FIR Filter of DS-CDMA UWB Modem Transmitter

NASA Astrophysics Data System (ADS)

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

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

Validation of the Operating and Support Cost Model for Avionics Automatic Test Equipment (OSCATE).

DTIC Science & Technology

1980-06-01

AFLCR 65-1 (56) DOD 4140 -32 (74) CODES DATA LISTED BY. ALC code, Division Code, Equipment Specialist Code, NSN DATA ORDERING SEQUENCEs This data is...PAJ6A 4140 -01-043-5035 .... IL0UERft1TfR 1002 1 319.55 22720 1 0 0 1003 0 14.55 0 0 0 10.00 0 0 1004 0 0 32.454 16.42 0 0 0 0 0 0 0 127 1101 PAJHA 4920...5320 480 CONTINUE 5330 60 To 150 5340 5350C *...*~****.*.s*..** 5360C *****eOUTPUT OPTION 7 5370C e**ss*** sae ******* 5380 500 PRINT 510 5390 510

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

DTIC Science & Technology

2009-10-01

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

A Golay complementary TS-based symbol synchronization scheme in variable rate LDPC-coded MB-OFDM UWBoF system

NASA Astrophysics Data System (ADS)

He, Jing; Wen, Xuejie; Chen, Ming; Chen, Lin

2015-09-01

In this paper, a Golay complementary training sequence (TS)-based symbol synchronization scheme is proposed and experimentally demonstrated in multiband orthogonal frequency division multiplexing (MB-OFDM) ultra-wideband over fiber (UWBoF) system with a variable rate low-density parity-check (LDPC) code. Meanwhile, the coding gain and spectral efficiency in the variable rate LDPC-coded MB-OFDM UWBoF system are investigated. By utilizing the non-periodic auto-correlation property of the Golay complementary pair, the start point of LDPC-coded MB-OFDM UWB signal can be estimated accurately. After 100 km standard single-mode fiber (SSMF) transmission, at the bit error rate of 1×10-3, the experimental results show that the short block length 64QAM-LDPC coding provides a coding gain of 4.5 dB, 3.8 dB and 2.9 dB for a code rate of 62.5%, 75% and 87.5%, respectively.

Towers of generalized divisible quantum codes

NASA Astrophysics Data System (ADS)

Haah, Jeongwan

2018-04-01

A divisible binary classical code is one in which every code word has weight divisible by a fixed integer. If the divisor is 2ν for a positive integer ν , then one can construct a Calderbank-Shor-Steane (CSS) code, where X -stabilizer space is the divisible classical code, that admits a transversal gate in the ν th level of Clifford hierarchy. We consider a generalization of the divisibility by allowing a coefficient vector of odd integers with which every code word has zero dot product modulo the divisor. In this generalized sense, we construct a CSS code with divisor 2ν +1 and code distance d from any CSS code of code distance d and divisor 2ν where the transversal X is a nontrivial logical operator. The encoding rate of the new code is approximately d times smaller than that of the old code. In particular, for large d and ν ≥2 , our construction yields a CSS code of parameters [[O (dν -1) ,Ω (d ) ,d ] ] admitting a transversal gate at the ν th level of Clifford hierarchy. For our construction we introduce a conversion from magic state distillation protocols based on Clifford measurements to those based on codes with transversal T gates. Our tower contains, as a subclass, generalized triply even CSS codes that have appeared in so-called gauge fixing or code switching methods.

Optimal power allocation and joint source-channel coding for wireless DS-CDMA visual sensor networks

NASA Astrophysics Data System (ADS)

Pandremmenou, Katerina; Kondi, Lisimachos P.; Parsopoulos, Konstantinos E.

2011-01-01

In this paper, we propose a scheme for the optimal allocation of power, source coding rate, and channel coding rate for each of the nodes of a wireless Direct Sequence Code Division Multiple Access (DS-CDMA) visual sensor network. The optimization is quality-driven, i.e. the received quality of the video that is transmitted by the nodes is optimized. The scheme takes into account the fact that the sensor nodes may be imaging scenes with varying levels of motion. Nodes that image low-motion scenes will require a lower source coding rate, so they will be able to allocate a greater portion of the total available bit rate to channel coding. Stronger channel coding will mean that such nodes will be able to transmit at lower power. This will both increase battery life and reduce interference to other nodes. Two optimization criteria are considered. One that minimizes the average video distortion of the nodes and one that minimizes the maximum distortion among the nodes. The transmission powers are allowed to take continuous values, whereas the source and channel coding rates can assume only discrete values. Thus, the resulting optimization problem lies in the field of mixed-integer optimization tasks and is solved using Particle Swarm Optimization. Our experimental results show the importance of considering the characteristics of the video sequences when determining the transmission power, source coding rate and channel coding rate for the nodes of the visual sensor network.

Repetition as the essence of life on this earth: music and genes.

PubMed

Ohno, S

1987-01-01

In prebiotic nucleic acid replication, templates appear to have been in short supply. A single round of tandem duplication of existing oligomers assured progressive extension of templates to the length adequate for encoding of polypeptide chains. Thus, the first set of coding sequences had to be repeats of base oligomers encoding polypeptide chains of various periodicities. On one hand, the readiness of these periodical polypeptide chains to assume alpha-helical and/or beta-sheet secondary structures contributed to the extremely rapid initial functional diversification of these polypeptide chains. It would be recalled that most, if not all, of the sugar-metabolizing enzymes had already achieved the inviolable functional competence before the division of prokaryotes from eukaryotes. On the other hand, a certain (dipeptidic?) of the peptidic periodicities was apparently chosen as the timekeeping unit by the biological clock. Musical compositions too apparently evolved originally as a timekeeping device. Accordingly, repetitiousness is evident in all musical compositions. Evolution of musical compositions from the early Baroque to the late Romantic parallels that of coding sequences from rather exact repeats of base oligomers to more complex modern coding sequences in which repetitious elements are less conspicuous and more varied. Inasmuch as the earth is governed by the hierarchy of periodicities (days, months and years), such reliance on periodicities is rather expected.

An Overview of the Greyscales Lethality Assessment Methodology

DTIC Science & Technology

2011-01-01

code has already been integrated into the Weapon Systems Division MECA and DUEL missile engagement simulations. It can also be integrated into...incorporated into a variety of simulations. The code has already been integrated into the Weapon Systems Division MECA and DUEL missile engagement...capable of being incorporated into a variety of simulations. The code has already been integrated into the Weapon Systems Division MECA and DUEL missile

Iterative Overlap FDE for Multicode DS-CDMA

NASA Astrophysics Data System (ADS)

Takeda, Kazuaki; Tomeba, Hiromichi; Adachi, Fumiyuki

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

A theory that may explain the Hayflick limit--a means to delete one copy of a repeating sequence during each cell cycle in certain human cells such as fibroblasts.

PubMed

Naveilhan, P; Baudet, C; Jabbour, W; Wion, D

1994-09-01

A model that may explain the limited division potential of certain cells such as human fibroblasts in culture is presented. The central postulate of this theory is that there exists, prior to certain key exons that code for materials needed for cell division, a unique sequence of specific repeating segments of DNA. One copy of such repeating segments is deleted during each cell cycle in cells that are not protected from such deletion through methylation of their cytosine residues. According to this theory, the means through which such repeated sequences are removed, one per cycle, is through the sequential action of enzymes that act much as bacterial restriction enzymes do--namely to produce scissions in both strands of DNA in areas that correspond to the DNA base sequence recognition specificities of such enzymes. After the first scission early in a replicative cycle, that enzyme becomes inhibited, but the cleavage of the first site exposes the closest site in the repetitive element to the action of a second restriction enzyme after which that enzyme also becomes inhibited. Then repair occurs, regenerating the original first site. Through this sequential activation and inhibition of two different restriction enzymes, only one copy of the repeating sequence is deleted during each cell cycle. In effect, the repeating sequence operates as a precise counter of the numbers of cell doubling that have occurred since the cells involved differentiated during development.

Development of the Average Likelihood Function for Code Division Multiple Access (CDMA) Using BPSK and QPSK Symbols

DTIC Science & Technology

2015-01-01

This research has the purpose to establish a foundation for new classification and estimation of CDMA signals. Keywords: DS / CDMA signals, BPSK, QPSK...DEVELOPMENT OF THE AVERAGE LIKELIHOOD FUNCTION FOR CODE DIVISION MULTIPLE ACCESS ( CDMA ) USING BPSK AND QPSK SYMBOLS JANUARY 2015...To) OCT 2013 – OCT 2014 4. TITLE AND SUBTITLE DEVELOPMENT OF THE AVERAGE LIKELIHOOD FUNCTION FOR CODE DIVISION MULTIPLE ACCESS ( CDMA ) USING BPSK

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

NASA Technical Reports Server (NTRS)

Wallett, Thomas M.

2009-01-01

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

The Application of SERS (Surface Enhanced Raman Scattering) to Study Surface Oxidation Reactions of Phosphonates.

DTIC Science & Technology

1988-02-15

Center Attn: Dr. Ron Atkins Code 50C Chemistry Division Crane, Indiana 47522-5050 China Lake, California 93555 Scientific Advisor INaval Civil...Superintendent Marine Sciences Division Chemistry Division, Code 6100 San Diego, California 91232 Naval Research Laboratory Washington, D.C. 20375-5000 ,! .1

Measuring Time-of-Flight in an Ultrasonic LPS System Using Generalized Cross-Correlation

PubMed Central

Villladangos, José Manuel; Ureña, Jesús; García, Juan Jesús; Mazo, Manuel; Hernández, Álvaro; Jiménez, Ana; Ruíz, Daniel; De Marziani, Carlos

2011-01-01

In this article, a time-of-flight detection technique in the frequency domain is described for an ultrasonic Local Positioning System (LPS) based on encoded beacons. Beacon transmissions have been synchronized and become simultaneous by means of the DS-CDMA (Direct-Sequence Code Division Multiple Access) technique. Every beacon has been associated to a 255-bit Kasami code. The detection of signal arrival instant at the receiver, from which the distance to each beacon can be obtained, is based on the application of the Generalized Cross-Correlation (GCC), by using the cross-spectral density between the received signal and the sequence to be detected. Prior filtering to enhance the frequency components around the carrier frequency (40 kHz) has improved estimations when obtaining the correlation function maximum, which implies an improvement in distance measurement precision. Positioning has been achieved by using hyperbolic trilateration, based on the Time Differences of Arrival (TDOA) between a reference beacon and the others. PMID:22346645

Measuring time-of-flight in an ultrasonic LPS system using generalized cross-correlation.

PubMed

Villladangos, José Manuel; Ureña, Jesús; García, Juan Jesús; Mazo, Manuel; Hernández, Alvaro; Jiménez, Ana; Ruíz, Daniel; De Marziani, Carlos

2011-01-01

In this article, a time-of-flight detection technique in the frequency domain is described for an ultrasonic local positioning system (LPS) based on encoded beacons. Beacon transmissions have been synchronized and become simultaneous by means of the DS-CDMA (direct-sequence code Division multiple access) technique. Every beacon has been associated to a 255-bit Kasami code. The detection of signal arrival instant at the receiver, from which the distance to each beacon can be obtained, is based on the application of the generalized cross-correlation (GCC), by using the cross-spectral density between the received signal and the sequence to be detected. Prior filtering to enhance the frequency components around the carrier frequency (40 kHz) has improved estimations when obtaining the correlation function maximum, which implies an improvement in distance measurement precision. Positioning has been achieved by using hyperbolic trilateration, based on the time differences of arrival (TDOA) between a reference beacon and the others.

Multiuser receiver for DS-CDMA signals in multipath channels: an enhanced multisurface method.

PubMed

Mahendra, Chetan; Puthusserypady, Sadasivan

2006-11-01

This paper deals with the problem of multiuser detection in direct-sequence code-division multiple-access (DS-CDMA) systems in multipath environments. The existing multiuser detectors can be divided into two categories: (1) low-complexity poor-performance linear detectors and (2) high-complexity good-performance nonlinear detectors. In particular, in channels where the orthogonality of the code sequences is destroyed by multipath, detectors with linear complexity perform much worse than the nonlinear detectors. In this paper, we propose an enhanced multisurface method (EMSM) for multiuser detection in multipath channels. EMSM is an intermediate piecewise linear detection scheme with a run-time complexity linear in the number of users. Its bit error rate performance is compared with existing linear detectors, a nonlinear radial basis function detector trained by the new support vector learning algorithm, and Verdu's optimal detector. Simulations in multipath channels, for both synchronous and asynchronous cases, indicate that it always outperforms all other linear detectors, performing nearly as well as nonlinear detectors.

The Bauschinger Effect in Autofrettaged Tubes- A Comparison of Models Including the ASME Code

DTIC Science & Technology

1998-06-01

possible error in Division 3 of Section Vm of the ASME Boiler and Pressure Vessel Code . They show that the empirical method used in the code to...Discussion presented by DP Kendall We appreciate the acknowledgement in the Kendall discussion that Division 3 of Section VIII of the ASME Boiler and Pressure Vessel Code may

A Guide for Recertification of Ground Based Pressure Vessels and Liquid Holding Tanks

DTIC Science & Technology

1987-12-15

Boiler and Pressure Vessel Code , Section...Requirements 202 Calculate Vessel MAWP Using ASME Boiler and Pressure Vessel Code Section VUI, Division 1. 203 Assess Vessel MAWP Using ASME Boiler and Pressure Vessel Code Section...Engineers (ASME) Boiler and Pressure Vessel Code (B&PV) Section VIll, Division 1, or other applicable standard. This activity involves the

14 CFR 1215.108 - Defining user service requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... to NASA Headquarters, Code OX, Space Network Division, Washington, DC 20546. Upon review and... submitted in writing to both NASA Headquarters, Code OX, Space Network Division, and GSFC, Code 501.... Request for services within priority groups shall be negotiated with non-NASA users on a first come, first...

dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

PubMed Central

Vincent, Jonathan; Dai, Zhanwu; Ravel, Catherine; Choulet, Frédéric; Mouzeyar, Said; Bouzidi, M. Fouad; Agier, Marie; Martre, Pierre

2013-01-01

The functional annotation of genes based on sequence homology with genes from model species genomes is time-consuming because it is necessary to mine several unrelated databases. The aim of the present work was to develop a functional annotation database for common wheat Triticum aestivum (L.). The database, named dbWFA, is based on the reference NCBI UniGene set, an expressed gene catalogue built by expressed sequence tag clustering, and on full-length coding sequences retrieved from the TriFLDB database. Information from good-quality heterogeneous sources, including annotations for model plant species Arabidopsis thaliana (L.) Heynh. and Oryza sativa L., was gathered and linked to T. aestivum sequences through BLAST-based homology searches. Even though the complexity of the transcriptome cannot yet be fully appreciated, we developed a tool to easily and promptly obtain information from multiple functional annotation systems (Gene Ontology, MapMan bin codes, MIPS Functional Categories, PlantCyc pathway reactions and TAIR gene families). The use of dbWFA is illustrated here with several query examples. We were able to assign a putative function to 45% of the UniGenes and 81% of the full-length coding sequences from TriFLDB. Moreover, comparison of the annotation of the whole T. aestivum UniGene set along with curated annotations of the two model species assessed the accuracy of the annotation provided by dbWFA. To further illustrate the use of dbWFA, genes specifically expressed during the early cell division or late storage polymer accumulation phases of T. aestivum grain development were identified using a clustering analysis and then annotated using dbWFA. The annotation of these two sets of genes was consistent with previous analyses of T. aestivum grain transcriptomes and proteomes. Database URL: urgi.versailles.inra.fr/dbWFA/ PMID:23660284

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

NASA Astrophysics Data System (ADS)

Shima, Tomoyuki; Tomeba, Hiromichi; Adachi, Fumiyuki

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

Advanced Code-Division Multiplexers for Superconducting Detector Arrays

NASA Astrophysics Data System (ADS)

Irwin, K. D.; Cho, H. M.; Doriese, W. B.; Fowler, J. W.; Hilton, G. C.; Niemack, M. D.; Reintsema, C. D.; Schmidt, D. R.; Ullom, J. N.; Vale, L. R.

2012-06-01

Multiplexers based on the modulation of superconducting quantum interference devices are now regularly used in multi-kilopixel arrays of superconducting detectors for astrophysics, cosmology, and materials analysis. Over the next decade, much larger arrays will be needed. These larger arrays require new modulation techniques and compact multiplexer elements that fit within each pixel. We present a new in-focal-plane code-division multiplexer that provides multiplexing elements with the required scalability. This code-division multiplexer uses compact lithographic modulation elements that simultaneously multiplex both signal outputs and superconducting transition-edge sensor (TES) detector bias voltages. It eliminates the shunt resistor used to voltage bias TES detectors, greatly reduces power dissipation, allows different dc bias voltages for each TES, and makes all elements sufficiently compact to fit inside the detector pixel area. These in-focal plane code-division multiplexers can be combined with multi-GHz readout based on superconducting microresonators to scale to even larger arrays.

Orthogonal Pilot Channel Using Combination of FDMA and CDMA in Single-Carrier FDMA-Based Evolved UTRA Uplink

NASA Astrophysics Data System (ADS)

Kawamura, Teruo; Kishiyama, Yoshihisa; Higuchi, Kenichi; Sawahashi, Mamoru

In the Evolved UTRA (UMTS Terrestrial Radio Access) uplink, single-carrier frequency division multiple access (SC-FDMA) radio access was adopted owing to its advantageous low peak-to-average power ratio (PAPR) feature, which leads to wide coverage area provisioning with limited peak transmission power of user equipments. This paper proposes orthogonal pilot channel generation using the combination of FDMA and CDMA in the SC-FDMA-based Evolved UTRA uplink. In the proposed method, we employ distributed FDMA transmission for simultaneous accessing users with different transmission bandwidths, and employ CDMA transmission for simultaneous accessing users with identical transmission bandwidth. Moreover, we apply a code sequence with a good auto-correlation property such as a Constant Amplitude Zero Auto-Correlation (CAZAC) sequence employing a cyclic shift to increase the number of sequences. Simulation results show that the average packet error rate performance using an orthogonal pilot channel with the combination of FDMA and CDMA in a six-user environment, i. e., four users each with a 1.25-MHz transmission bandwidth and two users each with a 5-MHz transmission bandwidth, employing turbo coding with the coding r of R=1/2 and QPSK and 16QAM data modulation coincides well with that in a single-user environment with the same transmission bandwidth. We show that the proposed orthogonal pilot channel structure using the combination of distributed FDMA and CDMA transmissions and the application of the CAZAC sequence is effective in the SC-FDMA-based Evolved UTRA uplink.

Optical digital chaos cryptography

NASA Astrophysics Data System (ADS)

Arenas-Pingarrón, Álvaro; González-Marcos, Ana P.; Rivas-Moscoso, José M.; Martín-Pereda, José A.

2007-10-01

In this work we present a new way to mask the data in a one-user communication system when direct sequence - code division multiple access (DS-CDMA) techniques are used. The code is generated by a digital chaotic generator, originally proposed by us and previously reported for a chaos cryptographic system. It is demonstrated that if the user's data signal is encoded with a bipolar phase-shift keying (BPSK) technique, usual in DS-CDMA, it can be easily recovered from a time-frequency domain representation. To avoid this situation, a new system is presented in which a previous dispersive stage is applied to the data signal. A time-frequency domain analysis is performed, and the devices required at the transmitter and receiver end, both user-independent, are presented for the optical domain.

A narrowband CDMA communications payload for little LEOS applications

NASA Astrophysics Data System (ADS)

Michalik, H.; Hävecker, W.; Ginati, A.

1996-09-01

In recent years Code Division Multiple Access (CDMA) techniques have been investigated for application in Local Area Networks [J. A. Salehi, IEEE Trans. Commun. 37 (1989)]as well as in Mobile Communications [R. Kohno et al., IEEE Commun. Mag. Jan (1995)]. The main attraction of these techniques is due to potential higher throughput and capacity of such systems under certain conditions compared to conventional multi-access schemes like frequency and time division multiplexing. Mobile communication over a Satellite Link represents in some terms the "worst case" for operating a CDMA-system. Considering e.g. the uplink case from mobile to satellite, the imperfections due to different and time varying channel conditions will add to the well known effects of Multiple Access Interference (MAI) between the simultaneously active users at the satellite receiver. In addition, bandwidth constraints due to the non-availability of large bandwidth channels in the interesting frequency bands, exist for small systems. As a result, for a given service in terms of user data rates, the practical code sequence lengths are limited as well as the available number of codes within a code set. In this paper a communications payload for Small Satellite Applications with CDMA uplink and C/TDMA downlink under the constraint of bandwidth limitations is proposed. To optimise the performance under the above addressed imperfections the system provides ability for power control and synchronisation for the CDMA uplink. The major objectives of this project are studying, development and testing of such a system for educational purposes and technology development at Hochschule Bremen.

Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus.

PubMed

Collart, F R; Osipiuk, J; Trent, J; Olsen, G J; Huberman, E

1996-10-03

We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Pyrococcus furiosus (Pf), a hyperthermophillic archeon. Sequence analysis of the Pf gene indicated an open reading frame specifying a protein of 485 amino acids (aa) with a calculated M(r) of 52900. Canonical Archaea promoter elements, Box A and Box B, are located -49 and -17 nucleotides (nt), respectively, upstream of the putative start codon. The sequence of the putative active-site region conforms to the IMPDH signature motif and contains a putative active-site cysteine. Phylogenetic relationships derived by using all available IMPDH sequences are consistent with trees developed for other molecules; they do not precisely resolve the history of Pf IMPDH but indicate a close similarity to bacterial IMPDH proteins. The phylogenetic analysis indicates that a gene duplication occurred prior to the division between rodents and humans, accounting for the Type I and II isoforms identified in mice and humans.

The Professional Socialization of Certified Athletic Trainers in the National Collegiate Athletic Association Division I Context

PubMed Central

Pitney, William A.; Ilsley, Paul; Rintala, Jan

2002-01-01

Objective: To describe the professional socialization process of certified athletic trainers (ATCs) in National Collegiate Athletic Association (NCAA) Division I to guide athletic training education and professional development. Design and Setting: We conducted a qualitative study to explore the experiences related to how participants were socialized into their professional roles in Division I. Subjects: A total of 16 interviews were conducted with 11 male (68.75%) and 5 female (31.25%) participants who were either currently or formerly affiliated with an NCAA Division I athletic program. Data Analysis: The interviews were transcribed, coded, and analyzed inductively using a modified grounded theory approach. Trustworthiness was obtained by peer review, data source triangulation, and member checks. Results: We identified a discernible pattern of socialization experiences and perceptions among the participants. The professional socialization processes of Division I collegiate ATCs is explained as a 5-phase developmental sequence: (1) envisioning the role, (2) formal preparation, (3) organizational entry, (4) role evolution, and (5) gaining stability. Conclusions: Examining the professional socialization process provides insights into the experiences of Division I collegiate ATCs as they prepare for their job responsibilities and develop professionally. Appropriate socialization tactics, such as the use of a structured mentoring experience, formal orientation, and staff development programming, can be implemented to promote effective professional development. Additionally, undergraduate students may be well served if they are educated to better use informal learning situations during their initial socializing events. PMID:12937446

46 CFR 54.01-2 - Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 2 2013-10-01 2013-10-01 false Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code. 54.01-2 Section 54.01-2 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS General Requirements § 54.01-2 Adoption of division 1 of section VIII of the ASME Boiler and...

46 CFR 54.01-2 - Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code. 54.01-2 Section 54.01-2 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS General Requirements § 54.01-2 Adoption of division 1 of section VIII of the ASME Boiler and...

46 CFR 54.01-2 - Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 2 2012-10-01 2012-10-01 false Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code. 54.01-2 Section 54.01-2 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS General Requirements § 54.01-2 Adoption of division 1 of section VIII of the ASME Boiler and...

46 CFR 54.01-2 - Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code. 54.01-2 Section 54.01-2 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS General Requirements § 54.01-2 Adoption of division 1 of section VIII of the ASME Boiler and...

46 CFR 54.01-2 - Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 2 2014-10-01 2014-10-01 false Adoption of division 1 of section VIII of the ASME Boiler and Pressure Vessel Code. 54.01-2 Section 54.01-2 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS General Requirements § 54.01-2 Adoption of division 1 of section VIII of the ASME Boiler and...

Annual Historical Report Calendar Year 1993

DTIC Science & Technology

1994-04-01

Physical Training, 16. PRICE CODE Military Performance, Military Nutrition , Military Psychology. 17. SECURITY CLASSIFICATION 18. SECURITY CLASSIFICATION 19... Nutrition Division . . . . . . . . . . 97 Military Performance & Neuroscience Division . 115 Occupational Medicine Division ........ .130 Occupational...Directorate, Dr. James A. Vogel, Director. The Directorate incorporates the Military Nutrition Division, the Military Performance and Neuroscience Division

A satellite mobile communication system based on Band-Limited Quasi-Synchronous Code Division Multiple Access (BLQS-CDMA)

NASA Technical Reports Server (NTRS)

Degaudenzi, R.; Elia, C.; Viola, R.

1990-01-01

Discussed here is a new approach to code division multiple access applied to a mobile system for voice (and data) services based on Band Limited Quasi Synchronous Code Division Multiple Access (BLQS-CDMA). The system requires users to be chip synchronized to reduce the contribution of self-interference and to make use of voice activation in order to increase the satellite power efficiency. In order to achieve spectral efficiency, Nyquist chip pulse shaping is used with no detection performance impairment. The synchronization problems are solved in the forward link by distributing a master code, whereas carrier forced activation and closed loop control techniques have been adopted in the return link. System performance sensitivity to nonlinear amplification and timing/frequency synchronization errors are analyzed.

The complete mitochondrial genome of the dwarf tapeworm Hymenolepis nana--a neglected zoonotic helminth.

PubMed

Cheng, Tian; Liu, Guo-Hua; Song, Hui-Qun; Lin, Rui-Qing; Zhu, Xing-Quan

2016-03-01

Hymenolepis nana, commonly known as the dwarf tapeworm, is one of the most common tapeworms of humans and rodents and can cause hymenolepiasis. Although this zoonotic tapeworm is of socio-economic significance in many countries of the world, its genetics, systematics, epidemiology, and biology are poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of H. nana. The mt genome is 13,764 bp in size and encodes 36 genes, including 12 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA genes. All genes are transcribed in the same direction. The gene order and genome content are completely identical with their congener Hymenolepis diminuta. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference, Maximum likelihood, and Maximum parsimony showed the division of class Cestoda into two orders, supported the monophylies of both the orders Cyclophyllidea and Pseudophyllidea. Analyses of mt genome sequences also support the monophylies of the three families Taeniidae, Hymenolepididae, and Diphyllobothriidae. This novel mt genome provides a useful genetic marker for studying the molecular epidemiology, systematics, and population genetics of the dwarf tapeworm and should have implications for the diagnosis, prevention, and control of hymenolepiasis in humans.

Development of authentication code for multi-access optical code division multiplexing based quantum key distribution

NASA Astrophysics Data System (ADS)

Taiwo, Ambali; Alnassar, Ghusoon; Bakar, M. H. Abu; Khir, M. F. Abdul; Mahdi, Mohd Adzir; Mokhtar, M.

2018-05-01

One-weight authentication code for multi-user quantum key distribution (QKD) is proposed. The code is developed for Optical Code Division Multiplexing (OCDMA) based QKD network. A unique address assigned to individual user, coupled with degrading probability of predicting the source of the qubit transmitted in the channel offer excellent secure mechanism against any form of channel attack on OCDMA based QKD network. Flexibility in design as well as ease of modifying the number of users are equally exceptional quality presented by the code in contrast to Optical Orthogonal Code (OOC) earlier implemented for the same purpose. The code was successfully applied to eight simultaneous users at effective key rate of 32 bps over 27 km transmission distance.

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

PubMed

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

2001-01-01

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

Annual Historical Report Calendar Year 1992

DTIC Science & Technology

1993-04-01

Environmental Stress, Exercise Physiology, Physical Training, 16. PRICE CODE Military Performance, Military Nutrition , Military Psychology. 17. SECURITY...63 Occupational Health & Performance Directorate . . . 84 Military Nutrition Division ........ ........... 87 Military Performance...Military Nutrition Division, the Military Performance and Neuroscience Division, the Occupational Medicine Division, and the Occupational Physiology

Cognitive Code-Division Channelization

DTIC Science & Technology

2011-04-01

22] G. N. Karystinos and D. A. Pados, “New bounds on the total squared correlation and optimum design of DS - CDMA binary signature sets,” IEEE Trans...Commun., vol. 51, pp. 48-51, Jan. 2003. [23] C. Ding, M. Golin, and T. Klve, “Meeting the Welch and Karystinos- Pados bounds on DS - CDMA binary...receiver pair coexisting with a primary code-division multiple-access ( CDMA ) system. Our objective is to find the optimum transmitting power and code

Aerospace Human Factors

NASA Technical Reports Server (NTRS)

Jordan, Kevin

1999-01-01

The following contains the final report on the activities related to the Cooperative Agreement between the human factors research group at NASA Ames Research Center and the Psychology Department at San Jose State University. The participating NASA Ames division has been, as the organization has changed, the Aerospace Human Factors Research Division (ASHFRD and Code FL), the Flight Management and Human Factors Research Division (Code AF), and the Human Factors Research and Technology Division (Code IH). The inclusive dates for the report are November 1, 1984 to January 31, 1999. Throughout the years, approximately 170 persons worked on the cooperative agreements in one capacity or another. The Cooperative Agreement provided for research personnel to collaborate with senior scientists in ongoing NASA ARC research. Finally, many post-MA/MS and post-doctoral personnel contributed to the projects. It is worth noting that 10 former cooperative agreement personnel were hired into civil service positions directly from the agreements.

75 FR 58373 - Notice of Intent To Grant Exclusive Patent License; DQE, Inc.

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-24

... objections are to be filed with Naval Surface Warfare Center, Crane Division, Code OOL, Bldg 2, 300 Highway 361, Crane, IN 47522-5001. FOR FURTHER INFORMATION CONTACT: Mr. Christopher Monsey, Naval Surface Warfare Center, Crane Division, Code OOL, Bldg 2, 300 Highway 361, Crane, IN 47522-5001, telephone 812-854...

75 FR 9434 - Civil Rights Division, Disability Rights Section; Agency Information Collection Activities Under...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-02

... Rights (or his or her designee) may certify that a State or local building code or similar ordinance that establishes accessibility requirements (Code) meets or exceeds the minimum requirements of the ADA for..., Policy and Planning Staff, Justice Management Division, Patrick Henry Building, Suite 1600, 601 D Street...

75 FR 27816 - Civil Rights Division, Disability Rights Section; Agency Information Collection Activities Under...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-18

... certify that a State or local building code or similar ordinance that establishes accessibility requirements (Code) meets or exceeds the minimum requirements of the ADA for accessibility and usability of... Management Division, Patrick Henry Building, Suite 1600, 601 D Street, NW., Washington, DC 20530. Dated: May...

Performance Analysis of a De-correlated Modified Code Tracking Loop for Synchronous DS-CDMA System under Multiuser Environment

NASA Astrophysics Data System (ADS)

Wu, Ya-Ting; Wong, Wai-Ki; Leung, Shu-Hung; Zhu, Yue-Sheng

This paper presents the performance analysis of a De-correlated Modified Code Tracking Loop (D-MCTL) for synchronous direct-sequence code-division multiple-access (DS-CDMA) systems under multiuser environment. Previous studies have shown that the imbalance of multiple access interference (MAI) in the time lead and time lag portions of the signal causes tracking bias or instability problem in the traditional correlating tracking loop like delay lock loop (DLL) or modified code tracking loop (MCTL). In this paper, we exploit the de-correlating technique to combat the MAI at the on-time code position of the MCTL. Unlike applying the same technique to DLL which requires an extensive search algorithm to compensate the noise imbalance which may introduce small tracking bias under low signal-to-noise ratio (SNR), the proposed D-MCTL has much lower computational complexity and exhibits zero tracking bias for the whole range of SNR, regardless of the number of interfering users. Furthermore, performance analysis and simulations based on Gold codes show that the proposed scheme has better mean square tracking error, mean-time-to-lose-lock and near-far resistance than the other tracking schemes, including traditional DLL (T-DLL), traditional MCTL (T-MCTL) and modified de-correlated DLL (MD-DLL).

76 FR 23314 - Notice of Intent To Grant Partially Exclusive Patent License; Sean Linehan

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-26

... are to be filed with Naval Surface Warfare Center, Crane Division, Code OOL, Bldg 2, 300 Highway 361, Crane, IN 47522-5001. FOR FURTHER INFORMATION CONTACT: Mr. Christopher Monsey, Naval Surface Warfare Center, Crane Division, Code OOL, Bldg 2, 300 Highway 361, Crane, IN 47522-5001, telephone 812-854-4100...

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

NASA Astrophysics Data System (ADS)

Braun, Walter; Eglin, Peter; Abello, Ricard

1993-02-01

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

A Review on Spectral Amplitude Coding Optical Code Division Multiple Access

NASA Astrophysics Data System (ADS)

Kaur, Navpreet; Goyal, Rakesh; Rani, Monika

2017-06-01

This manuscript deals with analysis of Spectral Amplitude Coding Optical Code Division Multiple Access (SACOCDMA) system. The major noise source in optical CDMA is co-channel interference from other users known as multiple access interference (MAI). The system performance in terms of bit error rate (BER) degrades as a result of increased MAI. It is perceived that number of users and type of codes used for optical system directly decide the performance of system. MAI can be restricted by efficient designing of optical codes and implementing them with unique architecture to accommodate more number of users. Hence, it is a necessity to design a technique like spectral direct detection (SDD) technique with modified double weight code, which can provide better cardinality and good correlation property.

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

NASA Astrophysics Data System (ADS)

Sikder, Somali; Ghosh, Shila

2018-02-01

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

Cognitive Jointly Optimal Code-Division Channelization and Routing Over Cooperative Links

DTIC Science & Technology

2014-04-01

i List of Figures Fig. 1: Comparison between code-division channelization and FDM. Fig. 2: Secondary receiver SINR as a function of the iteration step...transmission percentage as a function of the number of active links under Cases rank(X′′) = 1 and > 1 (the study includes also the random code assignment...scheme); (b) Instantaneous output SINR of a primary signal against primary SINR-QoS threshold SINRthPU (thick line) and instanta- neous output SINR of

Joint Frequency-Domain Equalization and Despreading for Multi-Code DS-CDMA Using Cyclic Delay Transmit Diversity

NASA Astrophysics Data System (ADS)

Yamamoto, Tetsuya; Takeda, Kazuki; Adachi, Fumiyuki

Frequency-domain equalization (FDE) based on the minimum mean square error (MMSE) criterion can provide a better bit error rate (BER) performance than rake combining. To further improve the BER performance, cyclic delay transmit diversity (CDTD) can be used. CDTD simultaneously transmits the same signal from different antennas after adding different cyclic delays to increase the number of equivalent propagation paths. Although a joint use of CDTD and MMSE-FDE for direct sequence code division multiple access (DS-CDMA) achieves larger frequency diversity gain, the BER performance improvement is limited by the residual inter-chip interference (ICI) after FDE. In this paper, we propose joint FDE and despreading for DS-CDMA using CDTD. Equalization and despreading are simultaneously performed in the frequency-domain to suppress the residual ICI after FDE. A theoretical conditional BER analysis is presented for the given channel condition. The BER analysis is confirmed by computer simulation.

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

NASA Astrophysics Data System (ADS)

Wang, Shaowei; Ji, Xiaoyong

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

Evaluation of CDMA system capacity for mobile satellite system applications

NASA Technical Reports Server (NTRS)

Smith, Partrick O.; Geraniotis, Evaggelos A.

1988-01-01

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

LIDAR pulse coding for high resolution range imaging at improved refresh rate.

PubMed

Kim, Gunzung; Park, Yongwan

2016-10-17

In this study, a light detection and ranging system (LIDAR) was designed that codes pixel location information in its laser pulses using the direct- sequence optical code division multiple access (DS-OCDMA) method in conjunction with a scanning-based microelectromechanical system (MEMS) mirror. This LIDAR can constantly measure the distance without idle listening time for the return of reflected waves because its laser pulses include pixel location information encoded by applying the DS-OCDMA. Therefore, this emits in each bearing direction without waiting for the reflected wave to return. The MEMS mirror is used to deflect and steer the coded laser pulses in the desired bearing direction. The receiver digitizes the received reflected pulses using a low-temperature-grown (LTG) indium gallium arsenide (InGaAs) based photoconductive antenna (PCA) and the time-to-digital converter (TDC) and demodulates them using the DS-OCDMA. When all of the reflected waves corresponding to the pixels forming a range image are received, the proposed LIDAR generates a point cloud based on the time-of-flight (ToF) of each reflected wave. The results of simulations performed on the proposed LIDAR are compared with simulations of existing LIDARs.

Kalai-Smorodinsky bargaining solution for optimal resource allocation over wireless DS-CDMA visual sensor networks

NASA Astrophysics Data System (ADS)

Pandremmenou, Katerina; Kondi, Lisimachos P.; Parsopoulos, Konstantinos E.

2012-01-01

Surveillance applications usually require high levels of video quality, resulting in high power consumption. The existence of a well-behaved scheme to balance video quality and power consumption is crucial for the system's performance. In the present work, we adopt the game-theoretic approach of Kalai-Smorodinsky Bargaining Solution (KSBS) to deal with the problem of optimal resource allocation in a multi-node wireless visual sensor network (VSN). In our setting, the Direct Sequence Code Division Multiple Access (DS-CDMA) method is used for channel access, while a cross-layer optimization design, which employs a central processing server, accounts for the overall system efficacy through all network layers. The task assigned to the central server is the communication with the nodes and the joint determination of their transmission parameters. The KSBS is applied to non-convex utility spaces, efficiently distributing the source coding rate, channel coding rate and transmission powers among the nodes. In the underlying model, the transmission powers assume continuous values, whereas the source and channel coding rates can take only discrete values. Experimental results are reported and discussed to demonstrate the merits of KSBS over competing policies.

Coding and decoding for code division multiple user communication systems

NASA Technical Reports Server (NTRS)

Healy, T. J.

1985-01-01

A new algorithm is introduced which decodes code division multiple user communication signals. The algorithm makes use of the distinctive form or pattern of each signal to separate it from the composite signal created by the multiple users. Although the algorithm is presented in terms of frequency-hopped signals, the actual transmitter modulator can use any of the existing digital modulation techniques. The algorithm is applicable to error-free codes or to codes where controlled interference is permitted. It can be used when block synchronization is assumed, and in some cases when it is not. The paper also discusses briefly some of the codes which can be used in connection with the algorithm, and relates the algorithm to past studies which use other approaches to the same problem.

Design and fabrication considerations for stainless steel liquid helium jackets surrounding SCRF cavities

NASA Astrophysics Data System (ADS)

Bonnema, E. C.; Cunningham, E. K.; Rumel, J. D.

2014-01-01

The Department of Energy requires its subcontractors to meet 10 CFR 851 Appendix A Part 4 for all new pressure vessels and pressure piping. The stainless steel pressure vessel boundaries surrounding SCRF cavities fall under this requirement. Methods for meeting this requirement include design and fabrication of the pressure vessels to meet the requirements of the ASME Boiler & Pressure Vessel Code Section VIII Division 1 or Division 2. Design considerations include determining whether the configuration of the SCRF cavity can be accommodated under the rules of Division 1 or must be analyzed under Division 2 Part 4 Design by Rule Requirements or Part 5 Design by Analysis Requirements. Regardless of the Division or Part choice, designers will find the rules of the ASME Code require thicker pressure boundary members, larger welds, and additional non-destructive testing and quality assurance requirements. These challenges must be met and overcome by the fabricator through the development of robust, detailed, and repeatable manufacturing processes. In this paper we discuss the considerations for stainless steel pressure vessels that must meet the ASME Code and illustrate the discussion with examples from direct experience fabricating such vessels.

75 FR 21963 - Regulatory Flexibility Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

... Materials 3235-AK25 DIVISION OF INVESTMENT MANAGEMENT--Proposed Rule Stage Regulation Sequence Title... 3235-AI17 DIVISION OF INVESTMENT MANAGEMENT--Completed Actions Regulation Sequence Title Identifier... Management Investment Company 3235-AJ11 Shares, Unit Investment Trust Interests, and Municipal Fund...

Dynamic quality of service differentiation using fixed code weight in optical CDMA networks

NASA Astrophysics Data System (ADS)

Kakaee, Majid H.; Essa, Shawnim I.; Abd, Thanaa H.; Seyedzadeh, Saleh

2015-11-01

The emergence of network-driven applications, such as internet, video conferencing, and online gaming, brings in the need for a network the environments with capability of providing diverse Quality of Services (QoS). In this paper, a new code family of novel spreading sequences, called a Multi-Service (MS) code, has been constructed to support multiple services in Optical- Code Division Multiple Access (CDMA) system. The proposed method uses fixed weight for all services, however reducing the interfering codewords for the users requiring higher QoS. The performance of the proposed code is demonstrated using mathematical analysis. It shown that the total number of served users with satisfactory BER of 10-9 using NB=2 is 82, while they are only 36 and 10 when NB=3 and 4 respectively. The developed MS code is compared with variable-weight codes such as Variable Weight-Khazani Syed (VW-KS) and Multi-Weight-Random Diagonal (MW-RD). Different numbers of basic users (NB) are used to support triple-play services (audio, data and video) with different QoS requirements. Furthermore, reference to the BER of 10-12, 10-9, and 10-3 for video, data and audio, respectively, the system can support up to 45 total users. Hence, results show that the technique can clearly provide a relative QoS differentiation with lower value of basic users can support larger number of subscribers as well as better performance in terms of acceptable BER of 10-9 at fixed code weight.

