Airborne data measurement system errors reduction through state estimation and control optimization

NASA Astrophysics Data System (ADS)

Sebryakov, G. G.; Muzhichek, S. M.; Pavlov, V. I.; Ermolin, O. V.; Skrinnikov, A. A.

2018-02-01

The paper discusses the problem of airborne data measurement system errors reduction through state estimation and control optimization. The approaches are proposed based on the methods of experiment design and the theory of systems with random abrupt structure variation. The paper considers various control criteria as applied to an aircraft data measurement system. The physics of criteria is explained, the mathematical description and the sequence of steps for each criterion application is shown. The formula is given for airborne data measurement system state vector posterior estimation based for systems with structure variations.

Data-Aware Retrodiction for Asynchronous Harmonic Measurement in a Cyber-Physical Energy System.

PubMed

Liu, Youda; Wang, Xue; Liu, Yanchi; Cui, Sujin

2016-08-18

Cyber-physical energy systems provide a networked solution for safety, reliability and efficiency problems in smart grids. On the demand side, the secure and trustworthy energy supply requires real-time supervising and online power quality assessing. Harmonics measurement is necessary in power quality evaluation. However, under the large-scale distributed metering architecture, harmonic measurement faces the out-of-sequence measurement (OOSM) problem, which is the result of latencies in sensing or the communication process and brings deviations in data fusion. This paper depicts a distributed measurement network for large-scale asynchronous harmonic analysis and exploits a nonlinear autoregressive model with exogenous inputs (NARX) network to reorder the out-of-sequence measuring data. The NARX network gets the characteristics of the electrical harmonics from practical data rather than the kinematic equations. Thus, the data-aware network approximates the behavior of the practical electrical parameter with real-time data and improves the retrodiction accuracy. Theoretical analysis demonstrates that the data-aware method maintains a reasonable consumption of computing resources. Experiments on a practical testbed of a cyber-physical system are implemented, and harmonic measurement and analysis accuracy are adopted to evaluate the measuring mechanism under a distributed metering network. Results demonstrate an improvement of the harmonics analysis precision and validate the asynchronous measuring method in cyber-physical energy systems.

Logic system aids in evaluation of project readiness

NASA Technical Reports Server (NTRS)

Maris, S. J.; Obrien, T. J.

1966-01-01

Measurement Operational Readiness Requirements /MORR/ assignments logic is used for determining the readiness of a complex project to go forward as planned. The system used logic network which assigns qualities to all important criteria in a project and establishes a logical sequence of measurements to determine what the conditions are.

Volume comparison of radiofrequency ablation at 3- and 5-cm target volumes for four different radiofrequency generators: MR volumetry in an open 1-T MRI system versus macroscopic measurement.

PubMed

Rathke, Hendrik; Hamm, Bernd; Guettler, Felix; Lohneis, Philipp; Stroux, Andrea; Suttmeyer, Britta; Jonczyk, Martin; Teichgräber, Ulf; de Bucourt, Maximilian

2015-12-01

In a patient, it is usually not macroscopically possible to estimate the non-viable volume induced by radiofrequency ablation (RFA) after the procedure. The purpose of this study was to use an ex vivo bovine liver model to perform magnetic resonance (MR) volumetry of the visible tissue signal change induced by RFA and to correlate the MR measurement with the actual macroscopic volume measured in the dissected specimens. Sixty-four liver specimens cut from 16 bovine livers were ablated under constant simulated, close physiological conditions with target volumes set to 14.14 ml (3-cm lesion) and 65.45 ml (5-cm lesion). Four commercially available radiofrequency (RF) systems were tested (n=16 for each system; n=8 for 3 cm and n=8 for 5 cm). A T1-weighted turbo spin echo (TSE) sequence with inversion recovery and a proton-density (PD)-weighted TSE sequence were acquired in a 1.0-T open magnetic resonance imaging (MRI) system. After manual dissection, actual macroscopic ablation diameters were measured and volumes calculated. MR volumetry was performed using a semiautomatic software tool. To validate the correctness and feasibility of the volume formula in macroscopic measurements, MR multiplanar reformation diameter measurements with subsequent volume calculation and semiautomatic MR volumes were correlated. Semiautomatic MR volumetry yielded smaller volumes than manual measurement after dissection, irrespective of RF system used, target lesion size, and MR sequence. For the 3-cm lesion, only 43.3% (T1) and 41.5% (PD) of the entire necrosis are detectable. For the 5-cm lesion, only 40.8% (T1) and 37.2% (PD) are visualized in MRI directly after intervention. The correlation between semiautomatic MR volumes and calculated MR volumes was 0.888 for the T1-weighted sequence and 0.875 for the PD sequence. After correlation of semiautomatic MR volumes and calculated MR volumes, it seems reasonable to use the respective volume formula for macroscopic volume calculation. Hyperacute MRI after ex vivo intervention may result in the underestimation of the real expansion of the produced necrosis zone. This must be kept in mind when using MRI for validating ablation success directly after RFA. One reason for the discrepancy between macroscopic and MRI appearance immediately after RFA may be that the transitional zone shows no or only partially visible MR signal change.

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Test sequence; general requirements. 92...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Test sequence; general requirements...

Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.

PubMed

Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce

2016-09-01

Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.

The use of network analysis to study complex animal communication systems: a study on nightingale song.

PubMed

Weiss, Michael; Hultsch, Henrike; Adam, Iris; Scharff, Constance; Kipper, Silke

2014-06-22

The singing of song birds can form complex signal systems comprised of numerous subunits sung with distinct combinatorial properties that have been described as syntax-like. This complexity has inspired inquiries into similarities of bird song to human language; but the quantitative analysis and description of song sequences is a challenging task. In this study, we analysed song sequences of common nightingales (Luscinia megarhynchos) by means of a network analysis. We translated long nocturnal song sequences into networks of song types with song transitions as connectors. As network measures, we calculated shortest path length and transitivity and identified the 'small-world' character of nightingale song networks. Besides comparing network measures with conventional measures of song complexity, we also found a correlation between network measures and age of birds. Furthermore, we determined the numbers of in-coming and out-going edges of each song type, characterizing transition patterns. These transition patterns were shared across males for certain song types. Playbacks with different transition patterns provided first evidence that these patterns are responded to differently and thus play a role in singing interactions. We discuss potential functions of the network properties of song sequences in the framework of vocal leadership. Network approaches provide biologically meaningful parameters to describe the song structure of species with extremely large repertoires and complex rules of song retrieval.

The use of network analysis to study complex animal communication systems: a study on nightingale song

PubMed Central

Weiss, Michael; Hultsch, Henrike; Adam, Iris; Scharff, Constance; Kipper, Silke

2014-01-01

The singing of song birds can form complex signal systems comprised of numerous subunits sung with distinct combinatorial properties that have been described as syntax-like. This complexity has inspired inquiries into similarities of bird song to human language; but the quantitative analysis and description of song sequences is a challenging task. In this study, we analysed song sequences of common nightingales (Luscinia megarhynchos) by means of a network analysis. We translated long nocturnal song sequences into networks of song types with song transitions as connectors. As network measures, we calculated shortest path length and transitivity and identified the ‘small-world’ character of nightingale song networks. Besides comparing network measures with conventional measures of song complexity, we also found a correlation between network measures and age of birds. Furthermore, we determined the numbers of in-coming and out-going edges of each song type, characterizing transition patterns. These transition patterns were shared across males for certain song types. Playbacks with different transition patterns provided first evidence that these patterns are responded to differently and thus play a role in singing interactions. We discuss potential functions of the network properties of song sequences in the framework of vocal leadership. Network approaches provide biologically meaningful parameters to describe the song structure of species with extremely large repertoires and complex rules of song retrieval. PMID:24807258

Evaluation of 2-point, 3-point, and 6-point Dixon magnetic resonance imaging with flexible echo timing for muscle fat quantification.

PubMed

Grimm, Alexandra; Meyer, Heiko; Nickel, Marcel D; Nittka, Mathias; Raithel, Esther; Chaudry, Oliver; Friedberger, Andreas; Uder, Michael; Kemmler, Wolfgang; Quick, Harald H; Engelke, Klaus

2018-06-01

The purpose of this study is to evaluate and compare 2-point (2pt), 3-point (3pt), and 6-point (6pt) Dixon magnetic resonance imaging (MRI) sequences with flexible echo times (TE) to measure proton density fat fraction (PDFF) within muscles. Two subject groups were recruited (G1: 23 young and healthy men, 31 ± 6 years; G2: 50 elderly men, sarcopenic, 77 ± 5 years). A 3-T MRI system was used to perform Dixon imaging on the left thigh. PDFF was measured with six Dixon prototype sequences: 2pt, 3pt, and 6pt sequences once with optimal TEs (in- and opposed-phase echo times), lower resolution, and higher bandwidth (optTE sequences) and once with higher image resolution (highRes sequences) and shortest possible TE, respectively. Intra-fascia PDFF content was determined. To evaluate the comparability among the sequences, Bland-Altman analysis was performed. The highRes 6pt Dixon sequences served as reference as a high correlation of this sequence to magnetic resonance spectroscopy has been shown before. The PDFF difference between the highRes 6pt Dixon sequence and the optTE 6pt, both 3pt, and the optTE 2pt was low (between 2.2% and 4.4%), however, not to the highRes 2pt Dixon sequence (33%). For the optTE sequences, difference decreased with the number of echoes used. In conclusion, for Dixon sequences with more than two echoes, the fat fraction measurement was reliable with arbitrary echo times, while for 2pt Dixon sequences, it was reliable with dedicated in- and opposed-phase echo timing. Copyright © 2018 Elsevier B.V. All rights reserved.

Noise-robust speech recognition through auditory feature detection and spike sequence decoding.

PubMed

Schafer, Phillip B; Jin, Dezhe Z

2014-03-01

Speech recognition in noisy conditions is a major challenge for computer systems, but the human brain performs it routinely and accurately. Automatic speech recognition (ASR) systems that are inspired by neuroscience can potentially bridge the performance gap between humans and machines. We present a system for noise-robust isolated word recognition that works by decoding sequences of spikes from a population of simulated auditory feature-detecting neurons. Each neuron is trained to respond selectively to a brief spectrotemporal pattern, or feature, drawn from the simulated auditory nerve response to speech. The neural population conveys the time-dependent structure of a sound by its sequence of spikes. We compare two methods for decoding the spike sequences--one using a hidden Markov model-based recognizer, the other using a novel template-based recognition scheme. In the latter case, words are recognized by comparing their spike sequences to template sequences obtained from clean training data, using a similarity measure based on the length of the longest common sub-sequence. Using isolated spoken digits from the AURORA-2 database, we show that our combined system outperforms a state-of-the-art robust speech recognizer at low signal-to-noise ratios. Both the spike-based encoding scheme and the template-based decoding offer gains in noise robustness over traditional speech recognition methods. Our system highlights potential advantages of spike-based acoustic coding and provides a biologically motivated framework for robust ASR development.

Data-Aware Retrodiction for Asynchronous Harmonic Measurement in a Cyber-Physical Energy System

PubMed Central

Liu, Youda; Wang, Xue; Liu, Yanchi; Cui, Sujin

2016-01-01

Cyber-physical energy systems provide a networked solution for safety, reliability and efficiency problems in smart grids. On the demand side, the secure and trustworthy energy supply requires real-time supervising and online power quality assessing. Harmonics measurement is necessary in power quality evaluation. However, under the large-scale distributed metering architecture, harmonic measurement faces the out-of-sequence measurement (OOSM) problem, which is the result of latencies in sensing or the communication process and brings deviations in data fusion. This paper depicts a distributed measurement network for large-scale asynchronous harmonic analysis and exploits a nonlinear autoregressive model with exogenous inputs (NARX) network to reorder the out-of-sequence measuring data. The NARX network gets the characteristics of the electrical harmonics from practical data rather than the kinematic equations. Thus, the data-aware network approximates the behavior of the practical electrical parameter with real-time data and improves the retrodiction accuracy. Theoretical analysis demonstrates that the data-aware method maintains a reasonable consumption of computing resources. Experiments on a practical testbed of a cyber-physical system are implemented, and harmonic measurement and analysis accuracy are adopted to evaluate the measuring mechanism under a distributed metering network. Results demonstrate an improvement of the harmonics analysis precision and validate the asynchronous measuring method in cyber-physical energy systems. PMID:27548171

Robust sensorimotor representation to physical interaction changes in humanoid motion learning.

PubMed

Shimizu, Toshihiko; Saegusa, Ryo; Ikemoto, Shuhei; Ishiguro, Hiroshi; Metta, Giorgio

2015-05-01

This paper proposes a learning from demonstration system based on a motion feature, called phase transfer sequence. The system aims to synthesize the knowledge on humanoid whole body motions learned during teacher-supported interactions, and apply this knowledge during different physical interactions between a robot and its surroundings. The phase transfer sequence represents the temporal order of the changing points in multiple time sequences. It encodes the dynamical aspects of the sequences so as to absorb the gaps in timing and amplitude derived from interaction changes. The phase transfer sequence was evaluated in reinforcement learning of sitting-up and walking motions conducted by a real humanoid robot and compatible simulator. In both tasks, the robotic motions were less dependent on physical interactions when learned by the proposed feature than by conventional similarity measurements. Phase transfer sequence also enhanced the convergence speed of motion learning. Our proposed feature is original primarily because it absorbs the gaps caused by changes of the originally acquired physical interactions, thereby enhancing the learning speed in subsequent interactions.

Designing Effective In-vehicle Icons

DOT National Transportation Integrated Search

1975-04-01

The design of a system for scanning sequences of aerial photographs with a computer-controlled flying-spot scanner and automatically measuring vehicle locations is described. Hardware and software requirements for an operational system of this type a...

Gradient-Induced Voltages on 12-Lead ECGs during High Duty-Cycle MRI Sequences and a Method for Their Removal considering Linear and Concomitant Gradient Terms

PubMed Central

Zhang, Shelley HuaLei; Ho Tse, Zion Tsz; Dumoulin, Charles L.; Kwong, Raymond Y.; Stevenson, William G.; Watkins, Ronald; Ward, Jay; Wang, Wei; Schmidt, Ehud J.

2015-01-01

Purpose To restore 12-lead ECG signal fidelity inside MRI by removing magnetic-field gradient induced-voltages during high gradient-duty-cycle sequences. Theory and Methods A theoretical equation was derived, providing first- and second-order electrical fields induced at individual ECG electrode as a function of gradient fields. Experiments were performed at 3T on healthy volunteers, using a customized acquisition system which captured full amplitude and frequency response of ECGs, or a commercial recording system. The 19 equation coefficients were derived by linear regression of data from accelerated sequences, and used to compute induced-voltages in real-time during full-resolution sequences to remove ECG artifacts. Restored traces were evaluated relative to ones acquired without imaging. Results Measured induced-voltages were 0.7V peak-to-peak during balanced Steady-State Free Precession (bSSFP) with heart at the isocenter. Applying the equation during gradient echo sequencing, three-dimensional fast spin echo and multi-slice bSSFP imaging restored nonsaturated traces and second-order concomitant terms showed larger contributions in electrodes farther from the magnet isocenter. Equation coefficients are evaluated with high repeatability (ρ = 0.996) and are subject, sequence, and slice-orientation dependent. Conclusion Close agreement between theoretical and measured gradient-induced voltages allowed for real-time removal. Prospective estimation of sequence-periods where large induced-voltages occur may allow hardware removal of these signals. PMID:26101951

Auto-tracking system for human lumbar motion analysis.

PubMed

Sui, Fuge; Zhang, Da; Lam, Shing Chun Benny; Zhao, Lifeng; Wang, Dongjun; Bi, Zhenggang; Hu, Yong

2011-01-01

Previous lumbar motion analyses suggest the usefulness of quantitatively characterizing spine motion. However, the application of such measurements is still limited by the lack of user-friendly automatic spine motion analysis systems. This paper describes an automatic analysis system to measure lumbar spine disorders that consists of a spine motion guidance device, an X-ray imaging modality to acquire digitized video fluoroscopy (DVF) sequences and an automated tracking module with a graphical user interface (GUI). DVF sequences of the lumbar spine are recorded during flexion-extension under a guidance device. The automatic tracking software utilizing a particle filter locates the vertebra-of-interest in every frame of the sequence, and the tracking result is displayed on the GUI. Kinematic parameters are also extracted from the tracking results for motion analysis. We observed that, in a bone model test, the maximum fiducial error was 3.7%, and the maximum repeatability error in translation and rotation was 1.2% and 2.6%, respectively. In our simulated DVF sequence study, the automatic tracking was not successful when the noise intensity was greater than 0.50. In a noisy situation, the maximal difference was 1.3 mm in translation and 1° in the rotation angle. The errors were calculated in translation (fiducial error: 2.4%, repeatability error: 0.5%) and in the rotation angle (fiducial error: 1.0%, repeatability error: 0.7%). However, the automatic tracking software could successfully track simulated sequences contaminated by noise at a density ≤ 0.5 with very high accuracy, providing good reliability and robustness. A clinical trial with 10 healthy subjects and 2 lumbar spondylolisthesis patients were enrolled in this study. The measurement with auto-tacking of DVF provided some information not seen in the conventional X-ray. The results proposed the potential use of the proposed system for clinical applications.

From carbon to actinides: A new universal 1MV accelerator mass spectrometer at ANSTO

NASA Astrophysics Data System (ADS)

Wilcken, K. M.; Hotchkis, M.; Levchenko, V.; Fink, D.; Hauser, T.; Kitchen, R.

2015-10-01

A new 1 MV NEC pelletron AMS system at ANSTO is presented. The spectrometer comprises large radius magnets for actinide measurements. A novel feature of the system is fast switching between isotopes both at low and high energy sections allowing measurements of up to 8 isotopes within a single sequence. Technical details and layout of the spectrometer is presented. Performance data for 14C, 10Be, 26Al and actinides demonstrate the system is ready for routine AMS measurements.

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.

Polarized radiance distribution measurements of skylight. I. System description and characterization.

PubMed

Voss, K J; Liu, Y

1997-08-20

A new system to measure the natural skylight polarized radiance distribution has been developed. The system is based on a fish-eye lens, CCD camera system, and filter changer. With this system sequences of images can be combined to determine the linear polarization components of the incident light field. Calibration steps to determine the system 's polarization characteristics are described. Comparisons of the radiance measurements of this system and a simple pointing radiometer were made in the field and agreed within 10 % for measurements at 560 and 670 nm and 25 % at 860 nm. Polarization tests were done in the laboratory. The accuracy of the intensity measurements is estimated to be 10 %, while the accuracy of measurements of elements of the Mueller matrix are estimated to be 2 %.

Security Analysis of a Block Encryption Algorithm Based on Dynamic Sequences of Multiple Chaotic Systems

NASA Astrophysics Data System (ADS)

Du, Mao-Kang; He, Bo; Wang, Yong

2011-01-01

Recently, the cryptosystem based on chaos has attracted much attention. Wang and Yu (Commun. Nonlin. Sci. Numer. Simulat. 14 (2009) 574) proposed a block encryption algorithm based on dynamic sequences of multiple chaotic systems. We analyze the potential flaws in the algorithm. Then, a chosen-plaintext attack is presented. Some remedial measures are suggested to avoid the flaws effectively. Furthermore, an improved encryption algorithm is proposed to resist the attacks and to keep all the merits of the original cryptosystem.

Cordless hand-held optical 3D sensor

NASA Astrophysics Data System (ADS)

Munkelt, Christoph; Bräuer-Burchardt, Christian; Kühmstedt, Peter; Schmidt, Ingo; Notni, Gunther

2007-07-01

A new mobile optical 3D measurement system using phase correlation based fringe projection technique will be presented. The sensor consist of a digital projection unit and two cameras in a stereo arrangement, whereby both are battery powered. The data transfer to a base station will be done via WLAN. This gives the possibility to use the system in complicate, remote measurement situations, which are typical in archaeology and architecture. In the measurement procedure the sensor will be hand-held by the user, illuminating the object with a sequence of less than 10 fringe patterns, within a time below 200 ms. This short sequence duration was achieved by a new approach, which combines the epipolar constraint with robust phase correlation utilizing a pre-calibrated sensor head, containing two cameras and a digital fringe projector. Furthermore, the system can be utilized to acquire the all around shape of objects by using the phasogrammetric approach with virtual land marks introduced by the authors 1, 2. This way no matching procedures or markers are necessary for the registration of multiple views, which makes the system very flexible in accomplishing different measurement tasks. The realized measurement field is approx. 100 mm up to 400 mm in diameter. The mobile character makes the measurement system useful for a wide range of applications in arts, architecture, archaeology and criminology, which will be shown in the paper.

Sustained State-Independent Quantum Contextual Correlations from a Single Ion

NASA Astrophysics Data System (ADS)

Leupold, F. M.; Malinowski, M.; Zhang, C.; Negnevitsky, V.; Alonso, J.; Home, J. P.; Cabello, A.

