such as polarisation, large-scale structure and forthcoming 21-cm line observations which will enable these anomalies to be investigated further.

Development of Pistachio (Pistacia vera L.) spread.

Science.gov (United States)

Shakerardekani, Ahmad; Karim, Roselina; Ghazali, Hasanah Mohd; Chin, Nyuk Ling

2013-03-01

Pistachio nut (Pistacia vera L.) is one of the most delicious and nutritious nuts in the world. Pistachio spreads were developed using pistachio paste as the main component, icing sugar, soy protein isolate (SPI), and red palm oil (RPO), at different ratios. The highest mean scores of all the sensory attributes were depicted by spreads that were made without addition of SPI. It was found that the work of shear was 0 to 11.0 kg s for an acceptable spread. Sensory spreadability, overall texture, spreadability, and overall acceptability were negatively correlated (R > 0.83) with the work of shear of spreads. The findings indicated that the presence of RPO had a direct effect on the viscoelastic behavior of the pistachio spreads. The a values, which are related to the green color of the pistachio product ranged from 1.7 to 3.9 for spread without addition of RPO, and 4.0 to 5.3 in the presence of RPO. The development of pistachio spread would potentially increase the food uses of pistachio and introduce consumers with a healthier snack food. © 2013 Institute of Food Technologists®

Whole-Exome Sequencing Identifies One De Novo Variant in the FGD6 Gene in a Thai Family with Autism Spectrum Disorder

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Chuphong Thongnak

2018-01-01

Full Text Available Autism spectrum disorder (ASD has a strong genetic basis, although the genetics of autism is complex and it is unclear. Genetic testing such as microarray or sequencing was widely used to identify autism markers, but they are unsuccessful in several cases. The objective of this study is to identify causative variants of autism in two Thai families by using whole-exome sequencing technique. Whole-exome sequencing was performed with autism-affected children from two unrelated families. Each sample was sequenced on SOLiD 5500xl Genetic Analyzer system followed by combined bioinformatics pipeline including annotation and filtering process to identify candidate variants. Candidate variants were validated, and the segregation study with other family members was performed using Sanger sequencing. This study identified a possible causative variant for ASD, c.2951G>A, in the FGD6 gene. We demonstrated the potential for ASD genetic variants associated with ASD using whole-exome sequencing and a bioinformatics filtering procedure. These techniques could be useful in identifying possible causative ASD variants, especially in cases in which variants cannot be identified by other techniques.

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

Science.gov (United States)

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

2016-07-01

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

Plume spread and atmospheric stability

Energy Technology Data Exchange (ETDEWEB)

Weber, R O [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

1999-08-01

The horizontal spread of a plume in atmospheric dispersion can be described by the standard deviation of horizontal direction. The widely used Pasquill-Gifford classes of atmospheric stability have assigned typical values of the standard deviation of horizontal wind direction and of the lapse rate. A measured lapse rate can thus be used to estimate the standard deviation of wind direction. It is examined by means of a large dataset of fast wind measurements how good these estimates are. (author) 1 fig., 2 refs.

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

Science.gov (United States)

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.

Flame spread along thermally thick horizontal rods

Science.gov (United States)

Higuera, F. J.

2002-06-01

An analysis is carried out of the spread of a flame along a horizontal solid fuel rod, for which a weak aiding natural convection flow is established in the underside of the rod by the action of the axial gradient of the pressure variation that gravity generates in the warm gas surrounding the flame. The spread rate is determined in the limit of infinitely fast kinetics, taking into account the effect of radiative losses from the solid surface. The effect of a small inclination of the rod is discussed, pointing out a continuous transition between upward and downward flame spread. Flame spread along flat-bottomed solid cylinders, for which the gradient of the hydrostatically generated pressure drives the flow both along and across the direction of flame propagation, is also analysed.

Epidemic spreading on random surfer networks with infected avoidance strategy

Science.gov (United States)

Feng, Yun; Ding, Li; Huang, Yun-Han; Guan, Zhi-Hong

2016-12-01

In this paper, we study epidemic spreading on random surfer networks with infected avoidance (IA) strategy. In particular, we consider that susceptible individuals’ moving direction angles are affected by the current location information received from infected individuals through a directed information network. The model is mainly analyzed by discrete-time numerical simulations. The results indicate that the IA strategy can restrain epidemic spreading effectively. However, when long-distance jumps of individuals exist, the IA strategy’s effectiveness on restraining epidemic spreading is heavily reduced. Finally, it is found that the influence of the noises from information transferring process on epidemic spreading is indistinctive. Project supported in part by the National Natural Science Foundation of China (Grant Nos. 61403284, 61272114, 61673303, and 61672112) and the Marine Renewable Energy Special Fund Project of the State Oceanic Administration of China (Grant No. GHME2013JS01).

Rectal carriage of extended-spectrum beta-lactamase-producing gram-negative bacilli in community settings in Madagascar.

Directory of Open Access Journals (Sweden)

Perlinot Herindrainy

Full Text Available BACKGROUND: Extended-spectrum ß-lactamase-producing Enterobacteria (ESBL-PE emerged at the end of the 1980s, causing nosocomial outbreaks and/or hyperendemic situations in hospitals and long-term care facilities. In recent years, community-acquired infections due to ESBL-PE have spread worldwide, especially across developing countries including Madagascar. OBJECTIVES: This study aimed to determine the prevalence and risk factors of intestinal carriage of ESBL-PE in the community of Antananarivo. METHODS: Non-hospitalized patients were recruited in three health centers in different socio economic settings. Fresh stool collected were immediately plated on Drigalski agar containing 3 mg/liter of ceftriaxone. Gram-negative bacilli species were identified and ESBL production was tested by a double disk diffusion (cefotaxime and ceftazidime +/- clavulanate assay. Characterization of ESBLs were perfomed by PCR and direct sequencing. Molecular epidemiology was analysed by Rep-PCR and ERIC-PCR. RESULTS: 484 patients were screened (sex ratio  =  1.03, median age 28 years. 53 ESBL-PE were isolated from 49 patients (carrier rate 10.1%. The isolates included Escherichia coli (31, Klebsiella pneumoniae (14, Enterobacter cloacae (3, Citrobacter freundii (3, Kluyvera spp. (1 and Pantoae sp. (1. In multivariate analysis, only the socioeconomic status of the head of household was independently associated with ESBL-PE carriage, poverty being the predominant risk factor. CONCLUSIONS: The prevalence of carriage of ESBL in the community of Antananarivo is one of the highest reported worldwide. This alarming spread of resistance genes should be stopped urgently by improving hygiene and streamlining the distribution and consumption of antibiotics.

DeepProbe: Information Directed Sequence Understanding and Chatbot Design via Recurrent Neural Networks

OpenAIRE

Yin, Zi; Chang, Keng-hao; Zhang, Ruofei

2017-01-01

Information extraction and user intention identification are central topics in modern query understanding and recommendation systems. In this paper, we propose DeepProbe, a generic information-directed interaction framework which is built around an attention-based sequence to sequence (seq2seq) recurrent neural network. DeepProbe can rephrase, evaluate, and even actively ask questions, leveraging the generative ability and likelihood estimation made possible by seq2seq models. DeepProbe makes...

DNA sequence analysis of X-ray induced Adh null mutations in Drosophila melanogaster

International Nuclear Information System (INIS)

Mahmoud, J.; Fossett, N.G.; Arbour-Reily, P.; McDaniel, M.; Tucker, A.; Chang, S.H.; Lee, W.R.

1991-01-01

The mutational spectrum for 28 X-ray induced mutations and 2 spontaneous mutations, previously determined by genetic and cytogenetic methods, consisted of 20 multilocus deficiencies (19 induced and 1 spontaneous) and 10 intragenic mutations (9 induced and 1 spontaneous). One of the X-ray induced intragenic mutations was lost, and another was determined to be a recombinant with the allele used in the recovery scheme. The DNA sequence of two X-ray induced intragenic mutations has been published. This paper reports the results of DNA sequence analysis of the remaining intragenic mutations and a summary of the X-ray induced mutational spectrum. The combination of DNA sequence analysis with genetic complementation analysis shows a continuous distribution in size of deletions rather than two different types of mutations consisting of deletions and 'point mutations'. Sequencing is shown to be essential for detecting intragenic deletions. Of particular importance for future studies is the observation that all of the intragenic deletions consist of a direct repeat adjacent to the breakpoint with one of the repeats deleted

Design of Spreading-Codes-Assisted Active Imaging System

Directory of Open Access Journals (Sweden)

Alexey Volkov

2015-07-01

Full Text Available This work discusses an innovative approach to imaging which can improve the robustness of existing active-range measurement methods and potentially enhance their use in a variety of outdoor applications. By merging a proven modulation technique from the domain of spread-spectrum communications with the bleeding-edge CMOS sensor technology, the prototype of the modulated range sensor is designed and evaluated. A suitable set of application-specific spreading codes is proposed, evaluated and tested on the prototype. Experimental results show that the introduced modulation technique significantly reduces the impacts of environmental factors such as sunlight and external light sources, as well as mutual interference of identical devices. The proposed approach can be considered as a promising basis for a new generation of robust and cost-efficient range-sensing solutions for automotive applications, autonomous vehicles or robots.

Dynamics of Ionic Shifts in Cortical Spreading Depression.

Science.gov (United States)

Enger, Rune; Tang, Wannan; Vindedal, Gry Fluge; Jensen, Vidar; Johannes Helm, P; Sprengel, Rolf; Looger, Loren L; Nagelhus, Erlend A

2015-11-01

Cortical spreading depression is a slowly propagating wave of near-complete depolarization of brain cells followed by temporary suppression of neuronal activity. Accumulating evidence indicates that cortical spreading depression underlies the migraine aura and that similar waves promote tissue damage in stroke, trauma, and hemorrhage. Cortical spreading depression is characterized by neuronal swelling, profound elevation of extracellular potassium and glutamate, multiphasic blood flow changes, and drop in tissue oxygen tension. The slow speed of the cortical spreading depression wave implies that it is mediated by diffusion of a chemical substance, yet the identity of this substance and the pathway it follows are unknown. Intercellular spread between gap junction-coupled neurons or glial cells and interstitial diffusion of K(+) or glutamate have been proposed. Here we use extracellular direct current potential recordings, K(+)-sensitive microelectrodes, and 2-photon imaging with ultrasensitive Ca(2+) and glutamate fluorescent probes to elucidate the spatiotemporal dynamics of ionic shifts associated with the propagation of cortical spreading depression in the visual cortex of adult living mice. Our data argue against intercellular spread of Ca(2+) carrying the cortical spreading depression wavefront and are in favor of interstitial K(+) diffusion, rather than glutamate diffusion, as the leading event in cortical spreading depression. © The Author 2015. Published by Oxford University Press.

PHKA2 mutation spectrum in Korean patients with glycogen storage disease type IX: prevalence of deletion mutations.

Science.gov (United States)

Choi, Rihwa; Park, Hyung-Doo; Kang, Ben; Choi, So Yoon; Ki, Chang-Seok; Lee, Soo-Youn; Kim, Jong-Won; Song, Junghan; Choe, Yon Ho

2016-04-21

Molecular diagnosis of glycogen storage diseases (GSDs) is important to enable accurate diagnoses and make appropriate therapeutic plans. The aim of this study was to evaluate the PHKA2 mutation spectrum in Korean patients with GSD type IX. Thirteen Korean patients were tested for PHKA2 mutations using direct sequencing and a multiplex polymerase chain reaction method. A comprehensive review of the literature on previously reported PHKA2 mutations in other ethnic populations was conducted for comparison. Among 13 patients tested, six unrelated male patients with GSD IX aged 2 to 6 years at the first diagnostic work-up for hepatomegaly with elevated aspartate transaminase (AST) and alanine transaminase (ALT) were found to have PHKA2 mutations. These patients had different PHKA2 mutations: five were known mutations (c.537 + 5G > A, c.884G > A [p.Arg295His], c.3210_3212delGAG [p.Arg1072del], exon 8 deletion, and exons 27-33 deletion) and one was a novel mutation (exons 18-33 deletion). Notably, the most common type of mutation was gross deletion, in contrast to other ethnic populations in which the most common mutation type was sequence variant. This study expands our knowledge of the PHKA2 mutation spectrum of GSD IX. Considering the PHKA2 mutation spectrum in Korean patients with GSD IX, molecular diagnostic methods for deletions should be conducted in conjunction with direct sequence analysis to enable accurate molecular diagnosis of this disease in the Korean population.

A performance analysis of DS-CDMA and SCPC VSAT networks

Science.gov (United States)

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.

Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.

Directory of Open Access Journals (Sweden)

Sandeep J Joseph

Full Text Available Sequencing bacterial genomes from DNA isolated directly from clinical samples offers the promise of rapid and precise acquisition of informative genetic information. In the case of Chlamydia trachomatis, direct sequencing is particularly desirable because it obviates the requirement for culture in mammalian cells, saving time, cost and the possibility of missing low abundance strains. In this proof of concept study, we developed methodology that would allow genome-scale direct sequencing, using a multiplexed microdroplet PCR enrichment technology to amplify a 100 kb region of the C. trachomatis genome with 500 1.1-1.3 kb overlapping amplicons (5-fold amplicon redundancy. We integrated comparative genomic data into a pipeline to preferentially select conserved sites for amplicon design. The 100 kb target region could be amplified from clinical samples, including remnants from diagnostics tests, originating from the cervix, urethra and urine, For rapid analysis of these data, we developed a framework for whole-genome based genotyping called binstrain. We used binstrain to estimate the proportion of SNPs originating from 14 C. trachomatis reference serotype genomes in each sample. Direct DNA sequencing methods such as the one described here may have an important role in understanding the biology of C. trachomatis mixed infections and the natural genetic variation of the species within clinically relevant ecological niches.

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

Science.gov (United States)

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.

Direct whole-genome sequencing of Plasmodium falciparum specimens from dried erythrocyte spots

DEFF Research Database (Denmark)

Nag, Sidsel; Kofoed, Poul Erik; Ursing, Johan

2018-01-01

-infected individuals living in rural areas, away from main infrastructure and the electrical grid. The aim of this study was to describe a low-tech procedure to sample P. falciparum specimens for direct whole genome sequencing (WGS), without use of electricity and cold-chain. Methods: Venous blood samples were...

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

Science.gov (United States)

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.

Multiscale analysis of spreading in a large communication network

International Nuclear Information System (INIS)

Kivelä, Mikko; Pan, Raj Kumar; Kaski, Kimmo; Kertész, János; Saramäki, Jari; Karsai, Márton

2012-01-01

In temporal networks, both the topology of the underlying network and the timings of interaction events can be crucial in determining how a dynamic process mediated by the network unfolds. We have explored the limiting case of the speed of spreading in the SI model, set up such that an event between an infectious and a susceptible individual always transmits the infection. The speed of this process sets an upper bound for the speed of any dynamic process that is mediated through the interaction events of the network. With the help of temporal networks derived from large-scale time-stamped data on mobile phone calls, we extend earlier results that indicate the slowing-down effects of burstiness and temporal inhomogeneities. In such networks, links are not permanently active, but dynamic processes are mediated by recurrent events taking place on the links at specific points in time. We perform a multiscale analysis and pinpoint the importance of the timings of event sequences on individual links, their correlations with neighboring sequences, and the temporal pathways taken by the network-scale spreading process. This is achieved by studying empirically and analytically different characteristic relay times of links, relevant to the respective scales, and a set of temporal reference models that allow for removing selected time-domain correlations one by one. Our analysis shows that for the spreading velocity, time-domain inhomogeneities are as important as the network topology, which indicates the need to take time-domain information into account when studying spreading dynamics. In particular, results for the different characteristic relay times underline the importance of the burstiness of individual links

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

Science.gov (United States)

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...

Asymmetric liquid wetting and spreading on surfaces with slanted micro-pillar arrays

KAUST Repository

Yang, Xiaoming

2013-01-01

Uni-directional liquid spreading on asymmetric silicone-fabricated nanostructured surfaces has recently been reported. In this work, uniformly deflected polydimethylsiloxane (PDMS) micro-pillars covered with silver films were fabricated. Asymmetric liquid wetting and spreading behaviors in a preferential direction were observed on the slanted micro-pillar surfaces and a micro-scale thin liquid film advancing ahead of the bulk liquid droplet was clearly observed by high-speed video imaging. It is found that the slanted micro-pillar array is able to promote or inhibit the propagation of this thin liquid film in different directions by the asymmetric capillary force. The spreading behavior of the bulk liquid was guided and finally controlled by this micro-scale liquid film. Different spreading regimes are defined by the relationship between the liquid intrinsic contact angle and the critical angles, which were determined by the pillar height, pillar deflection angle and inter-pillar spacing. © The Royal Society of Chemistry 2013.

Quantitative diffusion characteristics of the human brain depend on MRI sequence parameters

International Nuclear Information System (INIS)

Wilson, M.; Blumhardt, L.D.; Morgan, P.S.

2002-01-01

Quantitative diffusion-weighted MRI has been applied to the study of neurological diseases, including multiple sclerosis, where the molecular self-diffusion coefficient D has been measured in both lesions and normal-appearing white matter. Histograms of D have been used as a novel measure of the ''lesion load'', with potential applications that include the monitoring of efficacy in new treatment trials. However different ways of measuring D may affect its value, making comparison between different centres and research groups impossible. We aimed to assess the effect, if any, of using two different MRI sequences on the value of D. We studied 13 healthy volunteers, using two different quantitative diffusion sequences (including different b max values and gradient applications). Maps of D were analysed using both regions of interest (ROI) in white matter and ''whole brain'' histograms, and compared between the two sequences. In addition, we studied three standardised test liquids (with known values of D) using both sequences. Histograms from the two sequences had different distributions, with a greater spread and higher peak position from the sequence with lower b max . This greater spread of D was also evident in the white matter and test liquid ROI. ''Limits of agreement'' analysis demonstrated that the differences could be clinically relevant, despite significant correlations between the sequences obtained using simple rank methods. We conclude that different quantitative diffusion sequences are unlikely to produce directly comparable values of D, particularly if different b max values are used. In addition, the use of inappropriate statistical tests may give false impressions of close agreement. Standardisation of methods for the measurement of D are required if these techniques are to become useful tools, for example in monitoring changes in the disease burden of multiple sclerosis. (orig.)

Quantitative diffusion characteristics of the human brain depend on MRI sequence parameters

Energy Technology Data Exchange (ETDEWEB)

Wilson, M.; Blumhardt, L.D. [University of Nottingham, Department of Neurology, Royal Preston Hospital, Preston (United Kingdom); Morgan, P.S. [Division of Academic Radiology, Queens Medical Centre, Nottingham (United Kingdom)

2002-07-01

Quantitative diffusion-weighted MRI has been applied to the study of neurological diseases, including multiple sclerosis, where the molecular self-diffusion coefficient D has been measured in both lesions and normal-appearing white matter. Histograms of D have been used as a novel measure of the ''lesion load'', with potential applications that include the monitoring of efficacy in new treatment trials. However different ways of measuring D may affect its value, making comparison between different centres and research groups impossible. We aimed to assess the effect, if any, of using two different MRI sequences on the value of D. We studied 13 healthy volunteers, using two different quantitative diffusion sequences (including different b{sub max} values and gradient applications). Maps of D were analysed using both regions of interest (ROI) in white matter and ''whole brain'' histograms, and compared between the two sequences. In addition, we studied three standardised test liquids (with known values of D) using both sequences. Histograms from the two sequences had different distributions, with a greater spread and higher peak position from the sequence with lower b{sub max}. This greater spread of D was also evident in the white matter and test liquid ROI. ''Limits of agreement'' analysis demonstrated that the differences could be clinically relevant, despite significant correlations between the sequences obtained using simple rank methods. We conclude that different quantitative diffusion sequences are unlikely to produce directly comparable values of D, particularly if different b{sub max} values are used. In addition, the use of inappropriate statistical tests may give false impressions of close agreement. Standardisation of methods for the measurement of D are required if these techniques are to become useful tools, for example in monitoring changes in the disease burden of multiple sclerosis. (orig.)

An Extended Multilocus Sequence Typing (MLST) Scheme for Rapid Direct Typing of Leptospira from Clinical Samples

OpenAIRE

Weiss, Sabrina; Menezes, Angela; Woods, Kate; Chanthongthip, Anisone; Dittrich, Sabine; Opoku-Boateng, Agatha; Kimuli, Maimuna; Chalker, Victoria

2016-01-01

Background Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST) data direct from patient specimens while minimising costs for subsequent sequencing. Methodology and Findings An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen t...

Nonlinear theory of the collisional Rayleigh-Taylor instability in equatorial spread F

International Nuclear Information System (INIS)

Chaturvedi, P.K.; Ossakow, S.L.

1977-01-01

The nonlinear behavior of the collisional Rayleigh-Taylor instability is studied in equatorial Spread F by including a dominant two-dimensional nonlinearity. It is found that on account of this nonlinearity the instability saturates by generating damped higher spatial harmonics. The saturated power spectrum for the density fluctuations is discussed. A comparison between experimental observations and theory is presented

Email networks and the spread of computer viruses

Science.gov (United States)

Newman, M. E.; Forrest, Stephanie; Balthrop, Justin

2002-09-01

Many computer viruses spread via electronic mail, making use of computer users' email address books as a source for email addresses of new victims. These address books form a directed social network of connections between individuals over which the virus spreads. Here we investigate empirically the structure of this network using data drawn from a large computer installation, and discuss the implications of this structure for the understanding and prevention of computer virus epidemics.

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

DEFF Research Database (Denmark)

Gloster, John; Jones, Andrew; Redington, Alison

2010-01-01

Foot-and-mouth disease virus (FMDV) 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....... Atmospheric dispersion models have been developed to assess airborne spread of FMDV in a number of countries, including the UK, Denmark, Australia, New Zealand, USA and Canada. These models were compared at a Workshop hosted by the Institute for Animal Health/Met Office in 2008. Each modeller was provided...... with data relating to the 1967 outbreak of FMD in Hampshire, UK, and asked to predict the spread of FMDV by the airborne route. A number of key issues emerged from the Workshop and subsequent modelling work: (1) in general all models predicted similar directions for livestock at risk, with much...

Competing spreading processes on multiplex networks: awareness and epidemics.

Science.gov (United States)

Granell, Clara; Gómez, Sergio; Arenas, Alex

2014-07-01

Epidemiclike spreading processes on top of multilayered interconnected complex networks reveal a rich phase diagram of intertwined competition effects. A recent study by the authors [C. Granell et al., Phys. Rev. Lett. 111, 128701 (2013).] presented an analysis of the interrelation between two processes accounting for the spreading of an epidemic, and the spreading of information awareness to prevent infection, on top of multiplex networks. The results in the case in which awareness implies total immunization to the disease revealed the existence of a metacritical point at which the critical onset of the epidemics starts, depending on completion of the awareness process. Here we present a full analysis of these critical properties in the more general scenario where the awareness spreading does not imply total immunization, and where infection does not imply immediate awareness of it. We find the critical relation between the two competing processes for a wide spectrum of parameters representing the interaction between them. We also analyze the consequences of a massive broadcast of awareness (mass media) on the final outcome of the epidemic incidence. Importantly enough, the mass media make the metacritical point disappear. The results reveal that the main finding, i.e., existence of a metacritical point, is rooted in the competition principle and holds for a large set of scenarios.

Analysis of a gamma-ray spectrum by using a standard spectrum

International Nuclear Information System (INIS)

Tasaka, Kanji

1975-06-01

The standard spectrum method has been extended to take into account the energy dependence of a standard spectrum. The method analyses the observed gamma-ray spectrum by the least-square method, using an interpolated standard spectrum for expressing the line shape and a linear function for the background continuum. The interpolated standard spectrum is defined for each fitting interval by interpolating several standard spectra, which are derived directly from the observed spectra of single photopeaks each corresponding to the incident monochromatic gamma-rays by subtracting the background and smoothing the data. (author)

PMS2 gene mutational analysis: direct cDNA sequencing to circumvent pseudogene interference.

Science.gov (United States)

Wimmer, Katharina; Wernstedt, Annekatrin

2014-01-01

The presence of highly homologous pseudocopies can compromise the mutation analysis of a gene of interest. In particular, when using PCR-based strategies, pseudogene co-amplification has to be effectively prevented. This is often achieved by using primers designed to be parental gene specific according to the reference sequence and by applying stringent PCR conditions. However, there are cases in which this approach is of limited utility. For example, it has been shown that the PMS2 gene exchanges sequences with one of its pseudogenes, named PMS2CL. This results in functional PMS2 alleles containing pseudogene-derived sequences at their 3'-end and in nonfunctional PMS2CL pseudogene alleles that contain gene-derived sequences. Hence, the paralogues cannot be distinguished according to the reference sequence. This shortcoming can be effectively circumvented by using direct cDNA sequencing. This approach is based on the selective amplification of PMS2 transcripts in two overlapping 1.6-kb RT-PCR products. In addition to avoiding pseudogene co-amplification and allele dropout, this method has also the advantage that it allows to effectively identify deletions, splice mutations, and de novo retrotransposon insertions that escape the detection of most DNA-based mutation analysis protocols.

Verona Coding Definitions of Emotional Sequences (VR-CoDES): Conceptual framework and future directions.

Science.gov (United States)

Piccolo, Lidia Del; Finset, Arnstein; Mellblom, Anneli V; Figueiredo-Braga, Margarida; Korsvold, Live; Zhou, Yuefang; Zimmermann, Christa; Humphris, Gerald

2017-12-01

To discuss the theoretical and empirical framework of VR-CoDES and potential future direction in research based on the coding system. The paper is based on selective review of papers relevant to the construction and application of VR-CoDES. VR-CoDES system is rooted in patient-centered and biopsychosocial model of healthcare consultations and on a functional approach to emotion theory. According to the VR-CoDES, emotional interaction is studied in terms of sequences consisting of an eliciting event, an emotional expression by the patient and the immediate response by the clinician. The rationale for the emphasis on sequences, on detailed classification of cues and concerns, and on the choices of explicit vs. non-explicit responses and providing vs. reducing room for further disclosure, as basic categories of the clinician responses, is described. Results from research on VR-CoDES may help raise awareness of emotional sequences. Future directions in applying VR-CoDES in research may include studies on predicting patient and clinician behavior within the consultation, qualitative analyses of longer sequences including several VR-CoDES triads, and studies of effects of emotional communication on health outcomes. VR-CoDES may be applied to develop interventions to promote good handling of patients' emotions in healthcare encounters. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

Science.gov (United States)

Scholz, Christian F P; Jensen, Anders

2017-01-01

The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.

Assignment of histidine resonances in the 1H NMR (500 MHz) spectrum of subtilisin BPN' using site-directed mutagenesis

International Nuclear Information System (INIS)

Bycroft, M.; Fersht, A.R.

1988-01-01

A spin-echo pulse sequence has been used to resolve the six histidine C-2H protons in the 500-MHz NMR spectrum of subtilisin BPN'. Five of these residues have been substituted by site-directed mutagenesis, and this has enabled a complete assignment of these protons to be obtained. Analysis of the pH titration curves of these signals has provided microscopic pK a 's for the six histidines in this enzyme. The pK a 's of the histidine residues in subtilisin BPN' have been compared with the values obtained for the histidines in the homologous enzyme from Bacillus licheniformis (subtilisin Carlsberg). Four of the five conserved histidines titrate with essentially identical pK a 's in the two enzymes. It therefore appears that the assignments made for these residues in subtilisin BPN' can be transferred to subtilisin Carlsberg. On the basis of these assignments, the one histidine that titrates with a substantially different pK a in the two enzymes can be assigned to histidine-238. This difference in pK a has been attributed to a Trp to Lys substitution at position 241 in subtilisin Carlsberg

The sequence spectrum of frameshift reversions obtained with a novel adaptive mutation assay in Saccharomyces cerevisiae

Directory of Open Access Journals (Sweden)

Erich Heidenreich

2016-12-01

Full Text Available Research on the mechanisms of adaptive mutagenesis in resting, i.e. non-replicating cells relies on appropriate mutation assays. Here we provide a novel procedure for the detection of frameshift-reverting mutations in yeast. Proliferation of non-reverted cells in this assay is suppressed by the lack of a fermentable carbon source. The test allele was constructed in a way that the reversions mimic microsatellite instability, a condition often found in cancer cells. We show the cell numbers during these starvation conditions and provide a DNA sequence spectrum of a representative set of revertants. The data in this article support the publication "Glucose starvation as a selective tool for the study of adaptive mutations in Saccharomyces cerevisiae" (Heidenreich and Steinboeck, 2016 [1].