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

NASA Astrophysics Data System (ADS)

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

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

Quantum internet using code division multiple access

PubMed Central

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

2013-01-01

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

Near Field HF Antenna Pattern Measurement Method Using an Antenna Pattern Range

DTIC Science & Technology

2015-12-01

Year 2015 by the Applied Electromagnetics Branch (Code 52250) of the System of Systems (SoS) & Platform Design Division (Code 52200), Space and...Head SoS & Platform Design Division iii EXECUTIVE SUMMARY The Antenna Pattern Range (APR) is an essential measurement facility operated at Space...14 1 INTRODUCTION Accurate characterization of antennas designed to support the warfighter is a critical

Background Perchlorate Source Identification Technical Guidance

DTIC Science & Technology

2013-12-01

Sciences Branch (Code 71752) of the Advanced Systems and Applied Sciences Division (Code 71700), Space and Naval Warfare Systems Center (SSC Pacific), San...Head Advanced Systems & Applied Sciences Division iii EXECUTIVE SUMMARY The objective of this document is to outline the approach, tools, and...Helium HMX Octahydro-1,3,5,7-Tetranitro-1,3,5,7- Tetrazocine IR Installation Restoration IRIS Integrated Risk Information System IR-MS Isotope-Ratio

Novel division level bacterial diversity in a Yellowstone hot spring.

PubMed

Hugenholtz, P; Pitulle, C; Hershberger, K L; Pace, N R

1998-01-01

A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609-1613, 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved or Bacteria-specific rDNA primers and cloned. Unique rDNA types among > 300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (> or = 98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing delta-Proteobacteria. The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.

Cognitive and Neural Sciences Division, 1991 Programs.

ERIC Educational Resources Information Center

Vaughan, Willard S., Ed.

This report documents research and development performed under the sponsorship of the Cognitive and Neural Sciences Division of the Office of Naval Research in fiscal year 1991. It provides abstracts (title, principal investigator, project code, objective, approach, progress, and related reports) of projects of three program divisions (cognitive…

DOD Residential Proton Exchange Membrane (PEM) Fuel Cell Demonstration Program. Volume 1. Summary of the Fiscal Year 2001 Program

DTIC Science & Technology

2004-02-01

Potential new stan- dard ASME Boiler and Pressure Vessel Code, Section VIII ( BPVC -VIII), Division 1 Rules for Construction of Pressure Vessels...Published and avail- able for sale. ASME BPVC -VIII Division 2 Rules for Construction of Pressure Vessels, Division 2, Gerry Eisenberg, ASME ...Vessels, Division 3, Alternate ASME BPVC -VIII Division 3 Gerry Eisenberg, ASME Published and avail- able for sale. Rules High

Goddard Visiting Scientist Program

NASA Technical Reports Server (NTRS)

2000-01-01

Under this Indefinite Delivery Indefinite Quantity (IDIQ) contract, USRA was expected to provide short term (from I day up to I year) personnel as required to provide a Visiting Scientists Program to support the Earth Sciences Directorate (Code 900) at the Goddard Space Flight Center. The Contractor was to have a pool, or have access to a pool, of scientific talent, both domestic and international, at all levels (graduate student to senior scientist), that would support the technical requirements of the following laboratories and divisions within Code 900: 1) Global Change Data Center (902); 2) Laboratory for Atmospheres (Code 910); 3) Laboratory for Terrestrial Physics (Code 920); 4) Space Data and Computing Division (Code 930); 5) Laboratory for Hydrospheric Processes (Code 970). The research activities described below for each organization within Code 900 were intended to comprise the general scope of effort covered under the Visiting Scientist Program.

LexA Binds to Transcription Regulatory Site of Cell Division Gene ftsZ in Toxic Cyanobacterium Microcystis aeruginosa.

PubMed

Honda, Takashi; Morimoto, Daichi; Sako, Yoshihiko; Yoshida, Takashi

2018-05-17

Previously, we showed that DNA replication and cell division in toxic cyanobacterium Microcystis aeruginosa are coordinated by transcriptional regulation of cell division gene ftsZ and that an unknown protein specifically bound upstream of ftsZ (BpFz; DNA-binding protein to an upstream site of ftsZ) during successful DNA replication and cell division. Here, we purified BpFz from M. aeruginosa strain NIES-298 using DNA-affinity chromatography and gel-slicing combined with gel electrophoresis mobility shift assay (EMSA). The N-terminal amino acid sequence of BpFz was identified as TNLESLTQ, which was identical to that of transcription repressor LexA from NIES-843. EMSA analysis using mutant probes showed that the sequence GTACTAN 3 GTGTTC was important in LexA binding. Comparison of the upstream regions of lexA in the genomes of closely related cyanobacteria suggested that the sequence TASTRNNNNTGTWC could be a putative LexA recognition sequence (LexA box). Searches for TASTRNNNNTGTWC as a transcriptional regulatory site (TRS) in the genome of M. aeruginosa NIES-843 showed that it was present in genes involved in cell division, photosynthesis, and extracellular polysaccharide biosynthesis. Considering that BpFz binds to the TRS of ftsZ during normal cell division, LexA may function as a transcriptional activator of genes related to cell reproduction in M. aeruginosa, including ftsZ. This may be an example of informality in the control of bacterial cell division.

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. [74...

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. [74...

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. [74...

A code-aided carrier synchronization algorithm based on improved nonbinary low-density parity-check codes

NASA Astrophysics Data System (ADS)

Bai, Cheng-lin; Cheng, Zhi-hui

2016-09-01

In order to further improve the carrier synchronization estimation range and accuracy at low signal-to-noise ratio ( SNR), this paper proposes a code-aided carrier synchronization algorithm based on improved nonbinary low-density parity-check (NB-LDPC) codes to study the polarization-division-multiplexing coherent optical orthogonal frequency division multiplexing (PDM-CO-OFDM) system performance in the cases of quadrature phase shift keying (QPSK) and 16 quadrature amplitude modulation (16-QAM) modes. The simulation results indicate that this algorithm can enlarge frequency and phase offset estimation ranges and enhance accuracy of the system greatly, and the bit error rate ( BER) performance of the system is improved effectively compared with that of the system employing traditional NB-LDPC code-aided carrier synchronization algorithm.

Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing.

PubMed

Kim, Bong-Soo; Kim, Byung Kwon; Lee, Jae-Hak; Kim, Myungjin; Lim, Young Woon; Chun, Jongsik

2008-08-01

Dissection of prokaryotic community structure is prerequisite to understand their ecological roles. Various methods are available for such a purpose which amplification and sequencing of 16S rRNA genes gained its popularity. However, conventional methods based on Sanger sequencing technique require cloning process prior to sequencing, and are expensive and labor-intensive. We investigated prokaryotic community structure in tidal flat sediments, Korea, using pyrosequencing and a subsequent automated bioinformatic pipeline for the rapid and accurate taxonomic assignment of each amplicon. The combination of pyrosequencing and bioinformatic analysis showed that bacterial and archaeal communities were more diverse than previously reported in clone library studies. Pyrosequencing analysis revealed 21 bacterial divisions and 37 candidate divisions. Proteobacteria was the most abundant division in the bacterial community, of which Gamma-and Delta-Proteobacteria were the most abundant. Similarly, 4 archaeal divisions were found in tidal flat sediments. Euryarchaeota was the most abundant division in the archaeal sequences, which were further divided into 8 classes and 11 unclassified euryarchaeota groups. The system developed here provides a simple, in-depth and automated way of dissecting a prokaryotic community structure without extensive pretreatment such as cloning.

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

NASA Astrophysics Data System (ADS)

Hortos, William S.

1998-03-01

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

Statistical physics inspired energy-efficient coded-modulation for optical communications.

PubMed

Djordjevic, Ivan B; Xu, Lei; Wang, Ting

2012-04-15

Because Shannon's entropy can be obtained by Stirling's approximation of thermodynamics entropy, the statistical physics energy minimization methods are directly applicable to the signal constellation design. We demonstrate that statistical physics inspired energy-efficient (EE) signal constellation designs, in combination with large-girth low-density parity-check (LDPC) codes, significantly outperform conventional LDPC-coded polarization-division multiplexed quadrature amplitude modulation schemes. We also describe an EE signal constellation design algorithm. Finally, we propose the discrete-time implementation of D-dimensional transceiver and corresponding EE polarization-division multiplexed system. © 2012 Optical Society of America

Ancient DNA sequence revealed by error-correcting codes.

PubMed

Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

2015-07-10

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

Ancient DNA sequence revealed by error-correcting codes

PubMed Central

Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

2015-01-01

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

CP decomposition approach to blind separation for DS-CDMA system using a new performance index

NASA Astrophysics Data System (ADS)

Rouijel, Awatif; Minaoui, Khalid; Comon, Pierre; Aboutajdine, Driss

2014-12-01

In this paper, we present a canonical polyadic (CP) tensor decomposition isolating the scaling matrix. This has two major implications: (i) the problem conditioning shows up explicitly and could be controlled through a constraint on the so-called coherences and (ii) a performance criterion concerning the factor matrices can be exactly calculated and is more realistic than performance metrics used in the literature. Two new algorithms optimizing the CP decomposition based on gradient descent are proposed. This decomposition is illustrated by an application to direct-sequence code division multiplexing access (DS-CDMA) systems; computer simulations are provided and demonstrate the good behavior of these algorithms, compared to others in the literature.

Soldier communication net for the 21st century digitized battlespace

NASA Astrophysics Data System (ADS)

Mu, Libo; Zhang, Yutian

1999-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Enhanced intercarrier interference mitigation based on encoded bit-sequence distribution inside optical superchannels

NASA Astrophysics Data System (ADS)

Torres, Jhon James Granada; Soto, Ana María Cárdenas; González, Neil Guerrero

2016-10-01

In the context of gridless optical multicarrier systems, we propose a method for intercarrier interference (ICI) mitigation which allows bit error correction in scenarios of nonspectral flatness between the subcarriers composing the multicarrier system and sub-Nyquist carrier spacing. We propose a hybrid ICI mitigation technique which exploits the advantages of signal equalization at both levels: the physical level for any digital and analog pulse shaping, and the bit-data level and its ability to incorporate advanced correcting codes. The concatenation of these two complementary techniques consists of a nondata-aided equalizer applied to each optical subcarrier, and a hard-decision forward error correction applied to the sequence of bits distributed along the optical subcarriers regardless of prior subchannel quality assessment as performed in orthogonal frequency-division multiplexing modulations for the implementation of the bit-loading technique. The impact of the ICI is systematically evaluated in terms of bit-error-rate as a function of the carrier frequency spacing and the roll-off factor of the digital pulse-shaping filter for a simulated 3×32-Gbaud single-polarization quadrature phase shift keying Nyquist-wavelength division multiplexing system. After the ICI mitigation, a back-to-back error-free decoding was obtained for sub-Nyquist carrier spacings of 28.5 and 30 GHz and roll-off values of 0.1 and 0.4, respectively.

Two-terminal video coding.

PubMed

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

Identification and Classification of Orthogonal Frequency Division Multiple Access (OFDMA) Signals Used in Next Generation Wireless Systems

DTIC Science & Technology

2012-03-01

advanced antenna systems AMC adaptive modulation and coding AWGN additive white Gaussian noise BPSK binary phase shift keying BS base station BTC ...QAM-16, and QAM-64, and coding types include convolutional coding (CC), convolutional turbo coding (CTC), block turbo coding ( BTC ), zero-terminating

75 FR 14359 - FM TABLE OF ALLOTMENTS, Stonewall, Texas

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-25

.... SUMMARY: The Audio Division denies the petition for rule making filed by Katherine Pyeatt, proposing the...-making proposals. For that reason, the Audio Division denied the petition for rule making and terminated..., Audio Division, Media Bureau. [FR Doc. 2010-6385 Filed 3-24-10; 8:45 am] BILLING CODE 6712-01-S ...

Coastal Processes: Challenges for Monitoring and Prediction

DTIC Science & Technology

2009-01-01

Code 1008.3 ADOR/Director NCST E. R. Franchi , 7000 Public Affairs (Unclassified/ Unlimited Only). Code 703o 4 Division, Code Author, Code n...Research Global and the Fondazione Cassa di Risparmio di La Spezia for the financial support provided for the conference and the special issue.

Cognitive and Neural Sciences Division 1991 Programs

DTIC Science & Technology

1991-08-01

FUNDING NUMBERS Cognitive and Neural Sciences Division 1991 Programs PE 61153N 6. AUTHOR(S) Edited by Willard S. Vaughan 7. PERFORMING ORGANIZATION...NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER Office of Naval Research 0CNR !1491-19 Cognitive and Neural Sciences Division Code 1142...NOTES iN This is a compilation of abstracts representing R&D sponsored by the ONR Cognitive and Neural Sciences Division. 12a. DISTRIBUTION

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

PubMed

Waheed, Khuram; Salem, Fathi M

2005-07-01

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

Cell genealogies in a plant meristem deduced with the aid of a 'bootstrap' L-system.

PubMed

Lück, J; Barlow, P W; Lück, H B

1994-01-01

The primary root meristem of maize (Zea mays L.) contains longitudinal files of cells arranged in groups of familial descent (sisters, cousins, etc.). These groups, or packets, show ordered sequences of cell division which are transverse with respect to the apico-basal axis of the root. The sequences have been analysed in three zones of the meristem during the course of the first four cell generations following germination. In this period, the number of cells in the packets increases from one to 16. Theoretically, there are 48 possible division pathways that lead to the eight-cell stage, and nearly 2 x 10(6) that lead to the 16-cell stage. However, analysis shows that only a few of all the possible pathways are used in any particular zone of the root. This restriction of pathways results from inherited sequences of asymmetric cell divisions which lead to sister cells of unequal length. All possible division pathways can be generated by deterministic 'bootstrap' L-systems which assign different lifespans to sister cells of successive generations and hence specify their subsequent sequence of divisions. These systems simulate propagating patterns of cell divisions which agree with those actually found within the growing packets that comprise the root meristem. The patterns of division are specific to cells originating in various regions of the meristem of the germinating root. The importance of such systems is that they simulate patterns of cellular proliferation where there is ancestral dependency. They can therefore be applied in other growing and proliferating systems where this is suspected.

The histone codes for meiosis.

PubMed

Wang, Lina; Xu, Zhiliang; Khawar, Muhammad Babar; Liu, Chao; Li, Wei

2017-09-01

Meiosis is a specialized process that produces haploid gametes from diploid cells by a single round of DNA replication followed by two successive cell divisions. It contains many special events, such as programmed DNA double-strand break (DSB) formation, homologous recombination, crossover formation and resolution. These events are associated with dynamically regulated chromosomal structures, the dynamic transcriptional regulation and chromatin remodeling are mainly modulated by histone modifications, termed 'histone codes'. The purpose of this review is to summarize the histone codes that are required for meiosis during spermatogenesis and oogenesis, involving meiosis resumption, meiotic asymmetric division and other cellular processes. We not only systematically review the functional roles of histone codes in meiosis but also discuss future trends and perspectives in this field. © 2017 Society for Reproduction and Fertility.

NASA. Lewis Research Center Advanced Modulation and Coding Project: Introduction and overview

NASA Technical Reports Server (NTRS)

Budinger, James M.

1992-01-01

The Advanced Modulation and Coding Project at LeRC is sponsored by the Office of Space Science and Applications, Communications Division, Code EC, at NASA Headquarters and conducted by the Digital Systems Technology Branch of the Space Electronics Division. Advanced Modulation and Coding is one of three focused technology development projects within the branch's overall Processing and Switching Program. The program consists of industry contracts for developing proof-of-concept (POC) and demonstration model hardware, university grants for analyzing advanced techniques, and in-house integration and testing of performance verification and systems evaluation. The Advanced Modulation and Coding Project is broken into five elements: (1) bandwidth- and power-efficient modems; (2) high-speed codecs; (3) digital modems; (4) multichannel demodulators; and (5) very high-data-rate modems. At least one contract and one grant were awarded for each element.

Analysis of Optical CDMA Signal Transmission: Capacity Limits and Simulation Results

NASA Astrophysics Data System (ADS)

Garba, Aminata A.; Yim, Raymond M. H.; Bajcsy, Jan; Chen, Lawrence R.

2005-12-01

We present performance limits of the optical code-division multiple-access (OCDMA) networks. In particular, we evaluate the information-theoretical capacity of the OCDMA transmission when single-user detection (SUD) is used by the receiver. First, we model the OCDMA transmission as a discrete memoryless channel, evaluate its capacity when binary modulation is used in the interference-limited (noiseless) case, and extend this analysis to the case when additive white Gaussian noise (AWGN) is corrupting the received signals. Next, we analyze the benefits of using nonbinary signaling for increasing the throughput of optical CDMA transmission. It turns out that up to a fourfold increase in the network throughput can be achieved with practical numbers of modulation levels in comparison to the traditionally considered binary case. Finally, we present BER simulation results for channel coded binary and[InlineEquation not available: see fulltext.]-ary OCDMA transmission systems. In particular, we apply turbo codes concatenated with Reed-Solomon codes so that up to several hundred concurrent optical CDMA users can be supported at low target bit error rates. We observe that unlike conventional OCDMA systems, turbo-empowered OCDMA can allow overloading (more active users than is the length of the spreading sequences) with good bit error rate system performance.

Elliptic net and its cryptographic application

NASA Astrophysics Data System (ADS)

Muslim, Norliana; Said, Mohamad Rushdan Md

2017-11-01

Elliptic net is a generalization of elliptic divisibility sequence and in cryptography field, most cryptographic pairings that are based on elliptic curve such as Tate pairing can be improved by applying elliptic nets algorithm. The elliptic net is constructed by using n dimensional array of values in rational number satisfying nonlinear recurrence relations that arise from elliptic divisibility sequences. The two main properties hold in the recurrence relations are for all positive integers m>n, hm +nhm -n=hm +1hm -1hn2-hn +1hn -1hm2 and hn divides hm whenever n divides m. In this research, we discuss elliptic divisibility sequence associated with elliptic nets based on cryptographic perspective and its possible research direction.

A pulse coding and decoding strategy to perform Lamb wave inspections using simultaneously multiple actuators

NASA Astrophysics Data System (ADS)

De Marchi, Luca; Marzani, Alessandro; Moll, Jochen; Kudela, Paweł; Radzieński, Maciej; Ostachowicz, Wiesław

2017-07-01

The performance of Lamb wave based monitoring systems, both in terms of diagnosis time and data complexity, can be enhanced by increasing the number of transducers used to actuate simultaneously the guided waves in the inspected medium. However, in case of multiple simultaneously-operated actuators the interference among the excited wave modes within the acquired signals has to be considered for the further processing. To this aim, in this work a code division strategy based on the Warped Frequency Transform is presented. At first, the proposed procedure encodes actuation pulses using Gold sequences. Next, for each considered actuator the acquired signals are compensated from dispersion by cross correlating the warped version of the actuated and received signals. Compensated signals form the base for a final wavenumber imaging meant at emphasizing defects and or anomalies by removing incident wavefield and edge reflections. The proposed strategy is tested numerically, and validated through an experiment in which guided waves are actuated in a plate by four piezoelectric transducers operating simultaneously.

Sharing Resources In Mobile/Satellite Communications

NASA Technical Reports Server (NTRS)

Yan, Tsun-Yee; Sue, Miles K.

1992-01-01

Report presents preliminary theoretical analysis of several alternative schemes for allocation of satellite resource among terrestrial subscribers of landmobile/satellite communication system. Demand-access and random-access approaches under code-division and frequency-division concepts compared.

Evaluation of Evidence for Altered Behavior and Auditory Deficits in Fishes Due to Human-Generated Noise Sources

DTIC Science & Technology

2006-04-01

prepared by the Research and Animal Care Branch, Code 2351, of the Biosciences Division, Code 235, SSC San Diego. This is a work of the United...and Animal Care Branch Under authority of M. Rothe, Head Biosciences Division i EXECUTIVE SUMMARY In this study, we have evaluated peer... sharks , skates, and rays) and teleost fishes (modern bony fishes) and provide recommendations for research to address remaining issues. Clear responses

Performance Analysis of a New Coded TH-CDMA Scheme in Dispersive Infrared Channel with Additive Gaussian Noise

NASA Astrophysics Data System (ADS)

Hamdi, Mazda; Kenari, Masoumeh Nasiri

2013-06-01

We consider a time-hopping based multiple access scheme introduced in [1] for communication over dispersive infrared links, and evaluate its performance for correlator and matched filter receivers. In the investigated time-hopping code division multiple access (TH-CDMA) method, the transmitter benefits a low rate convolutional encoder. In this method, the bit interval is divided into Nc chips and the output of the encoder along with a PN sequence assigned to the user determines the position of the chip in which the optical pulse is transmitted. We evaluate the multiple access performance of the system for correlation receiver considering background noise which is modeled as White Gaussian noise due to its large intensity. For the correlation receiver, the results show that for a fixed processing gain, at high transmit power, where the multiple access interference has the dominant effect, the performance improves by the coding gain. But at low transmit power, in which the increase of coding gain leads to the decrease of the chip time, and consequently, to more corruption due to the channel dispersion, there exists an optimum value for the coding gain. However, for the matched filter, the performance always improves by the coding gain. The results show that the matched filter receiver outperforms the correlation receiver in the considered cases. Our results show that, for the same bandwidth and bit rate, the proposed system excels other multiple access techniques, like conventional CDMA and time hopping scheme.

Cell cycle dependent intracellular distribution of two spliced isoforms of TCP/ILF3 proteins.

PubMed

Xu, You Hai; Leonova, Tatyana; Grabowski, Gregory A

2003-12-01

TCP80 is an approximately 80kDa mammalian cytoplasmic protein that binds to a set of mRNAs and inhibits their translation in vitro and ex vivo. This protein has high sequence similarity to interleukin-2 enhancer-binding factors (NF90/ILF3) and the M-phase phosphoprotein (MPP4)/DRBP76. A 110kDa immunologic isoform of TCP80/NF90/MPP4/DRBP76, termed TCP110, also is present in cytoplasm and nuclei of many types of cells. A cDNA sequence coding for TCP110 was derived by 5(')RACE. The TCP110 sequence is identical to ILF3. The gene coding for TCP110/ILF3 mapped to human chromosome 19 and the gene organization was analyzed using TCP80 and TCP110/ILF3 cDNA sequences. The TCP/ILF3 gene spans >34.8kb and contains 21 exons. At least one alternatively spliced product involving exons 19-21 exists and predicts the formation of either TCP80 or TCP110/ILF3. However, the functional relationships of TCP80 and TCP110/ILF3 required elucidation. The metabolic turnover rates and subcellular distribution of TCP80 and TCP110/ILF3 during the cell cycle showed TCP80 to be relatively stable (t(1/2)=5 days) in the cytoplasmic compartment. In comparison, TCP110/ILF3 migrated between the cytoplasmic and nuclear compartments during the cell cycle. The TCP110 C-terminal segment contains an additional nuclear localizing signal that plays a role in its nuclear translocation. This study indicates that the multiple cellular functions, i.e., translation control, interleukin-2 enhancer binding, or cell division, of TCP/ILF3 are fulfilled by alternatively spliced isoforms.

Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)

PubMed Central

Yang, Yaodong; Mason, Annaliese S.; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. PMID:23951162

Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

PubMed

Xiao, Yong; Xia, Wei; Yang, Yaodong; Mason, Annaliese S; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2011 CFR

2011-07-01

... submitted to the following address: (a) For U.S. mail. Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. ...

75 FR 13236 - FM Table of Allotments, Port Angeles, Washington

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-19

... rule. SUMMARY: The Audio Division grants a rulemaking petition filed by Jodesha Broadcasting, Inc., the..., Assistant Chief, Audio Division, Media Bureau. [FR Doc. 2010-6017 Filed 3-18-10; 8:45 am] BILLING CODE 6712...

40 CFR 98.9 - Addresses.

Code of Federal Regulations, 2010 CFR

2010-07-01

... submitted to the following address: (a) For U.S. mail. Director, Climate Change Division, 1200 Pennsylvania Ave., NW., Mail Code: 6207J, Washington, DC 20460. (b) For package deliveries. Director, Climate Change Division, 1310 L St, NW., Washington, DC 20005. ...

Research on compression performance of ultrahigh-definition videos

NASA Astrophysics Data System (ADS)

Li, Xiangqun; He, Xiaohai; Qing, Linbo; Tao, Qingchuan; Wu, Di

2017-11-01

With the popularization of high-definition (HD) images and videos (1920×1080 pixels and above), there are even 4K (3840×2160) television signals and 8 K (8192×4320) ultrahigh-definition videos. The demand for HD images and videos is increasing continuously, along with the increasing data volume. The storage and transmission cannot be properly solved only by virtue of the expansion capacity of hard disks and the update and improvement of transmission devices. Based on the full use of the coding standard high-efficiency video coding (HEVC), super-resolution reconstruction technology, and the correlation between the intra- and the interprediction, we first put forward a "division-compensation"-based strategy to further improve the compression performance of a single image and frame I. Then, by making use of the above thought and HEVC encoder and decoder, a video compression coding frame is designed. HEVC is used inside the frame. Last, with the super-resolution reconstruction technology, the reconstructed video quality is further improved. The experiment shows that by the proposed compression method for a single image (frame I) and video sequence here, the performance is superior to that of HEVC in a low bit rate environment.

EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

PubMed Central

Nahum, Laila A; Reynolds, Matthew T; Wang, Zhengyuan O; Faith, Jeremiah J; Jonna, Rahul; Jiang, Zhi J; Meyer, Thomas J; Pollock, David D

2006-01-01

Background Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. Description EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. Conclusion EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. PMID:17118150

Code division multiple access signaling for modulated reflector technology

DOEpatents

Briles, Scott D [Los Alamos, NM

2012-05-01

A method and apparatus for utilizing code division multiple access in modulated reflectance transmissions comprises the steps of generating a phase-modulated reflectance data bit stream; modifying the modulated reflectance data bit stream; providing the modified modulated reflectance data bit stream to a switch that connects an antenna to an infinite impedance in the event a "+1" is to be sent, or connects the antenna to ground in the event a "0" or a "-1" is to be sent.

Performance Analysis of Hybrid ARQ Protocols in a Slotted Code Division Multiple-Access Network

DTIC Science & Technology

1989-08-01

Convolutional Codes . in Proc Int. Conf. Commun., 21.4.1-21.4.5, 1987. [27] J. Hagenauer. Rate Compatible Punctured Convolutional Codes . in Proc Int. Conf...achieved by using a low rate (r = 0.5), high constraint length (e.g., 32) punctured convolutional code . Code puncturing provides for a variable rate code ...investigated the use of convolutional codes in Type II Hybrid ARQ protocols. The error

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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

NASA Astrophysics Data System (ADS)

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

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

2-Step Maximum Likelihood Channel Estimation for Multicode DS-CDMA with Frequency-Domain Equalization

NASA Astrophysics Data System (ADS)

Kojima, Yohei; Takeda, Kazuaki; Adachi, Fumiyuki

Frequency-domain equalization (FDE) based on the minimum mean square error (MMSE) criterion can provide better downlink bit error rate (BER) performance of direct sequence code division multiple access (DS-CDMA) than the conventional rake combining in a frequency-selective fading channel. FDE requires accurate channel estimation. In this paper, we propose a new 2-step maximum likelihood channel estimation (MLCE) for DS-CDMA with FDE in a very slow frequency-selective fading environment. The 1st step uses the conventional pilot-assisted MMSE-CE and the 2nd step carries out the MLCE using decision feedback from the 1st step. The BER performance improvement achieved by 2-step MLCE over pilot assisted MMSE-CE is confirmed by computer simulation.

Performance Analysis of Blind Subspace-Based Signature Estimation Algorithms for DS-CDMA Systems with Unknown Correlated Noise

NASA Astrophysics Data System (ADS)

Zarifi, Keyvan; Gershman, Alex B.

2006-12-01

We analyze the performance of two popular blind subspace-based signature waveform estimation techniques proposed by Wang and Poor and Buzzi and Poor for direct-sequence code division multiple-access (DS-CDMA) systems with unknown correlated noise. Using the first-order perturbation theory, analytical expressions for the mean-square error (MSE) of these algorithms are derived. We also obtain simple high SNR approximations of the MSE expressions which explicitly clarify how the performance of these techniques depends on the environmental parameters and how it is related to that of the conventional techniques that are based on the standard white noise assumption. Numerical examples further verify the consistency of the obtained analytical results with simulation results.

MAI statistics estimation and analysis in a DS-CDMA system

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

47 CFR 73.3549 - Requests for extension of time to operate without required monitors, indicating instruments, and...

Code of Federal Regulations, 2010 CFR

2010-10-01

... decoders for monitoring and generating the EAS codes and Attention Signal should be made to the FCC in Washington, DC, Attention: Audio Division (radio) or Video Division (television), Media Bureau. Such requests...

Archaebacterial phylogeny: perspectives on the urkingdoms

NASA Technical Reports Server (NTRS)

Woese, C. R.; Olsen, G. J.

1986-01-01

Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

Detecting cell division of Pseudomonas aeruginosa bacteria from bright-field microscopy images with hidden conditional random fields.

PubMed

Ong, Lee-Ling S; Xinghua Zhang; Kundukad, Binu; Dauwels, Justin; Doyle, Patrick; Asada, H Harry

2016-08-01

An approach to automatically detect bacteria division with temporal models is presented. To understand how bacteria migrate and proliferate to form complex multicellular behaviours such as biofilms, it is desirable to track individual bacteria and detect cell division events. Unlike eukaryotic cells, prokaryotic cells such as bacteria lack distinctive features, causing bacteria division difficult to detect in a single image frame. Furthermore, bacteria may detach, migrate close to other bacteria and may orientate themselves at an angle to the horizontal plane. Our system trains a hidden conditional random field (HCRF) model from tracked and aligned bacteria division sequences. The HCRF model classifies a set of image frames as division or otherwise. The performance of our HCRF model is compared with a Hidden Markov Model (HMM). The results show that a HCRF classifier outperforms a HMM classifier. From 2D bright field microscopy data, it is a challenge to separate individual bacteria and associate observations to tracks. Automatic detection of sequences with bacteria division will improve tracking accuracy.

One-dimensional photonic crystals for code-division multiple access

NASA Astrophysics Data System (ADS)

Wang, Shamino Yuanliang

One-dimensional photonic crystals exhibit reduced group velocity and huge dispersion at their rejection band edge frequencies. Therefore they are natural candidates as optical delay lines, dispersion compensators, and pulse reshapers. Using wavelength tunable pulses spectrally sliced from a mode-locked fiber laser, the transmission mode measurement was performed in the time domain with single picosecond resolution. Group delays and dispersion were measured with an autocorrelator as an ultrafast optical detector and cross-correlator. Our experimental results agree qualitatively with the theoretical and simulation predictions. A maximum group delay of 10 ps for a commercial 3 mm long uniform fiber Bragg grating and that of 22.6 ps for a research laboratory fabricated 1 cm grating were measured, corresponding to a group velocity 66% of the speed of light in bare fiber. We have also demonstrated in the overlap transmission region of a grating pair both gratings contribute to the group delay while the group velocity dispersion was canceled, resulting in additive delay in transmission with minimal pulse reshaping. This compound grating configuration was further expanded as specially designed grating sequence encoders and decoders in matched filter CDMA. The transmitter grating sequence temporally stretched the input pulse into a long time scale low peak intensity pseudorandom noise, while the conjugate grating sequence in the receiver performed pulse reconstruction and data recovery. A temporal FWHM contrast ratio of 2.5 and a peak intensity contrast ratio of 10 between the correctly and incorrectly decoded signals were achieved. Armed with more sophisticated grating designs we believe this would be a powerful solution to CDMA orthogonal code requirements.

A korarchaeal genome reveals insights into the evolution of the Archaea

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

Anderson, Iain J; Elkins, James G.; Podar, Mircea

2008-06-05

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name,"Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent. Ofmore » the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.« less

A Korarchael Genome Reveals Insights into the Evolution of the Archaea

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

Lapidus, Alla; Elkins, James G.; Podar, Mircea

2008-01-07

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, ?Candidatus Korarchaeum cryptofilum,? which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent.more » Of the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.« less

Microbial Diversity in a Hydrocarbon- and Chlorinated-Solvent-Contaminated Aquifer Undergoing Intrinsic Bioremediation

PubMed Central

Dojka, Michael A.; Hugenholtz, Philip; Haack, Sheridan K.; Pace, Norman R.

1998-01-01

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- or Archaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OP5, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association. PMID:9758812

Microbial diversity in a hydrocarbon- and chlorinated-solvent- contaminated aquifer undergoing intrinsic bioremediation

USGS Publications Warehouse

Dojka, M.A.; Hugenholtz, P.; Haack, S.K.; Pace, N.R.

1998-01-01

A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and chlorinated solvents undergoing intrinsic bioremediation. Samples were obtained from three redox zones: methanogenic, methanogenic-sulfate reducing, and iron or sulfate reducing. Small-subunit rRNA genes were amplified directly from aquifer material DNA by PCR with universally conserved or Bacteria- or Archaea-specific primers and were cloned. A total of 812 clones were screened by restriction fragment length polymorphisms (RFLP), approximately 50% of which were unique. All RFLP types that occurred more than once in the libraries, as well as many of the unique types, were sequenced. A total of 104 (94 bacterial and 10 archaeal) sequence types were determined. Of the 94 bacterial sequence types, 10 have no phylogenetic association with known taxonomic divisions and are phylogenetically grouped in six novel division level groups (candidate divisions WS1 to WS6); 21 belong to four recently described candidate divisions with no cultivated representatives (OPS, OP8, OP10, and OP11); and 63 are phylogenetically associated with 10 well-recognized divisions. The physiology of two particularly abundant sequence types obtained from the methanogenic zone could be inferred from their phylogenetic association with groups of microorganisms with a consistent phenotype. One of these sequence types is associated with the genus Syntrophus; Syntrophus spp. produce energy from the anaerobic oxidation of organic acids, with the production of acetate and hydrogen. The organism represented by the other sequence type is closely related to Methanosaeta spp., which are known to be capable of energy generation only through aceticlastic methanogenesis. We hypothesize, therefore, that the terminal step of hydrocarbon degradation in the methanogenic zone of the aquifer is aceticlastic methanogenesis and that the microorganisms represented by these two sequence types occur in syntrophic association.

29 CFR 510.21 - SIC codes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 29 Labor 3 2010-07-01 2010-07-01 false SIC codes. 510.21 Section 510.21 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR REGULATIONS IMPLEMENTATION OF THE... Classification of Industries § 510.21 SIC codes. (a) The Conference Report specifically cites Puerto Rico's...

49 CFR 173.52 - Classification codes and compatibility groups of explosives.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 2 2014-10-01 2014-10-01 false Classification codes and compatibility groups of... Class 1 § 173.52 Classification codes and compatibility groups of explosives. (a) The classification..., consists of the division number followed by the compatibility group letter. Compatibility group letters are...

ARC-2001-ACD01-0018

NASA Image and Video Library

2001-02-16

New Center Network Deployment ribbon Cutting: from left to right: Maryland Edwards, Code JT upgrade project deputy task manager; Ed Murphy, foundry networks systems engineer; Bohdan Cmaylo, Code JT upgrade project task manager, Scott Santiago, Division Chief, Code JT; Greg Miller, Raytheon Network engineer and Frank Daras, Raytheon network engineering manager.

Layered video transmission over multirate DS-CDMA wireless systems

NASA Astrophysics Data System (ADS)

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

2003-05-01

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

Comparison of FDMA and CDMA for second generation land-mobile satellite communications

NASA Technical Reports Server (NTRS)

Yongacoglu, A.; Lyons, R. G.; Mazur, B. A.

1990-01-01

Code Division Multiple Access (CDMA) and Frequency Division Multiple Access (FDMA) (both analog and digital) systems capacities are compared on the basis of identical link availabilities and physical propagation models. Parameters are optimized for a bandwidth limited, multibeam environment. For CDMA, the benefits of voice activated carriers, antenna discrimination, polarization reuse, return link power control and multipath suppression are included in the analysis. For FDMA, the advantages of bandwidth efficient modulation/coding combinations, voice activated carriers, polarization reuse, beam placement, and frequency staggering were taken into account.

Presentations - Herriott, T.M. and others, 2015 | Alaska Division of

Science.gov Websites

Details Title: Sequence stratigraphic framework of the Upper Jurassic Naknek Formation, Cook Inlet forearc Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of ., Wartes, M.A., and Decker, P.L., 2015, Sequence stratigraphic framework of the Upper Jurassic Naknek

Fiber-Bragg-Grating-Based Optical Code-Division Multiple Access Passive Optical Network Using Dual-Baseband Modulation Scheme

NASA Astrophysics Data System (ADS)

Lin, Wen-Piao; Wu, He-Long

2005-08-01

We propose a fiber-Bragg-grating (FBG)-based optical code-division multiple access passive optical network (OCDMA-PON) using a dual-baseband modulation scheme. A mathematical model is developed to study the performance of this scheme. According to the analyzed results, this scheme can allow a tolerance of the spectral power distortion (SPD) ratio of 25% with a bit error rate (BER) of 10-9 when the modified pseudorandom noise (PN) code length is 16. Moreover, we set up a simulated system to evaluate the baseband and radio frequency (RF) band transmission characteristics. The simulation results demonstrate that our proposed OCDMA-PON can provide a cost-effective and scalable fiber-to-the-home solution.

Stress analysis and evaluation of a rectangular pressure vessel

NASA Astrophysics Data System (ADS)

Rezvani, M. A.; Ziada, H. H.; Shurrab, M. S.

1992-10-01

This study addresses structural analysis and evaluation of an abnormal rectangular pressure vessel, designed to house equipment for drilling and collecting samples from Hanford radioactive waste storage tanks. It had to be qualified according to ASME boiler and pressure vessel code, section 8; however, it had the cover plate bolted along the long face, a configuration not addressed by the code. Finite element method was used to calculate stresses resulting from internal pressure; these stresses were then used to evaluate and qualify the vessel. Fatigue is not a concern; thus, it can be built according to section 8, division 1 instead of division 2. Stress analysis was checked against the code. A stayed plate was added to stiffen the long side of the vessel.

[Transposition errors during learning to reproduce a sequence by the right- and the left-hand movements: simulation of positional and movement coding].

PubMed

Liakhovetskiĭ, V A; Bobrova, E V; Skopin, G N

2012-01-01

Transposition errors during the reproduction of a hand movement sequence make it possible to receive important information on the internal representation of this sequence in the motor working memory. Analysis of such errors showed that learning to reproduce sequences of the left-hand movements improves the system of positional coding (coding ofpositions), while learning of the right-hand movements improves the system of vector coding (coding of movements). Learning of the right-hand movements after the left-hand performance involved the system of positional coding "imposed" by the left hand. Learning of the left-hand movements after the right-hand performance activated the system of vector coding. Transposition errors during learning to reproduce movement sequences can be explained by neural network using either vector coding or both vector and positional coding.

Informational structure of genetic sequences and nature of gene splicing

NASA Astrophysics Data System (ADS)

Trifonov, E. N.

1991-10-01

Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

Dynamic Divisive Normalization Predicts Time-Varying Value Coding in Decision-Related Circuits

PubMed Central

LoFaro, Thomas; Webb, Ryan; Glimcher, Paul W.

2014-01-01

Normalization is a widespread neural computation, mediating divisive gain control in sensory processing and implementing a context-dependent value code in decision-related frontal and parietal cortices. Although decision-making is a dynamic process with complex temporal characteristics, most models of normalization are time-independent and little is known about the dynamic interaction of normalization and choice. Here, we show that a simple differential equation model of normalization explains the characteristic phasic-sustained pattern of cortical decision activity and predicts specific normalization dynamics: value coding during initial transients, time-varying value modulation, and delayed onset of contextual information. Empirically, we observe these predicted dynamics in saccade-related neurons in monkey lateral intraparietal cortex. Furthermore, such models naturally incorporate a time-weighted average of past activity, implementing an intrinsic reference-dependence in value coding. These results suggest that a single network mechanism can explain both transient and sustained decision activity, emphasizing the importance of a dynamic view of normalization in neural coding. PMID:25429145

Characterization and Evolution of Cell Division and Cell Wall Synthesis Genes in the Bacterial Phyla Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes and Phylogenetic Comparison with rRNA Genes▿ †

PubMed Central

Pilhofer, Martin; Rappl, Kristina; Eckl, Christina; Bauer, Andreas Peter; Ludwig, Wolfgang; Schleifer, Karl-Heinz; Petroni, Giulio

2008-01-01

In the past, studies on the relationships of the bacterial phyla Planctomycetes, Chlamydiae, Lentisphaerae, and Verrucomicrobia using different phylogenetic markers have been controversial. Investigations based on 16S rRNA sequence analyses suggested a relationship of the four phyla, showing the branching order Planctomycetes, Chlamydiae, Verrucomicrobia/Lentisphaerae. Phylogenetic analyses of 23S rRNA genes in this study also support a monophyletic grouping and their branching order—this grouping is significant for understanding cell division, since the major bacterial cell division protein FtsZ is absent from members of two of the phyla Chlamydiae and Planctomycetes. In Verrucomicrobia, knowledge about cell division is mainly restricted to the recent report of ftsZ in the closely related genera Prosthecobacter and Verrucomicrobium. In this study, genes of the conserved division and cell wall (dcw) cluster (ddl, ftsQ, ftsA, and ftsZ) were characterized in all verrucomicrobial subdivisions (1 to 4) with cultivable representatives (1 to 4). Sequence analyses and transcriptional analyses in Verrucomicrobia and genome data analyses in Lentisphaerae suggested that cell division is based on FtsZ in all verrucomicrobial subdivisions and possibly also in the sister phylum Lentisphaerae. Comprehensive sequence analyses of available genome data for representatives of Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes strongly indicate that their last common ancestor possessed a conserved, ancestral type of dcw gene cluster and an FtsZ-based cell division mechanism. This implies that Planctomycetes and Chlamydiae may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with Verrucomicrobia. PMID:18310338

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2011 CFR

2011-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2013 CFR

2013-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2014 CFR

2014-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2012 CFR

2012-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

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

NASA Astrophysics Data System (ADS)

Silvester, J. A.

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

SEQassembly: A Practical Tools Program for Coding Sequences Splicing

NASA Astrophysics Data System (ADS)

Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

Cognitive and Neural Sciences Division, 1988 Programs.

ERIC Educational Resources Information Center

Vaughan, Willard S., Ed.