2018-05-01

We use a single trapped-ion qutrit to demonstrate the quantum-state-independent violation of noncontextuality inequalities using a sequence of randomly chosen quantum nondemolition projective measurements. We concatenate 53 ×106 sequential measurements of 13 observables, and unambiguously violate an optimal noncontextual bound. We use the same data set to characterize imperfections including signaling and repeatability of the measurements. The experimental sequence was generated in real time with a quantum random number generator integrated into our control system to select the subsequent observable with a latency below 50 μ s , which can be used to constrain contextual hidden-variable models that might describe our results. The state-recycling experimental procedure is resilient to noise and independent of the qutrit state, substantiating the fact that the contextual nature of quantum physics is connected to measurements and not necessarily to designated states. The use of extended sequences of quantum nondemolition measurements finds applications in the fields of sensing and quantum information.

RHETT/EPDM Performance Characterization

NASA Technical Reports Server (NTRS)

Haag, T.; Osborn, M.

1998-01-01

The 0.6 kW Electric Propulsion Demonstration Module (EPDM) flight thruster system was tested in a large vacuum facility for performance measurements and functional checkout. The thruster was operated at a xenon flow rate of 3.01 mg/s, which was supplied through a self-contained propellant system. All power was provided through a flight-packaged power processing unit, which was mounted in vacuum on a cold plate. The thruster was cycled through 34 individual startup and shutdown sequences. Operating periods ranged from 3 to 3600 seconds. The system responded promptly to each command sequence and there were no involuntary shutdowns. Direct thrust measurements indicated that steady state thrust was temperature sensitive, and varied from a high of 41.7 mN at 16 C, to a low of 34.8 mN at 110 C. Short duration thruster firings showed rapid response and good repeatability.

Safety Analysis and Protection Measures of the Control System of the Pulsed High Magnetic Field Facility in WHMFC

NASA Astrophysics Data System (ADS)

Shi, J. T.; Han, X. T.; Xie, J. F.; Yao, L.; Huang, L. T.; Li, L.

2013-03-01

A Pulsed High Magnetic Field Facility (PHMFF) has been established in Wuhan National High Magnetic Field Center (WHMFC) and various protection measures are applied in its control system. In order to improve the reliability and robustness of the control system, the safety analysis of the PHMFF is carried out based on Fault Tree Analysis (FTA) technique. The function and realization of 5 protection systems, which include sequence experiment operation system, safety assistant system, emergency stop system, fault detecting and processing system and accident isolating protection system, are given. The tests and operation indicate that these measures improve the safety of the facility and ensure the safety of people.

W134: A new pre-main-sequence double-lined spectroscopic binary

NASA Technical Reports Server (NTRS)

Padgett, Deborah L.; Stapelfeldt, Karl R.

1994-01-01

We report the discovery that the pre-main-sequence star Walker 134 in the young cluster NGC 2264 is a double-lined spectroscopic binary. Both components are G stars with strong Li I 6708 A absorption lines. Twenty radial velocity measurements have been used to determined the orbital elements of this system. The orbit has a period of 6.3532 +/- 0.0012 days and is circular within the limits of our velocity resolution; e less than 0.01. The total system mass is stellar mass sin(exp 3) i = 3.16 solar mass with a mass ratio of 1.04. Estimates for the orbit inclination angle and stellar radii place the system near the threshold for eclipse observability; howerver, no decrease in brightness was seen during two attempts at photometric monitoring. The circular orbit of W 134 fills an important gap in the period distribution of pre-main-sequence binaries and thereby constrains the effectiveness of tidal orbital circularization during the pre-main sequence.

Ultrasonic Multiple-Access Ranging System Using Spread Spectrum and MEMS Technology for Indoor Localization

PubMed Central

Segers, Laurent; Tiete, Jelmer; Braeken, An; Touhafi, Abdellah

2014-01-01

Indoor localization of persons and objects poses a great engineering challenge. Previously developed localization systems demonstrate the use of wideband techniques in ultrasound ranging systems. Direct sequence and frequency hopping spread spectrum ultrasound signals have been proven to achieve a high level of accuracy. A novel ranging method using the frequency hopping spread spectrum with finite impulse response filtering will be investigated and compared against the direct sequence spread spectrum. In the first setup, distances are estimated in a single-access environment, while in the second setup, two senders and one receiver are used. During the experiments, the micro-electromechanical systems are used as ultrasonic sensors, while the senders were implemented using field programmable gate arrays. Results show that in a single-access environment, the direct sequence spread spectrum method offers slightly better accuracy and precision performance compared to the frequency hopping spread spectrum. When two senders are used, measurements point out that the frequency hopping spread spectrum is more robust to near-far effects than the direct sequence spread spectrum. PMID:24553084

Discovery and characterization of 3000+ main-sequence binaries from APOGEE spectra

NASA Astrophysics Data System (ADS)

El-Badry, Kareem; Ting, Yuan-Sen; Rix, Hans-Walter; Quataert, Eliot; Weisz, Daniel R.; Cargile, Phillip; Conroy, Charlie; Hogg, David W.; Bergemann, Maria; Liu, Chao

2018-05-01

We develop a data-driven spectral model for identifying and characterizing spatially unresolved multiple-star systems and apply it to APOGEE DR13 spectra of main-sequence stars. Binaries and triples are identified as targets whose spectra can be significantly better fit by a superposition of two or three model spectra, drawn from the same isochrone, than any single-star model. From an initial sample of ˜20 000 main-sequence targets, we identify ˜2500 binaries in which both the primary and secondary stars contribute detectably to the spectrum, simultaneously fitting for the velocities and stellar parameters of both components. We additionally identify and fit ˜200 triple systems, as well as ˜700 velocity-variable systems in which the secondary does not contribute detectably to the spectrum. Our model simplifies the process of simultaneously fitting single- or multi-epoch spectra with composite models and does not depend on a velocity offset between the two components of a binary, making it sensitive to traditionally undetectable systems with periods of hundreds or thousands of years. In agreement with conventional expectations, almost all the spectrally identified binaries with measured parallaxes fall above the main sequence in the colour-magnitude diagram. We find excellent agreement between spectrally and dynamically inferred mass ratios for the ˜600 binaries in which a dynamical mass ratio can be measured from multi-epoch radial velocities. We obtain full orbital solutions for 64 systems, including 14 close binaries within hierarchical triples. We make available catalogues of stellar parameters, abundances, mass ratios, and orbital parameters.

Reactivity ratios and sequence structures of the copolymers prepared using photo-induced copolymerization of MMA with MTMP.

PubMed

Liu, Xiaoxuan; Zhang, Yongtao; Cui, Yanyan; Dong, Zhixian

2012-05-01

4-Methacryloyl-2,2,6,6-tetramethyl-piperidine (MTMP) was applied as reactive hindered amine piperidine. Photo-induced copolymerization of methyl methacrylate (MMA, M(1)) with MTMP (M(2)) was carried out in benzene solution at ambient temperature. The reactivity ratios for these monomers were measured by running a series of reactions at various feed ratios of initial monomers, and the monomer incorporation into copolymer was determined using (1)H NMR. Reactivity ratios of the MMA/MTMP system were measured to be r(1)= 0.37 and r(2)= 1.14 from extended Kelen-Tüdos method. The results show that monomer MTMP prefers homopolymerization to copolymerization in the system, whereas monomer MMA prefers copolymerization to homopolymerization. Sequence structures of the MMA/MTMP copolymers were characterized using (1)H NMR. The results show that the sequence structure for the main chain of the MMA/MTMP copolymers is mainly composed of a syndiotactic configuration, only with a little heterotactic configuration. Three kinds of the sequences of rr, rr', and lr' in the syndiotactic configuration are found. The sequence-length distribution in the MMA/MTMP copolymers is also obtained. For f(1)= 0.2, the monomer unit of MMA is mostly separated by MTMP units, and for f(1)= 0.6, the alternating tendency prevails and a large number of mono-sequences are formed; further up to f(1)= 0.8, the monomer unit of MTMP with the sequence of one unit is interspersed among the chain of MMA. Copyright © 2012 John Wiley & Sons, Ltd.

Wideband propagation measurement system using spread spectrum signaling and TDRS

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

OPEN PROBLEM: Orbits' statistics in chaotic dynamical systems

NASA Astrophysics Data System (ADS)

Arnold, V.

2008-07-01

This paper shows how the measurement of the stochasticity degree of a finite sequence of real numbers, published by Kolmogorov in Italian in a journal of insurances' statistics, can be usefully applied to measure the objective stochasticity degree of sequences, originating from dynamical systems theory and from number theory. Namely, whenever the value of Kolmogorov's stochasticity parameter of a given sequence of numbers is too small (or too big), one may conclude that the conjecture describing this sequence as a sample of independent values of a random variables is highly improbable. Kolmogorov used this strategy fighting (in a paper in 'Doklady', 1940) against Lysenko, who had tried to disprove the classical genetics' law of Mendel experimentally. Calculating his stochasticity parameter value for the numbers from Lysenko's experiment reports, Kolmogorov deduced, that, while these numbers were different from the exact fulfilment of Mendel's 3 : 1 law, any smaller deviation would be a manifestation of the report's number falsification. The calculation of the values of the stochasticity parameter would be useful for many other generators of pseudorandom numbers and for many other chaotically looking statistics, including even the prime numbers distribution (discussed in this paper as an example).

Ultrasonic Shear Wave Elasticity Imaging (SWEI) Sequencing and Data Processing Using a Verasonics Research Scanner

PubMed Central

Deng, Yufeng; Rouze, Ned C.; Palmeri, Mark L.; Nightingale, Kathryn R.

2017-01-01

Ultrasound elasticity imaging has been developed over the last decade to estimate tissue stiffness. Shear wave elasticity imaging (SWEI) quantifies tissue stiffness by measuring the speed of propagating shear waves following acoustic radiation force excitation. This work presents the sequencing and data processing protocols of SWEI using a Verasonics system. The selection of the sequence parameters in a Verasonics programming script is discussed in detail. The data processing pipeline to calculate group shear wave speed (SWS), including tissue motion estimation, data filtering, and SWS estimation is demonstrated. In addition, the procedures for calibration of beam position, scanner timing, and transducer face heating are provided to avoid SWS measurement bias and transducer damage. PMID:28092508

Comprehensive analysis of the T-cell receptor beta chain gene in rhesus monkey by high throughput sequencing

PubMed Central

Li, Zhoufang; Liu, Guangjie; Tong, Yin; Zhang, Meng; Xu, Ying; Qin, Li; Wang, Zhanhui; Chen, Xiaoping; He, Jiankui

2015-01-01

Profiling immune repertoires by high throughput sequencing enhances our understanding of immune system complexity and immune-related diseases in humans. Previously, cloning and Sanger sequencing identified limited numbers of T cell receptor (TCR) nucleotide sequences in rhesus monkeys, thus their full immune repertoire is unknown. We applied multiplex PCR and Illumina high throughput sequencing to study the TCRβ of rhesus monkeys. We identified 1.26 million TCRβ sequences corresponding to 643,570 unique TCRβ sequences and 270,557 unique complementarity-determining region 3 (CDR3) gene sequences. Precise measurements of CDR3 length distribution, CDR3 amino acid distribution, length distribution of N nucleotide of junctional region, and TCRV and TCRJ gene usage preferences were performed. A comprehensive profile of rhesus monkey immune repertoire might aid human infectious disease studies using rhesus monkeys. PMID:25961410

Narration and Vividness as Measures of Event-Specificity in Autobiographical Memory

ERIC Educational Resources Information Center

Nelson, Kristin L.; Moskovitz, Damian J.; Steiner, Hans

2008-01-01

The event specificity of autobiographical memories refers to the degree to which retold memories include specific details about a unique personal experience from a variety of representational systems supported by different brain areas. This article proposes 2 text measures as indicators of event specificity: (a) a measure of temporal sequence in…

Orbital motion in pre-main sequence binaries

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

Schaefer, G. H.; Prato, L.; Simon, M.

2014-06-01

We present results from our ongoing program to map the visual orbits of pre-main sequence (PMS) binaries in the Taurus star forming region using adaptive optics imaging at the Keck Observatory. We combine our results with measurements reported in the literature to analyze the orbital motion for each binary. We present preliminary orbits for DF Tau, T Tau S, ZZ Tau, and the Pleiades binary HBC 351. Seven additional binaries show curvature in their relative motion. Currently, we can place lower limits on the orbital periods for these systems; full solutions will be possible with more orbital coverage. Five othermore » binaries show motion that is indistinguishable from linear motion. We suspect that these systems are bound and might show curvature with additional measurements in the future. The observations reported herein lay critical groundwork toward the goal of measuring precise masses for low-mass PMS stars.« less

Development of a feed monitor system for a helium-cooled Michelson intererometer for the Spacelab

NASA Technical Reports Server (NTRS)

Essenwanger, P.

1980-01-01

A Michelson interferometer feed monitor system developed for Spacelab is described. The device is helium cooled and is to be used to measure far infrared radiation sources in space. Performance data and development sequence are presented.

TU-AB-BRA-07: Distortion-Free 3D Diffusion MRI On An MRI-Guided Radiotherapy System for Longitudinal Tumor Response Assessment

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

Gao, Y; Yang, Y; Rangwala, N

Purpose: To develop a reliable, 3D distortion-free diffusion MRI technique for longitudinal tumor response assessment and MRI-guided adaptive radiotherapy(RT). Methods: A diffusion prepared 3D turbo spin echo readout (DP-TSE) sequence was developed and compared with the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) sequence in a commercially available diffusion phantom, and one head-and-neck and one brain cancer patient on an MRI-guided RT system (ViewRay). In phantom study, the geometric fidelity was quantified as the ratio between the left-right (RL) and anterior-posterior (AP) dimension. Ten slices were measured on DP-TSE, DW-ssEPI and standard TSE images where the later was used as the geometricmore » reference. ADC accuracy was verified at both 0°C (reference ADC available) and room temperature with a range of diffusivity between 0.35 and 2.0*10{sup −3}mm{sup 2}/s. The ADC reproducibility was assessed based on 8 room-temperature measurements on 6 different days. In the pilot single-slice in-vivo study, CT images were used as the geometric reference, and ADC maps from both diffusion sequences were compared. Results: Distortion and susceptive-related artifact were severe in DW-ssEPI, with significantly lower RL/AP ratio (0.9579±0.0163) than DP-TSE (0.9990±0.0031) and TSE (0.9995±0.0031). ADCs from the two diffusion sequences both matched well with the vendor-provided values at 0°C; however DW-ssEPI fails to provide accurate ADC for high diffusivity vials at room temperature due to high noise level (10 times higher than DP-TSE). The DP-TSE sequence had excellent ADC reproducibility with <4% ADC variation among 8 separate measurements. In patient study, DP-TSE exhibited substantially improved geometric reliability. ROI analysis in ADC maps generated from DP-TSE and DW-ssEPI showed <5% difference where high b-value images were excluded from the latter approach due to excessive noise level. Conclusion: A diffusion MRI sequence with excellent geometric fidelity, accurate and highly reproducible ADC measurements was proposed for longitudinal tumor response assessment using an MRI-guided RT system. Yu Gao acknowledges research support from ViewRay.« less

Assessment of an automated capillary system for Plasmodium vivax microsatellite genotyping.

PubMed

Manrique, Paulo; Hoshi, Mari; Fasabi, Manuel; Nolasco, Oscar; Yori, Pablo; Calderón, Martiza; Gilman, Robert H; Kosek, Margaret N; Vinetz, Joseph M; Gamboa, Dionicia

2015-08-21

Several platforms have been used to generate the primary data for microsatellite analysis of malaria parasite genotypes. Each has relative advantages but share a limitation of being time- and cost-intensive. A commercially available automated capillary gel cartridge system was assessed in the microsatellite analysis of Plasmodium vivax diversity in the Peruvian Amazon. The reproducibility and accuracy of a commercially-available automated capillary system, QIAxcel, was assessed using a sequenced PCR product of 227 base pairs. This product was measured 42 times, then 27 P. vivax samples from Peruvian Amazon subjects were analyzed with this instrument using five informative microsatellites. Results from the QIAxcel system were compared with a Sanger-type sequencing machine, the ABI PRISM(®) 3100 Genetic Analyzer. Significant differences were seen between the sequenced amplicons and the results from the QIAxcel instrument. Different runs, plates and cartridges yielded significantly different results. Additionally, allele size decreased with each run by 0.045, or 1 bp, every three plates. QIAxcel and ABI PRISM systems differed in giving different values than those obtained by ABI PRISM, and too many (i.e. inaccurate) alleles per locus were also seen with the automated instrument. While P. vivax diversity could generally be estimated using an automated capillary gel cartridge system, the data demonstrate that this system is not sufficiently precise for reliably identifying parasite strains via microsatellite analysis. This conclusion reached after systematic analysis was due both to inadequate precision and poor reproducibility in measuring PCR product size.

An Adaptive Low-Cost GNSS/MEMS-IMU Tightly-Coupled Integration System with Aiding Measurement in a GNSS Signal-Challenged Environment.

PubMed

Zhou, Qifan; Zhang, Hai; Li, You; Li, Zheng

2015-09-18

The main aim of this paper is to develop a low-cost GNSS/MEMS-IMU tightly-coupled integration system with aiding information that can provide reliable position solutions when the GNSS signal is challenged such that less than four satellites are visible in a harsh environment. To achieve this goal, we introduce an adaptive tightly-coupled integration system with height and heading aiding (ATCA). This approach adopts a novel redundant measurement noise estimation method for an adaptive Kalman filter application and also augments external measurements in the filter to aid the position solutions, as well as uses different filters to deal with various situations. On the one hand, the adaptive Kalman filter makes use of the redundant measurement system's difference sequence to estimate and tune noise variance instead of employing a traditional innovation sequence to avoid coupling with the state vector error. On the other hand, this method uses the external height and heading angle as auxiliary references and establishes a model for the measurement equation in the filter. In the meantime, it also changes the effective filter online based on the number of tracked satellites. These measures have increasingly enhanced the position constraints and the system observability, improved the computational efficiency and have led to a good result. Both simulated and practical experiments have been carried out, and the results demonstrate that the proposed method is effective at limiting the system errors when there are less than four visible satellites, providing a satisfactory navigation solution.

State estimator for multisensor systems with irregular sampling and time-varying delays

NASA Astrophysics Data System (ADS)

Peñarrocha, I.; Sanchis, R.; Romero, J. A.

2012-08-01

This article addresses the state estimation in linear time-varying systems with several sensors with different availability, randomly sampled in time and whose measurements have a time-varying delay. The approach is based on a modification of the Kalman filter with the negative-time measurement update strategy, avoiding running back the full standard Kalman filter, the use of full augmented order models or the use of reorganisation techniques, leading to a lower implementation cost algorithm. The update equations are run every time a new measurement is available, independently of the time when it was taken. The approach is useful for networked control systems, systems with long delays and scarce measurements and for out-of-sequence measurements.

Measure-valued solutions to the complete Euler system revisited

NASA Astrophysics Data System (ADS)

Březina, Jan; Feireisl, Eduard

2018-06-01

We consider the complete Euler system describing the time evolution of a general inviscid compressible fluid. We introduce a new concept of measure-valued solution based on the total energy balance and entropy inequality for the physical entropy without any renormalization. This class of so-called dissipative measure-valued solutions is large enough to include the vanishing dissipation limits of the Navier-Stokes-Fourier system. Our main result states that any sequence of weak solutions to the Navier-Stokes-Fourier system with vanishing viscosity and heat conductivity coefficients generates a dissipative measure-valued solution of the Euler system under some physically grounded constitutive relations. Finally, we discuss the same asymptotic limit for the bi-velocity fluid model introduced by H.Brenner.

RoboPIV: how robotics enable PIV on a large industrial scale

NASA Astrophysics Data System (ADS)

Michaux, F.; Mattern, P.; Kallweit, S.

2018-07-01

This work demonstrates how the interaction between particle image velocimetry (PIV) and robotics can massively increase measurement efficiency. The interdisciplinary approach is shown using the complex example of an automated, large scale, industrial environment: a typical automotive wind tunnel application. Both the high degree of flexibility in choosing the measurement region and the complete automation of stereo PIV measurements are presented. The setup consists of a combination of three robots, individually used as a 6D traversing unit for the laser illumination system as well as for each of the two cameras. Synchronised movements in the same reference frame are realised through a master-slave setup with a single interface to the user. By integrating the interface into the standard wind tunnel management system, a single measurement plane or a predefined sequence of several planes can be requested through a single trigger event, providing the resulting vector fields within minutes. In this paper, a brief overview on the demands of large scale industrial PIV and the existing solutions is given. Afterwards, the concept of RoboPIV is introduced as a new approach. In a first step, the usability of a selection of commercially available robot arms is analysed. The challenges of pose uncertainty and importance of absolute accuracy are demonstrated through comparative measurements, explaining the individual pros and cons of the analysed systems. Subsequently, the advantage of integrating RoboPIV directly into the existing wind tunnel management system is shown on basis of a typical measurement sequence. In a final step, a practical measurement procedure, including post-processing, is given by using real data and results. Ultimately, the benefits of high automation are demonstrated, leading to a drastic reduction in necessary measurement time compared to non-automated systems, thus massively increasing the efficiency of PIV measurements.