Analytical procedure in aseismic design of eccentric structure using response spectrum

International Nuclear Information System (INIS)

Takemori, T.; Kuwabara, Y.; Suwabe, A.; Mitsunobu, S.

1977-01-01

In this paper, the response are evaluated by the following two methods by the use of the typical torsional analytical models in which masses, rigidities, eccentricities between the centers thereof and several actual earthquake waves are taken as the parameters: (1) the root mean square of responses by using the response spectra derived from the earthquake waves, (2) the time history analysis by using the earthquake wave. The earthquake waves used are chosen to present the different frequency content and magnitude of the response spectra. The typical results derived from the study are as follows: (a) the response accelerations of mass center in the input earthquake direction by the (1) method coincide comparatively well with those by the (2) method, (b) the response accelerations perpendicular to the input earthquake direction by (1) method are 2 to 3 times as much as those by the (2) method, (c) the amplification of the response accelerations at arbitrary points distributed on the spread mass to those of center of the lumped mass by the (1) method are remarkably large compared with those by the (2) method in both directions respectively. These problems on the response spectrum analysis for the above-mentioned eccentric structure are discussed, and an improved analytical method applying the amplification coefficients of responses derived from this parametric time history analysis is proposed to the actual seismic design by the using of the given design ground response spectrum with root mean square technique

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

Science.gov (United States)

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

2017-01-01

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

Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

Science.gov (United States)

Tan, M K

1991-08-01

A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

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

Science.gov (United States)

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.

Maximum likelihood sequence estimation for optical complex direct modulation.

Science.gov (United States)

Che, Di; Yuan, Feng; Shieh, William

2017-04-17

Semiconductor lasers are versatile optical transmitters in nature. Through the direct modulation (DM), the intensity modulation is realized by the linear mapping between the injection current and the light power, while various angle modulations are enabled by the frequency chirp. Limited by the direct detection, DM lasers used to be exploited only as 1-D (intensity or angle) transmitters by suppressing or simply ignoring the other modulation. Nevertheless, through the digital coherent detection, simultaneous intensity and angle modulations (namely, 2-D complex DM, CDM) can be realized by a single laser diode. The crucial technique of CDM is the joint demodulation of intensity and differential phase with the maximum likelihood sequence estimation (MLSE), supported by a closed-form discrete signal approximation of frequency chirp to characterize the MLSE transition probability. This paper proposes a statistical method for the transition probability to significantly enhance the accuracy of the chirp model. Using the statistical estimation, we demonstrate the first single-channel 100-Gb/s PAM-4 transmission over 1600-km fiber with only 10G-class DM lasers.

Term structure of 4d-electron configurations and calculated spectrum in Sn-isonuclear sequence

International Nuclear Information System (INIS)

Al-Rabban, Moza M.

2006-01-01

Theoretical calculations of term structure are carried out for the ground configurations 4d w , of atomic ions in the Sn isonuclear sequence. Atomic computations are performed to give a detailed account of the transitions in Sn +6 to Sn +13 ions. The spectrum is calculated for the most important excited configurations 4p 5 4d n+1 , 4d n-1 4f 1 , and 4d n-1 5p 1 with respect to the ground configuration 4d n , with n=8-1, respectively. The importance of 4p-4d, 4d-4f, and 4d-5p transitions is stressed, as well as the need for the configuration-interaction CI treatment of the Δn=0 transitions. In the region of importance for extreme ultraviolet (EUV) lithography around 13.4nm, the strongest lines were expected to be 4d n -4p 5 4d n+1 and 4d n -4d n-1 4f 1

The noise power spectrum in CT with direct fan beam reconstruction

International Nuclear Information System (INIS)

Baek, Jongduk; Pelc, Norbert J.

2010-01-01

The noise power spectrum (NPS) is a useful metric for understanding the noise content in images. To examine some unique properties of the NPS of fan beam CT, the authors derived an analytical expression for the NPS of fan beam CT and validated it with computer simulations. The nonstationary noise behavior of fan beam CT was examined by analyzing local regions and the entire field-of-view (FOV). This was performed for cases with uniform as well as nonuniform noise across the detector cells and across views. The simulated NPS from the entire FOV and local regions showed good agreement with the analytically derived NPS. The analysis shows that whereas the NPS of a large FOV in parallel beam CT (using a ramp filter) is proportional to frequency, the NPS with direct fan beam FBP reconstruction shows a high frequency roll off. Even in small regions, the fan beam NPS can show a sharp transition (discontinuity) at high frequencies. These effects are due to the variable magnification and therefore are more pronounced as the fan angle increases. For cases with nonuniform noise, the NPS can show the directional dependence and additional effects.

Direct and indirect impact of sewage sludge compost spreading on Quercus coccifera monoterpene emissions in a Mediterranean shrubland

Energy Technology Data Exchange (ETDEWEB)

Olivier, Romain [Aix-Marseille Universite - Institut Mediterraneen d' Ecologie et de Paleoecologie (IMEP), UMR 6111, Equipe Diversite Fonctionnelle des Communautes Vegetales - Centre de St Charles, Case 4, 13331 Marseille Cedex 03 (France); Staudt, Michael [Departement Fonctionnement des Ecosystemes, Centre d' Ecologie Fonctionnelle et Evolutive (CEFE, UMR 5175), 1919 Route de Mende, 34293 Montpellier Cedex 5 (France); Lavoir, Anne-Violette; Ormeno, Elena; Rizvi, Syed Hussain; Baldy, Virginie; Rivoal, Annabelle; Greff, Stephane; Lecareux, Caroline [Aix-Marseille Universite - Institut Mediterraneen d' Ecologie et de Paleoecologie (IMEP), UMR 6111, Equipe Diversite Fonctionnelle des Communautes Vegetales - Centre de St Charles, Case 4, 13331 Marseille Cedex 03 (France); Fernandez, Catherine, E-mail: catherine.fernandez@univ-provence.fr [Aix-Marseille Universite - Institut Mediterraneen d' Ecologie et de Paleoecologie (IMEP), UMR 6111, Equipe Diversite Fonctionnelle des Communautes Vegetales - Centre de St Charles, Case 4, 13331 Marseille Cedex 03 (France)

2011-04-15

Monoterpene emissions of Quercus coccifera L. were repeatedly measured during the two years following the spreading of a sewage sludge compost at rates of 50 Mg ha{sup -1} and 100 Mg ha{sup -1}, in a twelve-year-old post-fire Mediterranean shrubland. We also monitored the patterns of change in soil and leaf nutrient content, plant water potential, chlorophyll fluorescence, and plant growth. Compost spreading resulted in weak changes in leaf nutrient content and plant water status, and therefore no significant effect on monoterpene emissions at leaf scale, except during one summer sampling, probably related to advanced leaf maturity with the highest compost rate. However, compost increased plant growth, particularly the leaf biomass. The results suggest that compost spreading in Mediterranean shrublands has no strong short-term effect on Q. coccifera monoterpene emissions at leaf level, but may indirectly increase volatile organic compound fluxes at the stand scale, which may contribute to regional ozone pollution. - Research highlights: > Compost spreading had weak effects on leaf terpene emissions of Quercus coccifera. > Compost spreading increased leaf biomass of Q. coccifera. > Compost spreading indirectly increased Q. coccifera biogenic emissions, at the landscape scale. - Compost spreading in Mediterranean shrublands has no strong short-term effect on Q. coccifera monoterpene emissions at leaf level.

Direct and indirect impact of sewage sludge compost spreading on Quercus coccifera monoterpene emissions in a Mediterranean shrubland

International Nuclear Information System (INIS)

Olivier, Romain; Staudt, Michael; Lavoir, Anne-Violette; Ormeno, Elena; Rizvi, Syed Hussain; Baldy, Virginie; Rivoal, Annabelle; Greff, Stephane; Lecareux, Caroline; Fernandez, Catherine

2011-01-01

Monoterpene emissions of Quercus coccifera L. were repeatedly measured during the two years following the spreading of a sewage sludge compost at rates of 50 Mg ha -1 and 100 Mg ha -1 , in a twelve-year-old post-fire Mediterranean shrubland. We also monitored the patterns of change in soil and leaf nutrient content, plant water potential, chlorophyll fluorescence, and plant growth. Compost spreading resulted in weak changes in leaf nutrient content and plant water status, and therefore no significant effect on monoterpene emissions at leaf scale, except during one summer sampling, probably related to advanced leaf maturity with the highest compost rate. However, compost increased plant growth, particularly the leaf biomass. The results suggest that compost spreading in Mediterranean shrublands has no strong short-term effect on Q. coccifera monoterpene emissions at leaf level, but may indirectly increase volatile organic compound fluxes at the stand scale, which may contribute to regional ozone pollution. - Research highlights: → Compost spreading had weak effects on leaf terpene emissions of Quercus coccifera. → Compost spreading increased leaf biomass of Q. coccifera. → Compost spreading indirectly increased Q. coccifera biogenic emissions, at the landscape scale. - Compost spreading in Mediterranean shrublands has no strong short-term effect on Q. coccifera monoterpene emissions at leaf level.

Off-axis holographic lens spectrum-splitting photovoltaic system for direct and diffuse solar energy conversion.

Science.gov (United States)

Vorndran, Shelby D; Chrysler, Benjamin; Wheelwright, Brian; Angel, Roger; Holman, Zachary; Kostuk, Raymond

2016-09-20

This paper describes a high-efficiency, spectrum-splitting photovoltaic module that uses an off-axis volume holographic lens to focus and disperse incident solar illumination to a rectangular shaped high-bandgap indium gallium phosphide cell surrounded by strips of silicon cells. The holographic lens design allows efficient collection of both direct and diffuse illumination to maximize energy yield. We modeled the volume diffraction characteristics using rigorous coupled-wave analysis, and simulated system performance using nonsequential ray tracing and PV cell data from the literature. Under AM 1.5 illumination conditions the simulated module obtained a 30.6% conversion efficiency. This efficiency is a 19.7% relative improvement compared to the more efficient cell in the system (silicon). The module was also simulated under a typical meteorological year of direct and diffuse irradiance in Tucson, Arizona, and Seattle, Washington. Compared to a flat panel silicon module, the holographic spectrum splitting module obtained a relative improvement in energy yield of 17.1% in Tucson and 14.0% in Seattle. An experimental proof-of-concept volume holographic lens was also fabricated in dichromated gelatin to verify the main characteristics of the system. The lens obtained an average first-order diffraction efficiency of 85.4% across the aperture at 532 nm.

Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

Directory of Open Access Journals (Sweden)

Sara Imari Walker

Full Text Available 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

Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

DEFF Research Database (Denmark)

Binladen, Jonas; Wiuf, Carsten Henrik; Gilbert, M. Thomas P.

2006-01-01

To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved...... in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from...... adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nu...

Illusory spreading of watercolor.

Science.gov (United States)

Devinck, Frédéric; Hardy, Joseph L; Delahunt, Peter B; Spillmann, Lothar; Werner, John S

2006-05-04

The watercolor effect (WCE) is a phenomenon of long-range color assimilation occurring when a dark chromatic contour delineating a figure is flanked on the inside by a brighter chromatic contour; the brighter color spreads into the entire enclosed area. Here, we determined the optimal chromatic parameters and the cone signals supporting the WCE. To that end, we quantified the effect of color assimilation using hue cancellation as a function of hue, colorimetric purity, and cone modulation of inducing contours. When the inner and outer contours had chromaticities that were in opposite directions in color space, a stronger WCE was obtained as compared with other color directions. Additionally, equal colorimetric purity between the outer and inner contours was necessary to obtain a large effect compared with conditions in which the contours differed in colorimetric purity. However, there was no further increase in the magnitude of the effect when the colorimetric purity increased beyond a value corresponding to an equal vector length between the inner and outer contours. Finally, L-M-cone-modulated WCE was perceptually stronger than S-cone-modulated WCE for our conditions. This last result demonstrates that both L-M-cone and S-cone pathways are important for watercolor spreading. Our data suggest that the WCE depends critically upon the particular spatiochromatic arrangement in the display, with the relative chromatic contrast between the inducing contours being particularly important.

Radiation-induced germ-line mutations detected by a direct comparison of parents and children DNA sequences containing SNPs

International Nuclear Information System (INIS)

Morimyo, M.; Hongo, E.; Higashi, T.; Wu, J.; Matsumoto, I.; Okamoto, M.; Kawano, A.; Tsuji, S.

2003-01-01

Full text: Germ-line mutation is detected in mice but not in humans. To estimate genetic risk of humans, a new approach to extrapolate from animal data to humans or to directly detect radiation-induced mutations in man is expected. We have developed a new method to detect germ-line mutations by directly comparing DNA sequences of parents and children. The nucleotide sequences among mouse strains are almost identical except SNP markers that are detected at 1/1000 frequency. When gamma-irradiated male mice are mated with female mice, heterogeneous nucleotide sequences induced in children DNA are a candidate of mutation, whose assignment can be done by SNP analysis. This system can easily detect all types of mutations such as transition, transversion, frameshift and deletion induced by radiation and can be applied to humans having genetically heterogeneous nucleotide sequences and many SNP markers. C3H male mice of 8 weeks of gestation were irradiated with gamma rays of 3 and 1 Gy and after 3 weeks, they were mated with the same aged C57BL female mice. After 3 weeks breeding, DNA was extracted from parents and children mice. The nucleotide sequences of 150 STS markers containing 300-900 bp and SNPs of parents and children DNA were determined by a direct sequencing; amplification of STS markers by Taq DNA polymerase, purification of PCR products, and DNA sequencing with a dye-terminator method. At each radiation dose, a total amount of 5 Mb DNA sequences were examined to detect radiation-induced mutations. We could find 6 deletions in 3 Gy irradiated mice but not in 1 Gy and control mice. The mutation frequency was about 4.0 x 10 -7 /bp/ Gy or 1.6 x 10 -4 /locus/Gy, and suggested the non-linear increase of mutation rate with dose

[SPREADING OF NCTC CLONE 929 CELLS AFTER RESEEDING].

Science.gov (United States)

Petrov, Yu P; Negulyaev, Yu A; Tsupkina, N V

2015-01-01

The period (1 h after reseeding) of behaviour of mouse NCTC clone 929 cells to the conditions of artificial cultivation was studied. The time-lapse imaging followed the processing of the cells with ImageJ program was applied. To characterize the parametres cell status we used the cell area (projection of the cell on substrate) and Rp/Ra ratio introduced earlier as a spreading coefficient (Kuz'minykh, Petrov, 2004). After attaching a substratum, cells have a form of sphere (the phase "sphere") as the daughter cells after a mitosis. We revealed however that after this phase the reseeded cells do not start usual spreading and migration along substratum. They pass a phase of equally spreading in all directions and shaping their area as a circle (phase "circle"). This phase is absent of the daughter cells spreading after mitosis. We assume that the phase "circle" is a result of adaptation of the cells to reseedings at artificial cultivation. It is necessary for formation of a substrate composed of own extracellular matrix components (ECM) of the cells. Own ECM facilitates transition of the cells to their usual spreading and migration along substratum.

Spreading depolarizations increase delayed brain injury in a rat model of subarachnoid hemorrhage

NARCIS (Netherlands)

Hamming, Arend M.; Wermer, Marieke J. H.; Rudrapatna, S. Umesh; Lanier, Christian; van Os, Hine J. A.; van den Bergh, Walter M.; Ferrari, Michel D.; van der Toorn, Annette; van den Maagdenberg, Arn M. J. M.; Stowe, Ann M.; Dijkhuizen, Rick M.

Spreading depolarizations may contribute to delayed cerebral ischemia after aneurysmal subarachnoid hemorrhage, but the effect of spreading depolarizations on brain lesion progression after subarachnoid hemorrhage has not yet been assessed directly. Therefore, we tested the hypothesis that

Teaching Reading Comprehension and Language Skills to Students with Autism Spectrum Disorders and Developmental Disabilities Using Direct Instruction

Science.gov (United States)

Flores, Margaret M.; Nelson, Cynthia; Hinton, Vanessa; Franklin, Toni M.; Strozier, Shaunita D.; Terry, LaTonya; Franklin, Susan

2013-01-01

There is limited research demonstrating Direct Instruction (DI) as an effective reading comprehension intervention for students with autism spectrum disorders (ASD) and developmental disabilities (DD). Previous research has shown that DI, when portions of the program were implemented, resulted in increased skills (Flores & Ganz, 2007; Flores…

Filovirus Glycoprotein Sequence, Structure and Virulence

OpenAIRE

Phillips, J. C.

2014-01-01

Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range. Significance statement: Ebola virus is spreading rapidly in Africa. The connection between protein amino acid sequence and mortality is identified here.

Direct gaze elicits atypical activation of the theory-of-mind network in autism spectrum conditions.

Science.gov (United States)

von dem Hagen, Elisabeth A H; Stoyanova, Raliza S; Rowe, James B; Baron-Cohen, Simon; Calder, Andrew J

2014-06-01

Eye contact plays a key role in social interaction and is frequently reported to be atypical in individuals with autism spectrum conditions (ASCs). Despite the importance of direct gaze, previous functional magnetic resonance imaging in ASC has generally focused on paradigms using averted gaze. The current study sought to determine the neural processing of faces displaying direct and averted gaze in 18 males with ASC and 23 matched controls. Controls showed an increased response to direct gaze in brain areas implicated in theory-of-mind and gaze perception, including medial prefrontal cortex, temporoparietal junction, posterior superior temporal sulcus region, and amygdala. In contrast, the same regions showed an increased response to averted gaze in individuals with an ASC. This difference was confirmed by a significant gaze direction × group interaction. Relative to controls, participants with ASC also showed reduced functional connectivity between these regions. We suggest that, in the typical brain, perceiving another person gazing directly at you triggers spontaneous attributions of mental states (e.g. he is "interested" in me), and that such mental state attributions to direct gaze may be reduced or absent in the autistic brain.

KPC-mediated resistance in Klebsiella pneumoniae in two hospitals in Padua, Italy, June 2009-December 2011: massive spreading of a KPC-3-encoding plasmid and involvement of non-intensive care units

Directory of Open Access Journals (Sweden)

Richter Sara N

2012-07-01

Full Text Available Abstract Background Klebsiella pneumoniae carbapenemases (KPCs producing bacteria have emerged as a cause of multidrug-resistant nosocomial infections worldwide. KPCs are plasmid-encoded enzymes capable of hydrolysing a broad spectrum of beta-lactams, including carbapenems and monobactams, therefore worryingly limiting antimicrobial treatment options. Analysis of circulating bacterial strains and KPC alleles may help understanding the route of KPC dissemination and therefore help containing the infection. Methods KPC-producing Klebsiella pneumoniae dissemination in two 1580- and 300- bed hospitals in Padua, Italy, from initial outbreak in 2009 to late 2011 was analysed. Molecular and clinical epidemiology, including bacterial strains, KPC-encoding plasmid sequences and associated resistance genes, involved hospital wards and relocation of patients were described. Routine antimicrobial susceptibility testing and MIC of carbapenems on clinical isolates were performed. Detection of resistance genes was obtained by PCR and sequencing. MLST, PFGE and ERIC were used for molecular genotyping. Plasmid analysis was obtained by digestion with restriction enzymes and deep sequencing. Results KPC-positive clinical samples were isolated from nearly 200 patients. In the initial outbreak intensive care units were almost exclusively involved, while medical, surgical and long-term wards were successively massively concerned. Analysis of KPC alleles, plasmids and bacterial sequence types (STs indicated that during the initial outbreak KPC-3 in ST258 and KPC-2 in ST147 were each confined in one of the two surveilled hospitals. While KPC-2 dissemination was effectively contained, KPC-3 in ST258 cross-spreading was observed. The simultaneous presence of two carbapenemases, VIM-1 and KPC-2, in the same isolate was also observed in three patients. Total sequencing of plasmid content of two KPC-3 strains showed novel association of resistance plasmids. Conclusions The

Cell spreading on titanium dioxide film formed and modified with aerosol beam and femtosecond laser

International Nuclear Information System (INIS)

Shinonaga, Togo; Tsukamoto, Masahiro; Nagai, Akiko; Yamashita, Kimihiro; Hanawa, Takao; Matsushita, Nobuhiro; Xie, Guoqiang; Abe, Nobuyuki

2014-01-01

Titanium (Ti) is widely used in biomaterials because of its excellent anti-corrosion properties and high strength. However, Ti has no biological function, so its bioactivity must be improved. Coating a titanium dioxide (TiO 2 ) film on a Ti plate surface has been shown to improve the biocompatibility of Ti plates. If periodic nanostructures were formed on the film surface, the direction of cell spreading might be controlled by the direction of the grooves. Controlling cell spreading on biomaterials would contribute to the creation of advanced biomaterials. In this paper, a TiO 2 film was formed on a Ti plate with an aerosol beam composed of sub micron-sized TiO 2 particles and helium gas. Periodic nanostructures, lying perpendicular to the laser electric field polarization vector, were formed on the film by scanning the femtosecond laser focusing spot. The period and height of the periodic nanostructures were about 230 nm and 150 nm, respectively. In a cell test, cell spreading was observed along the grooves of the periodic nanostructures; in contrast, cell spreading did not show a definite direction on TiO 2 a film without periodic nanostructures. These results suggest that the direction of cell spreading on the film can be controlled by periodic nanostructure formation generated using a femtosecond laser.

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

Science.gov (United States)

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.

Spectrum of benzo[a]pyrene-induced mutations in the Pig-a gene of L5178YTk+/- cells identified with next generation sequencing.

Science.gov (United States)

Revollo, Javier; Wang, Yiying; McKinzie, Page; Dad, Azra; Pearce, Mason; Heflich, Robert H; Dobrovolsky, Vasily N

2017-12-01

We used Sanger sequencing and next generation sequencing (NGS) for analysis of mutations in the endogenous X-linked Pig-a gene of clonally expanded L5178YTk +/- cells. The clones developed from single cells that were sorted on a flow cytometer based upon the expression pattern of the GPI-anchored marker, CD90, on their surface. CD90-deficient and CD90-proficient cells were sorted from untreated cultures and CD90-deficient cells were sorted from cultures treated with benzo[a]pyrene (B[a]P). Pig-a mutations were identified in all clones developed from CD90-deficient cells; no Pig-a mutations were found in clones of CD90-proficient cells. The spectrum of B[a]P-induced Pig-a mutations was dominated by basepair substitutions, small insertions and deletions at G:C, or at sequences rich in G:C content. We observed high concordance between Pig-a mutations determined by Sanger sequencing and by NGS, but NGS was able to identify mutations in samples that were difficult to analyze by Sanger sequencing (e.g., mixtures of two mutant clones). Overall, the NGS method is a cost and labor efficient high throughput approach for analysis of a large number of mutant clones. Published by Elsevier B.V.

Demostration of 520 Gb/s/λ pre-equalized DFT-spread PDM-16QAM-OFDM signal transmission.

Science.gov (United States)

Li, Fan; Yu, Jianjun; Cao, Zizheng; Chen, Ming; Zhang, Junwen; Li, Xinying

2016-02-08

In this paper, we successfully transmit 8 × 520 Gb/s pre-equalized DFT-spread PDM-16QAM orthogonal frequency-division multiplexing (OFDM) signal over 840 km SMF with BER under 2.4 × 10(-2). We discuss how to obtain accurate tranceivers' response during pre-equalization for DFT-spread OFDM with coherent detection and we find conventional OFDM symbols training sequences (TSs) outperform DFT-spread OFDM symbols TSs in obtaining channel response for pre-equalization and equalization. Additionally, the optimal IFFT/FFT size is explored for the pre-equalized DFT-spread PDM-16QAM-OFDM transmission systems. It is the first time to realize 400 Gb/s/λ net rate OFDM signal transmission.

Gradient-recalled echo sequences in direct shoulder MR arthrography for evaluating the labrum

International Nuclear Information System (INIS)

Lee, Marc J.; Motamedi, Kambiz; Chow, Kira; Seeger, Leanne L.

2008-01-01

The purpose of this study was to determine the utility of fat-suppressed gradient-recalled echo (GRE) compared with conventional spin echo T1-weighted (T1W) sequences in direct shoulder MR arthrography for evaluating labral tears. Three musculoskeletal radiologists retrospectively reviewed MR arthrograms performed over a 12-month period for which surgical correlation was available. Of 180 serial arthrograms, 31 patients had surgery with a mean of 48 days following imaging. Paired coronal oblique and axial T1W or GRE sequences were analyzed by consensus for labral tear (coronal oblique two-dimensional multi-echo data image combination, 2D MEDIC; and axial three-dimensional double-echo steady-state, 3D DESS; Siemens MAGNETOM Sonata 1.5-T MR system). Interpretations were correlated with operative reports. Of 31 shoulders, 25 had labral tears at surgery. The GRE sequences depicted labral tears in 22, while T1W images depicted tears in 16 (sensitivity 88% versus 64%; p 0.7). Specificities were somewhat lower for GRE. Thin section GRE sequences are more sensitive than T1W for the detection of anterior and posterior labral tears. As the specificity of GRE was lower, it should be considered as an adjunctive imaging sequence that may improve depiction of labral tears, particularly smaller tears, in routine MR arthrography protocols. (orig.)

Evaluation of geometrical contributions to the spread of the Compton-scatter energy distribution

International Nuclear Information System (INIS)

Hanson, A.L.; Gigante, G.E.; Dipartimento di Fisica, Universita degli Studi di Roma I, ''La Sapienza,'' Corso Vittorio Emanuele II, 244, 00186 Roma, Italy)

1989-01-01

The spectrum from Compton-scattered x rays is an inherently broad distribution. This distribution is the sum of several Gaussian-like distributions, which gives the sum its unique shape. The Gaussian-like distributions are the result of convoluting the so-called Compton profile, the spread in the scattered-x-ray energies due to the momentum distributions of the target electrons, with the detector response and the geometrical effects. The distribution is then further modified by the absorption within the sample. A formulation for both qualitatively and quantitatively determining the magnitude of the geometrical contributions is presented. This formulation is based on a recently devised approach to the scattering geometry [Hanson, Gigante, Meron, Phys. Rev. Lett. 61, 135 (1988)]. A methodology for determining the geometrical spread in the energy of the scattered x rays is presented. The results can be conveniently used to optimize scattering geometries for the reduction of the geometry-caused spread

Spreading Depression, Spreading Depolarizations, and the Cerebral Vasculature

DEFF Research Database (Denmark)

Ayata, Cenk; Lauritzen, Martin

2015-01-01

Spreading depression (SD) is a transient wave of near-complete neuronal and glial depolarization associated with massive transmembrane ionic and water shifts. It is evolutionarily conserved in the central nervous systems of a wide variety of species from locust to human. The depolarization spreads...

Sequence History Update Tool

Science.gov (United States)

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

2008-01-01

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

Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria.

Science.gov (United States)

Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

2017-05-10

Bacillus velezensis LS69 was found to exhibit antagonistic activity against a diverse spectrum of pathogenic bacteria. It has one circular chromosome of 3,917,761bp with 3,643 open reading frames. Genome analysis identified ten gene clusters involved in nonribosomal synthesis of polyketides (macrolactin, bacillaene and difficidin), lipopeptides (surfactin, fengycin, bacilysin and iturin A) and bacteriocins (amylolysin and amylocyclicin). In addition, B. velezensis LS69 was found to contain a series of genes involved in enhancing plant growth and triggering plant immunity. Whole genome sequencing of Bacillus velezensis LS69 will provide a basis for elucidation of its biocontrol mechanisms and facilitate its applications in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

Flame spread over electrical wire with AC electric fields: Internal circulation, fuel vapor-jet, spread rate acceleration, and molten insulator dripping

KAUST Repository

Lim, Seungjae

2015-04-01

The effect of electric field on the characteristics of flame spread along a polyethylene (PE) insulated electrical wire was investigated experimentally by varying the AC frequency and voltage applied to the wire. The results showed that the flame spread rate was accelerated due to the convergence of electric flux near the end of wire, having three distinct regimes depending on applied voltage. In each regime, several subregimes could be identified depending on AC frequency. Flame shape (height and width) and slanted direction of the spreading flame were influenced differently. Fuel-vapor jets were ejected from the molten PE surface even for the baseline case without the application of an electric field; this could be attributed to the bursting of fuel vapor bubbles generated from internal boiling at the molten PE surface. An internal circulation of molten-PE was also observed as a result of non-uniform heating by the spreading flame. In the high voltage regime with a high AC frequency, excessive dripping of molten PE led to flame extinction.