The research and development efforts performed by principal investigators under sponsorship of the Office of Naval Research Cognitive and Neural Sciences Division during 1988 are documented. The title, name and affiliation of the principal investigator, project code, contract number, current end date, technical objective, approach, and progress of…

Correlation approach to identify coding regions in DNA sequences

NASA Technical Reports Server (NTRS)

Ossadnik, S. M.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

1994-01-01

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

Statistical properties of DNA sequences

NASA Technical Reports Server (NTRS)

Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

1995-01-01

We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

Cellulases and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2001-02-20

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Cellulases and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2001-01-01

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Space-time adaptive decision feedback neural receivers with data selection for high-data-rate users in DS-CDMA systems.

PubMed

de Lamare, Rodrigo C; Sampaio-Neto, Raimundo

2008-11-01

A space-time adaptive decision feedback (DF) receiver using recurrent neural networks (RNNs) is proposed for joint equalization and interference suppression in direct-sequence code-division multiple-access (DS-CDMA) systems equipped with antenna arrays. The proposed receiver structure employs dynamically driven RNNs in the feedforward section for equalization and multiaccess interference (MAI) suppression and a finite impulse response (FIR) linear filter in the feedback section for performing interference cancellation. A data selective gradient algorithm, based upon the set-membership (SM) design framework, is proposed for the estimation of the coefficients of RNN structures and is applied to the estimation of the parameters of the proposed neural receiver structure. Simulation results show that the proposed techniques achieve significant performance gains over existing schemes.

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

NASA Astrophysics Data System (ADS)

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

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

A performance analysis of DS-CDMA and SCPC VSAT networks

NASA Technical Reports Server (NTRS)

Hayes, David P.; Ha, Tri T.

1990-01-01

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

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

PubMed

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

2004-03-01

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

Space experiment development process

NASA Technical Reports Server (NTRS)

Depauw, James F.

1987-01-01

Described is a process for developing space experiments utilizing the Space Shuttle. The role of the Principal Investigator is described as well as the Principal Investigator's relation with the project development team. Described also is the sequence of events from an early definition phase through the steps of hardware development. The major interactions between the hardware development program and the Shuttle integration and safety activities are also shown. The presentation is directed to people with limited Shuttle experiment experience. The objective is to summarize the development process, discuss the roles of major participants, and list some lessons learned. Two points should be made at the outset. First, no two projects are the same so the process varies from case to case. Second, the emphasis here is on Code EN/Microgravity Science and Applications Division (MSAD).

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

NASA Astrophysics Data System (ADS)

Hettiarachchi, Ranga; Yokoyama, Mitsuo; Uehara, Hideyuki

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

New Insights into the Formation of Viable but Nonculturable Escherichia coli O157:H7 Induced by High-Pressure CO2

PubMed Central

Zhao, Feng; Wang, Yongtao; An, Haoran; Hu, Xiaosong

2016-01-01

ABSTRACT The formation of viable but nonculturable (VBNC) Escherichia coli O157:H7 induced by high-pressure CO2 (HPCD) was investigated using RNA sequencing (RNA-Seq) transcriptomics and isobaric tag for relative and absolute quantitation (iTRAQ) proteomic methods. The analyses revealed that 97 genes and 56 proteins were significantly changed upon VBNC state entry. Genes and proteins related to membrane transport, central metabolisms, DNA replication, and cell division were mainly downregulated in the VBNC cells. This caused low metabolic activity concurrently with a division arrest in cells, which may be related to VBNC state formation. Cell division repression and outer membrane overexpression were confirmed to be involved in VBNC state formation by homologous expression of z2046 coding for transcriptional repressor and ompF encoding outer membrane protein F. Upon VBNC state entry, pyruvate catabolism in the cells shifted from the tricarboxylic acid (TCA) cycle toward the fermentative route; this led to a low level of ATP. Combating the low energy supply, ATP production in the VBNC cells was compensated by the degradation of l-serine and l-threonine, the increased AMP generation, and the enhanced electron transfer. Furthermore, tolerance of the cells with respect to HPCD-induced acid, oxidation, and high CO2 stresses was enhanced by promoting the production of ammonia and NADPH and by reducing CO2 production during VBNC state formation. Most genes and proteins related to pathogenicity were downregulated in the VBNC cells. This would decrease the cell pathogenicity, which was confirmed by adhesion assays. In conclusion, the decreased metabolic activity, repressed cell division, and enhanced survival ability in E. coli O157:H7 might cause HPCD-induced VBNC state formation. PMID:27578754

Analysis of secured Optical Orthogonal Frequency Division Multiplexed System

NASA Astrophysics Data System (ADS)

Gill, Harsimranjit Singh; Bhatia, Kamaljit Singh; Gill, Sandeep Singh

2017-05-01

In this paper, security issues for optical orthogonal frequency division multiplexed (OFDM) systems are emphasized. The encryption has been done on the data of coded OFDM symbols using data encryption standard (DES) algorithm before transmitting through the fiber. The results obtained justify that the DES provides better security to the input data without further bandwidth requirement. The data is transmitted to a distance of 1,000 km in a single-mode fiber with 16-quadrature amplitude modulation. The peak-to-average power ratio and optical signal-to-noise ratio of secure coded OFDM signal is fairly better than the conventional OFDM signal.

Dual-balanced detection scheme with optical hard-limiters in an optical code division multiple access system

NASA Astrophysics Data System (ADS)

Liu, Maw-Yang; Hsu, Yi-Kai

2017-03-01

Three-arm dual-balanced detection scheme is studied in an optical code division multiple access system. As the MAI and beat noise are the main deleterious source of system performance, we utilize optical hard-limiters to alleviate such channel impairment. In addition, once the channel condition is improved effectively, the proposed two-dimensional error correction code can remarkably enhance the system performance. In our proposed scheme, the optimal thresholds of optical hard-limiters and decision circuitry are fixed, and they will not change with other system parameters. Our proposed scheme can accommodate a large number of users simultaneously and is suitable for burst traffic with asynchronous transmission. Therefore, it is highly recommended as the platform for broadband optical access network.

Code-division multiple-access multiuser demodulator by using quantum fluctuations.

PubMed

Otsubo, Yosuke; Inoue, Jun-Ichi; Nagata, Kenji; Okada, Masato

2014-07-01

We examine the average-case performance of a code-division multiple-access (CDMA) multiuser demodulator in which quantum fluctuations are utilized to demodulate the original message within the context of Bayesian inference. The quantum fluctuations are built into the system as a transverse field in the infinite-range Ising spin glass model. We evaluate the performance measurements by using statistical mechanics. We confirm that the CDMA multiuser modulator using quantum fluctuations achieve roughly the same performance as the conventional CDMA multiuser modulator through thermal fluctuations on average. We also find that the relationship between the quality of the original information retrieval and the amplitude of the transverse field is somehow a "universal feature" in typical probabilistic information processing, viz., in image restoration, error-correcting codes, and CDMA multiuser demodulation.

Code-division multiple-access multiuser demodulator by using quantum fluctuations

NASA Astrophysics Data System (ADS)

Otsubo, Yosuke; Inoue, Jun-ichi; Nagata, Kenji; Okada, Masato

2014-07-01

We examine the average-case performance of a code-division multiple-access (CDMA) multiuser demodulator in which quantum fluctuations are utilized to demodulate the original message within the context of Bayesian inference. The quantum fluctuations are built into the system as a transverse field in the infinite-range Ising spin glass model. We evaluate the performance measurements by using statistical mechanics. We confirm that the CDMA multiuser modulator using quantum fluctuations achieve roughly the same performance as the conventional CDMA multiuser modulator through thermal fluctuations on average. We also find that the relationship between the quality of the original information retrieval and the amplitude of the transverse field is somehow a "universal feature" in typical probabilistic information processing, viz., in image restoration, error-correcting codes, and CDMA multiuser demodulation.

Multiple Access Schemes for Lunar Missions

NASA Technical Reports Server (NTRS)

Deutsch, Leslie; Hamkins, Jon; Stocklin, Frank J.

2010-01-01

Two years ago, the NASA Coding, Modulation, and Link Protocol (CMLP) study was completed. The study, led by the authors of this paper, recommended codes, modulation schemes, and desired attributes of link protocols for all space communication links in NASA's future space architecture. Portions of the NASA CMLP team were reassembled to resolve one open issue: the use of multiple access (MA) communication from the lunar surface. The CMLP-MA team analyzed and simulated two candidate multiple access schemes that were identified in the original CMLP study: Code Division MA (CDMA) and Frequency Division MA (FDMA) based on a bandwidth-efficient Continuous Phase Modulation (CPM) with a superimposed Pseudo-Noise (PN) ranging signal (CPM/PN). This paper summarizes the results of the analysis and simulation of the CMLP-MA study and describes the final recommendations.

Code Verification Results of an LLNL ASC Code on Some Tri-Lab Verification Test Suite Problems

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

Anderson, S R; Bihari, B L; Salari, K

As scientific codes become more complex and involve larger numbers of developers and algorithms, chances for algorithmic implementation mistakes increase. In this environment, code verification becomes essential to building confidence in the code implementation. This paper will present first results of a new code verification effort within LLNL's B Division. In particular, we will show results of code verification of the LLNL ASC ARES code on the test problems: Su Olson non-equilibrium radiation diffusion, Sod shock tube, Sedov point blast modeled with shock hydrodynamics, and Noh implosion.

Advanced MR Imaging of the Human Nucleus Accumbens--Additional Guiding Tool for Deep Brain Stimulation.

PubMed

Lucas-Neto, Lia; Reimão, Sofia; Oliveira, Edson; Rainha-Campos, Alexandre; Sousa, João; Nunes, Rita G; Gonçalves-Ferreira, António; Campos, Jorge G

2015-07-01

The human nucleus accumbens (Acc) has become a target for deep brain stimulation (DBS) in some neuropsychiatric disorders. Nonetheless, even with the most recent advances in neuroimaging it remains difficult to accurately delineate the Acc and closely related subcortical structures, by conventional MRI sequences. It is our purpose to perform a MRI study of the human Acc and to determine whether there are reliable anatomical landmarks that enable the precise location and identification of the nucleus and its core/shell division. For the Acc identification and delineation, based on anatomical landmarks, T1WI, T1IR and STIR 3T-MR images were acquired in 10 healthy volunteers. Additionally, 32-direction DTI was obtained for Acc segmentation. Seed masks for the Acc were generated with FreeSurfer and probabilistic tractography was performed using FSL. The probability of connectivity between the seed voxels and distinct brain areas was determined and subjected to k-means clustering analysis, defining 2 different regions. With conventional T1WI, the Acc borders are better defined through its surrounding anatomical structures. The DTI color-coded vector maps and IR sequences add further detail in the Acc identification and delineation. Additionally, using probabilistic tractography it is possible to segment the Acc into a core and shell division and establish its structural connectivity with different brain areas. Advanced MRI techniques allow in vivo delineation and segmentation of the human Acc and represent an additional guiding tool in the precise and safe target definition for DBS. © 2015 International Neuromodulation Society.

Sequence of structures in fine-grained turbidites: Comparison of recent deep-sea and ancient flysch sediments

NASA Astrophysics Data System (ADS)

Stow, Dorrik A. V.; Shanmugam, Ganapathy

1980-01-01

A comparative study of the sequence of sedimentary structures in ancient and modern fine-grained turbidites is made in three contrasting areas. They are (1) Holocene and Pleistocene deep-sea muds of the Nova Scotian Slope and Rise, (2) Middle Ordovician Sevier Shale of the Valley and Ridge Province of the Southern Appalachians, and (3) Cambro-Ordovician Halifax Slate of the Meguma Group in Nova Scotia. A standard sequence of structures is proposed for fine-grained turbidites. The complete sequence has nine sub-divisions that are here termed T 0 to T 8. "The lower subdivision (T 0) comprises a silt lamina which has a sharp, scoured and load-cast base, internal parallel-lamination and cross-lamination, and a sharp current-lineated or wavy surface with 'fading-ripples' (= Type C etc. …)." (= Type C ripple-drift cross-lamination, Jopling and Walker, 1968). The overlying sequence shows textural and compositional grading through alternating silt and mud laminae. A convolute-laminated sub-division (T 1) is overlain by low-amplitude climbing ripples (T 2), thin regular laminae (T 3), thin indistinct laminae (T 4), and thin wipsy or convolute laminae (T 5). The topmost three divisions, graded mud (T 6), ungraded mud (T 7) and bioturbated mud (T 8), do not have silt laminae but rare patchy silt lenses and silt pseudonodules and a thin zone of micro-burrowing near the upper surface. The proposed sequence is analogous to the Bouma (1962) structural scheme for sandy turbidites and is approximately equivalent to Bouma's (C)DE divisions. The repetition of partial sequences characterizes different parts of the slope/base-of-slope/basin plain environment, and represents deposition from different stages of evolution of a large, muddy, turbidity flow. Microstructural detail and sequence are well preserved in ancient and even slightly metamorphosed sediments. Their recognition is important for determining depositional processes and for palaeoenvironmental interpretation.

Population genetics of Vibrio vulnificus: identification of two divisions and a distinct eel-pathogenic clone.

PubMed

Gutacker, Michaela; Conza, Nadine; Benagli, Cinzia; Pedroli, Ambra; Bernasconi, Marco Valerio; Permin, Lise; Aznar, Rosa; Piffaretti, Jean-Claude

2003-06-01

Genetic relationships among 62 Vibrio vulnificus strains of different geographical and host origins were analyzed by multilocus enzyme electrophoresis (MLEE), random amplification of polymorphic DNA (RAPD), and sequence analyses of the recA and glnA genes. Out of 15 genetic loci analyzed by MLEE, 11 were polymorphic. Cluster analysis identified 43 distinct electrophoretic types (ETs) separating the V. vulnificus population into two divisions (divisions I and II). One ET (ET 35) included all indole-negative isolates from diseased eels worldwide (biotype 2). A second ET (ET 2) marked all of the strains from Israel isolated from patients who handled St. Peter's fish (biotype 3). RAPD analysis of the 62 V. vulnificus isolates identified 26 different profiles separated into two divisions as well. In general, this subdivision was comparable (but not identical) to that observed by MLEE. Phylogenetic analysis of 543 bp of the recA gene and of 402 bp of the glnA gene also separated the V. vulnificus population into two major divisions in a manner similar to that by MLEE and RAPD. Sequence data again indicated the overall subdivision of the V. vulnificus population into different biotypes. In particular, indole-negative eel-pathogenic isolates (biotype 2) on one hand and the Israeli isolates (biotype 3) on the other tended to cluster together in both gene trees. None of the methods showed an association between distinct clones and human clinical manifestations. Furthermore, except for the Israeli strains, only minor clusters comprising geographically related isolates were observed. In conclusion, all three approaches (MLEE, RAPD, and DNA sequencing) generated comparable but not always equivalent results. The significance of the two divisions (divisions I and II) still remains to be clarified, and a reevaluation of the definition of the biotypes is also needed.

75 FR 19339 - FM Table of Allotments, Amboy, California

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-14

.... SUMMARY: The Audio Division seeks comments on a petition filed by Sunnylands Broadcasting, LLC, proposing... disabilities (Braille, large print, electronic files, audio format), send an e-mail to [email protected] or call... Chief, Audio Division, Media Bureau. [FR Doc. 2010-8449 Filed 4-13-10; 8:45 am] BILLING CODE 6712-01-S ...

75 FR 37881 - Surety Companies Acceptable on Federal Bonds-Change in State of Incorporation United States...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-30

..., Financial Management Service, Financial Accounting and Services Division, Surety Bond Branch, 3700 East-West..., Financial Accounting and Services Division. [FR Doc. 2010-15614 Filed 6-29-10; 8:45 am] BILLING CODE 4810-35... State of Incorporation United States Fidelity and Guaranty Company AGENCY: Financial Management Service...

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

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

Expeditionary Warfare Division Meeting (10th) Held in Panama City, Florida on 24-27 October 2005

DTIC Science & Technology

2005-10-01

Seabasing a TRANSCOM Perspective, by Captain Craig Galloway, USN, US Transportation Command, J5A DLA Afloat, by Col Jeff Hill, Chief, Distribution ... Management Division, Defense Logistics Agency Sustaining the Seabase a View…, by Mr. Nicholas Linkowitz, HQMC I&L (Code LPV) Sustaining the Sea Base

Annual Report: Discipline, Crime, and Violence, School Year 2008-2009

ERIC Educational Resources Information Center

Virginia Department of Education, 2011

2011-01-01

The "Code of Virginia" requires school divisions statewide to submit data to the Virginia Department of Education (VDOE) on incidents of discipline, crime, and violence (DCV). School divisions began reporting such data in 1991. This annual report focuses primarily on DCV data submitted for school year 2008-2009, with selected comparisons…

Annual Report: Discipline, Crime, and Violence, School Year 2009-2010

ERIC Educational Resources Information Center

Virginia Department of Education, 2011

2011-01-01

The "Code of Virginia" requires school divisions statewide to submit data to the Virginia Department of Education (VDOE) on incidents of discipline, crime, and violence (DCV). School divisions began reporting such data in 1991. This annual report focuses primarily on DCV data submitted for school year 2009-2010, with selected comparisons…

77 FR 43859 - Notice of Lodging of Consent Decree Under the Comprehensive Environmental Response, Compensation...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-26

... Assistant Attorney General, Environment and Natural Resources Division, and either emailed to pubcomment-ees..., Environment and Natural Resources Division. [FR Doc. 2012-18191 Filed 7-25-12; 8:45 am] BILLING CODE 4410-15-P ... DEPARTMENT OF JUSTICE Notice of Lodging of Consent Decree Under the Comprehensive Environmental...

Annual Report: Discipline, Crime, and Violence, School Year 2007-2008

ERIC Educational Resources Information Center

Virginia Department of Education, 2009

2009-01-01

The "Code of Virginia" requires school divisions statewide to submit data to the Virginia Department of Education (VDOE) on incidents of discipline, crime, and violence (DCV). School divisions began reporting such data in 1991. This annual report focuses primarily on DCV data submitted for school year 2007-2008, with selected comparisons…

Annual Report: Discipline, Crime, and Violence, School Year 2006-2007

ERIC Educational Resources Information Center

Virginia Department of Education, 2008

2008-01-01

The "Code of Virginia" requires school divisions statewide to submit data to the Virginia Department of Education (VDOE) on incidents of discipline, crime, and violence (DCV). School divisions began reporting such data in 1991. This annual report focuses primarily on DCV data submitted for school year 2006-2007, with selected comparisons…

Annual Report: Discipline, Crime, and Violence, School Year 2004-2005

ERIC Educational Resources Information Center

Virginia Department of Education, 2006

2006-01-01

The "Code of Virginia" (Section 22.1-279.3:1) requires school divisions statewide to submit data annually to the Virginia Department of Education (VDOE) on incidents of discipline, crime, and violence (DCV). School divisions began reporting data on discipline, crime, and violence to the VDOE in 1991. The federal "Gun-Free Schools…

17 CFR 17.03 - Delegation of authority to the Director of the Division of Market Oversight.

Code of Federal Regulations, 2010 CFR

2010-04-01

... information using the format, coding structure or electronic data transmission procedures otherwise required...) Pursuant to § 17.00(a), the authority to approve a format and coding structure other than that set forth in...

Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

PubMed Central

Hall, L; Laird, J E; Craig, R K

1984-01-01

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375

DNA barcode goes two-dimensions: DNA QR code web server.

PubMed

Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

USGS Publications Warehouse

Sahl, J.W.; Schmidt, R.; Swanner, E.D.; Mandernack, K.W.; Templeton, A.S.; Kieft, Thomas L.; Smith, R.L.; Sanford, W.E.; Callaghan, R.L.; Mitton, J.B.; Spear, J.R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Lichenase and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2000-08-15

The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding sequence, recombinant DNA molecules comprising the lichenase coding sequences, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.

Construction and characterization of normalized cDNA libraries by 454 pyrosequencing and estimation of DNA methylation levels in three distantly related termite species.

PubMed

Hayashi, Yoshinobu; Shigenobu, Shuji; Watanabe, Dai; Toga, Kouhei; Saiki, Ryota; Shimada, Keisuke; Bourguignon, Thomas; Lo, Nathan; Hojo, Masaru; Maekawa, Kiyoto; Miura, Toru

2013-01-01

In termites, division of labor among castes, categories of individuals that perform specialized tasks, increases colony-level productivity and is the key to their ecological success. Although molecular studies on caste polymorphism have been performed in termites, we are far from a comprehensive understanding of the molecular basis of this phenomenon. To facilitate future molecular studies, we aimed to construct expressed sequence tag (EST) libraries covering wide ranges of gene repertoires in three representative termite species, Hodotermopsis sjostedti, Reticulitermes speratus and Nasutitermes takasagoensis. We generated normalized cDNA libraries from whole bodies, except for guts containing microbes, of almost all castes, sexes and developmental stages and sequenced them with the 454 GS FLX titanium system. We obtained >1.2 million quality-filtered reads yielding >400 million bases for each of the three species. Isotigs, which are analogous to individual transcripts, and singletons were produced by assembling the reads and annotated using public databases. Genes related to juvenile hormone, which plays crucial roles in caste differentiation of termites, were identified from the EST libraries by BLAST search. To explore the potential for DNA methylation, which plays an important role in caste differentiation of honeybees, tBLASTn searches for DNA methyltransferases (dnmt1, dnmt2 and dnmt3) and methyl-CpG binding domain (mbd) were performed against the EST libraries. All four of these genes were found in the H. sjostedti library, while all except dnmt3 were found in R. speratus and N. takasagoensis. The ratio of the observed to the expected CpG content (CpG O/E), which is a proxy for DNA methylation level, was calculated for the coding sequences predicted from the isotigs and singletons. In all of the three species, the majority of coding sequences showed depletion of CpG O/E (less than 1), and the distributions of CpG O/E were bimodal, suggesting the presence of DNA methylation.

Construction and Characterization of Normalized cDNA Libraries by 454 Pyrosequencing and Estimation of DNA Methylation Levels in Three Distantly Related Termite Species

PubMed Central

Hayashi, Yoshinobu; Shigenobu, Shuji; Watanabe, Dai; Toga, Kouhei; Saiki, Ryota; Shimada, Keisuke; Bourguignon, Thomas; Lo, Nathan; Hojo, Masaru; Maekawa, Kiyoto; Miura, Toru

2013-01-01

In termites, division of labor among castes, categories of individuals that perform specialized tasks, increases colony-level productivity and is the key to their ecological success. Although molecular studies on caste polymorphism have been performed in termites, we are far from a comprehensive understanding of the molecular basis of this phenomenon. To facilitate future molecular studies, we aimed to construct expressed sequence tag (EST) libraries covering wide ranges of gene repertoires in three representative termite species, Hodotermopsis sjostedti , Reticulitermessperatus and Nasutitermestakasagoensis . We generated normalized cDNA libraries from whole bodies, except for guts containing microbes, of almost all castes, sexes and developmental stages and sequenced them with the 454 GS FLX titanium system. We obtained >1.2 million quality-filtered reads yielding >400 million bases for each of the three species. Isotigs, which are analogous to individual transcripts, and singletons were produced by assembling the reads and annotated using public databases. Genes related to juvenile hormone, which plays crucial roles in caste differentiation of termites, were identified from the EST libraries by BLAST search. To explore the potential for DNA methylation, which plays an important role in caste differentiation of honeybees, tBLASTn searches for DNA methyltransferases (dnmt1, dnmt2 and dnmt3) and methyl-CpG binding domain (mbd) were performed against the EST libraries. All four of these genes were found in the H . sjostedti library, while all except dnmt3 were found in R . speratus and N . takasagoensis . The ratio of the observed to the expected CpG content (CpG O/E), which is a proxy for DNA methylation level, was calculated for the coding sequences predicted from the isotigs and singletons. In all of the three species, the majority of coding sequences showed depletion of CpG O/E (less than 1), and the distributions of CpG O/E were bimodal, suggesting the presence of DNA methylation. PMID:24098800

Dynamic divisive normalization predicts time-varying value coding in decision-related circuits.

PubMed

Louie, Kenway; LoFaro, Thomas; Webb, Ryan; Glimcher, Paul W

2014-11-26

Normalization is a widespread neural computation, mediating divisive gain control in sensory processing and implementing a context-dependent value code in decision-related frontal and parietal cortices. Although decision-making is a dynamic process with complex temporal characteristics, most models of normalization are time-independent and little is known about the dynamic interaction of normalization and choice. Here, we show that a simple differential equation model of normalization explains the characteristic phasic-sustained pattern of cortical decision activity and predicts specific normalization dynamics: value coding during initial transients, time-varying value modulation, and delayed onset of contextual information. Empirically, we observe these predicted dynamics in saccade-related neurons in monkey lateral intraparietal cortex. Furthermore, such models naturally incorporate a time-weighted average of past activity, implementing an intrinsic reference-dependence in value coding. These results suggest that a single network mechanism can explain both transient and sustained decision activity, emphasizing the importance of a dynamic view of normalization in neural coding. Copyright © 2014 the authors 0270-6474/14/3416046-12$15.00/0.

On the Application of Time-Reversed Space-Time Block Code to Aeronautical Telemetry

DTIC Science & Technology

2014-06-01

Keying (SOQPSK), bit error rate (BER), Orthogonal Frequency Division Multiplexing ( OFDM ), Generalized time-reversed space-time block codes (GTR-STBC) 16...Alamouti code [4]) is optimum [2]. Although OFDM is generally applied on a per subcarrier basis in frequency selective fading, it is not a viable...Calderbank, “Finite-length MIMO decision feedback equal- ization for space-time block-coded signals over multipath-fading channels,” IEEE Transac- tions on

Throughput of Coded Optical CDMA Systems with AND Detectors

NASA Astrophysics Data System (ADS)

Memon, Kehkashan A.; Umrani, Fahim A.; Umrani, A. W.; Umrani, Naveed A.

2012-09-01

Conventional detection techniques used in optical code-division multiple access (OCDMA) systems are not optimal and result in poor bit error rate performance. This paper analyzes the coded performance of optical CDMA systems with AND detectors for enhanced throughput efficiencies and improved error rate performance. The results show that the use of AND detectors significantly improve the performance of an optical channel.

Chiasmatic and achiasmatic inverted meiosis of plants with holocentric chromosomes

PubMed Central

Cabral, Gabriela; Marques, André; Schubert, Veit; Pedrosa-Harand, Andrea; Schlögelhofer, Peter

2014-01-01

Meiosis is a specialized cell division in sexually reproducing organisms before gamete formation. Following DNA replication, the canonical sequence in species with monocentric chromosomes is characterized by reductional segregation of homologous chromosomes during the first and equational segregation of sister chromatids during the second meiotic division. Species with holocentric chromosomes employ specific adaptations to ensure regular disjunction during meiosis. Here we present the analysis of two closely related plant species with holocentric chromosomes that display an inversion of the canonical meiotic sequence, with the equational division preceding the reductional. In-depth analysis of the meiotic divisions of Rhynchospora pubera and R. tenuis reveals that during meiosis I sister chromatids are bi-oriented, display amphitelic attachment to the spindle and are subsequently separated. During prophase II, chromatids are connected by thin chromatin threads that appear instrumental for the regular disjunction of homologous non-sister chromatids in meiosis II. PMID:25295686

Studying Functions of All Yeast Genes Simultaneously

NASA Technical Reports Server (NTRS)

Stolc, Viktor; Eason, Robert G.; Poumand, Nader; Herman, Zelek S.; Davis, Ronald W.; Anthony Kevin; Jejelowo, Olufisayo

2006-01-01

A method of studying the functions of all the genes of a given species of microorganism simultaneously has been developed in experiments on Saccharomyces cerevisiae (commonly known as baker's or brewer's yeast). It is already known that many yeast genes perform functions similar to those of corresponding human genes; therefore, by facilitating understanding of yeast genes, the method may ultimately also contribute to the knowledge needed to treat some diseases in humans. Because of the complexity of the method and the highly specialized nature of the underlying knowledge, it is possible to give only a brief and sketchy summary here. The method involves the use of unique synthetic deoxyribonucleic acid (DNA) sequences that are denoted as DNA bar codes because of their utility as molecular labels. The method also involves the disruption of gene functions through deletion of genes. Saccharomyces cerevisiae is a particularly powerful experimental system in that multiple deletion strains easily can be pooled for parallel growth assays. Individual deletion strains recently have been created for 5,918 open reading frames, representing nearly all of the estimated 6,000 genetic loci of Saccharomyces cerevisiae. Tagging of each deletion strain with one or two unique 20-nucleotide sequences enables identification of genes affected by specific growth conditions, without prior knowledge of gene functions. Hybridization of bar-code DNA to oligonucleotide arrays can be used to measure the growth rate of each strain over several cell-division generations. The growth rate thus measured serves as an index of the fitness of the strain.

FRAGS: estimation of coding sequence substitution rates from fragmentary data

PubMed Central

Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

2004-01-01

Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

Visual pattern image sequence coding

NASA Technical Reports Server (NTRS)

Silsbee, Peter; Bovik, Alan C.; Chen, Dapang

1990-01-01

The visual pattern image coding (VPIC) configurable digital image-coding process is capable of coding with visual fidelity comparable to the best available techniques, at compressions which (at 30-40:1) exceed all other technologies. These capabilities are associated with unprecedented coding efficiencies; coding and decoding operations are entirely linear with respect to image size and entail a complexity that is 1-2 orders of magnitude faster than any previous high-compression technique. The visual pattern image sequence coding to which attention is presently given exploits all the advantages of the static VPIC in the reduction of information from an additional, temporal dimension, to achieve unprecedented image sequence coding performance.

75 FR 61530 - Issuance of Regulatory Guides

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-05

... Materials Code Case Acceptability, ASME Section III,'' and RG 1.147, Rev. 16, ``Inservice Inspection Code Case Acceptability, ASME Section XI, Division 1.'' FOR FURTHER INFORMATION CONTACT: Wallace E. Norris... specific problems or postulated accidents, and data the staff needs in its review of applications for...

Distributed magnetic field positioning system using code division multiple access

NASA Technical Reports Server (NTRS)

Prigge, Eric A. (Inventor)

2003-01-01

An apparatus and methods for a magnetic field positioning system use a fundamentally different, and advantageous, signal structure and multiple access method, known as Code Division Multiple Access (CDMA). This signal architecture, when combined with processing methods, leads to advantages over the existing technologies, especially when applied to a system with a large number of magnetic field generators (beacons). Beacons at known positions generate coded magnetic fields, and a magnetic sensor measures a sum field and decomposes it into component fields to determine the sensor position and orientation. The apparatus and methods can have a large `building-sized` coverage area. The system allows for numerous beacons to be distributed throughout an area at a number of different locations. A method to estimate position and attitude, with no prior knowledge, uses dipole fields produced by these beacons in different locations.

Architecture design and performance evaluation of multigranularity optical networks based on optical code division multiplexing

NASA Astrophysics Data System (ADS)

Huang, Shaowei; Baba, Ken-Ichi; Murata, Masayuki; Kitayama, Ken-Ichi

2006-12-01

In traditional lambda-based multigranularity optical networks, a lambda is always treated as the basic routing unit, resulting in low wavelength utilization. On the basis of optical code division multiplexing (OCDM) technology, a novel OCDM-based multigranularity optical cross-connect (MG-OXC) is proposed. Compared with the traditional lambda-based MG-OXC, its switching capability has been extended to support fiber switching, waveband switching, lambda switching, and OCDM switching. In a network composed of OCDM-based MG-OXCs, a single wavelength can be shared by distinct label switched paths (LSPs) called OCDM-LSPs, and OCDM-LSP switching can be implemented in the optical domain. To improve the network flexibility for an OCDM-LSP provisioning, two kinds of switches enabling hybrid optical code (OC)-wavelength conversion are designed. Simulation results indicate that a blocking probability reduction of 2 orders can be obtained by deploying only five OCs to a single wavelength. Furthermore, compared with time-division-multiplexing LSP (TDM-LSP), owing to the asynchronous accessibility and the OC conversion, OCDM-LSPs have been shown to permit a simpler switch architecture and achieve better blocking performance than TDM-LSPs.

Quadriphase DS-CDMA wireless communication systems employing the generalized detector

NASA Astrophysics Data System (ADS)

Tuzlukov, Vyacheslav

2012-05-01

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

Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads

PubMed Central

Jiang, Guo-Feng; Hinsinger, Damien Daniel; Strijk, Joeri Sergej

2016-01-01

Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group. PMID:27558458

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

PubMed

Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

2011-01-01

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

Chromosome Dynamics Visualized with an Anti-Centromeric Histone H3 Antibody in Allium

PubMed Central

Nagaki, Kiyotaka; Yamamoto, Maki; Yamaji, Naoki; Mukai, Yasuhiko; Murata, Minoru

2012-01-01

Due to the ease with which chromosomes can be observed, the Allium species, and onion in particular, have been familiar materials employed in cytogenetic experiments in biology. In this study, centromeric histone H3 (CENH3)-coding cDNAs were identified in four Allium species (onion, welsh onion, garlic and garlic chives) and cloned. Anti-CENH3 antibody was then raised against a deduced amino acid sequence of CENH3 of welsh onion. The antibody recognized all CENH3 orthologs of the Allium species tested. Immunostaining with the antibody enabled clear visualization of chromosome behavior during mitosis in the species. Furthermore, three-dimensional (3D) observation of mitotic cell division was achieved by subjecting root sections to immunohistochemical techniques. The 3D dynamics of the cells and position of cell-cycle marker proteins (CENH3 and α-tubulin) were clearly revealed by immunohistochemical staining with the antibodies. The immunohistochemical analysis made it possible to establish an overview of the location of dividing cells in the root tissues. This breakthrough in technique, in addition to the two centromeric DNA sequences isolated from welsh onion by chromatin immuno-precipitation using the antibody, should lead to a better understanding of plant cell division. A phylogenetic analysis of Allium CENH3s together with the previously reported plant CENH3s showed two separate clades for monocot species tested. One clade was made from CENH3s of the Allium species with those of Poaceae species, and the other from CENH3s of a holocentric species (Luzula nivea). These data may imply functional differences of CENH3s between holocentric and monocentric species. Centromeric localization of DNA sequences isolated from welsh onion by chromatin immuno-precipitation (ChIP) using the antibody was confirmed by fluorescence in situ hybridization and ChIP-quantitative PCR. PMID:23236469

Physical structure and chromosomal localization of a gene encoding human p58[sup clk-1], a cell division control related protein kinase

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

Eipers, P.G.

1992-01-01

The gene for the human p58[sup clk[minus]1] protein kinase, a cell division control-related gene, has been mapped by somatic cell hybrid analyses, in situ localization with the chromosomal gene, and nested polymerase chain reaction amplification of microdissected chromosomes. These studies indicate that the expressed p58[sup clk[minus]1] chromosomal gene maps to 1p36, while a highly related p58[sup clk[minus]1] sequence of unknown nature maps to chromosome 15. Assignment of a p34[sup cdc2]-related gene to 1p36 region, including neuroblastoma, ductal carcinoma of the breast, malignant melanoma, Merkel cell carcinoma and endocrine neoplasia among others. Aberrant expression of this protein kinase negatively regulates normalmore » cellular growth. The p58[sup clk[minus]1] protein contains a central domain of 299 amino acids that is 46% identical to human p34[sup cdc2], the master mitotic protein kinase. This dissertation details the complete structure of the p58[sup clk[minus]1] chromosomal gene, including its putative promoter region, transcriptional start sites, exonic sequences, and intron/exon boundary sequences. The gene is 10 kb in size and contains 12 exons and 11 introns. Interestingly, the rather large 2.0 kb 3[prime] untranslated region is interrupted by an intron that separates a region containing numerous AUUUA destabilization motifs from the coding region. Furthermore, the expression of this gene in normal human tissues, as well as several human tumor cell samples and lines, is examined. The origin of multiple human transcripts from the same chromosomal gene, and the possible differential stability of these various transcripts, is discussed with regard to the transcriptional and post-transcriptional regulation of this gene. This is the first report of the chromosomal gene structure of a member of the p34[sup cdc2] supergene family.« less

75 FR 19338 - FM TABLE OF ALLOTMENTS, Milford, Utah

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-14

.... SUMMARY: The Audio Division seeks comments on a petition filed by Canyon Media Group, LLC, authorized..., large print, electronic files, audio format), send an e-mail to [email protected] or call the Consumer... Chief, Audio Division, Media Bureau. [FR Doc. 2010-8448 Filed 4-13-10; 8:45 am] BILLING CODE 6712-01-S ...

Technology Transfer Summary Report (FY92), Naval Surface Warfare Center Dahlgren Division

DTIC Science & Technology

1994-04-20

communications; no formal records are kept of these. Community Technical Outreach NSWCDD participates in the "Science and Engineering Apprentice" and the " Bay ...ADMINISTRATOR’S OFFICE NAVAL UNDERSEA WARFARE CENTER PO BOX 545 DIVISION NEWPORT SEQUIM WA 98382 NEWPORI’ RI 02841-5047 ATTN GIFT AND EXCHANGE DIV 4 ATTN CODE 00

78 FR 22295 - Notice of Lodging of Proposed Consent Decree Under the Comprehensive Environmental Response...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

... claims for natural resource damages and assessment costs (``NRD'') of the United States Department of... should be addressed to the Assistant Attorney General, Environment and Natural Resources Division, and..., Environment and Natural Resources Division. [FR Doc. 2013-08719 Filed 4-12-13; 8:45 am] BILLING CODE 4410-15-P ...

Management Auditing

DTIC Science & Technology

1975-09-01

Programs Psychological Sciences Division Office of Naval Research Contract No. N00014-74-A-0436-0001 NR 151-370 Approved for public release...Supported By Commandant of the Marine Corps (Code RD) And Monitored By Personnel and Training Research Programs Psychological Sciences Division...balance 6. Test for effectiveness 7. Search for problems 8. Ascertain solutions 9« Determine alternatives 10. Seek out methods for improvement

Annual Report: Discipline, Crime, and Violence, School Year 2010-2011

ERIC Educational Resources Information Center

Virginia Department of Education, 2012

2012-01-01

The "Code of Virginia" (Section 22.1-279.3:1) requires school divisions statewide to submit data to the Virginia Department of Education (VDOE) on incidents of discipline, crime, and violence (DCV). School divisions began reporting such data in 1991. This annual report focuses primarily on DCV data submitted for school year 2010-2011,…

Discrete Cosine Transform Image Coding With Sliding Block Codes

NASA Astrophysics Data System (ADS)

Divakaran, Ajay; Pearlman, William A.

1989-11-01

A transform trellis coding scheme for images is presented. A two dimensional discrete cosine transform is applied to the image followed by a search on a trellis structured code. This code is a sliding block code that utilizes a constrained size reproduction alphabet. The image is divided into blocks by the transform coding. The non-stationarity of the image is counteracted by grouping these blocks in clusters through a clustering algorithm, and then encoding the clusters separately. Mandela ordered sequences are formed from each cluster i.e identically indexed coefficients from each block are grouped together to form one dimensional sequences. A separate search ensues on each of these Mandela ordered sequences. Padding sequences are used to improve the trellis search fidelity. The padding sequences absorb the error caused by the building up of the trellis to full size. The simulations were carried out on a 256x256 image ('LENA'). The results are comparable to any existing scheme. The visual quality of the image is enhanced considerably by the padding and clustering.

DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

PubMed Central

Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, “DNA barcode” actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications. PMID:22574113

LDPC coded OFDM over the atmospheric turbulence channel.

PubMed

Djordjevic, Ivan B; Vasic, Bane; Neifeld, Mark A

2007-05-14

Low-density parity-check (LDPC) coded optical orthogonal frequency division multiplexing (OFDM) is shown to significantly outperform LDPC coded on-off keying (OOK) over the atmospheric turbulence channel in terms of both coding gain and spectral efficiency. In the regime of strong turbulence at a bit-error rate of 10(-5), the coding gain improvement of the LDPC coded single-side band unclipped-OFDM system with 64 sub-carriers is larger than the coding gain of the LDPC coded OOK system by 20.2 dB for quadrature-phase-shift keying (QPSK) and by 23.4 dB for binary-phase-shift keying (BPSK).

46 CFR 54.01-1 - Incorporation by reference.

Code of Federal Regulations, 2012 CFR

2012-10-01

...://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. The material is also...) American Society of Mechanical Engineers (ASME) International, Three Park Avenue, New York, NY 10016-5990: (1) ASME Boiler and Pressure Vessel Code, Section VIII, Division 1, Rules for Construction of...

46 CFR 54.01-1 - Incorporation by reference.

Code of Federal Regulations, 2011 CFR

2011-10-01

...://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. The material is also...) American Society of Mechanical Engineers (ASME) International, Three Park Avenue, New York, NY 10016-5990: (1) ASME Boiler and Pressure Vessel Code, Section VIII, Division 1, Rules for Construction of...

46 CFR 54.01-1 - Incorporation by reference.

Code of Federal Regulations, 2013 CFR

2013-10-01

...://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. The material is also... of Mechanical Engineers (ASME) International, Three Park Avenue, New York, NY 10016-5990: (1) ASME Boiler and Pressure Vessel Code, Section VIII, Division 1, Rules for Construction of Pressure Vessels...

46 CFR 54.01-1 - Incorporation by reference.

Code of Federal Regulations, 2014 CFR

2014-10-01

...://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html. The material is also... of Mechanical Engineers (ASME) International, Three Park Avenue, New York, NY 10016-5990: (1) ASME Boiler and Pressure Vessel Code, Section VIII, Division 1, Rules for Construction of Pressure Vessels...

USAF Hyperbaric Animal Transfer Chamber System.

DTIC Science & Technology

1988-01-01

in full accordance with the requirements of the ASME Boiler and Pressure Vessel Code , Section VIII, Division 2, including provisions for lethal and...possible application to military and aviation medicine. REFERENCES 1. ASME Boiler and Pressure Vessel Code , Sec III, Div 2, para AD-160, AF-402, . and

User's manual for a two-dimensional, ground-water flow code on the Octopus computer network

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

Naymik, T.G.

1978-08-30

A ground-water hydrology computer code, programmed by R.L. Taylor (in Proc. American Society of Civil Engineers, Journal of Hydraulics Division, 93(HY2), pp. 25-33 (1967)), has been adapted to the Octopus computer system at Lawrence Livermore Laboratory. Using an example problem, this manual details the input, output, and execution options of the code.