How weak values emerge in joint measurements on cloned quantum systems.

PubMed

Hofmann, Holger F

2012-07-13

A statistical analysis of optimal universal cloning shows that it is possible to identify an ideal (but nonpositive) copying process that faithfully maps all properties of the original Hilbert space onto two separate quantum systems, resulting in perfect correlations for all observables. The joint probabilities for noncommuting measurements on separate clones then correspond to the real parts of the complex joint probabilities observed in weak measurements on a single system, where the measurements on the two clones replace the corresponding sequence of weak measurement and postselection. The imaginary parts of weak measurement statics can be obtained by replacing the cloning process with a partial swap operation. A controlled-swap operation combines both processes, making the complete weak measurement statistics accessible as a well-defined contribution to the joint probabilities of fully resolved projective measurements on the two output systems.

The non-contact biometric identified bio signal measurement sensor and algorithms.

PubMed

Kim, Chan-Il; Lee, Jong-Ha

2018-01-01

In these days, wearable devices have been developed for effectively measuring biological data. However, these devices have tissue allege and noise problem. To solve these problems, biometric measurement based on a non-contact method, such as face image sequencing is developed. This makes it possible to measure biometric data without any operation and side effects. However, it is impossible for a remote center to identify the person whose data are measured by the novel methods. In this paper, we propose the novel non-contact heart rate and blood pressure imaging system, Deep Health Eye. This system has authentication process at the same time as measuring bio signals, through non-contact method. In the future, this system can be convenient home bio signal monitoring system by combined with smart mirror.

Non-Invasive Evaluation of the GABAergic/Glutamatergic System in Autistic Patients Observed by MEGA-Editing Proton MR Spectroscopy Using a Clinical 3 Tesla Instrument

ERIC Educational Resources Information Center

Harada, Masafumi; Taki, Masako M.; Nose, Ayumi; Kubo, Hitoshi; Mori, Kenji; Nishitani, Hiromu; Matsuda, Tsuyoshi

2011-01-01

Amino acids related to neurotransmitters and the GABAergic/glutamatergic system were measured using a 3 T-MRI instrument in 12 patients with autism and 10 normal controls. All measurements were performed in the frontal lobe (FL) and lenticular nuclei (LN) using a conventional sequence for n-acetyl aspartate (NAA) and glutamate (Glu), and the…

A new sequence for single-shot diffusion-weighted NMR spectroscopy by the trace of the diffusion tensor.

PubMed

Valette, Julien; Giraudeau, Céline; Marchadour, Charlotte; Djemai, Boucif; Geffroy, Françoise; Ghaly, Mohamed Ahmed; Le Bihan, Denis; Hantraye, Philippe; Lebon, Vincent; Lethimonnier, Franck

2012-12-01

Diffusion-weighted spectroscopy is a unique tool for exploring the intracellular microenvironment in vivo. In living systems, diffusion may be anisotropic, when biological membranes exhibit particular orientation patterns. In this work, a volume selective diffusion-weighted sequence is proposed, allowing single-shot measurement of the trace of the diffusion tensor, which does not depend on tissue anisotropy. With this sequence, the minimal echo time is only three times the diffusion time. In addition, cross-terms between diffusion gradients and other gradients are cancelled out. An adiabatic version, similar to localization by adiabatic selective refocusing sequence, is then derived, providing partial immunity against cross-terms. Proof of concept is performed ex vivo on chicken skeletal muscle by varying tissue orientation and intra-voxel shim. In vivo performance of the sequence is finally illustrated in a U87 glioblastoma mouse model, allowing the measurement of the trace apparent diffusion coefficient for six metabolites, including J-modulated metabolites. Although measurement performed along three separate orthogonal directions would bring similar accuracy on trace apparent diffusion coefficient under ideal conditions, the method described here should be useful for probing intimate properties of the cells with minimal experimental bias. Copyright © 2012 Wiley Periodicals, Inc.

Modal Identification Experiment accommodations review

NASA Technical Reports Server (NTRS)

Klich, Phillip J.; Stillwagen, Frederic H.; Mutton, Philip

1994-01-01

The Modal Identification Experiment (MIE) will monitor the structure of the Space Station Freedom (SSF), and measure its response to a sequence of induced disturbances. The MIE will determine the frequency, damping, and shape of the important modes during the SSF assembly sequence including the Permanently Manned Configuration. This paper describes the accommodations for the proposed instrumentation, the data processing hardware, and the communications data rates. An overview of the MIE operational modes for measuring SSF acceleration forces with accelerometers is presented. The SSF instrumentation channel allocations and the Data Management System (DMS) services required for MIE are also discussed.

Strategies in construction and interpretation of graphic-symbol sequences by individuals who use AAC systems.

PubMed

Trudeau, Natacha; Sutton, Ann; Morford, Jill P; Côté-Giroux, Patricia; Pauzé, Anne-Marie; Vallée, Véronique

2010-12-01

Given the frequent use of graphic symbols in augmentative and alternative communication (AAC) systems, some individuals who use AAC may have greater familiarity with constructing graphic-symbol sequences than do speaking individuals without disabilities. Whether this increased familiarity has an impact on the interpretation of such sequences or on the relationship between construction and interpretation is fundamental to our understanding of the mechanisms underlying communication using graphic symbols. In this study, individuals who use graphic-symbol AAC systems were asked to construct and interpret graphic-symbol sequences representing the same target content (simple and complex propositions). The majority of participants used stable response patterns on both tasks; a minority were inconsistent on both tasks. Asymmetrical patterns (stable on one task but not the other) were rare, suggesting that neither channel (construction or interpretation) preceded the other, in contrast to earlier findings with participants without disabilities (i.e., novice users of graphic symbols). Furthermore, there were differences between stable and less stable responders on measures of syntactic comprehension and cognitive level but not on chronological age, receptive vocabulary, or AAC system characteristics and length of use.

Force measurements on the molecular interactions between ligand (RGD) and human platelet α IIbβ 3 receptor system

NASA Astrophysics Data System (ADS)

Lee, ImShik; Marchant, Roger E.

2001-10-01

The peptide sequence arginine-glycine-aspartate (RGD) found in fibrinogen, von Willebrand factor, fibronectin, and vitronectin, plays a critical role in platelet adhesion and thrombus formation, when bound to the platelet α IIbβ 3 integrin receptor. Using atomic force microscopy (AFM), we have measured the debonding interaction between an RGD peptide-modified AFM probe tip and a human platelet surface from pN to nN levels of force. The peptide sequence, GSSSGRGDSPA, which contains the biologically active RGDSP sequence with a hydrophilic spacer sequence (GSSSG), was covalently coupled to AFM probe tips. Direct measurements on the debonding force for the RGD ligand - α IIbβ 3 platelet receptor system were carried out in Tyrode buffer at room temperature. Our results show three distinct distributions of debonding forces at a loading rate of 12 nN/s, from which we estimate the debonding force for the single ligand-receptor to be ˜93 pN. The results also show evidence for considerable extension in the flexible sample surface during the debonding process, and a linear correlation between the debonding force and the logarithm of the rate of loading. From our analysis, the zero kinetic off-rate Koff(0), the single molecular binding energy Eb, and the transition state xB, assuming rigid binding, were extracted from the data, and estimated to be 22.6 s -1, -2.64×10 -20 J and 0.1 nm, respectively.

Acoustic Imaging of Snowpack Physical Properties

NASA Astrophysics Data System (ADS)

Kinar, N. J.; Pomeroy, J. W.

2011-12-01

Measurements of snowpack depth, density, structure and temperature have often been conducted by the use of snowpits and invasive measurement devices. Previous research has shown that acoustic waves passing through snow are capable of measuring these properties. An experimental observation device (SAS2, System for the Acoustic Sounding of Snow) was used to autonomously send audible sound waves into the top of the snowpack and to receive and process the waves reflected from the interior and bottom of the snowpack. A loudspeaker and microphone array separated by an offset distance was suspended in the air above the surface of the snowpack. Sound waves produced from a loudspeaker as frequency-swept sequences and maximum length sequences were used as source signals. Up to 24 microphones measured the audible signal from the snowpack. The signal-to-noise ratio was compared between sequences in the presence of environmental noise contributed by wind and reflections from vegetation. Beamforming algorithms were used to reject spurious reflections and to compensate for movement of the sensor assembly during the time of data collection. A custom-designed circuit with digital signal processing hardware implemented an inversion algorithm to relate the reflected sound wave data to snowpack physical properties and to create a two-dimensional image of snowpack stratigraphy. The low power consumption circuit was powered by batteries and through WiFi and Bluetooth interfaces enabled the display of processed data on a mobile device. Acoustic observations were logged to an SD card after each measurement. The SAS2 system was deployed at remote field locations in the Rocky Mountains of Alberta, Canada. Acoustic snow properties data was compared with data collected from gravimetric sampling, thermocouple arrays, radiometers and snowpit observations of density, stratigraphy and crystal structure. Aspects for further research and limitations of the acoustic sensing system are also discussed.

Towards predicting the encoding capability of MR fingerprinting sequences.

PubMed

Sommer, K; Amthor, T; Doneva, M; Koken, P; Meineke, J; Börnert, P

2017-09-01

Sequence optimization and appropriate sequence selection is still an unmet need in magnetic resonance fingerprinting (MRF). The main challenge in MRF sequence design is the lack of an appropriate measure of the sequence's encoding capability. To find such a measure, three different candidates for judging the encoding capability have been investigated: local and global dot-product-based measures judging dictionary entry similarity as well as a Monte Carlo method that evaluates the noise propagation properties of an MRF sequence. Consistency of these measures for different sequence lengths as well as the capability to predict actual sequence performance in both phantom and in vivo measurements was analyzed. While the dot-product-based measures yielded inconsistent results for different sequence lengths, the Monte Carlo method was in a good agreement with phantom experiments. In particular, the Monte Carlo method could accurately predict the performance of different flip angle patterns in actual measurements. The proposed Monte Carlo method provides an appropriate measure of MRF sequence encoding capability and may be used for sequence optimization. Copyright © 2017 Elsevier Inc. All rights reserved.

Model-Based Analysis of Flow-Mediated Dilation and Intima-Media Thickness

PubMed Central

Bartoli, G.; Menegaz, G.; Lisi, M.; Di Stolfo, G.; Dragoni, S.; Gori, T.

2008-01-01

We present an end-to-end system for the automatic measurement of flow-mediated dilation (FMD) and intima-media thickness (IMT) for the assessment of the arterial function. The video sequences are acquired from a B-mode echographic scanner. A spline model (deformable template) is fitted to the data to detect the artery boundaries and track them all along the video sequence. The a priori knowledge about the image features and its content is exploited. Preprocessing is performed to improve both the visual quality of video frames for visual inspection and the performance of the segmentation algorithm without affecting the accuracy of the measurements. The system allows real-time processing as well as a high level of interactivity with the user. This is obtained by a graphical user interface (GUI) enabling the cardiologist to supervise the whole process and to eventually reset the contour extraction at any point in time. The system was validated and the accuracy, reproducibility, and repeatability of the measurements were assessed with extensive in vivo experiments. Jointly with the user friendliness, low cost, and robustness, this makes the system suitable for both research and daily clinical use. PMID:19360110

MR Scanner Systems Should Be Adequately Characterized in Diffusion-MRI of the Breast

PubMed Central

Giannelli, Marco; Sghedoni, Roberto; Iacconi, Chiara; Iori, Mauro; Traino, Antonio Claudio; Guerrisi, Maria; Mascalchi, Mario; Toschi, Nicola; Diciotti, Stefano

2014-01-01

Breast imaging represents a relatively recent and promising field of application of quantitative diffusion-MRI techniques. In view of the importance of guaranteeing and assessing its reliability in clinical as well as research settings, the aim of this study was to specifically characterize how the main MR scanner system-related factors affect quantitative measurements in diffusion-MRI of the breast. In particular, phantom acquisitions were performed on three 1.5 T MR scanner systems by different manufacturers, all equipped with a dedicated multi-channel breast coil as well as acquisition sequences for diffusion-MRI of the breast. We assessed the accuracy, inter-scan and inter-scanner reproducibility of the mean apparent diffusion coefficient measured along the main orthogonal directions () as well as of diffusion-tensor imaging (DTI)-derived mean diffusivity (MD) measurements. Additionally, we estimated spatial non-uniformity of (NU) and MD (NUMD) maps. We showed that the signal-to-noise ratio as well as overall calibration of high strength diffusion gradients system in typical acquisition sequences for diffusion-MRI of the breast varied across MR scanner systems, introducing systematic bias in the measurements of diffusion indices. While and MD values were not appreciably different from each other, they substantially varied across MR scanner systems. The mean of the accuracies of measured and MD was in the range [−2.3%,11.9%], and the mean of the coefficients of variation for and MD measurements across MR scanner systems was 6.8%. The coefficient of variation for repeated measurements of both and MD was < 1%, while NU and NUMD values were <4%. Our results highlight that MR scanner system-related factors can substantially affect quantitative diffusion-MRI of the breast. Therefore, a specific quality control program for assessing and monitoring the performance of MR scanner systems for diffusion-MRI of the breast is highly recommended at every site, especially in multicenter and longitudinal studies. PMID:24489711

Use of wavelet-packet transforms to develop an engineering model for multifractal characterization of mutation dynamics in pathological and nonpathological gene sequences

NASA Astrophysics Data System (ADS)

Walker, David Lee

1999-12-01

This study uses dynamical analysis to examine in a quantitative fashion the information coding mechanism in DNA sequences. This exceeds the simple dichotomy of either modeling the mechanism by comparing DNA sequence walks as Fractal Brownian Motion (fbm) processes. The 2-D mappings of the DNA sequences for this research are from Iterated Function System (IFS) (Also known as the ``Chaos Game Representation'' (CGR)) mappings of the DNA sequences. This technique converts a 1-D sequence into a 2-D representation that preserves subsequence structure and provides a visual representation. The second step of this analysis involves the application of Wavelet Packet Transforms, a recently developed technique from the field of signal processing. A multi-fractal model is built by using wavelet transforms to estimate the Hurst exponent, H. The Hurst exponent is a non-parametric measurement of the dynamism of a system. This procedure is used to evaluate gene- coding events in the DNA sequence of cystic fibrosis mutations. The H exponent is calculated for various mutation sites in this gene. The results of this study indicate the presence of anti-persistent, random walks and persistent ``sub-periods'' in the sequence. This indicates the hypothesis of a multi-fractal model of DNA information encoding warrants further consideration. This work examines the model's behavior in both pathological (mutations) and non-pathological (healthy) base pair sequences of the cystic fibrosis gene. These mutations both natural and synthetic were introduced by computer manipulation of the original base pair text files. The results show that disease severity and system ``information dynamics'' correlate. These results have implications for genetic engineering as well as in mathematical biology. They suggest that there is scope for more multi-fractal models to be developed.

Whole Transcriptome Sequencing Enables Discovery and Analysis of Viruses in Archived Primary Central Nervous System Lymphomas

PubMed Central

DeBoever, Christopher; Reid, Erin G.; Smith, Erin N.; Wang, Xiaoyun; Dumaop, Wilmar; Harismendy, Olivier; Carson, Dennis; Richman, Douglas; Masliah, Eliezer; Frazer, Kelly A.

2013-01-01

Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples. PMID:24023918

Measurement of 15N longitudinal relaxation rates in 15NH4+ spin systems to characterise rotational correlation times and chemical exchange

NASA Astrophysics Data System (ADS)

Hansen, D. Flemming

2017-06-01

Many chemical and biological processes rely on the movement of monovalent cations and an understanding of such processes can therefore only be achieved by characterising the dynamics of the involved ions. It has recently been shown that 15N-ammonium can be used as a proxy for potassium to probe potassium binding in bio-molecules such as DNA quadruplexes and enzymes. Moreover, equations have been derived to describe the time-evolution of 15N-based spin density operator elements of 15NH4+ spin systems. Herein NMR pulse sequences are derived to select specific spin density matrix elements of the 15NH4+ spin system and to measure their longitudinal relaxation in order to characterise the rotational correlation time of the 15NH4+ ion as well as report on chemical exchange events of the 15NH4+ ion. Applications to 15NH4+ in acidic aqueous solutions are used to cross-validate the developed pulse sequence while measurements of spin-relaxation rates of 15NH4+ bound to a 41 kDa domain of the bacterial Hsp70 homologue DnaK are presented to show the general applicability of the derived pulse sequence. The rotational correlation time obtained for 15N-ammonium bound to DnaK is similar to the correlation time that describes the rotation about the threefold axis of a methyl group. The methodology presented here provides, together with the previous theoretical framework, an important step towards characterising the motional properties of cations in macromolecular systems.

An Adaptive Low-Cost GNSS/MEMS-IMU Tightly-Coupled Integration System with Aiding Measurement in a GNSS Signal-Challenged Environment

PubMed Central

Zhou, Qifan; Zhang, Hai; Li, You; Li, Zheng

2015-01-01

The main aim of this paper is to develop a low-cost GNSS/MEMS-IMU tightly-coupled integration system with aiding information that can provide reliable position solutions when the GNSS signal is challenged such that less than four satellites are visible in a harsh environment. To achieve this goal, we introduce an adaptive tightly-coupled integration system with height and heading aiding (ATCA). This approach adopts a novel redundant measurement noise estimation method for an adaptive Kalman filter application and also augments external measurements in the filter to aid the position solutions, as well as uses different filters to deal with various situations. On the one hand, the adaptive Kalman filter makes use of the redundant measurement system’s difference sequence to estimate and tune noise variance instead of employing a traditional innovation sequence to avoid coupling with the state vector error. On the other hand, this method uses the external height and heading angle as auxiliary references and establishes a model for the measurement equation in the filter. In the meantime, it also changes the effective filter online based on the number of tracked satellites. These measures have increasingly enhanced the position constraints and the system observability, improved the computational efficiency and have led to a good result. Both simulated and practical experiments have been carried out, and the results demonstrate that the proposed method is effective at limiting the system errors when there are less than four visible satellites, providing a satisfactory navigation solution. PMID:26393605

Introduction of an automated user-independent quantitative volumetric magnetic resonance imaging breast density measurement system using the Dixon sequence: comparison with mammographic breast density assessment.

PubMed

Wengert, Georg Johannes; Helbich, Thomas H; Vogl, Wolf-Dieter; Baltzer, Pascal; Langs, Georg; Weber, Michael; Bogner, Wolfgang; Gruber, Stephan; Trattnig, Siegfried; Pinker, Katja

2015-02-01

The purposes of this study were to introduce and assess an automated user-independent quantitative volumetric (AUQV) breast density (BD) measurement system on the basis of magnetic resonance imaging (MRI) using the Dixon technique as well as to compare it with qualitative and quantitative mammographic (MG) BD measurements. Forty-three women with normal mammogram results (Breast Imaging Reporting and Data System 1) were included in this institutional review board-approved prospective study. All participants were subjected to BD assessment with MRI using the following sequence with the Dixon technique (echo time/echo time, 6 milliseconds/2.45 milliseconds/2.67 milliseconds; 1-mm isotropic; 3 minutes 38 seconds). To test the reproducibility, a second MRI after patient repositioning was performed. The AUQV magnetic resonance (MR) BD measurement system automatically calculated percentage (%) BD. The qualitative BD assessment was performed using the American College of Radiology Breast Imaging Reporting and Data System BD categories. Quantitative BD was estimated semiautomatically using the thresholding technique Cumulus4. Appropriate statistical tests were used to assess the agreement between the AUQV MR measurements and to compare them with qualitative and quantitative MG BD estimations. The AUQV MR BD measurements were successfully performed in all 43 women. There was a nearly perfect agreement of AUQV MR BD measurements between the 2 MR examinations for % BD (P < 0.001; intraclass correlation coefficient, 0.998) with no significant differences (P = 0.384). The AUQV MR BD measurements were significantly lower than quantitative and qualitative MG BD assessment (P < 0.001). The AUQV MR BD measurement system allows a fully automated, user-independent, robust, reproducible, as well as radiation- and compression-free volumetric quantitative BD assessment through different levels of BD. The AUQV MR BD measurements were significantly lower than the currently used qualitative and quantitative MG-based approaches, implying that the current assessment might overestimate breast density with MG.

PET Imaging Stability Measurements During Simultaneous Pulsing of Aggressive MR Sequences on the SIGNA PET/MR System.