Direct measurements of the spectrum of the near-millimeter cosmic background

International Nuclear Information System (INIS)

Richards, P.L.

1980-01-01

The spectrum of the cosmic background radiation peaks at 6 cm -1 and falls rapidly at higher frequencies. The experimental determination of this simple but important fact has had a long and troubled history. It remained in doubt long after the nature of the Rayleigh-Jeans region of the spectrum was firmly established. In this review the author describes the experimental difficulties which have plagued cosmic background measurements at and beyond the peak in the spectrum. A critical evaluation of the present status of the field is then given. (Auth.)

Several Families of Sequences with Low Correlation and Large Linear Span

Science.gov (United States)

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].

Typing of Staphylococcus aureus in order to determine the spread of drug resistant strains inside and outside hospital environment.

Science.gov (United States)

Pobiega, Monika; Wójkowska-Mach, Jadwiga; Heczko, Piotr B

2013-01-01

Staphylococcus aureus is one of the most important etiological factors of both nosocomial and community-acquired infections. Multidrug-resistant S. aureus is frequently isolated nowadays. Antibiotics used on the hospital ward exert a selective pressure on the strains and favor resistant strains. Multidrug-resistant and highly virulent strains can spread not only within the hospital but also between hospitals. Numerous studies show a predominance of one clone on a specific territory. The spread of such dangerous clones to neighboring countries and the entire continent is possible. Typing methods are very useful in infection control and prevention. Modern methods which are based on sequencing are necessary in rationalizing of infection control programs. Typing of Staphylococcus aureus includes methods that allow to determine the spread of drug-resistant pathogens. 'Gold standard' is pulsed-field gel electrophoresis (PFGE), which relies on separating the DNA fragments after restriction cutting. MLST (Multi Locus Sequence Typing) is based on a comparison of"housekeeping" gene sequences controlling the basic cell functions. With the MLST method, it is possible to demonstrate a broad, international spread of the specific clones. However, for epidemiological investigations, MLST seems to be too time-consuming and expensive to be used as a basic typing tool. The complementary method is spa typing, based on the sequencing of short repetitive sequences of the polymorphic X region from the gene encoding protein A. This method can be used for studying molecular evolution of S. aureus, as well as for testing for hospital outbreaks. It is faster and cheaper than MLST. It is also necessary to subtype the elements responsible for methycillin resistance (SCCmec), which allows to distinguish MRSA (Methicillin-resistant Staphylococcus aureus) clones with a common ancestor, but different epidemiological origin. All of those methods have their specific advantages and disadvantages and

Cell spreading on titanium dioxide film formed and modified with aerosol beam and femtosecond laser

Energy Technology Data Exchange (ETDEWEB)

Shinonaga, Togo, E-mail: togo@jwri.osaka-u.ac.jp [Graduate School of Engineering, Osaka University, 1-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Tsukamoto, Masahiro [Joining and Welding Research Institute, Osaka University, 11-1 Mihogaoka, Ibaraki, Osaka 567-0047 (Japan); Nagai, Akiko; Yamashita, Kimihiro; Hanawa, Takao [Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062 (Japan); Matsushita, Nobuhiro [Materials and Structures Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Xie, Guoqiang [Institute for Materials Research, Tohoku University, 2-1-1 Karahira, Aoba-ku, Sendai, Miyagi 980-8577 (Japan); Abe, Nobuyuki [Joining and Welding Research Institute, Osaka University, 11-1 Mihogaoka, Ibaraki, Osaka 567-0047 (Japan)

2014-01-01

Titanium (Ti) is widely used in biomaterials because of its excellent anti-corrosion properties and high strength. However, Ti has no biological function, so its bioactivity must be improved. Coating a titanium dioxide (TiO{sub 2}) film on a Ti plate surface has been shown to improve the biocompatibility of Ti plates. If periodic nanostructures were formed on the film surface, the direction of cell spreading might be controlled by the direction of the grooves. Controlling cell spreading on biomaterials would contribute to the creation of advanced biomaterials. In this paper, a TiO{sub 2} film was formed on a Ti plate with an aerosol beam composed of sub micron-sized TiO{sub 2} particles and helium gas. Periodic nanostructures, lying perpendicular to the laser electric field polarization vector, were formed on the film by scanning the femtosecond laser focusing spot. The period and height of the periodic nanostructures were about 230 nm and 150 nm, respectively. In a cell test, cell spreading was observed along the grooves of the periodic nanostructures; in contrast, cell spreading did not show a definite direction on TiO{sub 2} a film without periodic nanostructures. These results suggest that the direction of cell spreading on the film can be controlled by periodic nanostructure formation generated using a femtosecond laser.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Dennis Maletich Junqueira

Full Text Available 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.

Molecular phylogeography of canine distemper virus: Geographic origin and global spreading.

Science.gov (United States)

Panzera, Yanina; Sarute, Nicolás; Iraola, Gregorio; Hernández, Martín; Pérez, Ruben

2015-11-01

Canine distemper virus (CDV) (Paramyxoviridae-Morbillivirus) is a worldwide spread virus causing a fatal systemic disease in a broad range of carnivore hosts. In this study we performed Bayesian inferences using 208 full-length hemagglutinin gene nucleotide sequences isolated in 16 countries during 37 years (1975-2011). The estimated time to the most recent common ancestor suggested that current CDV strains emerged in the United States in the 1880s. This ancestor diversified through time into two ancestral clades, the current America 1 lineage that recently spread to Asia, and other ancestral clade that diversified and spread worldwide to originate the remaining eight lineages characterized to date. The spreading of CDV was characterized by several migratory events with posterior local differentiation, and expansion of the virus host range. A significant genetic flow between domestic and wildlife hosts is displayed; being domestic hosts the main viral reservoirs worldwide. This study is an extensive and integrative description of spatio/temporal population dynamics of CDV lineages that provides a novel evolutionary paradigm about the origin and dissemination of the current strains of the virus. Copyright © 2015 Elsevier Inc. All rights reserved.

Sadhana | Indian Academy of Sciences

Indian Academy of Sciences (India)

Because of the complex structure the sequences are very difficult to detect and analyse by an enemy's electronic support measures (ESMs). The synthesized sequences are promising for practical application to radar and spread spectrum communication systems. These sequences are found using the Modified Simulated ...

Fine structure and energy spectrum of exciton in direct band gap cubic semiconductors with degenerate valence bands

International Nuclear Information System (INIS)

Nguyen Toan Thang; Nguyen Ai Viet; Nguyen Que Huong

1987-06-01

The influence of the cubic structure on the energy spectrum of direct exciton is investigated, using the new method suggested by Nguyen Van Hieu and co-workers. Explicit expressions of the exciton energy levels 1S, 2S and 2P are derived. A comparison with the experiments and the other theory is done for ZnSe. (author). 10 refs, 1 fig., 2 tabs

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

Science.gov (United States)

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

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

Hanni S M Kiiski

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

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

Science.gov (United States)

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

Human genome sequencing with direct x-ray holographic imaging

International Nuclear Information System (INIS)

Rhodes, C.K.

1993-01-01

Direct holographic imaging of biological materials is widely applicable to the study of the structure, properties and action of genetic material. This particular application involves the sequencing of the human genome where prospective genomic imaging technology is composed of three subtechnologies, name an x-ray holographic camera, suitable chemistry and enzymology for the preparation of tagged DNA samples, and the illuminator in the form of an x-ray laser. We report appropriate x-ray camera, embodied by the instrument developed by MCR, is available and that suitable chemical and enzymatic procedures exist for the preparation of the necessary tagged DNA strands. Concerning the future development of the x-ray illuminator. We find that a practical small scale x-ray light source is indeed feasible. This outcome requires the use of unconventional physical processes in order to achieve the necessary power-compression in the amplifying medium. The understanding of these new physical mechanisms is developing rapidly. Importantly, although the x-ray source does not currently exist, the understanding of these new physical mechanisms is developing rapidly and the research has established the basic scaling laws that will determine the properties of the x-ray illuminator. When this x-ray source becomes available, an extremely rapid and cost effective instrument for 3-D imaging of biological materials can be applied to a wide range of biological structural assays, including the base-pair sequencing of the human genome and many questions regarding its higher levels of organization

The Symmetric Rudin-Shapiro Transform

DEFF Research Database (Denmark)

Harbo, Anders La-Cour

2003-01-01

A method for constructing spread spectrum sequences is presented. The method is based on a linear, orthogonal, symmetric transform, the Rudin-Shapiro transform (RST), which is in many respects quite similar to the Haar wavelet packet transform. The RST provides the means for generating large sets...... of spread spectrum signals. This presentation provides a simple definition of the symmetric RST that leads to a fast N log(N) and numerically stable implementation of the transform....

The impact of cerebellar transcranial direct current stimulation (tDCS) on learning fine-motor sequences.

Science.gov (United States)

Shimizu, Renee E; Wu, Allan D; Samra, Jasmine K; Knowlton, Barbara J

2017-01-05

The cerebellum has been shown to be important for skill learning, including the learning of motor sequences. We investigated whether cerebellar transcranial direct current stimulation (tDCS) would enhance learning of fine motor sequences. Because the ability to generalize or transfer to novel task variations or circumstances is a crucial goal of real world training, we also examined the effect of tDCS on performance of novel sequences after training. In Study 1, participants received either anodal, cathodal or sham stimulation while simultaneously practising three eight-element key press sequences in a non-repeating, interleaved order. Immediately after sequence practice with concurrent tDCS, a transfer session was given in which participants practised three interleaved novel sequences. No stimulation was given during transfer. An inhibitory effect of cathodal tDCS was found during practice, such that the rate of learning was slowed in comparison to the anodal and sham groups. In Study 2, participants received anodal or sham stimulation and a 24 h delay was added between the practice and transfer sessions to reduce mental fatigue. Although this consolidation period benefitted subsequent transfer for both tDCS groups, anodal tDCS enhanced transfer performance. Together, these studies demonstrate polarity-specific effects on fine motor sequence learning and generalization.This article is part of the themed issue 'New frontiers for statistical learning in the cognitive sciences'. © 2016 The Author(s).

Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples

DEFF Research Database (Denmark)

Hasman, Henrik; Saputra, Dhany; Sicheritz-Pontén, Thomas

2014-01-01

Whole genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples this could further reduce diagnostic time and thereby improve control and treatment. A major bottle-neck is the availability of fast and reliable bioinformatics...

Exploring the Complex Pattern of Information Spreading in Online Blog Communities

Science.gov (United States)

Pei, Sen; Muchnik, Lev; Tang, Shaoting; Zheng, Zhiming; Makse, Hernán A.

2015-01-01

Information spreading in online social communities has attracted tremendous attention due to its utmost practical values in applications. Despite that several individual-level diffusion data have been investigated, we still lack the detailed understanding of the spreading pattern of information. Here, by comparing information flows and social links in a blog community, we find that the diffusion processes are induced by three different spreading mechanisms: social spreading, self-promotion and broadcast. Although numerous previous studies have employed epidemic spreading models to simulate information diffusion, we observe that such models fail to reproduce the realistic diffusion pattern. In respect to users behaviors, strikingly, we find that most users would stick to one specific diffusion mechanism. Moreover, our observations indicate that the social spreading is not only crucial for the structure of diffusion trees, but also capable of inducing more subsequent individuals to acquire the information. Our findings suggest new directions for modeling of information diffusion in social systems, and could inform design of efficient propagation strategies based on users behaviors. PMID:25985081

Global stability of a two-mediums rumor spreading model with media coverage

Science.gov (United States)

Huo, Liang'an; Wang, Li; Song, Guoxiang

2017-09-01

Rumor spreading is a typical form of social communication and plays a significant role in social life, and media coverage has a great influence on the spread of rumor. In this paper, we present a new model with two media coverage to investigate the impact of the different mediums on rumor spreading. Then, we calculate the equilibria of the model and construct the reproduction number ℜ0. And we prove the global asymptotic stability of equilibria by using Lyapunov functions. Finally, we can conclude that the transition rate of the ignorants between two mediums has a direct effect on the scale of spreaders, and different media coverage has significant effects on the dynamics behaviors of rumor spreading.

Golay sequences coded coherent optical OFDM for long-haul transmission

Science.gov (United States)

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.

Roles of the spreading scope and effectiveness in spreading dynamics on multiplex networks

Science.gov (United States)

Li, Ming; Liu, Run-Ran; Peng, Dan; Jia, Chun-Xiao; Wang, Bing-Hong

2018-02-01

Comparing with single networks, the multiplex networks bring two main effects on the spreading process among individuals. First, the pathogen or information can be transmitted to more individuals through different layers at one time, which enlarges the spreading scope. Second, through different layers, an individual can also transmit the pathogen or information to the same individuals more than once at one time, which makes the spreading more effective. To understand the different roles of the spreading scope and effectiveness, we propose an epidemic model on multiplex networks with link overlapping, where the spreading effectiveness of each interaction as well as the variety of channels (spreading scope) can be controlled by the number of overlapping links. We find that for Poisson degree distribution, increasing the epidemic scope (the first effect) is more efficient than enhancing epidemic probability (the second effect) to facilitate the spreading process. However, for power-law degree distribution, the effects of the two factors on the spreading dynamics become complicated. Enhancing epidemic probability makes pathogen or rumor easier to outbreak in a finite system. But after that increasing epidemic scopes is still more effective for a wide spreading. Theoretical results along with reasonable explanation for these phenomena are all given in this paper, which indicates that the epidemic scope could play an important role in the spreading dynamics.

Gasification of the southern spread of Bolivia-Brazil gas pipeline

International Nuclear Information System (INIS)

Frisoli, Caetano; Senna, Ferando Jose Ennes de; Faria, Jose Aurelio Carvalho de

2000-01-01

As to the commissioning of the Northern spread, Inert Direct Purging was also adopted for purging the Southern Spread of Bolivia-Brazil Gas Pipeline. This section is 1191 km long and lies between the city of Paulinia in the State of Sao Paulo up to Canoas in the Sate of Rio Grande do Sul. The Inert Direct Purging is based on the principle of high gas injection flow rates at the initial point and the purging of air at the other end, separated by a nitrogen plug. A purging model, developed by The Gas Research Institute, was used in conjunction with the software Pipeline Studio for planning purposes. The arrival of gas at each valve and the size of gas/nitrogen/air interfaces were also recorded. Graphs and tables compare calculated and recorded data. Final results demonstrated model accuracy and its suitable applicability for purging, as well as the Inert Direct Purging method for gas pipelines of extensive lengths. (author)

Formation of hemoglobin (Hb)-octadecylamine (ODA) Langmuir-Blodgett (LB) film by spreading Hb solution directly onto subphase covered with a layer of ODA and its electrochemical property

International Nuclear Information System (INIS)

Yin Fan; Shin, Hoon-Kyu; Kwon, Young-Soo

2006-01-01

The formation of hemoglobin (Hb)-octadecylamine (ODA) Langmuir-Blotgett (LB) film by spreading Hb solution directly onto subphase covered with a layer of ODA and its electrochemical properties were studied in this paper. This method ensured better electrode activity because almost no protein was adsorbed onto electrode surface before depositing Hb-ODA monolayer onto electrode surface. The optimum equilibrium time of Hb interacted with ODA layer, the optimum protein amount spread onto subphase's interface and the optimum ionic strength and pH of subphase were obtained from the experimental results. The compressibility analyses of Hb-ODA films showed that the surface pressure of this film from liquid-expanded to liquid-condensed state ranged between 16 and 40 mN/m. Direct electron transfer of Hb immobilized on gold electrode by LB technique was observed by cyclic voltammetry. Results showed that Hb molecules still kept their electrochemical activity. The electrode with Hb-ODA LB film displayed the fastest electron transfer rate when the film transferred under the surface pressure of 35 mN/m

Formation of hemoglobin (Hb)-octadecylamine (ODA) Langmuir-Blodgett (LB) film by spreading Hb solution directly onto subphase covered with a layer of ODA and its electrochemical property

Energy Technology Data Exchange (ETDEWEB)

Yin Fan [Department of Electrical Engineering, Dong-A University, Busan 604-714 (Korea, Republic of); Department of Chemistry, Changshu Institute of Technology, Changshu, 215500 (China); Shin, Hoon-Kyu [Department of Electrical Engineering, Dong-A University, Busan 604-714 (Korea, Republic of); Kwon, Young-Soo [Department of Electrical Engineering, Dong-A University, Busan 604-714 (Korea, Republic of)]. E-mail: yskwon@daunet.donga.ac.kr

2006-03-21

The formation of hemoglobin (Hb)-octadecylamine (ODA) Langmuir-Blotgett (LB) film by spreading Hb solution directly onto subphase covered with a layer of ODA and its electrochemical properties were studied in this paper. This method ensured better electrode activity because almost no protein was adsorbed onto electrode surface before depositing Hb-ODA monolayer onto electrode surface. The optimum equilibrium time of Hb interacted with ODA layer, the optimum protein amount spread onto subphase's interface and the optimum ionic strength and pH of subphase were obtained from the experimental results. The compressibility analyses of Hb-ODA films showed that the surface pressure of this film from liquid-expanded to liquid-condensed state ranged between 16 and 40 mN/m. Direct electron transfer of Hb immobilized on gold electrode by LB technique was observed by cyclic voltammetry. Results showed that Hb molecules still kept their electrochemical activity. The electrode with Hb-ODA LB film displayed the fastest electron transfer rate when the film transferred under the surface pressure of 35 mN/m.

A theoretical and numerical study of polarimetric scattering and emission from random rough surfaces with anisotropic directional spectrum

Science.gov (United States)

Yueh, S. H.; Kwok, R.

1993-01-01

In this paper, theoretical and numerical results of the polarimetric scattering and emission from random rough surfaces with anisotropic directional spectrum are presented for the remote sensing of ocean and soil surfaces. The polarimetric scattered field for rough dielectric surfaces is derived to the second order by the small perturbation method (SPM). It is found that the second-order scattered field is coherent in nature, and its coefficients for different polarizations present the lowest-order corrections to the Fresnel reflection coefficients of the surfaces. In addition, the cross-polarized (HV and VH) components of the coherent fields are reciprocal and not zero for surfaces with anisotropic directional spectrum when the azimuth angle of the incident direction is not aligned with the symmetry directions of surfaces. In order to verify the energy conservation condition of the theoretical results, which is important if the theory is to be applied to the passive polarimetry of rough surfaces, a Monte Carlo simulation is performed to numerically calculate the polarimetric reflectivities of one-dimensional random rough surfaces which are generated with a prescribed power-law spectrum in the spectral domain and transformed to the spatial domain by the FFT. The surfaces simulated by this approach are periodic with the period corresponding to the low-wavenumber cutoff. To calculate the scattering from periodic dielectric surfaces, the authors present a new numerical technique which applies the Floquet theorem to reduce the problem to one period and does not require the evaluation of one-dimensional periodic Green's function used in the conventional method of moment formulation. Once the scattering coefficients are obtained, the polarimetric Stokes vectors for the emission from the random surfaces are then calculated according to the Kirchhoff's law and are illustrated as functions of relative azimuth observation and row directions. The second-order SPM is also

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

Science.gov (United States)

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

The Symmetric Rudin-Shapiro Transform

DEFF Research Database (Denmark)

Harbo, Anders La-Cour

2003-01-01

A method for constructing spread spectrum sequences is presented. The method is based on a linear, orthogonal, and symmetric transform given as the Rudin-Shapiro transform (RST), which is in many respects quite similar to the Haar wavelet packet transform. The RST provides the means for generatin...... large sets of spread spectrum signals. This presentation provides a simple definition of the symmetric RST that leads to a fast N log(N) and numerically stable implementation of the transform....

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

Science.gov (United States)

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.

Mechanistic movement models to understand epidemic spread.

Science.gov (United States)

Fofana, Abdou Moutalab; Hurford, Amy

2017-05-05

An overlooked aspect of disease ecology is considering how and why animals come into contact with one and other resulting in disease transmission. Mathematical models of disease spread frequently assume mass-action transmission, justified by stating that susceptible and infectious hosts mix readily, and foregoing any detailed description of host movement. Numerous recent studies have recorded, analysed and modelled animal movement. These movement models describe how animals move with respect to resources, conspecifics and previous movement directions and have been used to understand the conditions for the occurrence and the spread of infectious diseases when hosts perform a type of movement. Here, we summarize the effect of the different types of movement on the threshold conditions for disease spread. We identify gaps in the literature and suggest several promising directions for future research. The mechanistic inclusion of movement in epidemic models may be beneficial for the following two reasons. Firstly, the estimation of the transmission coefficient in an epidemic model is possible because animal movement data can be used to estimate the rate of contacts between conspecifics. Secondly, unsuccessful transmission events, where a susceptible host contacts an infectious host but does not become infected can be quantified. Following an outbreak, this enables disease ecologists to identify 'near misses' and to explore possible alternative epidemic outcomes given shifts in ecological or immunological parameters.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Author(s).

Spread effects - methodology

International Nuclear Information System (INIS)

2004-01-01

Diffusion of technology, environmental effects and rebound effects are the principal effects from the funding of renewable energy and energy economising. It is difficult to estimate the impact of the spread effects both prior to the measures are implemented and after the measures are carried out. Statistical methods can be used to estimate the spread effects, but they are insecure and always need to be complemented with qualitative and subjective evaluations. It is more adequate to evaluate potential spread effects from market and market data surveillance for a selection of technologies and parties. Based on this information qualitative indicators for spread effects can be constructed and used both ex ante and ex post (ml)

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

Science.gov (United States)

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

Complete Genome Sequence of the Goatpox Virus Strain Gorgan Obtained Directly from a Commercial Live Attenuated Vaccine

Science.gov (United States)

Mathijs, Elisabeth; Vandenbussche, Frank; Haegeman, Andy; Al-Majali, Ahmad; De Clercq, Kris

2016-01-01

This is a report of the complete genome sequence of the goatpox virus strain Gorgan, which was obtained directly from a commercial live attenuated vaccine (Caprivac, Jordan Bio-Industries Centre). PMID:27738031

Spontaneous Spreading of a Droplet: The Role of Solid Continuity and Advancing Contact Angle.

Science.gov (United States)

Jiang, Youhua; Sun, Yujin; Drelich, Jaroslaw W; Choi, Chang-Hwan

2018-05-01

Spontaneous spreading of a droplet on a solid surface is poorly understood from a macroscopic level down to a molecular level. Here, we investigate the effect of surface topography and wettability on spontaneous spreading of a water droplet. Spreading force is measured for a suspended droplet that minimizes interference of kinetic energy in the spontaneous spreading during its contact with solid surfaces of discontinuous (pillar) and continuous (pore) patterns with various shapes and dimensions. Results show that a droplet cannot spread spontaneously on pillared surfaces regardless of their shapes or dimensions because of the solid discontinuity. On the contrary, a droplet on pored surfaces can undergo spontaneous spreading whose force increases with a decrease in the advancing contact angle. Theoretical models based on both the system free energy and capillary force along the contact line validate the direct and universal dependency of the spontaneous spreading force on the advancing contact angle.

Minimization of spin tune spread by matching dispersion prime at RHIC

Energy Technology Data Exchange (ETDEWEB)

Liu, C. [Brookhaven National Lab. (BNL), Upton, NY (United States); Kewisch, J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Huang, H. [Brookhaven National Lab. (BNL), Upton, NY (United States)

2017-08-31

At RHIC, the spin polarization is preserved with a pair of Siberian snakes on the oppo- site sides in each ring. The polarized proton beam with finite spin tune spread might cross spin resonances multiple times in two cases, one is when beam going through strong spin intrinsic resonances during acceleration, the other is when sweeping spin flipper’ frequency across the spin tune to flip the direction of spin polarization. The consequence is loss of spin polarization in both cases. Therefore, a scheme of min- imizing the spin tune spread by matching the dispersion primes at the two snakes was introduced based on the fact that the spin tune spread is proportional to the difference of dispersion primes at the two snakes. The scheme was implemented at fixed energies for the spin flipper study and during beam acceleration for better spin polarization transmission efficiency. The effect of minimizing the spin tune spread by matching the dispersion primes was observed and confirmed experimentally. The principle of minimizing the spin tune spread by matching the dispersion primes, the impact on the beam optics, and the effect of a narrower spin tune spread are presented in this report.

Gradient-recalled echo sequences in direct shoulder MR arthrography for evaluating the labrum

Energy Technology Data Exchange (ETDEWEB)

Lee, Marc J.; Motamedi, Kambiz; Chow, Kira; Seeger, Leanne L. [David Geffen School of Medicine at UCLA, Department of Radiology, 200 UCLA Medical Plaza, Suite 165-59, Box 956952, Los Angeles, CA (United States)

2008-01-15

The purpose of this study was to determine the utility of fat-suppressed gradient-recalled echo (GRE) compared with conventional spin echo T1-weighted (T1W) sequences in direct shoulder MR arthrography for evaluating labral tears. Three musculoskeletal radiologists retrospectively reviewed MR arthrograms performed over a 12-month period for which surgical correlation was available. Of 180 serial arthrograms, 31 patients had surgery with a mean of 48 days following imaging. Paired coronal oblique and axial T1W or GRE sequences were analyzed by consensus for labral tear (coronal oblique two-dimensional multi-echo data image combination, 2D MEDIC; and axial three-dimensional double-echo steady-state, 3D DESS; Siemens MAGNETOM Sonata 1.5-T MR system). Interpretations were correlated with operative reports. Of 31 shoulders, 25 had labral tears at surgery. The GRE sequences depicted labral tears in 22, while T1W images depicted tears in 16 (sensitivity 88% versus 64%; p < 0.05). Subdividing the labrum, GRE was significantly more sensitive for the posterior labrum (75% versus 25%; p < 0.05) with a trend toward greater sensitivity at the anterior labrum (78% versus 56%; p = 0.157) but not significantly different for the superior labrum (50% versus 57%; p > 0.7). Specificities were somewhat lower for GRE. Thin section GRE sequences are more sensitive than T1W for the detection of anterior and posterior labral tears. As the specificity of GRE was lower, it should be considered as an adjunctive imaging sequence that may improve depiction of labral tears, particularly smaller tears, in routine MR arthrography protocols. (orig.)

Putting instruction sequences into effect

NARCIS (Netherlands)

Bergstra, J.A.

2011-01-01

An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

Digital hf radar observations of equatorial spread-F

International Nuclear Information System (INIS)

Argo, P.E.

1984-01-01

Modern digital ionosondes, with both direction finding and doppler capabilities can provide large scale pictures of the Spread-F irregularity regions. A morphological framework has been developed that allows interpretation of the hf radar data. A large scale irregularity structure is found to be nightward of the dusk terminator, stationary in the solar reference frame. As the plasma moves through this foehn-wall-like structure it descends, and irregularities may be generated. Localized upwellings, or bubbles, may be produced, and they drift with the background plasma. The spread-F irregularity region is found to be best characterized as a partly cloudy sky, due to the patchiness of the substructures. 13 references, 16 figures

A SOM clustering pattern sequence-based next symbol prediction method for day-ahead direct electricity load and price forecasting

International Nuclear Information System (INIS)

Jin, Cheng Hao; Pok, Gouchol; Lee, Yongmi; Park, Hyun-Woo; Kim, Kwang Deuk; Yun, Unil; Ryu, Keun Ho

2015-01-01

Highlights: • A novel pattern sequence-based direct time series forecasting method was proposed. • Due to the use of SOM’s topology preserving property, only SOM can be applied. • SCPSNSP only deals with the cluster patterns not each specific time series value. • SCPSNSP performs better than recently developed forecasting algorithms. - Abstract: In this paper, we propose a new day-ahead direct time series forecasting method for competitive electricity markets based on clustering and next symbol prediction. In the clustering step, pattern sequence and their topology relations are obtained from self organizing map time series clustering. In the next symbol prediction step, with each cluster label in the pattern sequence represented as a pair of its topologically identical coordinates, artificial neural network is used to predict the topological coordinates of next day by training the relationship between previous daily pattern sequence and its next day pattern. According to the obtained topology relations, the nearest nonzero hits pattern is assigned to next day so that the whole time series values can be directly forecasted from the assigned cluster pattern. The proposed method was evaluated on Spanish, Australian and New York electricity markets and compared with PSF and some of the most recently published forecasting methods. Experimental results show that the proposed method outperforms the best forecasting methods at least 3.64%

Detecting the influence of spreading in social networks with excitable sensor networks.