Development of a Pebble-Bed Liquid-Nitrogen Evaporator and Superheater for the Scaled Large Blast/Thermal Simulator Facility

DTIC Science & Technology

1991-04-01

Boiler and Pressure Vessel Code . Other design requirements are developed from standard safe... Boiler and Pressure Vessel Code . The following three condi- tions constitute the primary design parameters for pressure vessels: (a) Design Working...rules and practices of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code . Section VIII, Division 1 of the ASME

Integrated Modeling of the Battlespace Environment

DTIC Science & Technology

2010-10-01

Office of Counsel.Code 1008.3 ADOR/Director NCST E. R. Franchi , 7000 Public Affairs (Unclassified/ Unlimited Only). Code 7030 4 Division, Code...ESMF: the Hakamada- Akasofu-Fry version 2 (HAFv2) solar wind model and the global assimilation of ionospheric mea- surements (GAIM1) forecast...ground-truth measurements for comparison with the solar wind predictions. Global Assimilation of Ionospheric Measurements The GAIMv2.3 effort

CRITICA: coding region identification tool invoking comparative analysis

NASA Technical Reports Server (NTRS)

Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

1999-01-01

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

Flexible manipulation of terahertz wave reflection using polarization insensitive coding metasurfaces.

PubMed

Jiu-Sheng, Li; Ze-Jiang, Zhao; Jian-Quan, Yao

2017-11-27

In order to extend to 3-bit encoding, we propose notched-wheel structures as polarization insensitive coding metasurfaces to control terahertz wave reflection and suppress backward scattering. By using a coding sequence of "00110011…" along x-axis direction and 16 × 16 random coding sequence, we investigate the polarization insensitive properties of the coding metasurfaces. By designing the coding sequences of the basic coding elements, the terahertz wave reflection can be flexibly manipulated. Additionally, radar cross section (RCS) reduction in the backward direction is less than -10dB in a wide band. The present approach can offer application for novel terahertz manipulation devices.

Noncoding sequence classification based on wavelet transform analysis: part I

NASA Astrophysics Data System (ADS)

Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

2017-09-01

DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

Converting Panax ginseng DNA and chemical fingerprints into two-dimensional barcode.

PubMed

Cai, Yong; Li, Peng; Li, Xi-Wen; Zhao, Jing; Chen, Hai; Yang, Qing; Hu, Hao

2017-07-01

In this study, we investigated how to convert the Panax ginseng DNA sequence code and chemical fingerprints into a two-dimensional code. In order to improve the compression efficiency, GATC2Bytes and digital merger compression algorithms are proposed. HPLC chemical fingerprint data of 10 groups of P. ginseng from Northeast China and the internal transcribed spacer 2 (ITS2) sequence code as the DNA sequence code were ready for conversion. In order to convert such data into a two-dimensional code, the following six steps were performed: First, the chemical fingerprint characteristic data sets were obtained through the inflection filtering algorithm. Second, precompression processing of such data sets is undertaken. Third, precompression processing was undertaken with the P. ginseng DNA (ITS2) sequence codes. Fourth, the precompressed chemical fingerprint data and the DNA (ITS2) sequence code were combined in accordance with the set data format. Such combined data can be compressed by Zlib, an open source data compression algorithm. Finally, the compressed data generated a two-dimensional code called a quick response code (QR code). Through the abovementioned converting process, it can be found that the number of bytes needed for storing P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can be greatly reduced. After GTCA2Bytes algorithm processing, the ITS2 compression rate reaches 75% and the chemical fingerprint compression rate exceeds 99.65% via filtration and digital merger compression algorithm processing. Therefore, the overall compression ratio even exceeds 99.36%. The capacity of the formed QR code is around 0.5k, which can easily and successfully be read and identified by any smartphone. P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can form a QR code after data processing, and therefore the QR code can be a perfect carrier of the authenticity and quality of P. ginseng information. This study provides a theoretical basis for the development of a quality traceability system of traditional Chinese medicine based on a two-dimensional code.

Synthetic Division and Matrix Factorization

ERIC Educational Resources Information Center

Barabe, Samuel; Dubeau, Franc

2007-01-01

Synthetic division is viewed as a change of basis for polynomials written under the Newton form. Then, the transition matrices obtained from a sequence of changes of basis are used to factorize the inverse of a bidiagonal matrix or a block bidiagonal matrix.

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.

PubMed

Lin, Feng-Jiau; Liu, Yuan; Sha, Zhongli; Tsang, Ling Ming; Chu, Ka Hou; Chan, Tin-Yam; Liu, Ruiyu; Cui, Zhaoxia

2012-11-16

The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes

PubMed Central

2012-01-01

Background The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. Results We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Conclusions Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda. PMID:23153176

77 FR 59629 - Statutorily Mandated Designation of Difficult Development Areas for 2013

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... Economist, Economic Development and Public Finance Division, Office of Policy Development and Research... evaluative list of metropolitan zip codes that would be designated Small Area DDAs using this methodology and... Research. [FR Doc. 2012-23900 Filed 9-27-12; 8:45 am] BILLING CODE 4210-67-P ...

Cataloguing and Classification Section. Bibliographic Control Division. Papers.

ERIC Educational Resources Information Center

International Federation of Library Associations, The Hague (Netherlands).

Papers on cataloging, classification, and coding systems which were presented at the 1982 International Federation of Library Associations (IFLA) conference include: (1) "Numbering and Coding Systems for Bibliographic Control in Use in North America" by Lois Mai Chan (United States); (2) "A Project Undertaken by the Library of…

Studies of Heat Transfer in Complex Internal Flows.

DTIC Science & Technology

1982-01-01

D.C. 20362 (Tel 202-692-6874) Mr. Richard S. Carlton Director, Engines Division, Code 523 NC #4 Naval Sea Systems Command Washington, D.C. 20362...Walter Ritz Code 033C Naval Ships Systems Engineering Station Philadelphia, Pennsylvania 19112 (Tel. 215-755-3841) Dr. Simion Kuo United Tech. Res

78 FR 23558 - Pesticide Products; Registration Applications for New Active Ingredients

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-19

... 20460- 0001. As part of the mailing address, include the contact person's name, division, and mail code.... The following list of North American Industrial Classification System (NAICS) codes is not intended to... decision by the Agency on these applications. For actions being evaluated under the Agency's public...

78 FR 79363 - Hazardous Materials: Adoption of ASME Code Section XII and the National Board Inspection Code

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-30

... Rulemaking Division, (202) 366-8553, or Stanley Staniszewski, Engineering and Research [[Page 79364... increased capacity to transport product. A review of previous research by PHMSA's Engineering and Research..., knowledge-sharing, and skill development across all engineering disciplines. ASME is recognized globally for...

New Sequences with Low Correlation and Large Family Size

NASA Astrophysics Data System (ADS)

Zeng, Fanxin

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

Is a Genome a Codeword of an Error-Correcting Code?

PubMed Central

Kleinschmidt, João H.; Silva-Filho, Márcio C.; Bim, Edson; Herai, Roberto H.; Yamagishi, Michel E. B.; Palazzo, Reginaldo

2012-01-01

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction. PMID:22649495

[The Ethics and Deontology division of the French National Council of Medical Doctors, eight years of activity, 1993-2001].

PubMed

Hoerni, Bernard

2011-01-01

The activity of the division of Ethics and deontology of the French National council of medical doctors is analysed by its former president (1993-2001). Among a lot of topics, a new version of the professionnal Code of deontology and patients' information were the main subjects of reflection and action.

UGV Interoperability Profile (IOP) Communications Profile, Version 0

DTIC Science & Technology

2011-12-21

some UGV systems employ Orthogonal Frequency Division Multiplexing ( OFDM ) or Coded Orthogonal Frequency Division Multiplexing (COFDM) waveforms which...other portions of the IOP. Attribute Paragraph Title Values Waveform 3.3 Air Interface/ Waveform OFDM , COFDM, DDL, CDL, None OCU to Platform...Sight MANET Mobile Ad-hoc Network Mbps Megabits per second MC/PM Master Controller/ Payload Manager MHz Megahertz MIMO Multiple Input Multiple

U.S. Army Corps of Engineers Recreation Study. A Plan Prepared for the Assistant Secretary of the Army (Civil Works). Volume 2. Appendices

DTIC Science & Technology

1990-09-01

TELEPHONE (Include Area Code) 22c OFFICE SYMBOL WILLIAM J. HANSEN (703) 355-3089 CEWRC-IWR-R DD FORM 1473, 84 MAR 83 APR edition may be used until... William J. Hansen of the Institute for Water Resources was the Technical Study Manager. Mr. L. Leigh Skaggs of the Institute for Water Resources...Mr. William Thornton, Missouri River Division, Mr. Bruce Hardie, Southwestern Division and Mr. Allen Summers, North Pacific Division. U.S. ARMY

Acta Aeronautica et Astronautica Sinica.

DTIC Science & Technology

1982-07-28

AERONAUTICA ET ASTRONAUTICA SINICA - <,y English pages: 212 _r Source : Acta Aeronautica et Astronautica Sinica, Vol. 2, Nr. 4, December 1981 , . pp. 1...ADVOCATED OR IMPLIED ARE THOSE OP THE SOURCE ANDDO NOT NECESSARILY REFLECT THE POSITION TRANSLATION DIVISION OR OPINION OF THE FOREnjN TECHNOLOGY DI...axial) solution section code 2 Lower Corner Symbols i code of sectional cylindrical coordinate system j,k radial and peripheral codes of solution

ILIR 󈧅: SSC San Diego In-House Laboratory Independent Research 2001 Annual Report

DTIC Science & Technology

2002-05-01

canine distemper virus (CDV) (a morbillivirus closely related to one infecting marine mammals) by intramuscular or intradermal inoculation with a...data.* 3. Sixt, N., A. Cardoso, A. Vallier, J. Fayolle, R. Buckland, T. F. Wild. 1998. “Canine Distemper Virus DNA Vaccination Induces Humoral and...Complementary Code Keying CCSK Cyclic Code Shift Keying CDMA Code Division Multiplexing CDV Canine Distemper Virus CFAR Constant False Alarm

Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs

PubMed Central

Cheng, Chao; Ung, Matthew; Grant, Gavin D.; Whitfield, Michael L.

2013-01-01

Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and a combination of the two types of features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division. The model we propose here provides not only a practical tool for identifying novel cell cycle genes with high accuracy, but also new insights on cell cycle regulation by TFs and cis-regulatory elements. PMID:23874175

A murC gene in Porphyromonas gingivalis 381.

PubMed

Ansai, T; Yamashita, Y; Awano, S; Shibata, Y; Wachi, M; Nagai, K; Takehara, T

1995-09-01

The gene encoding a 51 kDa polypeptide of Porphyromonas gingivalis 381 was isolated by immunoblotting using an antiserum raised against P. gingivalis alkaline phosphatase. DNA sequence analysis of a 2.5 kb DNA fragment containing a gene encoding the 51 kDa protein revealed one complete and two incomplete ORFs. Database searches using the FASTA program revealed significant homology between the P. gingivalis 51 kDa protein and the MurC protein of Escherichia coli, which functions in peptidoglycan synthesis. The cloned 51 kDa protein encoded a functional product that complemented an E. coli murC mutant. Moreover, the ORF just upstream of murC coded for a protein that was 31% homologous with the E. coli MurG protein. The ORF just downstream of murC coded for a protein that was 17% homologous with the Streptococcus pneumoniae penicillin-binding protein 2B (PBP2B), which functions in peptidoglycan synthesis and is responsible for antibiotic resistance. These results suggest that P. gingivalis contains a homologue of the E. coli peptidoglycan synthesis gene murC and indicate the possibility of a cluster of genes responsible for cell division and cell growth, as in the E. coli mra region.

Motion-related resource allocation in dynamic wireless visual sensor network environments.

PubMed

Katsenou, Angeliki V; Kondi, Lisimachos P; Parsopoulos, Konstantinos E

2014-01-01

This paper investigates quality-driven cross-layer optimization for resource allocation in direct sequence code division multiple access wireless visual sensor networks. We consider a single-hop network topology, where each sensor transmits directly to a centralized control unit (CCU) that manages the available network resources. Our aim is to enable the CCU to jointly allocate the transmission power and source-channel coding rates for each node, under four different quality-driven criteria that take into consideration the varying motion characteristics of each recorded video. For this purpose, we studied two approaches with a different tradeoff of quality and complexity. The first one allocates the resources individually for each sensor, whereas the second clusters them according to the recorded level of motion. In order to address the dynamic nature of the recorded scenery and re-allocate the resources whenever it is dictated by the changes in the amount of motion in the scenery, we propose a mechanism based on the particle swarm optimization algorithm, combined with two restarting schemes that either exploit the previously determined resource allocation or conduct a rough estimation of it. Experimental simulations demonstrate the efficiency of the proposed approaches.

Distributed reservation-based code division multiple access

NASA Astrophysics Data System (ADS)

Wieselthier, J. E.; Ephremides, A.

1984-11-01

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

Heterodyne detection using spectral line pairing for spectral phase encoding optical code division multiple access and dynamic dispersion compensation.

PubMed

Yang, Yi; Foster, Mark; Khurgin, Jacob B; Cooper, A Brinton

2012-07-30

A novel coherent optical code-division multiple access (OCDMA) scheme is proposed that uses spectral line pairing to generate signals suitable for heterodyne decoding. Both signal and local reference are transmitted via a single optical fiber and a simple balanced receiver performs sourceless heterodyne detection, canceling speckle noise and multiple-access interference (MAI). To validate the idea, a 16 user fully loaded phase encoded system is simulated. Effects of fiber dispersion on system performance are studied as well. Both second and third order dispersion management is achieved by using a spectral phase encoder to adjust phase shifts of spectral components at the optical network unit (ONU).

Pattern recognition of electronic bit-sequences using a semiconductor mode-locked laser and spatial light modulators

NASA Astrophysics Data System (ADS)

Bhooplapur, Sharad; Akbulut, Mehmetkan; Quinlan, Franklyn; Delfyett, Peter J.

2010-04-01

A novel scheme for recognition of electronic bit-sequences is demonstrated. Two electronic bit-sequences that are to be compared are each mapped to a unique code from a set of Walsh-Hadamard codes. The codes are then encoded in parallel on the spectral phase of the frequency comb lines from a frequency-stabilized mode-locked semiconductor laser. Phase encoding is achieved by using two independent spatial light modulators based on liquid crystal arrays. Encoded pulses are compared using interferometric pulse detection and differential balanced photodetection. Orthogonal codes eight bits long are compared, and matched codes are successfully distinguished from mismatched codes with very low error rates, of around 10-18. This technique has potential for high-speed, high accuracy recognition of bit-sequences, with applications in keyword searches and internet protocol packet routing.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

An algebraic hypothesis about the primeval genetic code architecture.

PubMed

Sánchez, Robersy; Grau, Ricardo

2009-09-01

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

A most spectrum-efficient duplexing system: CDD

NASA Astrophysics Data System (ADS)

Lee, William C. Y.

2001-10-01

The game to play in wireless communications when it comes to increasing spectrum efficiency is to eliminate interference. Currently, all cellular systems use FDD (Frequency Division Duplexing) in an attempt to eliminate the interference from the adjacent cells. Through the use of many technologies only one type of interference remains and that is the adjacent base-tohome mobile interference. TDD (Time Division Duplexing) has not been used for mobile cellular systems, not only because of the adjacent base-to-home mobile interference, but also because of the additional adjacent base-to-home base interference, and adjacent mobile-to-home mobile interference. Therefore, TDD can only be used for small, confined area systems. CDD (Code Division Duplexing) can eliminate all three kinds of interference; the adjacent base-to-home mobile, the adjacent baseto-home base, and the adjacent mobile- to- home in cellular systems. Eliminating each of these interferences makes CDD the most spectrum efficient duplexing system. This talk will elaborate on a set of smart codes, which will make an efficient CDD system a reality.

Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

NASA Astrophysics Data System (ADS)

Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

2017-07-01

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

Code-division-multiplexed readout of large arrays of TES microcalorimeters

NASA Astrophysics Data System (ADS)

Morgan, K. M.; Alpert, B. K.; Bennett, D. A.; Denison, E. V.; Doriese, W. B.; Fowler, J. W.; Gard, J. D.; Hilton, G. C.; Irwin, K. D.; Joe, Y. I.; O'Neil, G. C.; Reintsema, C. D.; Schmidt, D. R.; Ullom, J. N.; Swetz, D. S.

2016-09-01

Code-division multiplexing (CDM) offers a path to reading out large arrays of transition edge sensor (TES) X-ray microcalorimeters with excellent energy and timing resolution. We demonstrate the readout of X-ray TESs with a 32-channel flux-summed code-division multiplexing circuit based on superconducting quantum interference device (SQUID) amplifiers. The best detector has energy resolution of 2.28 ± 0.12 eV FWHM at 5.9 keV and the array has mean energy resolution of 2.77 ± 0.02 eV over 30 working sensors. The readout channels are sampled sequentially at 160 ns/row, for an effective sampling rate of 5.12 μs/channel. The SQUID amplifiers have a measured flux noise of 0.17 μΦ0/√Hz (non-multiplexed, referred to the first stage SQUID). The multiplexed noise level and signal slew rate are sufficient to allow readout of more than 40 pixels per column, making CDM compatible with requirements outlined for future space missions. Additionally, because the modulated data from the 32 SQUID readout channels provide information on each X-ray event at the row rate, our CDM architecture allows determination of the arrival time of an X-ray event to within 275 ns FWHM with potential benefits in experiments that require detection of near-coincident events.

Performance Enhancement of MC-CDMA System through Novel Sensitive Bit Algorithm Aided Turbo Multi User Detection

PubMed Central

Kumaravel, Rasadurai; Narayanaswamy, Kumaratharan

2015-01-01

Multi carrier code division multiple access (MC-CDMA) system is a promising multi carrier modulation (MCM) technique for high data rate wireless communication over frequency selective fading channels. MC-CDMA system is a combination of code division multiple access (CDMA) and orthogonal frequency division multiplexing (OFDM). The OFDM parts reduce multipath fading and inter symbol interference (ISI) and the CDMA part increases spectrum utilization. Advantages of this technique are its robustness in case of multipath propagation and improve security with the minimize ISI. Nevertheless, due to the loss of orthogonality at the receiver in a mobile environment, the multiple access interference (MAI) appears. The MAI is one of the factors that degrade the bit error rate (BER) performance of MC-CDMA system. The multiuser detection (MUD) and turbo coding are the two dominant techniques for enhancing the performance of the MC-CDMA systems in terms of BER as a solution of overcome to MAI effects. In this paper a low complexity iterative soft sensitive bits algorithm (SBA) aided logarithmic-Maximum a-Posteriori algorithm (Log MAP) based turbo MUD is proposed. Simulation results show that the proposed method provides better BER performance with low complexity decoding, by mitigating the detrimental effects of MAI. PMID:25714917

Circular codes revisited: a statistical approach.

PubMed

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

PubMed Central

Turco, Gina; Schnable, James C.; Pedersen, Brent; Freeling, Michael

2013-01-01

Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by >12 kb of non-coding sequence. We have used this tool to characterize new motifs, associate CNSs with additional functions, and identify previously undetected genes encoding RNA and protein in the genomes of five grass species. We provide a list of 15,363 orthologous CNSs conserved across all grasses tested. We were also able to identify regulatory sequences present in the common ancestor of grasses that have been lost in one or more extant grass lineages. Lists of orthologous gene pairs and associated CNSs are provided for reference inbred lines of arabidopsis, Japonica rice, foxtail millet, sorghum, brachypodium, and maize. PMID:23874343

Teamwork in Task Analysis. Training Manual V

DTIC Science & Technology

1975-11-01

Research Programs Psychological Sciences Division Office of Naval Research Contract No. N00014-74-A-0436-0001 NR 151-370 Approved for public...Corps (Code RD) And Monitored By Personnel and Training Research Programs Psychological Sciences Division Office of Naval Research Contract No...survival in the hidden warfare of the destructive psychological win-lose game. Win-lose behavior stems from individual attitudes and manage- ment climate

INSTRUMENTATION AND CONTROLS DIVISION, ELECTRICAL DESIGN STANDARDS AND GRAPHICAL SYMBOLS

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

Bates, A.E.G.; Bowelle, M.M.; Horton, J.L.

1960-10-01

Recommendations of the Instrumentation and Controls Division Committee on Electrical and Electronic Symbols and Drawings are presented. The American Standards Associrtion Graphical Symbols for Electrical Diagrams are given, with certain variations or additions recommended by the Committee to clarify or more positively identify the device or element symbolized. Recommendations regarding electrical elementary diagram 1ayout, device coding, etc., are included. (W.D.M.)

Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (83rd, Phoenix, Arizona, August 9-12, 2000). Media Ethics Division.

ERIC Educational Resources Information Center

Association for Education in Journalism and Mass Communication.

The Media Ethics Division section of the proceedings contains the following seven papers: "The Concept of Media Accountability Reconsidered" (Patrick Lee Plaisance); "Of Joint Ventures, Sock Puppets and New Media Synergy: Codes of Ethics and the Emergence of Institutional Conflicts of Interest" (Charles N. Davis and Stephanie…

A VLT/UVES spectroscopy study of O2 stars in the LMC

NASA Astrophysics Data System (ADS)

Doran, Emile I.; Crowther, Paul A.

2011-01-01

We have analysed VLT/UVES spectra of six O2 stars within the Large Magellanic Cloud using the non-LTE atmospheric code CMFGEN. A range of physical properties was determined by employing a temperature calibration based upon N IV - N V diagnostics. Wind properties were also obtained from the Hα line, while CNO surface abundances were supplied through various diagnostics. Our results reveal effective temperatures in excess of T_{eff} ˜50 kK in all cases. We also addressed their evolutionary status and favour a mass dependent division. For lower masses ≤100 M⊙Mar, an O2 star follows the classical sequence, evolving from dwarf on to giant, through to supergiant. At higher masses, the dwarf phase may be circumvented and instead O2 stars begin their lives as giants or supergiants, evolving to the H-rich WN stage within ˜1.5 Myr.

DS-CDMA satellite diversity reception for personal satellite communication: Downlink performance analysis

NASA Technical Reports Server (NTRS)

DeGaudenzi, Riccardo; Giannetti, Filippo

1995-01-01

The downlink of a satellite-mobile personal communication system employing power-controlled Direct Sequence Code Division Multiple Access (DS-CDMA) and exploiting satellite-diversity is analyzed and its performance compared with a more traditional communication system utilizing single satellite reception. The analytical model developed has been thoroughly validated by means of extensive Monte Carlo computer simulations. It is shown how the capacity gain provided by diversity reception shrinks considerably in the presence of increasing traffic or in the case of light shadowing conditions. Moreover, the quantitative results tend to indicate that to combat system capacity reduction due to intra-system interference, no more than two satellites shall be active over the same region. To achieve higher system capacity, differently from terrestrial cellular systems, Multi-User Detection (MUD) techniques are likely to be required in the mobile user terminal, thus considerably increasing its complexity.

Handover aspects for a Low Earth Orbit (LEO) CDMA Land Mobile Satellite (LMS) system

NASA Technical Reports Server (NTRS)

Carter, P.; Beach, M. A.

1993-01-01

This paper addresses the problem of handoff in a land mobile satellite (LMS) system between adjacent satellites in a low earth orbit (LEO) constellation. In particular, emphasis is placed on the application of soft handoff in a direct sequence code division multiple access (DS-CDMA) LMS system. Soft handoff is explained in terms of terrestrial macroscopic diversity, in which signals transmitted via several independent fading paths are combined to enhance the link quality. This concept is then reconsidered in the context of a LEO LMS system. A two-state Markov channel model is used to simulate the effects of shadowing on the communications path from the mobile to each satellite during handoff. The results of the channel simulation form a platform for discussion regarding soft handoff, highlighting the potential merits of the scheme when applied in a LEO LMS environment.

Approximate equiangular tight frames for compressed sensing and CDMA applications

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Comparison of two underwater acoustic communications techniques for multi-user access

NASA Astrophysics Data System (ADS)

Hursky, Paul; Siderius, T. Martin; Kauaiex Group

2004-05-01

Frequency hopped frequency shift keying (FHFSK) and code division multiple access (CDMA) are two different modulation techniques for multiple users to communicate with a single receiver simultaneously. In July 2003, these two techniques were tested alongside each other in a shallow water coastal environment off the coast of Kauai. A variety of instruments were used to measure the prevailing oceanography, enabling detailed modeling of the channel. The channel was acoustically probed using LFM waveforms and m-sequences as well. We will present the results of demodulating the FHFSK and CDMA waveforms and discuss modeling the channel for the purpose of predicting multi-user communications performance. a)Michael B. Porter, Paul Hursky, Martin Siderius (SAIC), Mohsen Badiey (UD), Jerald Caruthers (USM), William S. Hodgkiss, Kaustubha Raghukumar (SIO), Dan Rouseff, Warren Fox (APL-UW), Christian de Moustier, Brian Calder, Barbara J. Kraft (UNH), Keyko McDonald (SPAWARSSC), Peter Stein, James K. Lewis, and Subramaniam Rajan (SSI).

A novel wireless local positioning system for airport (indoor) security

NASA Astrophysics Data System (ADS)

Zekavat, Seyed A.; Tong, Hui; Tan, Jindong

2004-09-01

A novel wireless local positioning system (WLPS) for airport (or indoor) security is introduced. This system is used by airport (indoor) security guards to locate all of, or a group of airport employees or passengers within the airport area. WLPS consists of two main parts: (1) a base station that is carried by security personnel; hence, introducing dynamic base station (DBS), and (2) a transponder (TRX) that is mounted on all people (including security personnel) present at the airport; thus, introducing them as active targets. In this paper, we (a) draw a futuristic view of the airport security systems, and the flow of information at the airports, (b) investigate the techniques of extending WLPS coverage area beyond the line-of-sight (LoS), and (c) study the performance of this system via standard transceivers, and direct sequence code division multiple access (DS-CDMA) systems with and without antenna arrays and conventional beamforming (BF).

Second-generation sequencing of entire mitochondrial coding-regions (∼15.4 kb) holds promise for study of the phylogeny and taxonomy of human body lice and head lice.

PubMed

Xiong, H; Campelo, D; Pollack, R J; Raoult, D; Shao, R; Alem, M; Ali, J; Bilcha, K; Barker, S C

2014-08-01

The Illumina Hiseq platform was used to sequence the entire mitochondrial coding-regions of 20 body lice, Pediculus humanus Linnaeus, and head lice, P. capitis De Geer (Phthiraptera: Pediculidae), from eight towns and cities in five countries: Ethiopia, France, China, Australia and the U.S.A. These data (∼310 kb) were used to see how much more informative entire mitochondrial coding-region sequences were than partial mitochondrial coding-region sequences, and thus to guide the design of future studies of the phylogeny, origin, evolution and taxonomy of body lice and head lice. Phylogenies were compared from entire coding-region sequences (∼15.4 kb), entire cox1 (∼1.5 kb), partial cox1 (∼700 bp) and partial cytb (∼600 bp) sequences. On the one hand, phylogenies from entire mitochondrial coding-region sequences (∼15.4 kb) were much more informative than phylogenies from entire cox1 sequences (∼1.5 kb) and partial gene sequences (∼600 to ∼700 bp). For example, 19 branches had > 95% bootstrap support in our maximum likelihood tree from the entire mitochondrial coding-regions (∼15.4 kb) whereas the tree from 700 bp cox1 had only two branches with bootstrap support > 95%. Yet, by contrast, partial cytb (∼600 bp) and partial cox1 (∼486 bp) sequences were sufficient to genotype lice to Clade A, B or C. The sequences of the mitochondrial genomes of the P. humanus, P. capitis and P. schaeffi Fahrenholz studied are in NCBI GenBank under the accession numbers KC660761-800, KC685631-6330, KC241882-97, EU219988-95, HM241895-8 and JX080388-407. © 2014 The Royal Entomological Society.

Effective Identification of Similar Patients Through Sequential Matching over ICD Code Embedding.

PubMed

Nguyen, Dang; Luo, Wei; Venkatesh, Svetha; Phung, Dinh

2018-04-11

Evidence-based medicine often involves the identification of patients with similar conditions, which are often captured in ICD (International Classification of Diseases (World Health Organization 2013)) code sequences. With no satisfying prior solutions for matching ICD-10 code sequences, this paper presents a method which effectively captures the clinical similarity among routine patients who have multiple comorbidities and complex care needs. Our method leverages the recent progress in representation learning of individual ICD-10 codes, and it explicitly uses the sequential order of codes for matching. Empirical evaluation on a state-wide cancer data collection shows that our proposed method achieves significantly higher matching performance compared with state-of-the-art methods ignoring the sequential order. Our method better identifies similar patients in a number of clinical outcomes including readmission and mortality outlook. Although this paper focuses on ICD-10 diagnosis code sequences, our method can be adapted to work with other codified sequence data.

Occupational Sequences: Auto Engines 1. AT 121.

ERIC Educational Resources Information Center

Korb, A. W.; And Others

In an attempt to individualize an automotive course, the Vocational-Technical Division of Northern Montana College has developed Occupational Sequences for an engine rebuilding course. Occupational Sequences, a learning or teaching aid, is an analysis of numbered operations involved in engine rebuilding. Job sheets, included in the book, provide a…

Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps.

PubMed

Aires-de-Sousa, João; Aires-de-Sousa, Luisa

2003-01-01

We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence. This is a compact representation of the neighbourhood of a base. The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code). It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques. To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G. It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions. For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second). Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment. Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep. Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Complete Coding Genome Sequence for Mogiana Tick Virus, a Jingmenvirus Isolated from Ticks in Brazil

DTIC Science & Technology

2017-05-04

and capable of infecting a wide range of animal hosts (1–5). Here, we report the complete coding genome sequence (i.e., only missing portions of...segmented nature of the genome was not under- stood. Therefore, only the two genome segments with detectable sequence homolo- gies to flaviviruses were...originally reported (2). We revisited the data set of Maruyama et al. (2) and assembled the complete coding sequences for all four genome segments. We

Transcription of Gypsy Elements in a Y-Chromosome Male Fertility Gene of Drosophila Hydei

PubMed Central

Hochstenbach, R.; Harhangi, H.; Schouren, K.; Bindels, P.; Suijkerbuijk, R.; Hennig, W.

1996-01-01

We have found that defective gypsy retrotransposons are a major constituent of the lampbrush loop pair Nooses in the short arm of the Y chromosome of Drosophila hydei. The loop pair is formed by male fertility gene Q during the primary spermatocyte stage of spermatogenesis, each loop being a single transcription unit with an estimated length of 260 kb. Using fluorescent in situ hybridization, we show that throughout the loop transcripts gypsy elements are interspersed with blocks of a tandemly repetitive Y-specific DNA sequence, ay1. Nooses transcripts containing both sequence types show a wide size range on Northern blots, do not migrate to the cytoplasm, and are degraded just before the first meiotic division. Only one strand of ay1 and only the coding strand of gypsy can be detected in the loop transcripts. However, as cloned genomic DNA fragments also display opposite orientations of ay1 and gypsy, such DNA sections cannot be part of the Nooses. Hence, they are most likely derived from the flanking heterochromatin. The direction of transcription of ay1 and gypsy thus appears to be of a functional significance. PMID:8852843

Epigenetic regulatory mechanisms in vertebrate eye development and disease

PubMed Central

Cvekl, A; Mitton, KP

2014-01-01

Eukaryotic DNA is organized as a nucleoprotein polymer termed chromatin with nucleosomes serving as its repetitive architectural units. Cellular differentiation is a dynamic process driven by activation and repression of specific sets of genes, partitioning the genome into transcriptionally active and inactive chromatin domains. Chromatin architecture at individual genes/loci may remain stable through cell divisions, from a single mother cell to its progeny during mitosis, and represents an example of epigenetic phenomena. Epigenetics refers to heritable changes caused by mechanisms distinct from the primary DNA sequence. Recent studies have shown a number of links between chromatin structure, gene expression, extracellular signaling, and cellular differentiation during eye development. This review summarizes recent advances in this field, and the relationship between sequence-specific DNA-binding transcription factors and their roles in recruitment of chromatin remodeling enzymes. In addition, lens and retinal differentiation is accompanied by specific changes in the nucleolar organization, expression of non-coding RNAs, and DNA methylation. Epigenetic regulatory mechanisms in ocular tissues represent exciting areas of research that have opened new avenues for understanding normal eye development, inherited eye diseases and eye diseases related to aging and the environment. PMID:20179734

Quantized phase coding and connected region labeling for absolute phase retrieval.

PubMed

Chen, Xiangcheng; Wang, Yuwei; Wang, Yajun; Ma, Mengchao; Zeng, Chunnian

2016-12-12

This paper proposes an absolute phase retrieval method for complex object measurement based on quantized phase-coding and connected region labeling. A specific code sequence is embedded into quantized phase of three coded fringes. Connected regions of different codes are labeled and assigned with 3-digit-codes combining the current period and its neighbors. Wrapped phase, more than 36 periods, can be restored with reference to the code sequence. Experimental results verify the capability of the proposed method to measure multiple isolated objects.

Functional interrogation of non-coding DNA through CRISPR genome editing

PubMed Central

Canver, Matthew C.; Bauer, Daniel E.; Orkin, Stuart H.

2017-01-01

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. PMID:28288828

Memorization of Sequences of Movements of the Right or the Left Hand by Right- and Left-Handers: Vector Coding.

PubMed

Bobrova, E V; Bogacheva, I N; Lyakhovetskii, V A; Fabinskaja, A A; Fomina, E V

2017-01-01

In order to test the hypothesis of hemisphere specialization for different types of information coding (the right hemisphere, for positional coding; the left one, for vector coding), we analyzed the errors of right and left-handers during a task involving the memorization of sequences of movements by the left or the right hand, which activates vector coding by changing the order of movements in memorized sequences. The task was first performed by the right or the left hand, then by the opposite hand. It was found that both'right- and left-handers use the information about the previous movements of the dominant hand, but not of the non-dom" inant one. After changing the hand, right-handers use the information about previous movements of the second hand, while left-handers do not. We compared our results with the data of previous experiments, in which positional coding was activated, and concluded that both right- and left-handers use vector coding for memorizing the sequences of their dominant hands and positional coding for memorizing the sequences of non-dominant hand. No similar patterns of errors were found between right- and left-handers after changing the hand, which suggests that in right- and left-handersthe skills are transferred in different ways depending on the type of coding.

Securities and Exchange Commission Semiannual Regulatory Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-26

... Insurance Contracts 3235-AK49 DIVISION OF INVESTMENT MANAGEMENT--Final Rule Stage Regulation Sequence Title Identifier Number Number 425 Amendments to Form ADV 3235-AI17 DIVISION OF INVESTMENT MANAGEMENT--Completed... 15c2-2: Confirmation of Transactions in Open-End Management Investment Company 3235-AJ11 Shares, Unit...

48 CFR 3.303 - Reporting suspected antitrust violations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... turn in sequence as low bidder, or so that certain competitors bid low only on some sizes of contracts and high on other sizes; (5) Division of the market, so that certain competitors bid low only for..., Attention: Assistant Attorney General, Antitrust Division, and shall include— (1) A brief statement...

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

Lewis Structures Technology, 1988. Volume 3: Structural Integrity Fatigue and Fracture Wind Turbines HOST

NASA Technical Reports Server (NTRS)

1988-01-01

The charter of the Structures Division is to perform and disseminate results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practioners of structural engineering mechanics beyond the aerospace arena. The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

Detection of somatic, subclonal and mosaic CNVs from sequencing | Division of Cancer Prevention

Cancer.gov

Progress in technology has made individual genome sequencing a clinical reality, with partial genome sequencing already in use in clinical care. In fact, it is expected that within a few years whole genome sequencing will be a standard procedure that will allow discovering personal genomic variants of all types and thus greatly facilitate individualized medicine. However, fast

Primer development to obtain complete coding sequence of HA and NA genes of influenza A/H3N2 virus.

PubMed

Agustiningsih, Agustiningsih; Trimarsanto, Hidayat; Setiawaty, Vivi; Artika, I Made; Muljono, David Handojo

2016-08-30

Influenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. An optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested. The developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.

VLSI implementation of RSA encryption system using ancient Indian Vedic mathematics

NASA Astrophysics Data System (ADS)

Thapliyal, Himanshu; Srinivas, M. B.

2005-06-01

This paper proposes the hardware implementation of RSA encryption/decryption algorithm using the algorithms of Ancient Indian Vedic Mathematics that have been modified to improve performance. The recently proposed hierarchical overlay multiplier architecture is used in the RSA circuitry for multiplication operation. The most significant aspect of the paper is the development of a division architecture based on Straight Division algorithm of Ancient Indian Vedic Mathematics and embedding it in RSA encryption/decryption circuitry for improved efficiency. The coding is done in Verilog HDL and the FPGA synthesis is done using Xilinx Spartan library. The results show that RSA circuitry implemented using Vedic division and multiplication is efficient in terms of area/speed compared to its implementation using conventional multiplication and division architectures.

GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less

Phylogenetic Network for European mtDNA

PubMed Central

Finnilä, Saara; Lehtonen, Mervi S.; Majamaa, Kari

2001-01-01

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in the coding region of mtDNA from 121 Finns, by conformation-sensitive gel electrophoresis and subsequent sequencing and by direct sequencing of the D loop. Furthermore, 71 sequences from our previous reports were included, so that the samples represented all the mtDNA haplogroups present in the Finnish population. We found a total of 297 variable sites in the coding region, which allowed the compilation of unambiguous phylogenetic networks. The D loop harbored 104 variable sites, and, in most cases, these could be localized within the coding-region networks, without discrepancies. Interestingly, many homoplasies were detected in the coding region. Nucleotide variation in the rRNA and tRNA genes was 6%, and that in the third nucleotide positions of structural genes amounted to 22% of that in the HVS-I. The complete networks enabled the relationships between the mtDNA haplogroups to be analyzed. Phylogenetic networks based on the entire coding-region sequence in mtDNA provide a rich source for further population genetic studies, and complete sequences make it easier to differentiate between disease-causing mutations and rare polymorphisms. PMID:11349229

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity.

PubMed

Ishikawa, Sohta A; Inagaki, Yuji; Hashimoto, Tetsuo

2012-01-01

In phylogenetic analyses of nucleotide sequences, 'homogeneous' substitution models, which assume the stationarity of base composition across a tree, are widely used, albeit individual sequences may bear distinctive base frequencies. In the worst-case scenario, a homogeneous model-based analysis can yield an artifactual union of two distantly related sequences that achieved similar base frequencies in parallel. Such potential difficulty can be countered by two approaches, 'RY-coding' and 'non-homogeneous' models. The former approach converts four bases into purine and pyrimidine to normalize base frequencies across a tree, while the heterogeneity in base frequency is explicitly incorporated in the latter approach. The two approaches have been applied to real-world sequence data; however, their basic properties have not been fully examined by pioneering simulation studies. Here, we assessed the performances of the maximum-likelihood analyses incorporating RY-coding and a non-homogeneous model (RY-coding and non-homogeneous analyses) on simulated data with parallel convergence to similar base composition. Both RY-coding and non-homogeneous analyses showed superior performances compared with homogeneous model-based analyses. Curiously, the performance of RY-coding analysis appeared to be significantly affected by a setting of the substitution process for sequence simulation relative to that of non-homogeneous analysis. The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity.

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.

PubMed

Suyama, Mikita; Lathe, Warren C; Bork, Peer

2005-10-10

We have identified 141 novel palindromic repetitive elements in the genome of euryarchaeon Methanocaldococcus jannaschii. The total length of these elements is 14.3kb, which corresponds to 0.9% of the total genomic sequence and 6.3% of all extragenic regions. The elements can be divided into three groups (MJRE1-3) based on the sequence similarity. The low sequence identity within each of the groups suggests rather old origin of these elements in M. jannaschii. Three MJRE2 elements were located within the protein coding regions without disrupting the coding potential of the host genes, indicating that insertion of repeats might be a widespread mechanism to enhance sequence diversity in coding regions.

An archaebacterial homologue of the essential eubacterial cell division protein FtsZ.

PubMed

Baumann, P; Jackson, S P

1996-06-25

Life falls into three fundamental domains--Archaea, Bacteria, and Eucarya (formerly archaebacteria, eubacteria, and eukaryotes,. respectively). Though Archaea lack nuclei and share many morphological features with Bacteria, molecular analyses, principally of the transcription and translation machineries, have suggested that Archaea are more related to Eucarya than to Bacteria. Currently, little is known about the archaeal cell division apparatus. In Bacteria, a crucial component of the cell division machinery is FtsZ, a GTPase that localizes to a ring at the site of septation. Interestingly, FtsZ is distantly related in sequence to eukaryotic tubulins, which also interact with GTP and are components of the eukaryotic cell cytoskeleton. By screening for the ability to bind radiolabeled nucleotides, we have identified a protein of the hyperthermophilic archaeon Pyrococcus woesei that interacts tightly and specifically with GTP. Furthermore, through screening an expression library of P. woesei genomic DNA, we have cloned the gene encoding this protein. Sequence comparisons reveal that the P. woesei GTP-binding protein is strikingly related in sequence to eubacterial FtsZ and is marginally more similar to eukaryotic tubulins than are bacterial FtsZ proteins. Phylogenetic analyses reinforce the notion that there is an evolutionary linkage between FtsZ and tubulins. These findings suggest that the archaeal cell division apparatus may be fundamentally similar to that of Bacteria and lead us to consider the evolutionary relationships between Archaea, Bacteria, and Eucarya.

Brain cDNA clone for human cholinesterase

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

McTiernan, C.; Adkins, S.; Chatonnet, A.

1987-10-01

A cDNA library from human basal ganglia was screened with oligonucleotide probes corresponding to portions of the amino acid sequence of human serum cholinesterase. Five overlapping clones, representing 2.4 kilobases, were isolated. The sequenced cDNA contained 207 base pairs of coding sequence 5' to the amino terminus of the mature protein in which there were four ATG translation start sites in the same reading frame as the protein. Only the ATG coding for Met-(-28) lay within a favorable consensus sequence for functional initiators. There were 1722 base pairs of coding sequence corresponding to the protein found circulating in human serum.more » The amino acid sequence deduced from the cDNA exactly matched the 574 amino acid sequence of human serum cholinesterase, as previously determined by Edman degradation. Therefore, our clones represented cholinesterase rather than acetylcholinesterase. It was concluded that the amino acid sequences of cholinesterase from two different tissues, human brain and human serum, were identical. Hybridization of genomic DNA blots suggested that a single gene, or very few genes coded for cholinesterase.« less

Functional interrogation of non-coding DNA through CRISPR genome editing.