PubMed

Deller, Timothy W; Khalighi, Mohammad Mehdi; Jansen, Floris P; Glover, Gary H

2018-01-01

The recent introduction of simultaneous whole-body PET/MR scanners has enabled new research taking advantage of the complementary information obtainable with PET and MRI. One such application is kinetic modeling, which requires high levels of PET quantitative stability. To accomplish the required PET stability levels, the PET subsystem must be sufficiently isolated from the effects of MR activity. Performance measurements have previously been published, demonstrating sufficient PET stability in the presence of MR pulsing for typical clinical use; however, PET stability during radiofrequency (RF)-intensive and gradient-intensive sequences has not previously been evaluated for a clinical whole-body scanner. In this work, PET stability of the GE SIGNA PET/MR was examined during simultaneous scanning of aggressive MR pulse sequences. Methods: PET performance tests were acquired with MR idle and during simultaneous MR pulsing. Recent system improvements mitigating RF interference and gain variation were used. A fast recovery fast spin echo MR sequence was selected for high RF power, and an echo planar imaging sequence was selected for its high heat-inducing gradients. Measurements were performed to determine PET stability under varying MR conditions using the following metrics: sensitivity, scatter fraction, contrast recovery, uniformity, count rate performance, and image quantitation. A final PET quantitative stability assessment for simultaneous PET scanning during functional MRI studies was performed with a spiral in-and-out gradient echo sequence. Results: Quantitation stability of a 68 Ge flood phantom was demonstrated within 0.34%. Normalized sensitivity was stable during simultaneous scanning within 0.3%. Scatter fraction measured with a 68 Ge line source in the scatter phantom was stable within the range of 40.4%-40.6%. Contrast recovery and uniformity were comparable for PET images acquired simultaneously with multiple MR conditions. Peak noise equivalent count rate was 224 kcps at an effective activity concentration of 18.6 kBq/mL, and the count rate curves and scatter fraction curve were consistent for the alternating MR pulsing states. A final test demonstrated quantitative stability during a spiral functional MRI sequence. Conclusion: PET stability metrics demonstrated that PET quantitation was not affected during simultaneous aggressive MRI. This stability enables demanding applications such as kinetic modeling. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

pO(2) measurements by phosphorescence quenching: characteristics and applications of an automated system.

PubMed

Kerger, Heinz; Groth, Gesine; Kalenka, Armin; Vajkoczy, Peter; Tsai, Amy G; Intaglietta, Marcos

2003-01-01

An automated system for pO(2) analysis based upon phosphorescence quenching was tested. The system was calibrated in vitro with capillary samples of saline and blood. Results were compared to a conventional measuring procedure wherein pO(2) was calculated off-line by computer fitting of phosphorescence decay signals. PO(2) measurements obtained by the automated system were correlated (r(2) = 0.98) with readings simultaneously generated by a blood gas analyzer, accuracy being highest in the low (0-20 mm Hg) and medium pO(2) ranges (21-70 mm Hg). Measurements in in vivo studies in the hamster skin-fold preparation were similar to previously reported results. The automated system fits the phosphorescence decay data to a single exponential and allows repeated pO(2) measurements in rapid sequence.

Measurements of RF heating during 3.0-T MRI of a pig implanted with deep brain stimulator.

PubMed

Gorny, Krzysztof R; Presti, Michael F; Goerss, Stephan J; Hwang, Sun C; Jang, Dong-Pyo; Kim, Inyong; Min, Hoon-Ki; Shu, Yunhong; Favazza, Christopher P; Lee, Kendall H; Bernstein, Matt A

2013-06-01

To present preliminary, in vivo temperature measurements during MRI of a pig implanted with a deep brain stimulation (DBS) system. DBS system (Medtronic Inc., Minneapolis, MN) was implanted in the brain of an anesthetized pig. 3.0-T MRI was performed with a T/R head coil using the low-SAR GRE EPI and IR-prepped GRE sequences (SAR: 0.42 and 0.39 W/kg, respectively), and the high-SAR 4-echo RF spin echo (SAR: 2.9 W/kg). Fluoroptic thermometry was used to directly measure RF-related heating at the DBS electrodes, and at the implantable pulse generator (IPG). For reference the measurements were repeated in the same pig at 1.5 T and, at both field strengths, in a phantom. At 3.0T, the maximal temperature elevations at DBS electrodes were 0.46 °C and 2.3 °C, for the low- and high-SAR sequences, respectively. No heating was observed on the implanted IPG during any of the measurements. Measurements of in vivo heating differed from those obtained in the phantom. The 3.0-T MRI using GRE EPI and IR-prepped GRE sequences resulted in local temperature elevations at DBS electrodes of no more than 0.46 °C. Although no extrapolation should be made to human exams and much further study will be needed, these preliminary data are encouraging for the future use 3.0-T MRI in patients with DBS. Copyright © 2013 Elsevier Inc. All rights reserved.

Measurements of RF Heating during 3.0T MRI of a Pig Implanted with Deep Brain Stimulator

PubMed Central

Gorny, Krzysztof R; Presti, Michael F; Goerss, Stephan J; Hwang, Sun C; Jang, Dong-Pyo; Kim, Inyong; Shu, Yunhong; Favazza, Christopher P; Lee, Kendall H; Bernstein, Matt A

2012-01-01

Purpose To present preliminary, in vivo temperature measurements during MRI of a pig implanted with a deep brain stimulation (DBS) system. Materials and Methods DBS system (Medtronic Inc., Minneapolis, MN) was implanted in the brain of an anesthetized pig. 3.0T MRI was performed with a T/R head coil using the low-SAR GRE EPI and IR-prepped GRE sequences (SAR: 0.42 W/kg and 0.39 W/kg, respectively), and the high-SAR 4-echo RF spin echo (SAR: 2.9 W/kg). Fluoroptic thermometry was used to directly measure RF-related heating at the DBS electrodes, and at the implantable pulse generator (IPG). For reference the measurements were repeated in the same pig at 1.5T and, at both field strengths, in a phantom. Results At 3.0T, the maximal temperature elevations at DBS electrodes were 0.46 °C and 2.3 °C, for the low- and high-SAR sequences, respectively. No heating was observed on the implanted IPG during any of the measurements. Measurements of in-vivo heating differed from those obtained in the phantom. Conclusion The 3.0T MRI using GRE EPI and IR-prepped GRE sequences resulted in local temperature elevations at DBS electrodes of no more than 0.46°C. Although no extrapolation should be made to human exams and much further study will be needed, these preliminary data are encouraging for the future use 3.0T MRI in patients with DBS. PMID:23228310

Magnetic Resonance Arterial Spin Tagging for Non-Invasive Pharmacokinetic Analysis of Breast Cancer

DTIC Science & Technology

2000-10-01

sequence software that we had developed for this project. In addition, we revised the pulse sequences to utilize the high performance gradients (40 mT/ m ...peak, 150 mT/ m /ms rise) of the system. We believe these revised sequences will provide better arterial spin tagged data for perfusion measurement. All...U.... ...... ... -- v p I _1 i-:F~ ----- ! - .Ag Jig. H aI .. M e fI6lo 3 ~ ~ 2 0’,~- A.11. I 1 1 9 - HP ~ ~ IM I 15 L 1 1 8 = NIAt I C J1 5

Gradient waveform pre-emphasis based on the gradient system transfer function.

PubMed

Stich, Manuel; Wech, Tobias; Slawig, Anne; Ringler, Ralf; Dewdney, Andrew; Greiser, Andreas; Ruyters, Gudrun; Bley, Thorsten A; Köstler, Herbert

2018-02-25

The gradient system transfer function (GSTF) has been used to describe the distorted k-space trajectory for image reconstruction. The purpose of this work was to use the GSTF to determine the pre-emphasis for an undistorted gradient output and intended k-space trajectory. The GSTF of the MR system was determined using only standard MR hardware without special equipment such as field probes or a field camera. The GSTF was used for trajectory prediction in image reconstruction and for a gradient waveform pre-emphasis. As test sequences, a gradient-echo sequence with phase-encoding gradient modulation and a gradient-echo sequence with a spiral read-out trajectory were implemented and subsequently applied on a structural phantom and in vivo head measurements. Image artifacts were successfully suppressed by applying the GSTF-based pre-emphasis. Equivalent results are achieved with images acquired using GSTF-based post-correction of the trajectory as a part of image reconstruction. In contrast, the pre-emphasis approach allows reconstruction using the initially intended trajectory. The artifact suppression shown for two sequences demonstrates that the GSTF can serve for a novel pre-emphasis. A pre-emphasis based on the GSTF information can be applied to any arbitrary sequence type. © 2018 International Society for Magnetic Resonance in Medicine.

Controlling Light Transmission Through Highly Scattering Media Using Semi-Definite Programming as a Phase Retrieval Computation Method.

PubMed

N'Gom, Moussa; Lien, Miao-Bin; Estakhri, Nooshin M; Norris, Theodore B; Michielssen, Eric; Nadakuditi, Raj Rao

2017-05-31

Complex Semi-Definite Programming (SDP) is introduced as a novel approach to phase retrieval enabled control of monochromatic light transmission through highly scattering media. In a simple optical setup, a spatial light modulator is used to generate a random sequence of phase-modulated wavefronts, and the resulting intensity speckle patterns in the transmitted light are acquired on a camera. The SDP algorithm allows computation of the complex transmission matrix of the system from this sequence of intensity-only measurements, without need for a reference beam. Once the transmission matrix is determined, optimal wavefronts are computed that focus the incident beam to any position or sequence of positions on the far side of the scattering medium, without the need for any subsequent measurements or wavefront shaping iterations. The number of measurements required and the degree of enhancement of the intensity at focus is determined by the number of pixels controlled by the spatial light modulator.

Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

PubMed

Bastien, Olivier; Maréchal, Eric

2008-08-07

Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the information hazard rate, and that pairwise sequence alignment scores should follow a Gumbel distribution, which parameters could find some theoretical rationale. In particular, one parameter corresponds to the information hazard rate. Extreme value distribution of alignment scores, assessed from high scoring segments pairs following the Karlin-Altschul model, can also be deduced from the Reliability Theory applied to molecular sequences. It reflects the redundancy of information between homologous sequences, under functional conservative pressure. This model also provides a link between concepts of biological sequence analysis and of systems biology.

Evaluation of balanced steady-state free precession (TrueFISP) and K-space segmented gradient echo sequences for 3D coronary MR angiography with navigator gating at 3 Tesla.

PubMed

Kaul, M G; Stork, A; Bansmann, P M; Nolte-Ernsting, C; Lund, G K; Weber, C; Adam, G

2004-11-01

To test the feasibility of k-space segmented gradient-echo pulse sequences for free-breathing coronary magnetic resonance angiography (cMRA) on a clinical 3T system. T2-prepared, fat-suppressed turbo field echo (TFE, turboFLASH, SFPGR) as well as balanced TFE (b-TFE, trueFISP, FIESTA, segmented SSFP) sequences with navigator gating for prospective motion correction were applied on a 3T system equipped with a six-element phased-array cardiac coil. In 15 healthy volunteers, the right coronary artery (RCA) was examined with TFE and b-TFE sequences. Due to examination time limitations, the left coronary artery (LM/LAD) was examined exclusively with the TFE sequence in ten volunteers. Image quality was graded on a five point scale (0 = not visualized to 4 = excellent). The length, diameter and sharpness of the vessels and the contrast-to-noise ratios (CNR) were measured. 98 % of all major segments (proximal/middle/distal) of the RCA could be seen with the TFE sequence and 82 % with the b-TFE sequence. The image quality for the three segments was graded higher for the TFE sequence (2.7/2.7/1.5) than for the b-TFE sequence (1.9/1.6/0.9) with P: (< or = 0.001/< or = 0.004/< or = 0.056). The kappa of the interobserver variability was 0.75 for the TFE sequence and 0.8 for the b-TFE sequence. The measured vessel lengths were longer for the TFE sequence (95 +/- 22 mm) than for the b-TFE sequence (80 +/- 40 mm; P < or = 0.115). No significant changes (P < or = 0.074, P < or = 0.145) in diameter and vessel sharpness of the RCAs were observed between the TFE (2.4 +/- 0.3 mm, 60 % +/- 5) and b-TFE sequences (2.4 +/- 0.3 mm, 62 % +/- 6). The CNR was higher for the TFE sequence (10.1 +/- 3.4) than for the b-TFE sequence (6.6 +/- 2.1; P < or = 0.014). All ten main and proximal segments of the LM/LAD, which were examined exclusively with the TFE sequence, were visible with grade 2.5 and 2.1. The middle segment was visible in seven cases with grade 1.3. In three cases, the distal segment was visible with grade 0.5. The vessel length was 78 +/- 27 mm and the CNR 11.9 +/- 2.4. The conventional TFE technique has demonstrated good feasibility for cMRA at 3T. In its operational availability at 3T, the b-TFE sequence is inferior to the TFE sequence.

Algebraic Approaches for Scalable End-to-End Monitoring and Diagnosis

NASA Astrophysics Data System (ADS)

Zhao, Yao; Chen, Yan

The rigidity of the Internet architecture led to flourish in the research of end-to-end based systems. In this chapter, we describe a linear algebra-based end-to-end monitoring and diagnosis system. We first propose a tomography-based overlay monitoring system (TOM). Given n end hosts, TOM selectively monitors a basis set of O(nlogn) paths out of all n(n - 1) end-to-end paths. Any end-to-end path can be written as a unique linear combination of paths in the basis set. Consequently, by monitoring loss rates for the paths in the basis set, TOM infers loss rates for all end-to-end paths. Furthermore, leveraging on the scalable measurements from the TOM system, we propose the Least-biased End-to-End Network Diagnosis (in short, LEND) system. We define a minimal identifiable link sequence (MILS) as a link sequence of minimal length whose properties can be uniquely identified from end-to-end measurements. LEND applies an algebraic approach to find out the MILSes and infers the properties of the MILSes efficiently. This also means LEND system achieves the finest diagnosis granularity under the least biased statistical assumptions.

Quantum predictions for an unmeasured system cannot be simulated with a finite-memory classical system

NASA Astrophysics Data System (ADS)

Tavakoli, Armin; Cabello, Adán

2018-03-01

We consider an ideal experiment in which unlimited nonprojective quantum measurements are sequentially performed on a system that is initially entangled with a distant one. At each step of the sequence, the measurements are randomly chosen between two. However, regardless of which measurement is chosen or which outcome is obtained, the quantum state of the pair always remains entangled. We show that the classical simulation of the reduced state of the distant system requires not only unlimited rounds of communication, but also that the distant system has infinite memory. Otherwise, a thermodynamical argument predicts heating at a distance. Our proposal can be used for experimentally ruling out nonlocal finite-memory classical models of quantum theory.

Short range spread-spectrum radiolocation system and method

DOEpatents

Smith, Stephen F.

2003-04-29

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

Sequence-specific inhibition of Dicer measured with a force-based microarray for RNA ligands.

PubMed

Limmer, Katja; Aschenbrenner, Daniela; Gaub, Hermann E

2013-04-01

Malfunction of protein translation causes many severe diseases, and suitable correction strategies may become the basis of effective therapies. One major regulatory element of protein translation is the nuclease Dicer that cuts double-stranded RNA independently of the sequence into pieces of 19-22 base pairs starting the RNA interference pathway and activating miRNAs. Inhibiting Dicer is not desirable owing to its multifunctional influence on the cell's gene regulation. Blocking specific RNA sequences by small-molecule binding, however, is a promising approach to affect the cell's condition in a controlled manner. A label-free assay for the screening of site-specific interference of small molecules with Dicer activity is thus needed. We used the Molecular Force Assay (MFA), recently developed in our lab, to measure the activity of Dicer. As a model system, we used an RNA sequence that forms an aptamer-binding site for paromomycin, a 615-dalton aminoglycoside. We show that Dicer activity is modulated as a function of concentration and incubation time: the addition of paromomycin leads to a decrease of Dicer activity according to the amount of ligand. The measured dissociation constant of paromomycin to its aptamer was found to agree well with literature values. The parallel format of the MFA allows a large-scale search and analysis for ligands for any RNA sequence.

RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

PubMed Central

Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

2000-01-01

The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be revealed by seven RISA systems within one month. PMID:11076861

The Electric Circuit as a System: A New Approach.

ERIC Educational Resources Information Center

Hartel, H.

1982-01-01

Traditionally, the terms "current,""voltage," and "resistance" are introduced in a linear sequence according to structure of the discipline and based on measurement operations. A new approach is discussed, the terms being introduced simultaneously in a qualitative way, using the system aspect of the electric circuit as an integrative base.…

Optimal rotation sequences for active perception

NASA Astrophysics Data System (ADS)

Nakath, David; Rachuy, Carsten; Clemens, Joachim; Schill, Kerstin

2016-05-01

One major objective of autonomous systems navigating in dynamic environments is gathering information needed for self localization, decision making, and path planning. To account for this, such systems are usually equipped with multiple types of sensors. As these sensors often have a limited field of view and a fixed orientation, the task of active perception breaks down to the problem of calculating alignment sequences which maximize the information gain regarding expected measurements. Action sequences that rotate the system according to the calculated optimal patterns then have to be generated. In this paper we present an approach for calculating these sequences for an autonomous system equipped with multiple sensors. We use a particle filter for multi- sensor fusion and state estimation. The planning task is modeled as a Markov decision process (MDP), where the system decides in each step, what actions to perform next. The optimal control policy, which provides the best action depending on the current estimated state, maximizes the expected cumulative reward. The latter is computed from the expected information gain of all sensors over time using value iteration. The algorithm is applied to a manifold representation of the joint space of rotation and time. We show the performance of the approach in a spacecraft navigation scenario where the information gain is changing over time, caused by the dynamic environment and the continuous movement of the spacecraft

TOWARD PRECISE AGES FOR SINGLE STARS IN THE FIELD. GYROCHRONOLOGY CONSTRAINTS AT SEVERAL Gyr USING WIDE BINARIES. I. AGES FOR INITIAL SAMPLE

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

Chaname, Julio; Ramirez, Ivan

2012-02-10

We present a program designed to obtain age-rotation measurements of solar-type dwarfs to be used in the calibration of gyrochronology relations at ages of several Gyr. This is a region of parameter space crucial for the large-scale study of the Milky Way, and where the only constraint available today is that provided by the Sun. Our program takes advantage of a set of wide binaries selected so that one component is an evolved star and the other is a main-sequence star of FGK type. In this way, we obtain the age of the system from the evolved star, while themore » rotational properties of the main-sequence component provide the information relevant for gyrochronology regarding the spin-down of solar-type stars. By mining currently available catalogs of wide binaries, we assemble a sample of 37 pairs well positioned for our purposes: 19 with turnoff or subgiant primaries and 18 with white dwarf components. Using high-resolution optical spectroscopy, we measure precise stellar parameters for a subset of 15 of the pairs with turnoff/subgiant components and use these to derive isochronal ages for the corresponding systems. Ages for 16 of the 18 pairs with white dwarf components are taken from the literature. The ages of this initial sample of 31 wide binaries range from 1 to 9 Gyr, with precisions better than {approx}20% for almost half of these systems. When combined with measurements of the rotation period of their main-sequence components, these wide binary systems would potentially provide a similar number of points useful for the calibration of gyrochronology relations at very old ages.« less

Choice of High-Efficacy Strains for the Annual Influenza Vaccine

NASA Astrophysics Data System (ADS)

Deem, Michael

2005-03-01

We introduce a model of protein evolution to explain limitations in the immune system response to vaccination and disease [1]. The phenomenon of original antigenic sin, wherein vaccination creates memory sequences that can increase susceptibility to future exposures to the same disease, is explained as stemming from localization of the immune system response in antibody sequence space. This localization is a result of the roughness in sequence space of the evolved antibody affinity constant for antigen and is observed for diseases with high year-to-year mutation rates, such as influenza. We show that the order parameter within this theory correlates well with efficacies of the H3N2 influenza A component of the annual vaccine between 1971 and 2004 [2,3]. This new measure of antigenic distance predicts vaccine efficacy significantly more accurately than do current state-of-the-art phylogenetic sequence analyses or ferret antisera inhibition assays. We discuss how this new measure of antigenic distance may be used in the context of annual influenza vaccine design and monitoring of vaccine efficacy. 1) M. W. Deem and H. Y. Lee, Phys. Rev. Lett. 91 (2003) 068101. 2) E. T. Munoz and M. W. Deem,q-bio.BM/0408016. 3) V. Gupta, D. J. Earl, and M. W. Deem, ``Choice of High-Efficacy Strains for the Annual Influenza Vaccine,'' submitted.

First experiment on LMJ facility: pointing and synchronisation qualification, sequences qualification

NASA Astrophysics Data System (ADS)

Henry, Olivier; Bretheau, Dominique; Luttmann, Michel; Graillot, Herve; Ferri, Michel; Seguineau, Frederic; Bar, Emmanuel; Patissou, Loic; Canal, Phillipe; Sautarel, Françoise; Tranquille Marques, Yves; Raffestin, Didier

2016-10-01

The LMJ (Laser mega Joule) facility at the CESTA site (Aquitaine, France) is a tool designed to deliver up to 1.2 MJ at 351 nm for plasma experiments. The experiment system will include 11 diagnostics: UV and X energy balances, imagers (Streak and stripe camera, CCD), spectrometers, and a Visar/pyrometer. The facility must be able to deliver, within the hour following the shot, all the results of the plasma diagnostics, alignment images and laser diagnostic measurements. These results have to be guaranteed in terms of conformity to the request and quality of measurement. The end of 2014 was devoted to the qualification of system pointing on target and synchronization within and between beams. The shots made with one chain (divided in 2 quads - 8 laser beams) have achieved 50 µm of misalignment accuracy (chain and quad channel) and a synchronization accuracy in the order of 50 ps. The performances achieved for plasma diagnostic (in the order of less 100 µm of alignment and timing accuracy less than 150 ps) comply with expectations. At the same time the first automatic sequences were tested. They allowed a shot on target every 6h:30 and in some case twice a day by reducing preparation actions, leading to a sequence of 4h:00. These shooting sequences are managed by an operating team of 7 people helped by 3 people for security aspects.