Directory of Open Access Journals (Sweden)

Sen Pei

Full Text Available Detecting spreading outbreaks in social networks with sensors is of great significance in applications. Inspired by the formation mechanism of humans' physical sensations to external stimuli, we propose a new method to detect the influence of spreading by constructing excitable sensor networks. Exploiting the amplifying effect of excitable sensor networks, our method can better detect small-scale spreading processes. At the same time, it can also distinguish large-scale diffusion instances due to the self-inhibition effect of excitable elements. Through simulations of diverse spreading dynamics on typical real-world social networks (Facebook, coauthor, and email social networks, we find that the excitable sensor networks are capable of detecting and ranking spreading processes in a much wider range of influence than other commonly used sensor placement methods, such as random, targeted, acquaintance and distance strategies. In addition, we validate the efficacy of our method with diffusion data from a real-world online social system, Twitter. We find that our method can detect more spreading topics in practice. Our approach provides a new direction in spreading detection and should be useful for designing effective detection methods.

Thread angle dependency on flame spread shape over kenaf/polyester combined fabric

Science.gov (United States)

Azahari Razali, Mohd; Sapit, Azwan; Nizam Mohammed, Akmal; Nor Anuar Mohamad, Md; Nordin, Normayati; Sadikin, Azmahani; Faisal Hushim, Mohd; Jaat, Norrizam; Khalid, Amir

2017-09-01

Understanding flame spread behavior is crucial to Fire Safety Engineering. It is noted that the natural fiber exhibits different flame spread behavior than the one of the synthetic fiber. This different may influences the flame spread behavior over combined fabric. There is a research has been done to examined the flame spread behavior over kenaf/polyester fabric. It is seen that the flame spread shape is dependent on the thread angle dependency. However, the explanation of this phenomenon is not described in detail in that research. In this study, explanation about this phenomenon is given in detail. Results show that the flame spread shape is dependent on the position of synthetic thread. For thread angle, θ = 0°, the polyester thread is breaking when the flame approach to the thread and the kenaf thread tends to move to the breaking direction. This behavior produces flame to be ‘V’ shape. However, for thread angle, θ = 90°, the polyester thread melts while the kenaf thread decomposed and burned. At this angle, the distance between kenaf threads remains constant as flame approaches.

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

Science.gov (United States)

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.

Detection of nucleic acid sequences by invader-directed cleavage

Science.gov (United States)

Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

High Prevalence of Escherichia coli-Producing CTX-M-15 Extended-Spectrum Beta-Lactamases in Poultry and Human Clinical Isolates in Romania.

Science.gov (United States)

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

DIRECT SPECTRUM OF THE BENCHMARK T DWARF HD 19467 B

Energy Technology Data Exchange (ETDEWEB)

Crepp, Justin R.; Matthews, Christopher T. [Department of Physics, University of Notre Dame, 225 Nieuwland Science Hall, Notre Dame, IN 46556 (United States); Rice, Emily L.; Giorla, Paige [College of Staten Island, CUNY, 2800 Victory Boulevard, Staten Island, NY 10314 (United States); Veicht, AAron; Nilsson, Ricky; Luszcz-Cook, Statia H.; Oppenheimer, Rebecca; Brenner, Douglas [American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 (United States); Aguilar, Jonathan; Pueyo, Laurent; Sivaramakrishnan, Anand; Soummer, Remi [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Hinkley, Sasha; Hillenbrand, Lynne A. [Department of Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Vasisht, Gautam; Cady, Eric; Lockhart, Thomas; Roberts, Lewis C. Jr. [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Beichman, Charles A., E-mail: jcrepp@nd.edu [NASA Exoplanet Science Institute, California Institute of Technology, Pasadena, CA 91125 (United States); and others

2015-01-10

HD 19467 B is presently the only directly imaged T dwarf companion known to induce a measurable Doppler acceleration around a solar-type star. We present spectroscopy measurements of this important benchmark object taken with the Project 1640 integral field unit at Palomar Observatory. Our high-contrast R ≈ 30 observations obtained simultaneously across the JH bands confirm the cold nature of the companion as reported from the discovery article and determine its spectral type for the first time. Fitting the measured spectral energy distribution to SpeX/IRTF T dwarf standards and synthetic spectra from BT-Settl atmospheric models, we find that HD 19467 B is a T5.5 ± 1 dwarf with effective temperature T{sub eff}=978{sub −43}{sup +20} K. Our observations reveal significant methane absorption affirming its substellar nature. HD 19467 B shows promise to become the first T dwarf that simultaneously reveals its mass, age, and metallicity independent from the spectrum of light that it emits.

Theoretical research relating to excitation spectrum of furan. Application of integral direct coupled cluster linear response (direct CCLR) method; Furan no reiki supekutoru ni kansuru ronriteki kenkyu. Integral-direct Coupled Cluster Linear Response (direct CCLR) ho no tekiyo

Energy Technology Data Exchange (ETDEWEB)

Shigemitsu, Yasuhiro. [Nagasaki Industrial Technology Center, Nagasaki (Japan)

1999-07-01

heoretical researches relating to excitation spectrum of furan have been carried out for many years, and they reveal the problems that should be solved in order to predict highly reliable excitation energy. In general, it is difficult to uniformly obtain highly reliable calculation results for all excitation states since different excitation states show different electronic correlative effects. Means for obtaining the electron states in ground state and excited state and calculating the energy difference thereof is the mainstream of the theoretical calculation of the excitation energy. CASSCF/CASPT 2 developed by Roos et al. is a typical method excellent in quantitative description. Recently, the comparison between direct CCLR and CASSCF/CASPT 2 as examples for calculating the excitation spectrum of furan was carried out by using the same ground function. For Rydberg excitation, CC3, CAS, CASPT 2 show good agreement with each other. (NEDO)

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.

OpenAIRE

Merker Matthias; Blin Camille; Mona Stefano; Duforet-Frebourg Nicolas; Lecher Sophie; Willery Eve; Blum Michael G B; Rüsch-Gerdes Sabine; Mokrousov Igor; Aleksic Eman; Allix-Béguec Caroline; Antierens Annick; Augustynowicz-Kopec Ewa; Ballif Marie; Barletta Francesca

2015-01-01

International audience; Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiat...

Wave directional spectrum from array measurements

Digital Repository Service at National Institute of Oceanography (India)

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

Using the method of Esteva (1976, 1977), whcih assumes that at the frequency band the waves approach from just a single "mean" wave direction, wave direction has been consistently, accurately and unambiguously evaluated as a function of frequency...

Age, spreading rates, and spreading asymmetry of the world's ocean crust

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The authors present four companion digital models of the age, age uncertainty, spreading rates and spreading asymmetries of the world's ocean basins as geographic...

Asymmetric gravitational spreading - Analogue experiments on the Svecofennian orogen

Science.gov (United States)

Nikkilä, Kaisa; Korja, Annakaisa; Koyi, Hemin; Eklund, Olav

2015-04-01

Over-thickened orogenic crust may suffer from rheological, gravitational and topographical unbalancing resulting in discharging via gravitational spreading. If the thickened orogen is also hot, then increased temperature may reduce the viscosity of the crust that may induce large-scale horizontal flow. The effect of flow on the crustal architecture has previously been modeled with symmetric two-way spreading or asymmetric one- or two-way spreading (like channel flow) experiments. Most models do not take into account of the contrasting mechanical properties of the juxtaposed terranes. We have made analogue experiments to study gravitational one-way spreading and the interplay between two crustal blocks with contrasting rheological properties. The models are 3 cm thick replicas of 60 km thick crust. They have three horizontal layers representing strong lower, weak middle and brittle upper crust. The models have cuts to study the effect of inherited crustal-scale weakness zones. The experiments have been conducted within a large centrifuge in the Hans Ramberg Tectonic Laboratory at Uppsala University. The analogue models propose that asymmetric, unilateral flow has different effect on the contrasting crustal units, in both horizontal and vertical directions. The laterally heterogeneous crust flows towards the direction of extension, and it rotates and extends the pre-existing weakness zones. The weakness zones facilitate exhumation and they increase strain rate. The weakness zones split the crust into subblocks, which stretch individually and which may show signatures of compression or rotation. The changes in thickness of the model reflect changes in the layers, which may thin or thicken depending on the mechanical properties of crustal layers. A consequence of this the total amount of flattening is less than the model extension. The results are compared to geophysical and geological data from Precambrian Svecofennian orogen in Fennoscandia. The comparison suggest

A base composition analysis of natural patterns for the preprocessing of metagenome sequences.

Science.gov (United States)

Bonham-Carter, Oliver; Ali, Hesham; Bastola, Dhundy

2013-01-01

On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy. We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code.

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

Science.gov (United States)

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.

Information hiding technique

Science.gov (United States)

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.

Pseudogene of dihydrolipoyl succinyltransferase (E2k) found by PCR amplification and direct sequencing of rodent-human cell hybrid DNAs

Energy Technology Data Exchange (ETDEWEB)

Cai, X.; Ali, G.; Blass, J.P. [Cornell Univ. Medical College, White Plains, NY (United States); Szabo, P. [Cornell Univ. Medical College, New York, NY (United States); Tanzi, R.E. [Massachusetts General Hospital, Boston, MA (United States)

1994-07-01

Previous studies have indicated that the cDNA for the E2k component of the human {alpha}-ketoglutarate dehydrogenase complex (KGDHC) hybridized not only to a major locus on chromosome 14q24.3 in a region associated with familial Alzheimer`s disease and with Joseph-Machado disease, but also to another locus on chromosome 1p31. The authors now report that PCR of genomic DNA and direct sequencing indicated that the chromosome 1 locus is an intronless pseudogene. PCR of genomic DNA amplified E2k fragments from mouse-human cell hybrids containing human chromosome 1 DNA but not from hybrids containing human chromosome 14 DNA. The resulting amplicons were of comparable sizes to those when the cDNA was used to template. The direct sequencing of these amplicons confirmed the lack of introns and indicated a frame shift, which led to the presence of four termination codons early in the coding region. PCR followed by direct sequencing of the amplicons appears to be a convenient method for identifying intronless pseudogenes.

Influence of Signal-to-Noise Ratio and Point Spread Function on Limits of Super-Resolution

NARCIS (Netherlands)

Pham, T.Q.; Vliet, L.J. van; Schutte, K.

2005-01-01

This paper presents a method to predict the limit of possible resolution enhancement given a sequence of low resolution images. Three important parameters influence the outcome of this limit: the total Point Spread Function (PSF), the Signal-to-Noise Ratio (SNR) and the number of input images.

Influence of signal-to-noise ratio and point spread function on limits of super-resolution

NARCIS (Netherlands)

Pham, T.Q.; Van Vliet, L.; Schutte, K.

2005-01-01

This paper presents a method to predict the limit of possible resolution enhancement given a sequence of lowresolution images. Three important parameters influence the outcome of this limit: the total Point Spread Function (PSF), the Signal-to-Noise Ratio (SNR) and the number of input images.

Dynamics of spread of intestinal colonization with extended-spectrum beta-lactamases in E.coli: a mathematical model

DEFF Research Database (Denmark)

Philipsen, Kirsten Riber; Bootsma, M. C. J.; Leverstein-van Hall, M.A.

In this study a mathematical model for the spread of ESBL resistant E.coli among patients in a hospital and the surrounding catchment population has been introduced and used to described prevalence data from the Netherlands. Several statistical methods have been applied to estimate the model...

An optimum analysis sequence for environmental gamma-ray spectrometry

International Nuclear Information System (INIS)

De la Torre, F.; Rios M, C.; Ruvalcaba A, M. G.; Mireles G, F.; Saucedo A, S.; Davila R, I.; Pinedo, J. L.

2010-10-01

This work aims to obtain an optimum analysis sequence for environmental gamma-ray spectroscopy by means of Genie 2000 (Canberra). Twenty different analysis sequences were customized using different peak area percentages and different algorithms for: 1) peak finding, and 2) peak area determination, and with or without the use of a library -based on evaluated nuclear data- of common gamma-ray emitters in environmental samples. The use of an optimum analysis sequence with certified nuclear information avoids the problems originated by the significant variations in out-of-date nuclear parameters of commercial software libraries. Interference-free gamma ray energies with absolute emission probabilities greater than 3.75% were included in the customized library. The gamma-ray spectroscopy system (based on a Ge Re-3522 Canberra detector) was calibrated both in energy and shape by means of the IAEA-2002 reference spectra for software intercomparison. To test the performance of the analysis sequences, the IAEA-2002 reference spectrum was used. The z-score and the reduced χ 2 criteria were used to determine the optimum analysis sequence. The results show an appreciable variation in the peak area determinations and their corresponding uncertainties. Particularly, the combination of second derivative peak locate with simple peak area integration algorithms provides the greater accuracy. Lower accuracy comes from the combination of library directed peak locate algorithm and Genie's Gamma-M peak area determination. (Author)

The East Pacific Rise and its flanks 8 18° N: History of segmentation, propagation and spreading direction based on SeaMARC II and Sea Beam studies

Science.gov (United States)

MacDonald, Ken C.; Fox, Paul J.; Miller, Steve; Carbotte, Suzanne; Edwards, Margo H.; Eisen, Mark; Fornari, Daniel J.; Perram, Laura; Pockalny, Rob; Scheirer, Dan; Tighe, Stacey; Weiland, Charles; Wilson, Doug

1992-12-01

SeaMARC II and Sea Beam bathymetric data are combined to create a chart of the East Pacific Rise (EPR) from 8°N to 18°N reaching at least 1 Ma onto the rise flanks in most places. Based on these data as well as SeaMARC II side scan sonar mosaics we offer the following observations and conclusions. The EPR is segmented by ridge axis discontinuities such that the average segment lengths in the area are 360 km for first-order segments, 140 km for second-order segments, 52 km for third-order segments, and 13 km for fourth-order segments. All three first-order discontinuities are transform faults. Where the rise axis is a bathymetric high, second-order discontinuities are overlapping spreading centers (OSCs), usually with a distinctive 3:1 overlap to offset ratio. The off-axis discordant zones created by the OSCs are V-shaped in plan view indicating along axis migration at rates of 40 100 mm yr-1. The discordant zones consist of discrete abandoned ridge tips and overlap basins within a broad wake of anomalously deep bathymetry and high crustal magnetization. The discordant zones indicate that OSCs have commenced at different times and have migrated in different directions. This rules out any linkage between OSCs and a hot spot reference frame. The spacing of abandoned ridges indicates a recurrence interval for ridge abandonment of 20,000 200,000 yrs for OSCs with an average interval of approximately 100,000 yrs. Where the rise axis is a bathymetric low, the only second-order discontinuity mapped is a right-stepping jog in the axial rift valley. The discordant zone consists of a V-shaped wake of elongated deeps and interlocking ridges, similar to the wakes of second-order discontinuities on slow-spreading ridges. At the second-order segment level, long segments tend to lengthen at the expense of neighboring shorter segments. This can be understood if segments can be approximated by cracks, because the propagation force at a crack tip is directly proportional to crack

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Comparison between pathogen directed antibiotic treatment and empirical broad spectrum antibiotic treatment in patients with community acquired pneumonia: a prospective randomised study

NARCIS (Netherlands)

van der Eerden, M. M.; Vlaspolder, F.; de Graaff, C. S.; Groot, T.; Bronsveld, W.; Jansen, H. M.; Boersma, W. G.

2005-01-01

Background: There is much controversy about the ideal approach to the management of community acquired pneumonia ( CAP). Recommendations differ from a pathogen directed approach to an empirical strategy with broad spectrum antibiotics. Methods: In a prospective randomised open study performed

Modelling fast spreading patterns of airborne infectious diseases using complex networks

Science.gov (United States)

Brenner, Frank; Marwan, Norbert; Hoffmann, Peter

2017-04-01

The pandemics of SARS (2002/2003) and H1N1 (2009) have impressively shown the potential of epidemic outbreaks of infectious diseases in a world that is strongly connected. Global air travelling established an easy and fast opportunity for pathogens to migrate globally in only a few days. This made epidemiological prediction harder. By understanding this complex development and its link to climate change we can suggest actions to control a part of global human health affairs. In this study we combine the following data components to simulate the outbreak of an airborne infectious disease that is directly transmitted from human to human: em{Global Air Traffic Network (from openflights.org) with information on airports, airport location, direct flight connection, airplane type} em{Global population dataset (from SEDAC, NASA)} em{Susceptible-Infected-Recovered (SIR) compartmental model to simulate disease spreading in the vicinity of airports. A modified Susceptible-Exposed-Infected-Recovered (SEIR) model to analyze the impact of the incubation period.} em{WATCH-Forcing-Data-ERA-Interim (WFDEI) climate data: temperature, specific humidity, surface air pressure, and water vapor pressure} These elements are implemented into a complex network. Nodes inside the network represent airports. Each single node is equipped with its own SIR/SEIR compartmental model with node specific attributes. Edges between those nodes represent direct flight connections that allow infected individuals to move between linked nodes. Therefore the interaction of the set of unique SIR models creates the model dynamics we will analyze. To better figure out the influence on climate change on disease spreading patterns, we focus on Influenza-like-Illnesses (ILI). The transmission rate of ILI has a dependency on climate parameters like humidity and temperature. Even small changes of environmental variables can trigger significant differences in the global outbreak behavior. Apart from the direct

The VULCANO spreading programme

Energy Technology Data Exchange (ETDEWEB)

Cognet, G.; Laffont, G.; Jegou, C.; Journeau, C.; Sudreau, F.; Pierre, J.; Ramacciotti, M. [CEA (Atomic Energy Commission), DRN/DER - Bat. 212, CEA Cadarache, 13108 St. Paul Lez Durance (France)

1999-07-01

Among the currently studied core-catcher projects, some of them suppose corium spreading before cooling, in particular the EPR (European Pressurized Reactor) core-catcher concept is based on mixing the corium with a special concrete, spreading the molten mixture on a large multi-layer surface cooled from the bottom and subsequently cooling by flooding with water. Therefore, melt spreading deserves intensive investigation in order to determine and quantify key phenomena which govern the stopping of spreading. In France, for some years, the Nuclear Reactor Division of the Atomic Energy Commission (CEA/DRN) has undertaken a large program to improve knowledge on corium behaviour and coolability. This program is based on experimental and theoretical investigations which are finally gathered in scenario and mechanistic computer codes. In this framework, the real material experimental programme, VULCANO, conducted within an European frame, is currently devoted to the study of corium spreading. In 1997 and 1998, several tests have been performed on dry corium spreading with various composition of melts. Although all the observed phenomena, in particular the differences between simulant and real material melts have not been yet totally explained, these tests have already provided a lot of information about: The behaviour of complex mixtures including refractory oxides, silica, iron oxides and in one case iron metal; Spreading progression, which was never stopped in any of these tests by a crust formation at the front; The structure of spread melts (porosity, crusts,...); Physico-chemical interaction between melt and the refractory substratum which was composed of zirconia bricks. (authors)

The VULCANO spreading programme

International Nuclear Information System (INIS)

Cognet, G.; Laffont, G.; Jegou, C.; Journeau, C.; Sudreau, F.; Pierre, J.; Ramacciotti, M.

1999-01-01

Among the currently studied core-catcher projects, some of them suppose corium spreading before cooling, in particular the EPR (European Pressurized Reactor) core-catcher concept is based on mixing the corium with a special concrete, spreading the molten mixture on a large multi-layer surface cooled from the bottom and subsequently cooling by flooding with water. Therefore, melt spreading deserves intensive investigation in order to determine and quantify key phenomena which govern the stopping of spreading. In France, for some years, the Nuclear Reactor Division of the Atomic Energy Commission (CEA/DRN) has undertaken a large program to improve knowledge on corium behaviour and coolability. This program is based on experimental and theoretical investigations which are finally gathered in scenario and mechanistic computer codes. In this framework, the real material experimental programme, VULCANO, conducted within an European frame, is currently devoted to the study of corium spreading. In 1997 and 1998, several tests have been performed on dry corium spreading with various composition of melts. Although all the observed phenomena, in particular the differences between simulant and real material melts have not been yet totally explained, these tests have already provided a lot of information about: The behaviour of complex mixtures including refractory oxides, silica, iron oxides and in one case iron metal; Spreading progression, which was never stopped in any of these tests by a crust formation at the front; The structure of spread melts (porosity, crusts,...); Physico-chemical interaction between melt and the refractory substratum which was composed of zirconia bricks. (authors)

A novel method to discover fluoroquinolone antibiotic resistance (qnr genes in fragmented nucleotide sequences

Directory of Open Access Journals (Sweden)

Boulund Fredrik

2012-12-01

Full Text Available Abstract Background Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail. Results In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature. Conclusions The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.

Hop limited epidemic-like information spreading in mobile social networks with selfish nodes

Science.gov (United States)

Wu, Yahui; Deng, Su; Huang, Hongbin

2013-07-01

Similar to epidemics, information can be transmitted directly among users in mobile social networks. Different from epidemics, we can control the spreading process by adjusting the corresponding parameters (e.g., hop count) directly. This paper proposes a theoretical model to evaluate the performance of an epidemic-like spreading algorithm, in which the maximal hop count of the information is limited. In addition, our model can be used to evaluate the impact of users’ selfish behavior. Simulations show the accuracy of our theoretical model. Numerical results show that the information hop count can have an important impact. In addition, the impact of selfish behavior is related to the information hop count.

Hop limited epidemic-like information spreading in mobile social networks with selfish nodes

International Nuclear Information System (INIS)

Wu, Yahui; Deng, Su; Huang, Hongbin

2013-01-01

Similar to epidemics, information can be transmitted directly among users in mobile social networks. Different from epidemics, we can control the spreading process by adjusting the corresponding parameters (e.g., hop count) directly. This paper proposes a theoretical model to evaluate the performance of an epidemic-like spreading algorithm, in which the maximal hop count of the information is limited. In addition, our model can be used to evaluate the impact of users’ selfish behavior. Simulations show the accuracy of our theoretical model. Numerical results show that the information hop count can have an important impact. In addition, the impact of selfish behavior is related to the information hop count. (paper)

Are the Intraday Effects of Central Bank Intervention on Exchange Rate Spreads Asymmetric and State Dependent?

DEFF Research Database (Denmark)

Fatum, Rasmus; Pedersen, Jesper; Sørensen, Peter Norman

This paper investigates the intraday effects of unannounced foreign exchange intervention on bid-ask exchange rate spreads using official intraday intervention data provided by the Danish central bank. Our starting point is a simple theoretical model of the bid-ask spread which we use to formulate...... exert a significant influence on the exchange rate spread, but in opposite directions: intervention purchases of the smaller currency, on average, reduce the spread while intervention sales, on average, increase the spread. We also show that intervention only affects the exchange rate spread when...... the state of the market is not abnormally volatile. Our results are consistent with the notion that illiquidity arises when traders fear speculative pressure against the smaller currency and confirms the asymmetry hypothesis of our theoretical model....

The genomic signatures of Shigella evolution, adaptation and geographical spread.

Science.gov (United States)

The, Hao Chung; Thanh, Duy Pham; Holt, Kathryn E; Thomson, Nicholas R; Baker, Stephen

2016-04-01

Shigella spp. are some of the key pathogens responsible for the global burden of diarrhoeal disease. These facultative intracellular bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Escherichia coli and Salmonella spp. The genus Shigella comprises four different species, each consisting of several serogroups, all of which show phenotypic similarity, including invasive pathogenicity. DNA sequencing suggests that this similarity results from the convergent evolution of different Shigella spp. founders. Here, we review the evolutionary relationships between Shigella spp. and E . coli, and we highlight how the genomic plasticity of these bacteria and their acquisition of a distinctive virulence plasmid have enabled the development of such highly specialized pathogens. Furthermore, we discuss the insights that genotyping and whole-genome sequencing have provided into the phylogenetics and intercontinental spread of Shigella spp.

Epidemic spreading with activity-driven awareness diffusion on multiplex network.

Science.gov (United States)

Guo, Quantong; Lei, Yanjun; Jiang, Xin; Ma, Yifang; Huo, Guanying; Zheng, Zhiming

2016-04-01

There has been growing interest in exploring the interplay between epidemic spreading with human response, since it is natural for people to take various measures when they become aware of epidemics. As a proper way to describe the multiple connections among people in reality, multiplex network, a set of nodes interacting through multiple sets of edges, has attracted much attention. In this paper, to explore the coupled dynamical processes, a multiplex network with two layers is built. Specifically, the information spreading layer is a time varying network generated by the activity driven model, while the contagion layer is a static network. We extend the microscopic Markov chain approach to derive the epidemic threshold of the model. Compared with extensive Monte Carlo simulations, the method shows high accuracy for the prediction of the epidemic threshold. Besides, taking different spreading models of awareness into consideration, we explored the interplay between epidemic spreading with awareness spreading. The results show that the awareness spreading can not only enhance the epidemic threshold but also reduce the prevalence of epidemics. When the spreading of awareness is defined as susceptible-infected-susceptible model, there exists a critical value where the dynamical process on the awareness layer can control the onset of epidemics; while if it is a threshold model, the epidemic threshold emerges an abrupt transition with the local awareness ratio α approximating 0.5. Moreover, we also find that temporal changes in the topology hinder the spread of awareness which directly affect the epidemic threshold, especially when the awareness layer is threshold model. Given that the threshold model is a widely used model for social contagion, this is an important and meaningful result. Our results could also lead to interesting future research about the different time-scales of structural changes in multiplex networks.

Epidemic spreading with activity-driven awareness diffusion on multiplex network

Science.gov (United States)

Guo, Quantong; Lei, Yanjun; Jiang, Xin; Ma, Yifang; Huo, Guanying; Zheng, Zhiming

2016-04-01

There has been growing interest in exploring the interplay between epidemic spreading with human response, since it is natural for people to take various measures when they become aware of epidemics. As a proper way to describe the multiple connections among people in reality, multiplex network, a set of nodes interacting through multiple sets of edges, has attracted much attention. In this paper, to explore the coupled dynamical processes, a multiplex network with two layers is built. Specifically, the information spreading layer is a time varying network generated by the activity driven model, while the contagion layer is a static network. We extend the microscopic Markov chain approach to derive the epidemic threshold of the model. Compared with extensive Monte Carlo simulations, the method shows high accuracy for the prediction of the epidemic threshold. Besides, taking different spreading models of awareness into consideration, we explored the interplay between epidemic spreading with awareness spreading. The results show that the awareness spreading can not only enhance the epidemic threshold but also reduce the prevalence of epidemics. When the spreading of awareness is defined as susceptible-infected-susceptible model, there exists a critical value where the dynamical process on the awareness layer can control the onset of epidemics; while if it is a threshold model, the epidemic threshold emerges an abrupt transition with the local awareness ratio α approximating 0.5. Moreover, we also find that temporal changes in the topology hinder the spread of awareness which directly affect the epidemic threshold, especially when the awareness layer is threshold model. Given that the threshold model is a widely used model for social contagion, this is an important and meaningful result. Our results could also lead to interesting future research about the different time-scales of structural changes in multiplex networks.

Direct measurement of the partial decay energy of 7Be inner bremstrahlung spectrum

International Nuclear Information System (INIS)

Sanjeeviah, H.; Sanjeeviah, B.