PubMed

Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

2017-05-15

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

Nonlinear, nonbinary cyclic group codes

NASA Technical Reports Server (NTRS)

Solomon, G.

1992-01-01

New cyclic group codes of length 2(exp m) - 1 over (m - j)-bit symbols are introduced. These codes can be systematically encoded and decoded algebraically. The code rates are very close to Reed-Solomon (RS) codes and are much better than Bose-Chaudhuri-Hocquenghem (BCH) codes (a former alternative). The binary (m - j)-tuples are identified with a subgroup of the binary m-tuples which represents the field GF(2 exp m). Encoding is systematic and involves a two-stage procedure consisting of the usual linear feedback register (using the division or check polynomial) and a small table lookup. For low rates, a second shift-register encoding operation may be invoked. Decoding uses the RS error-correcting procedures for the m-tuple codes for m = 4, 5, and 6.

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

PubMed

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

Streamlined Genome Sequence Compression using Distributed Source Coding

PubMed Central

Wang, Shuang; Jiang, Xiaoqian; Chen, Feng; Cui, Lijuan; Cheng, Samuel

2014-01-01

We aim at developing a streamlined genome sequence compression algorithm to support alternative miniaturized sequencing devices, which have limited communication, storage, and computation power. Existing techniques that require heavy client (encoder side) cannot be applied. To tackle this challenge, we carefully examined distributed source coding theory and developed a customized reference-based genome compression protocol to meet the low-complexity need at the client side. Based on the variation between source and reference, our protocol will pick adaptively either syndrome coding or hash coding to compress subsequences of changing code length. Our experimental results showed promising performance of the proposed method when compared with the state-of-the-art algorithm (GRS). PMID:25520552

Gravity and the orientation of cell division

NASA Technical Reports Server (NTRS)

Helmstetter, C. E.

1997-01-01

A novel culture system for mammalian cells was used to investigate division orientations in populations of Chinese hamster ovary cells and the influence of gravity on the positioning of division axes. The cells were tethered to adhesive sites, smaller in diameter than a newborn cell, distributed over a nonadhesive substrate positioned vertically. The cells grew and divided while attached to the sites, and the angles and directions of elongation during anaphase, projected in the vertical plane, were found to be random with respect to gravity. However, consecutive divisions of individual cells were generally along the same axis or at 90 degrees to the previous division, with equal probability. Thus, successive divisions were restricted to orthogonal planes, but the choice of plane appeared to be random, unlike the ordered sequence of cleavage orientations seen during early embryo development.

Preparation and Use of Liposomes in Immunological Studies

DTIC Science & Technology

1993-01-01

SYMBOL MFI RO W 0 E FANIZATION Division of Bioctmnistry El O9V09W399 6c. ADDRESS (City, State, and ZIP Code). DRESS(Ci State, and ZIP Code) "Walter Reed...Anuv Institute of Research 1 A Washington. DC 20307-5100 oC" 8a. NAME OF FUNDING/SPONSORING 8b. OFFICE SYMBOL 9. PROCUREMENT INSTRUMENT IDENTIFICATION...12a NAME OF RESPONSIBLE INDIVIDUAL 22b. TELEPHONE (Include Area Code) 22c. OFFICE SYMBOL OD Form 1473, JUN 86 Previous editions are obsolete

Combining Satellite Ocean Color Imagery and Circulation Modeling to Forecast Bio-Optical Properties: Comparison of Models and Advection Schemes

DTIC Science & Technology

2008-10-01

Director NCST E. R. Franchi , 7000 ^^M^4^k ro£— 4// 2^/s y Public Affairs (Unclassified/ Unlimited Only), Code 7030 4 Division, Code Author, Code...from the Navy Operational Global Atmospheric Prediction System (NOGAPS, Hogan and Rosmond, 1991) and assimilates data via the Navy Coupled Ocean...forecasts using Global , Atlantic, Gulf of Mexico, and northern Gulf of Mexico configurations of HYCOM. Proceedings, Ocean Optics XIX, Castelvecchio Pascoli

75 FR 57278 - Agency Information Collection Activities: Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-20

... Title 44, United States Code, as amended by the Paperwork Reduction Act of 1995, Pub. L. 104-13), the... encrypted before transfer to each client record, HRSA is able to link data for clients across Ryan White HIV..., Division of Policy and Information Coordination. [FR Doc. 2010-23416 Filed 9-17-10; 8:45 am] BILLING CODE...

Australian Aerodynamic Design Codes for Aerial Tow Bodies.

DTIC Science & Technology

1987-08-27

HTP -1, which deals with aerial targets, it was recognised that there was a need for a complete and well docL mented approach for their aerodynamic and...circular cables cannot be assessed with the programs in their present form. 10. none of the programs are well documented and user’s manuals are not...National Leader ANL TTCP HTP -1 Weapons Systems Research Laboratory Director Superintendent - Weapons Division - Combat Systems Division Navy Office Navy

75 FR 79937 - Regulatory Flexibility Agenda

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-20

... INVESTMENT MANAGEMENT--Final Rule Stage Regulation Sequence Title Identifier Number Number 617 Temporary Rule Regarding Principal Trades With Certain Advisory Clients 3235-AJ96 DIVISION OF INVESTMENT MANAGEMENT... Sequence Title Identifier Number Number 626 Confirmation of Transactions in Open-End Management Investment...

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

PubMed

Kanda, Kojun; Pflug, James M; Sproul, John S; Dasenko, Mark A; Maddison, David R

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

PubMed Central

Dasenko, Mark A.

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced. PMID:26716693

The Mitochondrial Cytochrome Oxidase Subunit I Gene Occurs on a Minichromosome with Extensive Heteroplasmy in Two Species of Chewing Lice, Geomydoecus aurei and Thomomydoecus minor

PubMed Central

Pietan, Lucas L.; Spradling, Theresa A.

2016-01-01

In animals, mitochondrial DNA (mtDNA) typically occurs as a single circular chromosome with 13 protein-coding genes and 22 tRNA genes. The various species of lice examined previously, however, have shown mitochondrial genome rearrangements with a range of chromosome sizes and numbers. Our research demonstrates that the mitochondrial genomes of two species of chewing lice found on pocket gophers, Geomydoecus aurei and Thomomydoecus minor, are fragmented with the 1,536 base-pair (bp) cytochrome-oxidase subunit I (cox1) gene occurring as the only protein-coding gene on a 1,916–1,964 bp minicircular chromosome in the two species, respectively. The cox1 gene of T. minor begins with an atypical start codon, while that of G. aurei does not. Components of the non-protein coding sequence of G. aurei and T. minor include a tRNA (isoleucine) gene, inverted repeat sequences consistent with origins of replication, and an additional non-coding region that is smaller than the non-coding sequence of other lice with such fragmented mitochondrial genomes. Sequences of cox1 minichromosome clones for each species reveal extensive length and sequence heteroplasmy in both coding and noncoding regions. The highly variable non-gene regions of G. aurei and T. minor have little sequence similarity with one another except for a 19-bp region of phylogenetically conserved sequence with unknown function. PMID:27589589

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.

PubMed

Mehmood, Tahir; Bohlin, Jon; Snipen, Lars

2015-01-01

The upstream region of coding genes is important for several reasons, for instance locating transcription factor, binding sites, and start site initiation in genomic DNA. Motivated by a recently conducted study, where multivariate approach was successfully applied to coding sequence modeling, we have introduced a partial least squares (PLS) based procedure for the classification of true upstream prokaryotic sequence from background upstream sequence. The upstream sequences of conserved coding genes over genomes were considered in analysis, where conserved coding genes were found by using pan-genomics concept for each considered prokaryotic species. PLS uses position specific scoring matrix (PSSM) to study the characteristics of upstream region. Results obtained by PLS based method were compared with Gini importance of random forest (RF) and support vector machine (SVM), which is much used method for sequence classification. The upstream sequence classification performance was evaluated by using cross validation, and suggested approach identifies prokaryotic upstream region significantly better to RF (p-value < 0.01) and SVM (p-value < 0.01). Further, the proposed method also produced results that concurred with known biological characteristics of the upstream region.

Wireless visual sensor network resource allocation using cross-layer optimization

NASA Astrophysics Data System (ADS)

Bentley, Elizabeth S.; Matyjas, John D.; Medley, Michael J.; Kondi, Lisimachos P.

2009-01-01

In this paper, we propose an approach to manage network resources for a Direct Sequence Code Division Multiple Access (DS-CDMA) visual sensor network where nodes monitor scenes with varying levels of motion. It uses cross-layer optimization across the physical layer, the link layer and the application layer. Our technique simultaneously assigns a source coding rate, a channel coding rate, and a power level to all nodes in the network based on one of two criteria that maximize the quality of video of the entire network as a whole, subject to a constraint on the total chip rate. One criterion results in the minimal average end-to-end distortion amongst all nodes, while the other criterion minimizes the maximum distortion of the network. Our approach allows one to determine the capacity of the visual sensor network based on the number of nodes and the quality of video that must be transmitted. For bandwidth-limited applications, one can also determine the minimum bandwidth needed to accommodate a number of nodes with a specific target chip rate. Video captured by a sensor node camera is encoded and decoded using the H.264 video codec by a centralized control unit at the network layer. To reduce the computational complexity of the solution, Universal Rate-Distortion Characteristics (URDCs) are obtained experimentally to relate bit error probabilities to the distortion of corrupted video. Bit error rates are found first by using Viterbi's upper bounds on the bit error probability and second, by simulating nodes transmitting data spread by Total Square Correlation (TSC) codes over a Rayleigh-faded DS-CDMA channel and receiving that data using Auxiliary Vector (AV) filtering.

BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.

PubMed

Ito, Eric Augusto; Katahira, Isaque; Vicente, Fábio Fernandes da Rocha; Pereira, Luiz Filipe Protasio; Lopes, Fabrício Martins

2018-06-05

With the emergence of Next Generation Sequencing (NGS) technologies, a large volume of sequence data in particular de novo sequencing was rapidly produced at relatively low costs. In this context, computational tools are increasingly important to assist in the identification of relevant information to understand the functioning of organisms. This work introduces BASiNET, an alignment-free tool for classifying biological sequences based on the feature extraction from complex network measurements. The method initially transform the sequences and represents them as complex networks. Then it extracts topological measures and constructs a feature vector that is used to classify the sequences. The method was evaluated in the classification of coding and non-coding RNAs of 13 species and compared to the CNCI, PLEK and CPC2 methods. BASiNET outperformed all compared methods in all adopted organisms and datasets. BASiNET have classified sequences in all organisms with high accuracy and low standard deviation, showing that the method is robust and non-biased by the organism. The proposed methodology is implemented in open source in R language and freely available for download at https://cran.r-project.org/package=BASiNET.

The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

PubMed

Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

2016-01-01

Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

Synthesis of 10-Ethyl Flavin: A Multistep Synthesis Organic Chemistry Laboratory Experiment for Upper-Division Undergraduate Students

ERIC Educational Resources Information Center

Sichula, Vincent A.

2015-01-01

A multistep synthesis of 10-ethyl flavin was developed as an organic chemistry laboratory experiment for upper-division undergraduate students. Students synthesize 10-ethyl flavin as a bright yellow solid via a five-step sequence. The experiment introduces students to various hands-on experimental organic synthetic techniques, such as column…

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

PubMed Central

Kress, W. John; Erickson, David L.

2007-01-01

Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination. PMID:17551588

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

PubMed

Cenik, Can; Chua, Hon Nian; Singh, Guramrit; Akef, Abdalla; Snyder, Michael P; Palazzo, Alexander F; Moore, Melissa J; Roth, Frederick P

2017-03-01

Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 ' proximal- i ntron- m inus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N 1 -methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N 1 -methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC. © 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A DS-UWB Cognitive Radio System Based on Bridge Function Smart Codes

NASA Astrophysics Data System (ADS)

Xu, Yafei; Hong, Sheng; Zhao, Guodong; Zhang, Fengyuan; di, Jinshan; Zhang, Qishan

This paper proposes a direct-sequence UWB Gaussian pulse of cognitive radio systems based on bridge function smart sequence matrix and the Gaussian pulse. As the system uses the spreading sequence code, that is the bridge function smart code sequence, the zero correlation zones (ZCZs) which the bridge function sequences' auto-correlation functions had, could reduce multipath fading of the pulse interference. The Modulated channel signal was sent into the IEEE 802.15.3a UWB channel. We analysis the ZCZs's inhibition to the interference multipath interference (MPI), as one of the main system sources interferences. The simulation in SIMULINK/MATLAB is described in detail. The result shows the system has better performance by comparison with that employing Walsh sequence square matrix, and it was verified by the formula in principle.

Assessment of myoblast circular RNA dynamics and its correlation with miRNA during myogenic differentiation.

PubMed

Zhang, Pengpeng; Xu, Haixia; Li, Rui; Wu, Wei; Chao, Zhe; Li, Cencen; Xia, Wei; Wang, Lei; Yang, Jinzeng; Xu, Yongjie

2018-06-01

Myoblast differentiation is a highly complex process that is regulated by proteins as well as by non-coding RNAs. Circular RNAs have been identified as an emerging new class of non-coding RNA in the modulation of skeletal muscle development, whereas their expression profiles and functional regulation in myoblast differentiation remain unknown. In the present study, we performed deep RNA-sequencing of C2C12 myoblasts during cell differentiation and uncovered 37,751 unique circular RNAs derived from 6943 hosting genes. The ensuing qRT-PCR and RNA fluorescence in situ hybridization verification were carried out to confirm the RNA-sequencing results. An unbiased analysis demonstrated dynamic circular RNA expression changes in the process of myoblast differentiation, and the circular RNA abundances were independent from their cognate linear RNAs. Gene ontology analysis showed that many down-regulated circular RNAs were exclusive to cell division and the cell cycle, whereas up-regulated circular RNAs were related to the cell development process. Furthermore, interaction networks of circular RNA-microRNA were constructed. Several microRNAs well-known for myoblast regulation, such as miR-133, miR-24 and miR-23a, were in this network. In summary, this study showed that circular RNA expression dynamics changed during myoblast differentiation. Circular RNAs play a role in regulating the myoblast cell cycle and development by acting as microRNA binding sites to facilitate their regulation of gene expression during myoblast differentiation. These findings open a new avenue for future investigation of this emerging RNA class in skeletal muscle growth and development. Copyright © 2018 Elsevier Ltd. All rights reserved.

The influence of viral coding sequences on pestivirus IRES activity reveals further parallels with translation initiation in prokaryotes.

PubMed Central

Fletcher, Simon P; Ali, Iraj K; Kaminski, Ann; Digard, Paul; Jackson, Richard J

2002-01-01

Classical swine fever virus (CSFV) is a member of the pestivirus family, which shares many features in common with hepatitis C virus (HCV). It is shown here that CSFV has an exceptionally efficient cis-acting internal ribosome entry segment (IRES), which, like that of HCV, is strongly influenced by the sequences immediately downstream of the initiation codon, and is optimal with viral coding sequences in this position. Constructs that retained 17 or more codons of viral coding sequence exhibited full IRES activity, but with only 12 codons, activity was approximately 66% of maximum in vitro (though close to maximum in transfected BHK cells), whereas with just 3 codons or fewer, the activity was only approximately 15% of maximum. The minimal coding region elements required for high activity were exchanged between HCV and CSFV. Although maximum activity was observed in each case with the homologous combination of coding region and 5' UTR, the heterologous combinations were sufficiently active to rule out a highly specific functional interplay between the 5' UTR and coding sequences. On the other hand, inversion of the coding sequences resulted in low IRES activity, particularly with the HCV coding sequences. RNA structure probing showed that the efficiency of internal initiation of these chimeric constructs correlated most closely with the degree of single-strandedness of the region around and immediately downstream of the initiation codon. The low activity IRESs could not be rescued by addition of supplementary eIF4A (the initiation factor with ATP-dependent RNA helicase activity). The extreme sensitivity to secondary structure around the initiation codon is likely to be due to the fact that the eIF4F complex (which has eIF4A as one of its subunits) is not required for and does not participate in initiation on these IRESs. PMID:12515388

Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado▿

PubMed Central

Sahl, Jason W.; Schmidt, Raleigh; Swanner, Elizabeth D.; Mandernack, Kevin W.; Templeton, Alexis S.; Kieft, Thomas L.; Smith, Richard L.; Sanford, William E.; Callaghan, Robert L.; Mitton, Jeffry B.; Spear, John R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. PMID:17981950

An archaebacterial homologue of the essential eubacterial cell division protein FtsZ.

PubMed Central

Baumann, P; Jackson, S P

1996-01-01

Life falls into three fundamental domains--Archaea, Bacteria, and Eucarya (formerly archaebacteria, eubacteria, and eukaryotes,. respectively). Though Archaea lack nuclei and share many morphological features with Bacteria, molecular analyses, principally of the transcription and translation machineries, have suggested that Archaea are more related to Eucarya than to Bacteria. Currently, little is known about the archaeal cell division apparatus. In Bacteria, a crucial component of the cell division machinery is FtsZ, a GTPase that localizes to a ring at the site of septation. Interestingly, FtsZ is distantly related in sequence to eukaryotic tubulins, which also interact with GTP and are components of the eukaryotic cell cytoskeleton. By screening for the ability to bind radiolabeled nucleotides, we have identified a protein of the hyperthermophilic archaeon Pyrococcus woesei that interacts tightly and specifically with GTP. Furthermore, through screening an expression library of P. woesei genomic DNA, we have cloned the gene encoding this protein. Sequence comparisons reveal that the P. woesei GTP-binding protein is strikingly related in sequence to eubacterial FtsZ and is marginally more similar to eukaryotic tubulins than are bacterial FtsZ proteins. Phylogenetic analyses reinforce the notion that there is an evolutionary linkage between FtsZ and tubulins. These findings suggest that the archaeal cell division apparatus may be fundamentally similar to that of Bacteria and lead us to consider the evolutionary relationships between Archaea, Bacteria, and Eucarya. Images Fig. 1 Fig. 2 PMID:8692886

Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics

PubMed Central

2012-01-01

Background Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, the accuracies of previous methods of finding borders based on entropy segmentation method still need to be improved. Methods In this study, we first applied a new recursive entropic segmentation method on DNA sequences to get preliminary significant cuts. A 22-symbol alphabet is used to capture the differential composition of nucleotide doublets and stop codon patterns along three phases in both DNA strands. This process requires no prior training datasets. Results Comparing with the previous segmentation methods, the experimental results on three bacteria genomes, Rickettsia prowazekii, Borrelia burgdorferi and E.coli, show that our approach improves the accuracy for finding the borders between coding and non-coding regions in DNA sequences. Conclusions This paper presents a new segmentation method in prokaryotes based on Jensen-Rényi divergence with a 22-symbol alphabet. For three bacteria genomes, comparing to A12_JR method, our method raised the accuracy of finding the borders between protein coding and non-coding regions in DNA sequences. PMID:23282225

Variable weight spectral amplitude coding for multiservice OCDMA networks

NASA Astrophysics Data System (ADS)

Seyedzadeh, Saleh; Rahimian, Farzad Pour; Glesk, Ivan; Kakaee, Majid H.

2017-09-01

The emergence of heterogeneous data traffic such as voice over IP, video streaming and online gaming have demanded networks with capability of supporting quality of service (QoS) at the physical layer with traffic prioritisation. This paper proposes a new variable-weight code based on spectral amplitude coding for optical code-division multiple-access (OCDMA) networks to support QoS differentiation. The proposed variable-weight multi-service (VW-MS) code relies on basic matrix construction. A mathematical model is developed for performance evaluation of VW-MS OCDMA networks. It is shown that the proposed code provides an optimal code length with minimum cross-correlation value when compared to other codes. Numerical results for a VW-MS OCDMA network designed for triple-play services operating at 0.622 Gb/s, 1.25 Gb/s and 2.5 Gb/s are considered.

Optical network security using unipolar Walsh code

NASA Astrophysics Data System (ADS)

Sikder, Somali; Sarkar, Madhumita; Ghosh, Shila

2018-04-01

Optical code-division multiple-access (OCDMA) is considered as a good technique to provide optical layer security. Many research works have been published to enhance optical network security by using optical signal processing. The paper, demonstrates the design of the AWG (arrayed waveguide grating) router-based optical network for spectral-amplitude-coding (SAC) OCDMA networks with Walsh Code to design a reconfigurable network codec by changing signature codes to against eavesdropping. In this paper we proposed a code reconfiguration scheme to improve the network access confidentiality changing the signature codes by cyclic rotations, for OCDMA system. Each of the OCDMA network users is assigned a unique signature code to transmit the information and at the receiving end each receiver correlates its own signature pattern a(n) with the receiving pattern s(n). The signal arriving at proper destination leads to s(n)=a(n).

Effects of Debris Entrainment and Multi-Phase Flow on Plug Loading in an MX Trench.

DTIC Science & Technology

1978-09-15

gas stream of density (pg) and velocity (Vg) is: -., * -) - * 2~ TD FD Pg (V P V) Vp-Vg I CD( TD ) (A.1) 4 where the drag coefficient (CD) is defined by...ATTN: FCPR ATTN: Code L53 , J. Forrest Field Command Naval Facilities Engineering Command Defense Nuclear Agency ATTN: Code 09M22C Livermore Division

Nonspatial Sequence Coding in CA1 Neurons

PubMed Central

Allen, Timothy A.; Salz, Daniel M.; McKenzie, Sam

2016-01-01

The hippocampus is critical to the memory for sequences of events, a defining feature of episodic memory. However, the fundamental neuronal mechanisms underlying this capacity remain elusive. While considerable research indicates hippocampal neurons can represent sequences of locations, direct evidence of coding for the memory of sequential relationships among nonspatial events remains lacking. To address this important issue, we recorded neural activity in CA1 as rats performed a hippocampus-dependent sequence-memory task. Briefly, the task involves the presentation of repeated sequences of odors at a single port and requires rats to identify each item as “in sequence” or “out of sequence”. We report that, while the animals' location and behavior remained constant, hippocampal activity differed depending on the temporal context of items—in this case, whether they were presented in or out of sequence. Some neurons showed this effect across items or sequence positions (general sequence cells), while others exhibited selectivity for specific conjunctions of item and sequence position information (conjunctive sequence cells) or for specific probe types (probe-specific sequence cells). We also found that the temporal context of individual trials could be accurately decoded from the activity of neuronal ensembles, that sequence coding at the single-cell and ensemble level was linked to sequence memory performance, and that slow-gamma oscillations (20–40 Hz) were more strongly modulated by temporal context and performance than theta oscillations (4–12 Hz). These findings provide compelling evidence that sequence coding extends beyond the domain of spatial trajectories and is thus a fundamental function of the hippocampus. SIGNIFICANCE STATEMENT The ability to remember the order of life events depends on the hippocampus, but the underlying neural mechanisms remain poorly understood. Here we addressed this issue by recording neural activity in hippocampal region CA1 while rats performed a nonspatial sequence memory task. We found that hippocampal neurons code for the temporal context of items (whether odors were presented in the correct or incorrect sequential position) and that this activity is linked with memory performance. The discovery of this novel form of temporal coding in hippocampal neurons advances our fundamental understanding of the neurobiology of episodic memory and will serve as a foundation for our cross-species, multitechnique approach aimed at elucidating the neural mechanisms underlying memory impairments in aging and dementia. PMID:26843637

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

Timeliness and Delay in the Cook County Juvenile Court Child Protection Division. Discussion Paper CS-45.

ERIC Educational Resources Information Center

Merry, Sheila M.; Peters, Clark M.; Goerge, Robert M.; Osuch, Ruth; Minor, Maria; Budde, Stephen

This study suggests that court procedures in Illinois must improve to assure that more children are placed in permanent homes in a timely way. The University of Chicago's Chapin Hall Center for Children examined the timeliness of the Circuit Court of Cook County, Illinois' Child Protection Division in completing the sequence of hearings and…

Comparison of simple sequence repeats in 19 Archaea.

PubMed

Trivedi, S

2006-12-05

All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.

Association of Amine-Receptor DNA Sequence Variants with Associative Learning in the Honeybee.

PubMed

Lagisz, Malgorzata; Mercer, Alison R; de Mouzon, Charlotte; Santos, Luana L S; Nakagawa, Shinichi

2016-03-01

Octopamine- and dopamine-based neuromodulatory systems play a critical role in learning and learning-related behaviour in insects. To further our understanding of these systems and resulting phenotypes, we quantified DNA sequence variations at six loci coding octopamine-and dopamine-receptors and their association with aversive and appetitive learning traits in a population of honeybees. We identified 79 polymorphic sequence markers (mostly SNPs and a few insertions/deletions) located within or close to six candidate genes. Intriguingly, we found that levels of sequence variation in the protein-coding regions studied were low, indicating that sequence variation in the coding regions of receptor genes critical to learning and memory is strongly selected against. Non-coding and upstream regions of the same genes, however, were less conserved and sequence variations in these regions were weakly associated with between-individual differences in learning-related traits. While these associations do not directly imply a specific molecular mechanism, they suggest that the cross-talk between dopamine and octopamine signalling pathways may influence olfactory learning and memory in the honeybee.

Operational evaluation of a DGPS / SATCOM VTS : final report

DOT National Transportation Integrated Search

1996-09-01

Satellite communications (SATCOM) using code division multiple access(CDMA) modulation and burst messaging, provided a new dimension to communication channel capacity, operating dependability, and area of coverage. This technology, together with diff...

AFB Directory of Services Listings

MedlinePlus

... 520) 770-3268 (TDD/TTY) Arizona Department of Economic Security: Rehabilitation Services Administration 1789 West Jefferson Street, ... Arizona Division Aging and Adult Services Department of Economic Security 1789 W. Jefferson, Site Code 950A-2SW ...

40 CFR 49.5511 - Identification of plan.

Code of Federal Regulations, 2012 CFR

2012-07-01

...-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations... Director, GRIC DEQ, to Deborah Jordan, Air Division Director, EPA Region 9, Re: Gila River Indian Community...

40 CFR 49.5511 - Identification of plan.

Code of Federal Regulations, 2014 CFR

2014-07-01

...-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations... Director, GRIC DEQ, to Deborah Jordan, Air Division Director, EPA Region 9, Re: Gila River Indian Community...

40 CFR 49.5511 - Identification of plan.

Code of Federal Regulations, 2013 CFR

2013-07-01

...-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations... Director, GRIC DEQ, to Deborah Jordan, Air Division Director, EPA Region 9, Re: Gila River Indian Community...

40 CFR 49.5511 - Identification of plan.

Code of Federal Regulations, 2011 CFR

2011-07-01

...-741-6030, or go to: http://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations... Director, GRIC DEQ, to Deborah Jordan, Air Division Director, EPA Region 9, Re: Gila River Indian Community...

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

PubMed

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

2007-07-01

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

National Combustion Code: A Multidisciplinary Combustor Design System

NASA Technical Reports Server (NTRS)

Stubbs, Robert M.; Liu, Nan-Suey

1997-01-01

The Internal Fluid Mechanics Division conducts both basic research and technology, and system technology research for aerospace propulsion systems components. The research within the division, which is both computational and experimental, is aimed at improving fundamental understanding of flow physics in inlets, ducts, nozzles, turbomachinery, and combustors. This article and the following three articles highlight some of the work accomplished in 1996. A multidisciplinary combustor design system is critical for optimizing the combustor design process. Such a system should include sophisticated computer-aided design (CAD) tools for geometry creation, advanced mesh generators for creating solid model representations, a common framework for fluid flow and structural analyses, modern postprocessing tools, and parallel processing. The goal of the present effort is to develop some of the enabling technologies and to demonstrate their overall performance in an integrated system called the National Combustion Code.

FOURTH SEMINAR TO THE MEMORY OF D.N. KLYSHKO: Algebraic solution of the synthesis problem for coded sequences

NASA Astrophysics Data System (ADS)

Leukhin, Anatolii N.

2005-08-01

The algebraic solution of a 'complex' problem of synthesis of phase-coded (PC) sequences with the zero level of side lobes of the cyclic autocorrelation function (ACF) is proposed. It is shown that the solution of the synthesis problem is connected with the existence of difference sets for a given code dimension. The problem of estimating the number of possible code combinations for a given code dimension is solved. It is pointed out that the problem of synthesis of PC sequences is related to the fundamental problems of discrete mathematics and, first of all, to a number of combinatorial problems, which can be solved, as the number factorisation problem, by algebraic methods by using the theory of Galois fields and groups.

Evaluating the protein coding potential of exonized transposable element sequences

PubMed Central

Piriyapongsa, Jittima; Rutledge, Mark T; Patel, Sanil; Borodovsky, Mark; Jordan, I King

2007-01-01

Background Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM) approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently exonized but unlikely to encode protein sequences. Conclusion The exaptation of the numerous TE sequences found in exons as bona fide protein coding sequences may prove to be far less common than has been suggested by the analysis of complete genomes. We hypothesize that many exonized TE sequences actually function as post-transcriptional regulators of gene expression, rather than coding sequences, which may act through a variety of double stranded RNA related regulatory pathways. Indeed, their relatively high copy numbers and similarity to sequences dispersed throughout the genome suggests that exonized TE sequences could serve as master regulators with a wide scope of regulatory influence. Reviewers: This article was reviewed by Itai Yanai, Kateryna D. Makova, Melissa Wilson (nominated by Kateryna D. Makova) and Cedric Feschotte (nominated by John M. Logsdon Jr.). PMID:18036258

Proceedings of the Mobile Satellite System Architectures and Multiple Access Techniques Workshop

NASA Technical Reports Server (NTRS)

Dessouky, Khaled

1989-01-01

The Mobile Satellite System Architectures and Multiple Access Techniques Workshop served as a forum for the debate of system and network architecture issues. Particular emphasis was on those issues relating to the choice of multiple access technique(s) for the Mobile Satellite Service (MSS). These proceedings contain articles that expand upon the 12 presentations given in the workshop. Contrasting views on Frequency Division Multiple Access (FDMA), Code Division Multiple Access (CDMA), and Time Division Multiple Access (TDMA)-based architectures are presented, and system issues relating to signaling, spacecraft design, and network management constraints are addressed. An overview article that summarizes the issues raised in the numerous discussion periods of the workshop is also included.

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Genomic Sequence around Butterfly Wing Development Genes: Annotation and Comparative Analysis

PubMed Central

Conceição, Inês C.; Long, Anthony D.; Gruber, Jonathan D.; Beldade, Patrícia

2011-01-01

Background Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. Methodology/Principal Findings We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations) and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes). Conclusions The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1) the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2) the high conservation of non-coding sequence around the genes wingless and Ecdysone receptor, both involved in multiple developmental processes including wing pattern formation. PMID:21909358

Speech processing using conditional observable maximum likelihood continuity mapping

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

Hogden, John; Nix, David

A computer implemented method enables the recognition of speech and speech characteristics. Parameters are initialized of first probability density functions that map between the symbols in the vocabulary of one or more sequences of speech codes that represent speech sounds and a continuity map. Parameters are also initialized of second probability density functions that map between the elements in the vocabulary of one or more desired sequences of speech transcription symbols and the continuity map. The parameters of the probability density functions are then trained to maximize the probabilities of the desired sequences of speech-transcription symbols. A new sequence ofmore » speech codes is then input to the continuity map having the trained first and second probability function parameters. A smooth path is identified on the continuity map that has the maximum probability for the new sequence of speech codes. The probability of each speech transcription symbol for each input speech code can then be output.« less

SequenceL: Automated Parallel Algorithms Derived from CSP-NT Computational Laws

NASA Technical Reports Server (NTRS)

Cooke, Daniel; Rushton, Nelson

2013-01-01

With the introduction of new parallel architectures like the cell and multicore chips from IBM, Intel, AMD, and ARM, as well as the petascale processing available for highend computing, a larger number of programmers will need to write parallel codes. Adding the parallel control structure to the sequence, selection, and iterative control constructs increases the complexity of code development, which often results in increased development costs and decreased reliability. SequenceL is a high-level programming language that is, a programming language that is closer to a human s way of thinking than to a machine s. Historically, high-level languages have resulted in decreased development costs and increased reliability, at the expense of performance. In recent applications at JSC and in industry, SequenceL has demonstrated the usual advantages of high-level programming in terms of low cost and high reliability. SequenceL programs, however, have run at speeds typically comparable with, and in many cases faster than, their counterparts written in C and C++ when run on single-core processors. Moreover, SequenceL is able to generate parallel executables automatically for multicore hardware, gaining parallel speedups without any extra effort from the programmer beyond what is required to write the sequen tial/singlecore code. A SequenceL-to-C++ translator has been developed that automatically renders readable multithreaded C++ from a combination of a SequenceL program and sample data input. The SequenceL language is based on two fundamental computational laws, Consume-Simplify- Produce (CSP) and Normalize-Trans - pose (NT), which enable it to automate the creation of parallel algorithms from high-level code that has no annotations of parallelism whatsoever. In our anecdotal experience, SequenceL development has been in every case less costly than development of the same algorithm in sequential (that is, single-core, single process) C or C++, and an order of magnitude less costly than development of comparable parallel code. Moreover, SequenceL not only automatically parallelizes the code, but since it is based on CSP-NT, it is provably race free, thus eliminating the largest quality challenge the parallelized software developer faces.

ANN modeling of DNA sequences: new strategies using DNA shape code.

PubMed

Parbhane, R V; Tambe, S S; Kulkarni, B D

2000-09-01

Two new encoding strategies, namely, wedge and twist codes, which are based on the DNA helical parameters, are introduced to represent DNA sequences in artificial neural network (ANN)-based modeling of biological systems. The performance of the new coding strategies has been evaluated by conducting three case studies involving mapping (modeling) and classification applications of ANNs. The proposed coding schemes have been compared rigorously and shown to outperform the existing coding strategies especially in situations wherein limited data are available for building the ANN models.

An Evaluation of Sea Turtle Populations and Survival Status on Vieques Island.

DTIC Science & Technology

1982-06-22

Pritchard T. H. Stubbs Florida Audubon Society (N66001-80-C-0560) 22 June 1982 Prepared for Marine Sciences Division Approved for public release...the Florida Audubon Society for NOSC Marine Sciences Division (Code 513). I Released by Under authority of S. Yamamoto. Head H.O. Porter. Head Marine ...Coollco so wo . i .0*W ow a AomY b block4 m.. Reptiles -. HawksbilIVieques Isand Loaesbsd Green turtle Nestn Turtles Loatharback 2 0. AGSTA ACT

The primitive code and repeats of base oligomers as the primordial protein-encoding sequence.

PubMed Central

Ohno, S; Epplen, J T

1983-01-01

Even if the prebiotic self-replication of nucleic acids and the subsequent emergence of primitive, enzyme-independent tRNAs are accepted as plausible, the origin of life by spontaneous generation still appears improbable. This is because the just-emerged primitive translational machinery had to cope with base sequences that were not preselected for their coding potentials. Particularly if the primitive mitochondria-like code with four chain-terminating base triplets preceded the universal code, the translation of long, randomly generated, base sequences at this critical stage would have merely resulted in the production of short oligopeptides instead of long polypeptide chains. We present the base sequence of a mouse transcript containing tetranucleotide repeats conserved during evolution. Even if translated in accordance with the primitive mitochondria-like code, this transcript in its three reading frames can yield 245-, 246-, and 251-residue-long tetrapeptidic periodical polypeptides that are already acquiring longer periodicities. We contend that the first set of base sequences translated at the beginning of life were such oligonucleotide repeats. By quickly acquiring longer periodicities, their products must have soon gained characteristic secondary structures--alpha-helical or beta-sheet or both. PMID:6574491

NRL Radar Division C++ Coding Standard

DTIC Science & Technology

2016-12-05

The coding standard provides tools aimed at helping C++ programmers develop programs that are free of common types of errors, maintainable by...different programmers , portable to other operating systems, easy to read and understand, and have a consistent style. Questions of design, such as how to...mandatory for any organization with quality goals. The purpose of this standard is to provide tools aimed at helping C++ programmers develop programs that

Validation and Intercomparison Studies Within GODAE

DTIC Science & Technology

2009-09-01

unlimited. 13. SUPPLEMENTARY NOTES 20091228154 14. ABSTRACT During the Global Ocean Data Assimilation Experiment (GODAE), seven international... global -ocean and basin-scale forecasting systems of different countries in routine interaction and continuous operation, (2) to assess the quality and... Franchi , 7000 Public Affairs (Unclassified/ Unlimited Only), Code 7o30 4 Division, Code ^VtcV Vs-Jc \\ -Vi<-’/c ••>’ 3^v’.-:5, w. 3Uo|eri 1

Productivity Enhancement Program (PEP) for the Power Plant Division, Naval Air Rework Facility, North Island, San Diego. Preliminary Data Required.

DTIC Science & Technology

1984-02-01

97322 C9 571H0 NOTE 1--Ht» 360214-77 M.ORKID MDRA i D - \\—r— .ofjTxx .05r51-8* 62 ZBJA 0 ZANA D YBFA 0 : : 1.S508-P81 2F-SEE...Navy Recruiting Command (Code 20) Commanding Officer, Naval Aerospace Medical Institute (Library Code 12) (2) Commanding Officer Naval Technical

High performance and cost effective CO-OFDM system aided by polar code.

PubMed

Liu, Ling; Xiao, Shilin; Fang, Jiafei; Zhang, Lu; Zhang, Yunhao; Bi, Meihua; Hu, Weisheng

2017-02-06

A novel polar coded coherent optical orthogonal frequency division multiplexing (CO-OFDM) system is proposed and demonstrated through experiment for the first time. The principle of a polar coded CO-OFDM signal is illustrated theoretically and the suitable polar decoding method is discussed. Results show that the polar coded CO-OFDM signal achieves a net coding gain (NCG) of more than 10 dB at bit error rate (BER) of 10^-3 over 25-Gb/s 480-km transmission in comparison with conventional CO-OFDM. Also, compared to the 25-Gb/s low-density parity-check (LDPC) coded CO-OFDM 160-km system, the polar code provides a NCG of 0.88 dB @BER = 10^-3. Moreover, the polar code can relieve the laser linewidth requirement massively to get a more cost-effective CO-OFDM system.

Adaptive receiver structures for asynchronous CDMA systems

NASA Astrophysics Data System (ADS)

Rapajic, Predrag B.; Vucetic, Branka S.

1994-05-01

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

Effect of Pointing Error on the BER Performance of an Optical CDMA FSO Link with SIK Receiver

NASA Astrophysics Data System (ADS)

Nazrul Islam, A. K. M.; Majumder, S. P.

2017-12-01

An analytical approach is presented for an optical code division multiple access (OCDMA) system over free space optical (FSO) channel considering the effect of pointing error between the transmitter and the receiver. Analysis is carried out with an optical sequence inverse keying (SIK) correlator receiver with intensity modulation and direct detection (IM/DD) to find the bit error rate (BER) with pointing error. The results are evaluated numerically in terms of signal-to-noise plus multi-access interference (MAI) ratio, BER and power penalty due to pointing error. It is noticed that the OCDMA FSO system is highly affected by pointing error with significant power penalty at a BER of 10-6 and 10-9. For example, penalty at BER 10-9 is found to be 9 dB corresponding to normalized pointing error of 1.4 for 16 users with processing gain of 256 and is reduced to 6.9 dB when the processing gain is increased to 1,024.

Genomics dataset of unidentified disclosed isolates.

PubMed

Rekadwad, Bhagwan N

2016-09-01

Analysis of DNA sequences is necessary for higher hierarchical classification of the organisms. It gives clues about the characteristics of organisms and their taxonomic position. This dataset is chosen to find complexities in the unidentified DNA in the disclosed patents. A total of 17 unidentified DNA sequences were thoroughly analyzed. The quick response codes were generated. AT/GC content of the DNA sequences analysis was carried out. The QR is helpful for quick identification of isolates. AT/GC content is helpful for studying their stability at different temperatures. Additionally, a dataset on cleavage code and enzyme code studied under the restriction digestion study, which helpful for performing studies using short DNA sequences was reported. The dataset disclosed here is the new revelatory data for exploration of unique DNA sequences for evaluation, identification, comparison and analysis.

CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences.

PubMed

Hazes, Bart

2014-02-28

Protein-coding DNA sequences and their corresponding amino acid sequences are routinely used to study relationships between sequence, structure, function, and evolution. The rapidly growing size of sequence databases increases the power of such comparative analyses but it makes it more challenging to prepare high quality sequence data sets with control over redundancy, quality, completeness, formatting, and labeling. Software tools for some individual steps in this process exist but manual intervention remains a common and time consuming necessity. CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5' and 3' ends, full taxonomic data, and a heuristic to rank the scientific interest of each species. This rich information allows fully automated data set preparation with a level of sophistication that aims to meet or exceed manual processing. Defaults ensure ease of use for typical scenarios while allowing great flexibility when needed. Access is via a free web server at http://hazeslab.med.ualberta.ca/CDSbank/. CDSbank presents a user-friendly web server to download, filter, format, and name large sequence data sets. Common usage scenarios can be accessed via pre-programmed default choices, while optional sections give full control over the processing pipeline. Particular strengths are: extract protein-coding DNA sequences just as easily as amino acid sequences, full access to taxonomy for labeling and filtering, awareness of incomplete sequences, and the ability to take one protein sequence and extract all synonymous CDS or identical protein sequences in other species. Finally, CDSbank can also create labeled property files to, for instance, annotate or re-label phylogenetic trees.