Realizing a Rasch measurement through instructionally- sequenced domains of test items.

NASA Astrophysics Data System (ADS)

Schulz, E. Matthew

2016-11-01

This paper presents results from a project in which instructionally-sequenced domains were defined for purposes of constructing measures that that conform to an ideal in Guttman scaling and Rasch measurement. A fundamental idea in these measurement systems is that every person higher on the measurement scale can do everything that lower-level persons can do, plus at least one more thing. This idea has had limited application in educational measurement due to the stochastic nature of item response data and the sheer number of items needed to obtain reliable measures. However, it has been shown by Schulz, Lee, and Mullen [1] that this ideal can be can be realized at a higher level of abstraction - when items within a content strand are aggregated into a small number of domains that are ordered in instructional timing and difficulty. The present paper shows how this was done, and the results, in an achievement level setting project for the 2007 Grade 12 NAEP Economics Assessment.

Rapid Polymer Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor (Inventor); Brock, Mathew W. (Inventor)

2011-01-01

Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

The Functional Human C-Terminome

PubMed Central

Hedden, Michael; Lyon, Kenneth F.; Brooks, Steven B.; David, Roxanne P.; Limtong, Justin; Newsome, Jacklyn M.; Novakovic, Nemanja; Rajasekaran, Sanguthevar; Thapar, Vishal; Williams, Sean R.; Schiller, Martin R.

2016-01-01

All translated proteins end with a carboxylic acid commonly called the C-terminus. Many short functional sequences (minimotifs) are located on or immediately proximal to the C-terminus. However, information about the function of protein C-termini has not been consolidated into a single source. Here, we built a new “C-terminome” database and web system focused on human proteins. Approximately 3,600 C-termini in the human proteome have a minimotif with an established molecular function. To help evaluate the function of the remaining C-termini in the human proteome, we inferred minimotifs identified by experimentation in rodent cells, predicted minimotifs based upon consensus sequence matches, and predicted novel highly repetitive sequences in C-termini. Predictions can be ranked by enrichment scores or Gene Evolutionary Rate Profiling (GERP) scores, a measurement of evolutionary constraint. By searching for new anchored sequences on the last 10 amino acids of proteins in the human proteome with lengths between 3–10 residues and up to 5 degenerate positions in the consensus sequences, we have identified new consensus sequences that predict instances in the majority of human genes. All of this information is consolidated into a database that can be accessed through a C-terminome web system with search and browse functions for minimotifs and human proteins. A known consensus sequence-based predicted function is assigned to nearly half the proteins in the human proteome. Weblink: http://cterminome.bio-toolkit.com. PMID:27050421

Reading biological processes from nucleotide sequences

NASA Astrophysics Data System (ADS)

Murugan, Anand

Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical mechanisms.

Real-time, portable genome sequencing for Ebola surveillance.

PubMed

Quick, Joshua; Loman, Nicholas J; Duraffour, Sophie; Simpson, Jared T; Severi, Ettore; Cowley, Lauren; Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan Hj; Becker-Ziaja, Beate; Boettcher, Jan-Peter; Cabeza-Cabrerizo, Mar; Camino-Sanchez, Alvaro; Carter, Lisa L; Doerrbecker, Juiliane; Enkirch, Theresa; Dorival, Isabel Graciela García; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigail; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallash, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Yasmin; Sachse, Andrea; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Trina, Racine; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N'Faly; Williams, Cecelia V; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Franck; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, Jamie; Rachwal, Philip; Turner, Daniel; Pollakis, Georgios; Hiscox, Julian A; Matthews, David A; O'Shea, Matthew K; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Woelfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A; Koivogui, Lamine; Diallo, Boubacar; Keita, Sakoba; Rambaut, Andrew; Formenty, Pierre; Gunther, Stephan; Carroll, Miles W

2016-02-11

The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterize the infectious agent and determine its evolutionary rate. Genome sequencing also allows the identification of signatures of host adaptation, identification and monitoring of diagnostic targets, and characterization of responses to vaccines and treatments. The Ebola virus (EBOV) genome substitution rate in the Makona strain has been estimated at between 0.87 × 10(-3) and 1.42 × 10(-3) mutations per site per year. This is equivalent to 16-27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions. Genomic surveillance during the epidemic has been sporadic owing to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities. To address this problem, here we devise a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. We present sequence data and analysis of 142 EBOV samples collected during the period March to October 2015. We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15-60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.

Turbulent boundary layers subjected to multiple curvatures and pressure gradients

NASA Technical Reports Server (NTRS)

Bandyopadhyay, Promode R.; Ahmed, Anwar

1993-01-01

The effects of abruptly applied cycles of curvatures and pressure gradients on turbulent boundary layers are examined experimentally. Two two-dimensional curved test surfaces are considered: one has a sequence of concave and convex longitudinal surface curvatures and the other has a sequence of convex and concave curvatures. The choice of the curvature sequences were motivated by a desire to study the asymmetric response of turbulent boundary layers to convex and concave curvatures. The relaxation of a boundary layer from the effects of these two opposite sequences has been compared. The effect of the accompaying sequences of pressure gradient has also been examined but the effect of curvature dominates. The growth of internal layers at the curvature junctions have been studied. Measurements of the Gortler and corner vortex systems have been made. The boundary layer recovering from the sequence of concave to convex curvature has a sustained lower skin friction level than in that recovering from the sequence of convex to concave curvature. The amplification and suppression of turbulence due to the curvature sequences have also been studied.

Device accurately measures and records low gas-flow rates

NASA Technical Reports Server (NTRS)

Branum, L. W.

1966-01-01

Free-floating piston in a vertical column accurately measures and records low gas-flow rates. The system may be calibrated, using an adjustable flow-rate gas supply, a low pressure gage, and a sequence recorder. From the calibration rates, a nomograph may be made for easy reduction. Temperature correction may be added for further accuracy.

High-precision relocation for aftershocks of the 2016 ML 5.8 Gyeongju earthquake in South Korea: Stress partitioning controlled by complex fault systems

NASA Astrophysics Data System (ADS)

Woo, J. U.; Rhie, J.; Kang, T. S.; Kim, S.; Chai, G.; Cho, E.

2017-12-01

Complex inherent fault system is one of key factors controlling the main shock occurrence and the pattern of aftershock sequence. Many field studies have shown that the fault systems in the Korean Peninsula are complex because they formed by various tectonic events since Proterozoic. Apart from that the mainshock is the largest one (ML 5.8) ever recorded in South Korea, the Gyeongju earthquake sequence shows particularly interesting features: ML 5.1 event preceded ML 5.8 event by 50 min and they are located closely to each other ( 1 km). In addition, ML 4.5 event occurred 2 3 km away from the two events after a week of the mainshock. Considering reported focal mechanisms and hypocenters of the three major events, it is unlikely that the earthquake sequence occurs on a single fault plane. To depict the detailed fault geometry associated with the sequence, we precisely determine the relative locations of 1,400 aftershocks recorded by 27 broadband stations, which started to be deployed less than one hour after the mainshock. Double difference algorithm is applied using relative travel time measurements by a waveform cross-correlation method. Relocated hypocenters show that a major fault striking NE-SW and some minor faults get involved in the sequence. In particular, aftershocks immediately following ML 4.5 event seem to occur on a fault striking NW-SE, which is orthogonal to the strike of a major fault. We expect that the Gyeongju earthquake sequence resulted from the stress transfer controlled by the complex inherent fault system in this region.

LinkFinder: An expert system that constructs phylogenic trees

NASA Technical Reports Server (NTRS)

Inglehart, James; Nelson, Peter C.

1991-01-01

An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time.

Implementation of a quantum random number generator based on the optimal clustering of photocounts

NASA Astrophysics Data System (ADS)

Balygin, K. A.; Zaitsev, V. I.; Klimov, A. N.; Kulik, S. P.; Molotkov, S. N.

2017-10-01

To implement quantum random number generators, it is fundamentally important to have a mathematically provable and experimentally testable process of measurements of a system from which an initial random sequence is generated. This makes sure that randomness indeed has a quantum nature. A quantum random number generator has been implemented with the use of the detection of quasi-single-photon radiation by a silicon photomultiplier (SiPM) matrix, which makes it possible to reliably reach the Poisson statistics of photocounts. The choice and use of the optimal clustering of photocounts for the initial sequence of photodetection events and a method of extraction of a random sequence of 0's and 1's, which is polynomial in the length of the sequence, have made it possible to reach a yield rate of 64 Mbit/s of the output certainly random sequence.

Orthogonal Polynomials on the Unit Circle with Fibonacci Verblunsky Coefficients, II. Applications

NASA Astrophysics Data System (ADS)

Damanik, David; Munger, Paul; Yessen, William N.

2013-10-01

We consider CMV matrices with Verblunsky coefficients determined in an appropriate way by the Fibonacci sequence and present two applications of the spectral theory of such matrices to problems in mathematical physics. In our first application we estimate the spreading rates of quantum walks on the line with time-independent coins following the Fibonacci sequence. The estimates we obtain are explicit in terms of the parameters of the system. In our second application, we establish a connection between the classical nearest neighbor Ising model on the one-dimensional lattice in the complex magnetic field regime, and CMV operators. In particular, given a sequence of nearest-neighbor interaction couplings, we construct a sequence of Verblunsky coefficients, such that the support of the Lee-Yang zeros of the partition function for the Ising model in the thermodynamic limit coincides with the essential spectrum of the CMV matrix with the constructed Verblunsky coefficients. Under certain technical conditions, we also show that the zeros distribution measure coincides with the density of states measure for the CMV matrix.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

PubMed

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-05-01

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

PubMed Central

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-01-01

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases

PubMed Central

Lu, Stephen M.; Lu, Wuyuan; Qasim, M. A.; Anderson, Stephen; Apostol, Izydor; Ardelt, Wojciech; Bigler, Theresa; Chiang, Yi Wen; Cook, James; James, Michael N. G.; Kato, Ikunoshin; Kelly, Clyde; Kohr, William; Komiyama, Tomoko; Lin, Tiao-Yin; Ogawa, Michio; Otlewski, Jacek; Park, Soon-Jae; Qasim, Sabiha; Ranjbar, Michael; Tashiro, Misao; Warne, Nicholas; Whatley, Harry; Wieczorek, Anna; Wieczorek, Maciej; Wilusz, Tadeusz; Wynn, Richard; Zhang, Wenlei; Laskowski, Michael

2001-01-01

An additivity-based sequence to reactivity algorithm for the interaction of members of the Kazal family of protein inhibitors with six selected serine proteinases is described. Ten consensus variable contact positions in the inhibitor were identified, and the 19 possible variants at each of these positions were expressed. The free energies of interaction of these variants and the wild type were measured. For an additive system, this data set allows for the calculation of all possible sequences, subject to some restrictions. The algorithm was extensively tested. It is exceptionally fast so that all possible sequences can be predicted. The strongest, the most specific possible, and the least specific inhibitors were designed, and an evolutionary problem was solved. PMID:11171964

High-resolution Fourier transform spectroscopy of the Meinel system of OH

NASA Technical Reports Server (NTRS)

Abrams, Mark C.; Davis, Sumner P.; Rao, M. L. P.; Engleman, Rolf, Jr.; Brault, James W.

1994-01-01

The infrared spectrum of the hydroxyl radical OH, between 1850 and 9000/cm has been measured with a Fourier transform spectrometer. The source, a hydrogen-ozone diffusion flame, was designed to study the excitation of rotation-vibration levels of the OH Meinel bands under conditions similar to those in the upper atmosphere which produce the nighttime OH airglow emission. Twenty-three bands were observed: nine bands in the Delta upsilon = 1 sequence, nine bands in the Delta upsilon = 2 sequence, and five bands in the Delta upsilon = 3 sequence. A global nonlinear least-squares fit of 1696 lines yielded molecular parameters with a standard deviation of 0.003/cm. Term values are computed, and transition frequencies in the Delta upsilon = 3, 4, 5, 6 sequences in the near-infrared are predicted.

Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.

PubMed

Jerison, Elizabeth R; Desai, Michael M

2015-12-01

Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Users guide for EASI graphics

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

Sasser, D.W.

1978-03-01

EASI (Estimate of Adversary Sequence Interruption) is an analytical technique for measuring the effectiveness of physical protection systems. EASI Graphics is a computer graphics extension of EASI which provides a capability for performing sensitivity and trade-off analyses of the parameters of a physical protection system. This document reports on the implementation of EASI Graphics and illustrates its application with some examples.

Synchronous high speed multi-point velocity profile measurement by heterodyne interferometry

NASA Astrophysics Data System (ADS)

Hou, Xueqin; Xiao, Wen; Chen, Zonghui; Qin, Xiaodong; Pan, Feng

2017-02-01

This paper presents a synchronous multipoint velocity profile measurement system, which acquires the vibration velocities as well as images of vibrating objects by combining optical heterodyne interferometry and a high-speed CMOS-DVR camera. The high-speed CMOS-DVR camera records a sequence of images of the vibrating object. Then, by extracting and processing multiple pixels at the same time, a digital demodulation technique is implemented to simultaneously acquire the vibrating velocity of the target from the recorded sequences of images. This method is validated with an experiment. A piezoelectric ceramic plate with standard vibration characteristics is used as the vibrating target, which is driven by a standard sinusoidal signal.

BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data.

PubMed

Chae, Heejoon; Lee, Sangseon; Seo, Seokjun; Jung, Daekyoung; Chang, Hyeonsook; Nephew, Kenneth P; Kim, Sun

2016-12-01

Measuring gene expression, DNA sequence variation, and DNA methylation status is routinely done using high throughput sequencing technologies. To analyze such multi-omics data and explore relationships, reliable bioinformatics systems are much needed. Existing systems are either for exploring curated data or for processing omics data in the form of a library such as R. Thus scientists have much difficulty in investigating relationships among gene expression, DNA sequence variation, and DNA methylation using multi-omics data. In this study, we report a system called BioVLAB-mCpG-SNP-EXPRESS for the integrated analysis of DNA methylation, sequence variation (SNPs), and gene expression for distinguishing cellular phenotypes at the pairwise and multiple phenotype levels. The system can be deployed on either the Amazon cloud or a publicly available high-performance computing node, and the data analysis and exploration of the analysis result can be conveniently done using a web-based interface. In order to alleviate analysis complexity, all the process are fully automated, and graphical workflow system is integrated to represent real-time analysis progression. The BioVLAB-mCpG-SNP-EXPRESS system works in three stages. First, it processes and analyzes multi-omics data as input in the form of the raw data, i.e., FastQ files. Second, various integrated analyses such as methylation vs. gene expression and mutation vs. methylation are performed. Finally, the analysis result can be explored in a number of ways through a web interface for the multi-level, multi-perspective exploration. Multi-level interpretation can be done by either gene, gene set, pathway or network level and multi-perspective exploration can be explored from either gene expression, DNA methylation, sequence variation, or their relationship perspective. The utility of the system is demonstrated by performing analysis of phenotypically distinct 30 breast cancer cell line data set. BioVLAB-mCpG-SNP-EXPRESS is available at http://biohealth.snu.ac.kr/software/biovlab_mcpg_snp_express/. Copyright © 2016 Elsevier Inc. All rights reserved.

Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging.

PubMed

Nolte-Ernsting, C C; Tacke, J; Adam, G B; Haage, P; Jung, P; Jakse, G; Günther, R W

2001-01-01

The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. In projection MR urography, the entire pelvicaliceal system was imaged by acquisition of a fast single-slice sequence and the conventional 2D GRE technique provided superior morphological accuracy than 2D GRE EPI projection images (p < 0.0003). Fast 3D GRE EPI sequences improve the clinical practicability of excretory MR urography especially in old or critically ill patients unable to suspend breathing for more than 20 s. Conventional GRE sequences are superior to EPI in high-resolution detail MR urograms and in projection imaging.

Image based performance analysis of thermal imagers

NASA Astrophysics Data System (ADS)

Wegner, D.; Repasi, E.

2016-05-01

Due to advances in technology, modern thermal imagers resemble sophisticated image processing systems in functionality. Advanced signal and image processing tools enclosed into the camera body extend the basic image capturing capability of thermal cameras. This happens in order to enhance the display presentation of the captured scene or specific scene details. Usually, the implemented methods are proprietary company expertise, distributed without extensive documentation. This makes the comparison of thermal imagers especially from different companies a difficult task (or at least a very time consuming/expensive task - e.g. requiring the execution of a field trial and/or an observer trial). For example, a thermal camera equipped with turbulence mitigation capability stands for such a closed system. The Fraunhofer IOSB has started to build up a system for testing thermal imagers by image based methods in the lab environment. This will extend our capability of measuring the classical IR-system parameters (e.g. MTF, MTDP, etc.) in the lab. The system is set up around the IR- scene projector, which is necessary for the thermal display (projection) of an image sequence for the IR-camera under test. The same set of thermal test sequences might be presented to every unit under test. For turbulence mitigation tests, this could be e.g. the same turbulence sequence. During system tests, gradual variation of input parameters (e. g. thermal contrast) can be applied. First ideas of test scenes selection and how to assembly an imaging suite (a set of image sequences) for the analysis of imaging thermal systems containing such black boxes in the image forming path is discussed.

A fully redundant double difference algorithm for obtaining minimum variance estimates from GPS observations

NASA Technical Reports Server (NTRS)

Melbourne, William G.

1986-01-01

In double differencing a regression system obtained from concurrent Global Positioning System (GPS) observation sequences, one either undersamples the system to avoid introducing colored measurement statistics, or one fully samples the system incurring the resulting non-diagonal covariance matrix for the differenced measurement errors. A suboptimal estimation result will be obtained in the undersampling case and will also be obtained in the fully sampled case unless the color noise statistics are taken into account. The latter approach requires a least squares weighting matrix derived from inversion of a non-diagonal covariance matrix for the differenced measurement errors instead of inversion of the customary diagonal one associated with white noise processes. Presented is the so-called fully redundant double differencing algorithm for generating a weighted double differenced regression system that yields equivalent estimation results, but features for certain cases a diagonal weighting matrix even though the differenced measurement error statistics are highly colored.

Translating visual information into action predictions: Statistical learning in action and nonaction contexts.

PubMed

Monroy, Claire D; Gerson, Sarah A; Hunnius, Sabine

2018-05-01

Humans are sensitive to the statistical regularities in action sequences carried out by others. In the present eyetracking study, we investigated whether this sensitivity can support the prediction of upcoming actions when observing unfamiliar action sequences. In two between-subjects conditions, we examined whether observers would be more sensitive to statistical regularities in sequences performed by a human agent versus self-propelled 'ghost' events. Secondly, we investigated whether regularities are learned better when they are associated with contingent effects. Both implicit and explicit measures of learning were compared between agent and ghost conditions. Implicit learning was measured via predictive eye movements to upcoming actions or events, and explicit learning was measured via both uninstructed reproduction of the action sequences and verbal reports of the regularities. The findings revealed that participants, regardless of condition, readily learned the regularities and made correct predictive eye movements to upcoming events during online observation. However, different patterns of explicit-learning outcomes emerged following observation: Participants were most likely to re-create the sequence regularities and to verbally report them when they had observed an actor create a contingent effect. These results suggest that the shift from implicit predictions to explicit knowledge of what has been learned is facilitated when observers perceive another agent's actions and when these actions cause effects. These findings are discussed with respect to the potential role of the motor system in modulating how statistical regularities are learned and used to modify behavior.

The determination of high-resolution spatio-temporal glacier motion fields from time-lapse sequences

NASA Astrophysics Data System (ADS)

Schwalbe, Ellen; Maas, Hans-Gerd

2017-12-01

This paper presents a comprehensive method for the determination of glacier surface motion vector fields at high spatial and temporal resolution. These vector fields can be derived from monocular terrestrial camera image sequences and are a valuable data source for glaciological analysis of the motion behaviour of glaciers. The measurement concepts for the acquisition of image sequences are presented, and an automated monoscopic image sequence processing chain is developed. Motion vector fields can be derived with high precision by applying automatic subpixel-accuracy image matching techniques on grey value patterns in the image sequences. Well-established matching techniques have been adapted to the special characteristics of the glacier data in order to achieve high reliability in automatic image sequence processing, including the handling of moving shadows as well as motion effects induced by small instabilities in the camera set-up. Suitable geo-referencing techniques were developed to transform image measurements into a reference coordinate system.The result of monoscopic image sequence analysis is a dense raster of glacier surface point trajectories for each image sequence. Each translation vector component in these trajectories can be determined with an accuracy of a few centimetres for points at a distance of several kilometres from the camera. Extensive practical validation experiments have shown that motion vector and trajectory fields derived from monocular image sequences can be used for the determination of high-resolution velocity fields of glaciers, including the analysis of tidal effects on glacier movement, the investigation of a glacier's motion behaviour during calving events, the determination of the position and migration of the grounding line and the detection of subglacial channels during glacier lake outburst floods.