1978-01-01

The inner bremsstrahlung spectrum accompanying orbital electron capture decay of 7 Be to the first excited state of 7 Li was measured in coincidence with 477 keV gamma rays. From the Jauch plot of the spectrum the partial decay energy was found to be 394 +- 16 keV. The shape factor of the inner bremsstrahlung spectrum close to the end point was accurately determined. It was found to be a constant X(1.001 +- 0.002) (author)

Frequency characteristic measurement of a fiber optic gyroscope using a correlation spectrum analysis method based on a pseudo-random sequence

International Nuclear Information System (INIS)

Li, Yang; Chen, Xingfan; Liu, Cheng

2015-01-01

The frequency characteristic is an important indicator of a system’s dynamic performance. The identification of a fiber optic gyroscope (FOG)’s frequency characteristic using a correlation spectrum analysis method based on a pseudo-random sequence is proposed. Taking the angle vibrator as the source of the test rotation stimulation and a pseudo-random sequence as the test signal, the frequency characteristic of a FOG is calculated according to the power spectral density of the rotation rate signal and the cross-power spectral density of the FOG’s output signal and rotation rate signal. A theoretical simulation is done to confirm the validity of this method. An experiment system is built and the test results indicate that the measurement error of the normalized amplitude–frequency response is less than 0.01, that the error of the phase–frequency response is less than 0.3 rad, and the overall measurement accuracy is superior to the traditional frequency-sweep method. By using this method, the FOG’s amplitude–frequency response and phase–frequency response can be measured simultaneously, quickly, accurately, and with a high frequency resolution. The described method meets the requirements of engineering applications. (paper)

Potential corridors and barriers for plague spread in central Asia

Science.gov (United States)

2013-01-01

Background Plague (Yersinia pestis infection) is a vector-borne disease which caused millions of human deaths in the Middle Ages. The hosts of plague are mostly rodents, and the disease is spread by the fleas that feed on them. Currently, the disease still circulates amongst sylvatic rodent populations all over the world, including great gerbil (Rhombomys opimus) populations in Central Asia. Great gerbils are social desert rodents that live in family groups in burrows, which are visible on satellite images. In great gerbil populations an abundance threshold exists, above which plague can spread causing epizootics. The spatial distribution of the host species is thought to influence the plague dynamics, such as the direction of plague spread, however no detailed analysis exists on the possible functional or structural corridors and barriers that are present in this population and landscape. This study aims to fill that gap. Methods Three 20 by 20 km areas with known great gerbil burrow distributions were used to analyse the spatial distribution of the burrows. Object-based image analysis was used to map the landscape at several scales, and was linked to the burrow maps. A novel object-based method was developed – the mean neighbour absolute burrow density difference (MNABDD) – to identify the optimal scale and evaluate the efficacy of using landscape objects as opposed to square cells. Multiple regression using raster maps was used to identify the landscape-ecological variables that explain burrow density best. Functional corridors and barriers were mapped using burrow density thresholds. Cumulative resistance of the burrow distribution to potential disease spread was evaluated using cost distance analysis. A 46-year plague surveillance dataset was used to evaluate whether plague spread was radially symmetric. Results The burrow distribution was found to be non-random and negatively correlated with Greenness, especially in the floodplain areas. Corridors and

Extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in local and imported poultry meat in Ghana.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Obtaining the Bunch Shape in a Linac from Beam Spectrum Measurements

International Nuclear Information System (INIS)

Bane, Karl LF

1999-01-01

In linacs with high single-bunch charge, and tight tolerances for energy spread and emittance growth, controlling the short-range wakefield effects becomes extremely important. The effects of the wakefields, in turn, depend on the bunch length and also on the bunch shape. It was shown in the linac of the Stanford Linear Collider (SLC), for example, that by shaping the bunch, the final rms energy spread could be greatly reduced, compared to for the standard Gaussian bunch shape[1]. Therefore, in machines with high single-bunch charge, a method of measuring bunch shape can be an important beam diagnostic. In a linac with low single-bunch charge, the longitudinal bunch shape can be obtained relatively easily from a single measurement of the beam's final energy spectrum, provided that the final to initial energy ratio is large. One merely shifts the average phase of the beam, so that it rides off-crest sufficiently to induce an energy variation that is monotonic with longitudinal position. Then, by knowing the initial and final energies, the rf wave number, and the average beam phase, one can directly map the spectrum into the bunch shape. In a linac with high single-bunch charge, however, due to the effect of the longitudinal wakefield, this method either does not work at all, or it requires such a large shift in beam phase as to become impractical. In earlier work[2],[3] it was shown that, even when wakefields are important, if one measures the final beam spectrum for two different (properly chosen) values of beam phase, then one can again obtain the bunch shape, and--as a by-product--also the form of the wakefield induced voltage; this method was then illustrated using data from the linac of the SLC. These SLC measurements, however, had been performed with the machine in a special configuration, where the current was low; in addition, the noise the data was low and the measured spectra were smooth distributions. Under normal SLC conditions, however, the currents

Post sunset equatorial spread-F at Kwajalein and interplanetary magnetic field

Science.gov (United States)

Rastogi, R. G.; Chandra, H.; Janardhan, P.; Reinisch, B. W.; Bisoi, Susanta Kumar

2017-10-01

We connect the time sequence of changes in the IMF-Bz to the development of spread-F at an equatorial station Kwajalein on three different nights in November 2004, one during a geomagnetic quiet period and other two during geomagnetic disturbed periods. The chosen days show clear and smooth variations of IMF-Bz without any large fluctuations thereby enabling one to correlate changes in equatorial spread-F with corresponding changes in IMF-Bz. It is shown that a slow and continuous increase in the IMF-Bz over a duration of few hours has a similar effect on the equatorial ionosphere as of a sudden northward turning of the IMF-Bz in causing an electric field through the polar region and then to the equator. We conclude that the Spread-F at equatorial and low latitudes are due to echoes from ionization irregularities that arise due to the plasma instabilities generated by an eastward electric field on the large plasma density gradient in or below the base of the F-layer during any period of the night time along with the gravity driven Rayleigh-Taylor instability.

A thaumatin-like genomic sequence identification in Vitis vinifera l., stormy wines and musts based on direct pcr

Directory of Open Access Journals (Sweden)

Jana Žiarovská

2018-03-01

Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 Direct polymerase chain reaction method was use to amplify a thaumatin-like sequence of Vitis vinifera L. in grapes as well as in stormy wines and musts. Thaumatin-like proteins (TLPs of Vitis vinifera possess beside its function in abiotic and biotic stress response another one - they are able to cause protein haze in wine unless removed prior to bottling. Direct PCR is an approach where omission of DNA extraction is typical prior the amplification of the target site of plant genome. Crude extract or small pieces of plant tissues are used in the analysis directly without steps of extraction and purification of gDNA. The biological material that was used in analysis was collected during August - October 2017 in local stores and winery Sabo and comprises from cultivars Iršai, Muškát, Savignon Blanc, Svätovavrinecké, Dornfelder and Pálava. Direct PCR was performed by a cutted piece of grape tissue and a dilution buffer was use in 1:2 for stormy wine or must, respectively. Direct amplification of thaumatin-like protein sequence of Vitis vinifera was performed along with the control reactions with the primers for conserved region of plant chloroplast. Possitive amplification of thaumatin-like allergen sequence resulted in 570 bp amplicon. The most abundant amplicons were amplified in stormy wines, followed by musts and the amplicons from grapes were weaker when comparing them to others. The amplicon specificity checking of obtained PCR product of thaumatin-like allergen was performed by restriction cleavage by Psi I and resulted in restriction amplicons of the 80 bp, 81 bp, 94 bp and 315 bp in length. Confirmation of the amplicon specificity by restriction cleavage support the potential of direct PCR to become a reproducible method that will be fully applicable in routine analysis of not only plant genomes in the future, but it was demonstrated, that it works in liquids, too.  

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

Energy Technology Data Exchange (ETDEWEB)

Köberl, Martina; White, Richard A.; Erschen, Sabine; El-Arabi, Tarek F.; Jansson, Janet K.; Berg, Gabriele

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.

High resolution sequence stratigraphy in China

International Nuclear Information System (INIS)

Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

2008-01-01

Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

Experimental study on the effects of AC electric fields on flame spreading over polyethylene-insulated electric-wire

KAUST Repository

Jin, Young Kyu

2010-11-01

In this present study, we experimentally investigated the effects of electric fields on the characteristics of flames spreading over electric-wires with AC fields. The dependence of the rate at which a flame spreads over polyethylene-insulated wires on the frequency and amplitude of the applied AC electric field was examined. The spreading of the flame can be categorized into linear spreading and non-linearly accelerated spreading of flame. This categorization is based on the axial distribution of the field strength of the applied electric field. The rate at which the flame spreads is highly dependent on the inclined direction of the wire fire. It could be possible to explain the spreading of the flame on the basis of thermal balance. © 2010 The Korean Society of Mechanical Engineers.

Average intensity and spreading of partially coherent model beams propagating in a turbulent biological tissue

International Nuclear Information System (INIS)

Wu, Yuqian; Zhang, Yixin; Wang, Qiu; Hu, Zhengda

2016-01-01

For Gaussian beams with three different partially coherent models, including Gaussian-Schell model (GSM), Laguerre-Gaussian Schell-model (LGSM) and Bessel-Gaussian Schell-model (BGSM) beams propagating through a biological turbulent tissue, the expression of the spatial coherence radius of a spherical wave propagating in a turbulent biological tissue, and the average intensity and beam spreading for GSM, LGSM and BGSM beams are derived based on the fractal model of power spectrum of refractive-index variations in biological tissue. Effects of partially coherent model and parameters of biological turbulence on such beams are studied in numerical simulations. Our results reveal that the spreading of GSM beams is smaller than LGSM and BGSM beams on the same conditions, and the beam with larger source coherence width has smaller beam spreading than that with smaller coherence width. The results are useful for any applications involved light beam propagation through tissues, especially the cases where the average intensity and spreading properties of the light should be taken into account to evaluate the system performance and investigations in the structures of biological tissue. - Highlights: • Spatial coherence radius of a spherical wave propagating in a turbulent biological tissue is developed. • Expressions of average intensity and beam spreading for GSM, LGSM and BGSM beams in a turbulent biological tissue are derived. • The contrast for the three partially coherent model beams is shown in numerical simulations. • The results are useful for any applications involved light beam propagation through tissues.

Oppositely directed pairs of propagating rifts in back-arc basins: Double saloon door seafloor spreading during subduction rollback

Science.gov (United States)

Martin, A. K.

2006-06-01

When a continent breaks up into two plates, which then separate from each other about a rotation pole, it can be shown that if initial movement is taken up by lithospheric extension, asthenospheric breakthrough and oceanic accretion propagate toward the pole of rotation. Such a propagating rift model is then applied to an embryonic centrally located rift which evolves into two rifts propagating in opposite directions. The resultant rhombic shape of the modeled basin, initially underlain entirely by thinned continental crust, is very similar to the Oligocene to Burdigalian back-arc evolution of the Valencia Trough and the Liguro-Provencal Basin in the western Mediterranean. Existing well and seismic stratigraphic data confirm that a rift did initiate in the Gulf of Lion and propagated southwest into the Valencia Trough. Similarly, seismic refraction, gravity, and heat flow data demonstrate that maximum extension within the Valencia Trough/Liguro-Provencal Basin occurred in an axial position close to the North Balearic Fracture Zone. The same model of oppositely propagating rifts, when applied to the Burdigalian/Langhian episode of back-arc oceanic accretion within the Liguro-Provencal and Algerian basins, predicts a number of features which are borne out by existing geological and geophysical, particularly magnetic data. These include the orientation of subparallel magnetic anomalies, presumed to be seafloor spreading isochrons, in both basins; concave-to-the-west fracture zones southwest of the North Balearic Fracture Zone, and concave-to-the-east fracture zones to its northeast; a spherical triangular area of NW oriented seafloor spreading isochrons southwest of Sardinia; the greater NW extension of the central (youngest?) magnetic anomaly within this triangular area, in agreement with the model-predicted northwestward propagation of a rift in this zone; successively more central (younger) magnetic anomalies abutting thinned continental crust nearer to the pole of

Information spreading dynamics in hypernetworks

Science.gov (United States)

Suo, Qi; Guo, Jin-Li; Shen, Ai-Zhong

2018-04-01

Contact pattern and spreading strategy fundamentally influence the spread of information. Current mathematical methods largely assume that contacts between individuals are fixed by networks. In fact, individuals are affected by all his/her neighbors in different social relationships. Here, we develop a mathematical approach to depict the information spreading process in hypernetworks. Each individual is viewed as a node, and each social relationship containing the individual is viewed as a hyperedge. Based on SIS epidemic model, we construct two spreading models. One model is based on global transmission, corresponding to RP strategy. The other is based on local transmission, corresponding to CP strategy. These models can degenerate into complex network models with a special parameter. Thus hypernetwork models extend the traditional models and are more realistic. Further, we discuss the impact of parameters including structure parameters of hypernetwork, spreading rate, recovering rate as well as information seed on the models. Propagation time and density of informed nodes can reveal the overall trend of information dissemination. Comparing these two models, we find out that there is no spreading threshold in RP, while there exists a spreading threshold in CP. The RP strategy induces a broader and faster information spreading process under the same parameters.

Age Spreads and the Temperature Dependence of Age Estimates in Upper Sco

Energy Technology Data Exchange (ETDEWEB)

Fang Qiliang; Herczeg, Gregory J. [Kavli Institute for Astronomy and Astrophysics, Peking University, Yiheyuan Lu 5, Haidian Qu, 100871 Beijing (China); Rizzuto, Aaron [Department of Astronomy, University of Texas, 2515 Speedway, Stop C1400, Austin, TX 78712 (United States)

2017-06-20

Past estimates for the age of the Upper Sco Association are typically 11–13 Myr for intermediate-mass stars and 4–5 Myr for low-mass stars. In this study, we simulate populations of young stars to investigate whether this apparent dependence of estimated age on spectral type may be explained by the star formation history of the association. Solar and intermediate mass stars begin their pre-main sequence evolution on the Hayashi track, with fully convective interiors and cool photospheres. Intermediate-mass stars quickly heat up and transition onto the radiative Henyey track. As a consequence, for clusters in which star formation occurs on a timescale similar to that of the transition from a convective to a radiative interior, discrepancies in ages will arise when ages are calculated as a function of temperature instead of mass. Simple simulations of a cluster with constant star formation over several Myr may explain about half of the difference in inferred ages versus photospheric temperature; speculative constructions that consist of a constant star formation followed by a large supernova-driven burst could fully explain the differences, including those between F and G stars where evolutionary tracks may be more accurate. The age spreads of low-mass stars predicted from these prescriptions for star formation are consistent with the observed luminosity spread of Upper Sco. The conclusion that a lengthy star formation history will yield a temperature dependence in ages is expected from the basic physics of pre-main sequence evolution, and is qualitatively robust to the large uncertainties in pre-main sequence evolutionary models.

Effects of mutation on the downfield proton nuclear magnetic resonance spectrum of the 5S RNA of Escherichia coli

International Nuclear Information System (INIS)

Gewirth, D.T.; Moore, P.B.

1987-01-01

The imino proton spectra of several mutants of the 5S RNA of Escherichia coli are compared with that of the wild type. Three of the variants discussed are point mutations, and the fourth is a deletion mutant lacking bases 11-69 of the parent sequence, all obtained by site-directed mutagenesis techniques. The spectroscopic effects of mutation are limited in all cases, and the differences between normal and mutant spectra can be used to make or confirm the assignments of resonances. Several new assignments in the 5S spectrum are reported. Spectroscopic differences due to sequence differences permit the products of single genes within the 5S gene family to be distinguished and their fates followed by NMR

A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

Energy Technology Data Exchange (ETDEWEB)

Somers, Garrett; Pinsonneault, Marc H., E-mail: somers@astronomy.ohio-state.edu, E-mail: pinsono@astronomy.ohio-state.edu [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43201 (United States)

2014-07-20

We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T{sub eff} is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

International Nuclear Information System (INIS)

Somers, Garrett; Pinsonneault, Marc H.

2014-01-01

We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T eff is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Joke J F A van Vugt

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

Energy spectrum of buoyancy-driven turbulence

KAUST Repository

Kumar, Abhishek; Chatterjee, Anando G.; Verma, Mahendra K.

2014-01-01

Using high-resolution direct numerical simulation and arguments based on the kinetic energy flux Πu, we demonstrate that, for stably stratified flows, the kinetic energy spectrum Eu(k)∼k-11/5, the potential energy spectrum Eθ(k)∼k-7/5, and Πu(k)∼k-4

Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort.

Science.gov (United States)

Lawyer, Glenn; Schülter, Eugen; Kaiser, Rolf; Reuter, Stefan; Oette, Mark; Lengauer, Thomas

2012-08-01

HIV's genetic instability means that sequence similarity can illuminate the underlying transmission network. Previous application of such methods to samples from the United Kingdom has suggested that as many as 86% of UK infections arose outside of the country, a conclusion contrary to usual patterns of disease spread. We investigated transmission networks in the Resina cohort, a 2,747 member sample from Nordrhein-Westfalen, Germany, sequenced at therapy start. Transmission networks were determined by thresholding the pairwise genetic distance in the pol gene at 96.8% identity. At first blush the results concurred with the UK studies. Closer examination revealed four large and growing transmission networks that encompassed all major transmission groups. One of these formed a supercluster containing 71% of the sex with men (MSM) subjects when the network was thresholded at levels roughly equivalent to those used in the UK studies, though methodological differences suggest that this threshold may be too generous in the current data. Examination of the endo- versus exogenesis hypothesis by testing whether infections that were exogenous to Cologne or to Dusseldorf were endogenous to the greater region supported endogenous spread in MSM subjects and exogenous spread in the endemic transmission group. In intravenous drug using group subjects, it depended on viral strain, with subtype B sequences appearing to have origin exogenous to the Resina data, while non-B sequences (primarily subtype A) were almost completely endogenous to their local community. These results suggest that, at least in Germany, the question of endogenous versus exogenous linkages depends on subject group.

DNA-directed alkylating ligands as potential antitumor agents: sequence specificity of alkylation by intercalating aniline mustards.

Science.gov (United States)

Prakash, A S; Denny, W A; Gourdie, T A; Valu, K K; Woodgate, P D; Wakelin, L P

1990-10-23

The sequence preferences for alkylation of a series of novel parasubstituted aniline mustards linked to the DNA-intercalating chromophore 9-aminoacridine by an alkyl chain of variable length were studied by using procedures analogous to Maxam-Gilbert reactions. The compounds alkylate DNA at both guanine and adenine sites. For mustards linked to the acridine by a short alkyl chain through a para O- or S-link group, 5'-GT sequences are the most preferred sites at which N7-guanine alkylation occurs. For analogues with longer chain lengths, the preference of 5'-GT sequences diminishes in favor of N7-adenine alkylation at the complementary 5'-AC sequence. Magnesium ions are shown to selectively inhibit alkylation at the N7 of adenine (in the major groove) by these compounds but not the alkylation at the N3 of adenine (in the minor groove) by the antitumor antibiotic CC-1065. Effects of chromophore variation were also studied by using aniline mustards linked to quinazoline and sterically hindered tert-butyl-9-aminoacridine chromophores. The results demonstrate that in this series of DNA-directed mustards the noncovalent interactions of the carrier chromophores with DNA significantly modify the sequence selectivity of alkylation by the mustard. Relationships between the DNA alkylation patterns of these compounds and their biological activities are discussed.

Transforming clinical microbiology with bacterial genome sequencing.

Science.gov (United States)

Didelot, Xavier; Bowden, Rory; Wilson, Daniel J; Peto, Tim E A; Crook, Derrick W

2012-09-01

Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

An optimum analysis sequence for environmental gamma-ray spectrometry

Energy Technology Data Exchange (ETDEWEB)

De la Torre, F.; Rios M, C.; Ruvalcaba A, M. G.; Mireles G, F.; Saucedo A, S.; Davila R, I.; Pinedo, J. L., E-mail: fta777@hotmail.co [Universidad Autonoma de Zacatecas, Centro Regional de Estudis Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico)

2010-10-15

This work aims to obtain an optimum analysis sequence for environmental gamma-ray spectroscopy by means of Genie 2000 (Canberra). Twenty different analysis sequences were customized using different peak area percentages and different algorithms for: 1) peak finding, and 2) peak area determination, and with or without the use of a library -based on evaluated nuclear data- of common gamma-ray emitters in environmental samples. The use of an optimum analysis sequence with certified nuclear information avoids the problems originated by the significant variations in out-of-date nuclear parameters of commercial software libraries. Interference-free gamma ray energies with absolute emission probabilities greater than 3.75% were included in the customized library. The gamma-ray spectroscopy system (based on a Ge Re-3522 Canberra detector) was calibrated both in energy and shape by means of the IAEA-2002 reference spectra for software intercomparison. To test the performance of the analysis sequences, the IAEA-2002 reference spectrum was used. The z-score and the reduced {chi}{sup 2} criteria were used to determine the optimum analysis sequence. The results show an appreciable variation in the peak area determinations and their corresponding uncertainties. Particularly, the combination of second derivative peak locate with simple peak area integration algorithms provides the greater accuracy. Lower accuracy comes from the combination of library directed peak locate algorithm and Genie's Gamma-M peak area determination. (Author)

Sequence assembly

DEFF Research Database (Denmark)

Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

2009-01-01

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

Sound spectrum of a pulsating optical discharge

Energy Technology Data Exchange (ETDEWEB)

Grachev, G N; Smirnov, A L; Tishchenko, V N [Institute of Laser Physics, Siberian Branch, Russian Academy of Sciences, Novosibirsk (Russian Federation); Dmitriev, A K; Miroshnichenko, I B [Novosibirsk State Technical University (Russian Federation)

2016-02-28

A spectrum of sound of an optical discharge generated by a repetitively pulsed (RP) laser radiation has been investigated. The parameters of laser radiation are determined at which the spectrum of sound may contains either many lines, or the main line at the pulse repetition rate and several weaker overtones, or a single line. The spectrum of sound produced by trains of RP radiation comprises the line (and overtones) at the repetition rate of train sequences and the line at the repetition rate of pulses in trains. A CO{sub 2} laser with the pulse repetition rate of f ≈ 3 – 180 kHz and the average power of up to 2 W was used in the experiments. (optical discharges)

Effect of applied DC electric fields in flame spread over polyethylene-coated electrical wire

KAUST Repository

Jin, Young Kyu

2011-03-01

We experimentally investigated the effect of applied DC electric fields on the flame spread over polyethylene-coated electrical wire. The flame-spread rates over electrical wire with negative and positive DC electric fields from 0 to ±7 kV were measured and analyzed. We compared the results for DC electric fields with previous results for AC electric fields. We explored whether or not various flame shapes could be obtained with DC electric fields and the main reason for the flame-spread acceleration, particularly at the end of the electrical wire, for AC electric fields. We found that DC electric fields do not significantly affect the flame-spread rates. However, the flame shape is mildly altered by the ionic wind effect even for DC electric fields. The flame-spread rate is relevant to the flame shape and the slanted direction in spite of the mild impact. A possible explanation for the flame spread is given by a thermal-balance mechanism and fuel-vapor jet. © 2011 The Korean Society of Mechanical Engineers.

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

Science.gov (United States)

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.

Next-Generation Sequencing for Typing and Detection of ESBL and MBL E. coli causing UTI

Directory of Open Access Journals (Sweden)

Nabakishore Nayak

2017-10-01

Full Text Available 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 can be evaluated the performance of a new NGS assay during an outbreak of sequence type 131 (ST131 Escherichia coli infections in a teaching hospital. The assay will be performed on 100 extended-spectrum- beta-lactamase (ESBL E. coli isolates collected from UTI during last 5 years. Typing results will be compared to those of amplified fragment length polymorphism (AFLP, whereby we will be visually assessed the agreement of the Bio-Detection phylogenetic tree with clusters defined by AFLP. A microarray will be considered the gold standard for detection of resistance genes. AFLP will be identified a large cluster of different indistinguishable isolates on adjacent departments, indicating clonal spread. The BioDetection phylogenetic tree will be showed that all isolates of this outbreak cluster will be strongly related, while the further arrangement of the tree also largely agreed with other clusters defined by AFLP. With these experiments we will detect the ESBL and MBL strains and the patient can be prescribed the antibiotics accordingly.

[Study on the method for the determination of trace boron, molybdenum, silver, tin and lead in geochemical samples by direct current arc full spectrum direct reading atomic emission spectroscopy (DC-Arc-AES)].

Science.gov (United States)

Hao, Zhi-hong; Yao, Jian-zhen; Tang, Rui-ling; Zhang, Xue-mei; Li, Wen-ge; Zhang, Qin

2015-02-01

The method for the determmation of trace boron, molybdenum, silver, tin and lead in geochemical samples by direct current are full spectrum direct reading atomic emission spectroscopy (DC-Arc-AES) was established. Direct current are full spectrum direct reading atomic emission spectrometer with a large area of solid-state detectors has functions of full spectrum direct reading and real-time background correction. The new electrodes and new buffer recipe were proposed in this paper, and have applied for national patent. Suitable analytical line pairs, back ground correcting points of elements and the internal standard method were selected, and Ge was used as internal standard. Multistage currents were selected in the research on current program, and each current set different holding time to ensure that each element has a good signal to noise ratio. Continuous rising current mode selected can effectively eliminate the splash of the sample. Argon as shielding gas can eliminate CN band generating and reduce spectral background, also plays a role in stabilizing the are, and argon flow 3.5 L x min(-1) was selected. Evaporation curve of each element was made, and it was concluded that the evaporation behavior of each element is consistent, and combined with the effects of different spectrographic times on the intensity and background, the spectrographic time of 35s was selected. In this paper, national standards substances were selected as a standard series, and the standard series includes different nature and different content of standard substances which meet the determination of trace boron, molybdenum, silver, tin and lead in geochemical samples. In the optimum experimental conditions, the detection limits for B, Mo, Ag, Sn and Pb are 1.1, 0.09, 0.01, 0.41, and 0.56 microg x g(-1) respectively, and the precisions (RSD, n=12) for B, Mo, Ag, Sn and Pb are 4.57%-7.63%, 5.14%-7.75%, 5.48%-12.30%, 3.97%-10.46%, and 4.26%-9.21% respectively. The analytical accuracy was

Nonlinearity effect of electro-optical modulator response in double spread CDMA radio-over-fiber transmissions

Science.gov (United States)

Huang, Jen-Fa; Yen, Chih-Ta; Li, Tzung-Yen

2008-07-01

This study presents a double-spread code-division multiple-access (CDMA) scheme for radio-over-fiber (RoF) transmissions. The network coder/decoders (codecs) are implemented using arrayed-waveguide grating (AWG) routers coded with maximal-length sequence ( M-sequence) codes. The effects of phase-induced intensity noise (PIIN) and multiple-access interference (MAI) on the system performance are evaluated numerically for different values of the optical modulation index (OMI) during the nonlinear electro-optical modulator (EOM) response. At low OMI optical device noise is dominant, but at high OMI nonlinear effect becomes significant. Numerical result shows that the system performance is highly sensitive to the OMI. Therefore, specifying an appropriate value of the OMI is essential in optimizing the system performance. The influence of the degree of polarization (DOP) in the system is also discussed. By employing the scrambler in front of the balanced photo-detector, the system performance can be enhanced. The high-performance, low-cost characteristics of the double-spread CDMA render the scheme an ideal solution for radio-CDMA wireless system cascaded with optical CDMA network.

Ranked solutions to a class of combinatorial optimizations—with applications in mass spectrometry based peptide sequencing and a variant of directed paths in random media

Science.gov (United States)

Doerr, Timothy P.; Alves, Gelio; Yu, Yi-Kuo

2005-08-01

Typical combinatorial optimizations are NP-hard; however, for a particular class of cost functions the corresponding combinatorial optimizations can be solved in polynomial time using the transfer matrix technique or, equivalently, the dynamic programming approach. This suggests a way to efficiently find approximate solutions-find a transformation that makes the cost function as similar as possible to that of the solvable class. After keeping many high-ranking solutions using the approximate cost function, one may then re-assess these solutions with the full cost function to find the best approximate solution. Under this approach, it is important to be able to assess the quality of the solutions obtained, e.g., by finding the true ranking of the kth best approximate solution when all possible solutions are considered exhaustively. To tackle this statistical issue, we provide a systematic method starting with a scaling function generated from the finite number of high-ranking solutions followed by a convergent iterative mapping. This method, useful in a variant of the directed paths in random media problem proposed here, can also provide a statistical significance assessment for one of the most important proteomic tasks-peptide sequencing using tandem mass spectrometry data. For directed paths in random media, the scaling function depends on the particular realization of randomness; in the mass spectrometry case, the scaling function is spectrum-specific.

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

Science.gov (United States)

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

2014-12-01

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

Reverse preferential spread in complex networks

Science.gov (United States)

Toyoizumi, Hiroshi; Tani, Seiichi; Miyoshi, Naoto; Okamoto, Yoshio

2012-08-01

Large-degree nodes may have a larger influence on the network, but they can be bottlenecks for spreading information since spreading attempts tend to concentrate on these nodes and become redundant. We discuss that the reverse preferential spread (distributing information inversely proportional to the degree of the receiving node) has an advantage over other spread mechanisms. In large uncorrelated networks, we show that the mean number of nodes that receive information under the reverse preferential spread is an upper bound among any other weight-based spread mechanisms, and this upper bound is indeed a logistic growth independent of the degree distribution.

Spectrum Fatigue Lifetime and Residual Strength for Fiberglass Laminates; TOPICAL

International Nuclear Information System (INIS)

WAHL, NEIL K.; MANDELL, JOHN F.; SAMBORSKY, DANIEL D.