OCDMA Over WDM PON—Solution Path to Gigabit-Symmetric FTTH

NASA Astrophysics Data System (ADS)

Kitayama, Ken-Ichi; Wang, Xu; Wada, Naoya

2006-04-01

It will be revealed that a myth of deploying low bit-rate uplink fiber-to-the-home (FTTH) services while providing a high bit-rate downlink is wrong. Therefore, for the future broadband FTTH services, the focus should be on the capability to provide gigabit-or even multigigabits-per-second both in up-and downlinks, namely gigabit symmetric systems. Optical code-division multiple access (OCDMA) now deserves a revisit as a powerful alternative to time-division multiple access and wavelength-division multiple (WDM) access in FTTH systems. In this paper, the authors will first highlight the OCDMA systems. The system architecture and its operation principle, code design, optical en/decoding, using a long superstructured fiber Bragg grating (SSFBG) en/decoder, and its system performance will be described. Next, an OCDMA over WDM passive optical network (PON) as a solution for the gigabit-symmetric FTTH systems will be proposed. The system architecture and the WDM interchannel crosstalk will be studied. It will be shown that by taking advantage of reflection spectrum notches of the SSFBG en/decoder, the WDM interchannel crosstalk can be suppressed and can enable OCDMA over WDM PON to simultaneously provide multigigabit-per-second up-and downlinks to a large number of users.

76 FR 70703 - Senior Executive Service: Membership of Performance Review Board

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-15

...;and investigations, committee meetings, agency decisions and rulings, #0;delegations of authority..., Employee and Labor Relations Division. [FR Doc. 2011-29427 Filed 11-14-11; 8:45 am] BILLING CODE P ...

48 CFR 1552.211-80 - Data standards for the transmission of laboratory measurement results.

Code of Federal Regulations, 2010 CFR

2010-10-01

... this contract. Copies of the Order may be obtained by written request to: Office of Information Resources Management, Information Management and Systems Division, Mail Code (3404), Ariel Rios Building...

48 CFR 1552.211-80 - Data standards for the transmission of laboratory measurement results.

Code of Federal Regulations, 2012 CFR

2012-10-01

... this contract. Copies of the Order may be obtained by written request to: Office of Information Resources Management, Information Management and Systems Division, Mail Code (3404), Ariel Rios Building...

48 CFR 1552.211-80 - Data standards for the transmission of laboratory measurement results.

Code of Federal Regulations, 2011 CFR

2011-10-01

... this contract. Copies of the Order may be obtained by written request to: Office of Information Resources Management, Information Management and Systems Division, Mail Code (3404), Ariel Rios Building...

Variability and transmission by Aphis glycines of North American and Asian Soybean mosaic virus isolates.

PubMed

Domier, L L; Latorre, I J; Steinlage, T A; McCoppin, N; Hartman, G L

2003-10-01

The variability of North American and Asian strains and isolates of Soybean mosaic virus was investigated. First, polymerase chain reaction (PCR) products representing the coat protein (CP)-coding regions of 38 SMVs were analyzed for restriction fragment length polymorphisms (RFLP). Second, the nucleotide and predicted amino acid sequence variability of the P1-coding region of 18 SMVs and the helper component/protease (HC/Pro) and CP-coding regions of 25 SMVs were assessed. The CP nucleotide and predicted amino acid sequences were the most similar and predicted phylogenetic relationships similar to those obtained from RFLP analysis. Neither RFLP nor sequence analyses of the CP-coding regions grouped the SMVs by geographical origin. The P1 and HC/Pro sequences were more variable and separated the North American and Asian SMV isolates into two groups similar to previously reported differences in pathogenic diversity of the two sets of SMV isolates. The P1 region was the most informative of the three regions analyzed. To assess the biological relevance of the sequence differences in the HC/Pro and CP coding regions, the transmissibility of 14 SMV isolates by Aphis glycines was tested. All field isolates of SMV were transmitted efficiently by A. glycines, but the laboratory isolates analyzed were transmitted poorly. The amino acid sequences from most, but not all, of the poorly transmitted isolates contained mutations in the aphid transmission-associated DAG and/or KLSC amino acid sequence motifs of CP and HC/Pro, respectively.

Closed Genome Sequence of Chryseobacterium piperi Strain CTMT/ATCC BAA-1782, a Gram-Negative Bacterium with Clostridial Neurotoxin-Like Coding Sequences

PubMed Central

Wentz, Travis G.; Muruvanda, Tim; Thirunavukkarasu, Nagarajan; Hoffmann, Maria; Allard, Marc W.; Hodge, David R.; Pillai, Segaran P.; Hammack, Thomas S.; Brown, Eric W.

2017-01-01

ABSTRACT Clostridial neurotoxins, including botulinum and tetanus neurotoxins, are among the deadliest known bacterial toxins. Until recently, the horizontal mobility of this toxin gene family appeared to be limited to the genus Clostridium. We report here the closed genome sequence of Chryseobacterium piperi, a Gram-negative bacterium containing coding sequences with homology to clostridial neurotoxin family proteins. PMID:29192076

Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.

PubMed

Schwientek, Patrick; Neshat, Armin; Kalinowski, Jörn; Klein, Andreas; Rückert, Christian; Schneiker-Bekel, Susanne; Wendler, Sergej; Stoye, Jens; Pühler, Alfred

2014-11-20

Actinoplanes sp. SE50/110 is the producer of the alpha-glucosidase inhibitor acarbose, which is an economically relevant and potent drug in the treatment of type-2 diabetes mellitus. In this study, we present the detection of transcription start sites on this genome by sequencing enriched 5'-ends of primary transcripts. Altogether, 1427 putative transcription start sites were initially identified. With help of the annotated genome sequence, 661 transcription start sites were found to belong to the leader region of protein-coding genes with the surprising result that roughly 20% of these genes rank among the class of leaderless transcripts. Next, conserved promoter motifs were identified for protein-coding genes with and without leader sequences. The mapped transcription start sites were finally used to improve the annotation of the Actinoplanes sp. SE50/110 genome sequence. Concerning protein-coding genes, 41 translation start sites were corrected and 9 novel protein-coding genes could be identified. In addition to this, 122 previously undetermined non-coding RNA (ncRNA) genes of Actinoplanes sp. SE50/110 were defined. Focusing on antisense transcription start sites located within coding genes or their leader sequences, it was discovered that 96 of those ncRNA genes belong to the class of antisense RNA (asRNA) genes. The remaining 26 ncRNA genes were found outside of known protein-coding genes. Four chosen examples of prominent ncRNA genes, namely the transfer messenger RNA gene ssrA, the ribonuclease P class A RNA gene rnpB, the cobalamin riboswitch RNA gene cobRS, and the selenocysteine-specific tRNA gene selC, are presented in more detail. This study demonstrates that sequencing of enriched 5'-ends of primary transcripts and the identification of transcription start sites are valuable tools for advanced genome annotation of Actinoplanes sp. SE50/110 and most probably also for other bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

LCMV beamforming for a novel wireless local positioning system: a stationarity analysis

NASA Astrophysics Data System (ADS)

Tong, Hui; Zekavat, Seyed A.

2005-05-01

In this paper, we discuss the implementation of Linear Constrained Minimum Variance (LCMV) beamforming (BF) for a novel Wireless Local Position System (WLPS). WLPS main components are: (a) a dynamic base station (DBS), and (b) a transponder (TRX), both mounted on mobiles. WLPS might be considered as a node in a Mobile Adhoc NETwork (MANET). Each TRX is assigned an identification (ID) code. DBS transmits periodic short bursts of energy which contains an ID request (IDR) signal. The TRX transmits back its ID code (a signal with a limited duration) to the DBS as soon as it detects the IDR signal. Hence, the DBS receives non-continuous signals transmitted by TRX. In this work, we assume asynchronous Direct-Sequence Code Division Multiple Access (DS-CDMA) transmission from the TRX with antenna array/LCMV BF mounted at the DBS, and we discuss the implementation of the observed signal covariance matrix for LCMV BF. In LCMV BF, the observed covariance matrix should be estimated. Usually sample covariance matrix (SCM) is used to estimate this covariance matrix assuming a stationary model for the observed data which is the case in many communication systems. However, due to the non-stationary behavior of the received signal in WLPS systems, SCM does not lead to a high WLPS performance compared to even a conventional beamformer. A modified covariance matrix estimation method which utilizes the cyclostationarity property of WLPS system is introduced as a solution to this problem. It is shown that this method leads to a significant improvement in the WLPS performance.

Motion Detection in Ultrasound Image-Sequences Using Tensor Voting

NASA Astrophysics Data System (ADS)

Inba, Masafumi; Yanagida, Hirotaka; Tamura, Yasutaka

2008-05-01

Motion detection in ultrasound image sequences using tensor voting is described. We have been developing an ultrasound imaging system adopting a combination of coded excitation and synthetic aperture focusing techniques. In our method, frame rate of the system at distance of 150 mm reaches 5000 frame/s. Sparse array and short duration coded ultrasound signals are used for high-speed data acquisition. However, many artifacts appear in the reconstructed image sequences because of the incompleteness of the transmitted code. To reduce the artifacts, we have examined the application of tensor voting to the imaging method which adopts both coded excitation and synthetic aperture techniques. In this study, the basis of applying tensor voting and the motion detection method to ultrasound images is derived. It was confirmed that velocity detection and feature enhancement are possible using tensor voting in the time and space of simulated ultrasound three-dimensional image sequences.

The primary structure of the Saccharomyces cerevisiae gene for 3-phosphoglycerate kinase.

PubMed Central

Hitzeman, R A; Hagie, F E; Hayflick, J S; Chen, C Y; Seeburg, P H; Derynck, R

1982-01-01

The DNA sequence of the gene for the yeast glycolytic enzyme, 3-phosphoglycerate kinase (PGK), has been obtained by sequencing part of a 3.1 kbp HindIII fragment obtained from the yeast genome. The structural gene sequence corresponds to a reading frame of 1251 bp coding for 416 amino acids with no intervening DNA sequences. The amino acid sequence is approximately 65 percent homologous with human and horse PGK protein sequences and is in general agreement with the published protein sequence for yeast PGK. As for other highly expressed structural genes in yeast, the coding sequence is highly codon biased with 95 percent of the amino acids coded for by a select 25 codons (out of 61 possible). Besides structural DNA sequence, 291 bp of 5'-flanking sequence and 286 bp of 3'-flanking sequence were determined. Transcription starts 36 nucleotides upstream from the translational start and stops 86-93 nucleotides downstream from the translational stop. These results suggest a non-polyadenylated mRNA length of 1373 to 1380 nucleotides, which is consistent with the observed length of 1500 nucleotides for polyadenylated PGK mRNA. A sequence TATATATAAA is found at 145 nucleotides upstream from the translational start. This sequence resembles the TATAAA box that is possibly associated with RNA polymerase II binding. Images PMID:6296791

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

NASA Technical Reports Server (NTRS)

Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis.

PubMed

Buldyrev, S V; Goldberger, A L; Havlin, S; Mantegna, R N; Matsa, M E; Peng, C K; Simons, M; Stanley, H E

1995-05-01

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

NASA Technical Reports Server (NTRS)

Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Matsa, M. E.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.

PubMed

Flannick, Jason; Fuchsberger, Christian; Mahajan, Anubha; Teslovich, Tanya M; Agarwala, Vineeta; Gaulton, Kyle J; Caulkins, Lizz; Koesterer, Ryan; Ma, Clement; Moutsianas, Loukas; McCarthy, Davis J; Rivas, Manuel A; Perry, John R B; Sim, Xueling; Blackwell, Thomas W; Robertson, Neil R; Rayner, N William; Cingolani, Pablo; Locke, Adam E; Tajes, Juan Fernandez; Highland, Heather M; Dupuis, Josee; Chines, Peter S; Lindgren, Cecilia M; Hartl, Christopher; Jackson, Anne U; Chen, Han; Huyghe, Jeroen R; van de Bunt, Martijn; Pearson, Richard D; Kumar, Ashish; Müller-Nurasyid, Martina; Grarup, Niels; Stringham, Heather M; Gamazon, Eric R; Lee, Jaehoon; Chen, Yuhui; Scott, Robert A; Below, Jennifer E; Chen, Peng; Huang, Jinyan; Go, Min Jin; Stitzel, Michael L; Pasko, Dorota; Parker, Stephen C J; Varga, Tibor V; Green, Todd; Beer, Nicola L; Day-Williams, Aaron G; Ferreira, Teresa; Fingerlin, Tasha; Horikoshi, Momoko; Hu, Cheng; Huh, Iksoo; Ikram, Mohammad Kamran; Kim, Bong-Jo; Kim, Yongkang; Kim, Young Jin; Kwon, Min-Seok; Lee, Juyoung; Lee, Selyeong; Lin, Keng-Han; Maxwell, Taylor J; Nagai, Yoshihiko; Wang, Xu; Welch, Ryan P; Yoon, Joon; Zhang, Weihua; Barzilai, Nir; Voight, Benjamin F; Han, Bok-Ghee; Jenkinson, Christopher P; Kuulasmaa, Teemu; Kuusisto, Johanna; Manning, Alisa; Ng, Maggie C Y; Palmer, Nicholette D; Balkau, Beverley; Stančáková, Alena; Abboud, Hanna E; Boeing, Heiner; Giedraitis, Vilmantas; Prabhakaran, Dorairaj; Gottesman, Omri; Scott, James; Carey, Jason; Kwan, Phoenix; Grant, George; Smith, Joshua D; Neale, Benjamin M; Purcell, Shaun; Butterworth, Adam S; Howson, Joanna M M; Lee, Heung Man; Lu, Yingchang; Kwak, Soo-Heon; Zhao, Wei; Danesh, John; Lam, Vincent K L; Park, Kyong Soo; Saleheen, Danish; So, Wing Yee; Tam, Claudia H T; Afzal, Uzma; Aguilar, David; Arya, Rector; Aung, Tin; Chan, Edmund; Navarro, Carmen; Cheng, Ching-Yu; Palli, Domenico; Correa, Adolfo; Curran, Joanne E; Rybin, Dennis; Farook, Vidya S; Fowler, Sharon P; Freedman, Barry I; Griswold, Michael; Hale, Daniel Esten; Hicks, Pamela J; Khor, Chiea-Chuen; Kumar, Satish; Lehne, Benjamin; Thuillier, Dorothée; Lim, Wei Yen; Liu, Jianjun; Loh, Marie; Musani, Solomon K; Puppala, Sobha; Scott, William R; Yengo, Loïc; Tan, Sian-Tsung; Taylor, Herman A; Thameem, Farook; Wilson, Gregory; Wong, Tien Yin; Njølstad, Pål Rasmus; Levy, Jonathan C; Mangino, Massimo; Bonnycastle, Lori L; Schwarzmayr, Thomas; Fadista, João; Surdulescu, Gabriela L; Herder, Christian; Groves, Christopher J; Wieland, Thomas; Bork-Jensen, Jette; Brandslund, Ivan; Christensen, Cramer; Koistinen, Heikki A; Doney, Alex S F; Kinnunen, Leena; Esko, Tõnu; Farmer, Andrew J; Hakaste, Liisa; Hodgkiss, Dylan; Kravic, Jasmina; Lyssenko, Valeri; Hollensted, Mette; Jørgensen, Marit E; Jørgensen, Torben; Ladenvall, Claes; Justesen, Johanne Marie; Käräjämäki, Annemari; Kriebel, Jennifer; Rathmann, Wolfgang; Lannfelt, Lars; Lauritzen, Torsten; Narisu, Narisu; Linneberg, Allan; Melander, Olle; Milani, Lili; Neville, Matt; Orho-Melander, Marju; Qi, Lu; Qi, Qibin; Roden, Michael; Rolandsson, Olov; Swift, Amy; Rosengren, Anders H; Stirrups, Kathleen; Wood, Andrew R; Mihailov, Evelin; Blancher, Christine; Carneiro, Mauricio O; Maguire, Jared; Poplin, Ryan; Shakir, Khalid; Fennell, Timothy; DePristo, Mark; de Angelis, Martin Hrabé; Deloukas, Panos; Gjesing, Anette P; Jun, Goo; Nilsson, Peter; Murphy, Jacquelyn; Onofrio, Robert; Thorand, Barbara; Hansen, Torben; Meisinger, Christa; Hu, Frank B; Isomaa, Bo; Karpe, Fredrik; Liang, Liming; Peters, Annette; Huth, Cornelia; O'Rahilly, Stephen P; Palmer, Colin N A; Pedersen, Oluf; Rauramaa, Rainer; Tuomilehto, Jaakko; Salomaa, Veikko; Watanabe, Richard M; Syvänen, Ann-Christine; Bergman, Richard N; Bharadwaj, Dwaipayan; Bottinger, Erwin P; Cho, Yoon Shin; Chandak, Giriraj R; Chan, Juliana Cn; Chia, Kee Seng; Daly, Mark J; Ebrahim, Shah B; Langenberg, Claudia; Elliott, Paul; Jablonski, Kathleen A; Lehman, Donna M; Jia, Weiping; Ma, Ronald C W; Pollin, Toni I; Sandhu, Manjinder; Tandon, Nikhil; Froguel, Philippe; Barroso, Inês; Teo, Yik Ying; Zeggini, Eleftheria; Loos, Ruth J F; Small, Kerrin S; Ried, Janina S; DeFronzo, Ralph A; Grallert, Harald; Glaser, Benjamin; Metspalu, Andres; Wareham, Nicholas J; Walker, Mark; Banks, Eric; Gieger, Christian; Ingelsson, Erik; Im, Hae Kyung; Illig, Thomas; Franks, Paul W; Buck, Gemma; Trakalo, Joseph; Buck, David; Prokopenko, Inga; Mägi, Reedik; Lind, Lars; Farjoun, Yossi; Owen, Katharine R; Gloyn, Anna L; Strauch, Konstantin; Tuomi, Tiinamaija; Kooner, Jaspal Singh; Lee, Jong-Young; Park, Taesung; Donnelly, Peter; Morris, Andrew D; Hattersley, Andrew T; Bowden, Donald W; Collins, Francis S; Atzmon, Gil; Chambers, John C; Spector, Timothy D; Laakso, Markku; Strom, Tim M; Bell, Graeme I; Blangero, John; Duggirala, Ravindranath; Tai, E Shyong; McVean, Gilean; Hanis, Craig L; Wilson, James G; Seielstad, Mark; Frayling, Timothy M; Meigs, James B; Cox, Nancy J; Sladek, Rob; Lander, Eric S; Gabriel, Stacey; Mohlke, Karen L; Meitinger, Thomas; Groop, Leif; Abecasis, Goncalo; Scott, Laura J; Morris, Andrew P; Kang, Hyun Min; Altshuler, David; Burtt, Noël P; Florez, Jose C; Boehnke, Michael; McCarthy, Mark I

2017-12-19

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

PubMed Central

Jason, Flannick; Fuchsberger, Christian; Mahajan, Anubha; Teslovich, Tanya M.; Agarwala, Vineeta; Gaulton, Kyle J.; Caulkins, Lizz; Koesterer, Ryan; Ma, Clement; Moutsianas, Loukas; McCarthy, Davis J.; Rivas, Manuel A.; Perry, John R. B.; Sim, Xueling; Blackwell, Thomas W.; Robertson, Neil R.; Rayner, N William; Cingolani, Pablo; Locke, Adam E.; Tajes, Juan Fernandez; Highland, Heather M.; Dupuis, Josee; Chines, Peter S.; Lindgren, Cecilia M.; Hartl, Christopher; Jackson, Anne U.; Chen, Han; Huyghe, Jeroen R.; van de Bunt, Martijn; Pearson, Richard D.; Kumar, Ashish; Müller-Nurasyid, Martina; Grarup, Niels; Stringham, Heather M.; Gamazon, Eric R.; Lee, Jaehoon; Chen, Yuhui; Scott, Robert A.; Below, Jennifer E.; Chen, Peng; Huang, Jinyan; Go, Min Jin; Stitzel, Michael L.; Pasko, Dorota; Parker, Stephen C. J.; Varga, Tibor V.; Green, Todd; Beer, Nicola L.; Day-Williams, Aaron G.; Ferreira, Teresa; Fingerlin, Tasha; Horikoshi, Momoko; Hu, Cheng; Huh, Iksoo; Ikram, Mohammad Kamran; Kim, Bong-Jo; Kim, Yongkang; Kim, Young Jin; Kwon, Min-Seok; Lee, Juyoung; Lee, Selyeong; Lin, Keng-Han; Maxwell, Taylor J.; Nagai, Yoshihiko; Wang, Xu; Welch, Ryan P.; Yoon, Joon; Zhang, Weihua; Barzilai, Nir; Voight, Benjamin F.; Han, Bok-Ghee; Jenkinson, Christopher P.; Kuulasmaa, Teemu; Kuusisto, Johanna; Manning, Alisa; Ng, Maggie C. Y.; Palmer, Nicholette D.; Balkau, Beverley; Stančáková, Alena; Abboud, Hanna E.; Boeing, Heiner; Giedraitis, Vilmantas; Prabhakaran, Dorairaj; Gottesman, Omri; Scott, James; Carey, Jason; Kwan, Phoenix; Grant, George; Smith, Joshua D.; Neale, Benjamin M.; Purcell, Shaun; Butterworth, Adam S.; Howson, Joanna M. M.; Lee, Heung Man; Lu, Yingchang; Kwak, Soo-Heon; Zhao, Wei; Danesh, John; Lam, Vincent K. L.; Park, Kyong Soo; Saleheen, Danish; So, Wing Yee; Tam, Claudia H. T.; Afzal, Uzma; Aguilar, David; Arya, Rector; Aung, Tin; Chan, Edmund; Navarro, Carmen; Cheng, Ching-Yu; Palli, Domenico; Correa, Adolfo; Curran, Joanne E.; Rybin, Dennis; Farook, Vidya S.; Fowler, Sharon P.; Freedman, Barry I.; Griswold, Michael; Hale, Daniel Esten; Hicks, Pamela J.; Khor, Chiea-Chuen; Kumar, Satish; Lehne, Benjamin; Thuillier, Dorothée; Lim, Wei Yen; Liu, Jianjun; Loh, Marie; Musani, Solomon K.; Puppala, Sobha; Scott, William R.; Yengo, Loïc; Tan, Sian-Tsung; Taylor, Herman A.; Thameem, Farook; Wilson, Gregory; Wong, Tien Yin; Njølstad, Pål Rasmus; Levy, Jonathan C.; Mangino, Massimo; Bonnycastle, Lori L.; Schwarzmayr, Thomas; Fadista, João; Surdulescu, Gabriela L.; Herder, Christian; Groves, Christopher J.; Wieland, Thomas; Bork-Jensen, Jette; Brandslund, Ivan; Christensen, Cramer; Koistinen, Heikki A.; Doney, Alex S. F.; Kinnunen, Leena; Esko, Tõnu; Farmer, Andrew J.; Hakaste, Liisa; Hodgkiss, Dylan; Kravic, Jasmina; Lyssenko, Valeri; Hollensted, Mette; Jørgensen, Marit E.; Jørgensen, Torben; Ladenvall, Claes; Justesen, Johanne Marie; Käräjämäki, Annemari; Kriebel, Jennifer; Rathmann, Wolfgang; Lannfelt, Lars; Lauritzen, Torsten; Narisu, Narisu; Linneberg, Allan; Melander, Olle; Milani, Lili; Neville, Matt; Orho-Melander, Marju; Qi, Lu; Qi, Qibin; Roden, Michael; Rolandsson, Olov; Swift, Amy; Rosengren, Anders H.; Stirrups, Kathleen; Wood, Andrew R.; Mihailov, Evelin; Blancher, Christine; Carneiro, Mauricio O.; Maguire, Jared; Poplin, Ryan; Shakir, Khalid; Fennell, Timothy; DePristo, Mark; de Angelis, Martin Hrabé; Deloukas, Panos; Gjesing, Anette P.; Jun, Goo; Nilsson, Peter; Murphy, Jacquelyn; Onofrio, Robert; Thorand, Barbara; Hansen, Torben; Meisinger, Christa; Hu, Frank B.; Isomaa, Bo; Karpe, Fredrik; Liang, Liming; Peters, Annette; Huth, Cornelia; O'Rahilly, Stephen P; Palmer, Colin N. A.; Pedersen, Oluf; Rauramaa, Rainer; Tuomilehto, Jaakko; Salomaa, Veikko; Watanabe, Richard M.; Syvänen, Ann-Christine; Bergman, Richard N.; Bharadwaj, Dwaipayan; Bottinger, Erwin P.; Cho, Yoon Shin; Chandak, Giriraj R.; Chan, Juliana CN; Chia, Kee Seng; Daly, Mark J.; Ebrahim, Shah B.; Langenberg, Claudia; Elliott, Paul; Jablonski, Kathleen A.; Lehman, Donna M.; Jia, Weiping; Ma, Ronald C. W.; Pollin, Toni I.; Sandhu, Manjinder; Tandon, Nikhil; Froguel, Philippe; Barroso, Inês; Teo, Yik Ying; Zeggini, Eleftheria; Loos, Ruth J. F.; Small, Kerrin S.; Ried, Janina S.; DeFronzo, Ralph A.; Grallert, Harald; Glaser, Benjamin; Metspalu, Andres; Wareham, Nicholas J.; Walker, Mark; Banks, Eric; Gieger, Christian; Ingelsson, Erik; Im, Hae Kyung; Illig, Thomas; Franks, Paul W.; Buck, Gemma; Trakalo, Joseph; Buck, David; Prokopenko, Inga; Mägi, Reedik; Lind, Lars; Farjoun, Yossi; Owen, Katharine R.; Gloyn, Anna L.; Strauch, Konstantin; Tuomi, Tiinamaija; Kooner, Jaspal Singh; Lee, Jong-Young; Park, Taesung; Donnelly, Peter; Morris, Andrew D.; Hattersley, Andrew T.; Bowden, Donald W.; Collins, Francis S.; Atzmon, Gil; Chambers, John C.; Spector, Timothy D.; Laakso, Markku; Strom, Tim M.; Bell, Graeme I.; Blangero, John; Duggirala, Ravindranath; Tai, E. Shyong; McVean, Gilean; Hanis, Craig L.; Wilson, James G.; Seielstad, Mark; Frayling, Timothy M.; Meigs, James B.; Cox, Nancy J.; Sladek, Rob; Lander, Eric S.; Gabriel, Stacey; Mohlke, Karen L.; Meitinger, Thomas; Groop, Leif; Abecasis, Goncalo; Scott, Laura J.; Morris, Andrew P.; Kang, Hyun Min; Altshuler, David; Burtt, Noël P.; Florez, Jose C.; Boehnke, Michael; McCarthy, Mark I.

2017-01-01

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1–5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D. PMID:29257133

Not All Order Memory Is Equal: Test Demands Reveal Dissociations in Memory for Sequence Information

ERIC Educational Resources Information Center

Jonker, Tanya R.; MacLeod, Colin M.

2017-01-01

Remembering the order of a sequence of events is a fundamental feature of episodic memory. Indeed, a number of formal models represent temporal context as part of the memory system, and memory for order has been researched extensively. Yet, the nature of the code(s) underlying sequence memory is still relatively unknown. Across 4 experiments that…

Complete mitochondrial genome sequence of the heart failure model of cardiomyopathic Syrian hamster (Mesocricetus auratus).

PubMed

Hu, Bo; Liu, Dong-Xing; Zhang, Yu-Qing; Song, Jian-Tao; Ji, Xian-Fei; Hou, Zhi-Qiang; Zhang, Zhen-Hai

2016-05-01

In this study we sequenced the complete mitochondrial genome sequencing of a heart failure model of cardiomyopathic Syrian hamster (Mesocricetus auratus) for the first time. The total length of the mitogenome was 16,267 bp. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region.

Code-Switching to Know a TL Equivalent of an L1 Word: Request-Provision-Acknowledgement (RPA) Sequence

ERIC Educational Resources Information Center

Lucero, Edgar

2011-01-01

This article focuses on the learner's use of Code-switching to learn the TL (Target Language) equivalent of an L1 word. The interactional pattern that this situation creates defines the Request-Provision-Acknowledgement (RPA) sequence. The article explains each of the turns of the sequence under the combination of the Ethnomethodological…

Quantitative analysis of the anti-noise performance of an m-sequence in an electromagnetic method

NASA Astrophysics Data System (ADS)

Yuan, Zhe; Zhang, Yiming; Zheng, Qijia

2018-02-01

An electromagnetic method with a transmitted waveform coded by an m-sequence achieved better anti-noise performance compared to the conventional manner with a square-wave. The anti-noise performance of the m-sequence varied with multiple coding parameters; hence, a quantitative analysis of the anti-noise performance for m-sequences with different coding parameters was required to optimize them. This paper proposes the concept of an identification system, with the identified Earth impulse response obtained by measuring the system output with the input of the voltage response. A quantitative analysis of the anti-noise performance of the m-sequence was achieved by analyzing the amplitude-frequency response of the corresponding identification system. The effects of the coding parameters on the anti-noise performance are summarized by numerical simulation, and their optimization is further discussed in our conclusions; the validity of the conclusions is further verified by field experiment. The quantitative analysis method proposed in this paper provides a new insight into the anti-noise mechanism of the m-sequence, and could be used to evaluate the anti-noise performance of artificial sources in other time-domain exploration methods, such as the seismic method.

21 CFR 510.600 - Names, addresses, and drug labeler codes of sponsors of approved applications.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 049185 Watson Laboratories, Inc., 311 Bonnie Circle, Corona, CA 92880. 000402 Wayne Feed Division... Olney Ave., Cherry Hill, NJ 08034. 000402 Watson Laboratories, Inc., 311 Bonnie Circle, Corona, CA 92880...

21 CFR 510.600 - Names, addresses, and drug labeler codes of sponsors of approved applications.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 50704 017139 Watson Laboratories, Inc., 311 Bonnie Circle, Corona, CA 92880. 000402 Wayne Feed Division... Hill, NJ 08034. 000402 Watson Laboratories, Inc., 311 Bonnie Circle, Corona, CA 92880. 000842 Texas...

Code AI Personal Web Pages

NASA Technical Reports Server (NTRS)

Garcia, Joseph A.; Smith, Charles A. (Technical Monitor)

1998-01-01

The document consists of a publicly available web site (george.arc.nasa.gov) for Joseph A. Garcia's personal web pages in the AI division. Only general information will be posted and no technical material. All the information is unclassified.

NIH Scientists Try to Crack the Brain's Memory Codes

MedlinePlus

... Strategy Current Research Research Funded by NINDS Basic Neuroscience Clinical Research Translational Research Research at NINDS Focus ... Diversity Resources Jobs at NINDS Director, Division of Neuroscience Director, NIH BRAIN Initiative® Health Scientist Administrator Channels ...

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

PubMed

Wright, Imogen A; Travers, Simon A

2014-07-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genomics dataset on unclassified published organism (patent US 7547531).

PubMed

Khan Shawan, Mohammad Mahfuz Ali; Hasan, Md Ashraful; Hossain, Md Mozammel; Hasan, Md Mahmudul; Parvin, Afroza; Akter, Salina; Uddin, Kazi Rasel; Banik, Subrata; Morshed, Mahbubul; Rahman, Md Nazibur; Rahman, S M Badier

2016-12-01

Nucleotide (DNA) sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531) is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR) code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5%) which was followed by GP445198 (61.8%) and GP445189 (59.44%), while lowest was in GP445178 (24.39%). In addition, New England BioLabs (NEB) database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms' hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

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

NASA Astrophysics Data System (ADS)

Ringbeck, Thorsten; Schwarte, Rudolf; Buxbaum, Bernd

1999-12-01

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

Aeronautical audio broadcasting via satellite

NASA Technical Reports Server (NTRS)

Tzeng, Forrest F.

1993-01-01

A system design for aeronautical audio broadcasting, with C-band uplink and L-band downlink, via Inmarsat space segments is presented. Near-transparent-quality compression of 5-kHz bandwidth audio at 20.5 kbit/s is achieved based on a hybrid technique employing linear predictive modeling and transform-domain residual quantization. Concatenated Reed-Solomon/convolutional codes with quadrature phase shift keying are selected for bandwidth and power efficiency. RF bandwidth at 25 kHz per channel, and a decoded bit error rate at 10(exp -6) with E(sub b)/N(sub o) at 3.75 dB are obtained. An interleaver, scrambler, modem synchronization, and frame format were designed, and frequency-division multiple access was selected over code-division multiple access. A link budget computation based on a worst-case scenario indicates sufficient system power margins. Transponder occupancy analysis for 72 audio channels demonstrates ample remaining capacity to accommodate emerging aeronautical services.

The effect of structural design parameters on FPGA-based feed-forward space-time trellis coding-orthogonal frequency division multiplexing channel encoders

NASA Astrophysics Data System (ADS)

Passas, Georgios; Freear, Steven; Fawcett, Darren

2010-08-01

Orthogonal frequency division multiplexing (OFDM)-based feed-forward space-time trellis code (FFSTTC) encoders can be synthesised as very high speed integrated circuit hardware description language (VHDL) designs. Evaluation of their FPGA implementation can lead to conclusions that help a designer to decide the optimum implementation, given the encoder structural parameters. VLSI architectures based on 1-bit multipliers and look-up tables (LUTs) are compared in terms of FPGA slices and block RAMs (area), as well as in terms of minimum clock period (speed). Area and speed graphs versus encoder memory order are provided for quadrature phase shift keying (QPSK) and 8 phase shift keying (8-PSK) modulation and two transmit antennas, revealing best implementation under these conditions. The effect of number of modulation bits and transmit antennas on the encoder implementation complexity is also investigated.

Investigation of adaptive filtering and MDL mitigation based on space-time block-coding for spatial division multiplexed coherent receivers

NASA Astrophysics Data System (ADS)

Weng, Yi; He, Xuan; Yao, Wang; Pacheco, Michelle C.; Wang, Junyi; Pan, Zhongqi

2017-07-01

In this paper, we explored the performance of space-time block-coding (STBC) assisted multiple-input multiple-output (MIMO) scheme for modal dispersion and mode-dependent loss (MDL) mitigation in spatial-division multiplexed optical communication systems, whereas the weight matrices of frequency-domain equalization (FDE) were updated heuristically using decision-directed recursive least squares (RLS) algorithm for convergence and channel estimation. The proposed STBC-RLS algorithm can achieve 43.6% enhancement on convergence rate over conventional least mean squares (LMS) for quadrature phase-shift keying (QPSK) signals with merely 16.2% increase in hardware complexity. The overall optical signal to noise ratio (OSNR) tolerance can be improved via STBC by approximately 3.1, 4.9, 7.8 dB for QPSK, 16-quadrature amplitude modulation (QAM) and 64-QAM with respective bit-error-rates (BER) and minimum-mean-square-error (MMSE).

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

PubMed Central

Washietl, Stefan; Findeiß, Sven; Müller, Stephan A.; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L.; Stadler, Peter F.; Goldman, Nick

2011-01-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied “out of the box,” without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as “noncoding.” RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode. PMID:21357752

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

PubMed

Washietl, Stefan; Findeiss, Sven; Müller, Stephan A; Kalkhof, Stefan; von Bergen, Martin; Hofacker, Ivo L; Stadler, Peter F; Goldman, Nick

2011-04-01

With the availability of genome-wide transcription data and massive comparative sequencing, the discrimination of coding from noncoding RNAs and the assessment of coding potential in evolutionarily conserved regions arose as a core analysis task. Here we present RNAcode, a program to detect coding regions in multiple sequence alignments that is optimized for emerging applications not covered by current protein gene-finding software. Our algorithm combines information from nucleotide substitution and gap patterns in a unified framework and also deals with real-life issues such as alignment and sequencing errors. It uses an explicit statistical model with no machine learning component and can therefore be applied "out of the box," without any training, to data from all domains of life. We describe the RNAcode method and apply it in combination with mass spectrometry experiments to predict and confirm seven novel short peptides in Escherichia coli and to analyze the coding potential of RNAs previously annotated as "noncoding." RNAcode is open source software and available for all major platforms at http://wash.github.com/rnacode.

High compression image and image sequence coding

NASA Technical Reports Server (NTRS)

Kunt, Murat

1989-01-01

The digital representation of an image requires a very large number of bits. This number is even larger for an image sequence. The goal of image coding is to reduce this number, as much as possible, and reconstruct a faithful duplicate of the original picture or image sequence. Early efforts in image coding, solely guided by information theory, led to a plethora of methods. The compression ratio reached a plateau around 10:1 a couple of years ago. Recent progress in the study of the brain mechanism of vision and scene analysis has opened new vistas in picture coding. Directional sensitivity of the neurones in the visual pathway combined with the separate processing of contours and textures has led to a new class of coding methods capable of achieving compression ratios as high as 100:1 for images and around 300:1 for image sequences. Recent progress on some of the main avenues of object-based methods is presented. These second generation techniques make use of contour-texture modeling, new results in neurophysiology and psychophysics and scene analysis.

Tipjet 80-inch Model Rotor Hover Test: Test No. 1198

DTIC Science & Technology

1993-09-01

primarily working papers Intended for internal use. They I carry an Identifying number which indicates their type and the numerical code of the oriwginatn...rotor lifting system, while exhbitin the highes aumntbnratio eve recorded for a CC rotor, sufer an induced power penalty due to the norilifting regon...INFORMATION This work was conducted by the Ship Systems and Programs DirectorateI (Code 22) of the Carderock Division, Naval Surface Warfare Center

Sesquinaries, Magnetics and Atmospheres: Studies of the Terrestrial Moons and Exoplanets

DTIC Science & Technology

2016-12-01

support provided by Red Sky Research, LLC. Computational support was provided by the NASA Ames Mission Design Division (Code RD) for research...Systems Branch (Code SST), NASA Ames Research Center, provided supercomputer access and computational resources for the work in Chapter 5. I owe a...huge debt of gratitude to Dr. Pete Worden, Dr. Steve Zornetzer, Dr. Alan Weston ( NASA ), and Col. Carol Welsch, Lt. Col Joe Nance and Lt. Col Brian

A Note on NCOM Temperature Forecast Error Calibration Using the Ensemble Transform

DTIC Science & Technology

2009-01-01

Division Head Ruth H. Preller, 7300 Security, Code 1226 Office of Counsel,Code 1008.3 ADOR/Director NCST E. R. Franchi , 7000 Public Affairs...problem, local unbiased (correlation) and persistent errors (bias) of the Navy Coastal Ocean Modeling (NCOM) System nested in global ocean domains, are...system were made available in real-time without performing local data assimilation, though remote sensing and global data was assimilated on the

Patterns of Indian Ocean Sea-Level Change in a Warming Climate

DTIC Science & Technology

2010-08-01

distribution is unlimited. 13. SUPPLEMENTARY NOTES 20110415461 14 ABSTRACT Global sea level has risen during the past decades as a result of thermal...expansion of the warming ocean and freshwater addition from melting continental icel However, sea-level rise is not globally uniforml, 2, 3, 4, 5...7320 Division Head Ruth H. Preller, 7300 Security. Code 1226 Office of Counsel,Code 1008.3 ADOR/Director NCST E. R. Franchi , 7000 Public

DNA transposons have colonized the genome of the giant virus Pandoravirus salinus.

PubMed

Sun, Cheng; Feschotte, Cédric; Wu, Zhiqiang; Mueller, Rachel Lockridge

2015-06-12

Transposable elements are mobile DNA sequences that are widely distributed in prokaryotic and eukaryotic genomes, where they represent a major force in genome evolution. However, transposable elements have rarely been documented in viruses, and their contribution to viral genome evolution remains largely unexplored. Pandoraviruses are recently described DNA viruses with genome sizes that exceed those of some prokaryotes, rivaling parasitic eukaryotes. These large genomes appear to include substantial noncoding intergenic spaces, which provide potential locations for transposable element insertions. However, no mobile genetic elements have yet been reported in pandoravirus genomes. Here, we report a family of miniature inverted-repeat transposable elements (MITEs) in the Pandoravirus salinus genome, representing the first description of a virus populated with a canonical transposable element family that proliferated by transposition within the viral genome. The MITE family, which we name Submariner, includes 30 copies with all the hallmarks of MITEs: short length, terminal inverted repeats, TA target site duplication, and no coding capacity. Submariner elements show signs of transposition and are undetectable in the genome of Pandoravirus dulcis, the closest known relative Pandoravirus salinus. We identified a DNA transposon related to Submariner in the genome of Acanthamoeba castellanii, a species thought to host pandoraviruses, which contains remnants of coding sequence for a Tc1/mariner transposase. These observations suggest that the Submariner MITEs of P. salinus belong to the widespread Tc1/mariner superfamily and may have been mobilized by an amoebozoan host. Ten of the 30 MITEs in the P. salinus genome are located within coding regions of predicted genes, while others are close to genes, suggesting that these transposons may have contributed to viral genetic novelty. Our discovery highlights the remarkable ability of DNA transposons to colonize and shape genomes from all domains of life, as well as giant viruses. Our findings continue to blur the division between viral and cellular genomes, adhering to the emerging view that the content, dynamics, and evolution of the genomes of giant viruses do not substantially differ from those of cellular organisms.

Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae).

PubMed

Liu, Ze-Xuan; Zhang, Yan; Liu, Yu-Ting; Chang, Qiao-Cheng; Su, Xin; Fu, Xue; Yue, Dong-Mei; Gao, Yuan; Wang, Chun-Ren

2016-04-01

Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans.

Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae)

PubMed Central

Liu, Ze-Xuan; Zhang, Yan; Liu, Yu-Ting; Chang, Qiao-Cheng; Su, Xin; Fu, Xue; Yue, Dong-Mei; Gao, Yuan; Wang, Chun-Ren

2016-01-01

Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans. PMID:27180575

The application of CFD for military aircraft design at transonic speeds

NASA Technical Reports Server (NTRS)

Smith, C. W.; Braymen, W. W.; Bhateley, I. C.; Londenberg, W. K.

1989-01-01

Numerous computational fluid dynamics (CFD) codes are available that solve any of several variations of the transonic flow equations from small disturbance to full Navier-Stokes. The design philosophy at General Dynamics Fort Worth Division involves use of all these levels of codes, depending on the stage of configuration development. Throughout this process, drag calculation is a central issue. An overview is provided for several transonic codes and representative test-to-theory comparisons for fighter-type configurations are presented. Correlations are shown for lift, drag, pitching moment, and pressure distributions. The future of applied CFD is also discussed, including the important task of code validation. With the progress being made in code development and the continued evolution in computer hardware, the routine application of these codes for increasingly more complex geometries and flow conditions seems apparent.