Analysis of codon usage in beta-tubulin sequences of helminths.

PubMed

von Samson-Himmelstjerna, G; Harder, A; Failing, K; Pape, M; Schnieder, T

2003-07-01

Codon usage bias has been shown to be correlated with gene expression levels in many organisms, including the nematode Caenorhabditis elegans. Here, the codon usage (cu) characteristics for a set of currently available beta-tubulin coding sequences of helminths were assessed by calculating several indices, including the effective codon number (Nc), the intrinsic codon deviation index (ICDI), the P2 value and the mutational response index (MRI). The P2 value gives a measure of translational pressure, which has been shown to be correlated to high gene expression levels in some organisms, but it has not yet been analysed in that respect in helminths. For all but two of the C. elegans beta-tubulin coding sequences investigated, the P2 value was the only index that indicated the presence of codon usage bias. Therefore, we propose that in general the helminth beta-tubulin sequences investigated here are not expressed at high levels. Furthermore, we calculated the correlation coefficients for the cu patterns of the helminth beta-tubulin sequences compared with those of highly expressed genes in organisms such as Escherichia coli and C. elegans. It was found that beta-tubulin cu patterns for all sequences of members of the Strongylida were significantly correlated to those for highly expressed C. elegans genes. This approach provides a new measure for comparing the adaptation of cu of a particular coding sequence with that of highly expressed genes in possible expression systems.Finally, using the cu patterns of the sequences studied, a phylogenetic tree was constructed. The topology of this tree was very much in concordance with that of a phylogeny based on small subunit ribosomal DNA sequence alignments.

Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison.

PubMed

Dai, Qi; Yang, Yanchun; Wang, Tianming

2008-10-15

Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r. The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.

An Imaging And Graphics Workstation For Image Sequence Analysis

NASA Astrophysics Data System (ADS)

Mostafavi, Hassan

1990-01-01

This paper describes an application-specific engineering workstation designed and developed to analyze imagery sequences from a variety of sources. The system combines the software and hardware environment of the modern graphic-oriented workstations with the digital image acquisition, processing and display techniques. The objective is to achieve automation and high throughput for many data reduction tasks involving metric studies of image sequences. The applications of such an automated data reduction tool include analysis of the trajectory and attitude of aircraft, missile, stores and other flying objects in various flight regimes including launch and separation as well as regular flight maneuvers. The workstation can also be used in an on-line or off-line mode to study three-dimensional motion of aircraft models in simulated flight conditions such as wind tunnels. The system's key features are: 1) Acquisition and storage of image sequences by digitizing real-time video or frames from a film strip; 2) computer-controlled movie loop playback, slow motion and freeze frame display combined with digital image sharpening, noise reduction, contrast enhancement and interactive image magnification; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored image sequence; 4) automatic and manual field-of-view and spatial calibration; 5) image sequence data base generation and management, including the measurement data products; 6) off-line analysis software for trajectory plotting and statistical analysis; 7) model-based estimation and tracking of object attitude angles; and 8) interface to a variety of video players and film transport sub-systems.

Analysis of dispatching rules in a stochastic dynamic job shop manufacturing system with sequence-dependent setup times

NASA Astrophysics Data System (ADS)

Sharma, Pankaj; Jain, Ajai

2014-12-01

Stochastic dynamic job shop scheduling problem with consideration of sequence-dependent setup times are among the most difficult classes of scheduling problems. This paper assesses the performance of nine dispatching rules in such shop from makespan, mean flow time, maximum flow time, mean tardiness, maximum tardiness, number of tardy jobs, total setups and mean setup time performance measures viewpoint. A discrete event simulation model of a stochastic dynamic job shop manufacturing system is developed for investigation purpose. Nine dispatching rules identified from literature are incorporated in the simulation model. The simulation experiments are conducted under due date tightness factor of 3, shop utilization percentage of 90% and setup times less than processing times. Results indicate that shortest setup time (SIMSET) rule provides the best performance for mean flow time and number of tardy jobs measures. The job with similar setup and modified earliest due date (JMEDD) rule provides the best performance for makespan, maximum flow time, mean tardiness, maximum tardiness, total setups and mean setup time measures.

A Highly Flexible, Automated System Providing Reliable Sample Preparation in Element- and Structure-Specific Measurements.

PubMed

Vorberg, Ellen; Fleischer, Heidi; Junginger, Steffen; Liu, Hui; Stoll, Norbert; Thurow, Kerstin

2016-10-01

Life science areas require specific sample pretreatment to increase the concentration of the analytes and/or to convert the analytes into an appropriate form for the detection and separation systems. Various workstations are commercially available, allowing for automated biological sample pretreatment. Nevertheless, due to the required temperature, pressure, and volume conditions in typical element and structure-specific measurements, automated platforms are not suitable for analytical processes. Thus, the purpose of the presented investigation was the design, realization, and evaluation of an automated system ensuring high-precision sample preparation for a variety of analytical measurements. The developed system has to enable system adaption and high performance flexibility. Furthermore, the system has to be capable of dealing with the wide range of required vessels simultaneously, allowing for less cost and time-consuming process steps. However, the system's functionality has been confirmed in various validation sequences. Using element-specific measurements, the automated system was up to 25% more precise compared to the manual procedure and as precise as the manual procedure using structure-specific measurements. © 2015 Society for Laboratory Automation and Screening.

Advanced Sine Wave Modulation of Continuous Wave Laser System for Atmospheric CO2 Differential Absorption Measurements

NASA Technical Reports Server (NTRS)

Campbell, Joel F.; Lin, Bing; Nehrir, Amin R.

2014-01-01

NASA Langley Research Center in collaboration with ITT Exelis have been experimenting with Continuous Wave (CW) laser absorption spectrometer (LAS) as a means of performing atmospheric CO2 column measurements from space to support the Active Sensing of CO2 Emissions over Nights, Days, and Seasons (ASCENDS) mission.Because range resolving Intensity Modulated (IM) CW lidar techniques presented here rely on matched filter correlations, autocorrelation properties without side lobes or other artifacts are highly desirable since the autocorrelation function is critical for the measurements of lidar return powers, laser path lengths, and CO2 column amounts. In this paper modulation techniques are investigated that improve autocorrelation properties. The modulation techniques investigated in this paper include sine waves modulated by maximum length (ML) sequences in various hardware configurations. A CW lidar system using sine waves modulated by ML pseudo random noise codes is described, which uses a time shifting approach to separate channels and make multiple, simultaneous online/offline differential absorption measurements. Unlike the pure ML sequence, this technique is useful in hardware that is band pass filtered as the IM sine wave carrier shifts the main power band. Both amplitude and Phase Shift Keying (PSK) modulated IM carriers are investigated that exibit perfect autocorrelation properties down to one cycle per code bit. In addition, a method is presented to bandwidth limit the ML sequence based on a Gaussian filter implemented in terms of Jacobi theta functions that does not seriously degrade the resolution or introduce side lobes as a means of reducing aliasing and IM carrier bandwidth.

Enhanced Monocular Visual Odometry Integrated with Laser Distance Meter for Astronaut Navigation

PubMed Central

Wu, Kai; Di, Kaichang; Sun, Xun; Wan, Wenhui; Liu, Zhaoqin

2014-01-01

Visual odometry provides astronauts with accurate knowledge of their position and orientation. Wearable astronaut navigation systems should be simple and compact. Therefore, monocular vision methods are preferred over stereo vision systems, commonly used in mobile robots. However, the projective nature of monocular visual odometry causes a scale ambiguity problem. In this paper, we focus on the integration of a monocular camera with a laser distance meter to solve this problem. The most remarkable advantage of the system is its ability to recover a global trajectory for monocular image sequences by incorporating direct distance measurements. First, we propose a robust and easy-to-use extrinsic calibration method between camera and laser distance meter. Second, we present a navigation scheme that fuses distance measurements with monocular sequences to correct the scale drift. In particular, we explain in detail how to match the projection of the invisible laser pointer on other frames. Our proposed integration architecture is examined using a live dataset collected in a simulated lunar surface environment. The experimental results demonstrate the feasibility and effectiveness of the proposed method. PMID:24618780

Stellar Diameters and Temperatures. III. Main-sequence A, F, G, and K Stars: Additional High-precision Measurements and Empirical Relations

NASA Astrophysics Data System (ADS)

Boyajian, Tabetha S.; von Braun, Kaspar; van Belle, Gerard; Farrington, Chris; Schaefer, Gail; Jones, Jeremy; White, Russel; McAlister, Harold A.; ten Brummelaar, Theo A.; Ridgway, Stephen; Gies, Douglas; Sturmann, Laszlo; Sturmann, Judit; Turner, Nils H.; Goldfinger, P. J.; Vargas, Norm

2013-07-01

Based on CHARA Array measurements, we present the angular diameters of 23 nearby, main-sequence stars, ranging from spectral types A7 to K0, 5 of which are exoplanet host stars. We derive linear radii, effective temperatures, and absolute luminosities of the stars using Hipparcos parallaxes and measured bolometric fluxes. The new data are combined with previously published values to create an Angular Diameter Anthology of measured angular diameters to main-sequence stars (luminosity classes V and IV). This compilation consists of 125 stars with diameter uncertainties of less than 5%, ranging in spectral types from A to M. The large quantity of empirical data is used to derive color-temperature relations to an assortment of color indices in the Johnson (BVR J I J JHK), Cousins (R C I C), Kron (R K I K), Sloan (griz), and WISE (W 3 W 4) photometric systems. These relations have an average standard deviation of ~3% and are valid for stars with spectral types A0-M4. To derive even more accurate relations for Sun-like stars, we also determined these temperature relations omitting early-type stars (T eff > 6750 K) that may have biased luminosity estimates because of rapid rotation; for this subset the dispersion is only ~2.5%. We find effective temperatures in agreement within a couple of percent for the interferometrically characterized sample of main-sequence stars compared to those derived via the infrared flux method and spectroscopic analysis.

Verification of real sensor motion for a high-dynamic 3D measurement inspection system

NASA Astrophysics Data System (ADS)

Breitbarth, Andreas; Correns, Martin; Zimmermann, Manuel; Zhang, Chen; Rosenberger, Maik; Schambach, Jörg; Notni, Gunther

2017-06-01

Inline three-dimensional measurements are a growing part of optical inspection. Considering increasing production capacities and economic aspects, dynamic measurements under motion are inescapable. Using a sequence of different pattern, like it is generally done in fringe projection systems, relative movements of the measurement object with respect to the 3d sensor between the images of one pattern sequence have to be compensated. Based on the application of fully automated optical inspection of circuit boards at an assembly line, the knowledge of the relative speed of movement between the measurement object and the 3d sensor system should be used inside the algorithms of motion compensation. Optimally, this relative speed is constant over the whole measurement process and consists of only one motion direction to avoid sensor vibrations. The quantified evaluation of this two assumptions and the error impact on the 3d accuracy are content of the research project described by this paper. For our experiments we use a glass etalon with non-transparent circles and transmitted light. Focused on the circle borders, this is one of the most reliable methods to determine subpixel positions using a couple of searching rays. The intersection point of all rays characterize the center of each circle. Based on these circle centers determined with a precision of approximately 1=50 pixel, the motion vector between two images could be calculated and compared with the input motion vector. Overall, the results are used to optimize the weight distribution of the 3d sensor head and reduce non-uniformly vibrations. Finally, there exists a dynamic 3d measurement system with an error of motion vectors about 4 micrometer. Based on this outcome, simulations result in a 3d standard deviation at planar object regions of 6 micrometers. The same system yields a 3d standard deviation of 9 µm without the optimization of weight distribution.

Characterization and correction of eddy-current artifacts in unipolar and bipolar diffusion sequences using magnetic field monitoring.

PubMed

Chan, Rachel W; von Deuster, Constantin; Giese, Daniel; Stoeck, Christian T; Harmer, Jack; Aitken, Andrew P; Atkinson, David; Kozerke, Sebastian

2014-07-01

Diffusion tensor imaging (DTI) of moving organs is gaining increasing attention but robust performance requires sequence modifications and dedicated correction methods to account for system imperfections. In this study, eddy currents in the "unipolar" Stejskal-Tanner and the velocity-compensated "bipolar" spin-echo diffusion sequences were investigated and corrected for using a magnetic field monitoring approach in combination with higher-order image reconstruction. From the field-camera measurements, increased levels of second-order eddy currents were quantified in the unipolar sequence relative to the bipolar diffusion sequence while zeroth and linear orders were found to be similar between both sequences. Second-order image reconstruction based on field-monitoring data resulted in reduced spatial misalignment artifacts and residual displacements of less than 0.43 mm and 0.29 mm (in the unipolar and bipolar sequences, respectively) after second-order eddy-current correction. Results demonstrate the need for second-order correction in unipolar encoding schemes but also show that bipolar sequences benefit from second-order reconstruction to correct for incomplete intrinsic cancellation of eddy-currents. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Impact of longer-term modest climate shifts on architecture of high-frequency sequences (Cyclothems), Pennsylvanian of midcontinent U.S.A

USGS Publications Warehouse

Feldman, H.R.; Franseen, E.K.; Joeckel, R.M.; Heckel, P.H.

2005-01-01

Pennsylvanian glacioeustatic cyclothems exposed in Kansas and adjacent areas provide a unique opportunity to test models of the impact of relative sea level and climate on stratal architecture. A succession of eight of these high-frequency sequences, traced along dip for 500 km, reveal that modest climate shifts from relatively dry-seasonal to relatively wet-seasonal with a duration of several sequences (???600,000 to 1 million years) had a dominant impact on facies, sediment dispersal patterns, and sequence architecture. The climate shifts documented herein are intermediate, both in magnitude and duration, between previously documented longer-term climate shifts throughout much of the Pennsylvanian and shorter-term shifts described within individual sequences. Climate indicators are best preserved at sequence boundaries and in incised-valley fills of the lowstand systems tracts (LST). Relatively drier climate indicators include high-chroma paleosols, typically with pedogenic carbonates, and plant assemblages that are dominated by gymnosperms, mostly xerophytic walchian conifers. The associated valleys are small (4 km wide and >20 m deep), and dominated by quartz sandstones derived from distant source areas, reflecting large drainage networks. Transgressive systems tracts (TST) in all eight sequences gen erally are characterized by thin, extensive limestones and thin marine shales, suggesting that the dominant control on TST facies distribution was the sequestration of siliciclastic sediment in updip positions. Highstand systems tracts (HST) were significantly impacted by the intermediate-scale climate cycle in that HSTs from relatively drier climates consist of thin marine shales overlain by extensive, thick regressive limestones, whereas HSTs from relatively wetter climates are dominated by thick marine shales. Previously documented relative sea-level changes do not track the climate cycles, indicating that climate played a role distinct from that of relative sea-level change. These intermediate-scale modest climate shifts had a dominant impact on sequence architecture. This independent measure of climate and relative sea level may allow the testing of models of climate and sediment supply based on modern systems. Copyright ?? 2005, SEPM.

Graphics modelling of non-contact thickness measuring robotics work cell

NASA Technical Reports Server (NTRS)

Warren, Charles W.

1990-01-01

A system was developed for measuring, in real time, the thickness of a sprayable insulation during its application. The system was graphically modelled, off-line, using a state-of-the-art graphics workstation and associated software. This model was to contain a 3D color model of a workcell containing a robot and an air bearing turntable. A communication link was established between the graphics workstations and the robot's controller. Sequences of robot motion generated by the computer simulation are transmitted to the robot for execution.

Hardware for dynamic quantum computing experiments: Part I

NASA Astrophysics Data System (ADS)

Johnson, Blake; Ryan, Colm; Riste, Diego; Donovan, Brian; Ohki, Thomas

Static, pre-defined control sequences routinely achieve high-fidelity operation on superconducting quantum processors. Efforts toward dynamic experiments depending on real-time information have mostly proceeded through hardware duplication and triggers, requiring a combinatorial explosion in the number of channels. We provide a hardware efficient solution to dynamic control with a complete platform of specialized FPGA-based control and readout electronics; these components enable arbitrary control flow, low-latency feedback and/or feedforward, and scale far beyond single-qubit control and measurement. We will introduce the BBN Arbitrary Pulse Sequencer 2 (APS2) control system and the X6 QDSP readout platform. The BBN APS2 features: a sequencer built around implementing short quantum gates, a sequence cache to allow long sequences with branching structures, subroutines for code re-use, and a trigger distribution module to capture and distribute steering information. The X6 QDSP features a single-stage DSP pipeline that combines demodulation with arbitrary integration kernels, and multiple taps to inspect data flow for debugging and calibration. We will show system performance when putting it all together, including a latency budget for feedforward operations. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Contract No. W911NF-10-1-0324.

X-Raying the Coronae of HD 155555

NASA Technical Reports Server (NTRS)

Lalitha, S.; Singh, K.P.; Drake, S. A.; Kashyap, V.

2015-01-01

We present an analysis of the high-resolution Chandra observation of the multiple system, HD 155555 (an RS CVn type binary system, HD 155555 AB, and its spatially resolved low-mass companion HD 155555 C). This is an intriguing system which shows properties of both an active pre-main sequence star and a synchronised (main sequence) binary. We obtain the emission measure distribution, temperature structures, plasma densities, and abundances of this system and compare them with the coronal properties of other young/active stars. HD 155555 AB and HD 155555 C produce copious X-ray emission with log L(sub x) of 30.54 and 29.30, respectively, in the 0.3-6.0 kiloelectronvolt energy band. The light curves of individual stars show variability on timescales of few minutes to hours. We analyse the dispersed spectra and reconstruct the emission measure distribution using spectral line analysis. The resulting elemental abundances exhibit inverse first ionisation potential effect in both cases. An analysis of He-like triplets yields a range of coronal electron densities 1010 - 1013 per cubic centimeter. Since HD 155555 AB is classified both as an RS CVn and a PMS star, we compare our results with those of other slightly older active main-sequence stars and T Tauri stars, which indicates that the coronal properties of HD 155555 AB closely resemble that of an older RS CVn binary rather than a younger PMS star. Our results also suggests that the properties of HD 155555 C is very similar to those of other active M dwarfs.

An SSVEP-actuated brain computer interface using phase-tagged flickering sequences: a cursor system.

PubMed

Lee, Po-Lei; Sie, Jyun-Jie; Liu, Yu-Ju; Wu, Chi-Hsun; Lee, Ming-Huan; Shu, Chih-Hung; Li, Po-Hung; Sun, Chia-Wei; Shyu, Kuo-Kai

2010-07-01

This study presents a new steady-state visual evoked potential (SSVEP)-based brain computer interface (BCI). SSVEPs, induced by phase-tagged flashes in eight light emitting diodes (LEDs), were used to control four cursor movements (up, right, down, and left) and four button functions (on, off, right-, and left-clicks) on a screen menu. EEG signals were measured by one EEG electrode placed at Oz position, referring to the international EEG 10-20 system. Since SSVEPs are time-locked and phase-locked to the onsets of SSVEP flashes, EEG signals were bandpass-filtered and segmented into epochs, and then averaged across a number of epochs to sharpen the recorded SSVEPs. Phase lags between the measured SSVEPs and a reference SSVEP were measured, and targets were recognized based on these phase lags. The current design used eight LEDs to flicker at 31.25 Hz with 45 degrees phase margin between any two adjacent SSVEP flickers. The SSVEP responses were filtered within 29.25-33.25 Hz and then averaged over 60 epochs. Owing to the utilization of high-frequency flickers, the induced SSVEPs were away from low-frequency noises, 60 Hz electricity noise, and eye movement artifacts. As a consequence, we achieved a simple architecture that did not require eye movement monitoring or other artifact detection and removal. The high-frequency design also achieved a flicker fusion effect for better visualization. Seven subjects were recruited in this study to sequentially input a command sequence, consisting of a sequence of eight cursor functions, repeated three times. The accuracy and information transfer rate (mean +/- SD) over the seven subjects were 93.14 +/- 5.73% and 28.29 +/- 12.19 bits/min, respectively. The proposed system can provide a reliable channel for severely disabled patients to communicate with external environments.

A Fuzzy Aproach For Facial Emotion Recognition

NASA Astrophysics Data System (ADS)

Gîlcă, Gheorghe; Bîzdoacă, Nicu-George

2015-09-01

This article deals with an emotion recognition system based on the fuzzy sets. Human faces are detected in images with the Viola - Jones algorithm and for its tracking in video sequences we used the Camshift algorithm. The detected human faces are transferred to the decisional fuzzy system, which is based on the variable fuzzyfication measurements of the face: eyebrow, eyelid and mouth. The system can easily determine the emotional state of a person.

Measurement Marker Recognition In A Time Sequence Of Infrared Images For Biomedical Applications

NASA Astrophysics Data System (ADS)

Fiorini, A. R.; Fumero, R.; Marchesi, R.