2002-01-01

This report addresses the effects of spectrum loading on lifetime and residual strength of a typical fiberglass laminate configuration used in wind turbine blade construction. Over 1100 tests have been run on laboratory specimens under a variety of load sequences. Repeated block loading at two or more load levels, either tensile-tensile, compressive-compressive, or reversing, as well as more random standard spectra have been studied. Data have been obtained for residual strength at various stages of the lifetime. Several lifetime prediction theories have been applied to the results. The repeated block loading data show lifetimes that are usually shorter than predicted by the most widely used linear damage accumulation theory, Miner's sum. Actual lifetimes are in the range of 10 to 20 percent of predicted lifetime in many cases. Linear and nonlinear residual strength models tend to fit the data better than Miner's sum, with the nonlinear providing a better fit of the two. Direct tests of residual strength at various fractions of the lifetime are consistent with the residual strength models. Load sequencing effects are found to be insignificant. The more a spectrum deviates from constant amplitude, the more sensitive predictions are to the damage law used. The nonlinear model provided improved correlation with test data for a modified standard wind turbine spectrum. When a single, relatively high load cycle was removed, all models provided similar, though somewhat non-conservative correlation with the experimental results. Predictions for the full spectrum, including tensile and compressive loads were slightly non-conservative relative to the experimental data, and accurately captured the trend with varying maximum load. The nonlinear residual strength based prediction with a power law S-N curve extrapolation provided the best fit to the data in most cases. The selection of the constant amplitude fatigue regression model becomes important at the lower stress, higher

The Eye Gaze Direction of an Observed Person Can Bias Perception, Memory, and Attention in Adolescents with and without Autism Spectrum Disorder

Science.gov (United States)

Freeth, M.; Ropar, D.; Chapman, P.; Mitchell, P.

2010-01-01

The reported experiments aimed to investigate whether a person and his or her gaze direction presented in the context of a naturalistic scene cause perception, memory, and attention to be biased in typically developing adolescents and high-functioning adolescents with autism spectrum disorder (ASD). A novel computerized image manipulation program…

Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland

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Lourdes de la Mata Saez

2015-12-01

Full Text Available Here we present draft-quality genome sequence assemblies for the oomycete Phytophthora ramorum genetic lineage EU2. We sequenced genomes of seven isolates collected in Northern Ireland between 2010 and 2012. Multiple genome sequences from P. ramorum EU2 will be valuable for identifying genetic variation within the clonal lineage that can be useful for tracking its spread.

Explaining the luminosity spread in young clusters: proto and pre-main sequence stellar evolution in a molecular cloud environment

Science.gov (United States)

Jensen, Sigurd S.; Haugbølle, Troels

2018-02-01

Hertzsprung-Russell diagrams of star-forming regions show a large luminosity spread. This is incompatible with well-defined isochrones based on classic non-accreting protostellar evolution models. Protostars do not evolve in isolation of their environment, but grow through accretion of gas. In addition, while an age can be defined for a star-forming region, the ages of individual stars in the region will vary. We show how the combined effect of a protostellar age spread, a consequence of sustained star formation in the molecular cloud, and time-varying protostellar accretion for individual protostars can explain the observed luminosity spread. We use a global magnetohydrodynamic simulation including a sub-scale sink particle model of a star-forming region to follow the accretion process of each star. The accretion profiles are used to compute stellar evolution models for each star, incorporating a model of how the accretion energy is distributed to the disc, radiated away at the accretion shock, or incorporated into the outer layers of the protostar. Using a modelled cluster age of 5 Myr, we naturally reproduce the luminosity spread and find good agreement with observations of the Collinder 69 cluster, and the Orion Nebular Cluster. It is shown how stars in binary and multiple systems can be externally forced creating recurrent episodic accretion events. We find that in a realistic global molecular cloud model massive stars build up mass over relatively long time-scales. This leads to an important conceptual change compared to the classic picture of non-accreting stellar evolution segmented into low-mass Hayashi tracks and high-mass Henyey tracks.

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

Science.gov (United States)

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

Effect of PVRC damping with independent support motion response spectrum analysis of piping systems

International Nuclear Information System (INIS)

Wang, Y.K.; Bezler, P.; Shteyngart, S.

1986-01-01

The Technical Committee for Piping Systems of the Pressure Vessel Research Committee (PVRC) has recommended new damping values to be used in the seismic analyses of piping systems in nuclear power plants. To evaluate the effects of coupling these recommendations with the use of independent support motion analyses methods, two sets of seismic analyses have been carried out for several piping systems. One set based on the use of uniform damping as specified in Regulatory Guide 1.61, the other based on the PVRC recommendations. In each set the analyses were performed using independent support motion time history and response spectrum methods as well as the envelope spectrum method. In the independent response spectrum analyses, 14 response estimates were in fact obtained by considering different combination procedures between the support group contributions and all sequences of combinations between support groups, modes and directions. For each analysis set, the response spectrum results were compared with time history estimates of those results. Comparison tables were then prepared depicting the percentage by which the response spectrum estimates exceeded the time history estimates. By comparing the result tables between both analysis sets, the impact of PVRC damping can be observed. Preliminary results show that the degree of exceedance of the response spectrum estimates based on PVRC damping is less than that based on uniform damping for the same piping problem. Expressed differently the results obtained if ISM methods are coupled with PVRC damping are not as conservative as those obtained using uniform damping

Revised South China Sea spreading history based on macrostructure analysis of IODP Expedition 349 core samples and geophysical data

Science.gov (United States)

Sun, Z.; Ding, W.; Zhao, X.; Qiu, N.; Lin, J.; Li, C.

2017-12-01

In Internaltional Ocean Discovery Program (IODP) Expedition 349, four sites were drilled and cored successfully in the South China Sea (SCS). Three of them are close to the central spreading ridge (Sites U1431, U1433 and U1434), and one (Site U1435) is located on an outer rise,,providingsignificant information on the spreading history of the SCS.In order to constrain the spreading historymore accurately with the core results, we analyzed the identifiable macrostructures (over 300 fractures, veins and slickensides)from all the consolidated samples of these four drill sites. Then we made a retrograde reconstruction of the SCS spreading history with the constraints of the estimated fractures and veins, post-spreading volcanism,seismic interpretation, as well as free-air gravity and magnetic anomaly and topography analysis. Our study indicates that the spreading of the SCS experienced at least one ridge jump event and two events of ridge orientation and spreading direction adjustment, which mademagnetic anomaly orientation, ridge positionand facture zone directionskeep changing in the South China Sea. During the last spreading stage, the spreading direction was north-southward but lasted for a very short time period. The oceanic crust is wider in the eastern SCS and tapers out toward west.Due to the subductionof SCS beneath the Philippine Sea plate, the seafloor began to develop new fractures:the NWW-to EW-trending R' shear faults and the NE-trending P faultsbecame dominant faults and controlled the eruption of post-drift volcanism.

Market-driven spectrum sharing in cognitive radio

CERN Document Server

Yi, Changyan

2016-01-01

This brief focuses on the current research on mechanism design for dynamic spectrum sharing in cognitive radio (CR) networks. Along with a review of CR architectures and characteristics, this brief presents the motivations, significances and unique challenges of implementing algorithmic mechanism design for encouraging both primary spectrum owners and secondary spectrum users to participate in dynamic spectrum sharing. The brief then focuses on recent advances in mechanism design in CR networks. With an emphasis on dealing with the uncertain spectrum availabilities, mechanisms based on spectrum recall, two-stage spectrum sharing and online spectrum allocation are introduced with the support of theoretic analyses and numerical illustrations. The brief concludes with a discussion of potential research directions and interests, which will motivate further studies on mechanism design for wireless communications. This brief is concise and approachable for researchers, professionals and advanced-level students in w...

Nicotiana small RNA sequences support a host genome origin of cucumber mosaic virus satellite RNA.

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Kiran Zahid

2015-01-01

Full Text Available Satellite RNAs (satRNAs are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. Despite many decades of research, the origin of satRNAs remains unknown. In this study we show that a β-glucuronidase (GUS transgene fused with a Cucumber mosaic virus (CMV Y satellite RNA (Y-Sat sequence (35S-GUS:Sat was transcriptionally repressed in N. tabacum in comparison to a 35S-GUS transgene that did not contain the Y-Sat sequence. This repression was not due to DNA methylation at the 35S promoter, but was associated with specific DNA methylation at the Y-Sat sequence. Both northern blot hybridization and small RNA deep sequencing detected 24-nt siRNAs in wild-type Nicotiana plants with sequence homology to Y-Sat, suggesting that the N. tabacum genome contains Y-Sat-like sequences that give rise to 24-nt sRNAs capable of guiding RNA-directed DNA methylation (RdDM to the Y-Sat sequence in the 35S-GUS:Sat transgene. Consistent with this, Southern blot hybridization detected multiple DNA bands in Nicotiana plants that had sequence homology to Y-Sat, suggesting that Y-Sat-like sequences exist in the Nicotiana genome as repetitive DNA, a DNA feature associated with 24-nt sRNAs. Our results point to a host genome origin for CMV satRNAs, and suggest novel approach of using small RNA sequences for finding the origin of other satRNAs.

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

Science.gov (United States)

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.

Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage.

Science.gov (United States)

Merker, Matthias; Blin, Camille; Mona, Stefano; Duforet-Frebourg, Nicolas; Lecher, Sophie; Willery, Eve; Blum, Michael G B; Rüsch-Gerdes, Sabine; Mokrousov, Igor; Aleksic, Eman; Allix-Béguec, Caroline; Antierens, Annick; Augustynowicz-Kopeć, Ewa; Ballif, Marie; Barletta, Francesca; Beck, Hans Peter; Barry, Clifton E; Bonnet, Maryline; Borroni, Emanuele; Campos-Herrero, Isolina; Cirillo, Daniela; Cox, Helen; Crowe, Suzanne; Crudu, Valeriu; Diel, Roland; Drobniewski, Francis; Fauville-Dufaux, Maryse; Gagneux, Sébastien; Ghebremichael, Solomon; Hanekom, Madeleine; Hoffner, Sven; Jiao, Wei-wei; Kalon, Stobdan; Kohl, Thomas A; Kontsevaya, Irina; Lillebæk, Troels; Maeda, Shinji; Nikolayevskyy, Vladyslav; Rasmussen, Michael; Rastogi, Nalin; Samper, Sofia; Sanchez-Padilla, Elisabeth; Savic, Branislava; Shamputa, Isdore Chola; Shen, Adong; Sng, Li-Hwei; Stakenas, Petras; Toit, Kadri; Varaine, Francis; Vukovic, Dragana; Wahl, Céline; Warren, Robin; Supply, Philip; Niemann, Stefan; Wirth, Thierry

2015-03-01

Mycobacterium tuberculosis strains of the Beijing lineage are globally distributed and are associated with the massive spread of multidrug-resistant (MDR) tuberculosis in Eurasia. Here we reconstructed the biogeographical structure and evolutionary history of this lineage by genetic analysis of 4,987 isolates from 99 countries and whole-genome sequencing of 110 representative isolates. We show that this lineage initially originated in the Far East, from where it radiated worldwide in several waves. We detected successive increases in population size for this pathogen over the last 200 years, practically coinciding with the Industrial Revolution, the First World War and HIV epidemics. Two MDR clones of this lineage started to spread throughout central Asia and Russia concomitantly with the collapse of the public health system in the former Soviet Union. Mutations identified in genes putatively under positive selection and associated with virulence might have favored the expansion of the most successful branches of the lineage.

Iterative normalization technique for reference sequence generation for zero-tail discrete fourier transform spread orthogonal frequency division multiplexing

DEFF Research Database (Denmark)

2017-01-01

, and performing an iterative manipulation of the input sequence. The performing of the iterative manipulation of the input sequence may include, for example: computing frequency domain response of the sequence, normalizing elements of the computed frequency domain sequence to unitary power while maintaining phase...

ON THE RELIABILITY OF STELLAR AGES AND AGE SPREADS INFERRED FROM PRE-MAIN-SEQUENCE EVOLUTIONARY MODELS

International Nuclear Information System (INIS)

Hosokawa, Takashi; Offner, Stella S. R.; Krumholz, Mark R.

2011-01-01

We revisit the problem of low-mass pre-main-sequence stellar evolution and its observational consequences for where stars fall on the Hertzsprung-Russell diagram (HRD). In contrast to most previous work, our models follow stars as they grow from small masses via accretion, and we perform a systematic study of how the stars' HRD evolution is influenced by their initial radius, by the radiative properties of the accretion flow, and by the accretion history, using both simple idealized accretion histories and histories taken from numerical simulations of star cluster formation. We compare our numerical results to both non-accreting isochrones and to the positions of observed stars in the HRD, with a goal of determining whether both the absolute ages and the age dispersions inferred from non-accreting isochrones are reliable. We show that non-accreting isochrones can sometimes overestimate stellar ages for more massive stars (those with effective temperatures above ∼3500 K), thereby explaining why non-accreting isochrones often suggest a systematic age difference between more and less massive stars in the same cluster. However, we also find the only way to produce a similar overestimate for the ages of cooler stars is if these stars grow from ∼0.01 M sun seed protostars that are an order of magnitude smaller than predicted by current theoretical models, and if the size of the seed protostar correlates systematically with the final stellar mass at the end of accretion. We therefore conclude that, unless both of these conditions are met, inferred ages and age spreads for cool stars are reliable, at least to the extent that the observed bolometric luminosities and temperatures are accurate. Finally, we note that the time dependence of the mass accretion rate has remarkably little effect on low-mass stars' evolution on the HRD, and that such time dependence may be neglected for all stars except those with effective temperatures above ∼4000 K.

Evaluation of the antibacterial spectrum of drosocin analogues

NARCIS (Netherlands)

Bikker, F.J.; Kaman-van Zanten, W.E.; Vries-van de Ruit, A.M.B.C. de; Voskamp-Visser, I.; Hooft, P.A.V. van; Mars-Groenendijk, R.H.; Visser, P.C. de; Noort, D.

2006-01-01

Drosocin is a 19-mer, cationic antimicrobial peptide from Drosophila melanogaster. The aim of the study was to examine the antibacterial spectrum of unglycosylated drosocin analogues. Furthermore, the amino acid sequence of DnaK, drosocin's intracellular target, from susceptible species was aligned

The qacC gene has recently spread between rolling circle plasmids of Staphylococcus, indicative of a novel gene transfer mechanism

Directory of Open Access Journals (Sweden)

Trudy M. Wassenaar

2016-09-01

Full Text Available Resistance of Staphylococcus species to quaternary ammonium compounds, frequently used as disinfectants and biocides, can be attributed to qac genes. These qac gene products belong to the Small Multidrug Resistant (SMR protein family, and are often encoded by rolling-circle (RC replicating plasmids. Four classes of SMR-type qac gene families have been described in Staphylococcus species: qacC, qacG, qacJ and qacH. Within their class, these genes are highly conserved, but qacC genes are extremely conserved, although they are found in variable plasmid backgrounds. The lower degree of sequence identity of these plasmids compared to the strict nucleotide conservation of their qacC means that this gene has recently spread. In the absence of insertion sequences or other genetic elements explaining the mobility, we sought for an explanation of mobilization by sequence comparison. Publically available sequences of qac genes, their flanking genes and the replication gene that is invariably present in RC-plasmids were compared to reconstruct the evolutionary history of these plasmids and to explain the recent spread of qacC. Here we propose a new model that explains how qacC is mobilized and transferred to acceptor RC-plasmids without assistance of other genes, by means of its location in between the Double Strand replication Origin (DSO and the Single-Strand replication Origin (SSO. The proposed mobilization model of this DSO-qacC-SSO element represents a novel mechanism of gene mobilization in RC-plasmids, which has also been employed by other genes, such as lnuA (conferring lincomycin resistance. The proposed gene mobility has aided to the wide spread of clinically relevant resistance genes in Staphylococcus populations.

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

DEFF Research Database (Denmark)

Liu, Siyang; Huang, Shujia; Rao, Junhua

2015-01-01

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......) 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...... 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...

The effectiveness of direct instruction for teaching language to children with autism spectrum disorders: identifying materials.

Science.gov (United States)

Ganz, Jennifer B; Flores, Margaret M

2009-01-01

Students with autism spectrum disorders (ASD) frequently demonstrate language delays (American Psychiatric Association 2000). This study investigated the effects of a Direct Instruction (DI) language program implemented with elementary students with ASD. There is little research in the area of DI as a language intervention for students with ASD. This study examined the effectiveness of DI with regard to students' oral language skills, specifically the identification of materials of which objects were made. A single-subject changing criterion design was employed. A functional relation between DI and oral language skills was demonstrated through replication of skill increase over three criterion changes and across three students. The results and their implications are discussed further.

Multilocus sequence typing of IncN plasmids

DEFF Research Database (Denmark)

García-Fernández, Aurora; Villa, Laura; Moodley, Arshnee

2011-01-01

that spread and persistence of this particular IncN-carrying blaVIM-1 lineage in Greece. CONCLUSIONS: This study proposes the use of pMLST as a suitable and rapid method for identification of IncN epidemic plasmid lineages. The recent spread of blaCTX-M-1 among humans and animals seems to be associated......OBJECTIVES: Incompatibility group N (IncN) plasmids have been associated with the dissemination of antimicrobial resistance and are a major vehicle for the spread of blaVIM-1 in humans and blaCTX-M-1 in animals. A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid...... in different countries from both animals and humans belonged to ST1, suggesting dissemination of an epidemic plasmid through the food chain. Fifteen of 17 plasmids carrying blaVIM-1 from Klebsiella pneumoniae and Escherichia coli, isolated during a 5year period in Greece were assigned to ST10, suggesting...

Image sequence analysis

CERN Document Server

1981-01-01

The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

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

Science.gov (United States)

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

Estimation of wave directional spreading in shallow water

Digital Repository Service at National Institute of Oceanography (India)

SanilKumar, V.; Deo, M.C.; Anand, N.M.; Chandramohan, P.

loads on offshore structures, long- term estimation of waves and estimation of sediment transport. According to the principle of superposition of linear waves, the sea state is com- posed of a large number of individual wave components, each having a..., who were involved in the data collection programme. NIO Contribution number 2569. References Benoit, M., 1992. Practical comparative performance survey of methods used for estimating directional wave spectra from heave–pitch–roll data. Proceedings...

Parametric spectro-temporal analyzer (PASTA) for real-time optical spectrum observation

Science.gov (United States)

Zhang, Chi; Xu, Jianbing; Chui, P. C.; Wong, Kenneth K. Y.

2013-06-01

Real-time optical spectrum analysis is an essential tool in observing ultrafast phenomena, such as the dynamic monitoring of spectrum evolution. However, conventional method such as optical spectrum analyzers disperse the spectrum in space and allocate it in time sequence by mechanical rotation of a grating, so are incapable of operating at high speed. A more recent method all-optically stretches the spectrum in time domain, but is limited by the allowable input condition. In view of these constraints, here we present a real-time spectrum analyzer called parametric spectro-temporal analyzer (PASTA), which is based on the time-lens focusing mechanism. It achieves a frame rate as high as 100 MHz and accommodates various input conditions. As a proof of concept and also for the first time, we verify its applications in observing the dynamic spectrum of a Fourier domain mode-locked laser, and the spectrum evolution of a laser cavity during its stabilizing process.

On the remarkable spectrum of a non-Hermitian random matrix model

International Nuclear Information System (INIS)

Holz, D E; Orland, H; Zee, A

2003-01-01

A non-Hermitian random matrix model proposed a few years ago has a remarkably intricate spectrum. Various attempts have been made to understand the spectrum, but even its dimension is not known. Using the Dyson-Schmidt equation, we show that the spectrum consists of a non-denumerable set of lines in the complex plane. Each line is the support of the spectrum of a periodic Hamiltonian, obtained by the infinite repetition of any finite sequence of the disorder variables. Our approach is based on the 'theory of words'. We make a complete study of all four-letter words. The spectrum is complicated because our matrix contains everything that will ever be written in the history of the universe, including this particular paper

Fungal communities in mycorrhizal roots of conifer seedlings in forest nurseries under different cultivation systems, assessed by morphotyping, direct sequencing and mycelial isolation.

Science.gov (United States)

Menkis, Audrius; Vasiliauskas, Rimvydas; Taylor, Andrew F S; Stenlid, Jan; Finlay, Roger

2005-12-01

Fungi colonising root tips of Pinus sylvestris and Picea abies grown under four different seedling cultivation systems were assessed by morphotyping, direct sequencing and isolation methods. Roots were morphotyped using two approaches: (1) 10% of the whole root system from 30 seedlings of each species and (2) 20 randomly selected tips per plant from 300 seedlings of each species. The first approach yielded 15 morphotypes, the second yielded 27, including 18 new morphotypes. The overall community consisted of 33 morphotypes. The level of mycorrhizal colonisation of roots determined by each approach was about 50%. The cultivation system had a marked effect on the level of mycorrhizal colonisation. In pine, the highest level of colonisation (48%) was observed in bare-root systems, while in spruce, colonisation was highest in polyethylene rolls (71%). Direct internal transcribed spacer ribosomal DNA sequencing and isolation detected a total of 93 fungal taxa, including 27 mycorrhizal. A total of 71 (76.3%) fungi were identified at least to a genus level. The overlap between the two methods was low. Only 13 (13.9%) of taxa were both sequenced and isolated, 47 (50.5%) were detected exclusively by sequencing and 33 (35.5%) exclusively by isolation. All isolated mycorrhizal fungi were also detected by direct sequencing. Characteristic mycorrhizas were Phialophora finlandia, Amphinema byssoides, Rhizopogon rubescens, Suillus luteus and Thelephora terrestris. There was a moderate similarity in mycorrhizal communities between pine and spruce and among different cultivation systems.

Measurement of Rank and Other Properties of Direct and Scattered Signals

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Svante Björklund

2016-01-01

Full Text Available We have designed an experiment for low-cost indoor measurements of rank and other properties of direct and scattered signals with radar interference suppression in mind. The signal rank is important also in many other applications, for example, DOA (Direction of Arrival estimation, estimation of the number of and location of transmitters in electronic warfare, and increasing the capacity in wireless communications. In real radar applications, such measurements can be very expensive, for example, involving airborne radars with array antennas. We have performed the measurements in an anechoic chamber with several transmitters, a receiving array antenna, and a moving reflector. Our experiment takes several aspects into account: transmitted signals with different correlation, decorrelation of the signals during the acquisition interval, covariance matrix estimation, noise eigenvalue spread, calibration, near-field compensation, scattering in a rough surface, and good control of the influencing factors. With our measurements we have observed rank, DOA spectrum, and eigenpatterns of direct and scattered signals. The agreement of our measured properties with theoretic and simulated results in the literature shows that our experiment is realistic and sound. The detailed description of our experiment could serve as help for conducting other well-controlled experiments.

Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens.

Science.gov (United States)

Hage, Elias; Wilkie, Gavin S; Linnenweber-Held, Silvia; Dhingra, Akshay; Suárez, Nicolás M; Schmidt, Julius J; Kay-Fedorov, Penelope C; Mischak-Weissinger, Eva; Heim, Albert; Schwarz, Anke; Schulz, Thomas F; Davison, Andrew J; Ganzenmueller, Tina

2017-06-01

Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Next-generation sequencing was performed on target enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast milk, respiratory samples, biopsies, and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients, and congenitally infected children). De novo-assembled HCMV genome sequences were obtained for 57 of 68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intraindividual blood samples from 9 of 15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in 6 individuals with sequential blood samples and upon compartmental analysis of 1 patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral-resistance mutations. In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Default Spread dan Term Spread sebagai Variabel Proxy Siklus Bisnis pada Model Fama-French

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Edwin Hendra

2015-08-01

Full Text Available This research aims to apply the Fama-French models and test the effect of alternative variable of bond yield spread, default spread (RBBB – RAAA and RAAA – RF, and the term spread (RSUN10-RSUN1, as proxy variables of the business cycle, in IDX stock data during 2005-2010. Four types of asset pricing models tested are Sharpe-Lintner CAPM, Fama-French models, Hwang et al.model, and hybrid model. The results showed that the size effect and value effect has an impact on excess stock returns. Slopes of market beta, SMB, and HML are more sensitive to stock big size and high B / M. Default spreads and term spreads in Hwang et al. model can explain the value effect, and weakly explain the size effect, meanwhile the power of explanation disappeared on Hybrid models. Based on the assessment adjusted R2 and the frequency of rejection of non-zero alpha, is found that the hybrid model is the most suitable model.  

Spreading and solidification behavior of molten Si droplets impinging on substrates

International Nuclear Information System (INIS)

Nagashio, K.; Murata, H.; Kuribayashi, K.

2004-01-01

This paper focuses on an effect of initial undercoolings on the spreading and solidification behavior of Si dropped on a silicon wafer, which was directly observed through it by the infrared imaging system. For an overheated droplet, the melt spreading occurred first and solidified later. The final splat shape was a typical disc. On the other hand, for a droplet with large initial undercooling, the solidification took place at the faster rate than the melt spreading, which resulted in a spherical shape of final splat. It is indicated that the final shape is considerably affected by the initial undercooling in the measurable-scale experiment with large droplets (∼mm size) and low impingement rates (∼m/s order). Moreover, equiaxed grains were found throughout the quenched surface by an electron backscatter pattern analysis. That is, the microstructure formation was nucleation-controlled since the growth parallel to the substrate was suppressed by the time-dependent contact of melt/substrate governed by the melt deformation

Spectrum of sequence variations in the FANCA gene: an International Fanconi Anemia Registry (IFAR) study.

Science.gov (United States)

Levran, Orna; Diotti, Raffaella; Pujara, Kanan; Batish, Sat D; Hanenberg, Helmut; Auerbach, Arleen D

2005-02-01

Fanconi anemia (FA) is an autosomal recessive disorder that is defined by cellular hypersensitivity to DNA cross-linking agents, and is characterized clinically by developmental abnormalities, progressive bone-marrow failure, and predisposition to leukemia and solid tumors. There is extensive genetic heterogeneity, with at least 11 different FA complementation groups. FA-A is the most common group, accounting for approximately 65% of all affected individuals. The mutation spectrum of the FANCA gene, located on chromosome 16q24.3, is highly heterogeneous. Here we summarize all sequence variations (mutations and polymorphisms) in FANCA described in the literature and listed in the Fanconi Anemia Mutation Database as of March 2004, and report 61 novel FANCA mutations identified in FA patients registered in the International Fanconi Anemia Registry (IFAR). Thirty-eight novel SNPs, previously unreported in the literature or in dbSNP, were also identified. We studied the segregation of common FANCA SNPs in FA families to generate haplotypes. We found that FANCA SNP data are highly useful for carrier testing, prenatal diagnosis, and preimplantation genetic diagnosis, particularly when the disease-causing mutations are unknown. Twenty-two large genomic deletions were identified by detection of apparent homozygosity for rare SNPs. In addition, a conserved SNP haplotype block spanning at least 60 kb of the FANCA gene was identified in individuals from various ethnic groups. (c) 2005 Wiley-Liss, Inc.

Spread of Extended Spectrum Cephalosporinase-Producing Escherichia coli Clones and Plasmids from Parent Animals to Broilers and to Broiler Meat in a Production Without Use of Cephalosporins

DEFF Research Database (Denmark)

Agersø, Yvonne; Jensen, Jacob Dyring; Hasman, Henrik

2014-01-01

Objectives: This study investigated the occurrence of extended spectrum cephalosporinase (ESC)–producing Escherichia coli in a broiler production with no cephalosporin use and a low use of antimicrobials in general. Furthermore, it investigated whether the current consumption of aminopenicillins....... Isolates with blaCMY-2 were subtyped by pulsed-field gel electrophoresis (PFGE), phylotyping, and antimicrobial susceptibility testing. Selected isolates were used as donors in filter-mating experiments, multilocus sequence typing (MLST), and plasmid replicons were typed. Aminopenicillin use at the farm...... (not flock) level was obtained from VetStat, a database for mandatory registration of veterinary prescriptions in Denmark. Results: ESC-producing E. coli occurred in 93% (27/29) of broiler parent farms in 2011, 27% (53/197) of broiler flocks in 2010, and 3.3% (4/121) of Danish retail broiler meat...

Clonal spread of blaOXA-72-carrying Acinetobacter baumannii sequence type 512 in Taiwan.

Science.gov (United States)

Kuo, Han-Yueh; Hsu, Po-Jui; Chen, Jiann-Yuan; Liao, Po-Cheng; Lu, Chia-Wei; Chen, Chang-Hua; Liou, Ming-Li

2016-07-01

This is the first report to show an insidious outbreak of armA- and blaOXA-72-carrying Acinetobacter baumannii sequence type 512 (ST512) at a study hospital in northern Taiwan. Multilocus sequence typing revealed that this was a ST512 clone. All of the isolates with ST512 carried a novel 12,056-bp repGR2 in combination with a repGR12-type plasmid. This plasmid, designated pAB-ML, had one copy of the blaOXA-72 gene that was flanked by XerC/XerD-like sites and conferred resistance to carbapenems. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

An Extended Multilocus Sequence Typing (MLST Scheme for Rapid Direct Typing of Leptospira from Clinical Samples.