The Navy’s Coupled Atmosphere-Ocean-Wave Prediction System

DTIC Science & Technology

2011-04-15

is provided below. llMurly lurtir llcai Mux. N. M,*!. Heal I luv . .tn.l Wind Sura f»f \\. Hu. Alia il.t.iujn 2«OX) i n.H 1 1 1 T 1 1...DATE IDD-MM YYYY) 15-04-201 I 2. REPORT TYPE Conference Proceeding 3. DATES COVERED (From To) 4. TITLE AND SUBTITLE The Navy’s Coupled...Code 7Q3n A I Division, Code I Author, Code i .y "f^****^ Cv^py>v’V/v^ 1. Release of this paper is approved. 2. To the best knowledge of

PMD compensation in fiber-optic communication systems with direct detection using LDPC-coded OFDM.

PubMed

Djordjevic, Ivan B

2007-04-02

The possibility of polarization-mode dispersion (PMD) compensation in fiber-optic communication systems with direct detection using a simple channel estimation technique and low-density parity-check (LDPC)-coded orthogonal frequency division multiplexing (OFDM) is demonstrated. It is shown that even for differential group delay (DGD) of 4/BW (BW is the OFDM signal bandwidth), the degradation due to the first-order PMD can be completely compensated for. Two classes of LDPC codes designed based on two different combinatorial objects (difference systems and product of combinatorial designs) suitable for use in PMD compensation are introduced.

SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

PubMed

Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

2016-06-15

Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

RNA polymerase beta-subunit gene (rpoB) sequence analysis for the identification of Bacteroides spp.

PubMed

Ko, K S; Kuwahara, T; Haehwa, L; Yoon, Y-J; Kim, B-J; Lee, K-H; Ohnishi, Y; Kook, Y-H

2007-01-01

Partial rpoB sequences (317 bp) of 11 species of Bacteroides, two Porphyromonas spp. and two Prevotella spp. were compared to delineate the genetic relationships among Bacteroides and closely related anaerobic species. The high level of inter-species sequence dissimilarities (7.6-20.8%) allowed the various Bacteroides spp. to be distinguished. The position of the Bacteroides distasonis and Bacteriodes merdae cluster in the rpoB tree was different from the position in the 16S rRNA gene tree. Based on rpoB sequence similarity and clustering in the rpoB tree, it was possible to correctly re-identify 80 clinical isolates of Bacteroides. In addition to two subgroups, cfiA-negative (division I) and cfiA-positive (division II), of Bacteroides fragilis isolates, two distinct subgroups were also found among Bacteroides ovatus and Bacteroides thetaiotaomicron isolates. Bacteroides genus-specific rpoB PCR and B. fragilis species-specific rpoB PCR allowed Bacteroides spp. to be differentiated from Porphyromonas and Prevotella spp., and also allowed B. fragilis to be differentiated from other non-fragilisBacteroides spp. included in the present study.

Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing

PubMed Central

Nunoura, Takuro; Takaki, Yoshihiro; Kazama, Hiromi; Hirai, Miho; Ashi, Juichiro; Imachi, Hiroyuki; Takai, Ken

2012-01-01

Microbial community structures in methane seep sediments in the Nankai Trough were analyzed by tag-sequencing analysis for the small subunit (SSU) rRNA gene using a newly developed primer set. The dominant members of Archaea were Deep-sea Hydrothermal Vent Euryarchaeotic Group 6 (DHVEG 6), Marine Group I (MGI) and Deep Sea Archaeal Group (DSAG), and those in Bacteria were Alpha-, Gamma-, Delta- and Epsilonproteobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. Diversity and richness were examined by 8,709 and 7,690 tag-sequences from sediments at 5 and 25 cm below the seafloor (cmbsf), respectively. The estimated diversity and richness in the methane seep sediment are as high as those in soil and deep-sea hydrothermal environments, although the tag-sequences obtained in this study were not sufficient to show whole microbial diversity in this analysis. We also compared the diversity and richness of each taxon/division between the sediments from the two depths, and found that the diversity and richness of some taxa/divisions varied significantly along with the depth. PMID:22510646

Efficient analysis of mouse genome sequences reveal many nonsense variants

PubMed Central

Steeland, Sophie; Timmermans, Steven; Van Ryckeghem, Sara; Hulpiau, Paco; Saeys, Yvan; Van Montagu, Marc; Vandenbroucke, Roosmarijn E.; Libert, Claude

2016-01-01

Genetic polymorphisms in coding genes play an important role when using mouse inbred strains as research models. They have been shown to influence research results, explain phenotypical differences between inbred strains, and increase the amount of interesting gene variants present in the many available inbred lines. SPRET/Ei is an inbred strain derived from Mus spretus that has ∼1% sequence difference with the C57BL/6J reference genome. We obtained a listing of all SNPs and insertions/deletions (indels) present in SPRET/Ei from the Mouse Genomes Project (Wellcome Trust Sanger Institute) and processed these data to obtain an overview of all transcripts having nonsynonymous coding sequence variants. We identified 8,883 unique variants affecting 10,096 different transcripts from 6,328 protein-coding genes, which is about 28% of all coding genes. Because only a subset of these variants results in drastic changes in proteins, we focused on variations that are nonsense mutations that ultimately resulted in a gain of a stop codon. These genes were identified by in silico changing the C57BL/6J coding sequences to the SPRET/Ei sequences, converting them to amino acid (AA) sequences, and comparing the AA sequences. All variants and transcripts affected were also stored in a database, which can be browsed using a SPRET/Ei M. spretus variants web tool (www.spretus.org), including a manual. We validated the tool by demonstrating the loss of function of three proteins predicted to be severely truncated, namely Fas, IRAK2, and IFNγR1. PMID:27147605

Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.

PubMed

Kuroshu, Reginaldo M; Watanabe, Junichi; Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka; Kasahara, Masahiro

2010-05-07

Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence approximately 800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only approximately US$3 per clone, demonstrating a significant advantage over previous approaches.

VaDiR: an integrated approach to Variant Detection in RNA.

PubMed

Neums, Lisa; Suenaga, Seiji; Beyerlein, Peter; Anders, Sara; Koestler, Devin; Mariani, Andrea; Chien, Jeremy

2018-02-01

Advances in next-generation DNA sequencing technologies are now enabling detailed characterization of sequence variations in cancer genomes. With whole-genome sequencing, variations in coding and non-coding sequences can be discovered. But the cost associated with it is currently limiting its general use in research. Whole-exome sequencing is used to characterize sequence variations in coding regions, but the cost associated with capture reagents and biases in capture rate limit its full use in research. Additional limitations include uncertainty in assigning the functional significance of the mutations when these mutations are observed in the non-coding region or in genes that are not expressed in cancer tissue. We investigated the feasibility of uncovering mutations from expressed genes using RNA sequencing datasets with a method called Variant Detection in RNA(VaDiR) that integrates 3 variant callers, namely: SNPiR, RVBoost, and MuTect2. The combination of all 3 methods, which we called Tier 1 variants, produced the highest precision with true positive mutations from RNA-seq that could be validated at the DNA level. We also found that the integration of Tier 1 variants with those called by MuTect2 and SNPiR produced the highest recall with acceptable precision. Finally, we observed a higher rate of mutation discovery in genes that are expressed at higher levels. Our method, VaDiR, provides a possibility of uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. In addition, our approach allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing datasets.

The TORMOZ Gene Encodes a Nucleolar Protein Required for Regulated Division Planes and Embryo Development in Arabidopsis[W

PubMed Central

Griffith, Megan E.; Mayer, Ulrike; Capron, Arnaud; Ngo, Quy A.; Surendrarao, Anandkumar; McClinton, Regina; Jürgens, Gerd; Sundaresan, Venkatesan

2007-01-01

Embryogenesis in Arabidopsis thaliana is marked by a predictable sequence of oriented cell divisions, which precede cell fate determination. We show that mutation of the TORMOZ (TOZ) gene yields embryos with aberrant cell division planes and arrested embryos that appear not to have established normal patterning. The defects in toz mutants differ from previously described mutations that affect embryonic cell division patterns. Longitudinal division planes of the proembryo are frequently replaced by transverse divisions and less frequently by oblique divisions, while divisions of the suspensor cells, which divide only transversely, appear generally unaffected. Expression patterns of selected embryo patterning genes are altered in the mutant embryos, implying that the positional cues required for their proper expression are perturbed by the misoriented divisions. The TOZ gene encodes a nucleolar protein containing WD repeats. Putative TOZ orthologs exist in other eukaryotes including Saccharomyces cerevisiae, where the protein is predicted to function in 18S rRNA biogenesis. We find that disruption of the Sp TOZ gene results in cell division defects in Schizosaccharomyces pombe. Previous studies in yeast and animal cells have identified nucleolar proteins that regulate the exit from M phase and cytokinesis, including factors involved in pre-rRNA processing. Our study suggests that in plant cells, nucleolar functions might interact with the processes of regulated cell divisions and influence the selection of longitudinal division planes during embryogenesis. PMID:17616738

Draft Genome Sequence of Cellulolytic and Xylanolytic Paenibacillus sp. A59, Isolated from Decaying Forest Soil from Patagonia, Argentina

PubMed Central

Ghio, Silvina; Martinez Cáceres, Alfredo I.; Talia, Paola; Grasso, Daniel H.

2015-01-01

Paenibacillus sp. A59 was isolated from decaying forest soil in Argentina and characterized as a xylanolytic strain. We report the draft genome sequence of this isolate, with an estimated genome size of 7 Mb which harbor 6,424 coding sequences. Genes coding for hydrolytic enzymes involved in lignocellulose deconstruction were predicted. PMID:26494679

75 FR 35076 - Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-21

... discussion are concept review of the following proposed FY 2011 Common Fund initiatives: (1) NIH-HMO Research... Canada): 866-695-1528. Conference code: 7626802625. Place: National Institutes of Health, Building 1...

77 FR 30972 - Certain Polybrominated Diphenylethers; Significant New Use Rule and Test Rule; Extension of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-24

... technical information contact: Catherine Roman, Chemical Control Division, Office of Pollution Prevention... Safety and Pollution Prevention. [FR Doc. 2012-12625 Filed 5-23-12; 8:45 am] BILLING CODE 6560-50-P ...

21 CFR 510.600 - Names, addresses, and drug labeler codes of sponsors of approved applications.

Code of Federal Regulations, 2014 CFR

2014-04-01

...., 311 Bonnie Circle, Corona, CA 92880. 000402 Wayne Feed Division, Continental Grain Co., P.O. Box 459..., CA 94544 000402 Watson Laboratories, Inc., 311 Bonnie Circle, Corona, CA 92880. 000409 Hospira Inc...

Concurrent error detecting codes for arithmetic processors

NASA Technical Reports Server (NTRS)

Lim, R. S.

1979-01-01

A method of concurrent error detection for arithmetic processors is described. Low-cost residue codes with check-length l and checkbase m = 2 to the l power - 1 are described for checking arithmetic operations of addition, subtraction, multiplication, division complement, shift, and rotate. Of the three number representations, the signed-magnitude representation is preferred for residue checking. Two methods of residue generation are described: the standard method of using modulo m adders and the method of using a self-testing residue tree. A simple single-bit parity-check code is described for checking the logical operations of XOR, OR, and AND, and also the arithmetic operations of complement, shift, and rotate. For checking complement, shift, and rotate, the single-bit parity-check code is simpler to implement than the residue codes.

Gene Identification Algorithms Using Exploratory Statistical Analysis of Periodicity

NASA Astrophysics Data System (ADS)

Mukherjee, Shashi Bajaj; Sen, Pradip Kumar

2010-10-01

Studying periodic pattern is expected as a standard line of attack for recognizing DNA sequence in identification of gene and similar problems. But peculiarly very little significant work is done in this direction. This paper studies statistical properties of DNA sequences of complete genome using a new technique. A DNA sequence is converted to a numeric sequence using various types of mappings and standard Fourier technique is applied to study the periodicity. Distinct statistical behaviour of periodicity parameters is found in coding and non-coding sequences, which can be used to distinguish between these parts. Here DNA sequences of Drosophila melanogaster were analyzed with significant accuracy.

Why is CDMA the solution for mobile satellite communication

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

National Program for Inspection of Non-Federal Dams. Williams Pond Dam (CT 00551), Thames River Basin, Lebanon, Connecticut. Phase I Inspection Program.

DTIC Science & Technology

1978-10-01

GRA&I UnTucea B WILLIAMS POND DAM ~~1Z~ CT 00551 _ Distribution/ Availabilit Y Codes Avail and/or Dis~tj pecialS RIVER BASIN ~lIILEBANON, COXNNECTICUT...Inspection Report. Alternatives to these recommendations r 1 would include reducing the Williams Pond water levels during expected periods of intense storm...Materials Branch Engi’neering Division FRED J. VNS. Jr., Member Chief, De ’ggn Branch Engineering Division SAUL COOPER, -r Chief, Water Control Branch

Cost Model/Data Base Catalog Non-DoD/Academic Survey. Volume 1. Project Summary

DTIC Science & Technology

1988-10-30

presented in two volumes: Volume 1- Project Summary, and L .JD Volume 2- Final Data Base. J Accesion - For NTIS C R A& Disiji( .. . U, L)~ .6I...218 47I I I I I I I I Exhibit 111-3. COMPLETE CATALOG BREAKOUT I MANAGEMENT CONSULTING & RESEARCH, INC. j 111-6 I IE-I Iu 0 HE-4 X C.) E- Ix UI.n 111...College/EDCCAir University Maxwell Air Force Base, AL 36112 2. AD (Armament Division) Department of the Air Force Armament Division/(subdiv code

Outbreak of poliomyelitis in Finland in 1984-85 - Re-analysis of viral sequences using the current standard approach.

PubMed

Simonen, Marja-Leena; Roivainen, Merja; Iber, Jane; Burns, Cara; Hovi, Tapani

2010-01-01

In 1984, a wild type 3 poliovirus (PV3/FIN84) spread all over Finland causing nine cases of paralytic poliomyelitis and one case of aseptic meningitis. The outbreak was ended in 1985 with an intensive vaccination campaign. By limited sequence comparison with previously isolated PV3 strains, closest relatives of PV3/FIN84 were found among strains circulating in the Mediterranean region. Now we wanted to reanalyse the relationships using approaches currently exploited in poliovirus surveillance. Cell lysates of 22 strains isolated during the outbreak and stored frozen were subjected to RT-PCR amplification in three genomic regions without prior subculture. Sequences of the entire VP1 coding region, 150 nucleotides in the VP1-2A junction, most of the 5' non-coding region, partial sequences of the 3D RNA polymerase coding region and partial 3' non-coding region were compared within the outbreak and with sequences available in data banks. In addition, complete nucleotide sequences were obtained for 2 strains isolated from two different cases of disease during the outbreak. The results confirmed the previously described wide intraepidemic variation of the strains, including amino acid substitutions in antigenic sites, as well as the likely Mediterranean region origin of the strains. Simplot and bootscanning analyses of the complete genomes indicated complicated evolutionary history of the non-capsid coding regions of the genome suggesting several recombinations with different HEV-C viruses in the past.

Divisions of geologic time-major chronostratigraphic and geochronologic units

USGS Publications Warehouse

,

2010-01-01

Effective communication in the geosciences requires consistent uses of stratigraphic nomenclature, especially divisions of geologic time. A geologic time scale is composed of standard stratigraphic divisions based on rock sequences and is calibrated in years. Over the years, the development of new dating methods and the refinement of previous methods have stimulated revisions to geologic time scales. Advances in stratigraphy and geochronology require that any time scale be periodically updated. Therefore, Divisions of Geologic Time, which shows the major chronostratigraphic (position) and geochronologic (time) units, is intended to be a dynamic resource that will be modified to include accepted changes of unit names and boundary age estimates. This fact sheet is a modification of USGS Fact Sheet 2007-3015 by the U.S. Geological Survey Geologic Names Committee.

Genetic code, hamming distance and stochastic matrices.

PubMed

He, Matthew X; Petoukhov, Sergei V; Ricci, Paolo E

2004-09-01

In this paper we use the Gray code representation of the genetic code C=00, U=10, G=11 and A=01 (C pairs with G, A pairs with U) to generate a sequence of genetic code-based matrices. In connection with these code-based matrices, we use the Hamming distance to generate a sequence of numerical matrices. We then further investigate the properties of the numerical matrices and show that they are doubly stochastic and symmetric. We determine the frequency distributions of the Hamming distances, building blocks of the matrices, decomposition and iterations of matrices. We present an explicit decomposition formula for the genetic code-based matrix in terms of permutation matrices, which provides a hypercube representation of the genetic code. It is also observed that there is a Hamiltonian cycle in a genetic code-based hypercube.

Mitochondrial genomes of the jungle crow Corvus macrorhynchos (Passeriformes: Corvidae) from shed feathers and a phylogenetic analysis of genus Corvus using mitochondrial protein-coding genes.

PubMed

Krzeminska, Urszula; Wilson, Robyn; Rahman, Sadequr; Song, Beng Kah; Seneviratne, Sampath; Gan, Han Ming; Austin, Christopher M

2016-07-01

The complete mitochondrial genomes of two jungle crows (Corvus macrorhynchos) were sequenced. DNA was extracted from tissue samples obtained from shed feathers collected in the field in Sri Lanka and sequenced using the Illumina MiSeq Personal Sequencer. Jungle crow mitogenomes have a structural organization typical of the genus Corvus and are 16,927 bp and 17,066 bp in length, both comprising 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal subunit genes, and a non-coding control region. In addition, we complement already available house crow (Corvus spelendens) mitogenome resources by sequencing an individual from Singapore. A phylogenetic tree constructed from Corvidae family mitogenome sequences available on GenBank is presented. We confirm the monophyly of the genus Corvus and propose to use complete mitogenome resources for further intra- and interspecies genetic studies.

Evolution of the alternative AQP2 gene: Acquisition of a novel protein-coding sequence in dolphins.

PubMed

Kishida, Takushi; Suzuki, Miwa; Takayama, Asuka

2018-01-01

Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron. Here, we show that the latter half of the third exon of the alternative AQP2 arose from a non-protein-coding sequence. Intact ORF of this de novo sequence is shared not by all cetaceans, but only by delphinoids. However, this sequence is conservative in all modern cetaceans, implying that this de novo sequence potentially plays important roles for marine adaptation in cetaceans. Copyright © 2017 Elsevier Inc. All rights reserved.

A Wideband Satcom Based Avionics Network with CDMA Uplink and TDM Downlink

NASA Technical Reports Server (NTRS)

Agrawal, D.; Johnson, B. S.; Madhow, U.; Ramchandran, K.; Chun, K. S.

2000-01-01

The purpose of this paper is to describe some key technical ideas behind our vision of a future satcom based digital communication network for avionics applications The key features of our design are as follows: (a) Packetized transmission to permit efficient use of system resources for multimedia traffic; (b) A time division multiplexed (TDM) satellite downlink whose physical layer is designed to operate the satellite link at maximum power efficiency. We show how powerful turbo codes (invented originally for linear modulation) can be used with nonlinear constant envelope modulation, thus permitting the satellite amplifier to operate in a power efficient nonlinear regime; (c) A code division multiple access (CDMA) satellite uplink, which permits efficient access to the satellite from multiple asynchronous users. Closed loop power control is difficult for bursty packetized traffic, especially given the large round trip delay to the satellite. We show how adaptive interference suppression techniques can be used to deal with the ensuing near-far problem; (d) Joint source-channel coding techniques are required both at the physical and the data transport layer to optimize the end-to-end performance. We describe a novel approach to multiple description image encoding at the data transport layer in this paper.

A Study of Dispersion Compensation of Polarization Multiplexing-Based OFDM-OCDMA for Radio-over-Fiber Transmissions

PubMed Central

Yen, Chih-Ta; Chen, Wen-Bin

2016-01-01

Chromatic dispersion from optical fiber is the most important problem that produces temporal skews and destroys the rectangular structure of code patterns in the spectra-amplitude-coding-based optical code-division multiple-access (SAC-OCDMA) system. Thus, the balance detection scheme does not work perfectly to cancel multiple access interference (MAI) and the system performance will be degraded. Orthogonal frequency-division multiplexing (OFDM) is the fastest developing technology in the academic and industrial fields of wireless transmission. In this study, the radio-over-fiber system is realized by integrating OFDM and OCDMA via polarization multiplexing scheme. The electronic dispersion compensation (EDC) equalizer element of OFDM integrated with the dispersion compensation fiber (DCF) is used in the proposed radio-over-fiber (RoF) system, which can efficiently suppress the chromatic dispersion influence in long-haul transmitted distance. A set of length differences for 10 km-long single-mode fiber (SMF) and 4 km-long DCF is to verify the compensation scheme by relative equalizer algorithms and constellation diagrams. In the simulation result, the proposed dispersion mechanism successfully compensates the dispersion from SMF and the system performance with dispersion equalizer is highly improved. PMID:27618042

Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

NASA Astrophysics Data System (ADS)

Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

2018-01-01

Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.

Weight distributions for turbo codes using random and nonrandom permutations

NASA Technical Reports Server (NTRS)

Dolinar, S.; Divsalar, D.

1995-01-01

This article takes a preliminary look at the weight distributions achievable for turbo codes using random, nonrandom, and semirandom permutations. Due to the recursiveness of the encoders, it is important to distinguish between self-terminating and non-self-terminating input sequences. The non-self-terminating sequences have little effect on decoder performance, because they accumulate high encoded weight until they are artificially terminated at the end of the block. From probabilistic arguments based on selecting the permutations randomly, it is concluded that the self-terminating weight-2 data sequences are the most important consideration in the design of constituent codes; higher-weight self-terminating sequences have successively decreasing importance. Also, increasing the number of codes and, correspondingly, the number of permutations makes it more and more likely that the bad input sequences will be broken up by one or more of the permuters. It is possible to design nonrandom permutations that ensure that the minimum distance due to weight-2 input sequences grows roughly as the square root of (2N), where N is the block length. However, these nonrandom permutations amplify the bad effects of higher-weight inputs, and as a result they are inferior in performance to randomly selected permutations. But there are 'semirandom' permutations that perform nearly as well as the designed nonrandom permutations with respect to weight-2 input sequences and are not as susceptible to being foiled by higher-weight inputs.

Division-induced DNA double strand breaks in the chromosome terminus region of Escherichia coli lacking RecBCD DNA repair enzyme

PubMed Central

Durand, Adeline; Desfontaines, Jean-Michel; Iurchenko, Ielyzaveta; Auger, Hélène; Leach, David R. F.

2017-01-01

Marker frequency analysis of the Escherichia coli recB mutant chromosome has revealed a deficit of DNA in a specific zone of the terminus, centred on the dif/TerC region. Using fluorescence microscopy of a marked chromosomal site, we show that the dif region is lost after replication completion, at the time of cell division, in one daughter cell only, and that the phenomenon is transmitted to progeny. Analysis by marker frequency and microscopy shows that the position of DNA loss is not defined by the replication fork merging point since it still occurs in the dif/TerC region when the replication fork trap is displaced in strains harbouring ectopic Ter sites. Terminus DNA loss in the recB mutant is also independent of dimer resolution by XerCD at dif and of Topo IV action close to dif. It occurs in the terminus region, at the point of inversion of the GC skew, which is also the point of convergence of specific sequence motifs like KOPS and Chi sites, regardless of whether the convergence of GC skew is at dif (wild-type) or a newly created sequence. In the absence of FtsK-driven DNA translocation, terminus DNA loss is less precisely targeted to the KOPS convergence sequence, but occurs at a similar frequency and follows the same pattern as in FtsK+ cells. Importantly, using ftsIts, ftsAts division mutants and cephalexin treated cells, we show that DNA loss of the dif region in the recB mutant is decreased by the inactivation of cell division. We propose that it results from septum-induced chromosome breakage, and largely contributes to the low viability of the recB mutant. PMID:28968392

Sedimentary record of erg migration

NASA Astrophysics Data System (ADS)

Porter, M. L.

1986-06-01

The sedimentary record of erg (eolian sand sea) migration consists of an idealized threefold division of sand-sea facies sequences. The basal division, here termed the fore-erg, is composed of a hierarchy of eolian sand bodies contained within sediments of the flanking depositional environment. These sand bodies consist of eolian strata deposited by small dune complexes, zibars, and sand sheets. The fore-erg represents the downwind, leading edge of the erg and records the onset of eolian sedimentation. Basin subsidence coupled with erg migration places the medial division, termed the central erg, over the fore-erg strata. The central erg, represented by a thick accumulation of large-scale, cross-stratified sandstone, is the product of large draa complexes. Eolian influence on regional sedimentation patterns is greatest in the central erg, and most of the sand transported and deposited in the erg is contained within this region. Reduction in sand supply and continued erg migration will cover the central-erg deposits with a veneer of back-erg deposits. This upper division of the erg facies sequence resembles closely the fore-erg region. Similar types of eolian strata are present and organized in sand bodies encased in sediments of the upwind flanking depositional environment(s). Back-erg deposits may be thin due to limited eolian influence on sedimentation or incomplete erg migration, or they may be completely absent because of great susceptibility to postdepositional erosion. Tectonic, climatic, and eustatic influences on sand-sea deposition will produce distinctive variations or modifications of the idealized erg facies sequence. The resulting variants in the sedimentary record of erg migration are illustrated with ancient examples from western North America, Europe, southern Africa, and South America.

Code Conversion Impact Factor and Cash Flow Impact of International Classification of Diseases, 10th Revision, on a Large Multihospital Radiology Practice.

PubMed

Jalilvand, Aryan; Fleming, Margaret; Moreno, Courtney; MacFarlane, Dan; Duszak, Richard

2018-01-01

The 2015 conversion of the International Classification of Diseases (ICD) system from the ninth revision (ICD-9) to the 10th revision (ICD-10) was widely projected to adversely impact physician practices. We aimed to assess code conversion impact factor (CCIF) projections and revenue delay impact to help radiology groups better prepare for eventual conversion to ICD, 11th revision (ICD-11). Studying 673,600 claims for 179 radiologists for the first year after ICD-10's implementation, we identified primary ICD-10 codes for the top 90th percentile of all examinations for the entire enterprise and each subspecialty division. Using established methodology, we calculated CCIFs (actual ICD-10 codes ÷ prior ICD-9 codes). To assess ICD-10's impact on cash flow, average monthly days in accounts receivable status was compared for the 12 months before and after conversion. Of all 69,823 ICD-10 codes, only 7,075 were used to report primary diagnoses across the entire practice, and just 562 were used to report 90% of all claims, compared with 348 under ICD-9. This translates to an overall CCIF of 1.6 for the department (far less than the literature-predicted 6). By subspecialty division, CCIFs ranged from 0.7 (breast) to 3.5 (musculoskeletal). Monthly average days in accounts receivable for the 12 months before and after ICD-10 conversion did not increase. The operational impact of the ICD-10 transition on radiology practices appears far less than anticipated with respect to both CCIF and delays in cash flow. Predictive models should be refined to help practices better prepare for ICD-11. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Next-generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparison of its divergence from the principal agent of human trichinellosis, Trichinella spiralis.

PubMed

Webb, Kristen M; Rosenthal, Benjamin M

2011-01-01

The mitochondrial genome's non-recombinant mode of inheritance and relatively rapid rate of evolution has promoted its use as a marker for studying the biogeographic history and evolutionary interrelationships among many metazoan species. A modest portion of the mitochondrial genome has been defined for 12 species and genotypes of parasites in the genus Trichinella, but its adequacy in representing the mitochondrial genome as a whole remains unclear, as the complete coding sequence has been characterized only for Trichinella spiralis. Here, we sought to comprehensively describe the extent and nature of divergence between the mitochondrial genomes of T. spiralis (which poses the most appreciable zoonotic risk owing to its capacity to establish persistent infections in domestic pigs) and Trichinella murrelli (which is the most prevalent species in North American wildlife hosts, but which poses relatively little risk to the safety of pork). Next generation sequencing methodologies and scaffold and de novo assembly strategies were employed. The entire protein-coding region was sequenced (13,917 bp), along with a portion of the highly repetitive non-coding region (1524 bp) of the mitochondrial genome of T. murrelli with a combined average read depth of 250 reads. The accuracy of base calling, estimated from coding region sequence was found to exceed 99.3%. Genome content and gene order was not found to be significantly different from that of T. spiralis. An overall inter-species sequence divergence of 9.5% was estimated. Significant variation was identified when the amount of variation between species at each gene is compared to the average amount of variation between species across the coding region. Next generation sequencing is a highly effective means to obtain previously unknown mitochondrial genome sequence. Particular to parasites, the extremely deep coverage achieved through this method allows for the detection of sequence heterogeneity between the multiple individuals that necessarily comprise such templates. Copyright © 2010 Elsevier B.V. All rights reserved.

Cloning and sequence determination of the gene coding for the pyruvate phosphate dikinase of Entamoeba histolytica.

PubMed

Saavedra-Lira, E; Pérez-Montfort, R

1994-05-16

We isolated three overlapping clones from a DNA genomic library of Entamoeba histolytica strain HM1:IMSS, whose translated nucleotide (nt) sequence shows similarities of 51, 48 and 47% with the amino acid (aa) sequences reported for the pyruvate phosphate dikinases from Bacteroides symbiosus, maize and Flaveria trinervia, respectively. The reading frame determined codes for a protein of 886 aa.

Draft Genome Sequence of Cellulolytic and Xylanolytic Paenibacillus sp. A59, Isolated from Decaying Forest Soil from Patagonia, Argentina.

PubMed

Ghio, Silvina; Martinez Cáceres, Alfredo I; Talia, Paola; Grasso, Daniel H; Campos, Eleonora

2015-10-22

Paenibacillus sp. A59 was isolated from decaying forest soil in Argentina and characterized as a xylanolytic strain. We report the draft genome sequence of this isolate, with an estimated genome size of 7 Mb which harbor 6,424 coding sequences. Genes coding for hydrolytic enzymes involved in lignocellulose deconstruction were predicted. Copyright © 2015 Ghio et al.

Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression

PubMed Central

Caldwell, Rachel; Lin, Yan-Xia; Zhang, Ren

2015-01-01

There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript) length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5′ and 3′ UTRs) between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length. PMID:26114098

The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae.

PubMed

Robertson, Helen E; Lapraz, François; Egger, Bernhard; Telford, Maximilian J; Schiffer, Philipp H

2017-05-12

Acoels are small, ubiquitous - but understudied - marine worms with a very simple body plan. Their internal phylogeny is still not fully resolved, and the position of their proposed phylum Xenacoelomorpha remains debated. Here we describe mitochondrial genome sequences from the acoels Paratomella rubra and Isodiametra pulchra, and the complete mitochondrial genome of the acoel Archaphanostoma ylvae. The P. rubra and A. ylvae sequences are typical for metazoans in size and gene content. The larger I. pulchra  mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome. The P. rubra, I. pulchra and A. ylvae mitochondria have a unique genome organisation in comparison to other metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap with little non-coding sequence in the compact P. rubra genome. Conversely, the A. ylvae and I. pulchra genomes have many long non-coding sequences between genes, likely driving genome size expansion in the latter. Phylogenetic trees inferred from mitochondrial genes retrieve Xenacoelomorpha as an early branching taxon in the deuterostomes. Sequence divergence analysis between P. rubra sampled in England and Spain indicates cryptic diversity.

Metal resistance sequences and transgenic plants

DOEpatents

Meagher, Richard Brian; Summers, Anne O.; Rugh, Clayton L.

1999-10-12

The present invention provides nucleic acid sequences encoding a metal ion resistance protein, which are expressible in plant cells. The metal resistance protein provides for the enzymatic reduction of metal ions including but not limited to divalent Cu, divalent mercury, trivalent gold, divalent cadmium, lead ions and monovalent silver ions. Transgenic plants which express these coding sequences exhibit increased resistance to metal ions in the environment as compared with plants which have not been so genetically modified. Transgenic plants with improved resistance to organometals including alkylmercury compounds, among others, are provided by the further inclusion of plant-expressible organometal lyase coding sequences, as specifically exemplified by the plant-expressible merB coding sequence. Furthermore, these transgenic plants which have been genetically modified to express the metal resistance coding sequences of the present invention can participate in the bioremediation of metal contamination via the enzymatic reduction of metal ions. Transgenic plants resistant to organometals can further mediate remediation of organic metal compounds, for example, alkylmetal compounds including but not limited to methyl mercury, methyl lead compounds, methyl cadmium and methyl arsenic compounds, in the environment by causing the freeing of mercuric or other metal ions and the reduction of the ionic mercury or other metal ions to the less toxic elemental mercury or other metals.

Writing and applications of fiber Bragg grating arrays

NASA Astrophysics Data System (ADS)

LaRochelle, Sophie; Cortes, Pierre-Yves; Fathallah, H.; Rusch, Leslie A.; Jaafar, H. B.

2000-12-01

Multiple Bragg gratings are written in a single fibre strand with accurate positioning to achieve predetermined time delays between optical channels. Applications of fibre Bragg grating arrays include encoders/decoders with series of identical gratings for optical code-division multiple access.

NRL Fact Book

DTIC Science & Technology

1997-07-01

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78 FR 72955 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change, as...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-04

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21 CFR 510.600 - Names, addresses, and drug labeler codes of sponsors of approved applications.

Code of Federal Regulations, 2010 CFR

2010-04-01

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Code of Federal Regulations, 2013 CFR

2013-04-01

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Management Sciences Division Annual Report (9th)

DTIC Science & Technology

1992-01-01

41 Actuarial Process Consolidation and Review ....................................... 43 How M alfunction Code Reduction...47 Sun W ork Stations ............................................................................... 48 Actuarial Process Consolidation and...Information System (WSMIS). Dyna-METRIC is used for wartime supply support capability assessments. The Aircraft Sustainability Model ( ASM ) is the

Cognitive and Neural Sciences Division 1990 Programs

DTIC Science & Technology

1990-08-01

operator skill acquisition for advanced manufacturing environments. In (W. Karawowski and M. Rahimi, Eds.) Ergonomics of Advanced Manufacturing and...PRINCIPAL INVESTIGATOR: John H. Maunsell University of Rochester Strong School of Medicine and Dentistry (716) 275-2076 R&T PROJECT CODE: 4424242 CONTRACT

On Learning Maps

DTIC Science & Technology

1975-09-01

Director, Office of Manpower Utilizatic Headquarters, Marine Corps (Code MPU ) MCB (Building 2009) Quantico, VA 22134 1 Dr. A.L. Slafkosky...National Defence HQ Ottawa, Canada K1A OK 2 1 Dr. Alma E. Lantz University of Denver Denver Research Institute Industrial Economics Division

Complete mitochondrial genome of the whiter-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Scarabaeidae).

PubMed

Kim, Min Jee; Im, Hyun Hwak; Lee, Kwang Youll; Han, Yeon Soo; Kim, Iksoo

2014-06-01

Abstract The complete nucleotide sequences of the mitochondrial genome from the whiter-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Scarabaeidae), was determined. The 20,319-bp long circular genome is the longest among completely sequenced Coleoptera. As is typical in animals, the P. brevitarsis genome consisted of two ribosomal RNAs, 22 transfer RNAs, 13 protein-coding genes and one A + T-rich region. Although the size of the coding genes was typical, the non-coding A + T-rich region was 5654 bp, which is the longest in insects. The extraordinary length of this region was composed of 28,117-bp tandem repeats and 782-bp tandem repeats. These repeat sequences were encompassed by three non-repeat sequences constituting 1804 bp.

Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany).

PubMed

Röske, Kerstin; Sachse, René; Scheerer, Carola; Röske, Isolde

2012-02-01

Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach. Multivariate statistic was used to reveal relationships between sequence diversity and the environmental conditions. The microbial communities were tremendously diverse with a Shannon index of diversity (H') ranging from 6.7 to 7.1. 18,986 sequences could be classified into 37 phyla including candidate divisions, but the full extent of genetic diversity was not captured. While CARD-FISH gave an overview about the community composition, more detailed information was gained by pyrosequencing. Bacteria were more abundant than Archaea. The dominating phylum in all samples was Proteobacteria, especially Betaproteobacteria and Deltaproteobacteria. Furthermore, sequences of Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Nitrospira, Spirochaetes, Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, and Gemmatimonadetes were found. The site ammonium concentration, water content and organic matter content revealed to be strongest environmental predictors explaining the observed significant differences in the community composition between sampling sites. Copyright © 2011 Elsevier GmbH. All rights reserved.

Rate adaptive multilevel coded modulation with high coding gain in intensity modulation direct detection optical communication

NASA Astrophysics Data System (ADS)

Xiao, Fei; Liu, Bo; Zhang, Lijia; Xin, Xiangjun; Zhang, Qi; Tian, Qinghua; Tian, Feng; Wang, Yongjun; Rao, Lan; Ullah, Rahat; Zhao, Feng; Li, Deng'ao

2018-02-01

A rate-adaptive multilevel coded modulation (RA-MLC) scheme based on fixed code length and a corresponding decoding scheme is proposed. RA-MLC scheme combines the multilevel coded and modulation technology with the binary linear block code at the transmitter. Bits division, coding, optional interleaving, and modulation are carried out by the preset rule, then transmitted through standard single mode fiber span equal to 100 km. The receiver improves the accuracy of decoding by means of soft information passing through different layers, which enhances the performance. Simulations are carried out in an intensity modulation-direct detection optical communication system using MATLAB®. Results show that the RA-MLC scheme can achieve bit error rate of 1E-5 when optical signal-to-noise ratio is 20.7 dB. It also reduced the number of decoders by 72% and realized 22 rate adaptation without significantly increasing the computing time. The coding gain is increased by 7.3 dB at BER=1E-3.

Performance optimization of spectral amplitude coding OCDMA system using new enhanced multi diagonal code

NASA Astrophysics Data System (ADS)

Imtiaz, Waqas A.; Ilyas, M.; Khan, Yousaf

2016-11-01

This paper propose a new code to optimize the performance of spectral amplitude coding-optical code division multiple access (SAC-OCDMA) system. The unique two-matrix structure of the proposed enhanced multi diagonal (EMD) code and effective correlation properties, between intended and interfering subscribers, significantly elevates the performance of SAC-OCDMA system by negating multiple access interference (MAI) and associated phase induce intensity noise (PIIN). Performance of SAC-OCDMA system based on the proposed code is thoroughly analyzed for two detection techniques through analytic and simulation analysis by referring to bit error rate (BER), signal to noise ratio (SNR) and eye patterns at the receiving end. It is shown that EMD code while using SDD technique provides high transmission capacity, reduces the receiver complexity, and provides better performance as compared to complementary subtraction detection (CSD) technique. Furthermore, analysis shows that, for a minimum acceptable BER of 10-9 , the proposed system supports 64 subscribers at data rates of up to 2 Gbps for both up-down link transmission.

EDGE 2017 R&D 100 Entry with Appendix

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

Chain, Patrick Sam Guy; Davenport, Karen Walston; Li, Po-E

Diabetes, infertility, cancer, and Alzheimer’s disease—the key to one day preventing or even curing such afflictions and diseases (both infectious and genetically driven) may be locked in our own genetic code and the code of microorganisms that inhabit our bodies. The study of this code, known as genomics, has recently become much more promising as a result of two things: (1) vast improvements in high-throughput, nextgeneration sequencing (NSG), and (2) an exponential decrease in the cost of such sequencing. For example, it originally cost approximately $3 billion to sequence the human genome; today, this genome could be resequenced for lessmore » than $1,000.« less

Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

PubMed Central

2011-01-01

Background Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships. Results In this paper, we have proposed a Vertical Decomposition with Genetic Algorithm (VDGA) for Multiple Sequence Alignment (MSA). In VDGA, we divide the sequences vertically into two or more subsequences, and then solve them individually using a guide tree approach. Finally, we combine all the subsequences to generate a new multiple sequence alignment. This technique is applied on the solutions of the initial generation and of each child generation within VDGA. We have used two mechanisms to generate an initial population in this research: the first mechanism is to generate guide trees with randomly selected sequences and the second is shuffling the sequences inside such trees. Two different genetic operators have been implemented with VDGA. To test the performance of our algorithm, we have compared it with existing well-known methods, namely PRRP, CLUSTALX, DIALIGN, HMMT, SB_PIMA, ML_PIMA, MULTALIGN, and PILEUP8, and also other methods, based on Genetic Algorithms (GA), such as SAGA, MSA-GA and RBT-GA, by solving a number of benchmark datasets from BAliBase 2.0. Conclusions The experimental results showed that the VDGA with three vertical divisions was the most successful variant for most of the test cases in comparison to other divisions considered with VDGA. The experimental results also confirmed that VDGA outperformed the other methods considered in this research. PMID:21867510

Scaling features of noncoding DNA

NASA Technical Reports Server (NTRS)

Stanley, H. E.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.

1999-01-01

We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong "background" effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.

Long-term, high-resolution confocal time lapse imaging of Arabidopsis cotyledon epidermis during germination.

PubMed

Peterson, Kylee M; Torii, Keiko U

2012-12-31

Imaging in vivo dynamics of cellular behavior throughout a developmental sequence can be a powerful technique for understanding the mechanics of tissue patterning. During animal development, key cell proliferation and patterning events occur very quickly. For instance, in Caenorhabditis elegans all cell divisions required for the larval body plan are completed within six hours after fertilization, with seven mitotic cycles(1); the sixteen or more mitoses of Drosophila embryogenesis occur in less than 24 hr(2). In contrast, cell divisions during plant development are slow, typically on the order of a day (3,4,5) . This imposes a unique challenge and a need for long-term live imaging for documenting dynamic behaviors of cell division and differentiation events during plant organogenesis. Arabidopsis epidermis is an excellent model system for investigating signaling, cell fate, and development in plants. In the cotyledon, this tissue consists of air- and water-resistant pavement cells interspersed with evenly distributed stomata, valves that open and close to control gas exchange and water loss. Proper spacing of these stomata is critical to their function, and their development follows a sequence of asymmetric division and cell differentiation steps to produce the organized epidermis (Fig. 1). This protocol allows observation of cells and proteins in the epidermis over several days of development. This time frame enables precise documentation of stem-cell divisions and differentiation of epidermal cells, including stomata and epidermal pavement cells. Fluorescent proteins can be fused to proteins of interest to assess their dynamics during cell division and differentiation processes. This technique allows us to understand the localization of a novel protein, POLAR(6), during the proliferation stage of stomatal-lineage cells in the Arabidopsis cotyledon epidermis, where it is expressed in cells preceding asymmetric division events and moves to a characteristic area of the cell cortex shortly before division occurs. Images can be registered and streamlined video easily produced using public domain software to visualize dynamic protein localization and cell types as they change over time.