1986-03-01

In thermographic measurements, quantitative surface temperature evaluation is often uncertain. The main reason is in the lack of available reference points in transient conditions. Reflective markers were used for automatic marker recognition and pixel coordinate computations. An algorithm selects marker icons to match marker references where particular luminance conditions are satisfied. Automatic marker recognition allows luminance compensation and temperature calibration of recorded infrared images. A biomedical application is presented: the dynamic behaviour of the surface temperature distributions is investigated in order to study the performance of two different pumping systems for extracorporeal circulation. Sequences of images are compared and results are discussed. Finally, the algorithm allows to monitor the experimental environment and to alert for the presence of unusual experimental conditions.

Simultaneously measuring multiple protein interactions and their correlations in a cell by Protein-interactome Footprinting

PubMed Central

Luo, Si-Wei; Liang, Zhi; Wu, Jia-Rui

2017-01-01

Quantitatively detecting correlations of multiple protein-protein interactions (PPIs) in vivo is a big challenge. Here we introduce a novel method, termed Protein-interactome Footprinting (PiF), to simultaneously measure multiple PPIs in one cell. The principle of PiF is that each target physical PPI in the interactome is simultaneously transcoded into a specific DNA sequence based on dimerization of the target proteins fused with DNA-binding domains. The interaction intensity of each target protein is quantified as the copy number of the specific DNA sequences bound by each fusion protein dimers. Using PiF, we quantitatively reveal dynamic patterns of PPIs and their correlation network in E. coli two-component systems. PMID:28338015

Fiber Optic Rosette Strain Gauge Development and Application on a Large-Scale Composite Structure

NASA Technical Reports Server (NTRS)

Moore, Jason P.; Przekop, Adam; Juarez, Peter D.; Roth, Mark C.

2015-01-01

A detailed description of the construction, application, and measurement of 196 FO rosette strain gauges that measured multi-axis strain across the outside upper surface of the forward bulkhead component of a multibay composite fuselage test article is presented. A background of the FO strain gauge and the FO measurement system as utilized in this application is given and results for the higher load cases of the testing sequence are shown.

Rapid Polymer Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

2013-01-01

Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

Noise and drift analysis of non-equally spaced timing data

NASA Technical Reports Server (NTRS)

Vernotte, F.; Zalamansky, G.; Lantz, E.

1994-01-01

Generally, it is possible to obtain equally spaced timing data from oscillators. The measurement of the drifts and noises affecting oscillators is then performed by using a variance (Allan variance, modified Allan variance, or time variance) or a system of several variances (multivariance method). However, in some cases, several samples, or even several sets of samples, are missing. In the case of millisecond pulsar timing data, for instance, observations are quite irregularly spaced in time. Nevertheless, since some observations are very close together (one minute) and since the timing data sequence is very long (more than ten years), information on both short-term and long-term stability is available. Unfortunately, a direct variance analysis is not possible without interpolating missing data. Different interpolation algorithms (linear interpolation, cubic spline) are used to calculate variances in order to verify that they neither lose information nor add erroneous information. A comparison of the results of the different algorithms is given. Finally, the multivariance method was adapted to the measurement sequence of the millisecond pulsar timing data: the responses of each variance of the system are calculated for each type of noise and drift, with the same missing samples as in the pulsar timing sequence. An estimation of precision, dynamics, and separability of this method is given.

An improved model for whole genome phylogenetic analysis by Fourier transform.

PubMed

Yin, Changchuan; Yau, Stephen S-T

2015-10-07

DNA sequence similarity comparison is one of the major steps in computational phylogenetic studies. The sequence comparison of closely related DNA sequences and genomes is usually performed by multiple sequence alignments (MSA). While the MSA method is accurate for some types of sequences, it may produce incorrect results when DNA sequences undergone rearrangements as in many bacterial and viral genomes. It is also limited by its computational complexity for comparing large volumes of data. Previously, we proposed an alignment-free method that exploits the full information contents of DNA sequences by Discrete Fourier Transform (DFT), but still with some limitations. Here, we present a significantly improved method for the similarity comparison of DNA sequences by DFT. In this method, we map DNA sequences into 2-dimensional (2D) numerical sequences and then apply DFT to transform the 2D numerical sequences into frequency domain. In the 2D mapping, the nucleotide composition of a DNA sequence is a determinant factor and the 2D mapping reduces the nucleotide composition bias in distance measure, and thus improving the similarity measure of DNA sequences. To compare the DFT power spectra of DNA sequences with different lengths, we propose an improved even scaling algorithm to extend shorter DFT power spectra to the longest length of the underlying sequences. After the DFT power spectra are evenly scaled, the spectra are in the same dimensionality of the Fourier frequency space, then the Euclidean distances of full Fourier power spectra of the DNA sequences are used as the dissimilarity metrics. The improved DFT method, with increased computational performance by 2D numerical representation, can be applicable to any DNA sequences of different length ranges. We assess the accuracy of the improved DFT similarity measure in hierarchical clustering of different DNA sequences including simulated and real datasets. The method yields accurate and reliable phylogenetic trees and demonstrates that the improved DFT dissimilarity measure is an efficient and effective similarity measure of DNA sequences. Due to its high efficiency and accuracy, the proposed DFT similarity measure is successfully applied on phylogenetic analysis for individual genes and large whole bacterial genomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.

PubMed

Smola, Matthew J; Rice, Greggory M; Busan, Steven; Siegfried, Nathan A; Weeks, Kevin M

2015-11-01

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small electrophilic reagents that react with 2'-hydroxyl groups to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues by using reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as can be done for simple model RNAs. This protocol describes the experimental steps, implemented over 3 d, that are required to perform SHAPE probing and to construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots and provides useful troubleshooting information. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures and visualize probable and alternative helices, often in under 1 d. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and entire transcriptomes.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2004-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2003-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, premain sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we developed much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measured disk accretion rates in these systems; and constructed detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

ODIN-object-oriented development interface for NMR.

PubMed

Jochimsen, Thies H; von Mengershausen, Michael

2004-09-01

A cross-platform development environment for nuclear magnetic resonance (NMR) experiments is presented. It allows rapid prototyping of new pulse sequences and provides a common programming interface for different system types. With this object-oriented interface implemented in C++, the programmer is capable of writing applications to control an experiment that can be executed on different measurement devices, even from different manufacturers, without the need to modify the source code. Due to the clear design of the software, new pulse sequences can be created, tested, and executed within a short time. To post-process the acquired data, an interface to well-known numerical libraries is part of the framework. This allows a transparent integration of the data processing instructions into the measurement module. The software focuses mainly on NMR imaging, but can also be used with limitations for spectroscopic experiments. To demonstrate the capabilities of the framework, results of the same experiment, carried out on two NMR imaging systems from different manufacturers are shown and compared with the results of a simulation.

Cross species analysis of microarray expression data

PubMed Central

Lu, Yong; Huggins, Peter; Bar-Joseph, Ziv

2009-01-01

Motivation: Many biological systems operate in a similar manner across a large number of species or conditions. Cross-species analysis of sequence and interaction data is often applied to determine the function of new genes. In contrast to these static measurements, microarrays measure the dynamic, condition-specific response of complex biological systems. The recent exponential growth in microarray expression datasets allows researchers to combine expression experiments from multiple species to identify genes that are not only conserved in sequence but also operated in a similar way in the different species studied. Results: In this review we discuss the computational and technical challenges associated with these studies, the approaches that have been developed to address these challenges and the advantages of cross-species analysis of microarray data. We show how successful application of these methods lead to insights that cannot be obtained when analyzing data from a single species. We also highlight current open problems and discuss possible ways to address them. Contact: zivbj@cs.cmu.edu PMID:19357096

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.

Sequence-Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies.

PubMed

Harris, Katherine E; Aldred, Shelley Force; Davison, Laura M; Ogana, Heather Anne N; Boudreau, Andrew; Brüggemann, Marianne; Osborn, Michael; Ma, Biao; Buelow, Benjamin; Clarke, Starlynn C; Dang, Kevin H; Iyer, Suhasini; Jorgensen, Brett; Pham, Duy T; Pratap, Payal P; Rangaswamy, Udaya S; Schellenberger, Ute; van Schooten, Wim C; Ugamraj, Harshad S; Vafa, Omid; Buelow, Roland; Trinklein, Nathan D

2018-01-01

We created a novel transgenic rat that expresses human antibodies comprising a diverse repertoire of heavy chains with a single common rearranged kappa light chain (IgKV3-15-JK1). This fixed light chain animal, called OmniFlic, presents a unique system for human therapeutic antibody discovery and a model to study heavy chain repertoire diversity in the context of a constant light chain. The purpose of this study was to analyze heavy chain variable gene usage, clonotype diversity, and to describe the sequence characteristics of antigen-specific monoclonal antibodies (mAbs) isolated from immunized OmniFlic animals. Using next-generation sequencing antibody repertoire analysis, we measured heavy chain variable gene usage and the diversity of clonotypes present in the lymph node germinal centers of 75 OmniFlic rats immunized with 9 different protein antigens. Furthermore, we expressed 2,560 unique heavy chain sequences sampled from a diverse set of clonotypes as fixed light chain antibody proteins and measured their binding to antigen by ELISA. Finally, we measured patterns and overall levels of somatic hypermutation in the full B-cell repertoire and in the 2,560 mAbs tested for binding. The results demonstrate that OmniFlic animals produce an abundance of antigen-specific antibodies with heavy chain clonotype diversity that is similar to what has been described with unrestricted light chain use in mammals. In addition, we show that sequence-based discovery is a highly effective and efficient way to identify a large number of diverse monoclonal antibodies to a protein target of interest.

Time-of-flight radio location system

DOEpatents

McEwan, T.E.

1996-04-23

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. 7 figs.

Time-of-flight radio location system

DOEpatents

McEwan, Thomas E.

1996-01-01

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence.

Nonclassicality of Temporal Correlations.

PubMed

Brierley, Stephen; Kosowski, Adrian; Markiewicz, Marcin; Paterek, Tomasz; Przysiężna, Anna

2015-09-18

The results of spacelike separated measurements are independent of distant measurement settings, a property one might call two-way no-signaling. In contrast, timelike separated measurements are only one-way no-signaling since the past is independent of the future but not vice versa. For this reason some temporal correlations that are formally identical to nonclassical spatial correlations can still be modeled classically. We propose a new formulation of Bell's theorem for temporal correlations; namely, we define nonclassical temporal correlations as the ones which cannot be simulated by propagating in time the classical information content of a quantum system given by the Holevo bound. We first show that temporal correlations between results of any projective quantum measurements on a qubit can be simulated classically. Then we present a sequence of general measurements on a single m-level quantum system that cannot be explained by propagating in time an m-level classical system and using classical computers with unlimited memory.

Cloud-based adaptive exon prediction for DNA analysis.

PubMed

Putluri, Srinivasareddy; Zia Ur Rahman, Md; Fathima, Shaik Yasmeen

2018-02-01

Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing. True identification of exon regions in a DNA sequence is a key task in bioinformatics, which helps in disease identification and design drugs. Three base periodicity property of exons forms the basis of all exon identification techniques. Adaptive signal processing techniques found to be promising in comparison with several other methods. Several adaptive exon predictors (AEPs) are developed using variable normalised least mean square and its maximum normalised variants to reduce computational complexity. Finally, performance evaluation of various AEPs is done based on measures such as sensitivity, specificity and precision using various standard genomic datasets taken from National Center for Biotechnology Information genomic sequence database.

NASBA: A detection and amplification system uniquely suited for RNA

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

Sooknanan, R.; Malek, L.T.

1995-06-01

The invention of PCR (polymerase chain reaction) has revolutionized our ability to amplify and manipulate a nucleic acid sequence in vitro. The commercial rewards of this revolution have driven the development of other nuclei acid amplification and detection methodologies. This has created an alphabet soup of technologies that use different amplification methods, including NASBA (nucleic acid sequence-based amplification), LCR (ligase chain reaction), SDA (strand displacement amplification), QBR (Q-beta replicase), CPR (cycling probe reaction), and bDNA (branched DNA). Despite the differences in their processes, these amplification systems can be separated into two broad categories based on how they achieve their goal:more » sequence-based amplification systems, such as PCR, NASBA, and SDA, amplify a target nucleic acid sequence. Signal-based amplification systems, such as LCR, QBR, CPR and bDNA, amplify or alter a signal from a detection reaction that is target-dependent. While the various methods have relative strengths and weaknesses, only NASBA offers the unique ability to homogeneously amplify an RNA analyte in the presence of homologous genomic DNA under isothermal conditions. Since the detection of RNA sequences almost invariably measures biological activity, it is an excellent prognostic indicator of activities as diverse as virus production, gene expression, and cell viability. The isothermal nature of the reaction makes NASBA especially suitable for large-scale manual screening. These features extend NASBA`s application range from research to commercial diagnostic applications. Field test kits are presently under development for human diagnostics as well as the burgeoning fields of food and environmental diagnostic testing. These developments suggest future integration of NASBA into robotic workstations for high-throughput screening as well. 17 refs., 1 tab.« less

Theory and practical application of out of sequence measurements with results for multi-static tracking

NASA Astrophysics Data System (ADS)

Iny, David

2007-09-01

This paper addresses the out-of-sequence measurement (OOSM) problem associated with multiple platform tracking systems. The problem arises due to different transmission delays in communication of detection reports across platforms. Much of the literature focuses on the improvement to the state estimate by incorporating the OOSM. As the time lag increases, there is diminishing improvement to the state estimate. However, this paper shows that optimal processing of OOSMs may still be beneficial by improving data association as part of a multi-target tracker. This paper derives exact multi-lag algorithms with the property that the standard log likelihood track scoring is independent of the order in which the measurements are processed. The orthogonality principle is applied to generalize the method of Bar- Shalom in deriving the exact A1 algorithm for 1-lag estimation. Theory is also developed for optimal filtering of time averaged measurements and measurements correlated through periodic updates of a target aim-point. An alternative derivation of the multi-lag algorithms is also achieved using an efficient variant of the augmented state Kalman filter (AS-KF). This results in practical and reasonably efficient multi-lag algorithms. Results are compared to a well known ad hoc algorithm for incorporating OOSMs. Finally, the paper presents some simulated multi-target multi-static scenarios where there is a benefit to processing the data out of sequence in order to improve pruning efficiency.

Concurrent validity of the Microsoft Kinect for Windows v2 for measuring spatiotemporal gait parameters.

PubMed

Dolatabadi, Elham; Taati, Babak; Mihailidis, Alex

2016-09-01

This paper presents a study to evaluate the concurrent validity of the Microsoft Kinect for Windows v2 for measuring the spatiotemporal parameters of gait. Twenty healthy adults performed several sequences of walks across a GAITRite mat under three different conditions: usual pace, fast pace, and dual task. Each walking sequence was simultaneously captured with two Kinect for Windows v2 and the GAITRite system. An automated algorithm was employed to extract various spatiotemporal features including stance time, step length, step time and gait velocity from the recorded Kinect v2 sequences. Accuracy in terms of reliability, concurrent validity and limits of agreement was examined for each gait feature under different walking conditions. The 95% Bland-Altman limits of agreement were narrow enough for the Kinect v2 to be a valid tool for measuring all reported spatiotemporal parameters of gait in all three conditions. An excellent intraclass correlation coefficient (ICC2, 1) ranging from 0.9 to 0.98 was observed for all gait measures across different walking conditions. The inter trial reliability of all gait parameters were shown to be strong for all walking types (ICC3, 1 > 0.73). The results of this study suggest that the Kinect for Windows v2 has the capacity to measure selected spatiotemporal gait parameters for healthy adults. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

A low-cost spectrometer for NMR measurements in the Earth's magnetic field

NASA Astrophysics Data System (ADS)

Michal, Carl A.

2010-10-01

We describe and demonstrate an inexpensive, easy-to-build, portable spectrometer for nuclear magnetic resonance measurements in the Earth's magnetic field. The spectrometer is based upon a widely available inexpensive microcontroller, which acts as a pulse programmer, audio-frequency synthesizer and digitizer, replacing what are typically the most expensive specialized components of the system. The microcontroller provides the capability to execute arbitrarily long and complicated sequences of phase-coherent, phase-modulated excitation pulses and acquire data sets of unlimited duration. Suitably packaged, the spectrometer is amenable to measurements in the research lab, in the field or in the teaching lab. The choice of components was heavily weighted by cost and availability, but required no significant sacrifice in performance. Using an existing personal computer, the resulting design can be assembled for as little as US200. The spectrometer performance is demonstrated with spin-echo and Carr-Purcell-Meiboom-Gill pulse sequences on a water sample.

A Module Experimental Process System Development Unit (MEPSDU)

NASA Technical Reports Server (NTRS)

1981-01-01

The purpose of this program is to demonstrate the technical readiness of a cost effective process sequence that has the potential for the production of flat plate photovoltaic modules which met the price goal in 1986 of $.70 or less per watt peak. Program efforts included: preliminary design review, preliminary cell fabrication using the proposed process sequence, verification of sandblasting back cleanup, study of resist parameters, evaluation of pull strength of the proposed metallization, measurement of contact resistance of Electroless Ni contacts, optimization of process parameter, design of the MEPSDU module, identification and testing of insulator tapes, development of a lamination process sequence, identification, discussions, demonstrations and visits with candidate equipment vendors, evaluation of proposals for tabbing and stringing machine.

Longitudinal diffusion MRI for treatment response assessment: Preliminary experience using an MRI-guided tri-cobalt 60 radiotherapy system.

PubMed

Yang, Yingli; Cao, Minsong; Sheng, Ke; Gao, Yu; Chen, Allen; Kamrava, Mitch; Lee, Percy; Agazaryan, Nzhde; Lamb, James; Thomas, David; Low, Daniel; Hu, Peng

2016-03-01

To demonstrate the preliminary feasibility of a longitudinal diffusion magnetic resonance imaging (MRI) strategy for assessing patient response to radiotherapy at 0.35 T using an MRI-guided radiotherapy system (ViewRay). Six patients (three head and neck cancer, three sarcoma) who underwent fractionated radiotherapy were enrolled in this study. A 2D multislice spin echo single-shot echo planar imaging diffusion pulse sequence was implemented on the ViewRay system and tested in phantom studies. The same pulse sequence was used to acquire longitudinal diffusion data (every 2-5 fractions) on the six patients throughout the entire course of radiotherapy. The reproducibility of the apparent diffusion coefficient (ADC) measurements was assessed using reference regions and the temporal variations of the tumor ADC values were evaluated. In diffusion phantom studies, the ADC values measured on the ViewRay system matched well with reference ADC values with <5% error for a range of ground truth diffusion coefficients of 0.4-1.1 × 10(-3) mm(2)/s. The remote reference regions (i.e., brainstem in head and neck patients) had consistent ADC values throughout the therapy for all three head and neck patients, indicating acceptable reproducibility of the diffusion imaging sequence. The tumor ADC values changed throughout therapy, with the change differing between patients, ranging from a 40% drop in ADC within the first week of therapy to gradually increasing throughout therapy. For larger tumors, intratumoral heterogeneity was observed. For one sarcoma patient, postradiotherapy biopsy showed less than 10% necrosis score, which correlated with the observed 40% decrease in ADC from the fifth fraction to the eighth treatment fraction. This pilot study demonstrated that longitudinal diffusion MRI is feasible using the 0.35 T ViewRay MRI. Larger patient cohort studies are warranted to correlate the longitudinal diffusion measurements to patient outcomes. Such an approach may enable response-guided adaptive radiotherapy.

Real Time Apnoea Monitoring of Children Using the Microsoft Kinect Sensor: A Pilot Study.

PubMed

Al-Naji, Ali; Gibson, Kim; Lee, Sang-Heon; Chahl, Javaan

2017-02-03

The objective of this study was to design a non-invasive system for the observation of respiratory rates and detection of apnoea using analysis of real time image sequences captured in any given sleep position and under any light conditions (even in dark environments). A Microsoft Kinect sensor was used to visualize the variations in the thorax and abdomen from the respiratory rhythm. These variations were magnified, analyzed and detected at a distance of 2.5 m from the subject. A modified motion magnification system and frame subtraction technique were used to identify breathing movements by detecting rapid motion areas in the magnified frame sequences. The experimental results on a set of video data from five subjects (3 h for each subject) showed that our monitoring system can accurately measure respiratory rate and therefore detect apnoea in infants and young children. The proposed system is feasible, accurate, safe and low computational complexity, making it an efficient alternative for non-contact home sleep monitoring systems and advancing health care applications.

Orbital Motion of Young Binaries in Ophiuchus and Upper Centaurus–Lupus

NASA Astrophysics Data System (ADS)

Schaefer, G. H.; Prato, L.; Simon, M.

2018-03-01

We present measurements of the orbital positions and flux ratios of 17 binary and triple systems in the Ophiuchus star-forming region and the Upper Centaurus–Lupus cluster based on adaptive optics imaging at the Keck Observatory. We report the detection of visual companions in MML 50 and MML 53 for the first time, as well as the possible detection of a third component in WSB 21. For six systems in our sample, our measurements provide a second orbital position following their initial discoveries over a decade ago. For eight systems with sufficient orbital coverage, we analyze the range of orbital solutions that fit the data. Ultimately, these observations will help provide the groundwork toward measuring precise masses for these pre-main-sequence stars and understanding the distribution of orbital parameters in young multiple systems.