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Sabrina Weiss

2016-09-01

Full Text Available Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST data direct from patient specimens while minimising costs for subsequent sequencing.An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK and the Lao Peoples Democratic Republic (Lao PDR. Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50% and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%. No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25% and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively. All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14].Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

Modelling the influence of human behaviour on the spread of infectious diseases: a review.

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Funk, Sebastian; Salathé, Marcel; Jansen, Vincent A A

2010-09-06

Human behaviour plays an important role in the spread of infectious diseases, and understanding the influence of behaviour on the spread of diseases can be key to improving control efforts. While behavioural responses to the spread of a disease have often been reported anecdotally, there has been relatively little systematic investigation into how behavioural changes can affect disease dynamics. Mathematical models for the spread of infectious diseases are an important tool for investigating and quantifying such effects, not least because the spread of a disease among humans is not amenable to direct experimental study. Here, we review recent efforts to incorporate human behaviour into disease models, and propose that such models can be broadly classified according to the type and source of information which individuals are assumed to base their behaviour on, and according to the assumed effects of such behaviour. We highlight recent advances as well as gaps in our understanding of the interplay between infectious disease dynamics and human behaviour, and suggest what kind of data taking efforts would be helpful in filling these gaps.

Multiplexed microsatellite recovery using massively parallel sequencing

Science.gov (United States)

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

Science.gov (United States)

Tam, Phuong Dinh; Trung, Tran; Tuan, Mai Anh; Chien, Nguyen Duc

2009-09-01

DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when immerged in double distilled water and kept refrigerated.

Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

International Nuclear Information System (INIS)

Phuong Dinh Tam; Mai Anh Tuan; Tran Trung; Nguyen Duc Chien

2009-01-01

DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when emerged in double distilled water and kept refrigerated.

Cooperative spreading processes in multiplex networks.

Science.gov (United States)

Wei, Xiang; Chen, Shihua; Wu, Xiaoqun; Ning, Di; Lu, Jun-An

2016-06-01

This study is concerned with the dynamic behaviors of epidemic spreading in multiplex networks. A model composed of two interacting complex networks is proposed to describe cooperative spreading processes, wherein the virus spreading in one layer can penetrate into the other to promote the spreading process. The global epidemic threshold of the model is smaller than the epidemic thresholds of the corresponding isolated networks. Thus, global epidemic onset arises in the interacting networks even though an epidemic onset does not arise in each isolated network. Simulations verify the analysis results and indicate that cooperative spreading processes in multiplex networks enhance the final infection fraction.

Antibiotic Susceptibilities and Genetic Characteristics of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Stools of Pediatric Diarrhea Patients in Surabaya, Indonesia.

Science.gov (United States)

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.

Spread effects - methodology; Spredningseffekter - metodegrunnlag

Energy Technology Data Exchange (ETDEWEB)

NONE

2004-07-01

Diffusion of technology, environmental effects and rebound effects are the principal effects from the funding of renewable energy and energy economising. It is difficult to estimate the impact of the spread effects both prior to the measures are implemented and after the measures are carried out. Statistical methods can be used to estimate the spread effects, but they are insecure and always need to be complemented with qualitative and subjective evaluations. It is more adequate to evaluate potential spread effects from market and market data surveillance for a selection of technologies and parties. Based on this information qualitative indicators for spread effects can be constructed and used both ex ante and ex post (ml)

Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China.

Science.gov (United States)

Zhang, Yuzhen; Vrancken, Bram; Feng, Yun; Dellicour, Simon; Yang, Qiqi; Yang, Weihong; Zhang, Yunzhi; Dong, Lu; Pybus, Oliver G; Zhang, Hailin; Tian, Huaiyu

2017-06-03

Rabies is an important but underestimated threat to public health, with most cases reported in Asia. Since 2000, a new epidemic wave of rabies has emerged in Yunnan Province, southwestern China, which borders three countries in Southeast Asia. We estimated gene-specific evolutionary rates for rabies virus using available data in GenBank, then used this information to calibrate the timescale of rabies virus (RABV) spread in Asia. We used 452 publicly available geo-referenced complete nucleoprotein (N) gene sequences, including 52 RABV sequences that were recently generated from samples collected in Yunnan between 2008 and 2012. The RABV N gene evolutionary rate was estimated to be 1.88 × 10 -4 (1.37-2.41 × 10 -4 , 95% Bayesian credible interval, BCI) substitutions per site per year. Phylogenetic reconstructions show that the currently circulating RABV lineages in Yunnan result from at least seven independent introductions (95% BCI: 6-9 introductions) and represent each of the three main Asian RABV lineages, SEA-1, -2 and -3. We find that Yunnan is a sink location for the domestic spread of RABV and connects RABV epidemics in North China, South China, and Southeast Asia. Cross-border spread from southeast Asia (SEA) into South China, and intermixing of the North and South China epidemics is also well supported. The influx of RABV into Yunnan from SEA was not well-supported, likely due to the poor sampling of SEA RABV diversity. We found evidence for a lineage displacement of the Yunnan SEA-2 and -3 lineages by Yunnan SEA-1 strains, and considered whether this could be attributed to fitness differences. Overall, our study contributes to a better understanding of the spread of RABV that could facilitate future rabies virus control and prevention efforts.

Density profile evolution and nonequilibrium effects in partial and full spreading measurements of surface diffusion

DEFF Research Database (Denmark)

Nikunen, P.; Vattulainen, Ilpo Tapio; Ala-Nissila, T.

2001-01-01

in D-C(theta) depend on the initial density gradient and the initial state from which the spreading starts. To this end, we carry out extensive Monte Carlo simulations for a lattice-gas model of the O/W(110) system. Studies of submonolayer spreading from an initially ordered p(2x1) phase at theta = 1....../2 reveal that the spreading and diffusion rates in directions parallel and perpendicular to rows of oxygen atoms are significantly different within the ordered phase. Aside from this effect, we find that the degree of ordering in the initial phase has a relatively small impact on the overall behavior of D...

Sequences in language and text

CERN Document Server

Mikros, George K

2015-01-01

The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

Spreading of correlations in the Falicov-Kimball model

Science.gov (United States)

Herrmann, Andreas J.; Antipov, Andrey E.; Werner, Philipp

2018-04-01

We study dynamical properties of the one- and two-dimensional Falicov-Kimball model using lattice Monte Carlo simulations. In particular, we calculate the spreading of charge correlations in the equilibrium model and after an interaction quench. The results show a reduction of the light-cone velocity with interaction strength at low temperature, while the phase velocity increases. At higher temperature, the initial spreading is determined by the Fermi velocity of the noninteracting system and the maximum range of the correlations decreases with increasing interaction strength. Charge order correlations in the disorder potential enhance the range of the correlations. We also use the numerically exact lattice Monte Carlo results to benchmark the accuracy of equilibrium and nonequilibrium dynamical cluster approximation calculations. It is shown that the bias introduced by the mapping to a periodized cluster is substantial, and that from a numerical point of view, it is more efficient to simulate the lattice model directly.

On the potential of zero-tail DFT-spread-OFDM in 5G networks

DEFF Research Database (Denmark)

Berardinelli, Gilberto; Tavares, Fernando Menezes Leitão; Sørensen, Troels Bundgaard

2014-01-01

Zero-tail Discrete Fourier Transform -spread OFDM (ZT DFT-s-OFDM) modulation allows to dynamically cope with the delay spread of the multipath channel, thus avoiding the limitations of hard-coded Cyclic Prefix (CP). In this paper, we discuss the potential of ZT DFT-s-OFDM modulation for the envis......, possibility of adopting unified radio numerology among different cells, reduced latency and support of agile link direction switching. The robustness of ZT DFT-s-OFDM towards non-idealities such as phase noise and non-linear power amplifier is also discussed....

Inferring Weighted Directed Association Networks from Multivariate Time Series with the Small-Shuffle Symbolic Transfer Entropy Spectrum Method

Directory of Open Access Journals (Sweden)

Yanzhu Hu

2016-09-01

Full Text Available Complex network methodology is very useful for complex system exploration. However, the relationships among variables in complex systems are usually not clear. Therefore, inferring association networks among variables from their observed data has been a popular research topic. We propose a method, named small-shuffle symbolic transfer entropy spectrum (SSSTES, for inferring association networks from multivariate time series. The method can solve four problems for inferring association networks, i.e., strong correlation identification, correlation quantification, direction identification and temporal relation identification. The method can be divided into four layers. The first layer is the so-called data layer. Data input and processing are the things to do in this layer. In the second layer, we symbolize the model data, original data and shuffled data, from the previous layer and calculate circularly transfer entropy with different time lags for each pair of time series variables. Thirdly, we compose transfer entropy spectrums for pairwise time series with the previous layer’s output, a list of transfer entropy matrix. We also identify the correlation level between variables in this layer. In the last layer, we build a weighted adjacency matrix, the value of each entry representing the correlation level between pairwise variables, and then get the weighted directed association network. Three sets of numerical simulated data from a linear system, a nonlinear system and a coupled Rossler system are used to show how the proposed approach works. Finally, we apply SSSTES to a real industrial system and get a better result than with two other methods.

Population History and Pathways of Spread of the Plant Pathogen Phytophthora plurivora

Science.gov (United States)

Schoebel, Corine N.; Stewart, Jane; Gruenwald, Niklaus J.; Rigling, Daniel; Prospero, Simone

2014-01-01

Human activity has been shown to considerably affect the spread of dangerous pests and pathogens worldwide. Therefore, strict regulations of international trade exist for particularly harmful pathogenic organisms. Phytophthora plurivora, which is not subject to regulations, is a plant pathogen frequently found on a broad range of host species, both in natural and artificial environments. It is supposed to be native to Europe while resident populations are also present in the US. We characterized a hierarchical sample of isolates from Europe and the US and conducted coalescent-, migration, and population genetic analysis of sequence and microsatellite data, to determine the pathways of spread and the demographic history of this pathogen. We found P. plurivora populations to be moderately diverse but not geographically structured. High levels of gene flow were observed within Europe and unidirectional from Europe to the US. Coalescent analyses revealed a signal of a recent expansion of the global P. plurivora population. Our study shows that P. plurivora has most likely been spread around the world by nursery trade of diseased plant material. In particular, P. plurivora was introduced into the US from Europe. International trade has allowed the pathogen to colonize new environments and/or hosts, resulting in population growth. PMID:24427303

Mutational spectrum of Xeroderma pigmentosum group A in Egyptian patients.

Science.gov (United States)

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.

Epidemic spreading and global stability of an SIS model with an infective vector on complex networks

Science.gov (United States)

Kang, Huiyan; Fu, Xinchu

2015-10-01

In this paper, we present a new SIS model with delay on scale-free networks. The model is suitable to describe some epidemics which are not only transmitted by a vector but also spread between individuals by direct contacts. In view of the biological relevance and real spreading process, we introduce a delay to denote average incubation period of disease in a vector. By mathematical analysis, we obtain the epidemic threshold and prove the global stability of equilibria. The simulation shows the delay will effect the epidemic spreading. Finally, we investigate and compare two major immunization strategies, uniform immunization and targeted immunization.

Resolving vorticity-driven lateral fire spread using the WRF-Fire coupled atmosphere–fire numerical model

OpenAIRE

Simpson, C. C.; Sharples, J. J.; Evans, J. P.

2014-01-01

Fire channelling is a form of dynamic fire behaviour, during which a wildland fire spreads rapidly across a steep lee-facing slope in a direction transverse to the background winds, and is often accompanied by a downwind extension of the active flaming region and extreme pyro-convection. Recent work using the WRF-Fire coupled atmosphere-fire model has demonstrated that fire channelling can be characterised as vorticity-driven lateral fire spread (VDLS). In t...

Experimental Study on Downwardly Spreading Flame over Inclined Polyethylene-insulated Electrical Wire with Applied AC Electric Fields

KAUST Repository

Lim, Seung Jae

2014-12-30

An experimental study on downwardly spreading flame over slanted electrical wire, which is insulated by Polyethylene (PE), was conducted with applied AC electric fields. The result showed that the flame spread rate decreased initially with increase in inclination angle of wire and then became nearly constant. The flame shape was modified significantly with applied AC electric field due to the effect of ionic wind. Such a variation in flame spread rate could be explained by a thermal balance mechanism, depending on flame shape and slanted direction of flame. Extinction of the spreading flame was not related to angle of inclination, and was described well by a functional dependency upon the frequency and voltage at extinction.

A fast computation method for MUSIC spectrum function based on circular arrays

Science.gov (United States)

Du, Zhengdong; Wei, Ping

2015-02-01

The large computation amount of multiple signal classification (MUSIC) spectrum function seriously affects the timeliness of direction finding system using MUSIC algorithm, especially in the two-dimensional directions of arrival (DOA) estimation of azimuth and elevation with a large antenna array. This paper proposes a fast computation method for MUSIC spectrum. It is suitable for any circular array. First, the circular array is transformed into a virtual uniform circular array, in the process of calculating MUSIC spectrum, for the cyclic characteristics of steering vector, the inner product in the calculation of spatial spectrum is realised by cyclic convolution. The computational amount of MUSIC spectrum is obviously less than that of the conventional method. It is a very practical way for MUSIC spectrum computation in circular arrays.

Research on the correlation between corona current spectrum and audible noise spectrum of HVDC transmission line

Science.gov (United States)

Liu, Yingyi; Zhou, Lijuan; Liu, Yuanqing; Yuan, Haiwen; Ji, Liang

2017-11-01

Audible noise is closely related to corona current on a high voltage direct current (HVDC) transmission line. In this paper, we measured a large amount of audible noise and corona current waveforms simultaneously based on the largest outdoor HVDC corona cage all over the world. By analyzing the experimental data, the related statistical regularities between a corona current spectrum and an audible noise spectrum were obtained. Furthermore, the generation mechanism of audible noise was analyzed theoretically, and the related mathematical expression between the audible noise spectrum and the corona current spectrum, which is suitable for all of these measuring points in the space, has been established based on the electro-acoustic conversion theory. Finally, combined with the obtained mathematical relation, the internal reasons for these statistical regularities appearing in measured corona current and audible noise data were explained. The results of this paper not only present the statistical association regularities between the corona current spectrum and the audible noise spectrum on a HVDC transmission line, but also reveal the inherent reasons of these associated rules.

An Auto sequence Code to Integrate a Neutron Unfolding Code with thePC-MCA Accuspec

International Nuclear Information System (INIS)

Darsono

2000-01-01

In a neutron spectrometry using proton recoil method, the neutronunfolding code is needed to unfold the measured proton spectrum to become theneutron spectrum. The process of the unfolding neutron in the existingneutron spectrometry which was successfully installed last year was doneseparately. This manuscript reports that the auto sequence code to integratethe neutron unfolding code UNFSPEC.EXE with the software facility of thePC-MCA Accuspec has been made and run successfully so that the new neutronspectrometry become compact. The auto sequence code was written based on therules in application program facility of PC-MCA Accuspec and then it wascompiled using AC-EXE. Result of the test of the auto sequence code showedthat for binning width 20, 30, and 40 giving a little different spectrumshape. The binning width around 30 gives a better spectrum in mean of givingsmall error compared to the others. (author)

Terrestrial spreading centers under Venus conditions - Evaluation of a crustal spreading model for Western Aphrodite Terra

Science.gov (United States)

Sotin, C.; Senske, D. A.; Head, J. W.; Parmentier, E. M.

1989-01-01

The model of Reid and Jackson (1981) for terrestrial spreading centers is applied to Venus conditions. On the basis of spreading rate, mantle temperature, and surface temperature, the model predicts both isostatic topography and crustal thickness. The model and Pioneer Venus altimetry and gravity data are used to test the hypothesis of Head and Crumpler (1987) that Western Aphrodite Terra is the location of crustal spreading on Venus. It is concluded that a spreading center model for Ovda Regio in Western Aphrodite Terra could account for the observed topography and line-of-sight gravity anomalies found in the Pioneer data.

Identifying influential spreaders in complex networks through local effective spreading paths

Science.gov (United States)

Wang, Xiaojie; Zhang, Xue; Yi, Dongyun; Zhao, Chengli

2017-05-01

How to effectively identify a set of influential spreaders in complex networks is of great theoretical and practical value, which can help to inhibit the rapid spread of epidemics, promote the sales of products by word-of-mouth advertising, and so on. A naive strategy is to select the top ranked nodes as identified by some centrality indices, and other strategies are mainly based on greedy methods and heuristic methods. However, most of those approaches did not concern the connections between nodes. Usually, the distances between the selected spreaders are very close, leading to a serious overlapping of their influence. As a consequence, the global influence of the spreaders in networks will be greatly reduced, which largely restricts the performance of those methods. In this paper, a simple and efficient method is proposed to identify a set of discrete yet influential spreaders. By analyzing the spreading paths in the network, we present the concept of effective spreading paths and measure the influence of nodes via expectation calculation. The numerical analysis in undirected and directed networks all show that our proposed method outperforms many other centrality-based and heuristic benchmarks, especially in large-scale networks. Besides, experimental results on different spreading models and parameters demonstrates the stability and wide applicability of our method.

Pseudorandom binary injection of levitons for electron quantum optics

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Yunus E. Beyhan

2017-09-01

Full Text Available Objectives: 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.

Microbial Community Structure of Deep-sea Hydrothermal Vents on the Ultraslow Spreading Southwest Indian Ridge

Directory of Open Access Journals (Sweden)

Jian Ding

2017-06-01

Full Text Available Southwest Indian Ridge (SWIR is a typical oceanic ultraslow spreading ridge with intensive hydrothermal activities. The microbial communities in hydrothermal fields including primary producers to support the entire ecosystem by utilizing geochemical energy generated from rock-seawater interactions. Here we have examined the microbial community structures on four hydrothermal vents from SWIR, representing distinct characteristics in terms of temperature, pH and metal compositions, by using Illumina sequencing of the 16S small subunit ribosomal RNA (rRNA genes, to correlate bacterial and archaeal populations with the nature of the vents influenced by ultraslow spreading features. Epsilon-, Gamma-, Alpha-, and Deltaproteobacteria and members of the phylum Bacteroidetes and Planctomycetes, as well as Thaumarchaeota, Woesearchaeota, and Euryarchaeota were dominant in all the samples. Both bacterial and archaeal community structures showed distinguished patterns compared to those in the fast-spreading East Pacific Ridge or the slow-spreading Mid-Atlantic Ridge as previously reported. Furthermore, within SWIR, the microbial communities are highly correlated with the local temperatures. For example, the sulfur-oxidizing bacteria were dominant within bacteria from low-temperature vents, but were not represented as the dominating group recovered from high temperature (over 300°C venting chimneys in SWIR. Meanwhile, Thaumarchaeota, the ammonium oxidizing archaea, only showed high relative abundance of amplicons in the vents with high-temperature in SWIR. These findings provide insights on the microbial community in ultraslow spreading hydrothermal fields, and therefore assist us in the understanding of geochemical cycling therein.

A single session of prefrontal cortex transcranial direct current stimulation does not modulate implicit task sequence learning and consolidation.

Science.gov (United States)

Savic, Branislav; Müri, René; Meier, Beat

Transcranial direct current stimulation (tDCS) is assumed to affect cortical excitability and dependent on the specific stimulation conditions either to increase or decrease learning. The purpose of this study was to modulate implicit task sequence learning with tDCS. As cortico-striatal loops are critically involved in implicit task sequence learning, tDCS was applied above the dorsolateral prefrontal cortex (DLPFC). In Experiment 1, anodal, cathodal, or sham tDCS was applied before the start of the sequence learning task. In Experiment 2, stimulation was applied during the sequence learning task. Consolidation of learning was assessed after 24 h. The results of both experiments showed that implicit task sequence learning occurred consistently but it was not modulated by different tDCS conditions. Similarly, consolidation measured after a 24 h-interval including sleep was also not affected by stimulation. These results indicate that a single session of DLPFC tDCS is not sufficient to modulate implicit task sequence learning. This study adds to the accumulating evidence that tDCS may not be as effective as originally thought. Copyright © 2017 Elsevier Inc. All rights reserved.

Pleiades rapid rotators - evidence for an evolutionary sequence

International Nuclear Information System (INIS)

Butler, R.P.; Marcy, G.W.; Cohen, R.D.; Duncan, D.K.; California Univ., La Jolla; Space Telescope Science Institute, Baltimore, MD)

1987-01-01

Four rapidly rotating early-K dwarfs in the Pleiades are shown to contain an order of magnitude more Li than four slow rotators of the same spectral type, as would be expected if they were systematically younger. This supports the idea that late-type stars first arrive on the main sequence with V(rot) greater than about 100 km/s, that they spin down to V(rot) less than about 10 km/s in 10 to the 7th to 10 to the 8th yr, and that the Pleiades lower main sequence shows such an age spread. 14 references

Volcanic spreading forcing and feedback in geothermal reservoir development, Amiata Volcano, Italia

Science.gov (United States)

Borgia, Andrea; Mazzoldi, Alberto; Brunori, Carlo Alberto; Allocca, Carmine; Delcroix, Carlo; Micheli, Luigi; Vercellino, Alberto; Grieco, Giovanni

2014-09-01

We made a stratigraphic, structural and morphologic study of the Amiata Volcano in Italy. We find that the edifice is dissected by intersecting grabens that accommodate the collapse of the higher sectors of the volcano. In turn, a number of compressive structures and diapirs exist around the margin of the volcano. These structures create an angular drainage pattern, with stream damming and captures, and a set of lakes within and around the volcano. We interpret these structures as the result of volcanic spreading of Amiata on its weak substratum, formed by the late Triassic evaporites (Burano Anhydrites) and the Middle-Jurassic to Early-Cretaceous clayey chaotic complexes (Ligurian Complex). Regional doming created a slope in the basement facilitating the outward flow and spreading of the ductile layers forced by the volcanic load. We model the dynamics of spreading with a scaled lubrication approximation of the Navier Stokes equations, and numerically study a set of solutions. In the model we include simple functions for volcanic deposition and surface erosion that change the topography over time. Scaling indicates that spreading at Amiata could still be active. The numerical solution shows that, as the central part of the edifice sinks into the weak basement, diapiric structures of the underlying formations form around the base of the volcano. Deposition of volcanic rocks within the volcano and surface erosion away from it both enhance spreading. In addition, a sloping basement may constitute a trigger for spreading and formation of trains of adjacent diapirs. As a feedback, the hot hydrothermal fluids decrease the shear strength of the anhydrites facilitating the spreading process. Finally, we observe that volcanic spreading has created ideal heat traps that constitute todays' exploited geothermal fields at Amiata. Normal faults generated by volcanic spreading, volcanic conduits, and direct contact between volcanic rocks (which host an extensive fresh

Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

NARCIS (Netherlands)

Collins, Ryan L; Brand, Harrison; Redin, Claire E.; Hanscom, Carrie; Antolik, Caroline; Stone, Matthew R; Glessner, Joseph T.; Mason, Tamara; Pregno, Giulia; Dorrani, Naghmeh; Mandrile, Giorgia; Giachino, Daniela; Perrin, Danielle; Walsh, Cole; Cipicchio, Michelle; Costello, Maura; Stortchevoi, Alexei; An, Joon Yong; Currall, Benjamin B; Seabra, Catarina M; Ragavendran, Ashok; Margolin, Lauren; Martinez-Agosto, Julian A.; Lucente, Diane; Levy, Brynn; Sanders, Jan-Stephan; Wapner, Ronald J.; Quintero-Rivera, Fabiola; Kloosterman, Wigard; Talkowski, Michael E.

2017-01-01

Background: Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. Results: We sequenced 689 participants with autism spectrum disorder (ASD) and other

Electrochemical direct immobilization of DNA sequences for label-free herpes virus detection

Energy Technology Data Exchange (ETDEWEB)

Phuong Dinh Tam; Mai Anh Tuan [International Training Institute for Materials Science (Viet Nam); Tran Trung [Department of Electrochemistry, Hung-Yen University of Technology and Education (Viet Nam); Nguyen Duc Chien [Institute of Engineering Physics, Hanoi University of Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam)], E-mail: tr_trunghut@yahoo.com

2009-09-01

DNA sequences/bio-macromolecules of herpes virus (5'-AT CAC CGA CCC GGA GAG GGA C-3') were directly immobilized into polypyrrole matrix by using the cyclic voltammetry method, and grafted onto arrays of interdigitated platinum microelectrodes. The morphology surface of the obtained PPy/DNA of herpes virus composite films was investigated by a FESEM Hitachi-S 4800. Fourier transform infrared spectroscopy (FTIR) was used to characterize the PPy/DNA film and to study the specific interactions that may exist between DNA biomacromolecules and PPy chains. Attempts are made to use these PPy/DNA composite films for label-free herpes virus detection revealed a response time of 60 s in solutions containing as low as 2 nM DNA concentration, and self life of six months when emerged in double distilled water and kept refrigerated.

Collective properties of injection-induced earthquake sequences: 1. Model description and directivity bias

Science.gov (United States)

Dempsey, David; Suckale, Jenny

2016-05-01

Induced seismicity is of increasing concern for oil and gas, geothermal, and carbon sequestration operations, with several M > 5 events triggered in recent years. Modeling plays an important role in understanding the causes of this seismicity and in constraining seismic hazard. Here we study the collective properties of induced earthquake sequences and the physics underpinning them. In this first paper of a two-part series, we focus on the directivity ratio, which quantifies whether fault rupture is dominated by one (unilateral) or two (bilateral) propagating fronts. In a second paper, we focus on the spatiotemporal and magnitude-frequency distributions of induced seismicity. We develop a model that couples a fracture mechanics description of 1-D fault rupture with fractal stress heterogeneity and the evolving pore pressure distribution around an injection well that triggers earthquakes. The extent of fault rupture is calculated from the equations of motion for two tips of an expanding crack centered at the earthquake hypocenter. Under tectonic loading conditions, our model exhibits a preference for unilateral rupture and a normal distribution of hypocenter locations, two features that are consistent with seismological observations. On the other hand, catalogs of induced events when injection occurs directly onto a fault exhibit a bias toward ruptures that propagate toward the injection well. This bias is due to relatively favorable conditions for rupture that exist within the high-pressure plume. The strength of the directivity bias depends on a number of factors including the style of pressure buildup, the proximity of the fault to failure and event magnitude. For injection off a fault that triggers earthquakes, the modeled directivity bias is small and may be too weak for practical detection. For two hypothetical injection scenarios, we estimate the number of earthquake observations required to detect directivity bias.

Relationship between line spread function (LSF), or slice sensitivity profile (SSP), and point spread function (PSF) in CT image system

International Nuclear Information System (INIS)

Ohkubo, Masaki; Wada, Shinichi; Kobayashi, Teiji; Lee, Yongbum; Tsai, Du-Yih

2004-01-01

In the CT image system, we revealed the relationship between line spread function (LSF), or slice sensitivity profile (SSP), and point spread function (PSF). In the system, the following equation has been reported; I(x,y)=O(x,y) ** PSF(x,y), in which I(x,y) and O(x,y) are CT image and object function, respectively, and ** is 2-dimensional convolution. In the same way, the following 3-dimensional expression applies; I'(x,y,z)=O'(x,y,z) *** PSF'(x,y,z), in which z-axis is the direction perpendicular to the x/y-scan plane. We defined that the CT image system was separable, when the above two equations could be transformed into following equations; I(x,y)=[O(x,y) * LSF x (x)] * LSF y (y) and I'(x,y,z) =[O'(x,y,z) * SSP(z)] ** PSF(x,y), respectively, in which LSF x (x) and LSF y (y) are LSFs in x- and y-direction, respectively. Previous reports for the LSF and SSP are considered to assume the separable-system. Under the condition of separable-system, we derived following equations; PSF(x,y)=LSF x (x) ·LSF y (y) and PSF'(x,y,z)=PSF(x,y)·SSP(z). They were validated by the computer-simulations. When the study based on 1-dimensional functions of LSF and SSP are expanded to that based on 2- or 3-dimensional functions of PSF, derived equations must be required. (author)

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

Science.gov (United States)

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

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

Directory of Open Access Journals (Sweden)

Lucas M Taniguti

Full Text Available 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.

Approaches for in silico finishing of microbial genome sequences

Directory of Open Access Journals (Sweden)

Frederico Schmitt Kremer

Full Text Available Abstract The introduction of next-generation sequencing (NGS had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases tools that are available to facilitate genome finishing.