New patterns in dust off the edge of Saturn’s main rings

NASA Astrophysics Data System (ADS)

Chancia, Robert Ormal; Hedman, Matthew M.; Ye, Shengyi; Kurth, William S.

2017-10-01

The Roche Division is a 3000-km-span of diffuse dust located at the outer edge of Saturn’s main ring system between the A and F rings. Several high-resolution images from Cassini’s orbit insertion revealed two regions with higher concentrations of dust within the Roche Division. These proposed dusty ringlets R/2004 S1 (radius=137,630 km) and R/2004 S2 (radius=138,900 km) lie coincident with the orbit of Atlas and slightly interior to the orbit of Prometheus respectively (Porco et al. 2005a Science). Using several image sequences later obtained by Cassini Hedman et al. 2009 (Icarus) found that these concentrations of dusty ring material are not simple ringlets, but are in fact organized into canted azimuthal brightness variations with a periodicity akin to a 3:4 resonance with Saturn’s rotation rate. The presumed perturbing phenomenon is Saturn’s kilometric radiation (SKR), a strong low wavelength component of the planet’s radio emissions, whose power oscillates near the planet’s rotation rate at a frequency matching the Roche Division structures. However, over the course of the Cassini mission the SKR period has varied by at least 7 minutes. As a result, the location of the resonance moved interior to the edge of the A ring and out of the Roche Division around the time of Saturn’s equinox. Subsequent observations of the Roche Division in the this time period show no evidence of the prominent structures previously observed during the first few years of the Cassini mission. Recently, the 3:4 resonant structures have reappeared in the Roche Division as one of the SKR periods has increased. Here we show that the these dusty Roche Division structures are present in sync with the varying SKR period using images sequences spanning the entire Cassini mission. We also highlight some particularly optimal observations, obtained during Cassini’s F-ring proximal and grand finale orbits, which reveal the dusty structure of the Roche Division in unprecedented detail.

Resource allocation for error resilient video coding over AWGN using optimization approach.

PubMed

An, Cheolhong; Nguyen, Truong Q

2008-12-01

The number of slices for error resilient video coding is jointly optimized with 802.11a-like media access control and the physical layers with automatic repeat request and rate compatible punctured convolutional code over additive white gaussian noise channel as well as channel times allocation for time division multiple access. For error resilient video coding, the relation between the number of slices and coding efficiency is analyzed and formulated as a mathematical model. It is applied for the joint optimization problem, and the problem is solved by a convex optimization method such as the primal-dual decomposition method. We compare the performance of a video communication system which uses the optimal number of slices with one that codes a picture as one slice. From numerical examples, end-to-end distortion of utility functions can be significantly reduced with the optimal slices of a picture especially at low signal-to-noise ratio.

Simulation realization of 2-D wavelength/time system utilizing MDW code for OCDMA system

NASA Astrophysics Data System (ADS)

Azura, M. S. A.; Rashidi, C. B. M.; Aljunid, S. A.; Endut, R.; Ali, N.

2017-11-01

This paper presents a realization of Wavelength/Time (W/T) Two-Dimensional Modified Double Weight (2-D MDW) code for Optical Code Division Multiple Access (OCDMA) system based on Spectral Amplitude Coding (SAC) approach. The MDW code has the capability to suppress Phase-Induce Intensity Noise (PIIN) and minimizing the Multiple Access Interference (MAI) noises. At the permissible BER 10-9, the 2-D MDW (APD) had shown minimum effective received power (Psr) = -71 dBm that can be obtained at the receiver side as compared to 2-D MDW (PIN) only received -61 dBm. The results show that 2-D MDW (APD) has better performance in achieving same BER with longer optical fiber length and with less received power (Psr). Also, the BER from the result shows that MDW code has the capability to suppress PIIN ad MAI.

The complete mitochondrial genome of the scab mite Psoroptes cuniculi (Arthropoda: Arachnida) provides insights into Acari phylogeny

PubMed Central

2014-01-01

Background Limited available sequence information has greatly impeded population genetics, phylogenetics and systematics studies in the subclass Acari (mites and ticks). Mitochondrial (mt) DNA is well known to provide genetic markers for investigations in these areas, but complete mt genomic data have been lacking for many Acari species. Herein, we present the complete mt genome of the scab mite Psoroptes cuniculi. Methods P. cuniculi was collected from a naturally infected New Zealand white rabbit from China and identified by morphological criteria. The complete mt genome of P. cuniculi was amplified by PCR and then sequenced. The relationships of this scab mite with selected members of the Acari were assessed by phylogenetic analysis of concatenated amino acid sequence datasets by Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP). Results This mt genome (14,247 bp) is circular and consists of 37 genes, including 13 genes for proteins, 22 genes for tRNA, 2 genes for rRNA. The gene arrangement in mt genome of P. cuniculi is the same as those of Dermatophagoides farinae (Pyroglyphidae) and Aleuroglyphus ovatus (Acaridae), but distinct from those of Steganacarus magnus (Steganacaridae) and Panonychus citri (Tetranychidae). Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (BI, ML and MP), showed the division of subclass Acari into two superorders, supported the monophylies of the both superorders Parasitiformes and Acariformes; and the three orders Ixodida and Mesostigmata and Astigmata, but rejected the monophyly of the order Prostigmata. Conclusions The mt genome of P. cuniculi represents the first mt genome of any member of the family Psoroptidae. Analysis of mt genome sequences in the present study has provided new insights into the phylogenetic relationships among several major lineages of Acari species. PMID:25052180

Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly

PubMed Central

Sugano, Sumio; Morishita, Shinichi; Suzuki, Yutaka

2010-01-01

Background Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. Methodology We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence ∼800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. Conclusions The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only ∼US$3 per clone, demonstrating a significant advantage over previous approaches. PMID:20479877

Cloning and expression of a cDNA coding for a human monocyte-derived plasminogen activator inhibitor.

PubMed

Antalis, T M; Clark, M A; Barnes, T; Lehrbach, P R; Devine, P L; Schevzov, G; Goss, N H; Stephens, R W; Tolstoshev, P

1988-02-01

Human monocyte-derived plasminogen activator inhibitor (mPAI-2) was purified to homogeneity from the U937 cell line and partially sequenced. Oligonucleotide probes derived from this sequence were used to screen a cDNA library prepared from U937 cells. One positive clone was sequenced and contained most of the coding sequence as well as a long incomplete 3' untranslated region (1112 base pairs). This cDNA sequence was shown to encode mPAI-2 by hybrid-select translation. A cDNA clone encoding the remainder of the mPAI-2 mRNA was obtained by primer extension of U937 poly(A)+ RNA using a probe complementary to the mPAI-2 coding region. The coding sequence for mPAI-2 was placed under the control of the lambda PL promoter, and the protein expressed in Escherichia coli formed a complex with urokinase that could be detected immunologically. By nucleotide sequence analysis, mPAI-2 cDNA encodes a protein containing 415 amino acids with a predicted unglycosylated Mr of 46,543. The predicted amino acid sequence of mPAI-2 is very similar to placental PAI-2 (3 amino acid differences) and shows extensive homology with members of the serine protease inhibitor (serpin) superfamily. mPAI-2 was found to be more homologous to ovalbumin (37%) than the endothelial plasminogen activator inhibitor, PAI-1 (26%). Like ovalbumin, mPAI-2 appears to have no typical amino-terminal signal sequence. The 3' untranslated region of the mPAI-2 cDNA contains a putative regulatory sequence that has been associated with the inflammatory mediators.

Cloning and expression of a cDNA coding for a human monocyte-derived plasminogen activator inhibitor.

PubMed Central

Antalis, T M; Clark, M A; Barnes, T; Lehrbach, P R; Devine, P L; Schevzov, G; Goss, N H; Stephens, R W; Tolstoshev, P

1988-01-01

Human monocyte-derived plasminogen activator inhibitor (mPAI-2) was purified to homogeneity from the U937 cell line and partially sequenced. Oligonucleotide probes derived from this sequence were used to screen a cDNA library prepared from U937 cells. One positive clone was sequenced and contained most of the coding sequence as well as a long incomplete 3' untranslated region (1112 base pairs). This cDNA sequence was shown to encode mPAI-2 by hybrid-select translation. A cDNA clone encoding the remainder of the mPAI-2 mRNA was obtained by primer extension of U937 poly(A)+ RNA using a probe complementary to the mPAI-2 coding region. The coding sequence for mPAI-2 was placed under the control of the lambda PL promoter, and the protein expressed in Escherichia coli formed a complex with urokinase that could be detected immunologically. By nucleotide sequence analysis, mPAI-2 cDNA encodes a protein containing 415 amino acids with a predicted unglycosylated Mr of 46,543. The predicted amino acid sequence of mPAI-2 is very similar to placental PAI-2 (3 amino acid differences) and shows extensive homology with members of the serine protease inhibitor (serpin) superfamily. mPAI-2 was found to be more homologous to ovalbumin (37%) than the endothelial plasminogen activator inhibitor, PAI-1 (26%). Like ovalbumin, mPAI-2 appears to have no typical amino-terminal signal sequence. The 3' untranslated region of the mPAI-2 cDNA contains a putative regulatory sequence that has been associated with the inflammatory mediators. Images PMID:3257578

[Learning and Repetive Reproduction of Memorized Sequences by the Right and the Left Hand].

PubMed

Bobrova, E V; Lyakhovetskii, V A; Bogacheva, I N

2015-01-01

An important stage of learning a new skill is repetitive reproduction of one and the same sequence of movements, which plays a significant role in forming of the movement stereotypes. Two groups of right-handers repeatedly memorized (6-10 repetitions) the sequences of their hand transitions by experimenter in 6 positions, firstly by the right hand (RH), and then--by the left hand (LH) or vice versa. Random sequences previously unknown to the volunteers were reproduced in the 11 series. Modified sequences were tested in the 2nd and 3rd series, where the same elements' positions were presented in different order. The processes of repetitive sequence reproduction were similar for RH and LH. However, the learning of the modified sequences differed: Information about elements' position disregarding the reproduction order was used only when LH initiated task performing. This information was not used when LH followed RH and when RH performed the task. Consequently, the type of information coding activated by LH helped learn the positions of sequence elements, while the type of information coding activated by RH prevented learning. It is supposedly connected with the predominant role of right hemisphere in the processes of positional coding and motor learning.

Sequence Polishing Library (SPL) v10.0

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

Oberortner, Ernst

The Sequence Polishing Library (SPL) is a suite of software tools in order to automate "Design for Synthesis and Assembly" workflows. Specifically: The SPL "Converter" tool converts files among the following sequence data exchange formats: CSV, FASTA, GenBank, and Synthetic Biology Open Language (SBOL); The SPL "Juggler" tool optimizes the codon usages of DNA coding sequences according to an optimization strategy, a user-specific codon usage table and genetic code. In addition, the SPL "Juggler" can translate amino acid sequences into DNA sequences.:The SPL "Polisher" verifies NA sequences against DNA synthesis constraints, such as GC content, repeating k-mers, and restriction sites.more » In case of violations, the "Polisher" reports the violations in a comprehensive manner. The "Polisher" tool can also modify the violating regions according to an optimization strategy, a user-specific codon usage table and genetic code;The SPL "Partitioner" decomposes large DNA sequences into smaller building blocks with partial overlaps that enable an efficient assembly. The "Partitioner" enables the user to configure the characteristics of the overlaps, which are mostly determined by the utilized assembly protocol, such as length, GC content, or melting temperature.« less

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)

PubMed Central

Martin, Andrew C. R.

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and ’dotifying’ repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/. PMID:25653836

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

PubMed

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Automotive Gas Turbine Power System-Performance Analysis Code

NASA Technical Reports Server (NTRS)

Juhasz, Albert J.

1997-01-01

An open cycle gas turbine numerical modelling code suitable for thermodynamic performance analysis (i.e. thermal efficiency, specific fuel consumption, cycle state points, working fluid flowrates etc.) of automotive and aircraft powerplant applications has been generated at the NASA Lewis Research Center's Power Technology Division. The use this code can be made available to automotive gas turbine preliminary design efforts, either in its present version, or, assuming that resources can be obtained to incorporate empirical models for component weight and packaging volume, in later version that includes the weight-volume estimator feature. The paper contains a brief discussion of the capabilities of the presently operational version of the code, including a listing of input and output parameters and actual sample output listings.

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

The complete validated mitochondrial genome of the silver gemfish Rexea solandri (Cuvier, 1832) (Perciformes, Gempylidae).

PubMed

Bustamante, Carlos; Ovenden, Jennifer R

2016-01-01

The silver gemfish Rexea solandri is an important economic resource but Vulnerable to overfishing in Australian waters. The complete mitochondrial genome sequence is described from 1.6 million reads obtained via next generation sequencing. The total length of the mitogenome is 16,350 bp comprising 2 rRNA, 13 protein-coding genes, 22 tRNA and 2 non-coding regions. The mitogenome sequence was validated against sequences of PCR fragments and BLAST queries of Genbank. Gene order was equivalent to that found in marine fishes.

High rate concatenated coding systems using bandwidth efficient trellis inner codes

NASA Technical Reports Server (NTRS)

Deng, Robert H.; Costello, Daniel J., Jr.

1989-01-01

High-rate concatenated coding systems with bandwidth-efficient trellis inner codes and Reed-Solomon (RS) outer codes are investigated for application in high-speed satellite communication systems. Two concatenated coding schemes are proposed. In one the inner code is decoded with soft-decision Viterbi decoding, and the outer RS code performs error-correction-only decoding (decoding without side information). In the other, the inner code is decoded with a modified Viterbi algorithm, which produces reliability information along with the decoded output. In this algorithm, path metrics are used to estimate the entire information sequence, whereas branch metrics are used to provide reliability information on the decoded sequence. This information is used to erase unreliable bits in the decoded output. An errors-and-erasures RS decoder is then used for the outer code. The two schemes have been proposed for high-speed data communication on NASA satellite channels. The rates considered are at least double those used in current NASA systems, and the results indicate that high system reliability can still be achieved.

Intact coding region of the serotonin transporter gene in obsessive-compulsive disorder

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

Altemus, M.; Murphy, D.L.; Greenberg, B.

1996-07-26

Epidemiologic studies indicate that obsessive-compulsive disorder is genetically transmitted in some families, although no genetic abnormalities have been identified in individuals with this disorder. The selective response of obsessive-compulsive disorder to treatment with agents which block serotonin reuptake suggests the gene coding for the serotonin transporter as a candidate gene. The primary structure of the serotonin-transporter coding region was sequenced in 22 patients with obsessive-compulsive disorder, using direct PCR sequencing of cDNA synthesized from platelet serotonin-transporter mRNA. No variations in amino acid sequence were found among the obsessive-compulsive disorder patients or healthy controls. These results do not support a rolemore » for alteration in the primary structure of the coding region of the serotonin-transporter gene in the pathogenesis of obsessive-compulsive disorder. 27 refs.« less

Novel coding, translation, and gene expression of a replicating covalently closed circular RNA of 220 nt.

PubMed

AbouHaidar, Mounir Georges; Venkataraman, Srividhya; Golshani, Ashkan; Liu, Bolin; Ahmad, Tauqeer

2014-10-07

The highly structured (64% GC) covalently closed circular (CCC) RNA (220 nt) of the virusoid associated with rice yellow mottle virus codes for a 16-kDa highly basic protein using novel modalities for coding, translation, and gene expression. This CCC RNA is the smallest among all known viroids and virusoids and the only one that codes proteins. Its sequence possesses an internal ribosome entry site and is directly translated through two (or three) completely overlapping ORFs (shifting to a new reading frame at the end of each round). The initiation and termination codons overlap UGAUGA (underline highlights the initiation codon AUG within the combined initiation-termination sequence). Termination codons can be ignored to obtain larger read-through proteins. This circular RNA with no noncoding sequences is a unique natural supercompact "nanogenome."

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades

PubMed Central

Blanga-Kanfi, Shani; Miranda, Hector; Penn, Osnat; Pupko, Tal; DeBry, Ronald W; Huchon, Dorothée

2009-01-01

Background Rodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes. Results We present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation. Conclusion Sequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset. PMID:19341461

[Prokaryotic expression and histological localization of the Taenia solium CDC37 gene].

PubMed

Huang, Jiang; Li, Bo; Dai, Jia-Lin; Zhang, Ai-Hua

2013-02-01

To express Taenia solium gene encoding cell division cycle 37 protein (TsCDC37) and investigate its antigenicity and localization in adults of Taenia solium. The complete coding sequence of TsCDC37 was amplified by PCR based on the recombinant plasmid clone from the cDNA library of adult Taenia solium. The PCR product was cloned into a prokaryotic expression vector pET-28a (+). The recombinant expression plasmid was identified by PCR, double endonuclease digestion and sequencing. The recombinant plasmid was transformed into E. coli BL21/DE3 and followed by expression of the protein induced by IPTG. The mice were immunized subcutaneously with purified recombinant TsCDC37 formulated in Freund's adjuvant. The antigenicity of the recombinant protein was examined by Western blotting. The localization of TsCDC37 in adult worms was demonstrated by immunofluorescent technique. The recombinant expression vector was constructed successfully. The recombinant protein was about M(r) 52 000, it was then purified and specifically recognized by immuno sera of SD rats and sera from patients infected with Taenia solium, Taenia saginata or Taenia asiatica. The immunofluorescence assay revealed that TsCDC37 located at the tegument of T. solium adult and the eggs. TsCDC37 gene has been expressed with immunoreactivity. The recombinant protein is mainly expressed in tegument and egg, and is a common antigen of the three human taenia cestodes.

Design of a Multicast Optical Packet Switch Based on Fiber Bragg Grating Technology for Future Networks

NASA Astrophysics Data System (ADS)

Cheng, Yuh-Jiuh; Yeh, Tzuoh-Chyau; Cheng, Shyr-Yuan

2011-09-01

In this paper, a non-blocking multicast optical packet switch based on fiber Bragg grating technology with optical output buffers is proposed. Only the header of optical packets is converted to electronic signals to control the fiber Bragg grating array of input ports and the packet payloads should be transparently destined to their output ports so that the proposed switch can reduce electronic interfaces as well as the bit rate. The modulation and the format of packet payloads may be non-standard where packet payloads could also include different wavelengths for increasing the volume of traffic. The advantage is obvious: the proposed switch could transport various types of traffic. An easily implemented architecture which can provide multicast services is also presented. An optical output buffer is designed to queue the packets if more than one incoming packet should reach to the same destination output port or including any waiting packets in optical output buffer that will be sent to the output port at a time slot. For preserving service-packet sequencing and fairness of routing sequence, a priority scheme and a round-robin algorithm are adopted at the optical output buffer. The fiber Bragg grating arrays for both input ports and output ports are designed for routing incoming packets using optical code division multiple access technology.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

PubMed

Smith, Chris R; Smith, Christopher D; Robertson, Hugh M; Helmkampf, Martin; Zimin, Aleksey; Yandell, Mark; Holt, Carson; Hu, Hao; Abouheif, Ehab; Benton, Richard; Cash, Elizabeth; Croset, Vincent; Currie, Cameron R; Elhaik, Eran; Elsik, Christine G; Favé, Marie-Julie; Fernandes, Vilaiwan; Gibson, Joshua D; Graur, Dan; Gronenberg, Wulfila; Grubbs, Kirk J; Hagen, Darren E; Viniegra, Ana Sofia Ibarraran; Johnson, Brian R; Johnson, Reed M; Khila, Abderrahman; Kim, Jay W; Mathis, Kaitlyn A; Munoz-Torres, Monica C; Murphy, Marguerite C; Mustard, Julie A; Nakamura, Rin; Niehuis, Oliver; Nigam, Surabhi; Overson, Rick P; Placek, Jennifer E; Rajakumar, Rajendhran; Reese, Justin T; Suen, Garret; Tao, Shu; Torres, Candice W; Tsutsui, Neil D; Viljakainen, Lumi; Wolschin, Florian; Gadau, Jürgen

2011-04-05

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

76 FR 41859 - Agency Information Collection Activities: Requests for Comments; Clearance of Renewed Approval of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

.... Estimated Average Burden per Response: 22 hours. Estimated Total Annual Burden: 100,132 hours. ADDRESSES... Business Services Division, AES-300. [FR Doc. 2011-17209 Filed 7-14-11; 8:45 am] BILLING CODE 4910-13-P ...

The Effectiveness of an Interactive Map Display in Tutoring Geography

DTIC Science & Technology

1976-08-01

MCIT LG Hanscom Field Bedford, MA 01730 Director, Office of Manpower Utilization Headquarters, Marine Corps (Code MPU ) MCB (Building 2009...Lantz University of Denver Denver Research Institute Industrial Economics Division Denver, CO 80210 Mr. Brian McNally Educational Testing Service

Gene and genon concept: coding versus regulation

PubMed Central

2007-01-01

We analyse here the definition of the gene in order to distinguish, on the basis of modern insight in molecular biology, what the gene is coding for, namely a specific polypeptide, and how its expression is realized and controlled. Before the coding role of the DNA was discovered, a gene was identified with a specific phenotypic trait, from Mendel through Morgan up to Benzer. Subsequently, however, molecular biologists ventured to define a gene at the level of the DNA sequence in terms of coding. As is becoming ever more evident, the relations between information stored at DNA level and functional products are very intricate, and the regulatory aspects are as important and essential as the information coding for products. This approach led, thus, to a conceptual hybrid that confused coding, regulation and functional aspects. In this essay, we develop a definition of the gene that once again starts from the functional aspect. A cellular function can be represented by a polypeptide or an RNA. In the case of the polypeptide, its biochemical identity is determined by the mRNA prior to translation, and that is where we locate the gene. The steps from specific, but possibly separated sequence fragments at DNA level to that final mRNA then can be analysed in terms of regulation. For that purpose, we coin the new term “genon”. In that manner, we can clearly separate product and regulative information while keeping the fundamental relation between coding and function without the need to introduce a conceptual hybrid. In mRNA, the program regulating the expression of a gene is superimposed onto and added to the coding sequence in cis - we call it the genon. The complementary external control of a given mRNA by trans-acting factors is incorporated in its transgenon. A consequence of this definition is that, in eukaryotes, the gene is, in most cases, not yet present at DNA level. Rather, it is assembled by RNA processing, including differential splicing, from various pieces, as steered by the genon. It emerges finally as an uninterrupted nucleic acid sequence at mRNA level just prior to translation, in faithful correspondence with the amino acid sequence to be produced as a polypeptide. After translation, the genon has fulfilled its role and expires. The distinction between the protein coding information as materialised in the final polypeptide and the processing information represented by the genon allows us to set up a new information theoretic scheme. The standard sequence information determined by the genetic code expresses the relation between coding sequence and product. Backward analysis asks from which coding region in the DNA a given polypeptide originates. The (more interesting) forward analysis asks in how many polypeptides of how many different types a given DNA segment is expressed. This concerns the control of the expression process for which we have introduced the genon concept. Thus, the information theoretic analysis can capture the complementary aspects of coding and regulation, of gene and genon. PMID:18087760

The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

PubMed Central

Oh, Chang Seok; Lee, Soong Deok; Kim, Yi-Suk; Shin, Dong Hoon

2015-01-01

Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods. PMID:26345190

Flexible and polarization-controllable diffusion metasurface with optical transparency

NASA Astrophysics Data System (ADS)

Zhuang, Yaqiang; Wang, Guangming; Liang, Jiangang; Cai, Tong; Guo, Wenlong; Zhang, Qingfeng

2017-11-01

In this paper, a novel coding metasurface is proposed to realize polarization-controllable diffusion scattering. The anisotropic Jerusalem-cross unit cell is employed as the basic coding element due to its polarization-dependent phase response. The isotropic random coding sequence is firstly designed to obtain diffusion scattering, and the anisotropic random coding sequence is subsequently realized by adding different periodic coding sequences to the original isotropic one along different directions. For demonstration, we designed and fabricated a flexible polarization-controllable diffusion metasurface (PCDM) with both chessboard diffusion and hedge diffusion under different polarizations. The specular scattering reduction performance of the anisotropic metasurface is better than the isotropic one because the scattered energies are redirected away from the specular reflection direction. For potential applications, the flexible PCDM wrapped around a cylinder structure is investigated and tested for polarization-controllable diffusion scattering. The numerical and experimental results coincide well, indicating anisotropic low scatterings with comparable performances. This paper provides an alternative approach for designing high-performance, flexible, low-scattering platforms.

Seepage and Piping through Levees and Dikes using 2D and 3D Modeling Codes

DTIC Science & Technology

2016-06-01

by the Hydrologic Systems Branch of the Flood and Storm Protection Division (CEERD-HF), U.S. Army Engineer Research and Development Center, Coastal ...ER D C/ CH L TR -1 6- 6 Flood & Coastal Storm Damage Reduction Program Seepage and Piping through Levees and Dikes Using 2D and 3D...Flood & Coastal Storm Damage Reduction Program ERDC/CHL TR-16-6 June 2016 Seepage and Piping through Levees and Dikes Using 2D and 3D Modeling Codes

CrossTalk: The Journal of Defense Software Engineering. Volume 25, Number 4, July/August 2012

DTIC Science & Technology

2012-08-01

understand the interface between various code components. For example, consider a situation in which handwrit - ten code produced by one team generates an...conclusively say that a division by zero will not occur. The abstract interpretation concept can be generalized as a tool set that can be used to determine...word what makes a good manager, I would say decisiveness. You can use the fan- ciest computers to gather the numbers, but in the end you have to set

Pulse Code Modulation (PCM) encoder handbook for Aydin Vector MMP-900 series system

NASA Technical Reports Server (NTRS)

Raphael, David

1995-01-01

This handbook explicates the hardware and software properties of a time division multiplex system. This system is used to sample analog and digital data. The data is then merged with frame synchronization information to produce a serial pulse coded modulation (PCM) bit stream. Information in this handbook is required by users to design congruous interface and attest effective utilization of this encoder system. Aydin Vector provides all of the components for these systems to Goddard Space Flight Center/Wallops Flight Facility.

Effects of Multipath and Oversampling on Navigation Using Orthogonal Frequency Division Multiplexed Signals of Opportunity

DTIC Science & Technology

2008-03-01

for military use. The L2 carrier frequency operates at 1227.6 MHz and transmits only the precise code . Each satellite transmits a unique pseudo ...random noise (PRN) code by which it is identified. GPS receivers require a LOS to four satellite signals to accurately estimate a position in three...receiver frequency errors, noise addition, and multipath ef- fects. He also developed four methods for estimating the cross- correlation peak within a sampled

Physical-Layer Network Coding for VPN in TDM-PON

NASA Astrophysics Data System (ADS)

Wang, Qike; Tse, Kam-Hon; Chen, Lian-Kuan; Liew, Soung-Chang

2012-12-01

We experimentally demonstrate a novel optical physical-layer network coding (PNC) scheme over time-division multiplexing (TDM) passive optical network (PON). Full-duplex error-free communications between optical network units (ONUs) at 2.5 Gb/s are shown for all-optical virtual private network (VPN) applications. Compared to the conventional half-duplex communications set-up, our scheme can increase the capacity by 100% with power penalty smaller than 3 dB. Synchronization of two ONUs is not required for the proposed VPN scheme

Coding visual features extracted from video sequences.

PubMed

Baroffio, Luca; Cesana, Matteo; Redondi, Alessandro; Tagliasacchi, Marco; Tubaro, Stefano

2014-05-01

Visual features are successfully exploited in several applications (e.g., visual search, object recognition and tracking, etc.) due to their ability to efficiently represent image content. Several visual analysis tasks require features to be transmitted over a bandwidth-limited network, thus calling for coding techniques to reduce the required bit budget, while attaining a target level of efficiency. In this paper, we propose, for the first time, a coding architecture designed for local features (e.g., SIFT, SURF) extracted from video sequences. To achieve high coding efficiency, we exploit both spatial and temporal redundancy by means of intraframe and interframe coding modes. In addition, we propose a coding mode decision based on rate-distortion optimization. The proposed coding scheme can be conveniently adopted to implement the analyze-then-compress (ATC) paradigm in the context of visual sensor networks. That is, sets of visual features are extracted from video frames, encoded at remote nodes, and finally transmitted to a central controller that performs visual analysis. This is in contrast to the traditional compress-then-analyze (CTA) paradigm, in which video sequences acquired at a node are compressed and then sent to a central unit for further processing. In this paper, we compare these coding paradigms using metrics that are routinely adopted to evaluate the suitability of visual features in the context of content-based retrieval, object recognition, and tracking. Experimental results demonstrate that, thanks to the significant coding gains achieved by the proposed coding scheme, ATC outperforms CTA with respect to all evaluation metrics.

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer.

PubMed

Wojcik, Sylwia E; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z; Rai, Kanti R; Kipps, Thomas J; Keating, Michael J; Croce, Carlo M; Calin, George A

2010-02-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas.

Non-codingRNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer

PubMed Central

Wojcik, Sylwia E.; Rossi, Simona; Shimizu, Masayoshi; Nicoloso, Milena S.; Cimmino, Amelia; Alder, Hansjuerg; Herlea, Vlad; Rassenti, Laura Z.; Rai, Kanti R.; Kipps, Thomas J.; Keating, Michael J.

2010-01-01

Cancer is a genetic disease in which the interplay between alterations in protein-coding genes and non-coding RNAs (ncRNAs) plays a fundamental role. In recent years, the full coding component of the human genome was sequenced in various cancers, whereas such attempts related to ncRNAs are still fragmentary. We screened genomic DNAs for sequence variations in 148 microRNAs (miRNAs) and ultraconserved regions (UCRs) loci in patients with chronic lymphocytic leukemia (CLL) or colorectal cancer (CRC) by Sanger technique and further tried to elucidate the functional consequences of some of these variations. We found sequence variations in miRNAs in both sporadic and familial CLL cases, mutations of UCRs in CLLs and CRCs and, in certain instances, detected functional effects of these variations. Furthermore, by integrating our data with previously published data on miRNA sequence variations, we have created a catalog of DNA sequence variations in miRNAs/ultraconserved genes in human cancers. These findings argue that ncRNAs are targeted by both germ line and somatic mutations as well as by single-nucleotide polymorphisms with functional significance for human tumorigenesis. Sequence variations in ncRNA loci are frequent and some have functional and biological significance. Such information can be exploited to further investigate on a genome-wide scale the frequency of genetic variations in ncRNAs and their functional meaning, as well as for the development of new diagnostic and prognostic markers for leukemias and carcinomas. PMID:19926640

Probability of coding of a DNA sequence: an algorithm to predict translated reading frames from their thermodynamic characteristics.

PubMed Central

Tramontano, A; Macchiato, M F

1986-01-01

An algorithm to determine the probability that a reading frame codifies for a protein is presented. It is based on the results of our previous studies on the thermodynamic characteristics of a translated reading frame. We also develop a prediction procedure to distinguish between coding and non-coding reading frames. The procedure is based on the characteristics of the putative product of the DNA sequence and not on periodicity characteristics of the sequence, so the prediction is not biased by the presence of overlapping translated reading frames or by the presence of translated reading frames on the complementary DNA strand. PMID:3753761

Validation of CFD/Heat Transfer Software for Turbine Blade Analysis

NASA Technical Reports Server (NTRS)

Kiefer, Walter D.

2004-01-01

I am an intern in the Turbine Branch of the Turbomachinery and Propulsion Systems Division. The division is primarily concerned with experimental and computational methods of calculating heat transfer effects of turbine blades during operation in jet engines and land-based power systems. These include modeling flow in internal cooling passages and film cooling, as well as calculating heat flux and peak temperatures to ensure safe and efficient operation. The branch is research-oriented, emphasizing the development of tools that may be used by gas turbine designers in industry. The branch has been developing a computational fluid dynamics (CFD) and heat transfer code called GlennHT to achieve the computational end of this analysis. The code was originally written in FORTRAN 77 and run on Silicon Graphics machines. However the code has been rewritten and compiled in FORTRAN 90 to take advantage of more modem computer memory systems. In addition the branch has made a switch in system architectures from SGI's to Linux PC's. The newly modified code therefore needs to be tested and validated. This is the primary goal of my internship. To validate the GlennHT code, it must be run using benchmark fluid mechanics and heat transfer test cases, for which there are either analytical solutions or widely accepted experimental data. From the solutions generated by the code, comparisons can be made to the correct solutions to establish the accuracy of the code. To design and create these test cases, there are many steps and programs that must be used. Before a test case can be run, pre-processing steps must be accomplished. These include generating a grid to describe the geometry, using a software package called GridPro. Also various files required by the GlennHT code must be created including a boundary condition file, a file for multi-processor computing, and a file to describe problem and algorithm parameters. A good deal of this internship will be to become familiar with these programs and the structure of the GlennHT code. Additional information is included in the original extended abstract.

mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

PubMed

Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

2013-08-15

Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.

PubMed

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-06

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an "extremophile collector" and may be a hot spot of novel extremophile biodiversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles

PubMed Central

Wall, Kate; Cornell, Jennifer; Bizzoco, Richard W; Kelley, Scott T

2015-01-01

Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an “extremophile collector” and may be a hot spot of novel extremophile biodiversity. PMID:25565172

Reduction of PAPR in coded OFDM using fast Reed-Solomon codes over prime Galois fields

NASA Astrophysics Data System (ADS)

Motazedi, Mohammad Reza; Dianat, Reza

2017-02-01

In this work, two new techniques using Reed-Solomon (RS) codes over GF(257) and GF(65,537) are proposed for peak-to-average power ratio (PAPR) reduction in coded orthogonal frequency division multiplexing (OFDM) systems. The lengths of these codes are well-matched to the length of OFDM frames. Over these fields, the block lengths of codes are powers of two and we fully exploit the radix-2 fast Fourier transform algorithms. Multiplications and additions are simple modulus operations. These codes provide desirable randomness with a small perturbation in information symbols that is essential for generation of different statistically independent candidates. Our simulations show that the PAPR reduction ability of RS codes is the same as that of conventional selected mapping (SLM), but contrary to SLM, we can get error correction capability. Also for the second proposed technique, the transmission of side information is not needed. To the best of our knowledge, this is the first work using RS codes for PAPR reduction in single-input single-output systems.

Recurrence time statistics: versatile tools for genomic DNA sequence analysis.

PubMed

Cao, Yinhe; Tung, Wen-Wen; Gao, J B

2004-01-01

With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

A candidate gene for choanal atresia in alpaca.

PubMed

Reed, Kent M; Bauer, Miranda M; Mendoza, Kristelle M; Armién, Aníbal G

2010-03-01

Choanal atresia (CA) is a common nasal craniofacial malformation in New World domestic camelids (alpaca and llama). CA results from abnormal development of the nasal passages and is especially debilitating to newborn crias. CA in camelids shares many of the clinical manifestations of a similar condition in humans (CHARGE syndrome). Herein we report on the regulatory gene CHD7 of alpaca, whose homologue in humans is most frequently associated with CHARGE. Sequence of the CHD7 coding region was obtained from a non-affected cria. The complete coding region was 9003 bp, corresponding to a translated amino acid sequence of 3000 aa. Additional genomic sequences corresponding to a significant portion of the CHD7 gene were identified and assembled from the 2x alpaca whole genome sequence, providing confirmatory sequence for much of the CHD7 coding region. The alpaca CHD7 mRNA sequence was 97.9% similar to the human sequence, with the greatest sequence difference being an insertion in exon 38 that results in a polyalanine repeat (A12). Polymorphism in this repeat was tested for association with CA in alpaca by cloning and sequencing the repeat from both affected and non-affected individuals. Variation in length of the poly-A repeat was not associated with CA. Complete sequencing of the CHD7 gene will be necessary to determine whether other mutations in CHD7 are the cause of CA in camelids.

Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

PubMed

Pang, Erli; Wu, Xiaomei; Lin, Kui

2016-06-01

Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution.

Translational resistivity/conductivity of coding sequences during exponential growth of Escherichia coli.

PubMed

Takai, Kazuyuki

2017-01-21

Codon adaptation index (CAI) has been widely used for prediction of expression of recombinant genes in Escherichia coli and other organisms. However, CAI has no mechanistic basis that rationalizes its application to estimation of translational efficiency. Here, I propose a model based on which we could consider how codon usage is related to the level of expression during exponential growth of bacteria. In this model, translation of a gene is considered as an analog of electric current, and an analog of electric resistance corresponding to each gene is considered. "Translational resistance" is dependent on the steady-state concentration and the sequence of the mRNA species, and "translational resistivity" is dependent only on the mRNA sequence. The latter is the sum of two parts: one is the resistivity for the elongation reaction (coding sequence resistivity), and the other comes from all of the other steps of the decoding reaction. This electric circuit model clearly shows that some conditions should be met for codon composition of a coding sequence to correlate well with its expression level. On the other hand, I calculated relative frequency of each of the 61 sense codon triplets translated during exponential growth of E. coli from a proteomic dataset covering over 2600 proteins. A tentative method for estimating relative coding sequence resistivity based on the data is presented. Copyright © 2016. Published by Elsevier Ltd.

Origins of Genes: "Big Bang" or Continuous Creation?

NASA Astrophysics Data System (ADS)

Kesse, Paul K.; Gibbs, Adrian

1992-10-01

Many protein families are common to all cellular organisms, indicating that many genes have ancient origins. Genetic variation is mostly attributed to processes such as mutation, duplication, and rearrangement of ancient modules. Thus it is widely assumed that much of present-day genetic diversity can be traced by common ancestry to a molecular "big bang." A rarely considered alternative is that proteins may arise continuously de novo. One mechanism of generating different coding sequences is by "overprinting," in which an existing nucleotide sequence is translated de novo in a different reading frame or from noncoding open reading frames. The clearest evidence for overprinting is provided when the original gene function is retained, as in overlapping genes. Analysis of their phylogenies indicates which are the original genes and which are their informationally novel partners. We report here the phylogenetic relationships of overlapping coding sequences from steroid-related receptor genes and from tymovirus, luteovirus, and lentivirus genomes. For each pair of overlapping coding sequences, one is confined to a single lineage, whereas the other is more widespread. This suggests that the phylogenetically restricted coding sequence arose only in the progenitor of that lineage by translating an out-of-frame sequence to yield the new polypeptide. The production of novel exons by alternative splicing in thyroid receptor and lentivirus genes suggests that introns can be a valuable evolutionary source for overprinting. New genes and their products may drive major evolutionary changes.

Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level.

PubMed

Brunak, S; Engelbrecht, J

1996-06-01

A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome.

Advanced multiple access concepts in mobile satellite systems

NASA Technical Reports Server (NTRS)

Ananasso, Fulvio

1990-01-01

Some multiple access strategies for Mobile Satellite Systems (MSS) are discussed. These strategies were investigated in the context of three separate studies conducted for the International Maritime Satellite Organization (INMARSAT) and the European Space Agency (ESA). Satellite-Switched Frequency Division Multiple Access (SS-FDMA), Code Division Multiple Access (CDMA), and Frequency-Addressable Beam architectures are addressed, discussing both system and technology aspects and outlining advantages and drawbacks of either solution with associated relevant hardware issues. An attempt is made to compare the considered option from the standpoint of user terminal/space segment complexity, synchronization requirements, spectral efficiency, and interference rejection.

Evolution and Diversity of the Human Hepatitis D Virus Genome

PubMed Central

Huang, Chi-Ruei; Lo, Szecheng J.

2010-01-01

Human hepatitis delta virus (HDV) is the smallest RNA virus in genome. HDV genome is divided into a viroid-like sequence and a protein-coding sequence which could have originated from different resources and the HDV genome was eventually constituted through RNA recombination. The genome subsequently diversified through accumulation of mutations selected by interactions between the mutated RNA and proteins with host factors to successfully form the infectious virions. Therefore, we propose that the conservation of HDV nucleotide sequence is highly related with its functionality. Genome analysis of known HDV isolates shows that the C-terminal coding sequences of large delta antigen (LDAg) are the highest diversity than other regions of protein-coding sequences but they still retain biological functionality to interact with the heavy chain of clathrin can be selected and maintained. Since viruses interact with many host factors, including escaping the host immune response, how to design a program to predict RNA genome evolution is a great challenging work. PMID:20204073

Visibility Data Filters for Europe

DTIC Science & Technology

1990-04-14

Manager Atmospheric Optics Branch FOR THE COMMANDER (Signature) R. Earl Good, Director Optical and Infrared Techn logy Division This report has been...recorded under code WW1, WW2 , etc. Unfortunately for most of the European stations contained in the DATSAV database, the precipitation flags are missing

USER MANUAL FOR EXPRESS, THE EXAMS-PRZM EXPOSURE SIMULATION SHELL

EPA Science Inventory

The Environmental Fate and Effects Division (EFED) of EPA's Office of Pesticide Programs(OPP) uses a suite of ORD simulation models for the exposure analysis portion of regulatory risk assessments. These models (PRZM, EXAMS, AgDisp) are complex, process-based simulation codes tha...

Sharing Teaching Ideas.

ERIC Educational Resources Information Center

Mathematics Teacher, 1985

1985-01-01

Discusses: (1) use of matrix techniques to write secret codes (includes ready-to-duplicate worksheets); (2) a method of multiplication and division of polynomials in one variable that is not tedius, time-consuming, or dependent on guesswork; and (3) adding and subtracting rational expressions and solving rational equations. (JN)

76 FR 36168 - Agency Information Collection Activities: Requests for Comments; Clearance of Renewed Approval of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-21

... at the following address: Ms. Carla Scott, Room 336, Federal Aviation Administration, AES-300, 950 L... Business Services Division, AES-200. [FR Doc. 2011-15378 Filed 6-20-11; 8:45 am] BILLING CODE 4910-13-P ...

76 FR 36168 - Agency Information Collection Activities; Requests for Comments; Clearance of Renewed Approval of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-21

... FAA at the following address: Ms. Carla Scott, Room 336, Federal Aviation Administration, AES-300, 950... Business Services Division, AES-200. [FR Doc. 2011-15405 Filed 6-20-11; 8:45 am] BILLING CODE 4910-13-P ...