Approaches for in silico finishing of microbial genome sequences.

Science.gov (United States)

Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

Direct measurement of the energy spectrum of an intense proton beam

International Nuclear Information System (INIS)

Leeper, R.J.; Lee, J.R.; Kissel, L.; Johnson, D.J.; Stygar, W.A.; Hebron, D.E.; Roose, L.D.

1983-01-01

A time-resolved magnetic spectrometer has been used to measure the energy spectrum of an intense (0.5 TW/cm 2 ) proton beam. A thin (2400 A) gold foil placed at the focus of an ion diode Rutherford scattered protons by 90 0 into the spectrometer, reducing the beam intensity to a level suitable for magnetic analysis. The scattered beam was collimated by two 1 mm diameter apertures separated by 12.3 cm. The collimated protons were deflected in a 12.7 cm diameter, 6.65 Kg samarium-cobalt permanent magnet. The deflected protons were recorded simultaneously on CR-39 and eight 1 mm 2 by 35 μm thick PIN diodes. A Monte Carlo computer code was used to calculate the sensitivity and resolution of the spectrometer. Data taken on Proto-I show a 150 keV to 250 keV wide proton energy spectrum at each instant in time

Spreading to localized targets in complex networks

Science.gov (United States)

Sun, Ye; Ma, Long; Zeng, An; Wang, Wen-Xu

2016-12-01

As an important type of dynamics on complex networks, spreading is widely used to model many real processes such as the epidemic contagion and information propagation. One of the most significant research questions in spreading is to rank the spreading ability of nodes in the network. To this end, substantial effort has been made and a variety of effective methods have been proposed. These methods usually define the spreading ability of a node as the number of finally infected nodes given that the spreading is initialized from the node. However, in many real cases such as advertising and news propagation, the spreading only aims to cover a specific group of nodes. Therefore, it is necessary to study the spreading ability of nodes towards localized targets in complex networks. In this paper, we propose a reversed local path algorithm for this problem. Simulation results show that our method outperforms the existing methods in identifying the influential nodes with respect to these localized targets. Moreover, the influential spreaders identified by our method can effectively avoid infecting the non-target nodes in the spreading process.

Effect of pollutant oscillations on oil spreading on the sea

International Nuclear Information System (INIS)

Abbey, T.M.; Amakiri, J.O.; Bestman, A.R.

1997-01-01

Analytical solutions for oil spreading on the sea are deduced when the pollutant source fluctuates with time for a simple rectangular geometry. Both asymmetrical and symmetrical solutions in the direction perpendicular to the uniform tidal stream are derived. The asymmetrical solution, though ad hoc, sheds light on the necessary adjustment to the simpler symmetric problem. Only a micro computer is necessary to simulate these solutions. (Author)

A system for measuring the energy spread of an accelerated beam

International Nuclear Information System (INIS)

Wilkerson, J.F.; Ludwig, E.J.; Clegg, T.B.; Anderson, R.E.

1987-01-01

A system has been implemented to monitor directly the energy spread of analyzed beams from a tandem electrostatic accelerator. The dispersion of a deflection magnet in the beam handling system is used to transform the energy distribution into a spatial distribution, which then is measured by electrostatically sweeping the spatially extended beam across a narrow slit. (orig.)

Magnetic resonance imaging of acute trauma of the cervical spine: spectrum of findings

Energy Technology Data Exchange (ETDEWEB)

Forster, B.B.; Koopmans, R.A. [British Columbia Univ., Vancouver, BC (Canada). Faculty of Medicine

1995-06-01

The magnetic resonance imaging (MRI) spectrum of acute injury to the cervical spine was illustrated in this pictorial essay. The appearance of the traumatized cord was discussed, including intramedullary hemorrhage, and the causes of spinal cord compression, such as disk herniation, epidural hematoma, fracture, dislocation and underlying spinal stenosis. The ability of MRI to directly reveal the severity of cord injury and simultaneously indicate the cause of cord compression proved particularly useful in the management of incomplete injury, for which surgical intervention may prevent further deterioration. The protocol for MRI of cervical spinal trauma included sagittal T1-weighted and T2-weighted conventional spin-echo sequences. In addition, transverse T2-weighted gradient-echo images were obtained. MRI`s ability to directly reveal the extent of cord injury was said to be a powerful tool in the management of incomplete injuries where further deterioration could be prevented by timely surgical intervention. 7 refs., 12 figs.

Spreading gossip in social networks

Science.gov (United States)

Lind, Pedro G.; da Silva, Luciano R.; Andrade, José S., Jr.; Herrmann, Hans J.

2007-09-01

We study a simple model of information propagation in social networks, where two quantities are introduced: the spread factor, which measures the average maximal reachability of the neighbors of a given node that interchange information among each other, and the spreading time needed for the information to reach such a fraction of nodes. When the information refers to a particular node at which both quantities are measured, the model can be taken as a model for gossip propagation. In this context, we apply the model to real empirical networks of social acquaintances and compare the underlying spreading dynamics with different types of scale-free and small-world networks. We find that the number of friendship connections strongly influences the probability of being gossiped. Finally, we discuss how the spread factor is able to be applied to other situations.

Spreading gossip in social networks.

Science.gov (United States)

Lind, Pedro G; da Silva, Luciano R; Andrade, José S; Herrmann, Hans J

2007-09-01

We study a simple model of information propagation in social networks, where two quantities are introduced: the spread factor, which measures the average maximal reachability of the neighbors of a given node that interchange information among each other, and the spreading time needed for the information to reach such a fraction of nodes. When the information refers to a particular node at which both quantities are measured, the model can be taken as a model for gossip propagation. In this context, we apply the model to real empirical networks of social acquaintances and compare the underlying spreading dynamics with different types of scale-free and small-world networks. We find that the number of friendship connections strongly influences the probability of being gossiped. Finally, we discuss how the spread factor is able to be applied to other situations.

COMBINED SURGERY OF SPREAD THYROID CANCER

Directory of Open Access Journals (Sweden)

V. Zh. Brzhezovsky

2014-01-01

Full Text Available Results of treating of 99 patients with differentiated thyroid cancer spreading beyond the capsule of the organ were analysed. In most cases with spreading the tumor to the tracheal rings performing of organ-preserving operations (from “window-like” tracheal resections to circular tracheal resection with intertracheal anastomosis is possible. Choosing of type of operation to be performed depends on localisation and spread of tumor invasion of trachea, pharynx and esophagus. Using of combined operations in patients with locally-spread thyroid cancer allows to achieve long and stable remission in most of the cases.

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

Science.gov (United States)

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.

Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa

Science.gov (United States)

Ranciaro, Alessia; Campbell, Michael C.; Hirbo, Jibril B.; Ko, Wen-Ya; Froment, Alain; Anagnostou, Paolo; Kotze, Maritha J.; Ibrahim, Muntaser; Nyambo, Thomas; Omar, Sabah A.; Tishkoff, Sarah A.

2014-01-01

In humans, the ability to digest lactose, the sugar in milk, declines after weaning because of decreasing levels of the enzyme lactase-phlorizin hydrolase, encoded by LCT. However, some individuals maintain high enzyme amounts and are able to digest lactose into adulthood (i.e., they have the lactase-persistence [LP] trait). It is thought that selection has played a major role in maintaining this genetically determined phenotypic trait in different human populations that practice pastoralism. To identify variants associated with the LP trait and to study its evolutionary history in Africa, we sequenced MCM6 introns 9 and 13 and ∼2 kb of the LCT promoter region in 819 individuals from 63 African populations and in 154 non-Africans from nine populations. We also genotyped four microsatellites in an ∼198 kb region in a subset of 252 individuals to reconstruct the origin and spread of LP-associated variants in Africa. Additionally, we examined the association between LP and genetic variability at candidate regulatory regions in 513 individuals from eastern Africa. Our analyses confirmed the association between the LP trait and three common variants in intron 13 (C-14010, G-13907, and G-13915). Furthermore, we identified two additional LP-associated SNPs in intron 13 and the promoter region (G-12962 and T-956, respectively). Using neutrality tests based on the allele frequency spectrum and long-range linkage disequilibrium, we detected strong signatures of recent positive selection in eastern African populations and the Fulani from central Africa. In addition, haplotype analysis supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa. PMID:24630847

Structure and Spectrum of Dust Coulomb Clusters

International Nuclear Information System (INIS)

Cheung, F.M.H.; Ford, C.; Barkby, S.; Samarian, A.A.; Vladimirov, S.V.

2005-01-01

In our study, the dynamics of Coulomb cluster systems were simulated for different number of particles. The spectra of energy states of dust Coulomb clusters corresponding to various packing sequences were obtained. The broadening of the spectrum due to inter-ring twist was discovered. It was found that the inter-ring twist will lead to a change in the energy spectrum of Coulomb cluster. This change was accompanied by a distortion of stable shells such that particles are able to compensate for any additional Coulomb energy (owing to the inter-ring twist) by further reducing their radial distance as much as possible. The overall effect is a change in the shape of the outer-shell from circular to elliptical

Neutralisation of HIV-1 cell-cell spread by human and llama antibodies.

Science.gov (United States)

McCoy, Laura E; Groppelli, Elisabetta; Blanchetot, Christophe; de Haard, Hans; Verrips, Theo; Rutten, Lucy; Weiss, Robin A; Jolly, Clare

2014-10-02

Direct cell-cell spread of HIV-1 is a very efficient mode of viral dissemination, with increasing evidence suggesting that it may pose a considerable challenge to controlling viral replication in vivo. Much current vaccine research involves the study of broadly neutralising antibodies (bNabs) that arise during natural infection with the aims of eliciting such antibodies by vaccination or incorporating them into novel therapeutics. However, whether cell-cell spread of HIV-1 can be effectively targeted by bNabs remains unclear, and there is much interest in identifying antibodies capable of efficiently neutralising virus transmitted by cell-cell contact. In this study we have tested a panel of bNAbs for inhibition of cell-cell spread, including some not previously evaluated for inhibition of this mode of HIV-1 transmission. We found that three CD4 binding site antibodies, one from an immunised llama (J3) and two isolated from HIV-1-positive patients (VRC01 and HJ16) neutralised cell-cell spread between T cells, while antibodies specific for glycan moieties (2G12, PG9, PG16) and the MPER (2F5) displayed variable efficacy. Notably, while J3 displayed a high level of potency during cell-cell spread we found that the small size of the llama heavy chain-only variable region (VHH) J3 is not required for efficient neutralisation since recombinant J3 containing a full-length human heavy chain Fc domain was significantly more potent. J3 and J3-Fc also neutralised cell-cell spread of HIV-1 from primary macrophages to CD4+ T cells. In conclusion, while bNabs display variable efficacy at preventing cell-cell spread of HIV-1, we find that some CD4 binding site antibodies can inhibit this mode of HIV-1 dissemination and identify the recently described llama antibody J3 as a particularly potent inhibitor. Effective neutralisation of cell-cell spread between physiologically relevant cell types by J3 and J3-Fc supports the development of VHH J3 nanobodies for therapeutic or

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

Science.gov (United States)

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…

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

Science.gov (United States)

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.

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

Science.gov (United States)

Sugathan, Aarathi; Biagioli, Marta; Golzio, Christelle; Erdin, Serkan; Blumenthal, Ian; Manavalan, Poornima; Ragavendran, Ashok; Brand, Harrison; Lucente, Diane; Miles, Judith; Sheridan, Steven D.; Stortchevoi, Alexei; Kellis, Manolis; Haggarty, Stephen J.; Katsanis, Nicholas; Gusella, James F.; Talkowski, Michael E.

2014-01-01

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis. PMID:25294932

Underground localization using dual magnetic field sequence measurement and pose graph SLAM for directional drilling

International Nuclear Information System (INIS)

Park, Byeolteo; Myung, Hyun

2014-01-01

With the development of unconventional gas, the technology of directional drilling has become more advanced. Underground localization is the key technique of directional drilling for real-time path following and system control. However, there are problems such as vibration, disconnection with external infrastructure, and magnetic field distortion. Conventional methods cannot solve these problems in real time or in various environments. In this paper, a novel underground localization algorithm using a re-measurement of the sequence of the magnetic field and pose graph SLAM (simultaneous localization and mapping) is introduced. The proposed algorithm exploits the property of the drilling system that the body passes through the previous pass. By comparing the recorded measurement from one magnetic sensor and the current re-measurement from another magnetic sensor, the proposed algorithm predicts the pose of the drilling system. The performance of the algorithm is validated through simulations and experiments. (paper)

Underground localization using dual magnetic field sequence measurement and pose graph SLAM for directional drilling

Science.gov (United States)

Park, Byeolteo; Myung, Hyun

2014-12-01

With the development of unconventional gas, the technology of directional drilling has become more advanced. Underground localization is the key technique of directional drilling for real-time path following and system control. However, there are problems such as vibration, disconnection with external infrastructure, and magnetic field distortion. Conventional methods cannot solve these problems in real time or in various environments. In this paper, a novel underground localization algorithm using a re-measurement of the sequence of the magnetic field and pose graph SLAM (simultaneous localization and mapping) is introduced. The proposed algorithm exploits the property of the drilling system that the body passes through the previous pass. By comparing the recorded measurement from one magnetic sensor and the current re-measurement from another magnetic sensor, the proposed algorithm predicts the pose of the drilling system. The performance of the algorithm is validated through simulations and experiments.

Direct processes in heavy ion reactions

International Nuclear Information System (INIS)

Bunakov, V.E.; Zagrebaev, V.I.

1983-01-01

Direct processes in heavy ion reactions are investigated. Relative theoretical contributions in the inclusive spectrum of α particles on processes of stripping breakup and inelastic breakup are estimated using the 22 Ne+ 181 Ta reaction as an example. The consideration is performed taking into account Coulomb and nuclear distortions in the inlet and outlet ion channels. It is shown that the hard edge of α spectrum and its maximum are well described by peripheral direct processes. The hard spectrum edge is conditioned by the pure process of ''incomplete fussion'' bringing about the production af a compound nucleus. The main part of inclusive spectrum is conditioned by reactions of inelastic and elastic breakup not connected with the production of a compound nucleus

Further spreading of canine oriental eyeworm in Europe: first report of Thelazia callipaeda in Romania.

Science.gov (United States)

Mihalca, Andrei Daniel; D'Amico, Gianluca; Scurtu, Iuliu; Chirilă, Ramona; Matei, Ioana Adriana; Ionică, Angela Monica

2015-01-27

Despite the increasing number of reports of autochthonous cases of ocular thelaziosis in dogs in several European countries, and the evident emergence of human cases, the distribution and spreading potential of this parasite is far for being fully known. In Romania, despite intensive surveillance performed over recent years on the typical hosts of T. callipaeda, the parasite has not been found until now. In October 2014 a German Shepherd was presented for consultation to a private veterinary practice from western Romania with a history of unilateral chronic conjunctivitis. Following a close examination of the affected eye, nematodes were noticed in the conjunctival sac. The specimens collected were used for morphological examination (light microscopy) and molecular analysis (amplification of the cytochrome c oxidase subunit 1 gene, followed by sequencing). Thirteen nematodes were collected, all identified morphologically as T. callipaeda. The history of the dog revealed no travel outside Romania, and during the last year, not even outside the home locality. The BLAST analysis of our sequence showed a 100% similarity T. callipaeda haplotype h1. This is the first report of T. callipaeda in Romania, which we consider to be with autochthonous transmission. These findings confirm the spreading trend of T callipaeda and the increased risk of emerging vector-borne zoonoses.

Towards Data-Driven Simulations of Wildfire Spread using Ensemble-based Data Assimilation

Science.gov (United States)

Rochoux, M. C.; Bart, J.; Ricci, S. M.; Cuenot, B.; Trouvé, A.; Duchaine, F.; Morel, T.

2012-12-01

Real-time predictions of a propagating wildfire remain a challenging task because the problem involves both multi-physics and multi-scales. The propagation speed of wildfires, also called the rate of spread (ROS), is indeed determined by complex interactions between pyrolysis, combustion and flow dynamics, atmospheric dynamics occurring at vegetation, topographical and meteorological scales. Current operational fire spread models are mainly based on a semi-empirical parameterization of the ROS in terms of vegetation, topographical and meteorological properties. For the fire spread simulation to be predictive and compatible with operational applications, the uncertainty on the ROS model should be reduced. As recent progress made in remote sensing technology provides new ways to monitor the fire front position, a promising approach to overcome the difficulties found in wildfire spread simulations is to integrate fire modeling and fire sensing technologies using data assimilation (DA). For this purpose we have developed a prototype data-driven wildfire spread simulator in order to provide optimal estimates of poorly known model parameters [*]. The data-driven simulation capability is adapted for more realistic wildfire spread : it considers a regional-scale fire spread model that is informed by observations of the fire front location. An Ensemble Kalman Filter algorithm (EnKF) based on a parallel computing platform (OpenPALM) was implemented in order to perform a multi-parameter sequential estimation where wind magnitude and direction are in addition to vegetation properties (see attached figure). The EnKF algorithm shows its good ability to track a small-scale grassland fire experiment and ensures a good accounting for the sensitivity of the simulation outcomes to the control parameters. As a conclusion, it was shown that data assimilation is a promising approach to more accurately forecast time-varying wildfire spread conditions as new airborne-like observations of

Spectrum of rhodopsin mutations in Korean patients with retinitis pigmentosa

Science.gov (United States)

Kim, Kwang Joong; Kim, Cinoo; Bok, Jeong; Kim, Kyung-Seon; Lee, Eun-Ju; Park, Sung Pyo; Chung, Hum; Han, Bok-Ghee; Kim, Hyung-Lae; Kimm, Kuchan; Yu, Hyeong Gon

2011-01-01

Purpose To determine the spectrum and frequency of rhodopsin gene (RHO) mutations in Korean patients with retinitis pigmentosa (RP) and to characterize genotype–phenotype correlations in patients with mutations. Methods The RHO mutations were screened by direct sequencing, and mutation prevalence was measured in patients and controls. The impact of missense mutations to RP was predicted by segregation analysis, peptide sequence alignment, and in silico analysis. The severity of disease in patients with the missense mutations was compared by visual acuity, electroretinography, optical coherence tomography, and kinetic visual field testing. Results Five heterozygous mutations were identified in six of 302 probands with RP, including a novel mutation (c.893C>A, p.A298D) and four known mutations (c.50C>T, p.T17M; c.533A>G, p.Y178C; c.888G>T, p.K296N; and c.1040C>T, p.P347L). The allele frequency of missense mutations was measured in 114 ethnically matched controls. p.A298D, newly identified in a sporadic patient, had never been found in controls and was predicted to be pathogenic. Among the patients with the missense mutations, we observed the most severe phenotype in patients with p.P347L, less severe phenotypes in patients with p.Y178C or p.A298D, and a relatively moderate phenotype in a patient with p.T17M. Conclusions The results reveal the spectrum of RHO mutations in Korean RP patients and clinical features that vary according to mutations. Our findings will be useful for understanding these genetic spectra and the genotype–phenotype correlations and will therefore help with predicting disease prognosis and facilitating the development of gene therapy. PMID:21677794

Spectrum sensing using single-radio switched-beam antenna systems

DEFF Research Database (Denmark)

Tsakalaki, Elpiniki; Wilcox, David; De Carvalho, Elisabeth

2012-01-01

of the reactive loads rotate the narrowband beampattern to different angular positions dividing the whole space around the cognitive receiver into several angular subspaces. The beampattern directionality leverages the performance of spectrum sensing algorithms like the energy detection by enhancing the receive......The paper describes spectrum sensing using single-radio switched-beam arrays with reactance-loaded parasitic elements. At a given frequency, the antenna's loading conditions (reactive loads) are optimized for maximum average beamforming gain in the beampattern look direction. Circular permutations...

Free energy analysis of cell spreading.

Science.gov (United States)

McEvoy, Eóin; Deshpande, Vikram S; McGarry, Patrick

2017-10-01

In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading. Simulations suggest that cell spreading can be viewed as a competition between (i) decreasing cytoskeletal free energy due to strain induced assembly of cytoskeletal proteins into contractile SFs, and (ii) increasing elastic free energy due to stretching of the mechanically passive components of the cell. The computed minimum free energy spread area is shown to be lower for a cell on a compliant substrate than on a rigid substrate. Furthermore, a low substrate ligand density is found to limit cell spreading. The predicted dependence of cell spread area on substrate stiffness and ligand density is in agreement with the experiments of Engler et al. (2003). We also simulate the experiments of Théry et al. (2006), whereby initially circular cells deform and adhere to "V-shaped" and "Y-shaped" ligand patches. Analysis of a number of different spread states reveals that deformed configurations with the lowest free energy exhibit a SF distribution that corresponds to experimental observations, i.e. a high concentration of highly aligned SFs occurs along free edges, with lower SF concentrations in the interior of the cell. In summary, the results of this study suggest that cell spreading is driven by free energy minimization based on a competition between decreasing

Epigenetics and cerebral organoids:promising directions in autism spectrum disorders

OpenAIRE

Forsberg, Sheena Louise; Ilieva, Mirolyuba; Maria Michel, Tanja

2018-01-01

Autism spectrum disorders (ASD) affect 1 in 68 children in the US according to the Centers for Disease Control and Prevention (CDC). It is characterized by impairments in social interactions and communication, restrictive and repetitive patterns of behaviors, and interests. Owing to disease complexity, only a limited number of treatment options are available mainly for children that alleviate but do not cure the debilitating symptoms. Studies confirm a genetic link, but environmental factors,...

The Spectrum of the Universe.

Science.gov (United States)

Hill, Ryley; Masui, Kiyoshi W; Scott, Douglas

2018-05-01

Cosmic background (CB) radiation, encompassing the sum of emission from all sources outside our own Milky Way galaxy across the entire electromagnetic spectrum, is a fundamental phenomenon in observational cosmology. Many experiments have been conceived to measure it (or its constituents) since the extragalactic Universe was first discovered; in addition to estimating the bulk (cosmic monopole) spectrum, directional variations have also been detected over a wide range of wavelengths. Here we gather the most recent of these measurements and discuss the current status of our understanding of the CB from radio to γ-ray energies. Using available data in the literature, we piece together the sky-averaged intensity spectrum and discuss the emission processes responsible for what is observed. We examine the effect of perturbations to the continuum spectrum from atomic and molecular line processes and comment on the detectability of these signals. We also discuss how one could, in principle, obtain a complete census of the CB by measuring the full spectrum of each spherical harmonic expansion coefficient. This set of spectra of multipole moments effectively encodes the entire statistical history of nuclear, atomic, and molecular processes in the Universe.

Forecasting oil price movements with crack spread futures

International Nuclear Information System (INIS)

Murat, Atilim; Tokat, Ekin

2009-01-01

In oil markets, the crack spread refers to the crude-product price relationship. Refiners are major participants in oil markets and they are primarily exposed to the crack spread. In other words, refiner activity is substantially driven by the objective of protecting the crack spread. Moreover, oil consumers are active participants in the oil hedging market and they are frequently exposed to the crack spread. From another perspective, hedge funds are heavily using crack spread to speculate in oil markets. Based on the high volume of crack spread futures trading in oil markets, the question we want to raise is whether the crack spread futures can be a good predictor of oil price movements. We investigated first whether there is a causal relationship between the crack spread futures and the spot oil markets in a vector error correction framework. We found the causal impact of crack spread futures on spot oil market both in the long- and the short-run after April 2003 where we detected a structural break in the model. To examine the forecasting performance, we use the random walk model (RWM) as a benchmark, and we also evaluate the forecasting power of crack spread futures against the crude oil futures. The results showed that (a) both the crack spread futures and the crude oil futures outperformed the RWM; and (b) the crack spread futures are almost as good as the crude oil futures in predicting the movements in spot oil markets. (author)

Effect of Heterogeneity of Vertex Activation on Epidemic Spreading in Temporal Networks

Directory of Open Access Journals (Sweden)

Yixin Zhu

2014-01-01

Full Text Available Development of sensor technologies and the prevalence of electronic communication services provide us with a huge amount of data on human communication behavior, including face-to-face conversations, e-mail exchanges, phone calls, message exchanges, and other types of interactions in various online forums. These indirect or direct interactions form potential bridges of the virus spread. For a long time, the study of virus spread is based on the aggregate static network. However, the interaction patterns containing diverse temporal properties may affect dynamic processes as much as the network topology does. Some empirical studies show that the activation time and duration of vertices and links are highly heterogeneous, which means intense activity may be followed by longer intervals of inactivity. We take heterogeneous distribution of the node interactivation time as the research background to build an asynchronous communication model. The two sides of the communication do not have to be active at the same time. One derives the threshold of virus spreading on the communication mode and analyzes the reason the heterogeneous distribution of the vertex interactivation time suppresses the spread of virus. At last, the analysis and results from the model are verified on the BA network.

The thickness of cover sequences in the Western Desert of Iraq from a power spectrum analysis of gravity and magnetic data

Science.gov (United States)

Mousa, Ahmed; Mickus, Kevin; Al-Rahim, Ali

2017-05-01

The Western Desert of Iraq is part of the stable shelf region on the Arabian Plate where the subsurface structural makeup is relatively unknown due to the lack of cropping out rocks, deep drill holes and deep seismic refraction and reflection profiles. To remedy this situation, magnetic and gravity data were analyzed to determine the thickness of the Phanerozoic cover sequences. The 2-D power spectrum method was used to estimate the depth to density and magnetic susceptibility interfaces by using 0.5° square windows. Additionally, the gravity data were analyzed using isostatic residual and decompensative methods to isolate gravity anomalies due to upper crustal density sources. The decompensative gravity anomaly and the differentially reduced to the pole magnetic map indicate a series of mainly north-south and northwest-southeast trending maxima and minima anomalies related to Proterozoic basement lithologies and the varying thickness of cover sequences. The magnetic and gravity derived thickness of cover sequences maps indicate that these thicknesses range from 4.5 to 11.5 km. Both maps in general are in agreement but more detail in the cover thicknesses was determined by the gravity analysis. The gravity-based cover thickness maps indicates regions with shallower depths than the magnetic-based cover thickness t map which may be due to density differences between limestone and shale units within the Paleozoic sediments. The final thickness maps indicate that the Western Desert is a complicated region of basins and uplifts that are more complex than have been shown on previous structural maps of the Western Desert. These basins and uplifts may be related to Paleozoic compressional tectonic events and possibly to the opening of the Tethys Ocean. In addition, petroleum exploration could be extended to three basins outlined by our analysis within the relatively unexplored western portions of the Western Desert.

Toward 3D Printing of Medical Implants: Reduced Lateral Droplet Spreading of Silicone Rubber under Intense IR Curing.

Science.gov (United States)

Stieghorst, Jan; Majaura, Daniel; Wevering, Hendrik; Doll, Theodor

2016-03-01

The direct fabrication of silicone-rubber-based individually shaped active neural implants requires high-speed-curing systems in order to prevent extensive spreading of the viscous silicone rubber materials during vulcanization. Therefore, an infrared-laser-based test setup was developed to cure the silicone rubber materials rapidly and to evaluate the resulting spreading in relation to its initial viscosity, the absorbed infrared radiation, and the surface tensions of the fabrication bed's material. Different low-adhesion materials (polyimide, Parylene-C, polytetrafluoroethylene, and fluorinated ethylenepropylene) were used as bed materials to reduce the spreading of the silicone rubber materials by means of their well-known weak surface tensions. Further, O2-plasma treatment was performed on the bed materials to reduce the surface tensions. To calculate the absorbed radiation, the emittance of the laser was measured, and the absorptances of the materials were investigated with Fourier transform infrared spectroscopy in attenuated total reflection mode. A minimum silicone rubber spreading of 3.24% was achieved after 2 s curing time, indicating the potential usability of the presented high-speed-curing process for the direct fabrication of thermal-curing silicone rubbers.

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

Energy Technology Data Exchange (ETDEWEB)

Li, Chengyuan [Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109 (Australia); De Grijs, Richard [Kavli Institute for Astronomy and Astrophysics and Department of Astronomy, Peking University, Yi He Yuan Lu 5, Hai Dian District, Beijing 100871 (China); Deng, Licai [Key Laboratory for Optical Astronomy, National Astronomical Observatories, Chinese Academy of Sciences, 20A Datun Road, Chaoyang District, Beijing 100012 (China); Milone, Antonino P. [Research School of Astronomy and Astrophysics, Australian National University, Mt. Stromlo Observatory, Cotter Road, Weston, ACT 2611 (Australia)

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.

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

Science.gov (United States)

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.

Gossip spread in social network Models