Sequence stratigraphy of upper Paleogene to Neogene carbonates exposed from Guánica bay to Guayanilla, Southern Puerto Rico.

NASA Astrophysics Data System (ADS)

Flores Hots, V. E.; Santos, H.

2016-12-01

Detailed stratigraphic columns were measured and microfacies analysis was performed in southwestern Puerto Rico to conduct a sequence stratigraphic analysis of Paleogene to Neogene strata. Two of the best exposed outcrops include the Guánica Bay and outcrops along Highway PR-132 in Guayanilla. Three depositional sequences, separated by two major sequence boundaries were found. The lower sequence occurs within the Juana Díaz Formation and is an open shelf to reef facies indicative of a Transgressive System Tract (TST), that is overlain by a High Stand System Tract (HST) marked by reef progradation. The HST in both Guánica Bay and Guayanilla is characterized by coral-rhodolith cyclicity however sections in Guánica Bay show pervasive recrystallization due to diagenetic alteration as a result of a long periods of exposure. This first sequence is Oligocene in age. The middle sequence, exposed at the eastern section of the Guánica Bay is also part of the Juana Díaz Formation and includes a turbiditic Lowstand System Tract (LST) of slope-like deposits flow, a TST constituted by coral rubble and skeletal grainstones belonging to a shallow island slope environment; and a HST that consists of an island slope chalk facies intercalated with turbidite grainstones derived storm events at the Guayanilla location. During the deposition of the middle sequence the Guánica Bay west section was topographically higher and exposed. The upper depositional sequence is Miocene in age and is composed of a TST with the transgression starting distally in the Guánica area and transgressing northward toward the Guayanilla area. These was correlated using high resolution 87Sr/86Sr isotope concentrations of shallow marine mollusks Kuphus incrassatus in the Ponce Formation at the Guánica Bay and Guayanilla locations. Facies patterns like the ones in the studied outcrops of southwestern Puerto Rico provide an exemplary environmental model of variability of paleodepositional relief, tectonic setting, variability in depositional setting of reef Sediment acumulations, the influence of storm events and variability in rock porosity by diagenetic processes yielding valuable models that may apply to potential Oligocene - Miocene hydrocarbon reservoirs.

Differentiating Visual from Response Sequencing during Long-term Skill Learning.

PubMed

Lynch, Brighid; Beukema, Patrick; Verstynen, Timothy

2017-01-01

The dual-system model of sequence learning posits that during early learning there is an advantage for encoding sequences in sensory frames; however, it remains unclear whether this advantage extends to long-term consolidation. Using the serial RT task, we set out to distinguish the dynamics of learning sequential orders of visual cues from learning sequential responses. On each day, most participants learned a new mapping between a set of symbolic cues and responses made with one of four fingers, after which they were exposed to trial blocks of either randomly ordered cues or deterministic ordered cues (12-item sequence). Participants were randomly assigned to one of four groups (n = 15 per group): Visual sequences (same sequence of visual cues across training days), Response sequences (same order of key presses across training days), Combined (same serial order of cues and responses on all training days), and a Control group (a novel sequence each training day). Across 5 days of training, sequence-specific measures of response speed and accuracy improved faster in the Visual group than any of the other three groups, despite no group differences in explicit awareness of the sequence. The two groups that were exposed to the same visual sequence across days showed a marginal improvement in response binding that was not found in the other groups. These results indicate that there is an advantage, in terms of rate of consolidation across multiple days of training, for learning sequences of actions in a sensory representational space, rather than as motoric representations.

Thermal imaging for cold air flow visualisation and analysis

NASA Astrophysics Data System (ADS)

Grudzielanek, M.; Pflitsch, A.; Cermak, J.

2012-04-01

In this work we present first applications of a thermal imaging system for animated visualization and analysis of cold air flow in field studies. The development of mobile thermal imaging systems advanced very fast in the last decades. The surface temperature of objects, which is detected with long-wave infrared radiation, affords conclusions in different problems of research. Modern thermal imaging systems allow infrared picture-sequences and a following data analysis; the systems are not exclusive imaging methods like in the past. Thus, the monitoring and analysing of dynamic processes became possible. We measured the cold air flow on a sloping grassland area with standard methods (sonic anemometers and temperature loggers) plus a thermal imaging system measuring in the range from 7.5 to 14µm. To analyse the cold air with the thermal measurements, we collected the surface infrared temperatures at a projection screen, which was located in cold air flow direction, opposite the infrared (IR) camera. The intention of using a thermal imaging system for our work was: 1. to get a general idea of practicability in our problem, 2. to assess the value of the extensive and more detailed data sets and 3. to optimise visualisation. The results were very promising. Through the possibility of generating time-lapse movies of the image sequences in time scaling, processes of cold air flow, like flow waves, turbulence and general flow speed, can be directly identified. Vertical temperature gradients and near-ground inversions can be visualised very well. Time-lapse movies will be presented. The extensive data collection permits a higher spatial resolution of the data than standard methods, so that cold air flow attributes can be explored in much more detail. Time series are extracted from the IR data series, analysed statistically, and compared to data obtained using traditional systems. Finally, we assess the usefulness of the additional measurement of cold air flow with thermal imaging systems.

Using the VentCam and Optical Plume Velocimetry to Measure High-Temperature Hydrothermal Fluid Flow Rates in the ASHES Vent Field on Axial Volcano

NASA Astrophysics Data System (ADS)

Crone, T. J.; Mittelstaedt, E. L.; Fornari, D. J.

2014-12-01

Fluid flow rates through high-temperature mid-ocean ridge hydrothermal vents are likely quite sensitive to poroelastic forcing mechanisms such as tidal loading and tectonic activity. Because poroelastic deformation and flow perturbations are estimated to extend to considerable depths within young oceanic crust, observations of flow rate changes at seafloor vents have the potential to provide constraints on the flow geometry and permeability structure of the underlying hydrothermal systems, as well as the quantities of heat and chemicals they exchange with overlying ocean, and the potential biological productivity of ecosystems they host. To help provide flow rate measurements in these challenging environments, we have developed two new optical flow oriented technologies. The first is a new form of Optical Plume Velocimetry (OPV) which relies on single-frame temporal cross-correlation to obtain time-averaged image velocity fields from short video sequences. The second is the VentCam, a deep sea camera system that can collect high-frame-rate video sequences at focused hydrothermal vents suitable for analysis with OPV. During the July 2014 R/V Atlantis/Alvin expedition to Axial Seamount, we deployed the VentCam at the ~300C Phoenix vent within the ASHES vent field and positioned it with DSRV Alvin. We collected 24 seconds of video at 50 frames per second every half-hour for approximately 10 days beginning July 22nd. We are currently applying single-frame lag OPV to these videos to estimate relative and absolute fluid flow rates through this vent. To explore the relationship between focused and diffuse venting, we deployed a second optical flow camera, the Diffuse Effluent Measurement System (DEMS), adjacent to this vent at a fracture within the lava carapace where low-T (~30C) fluids were exiting. This system collected video sequences and diffuse flow measurements at overlapping time intervals. Here we present the preliminary results of our work with VentCam and OPV, and comparisons with results from the DEMS camera.

Multirate and event-driven Kalman filters for helicopter flight

NASA Technical Reports Server (NTRS)

Sridhar, Banavar; Smith, Phillip; Suorsa, Raymond E.; Hussien, Bassam

1993-01-01

A vision-based obstacle detection system that provides information about objects as a function of azimuth and elevation is discussed. The range map is computed using a sequence of images from a passive sensor, and an extended Kalman filter is used to estimate range to obstacles. The magnitude of the optical flow that provides measurements for each Kalman filter varies significantly over the image depending on the helicopter motion and object location. In a standard Kalman filter, the measurement update takes place at fixed intervals. It may be necessary to use a different measurement update rate in different parts of the image in order to maintain the same signal to noise ratio in the optical flow calculations. A range estimation scheme that accepts the measurement only under certain conditions is presented. The estimation results from the standard Kalman filter are compared with results from a multirate Kalman filter and an event-driven Kalman filter for a sequence of helicopter flight images.

Generalized entropy production fluctuation theorems for quantum systems

NASA Astrophysics Data System (ADS)

Rana, Shubhashis; Lahiri, Sourabh; Jayannavar, A. M.

2013-02-01

Based on trajectory dependent path probability formalism in state space, we derive generalized entropy production fluctuation relations for a quantum system in the presence of measurement and feedback. We have obtained these results for three different cases: (i) the system is evolving in isolation from its surroundings; (ii) the system being weakly coupled to a heat bath; and (iii) system in contact with reservoir using quantum Crooks fluctuation theorem. In case (iii), we build on the treatment carried out in [H. T. Quan and H. Dong, arxiv/cond-mat: 0812.4955], where a quantum trajectory has been defined as a sequence of alternating work and heat steps. The obtained entropy production fluctuation theorems retain the same form as in the classical case. The inequality of second law of thermodynamics gets modified in the presence of information. These fluctuation theorems are robust against intermediate measurements of any observable performed with respect to von Neumann projective measurements as well as weak or positive operator valued measurements.

Influence of spatial and temporal spot distribution on the ocular surface quality and maximum ablation depth after photoablation with a 1050 Hz excimer laser system.

PubMed

Mrochen, Michael; Schelling, Urs; Wuellner, Christian; Donitzky, Christof

2009-02-01

To investigate the effect of temporal and spatial distributions of laser spots (scan sequences) on the corneal surface quality after ablation and the maximum ablation of a given refractive correction after photoablation with a high-repetition-rate scanning-spot laser. IROC AG, Zurich, Switzerland, and WaveLight AG, Erlangen, Germany. Bovine corneas and poly(methyl methacrylate) (PMMA) plates were photoablated using a 1050 Hz excimer laser prototype for corneal laser surgery. Four temporal and spatial spot distributions (scan sequences) with different temporal overlapping factors were created for 3 myopic, 3 hyperopic, and 3 phototherapeutic keratectomy ablation profiles. Surface quality and maximum ablation depth were measured using a surface profiling system. The surface quality factor increased (rough surfaces) as the amount of temporal overlapping in the scan sequence and the amount of correction increased. The rise in surface quality factor was less for bovine corneas than for PMMA. The scan sequence might cause systematic substructures at the surface of the ablated material depending on the overlapping factor. The maximum ablation varied within the scan sequence. The temporal and spatial distribution of the laser spots (scan sequence) during a corneal laser procedure affected the surface quality and maximum ablation depth of the ablation profile. Corneal laser surgery could theoretically benefit from smaller spot sizes and higher repetition rates. The temporal and spatial spot distributions are relevant to achieving these aims.

Problems in characterizing barrier performance

NASA Technical Reports Server (NTRS)

Jordan, Harry F.

1988-01-01

The barrier is a synchronization construct which is useful in separating a parallel program into parallel sections which are executed in sequence. The completion of a barrier requires cooperation among all executing processes. This requirement not only introduces the wait for the slowest process delay which is inherent in the definition of the synchronization, but also has implications for the efficient implementation and measurement of barrier performance in different systems. Types of barrier implementation and their relationship to different multiprocessor environments are described. Then the problem of measuring the performance of barrier implementations on specific machine architecture is discussed. The fact that the barrier synchronization requires the cooperation of all processes makes the problem of performance measurement similarly global. Making non-intrusive measurements of sufficient accuracy can be tricky on systems offering only rudimentary measurement tools.

Real-time, portable genome sequencing for Ebola surveillance

PubMed Central

Bore, Joseph Akoi; Koundouno, Raymond; Dudas, Gytis; Mikhail, Amy; Ouédraogo, Nobila; Afrough, Babak; Bah, Amadou; Baum, Jonathan HJ; Becker-Ziaja, Beate; Boettcher, Jan-Peter; Cabeza-Cabrerizo, Mar; Camino-Sanchez, Alvaro; Carter, Lisa L.; Doerrbecker, Juiliane; Enkirch, Theresa; Dorival, Isabel Graciela García; Hetzelt, Nicole; Hinzmann, Julia; Holm, Tobias; Kafetzopoulou, Liana Eleni; Koropogui, Michel; Kosgey, Abigail; Kuisma, Eeva; Logue, Christopher H; Mazzarelli, Antonio; Meisel, Sarah; Mertens, Marc; Michel, Janine; Ngabo, Didier; Nitzsche, Katja; Pallash, Elisa; Patrono, Livia Victoria; Portmann, Jasmine; Repits, Johanna Gabriella; Rickett, Natasha Yasmin; Sachse, Andrea; Singethan, Katrin; Vitoriano, Inês; Yemanaberhan, Rahel L; Zekeng, Elsa G; Trina, Racine; Bello, Alexander; Sall, Amadou Alpha; Faye, Ousmane; Faye, Oumar; Magassouba, N’Faly; Williams, Cecelia V.; Amburgey, Victoria; Winona, Linda; Davis, Emily; Gerlach, Jon; Washington, Franck; Monteil, Vanessa; Jourdain, Marine; Bererd, Marion; Camara, Alimou; Somlare, Hermann; Camara, Abdoulaye; Gerard, Marianne; Bado, Guillaume; Baillet, Bernard; Delaune, Déborah; Nebie, Koumpingnin Yacouba; Diarra, Abdoulaye; Savane, Yacouba; Pallawo, Raymond Bernard; Gutierrez, Giovanna Jaramillo; Milhano, Natacha; Roger, Isabelle; Williams, Christopher J; Yattara, Facinet; Lewandowski, Kuiama; Taylor, Jamie; Rachwal, Philip; Turner, Daniel; Pollakis, Georgios; Hiscox, Julian A.; Matthews, David A.; O’Shea, Matthew K.; Johnston, Andrew McD; Wilson, Duncan; Hutley, Emma; Smit, Erasmus; Di Caro, Antonino; Woelfel, Roman; Stoecker, Kilian; Fleischmann, Erna; Gabriel, Martin; Weller, Simon A.; Koivogui, Lamine; Diallo, Boubacar; Keita, Sakoba; Rambaut, Andrew; Formenty, Pierre; Gunther, Stephan; Carroll, Miles W.

2016-01-01

The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths 1. Genome sequencing in viral outbreaks is desirable in order to characterize the infectious agent to determine its evolutionary rate, signatures of host adaptation, identification and monitoring of diagnostic targets and responses to vaccines and treatments. The Ebola virus genome (EBOV) substitution rate in the Makona strain has been estimated at between 0.87 × 10−3 to 1.42 × 10−3 mutations per site per year. This is equivalent to 16 to 27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic 2-7. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought-after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions 8. Genomic surveillance during the epidemic has been sporadic due to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities 9. In order to address this problem, we devised a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. Here we present sequence data and analysis of 142 Ebola virus (EBOV) samples collected during the period March to October 2015. We were able to generate results in less than 24 hours after receiving an Ebola positive sample, with the sequencing process taking as little as 15-60 minutes. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks. PMID:26840485

The effects of the use of piezoelectric motors in a 1.5-Tesla high-field magnetic resonance imaging system (MRI).

PubMed

Wendt, O; Oellinger, J; Lüth, T C; Felix, R; Boenick, U

2000-01-01

This paper presents the results of an experimental investigation with two different rotatory piezomotors in a closed 1.5 Tesla high-field MRI. The focus of the investigation was on testing the functionality of these motors within the MRI and to determining the image interference they caused. To obtain a differentiated estimate of the interference the motors were tested in both the passive (turned off, i.e. without current flow) and active (turned on, i.e. with current flow) state during MRI scanning. Three different types of sequences were used for the test: Spin-Echo (SE), Gradient-Echo (GE) and Echo-Planar Imaging (EPI). A plastic container filled with a gadolinium-manganese solution was used for representation of the artefacts. The motors investigated were placed parallel to the container at predetermined distances during the experiment. The results show that the motors investigated suffered no functional limitations in the magnetic field of the MRI but, depending on the type of motor, the measurement distance and the state of the motor, the motors had different effects on the sequence images. A motor in the off-state placed immediately next to the object to be measured mainly causes artefacts because of its material properties. If, on the other hand, the piezomotor is in the on-state images with strong noise result when the motor is immediately next to the object being measured. The images regain their normal quality when the motor is approximately at a distance of 1 m from the object being investigated. Driving the motor inside the MRI, therefore, is only to be recommended during the pauses in scanning: this delivers artefact-free images if minimal, motor-specific distances are kept to. With regard to the three different types of sequences it was determined that the SE sequence was the least sensitive and the EPI sequence the most sensitive to disturbance. The GE sequence showed only minimal differences to the SE sequence with regard to signal-to-noise ratios. Since it requires considerably shorter scan-times it can be considered to be the most effective type of sequence under these conditions.

Three perspectives on complexity: entropy, compression, subsymmetry

NASA Astrophysics Data System (ADS)

Nagaraj, Nithin; Balasubramanian, Karthi

2017-12-01

There is no single universally accepted definition of `Complexity'. There are several perspectives on complexity and what constitutes complex behaviour or complex systems, as opposed to regular, predictable behaviour and simple systems. In this paper, we explore the following perspectives on complexity: effort-to-describe (Shannon entropy H, Lempel-Ziv complexity LZ), effort-to-compress (ETC complexity) and degree-of-order (Subsymmetry or SubSym). While Shannon entropy and LZ are very popular and widely used, ETC is relatively a new complexity measure. In this paper, we also propose a novel normalized complexity measure SubSym based on the existing idea of counting the number of subsymmetries or palindromes within a sequence. We compare the performance of these complexity measures on the following tasks: (A) characterizing complexity of short binary sequences of lengths 4 to 16, (B) distinguishing periodic and chaotic time series from 1D logistic map and 2D Hénon map, (C) analyzing the complexity of stochastic time series generated from 2-state Markov chains, and (D) distinguishing between tonic and irregular spiking patterns generated from the `Adaptive exponential integrate-and-fire' neuron model. Our study reveals that each perspective has its own advantages and uniqueness while also having an overlap with each other.

Stratigraphic evolution of the Late Jurassic Hanifa Formation along the Tuwaiq Escarpment, Saudi Arabia: Evidence for a carbonate ramp system

NASA Astrophysics Data System (ADS)

Fallatah, Mohammed I.; Kerans, Charles

2018-01-01

A sequence stratigraphic framework of the Late Jurassic (Oxfordian) Hanifa Formation at its exposure in Central Arabia is presented for the first time. This study offers the first high-resolution stratigraphic framework of the Hanifa along the Tuwaiq Escarpment by measuring 15 sections ( 770 m total thickness) over an oblique-to-dip distance of 260 km and collecting 295 samples for petrographic analysis. On the basis of these data, the Hanifa Formation can be subdivided into eight facies; 1) tabular cross-bedded quartz-peloidal-skeletal grainstone, 2) cross-bedded skeletal-peloidal grainstone, 3) bioturbated foraminiferal wackestone/mud-dominated packstone, 4) oncolitic rudstone, 5) stromatoporoid-coral biostrome/bioherm, 6) peloidal/composite-grain grain-dominated packstone/grainstone, 7) bioturbated spiculitic wackestone/mud-dominated packstone, and 8) thinly-bedded argillaceous mudstone/wackestone. The vertical and lateral distributions of these facies along the exposure define their sequence setting using the principals of sequence stratigraphy. By recognizing erosional surfaces, facies offset, and changes in facies proportions, five third-order sequences, with an average duration of 1.1 Myr, are interpreted for the Hanifa Formation. The correlation of the sequences across the study area shows that only four sequences are preserved in the north where shallow-water deposits are well-developed. Facies trends within these sequences are further illustrated in depositional models representing the highstand systems tracts (HST) and the transgressive systems tracts (TST) of the Hanifa Formation. These proposed models represent depositional settings of a carbonate ramp with normal open-marine conditions. The HST depositional model is characterized by a high-energy shoreline and depicts the presence of an offshore, structurally controlled skeletal-peloidal shoal body described here for the first time at the Hanifa exposure in the Hozwa area. This work provides a predictive framework and outcrop analog for applications in hydrocarbon exploration and development. Furthermore, a basinal setting predicted to the south of the study area is a potential site for unconventional plays.

New insights into phosphorus management in agriculture--A crop rotation approach.

PubMed

Łukowiak, Remigiusz; Grzebisz, Witold; Sassenrath, Gretchen F

2016-01-15

This manuscript presents research results examining phosphorus (P) management in a soil–plant system for three variables: i) internal resources of soil available phosphorus, ii) cropping sequence, and iii) external input of phosphorus (manure, fertilizers). The research was conducted in long-term cropping sequences with oilseed rape (10 rotations) and maize (six rotations) over three consecutive growing seasons (2004/2005, 2005/2006, and 2006/2007) in a production farm on soils originated from Albic Luvisols in Poland. The soil available phosphorus pool, measured as calcium chloride extractable P (CCE-P), constituted 28% to 67% of the total phosphorus input (PTI) to the soil–plant system in the spring. Oilseed rape and maize dominant cropping sequences showed a significant potential to utilize the CCE-P pool within the soil profile. Cropping sequences containing oilseed rape significantly affected the CCE-P pool, and in turn contributed to the P(TI). The P(TI) uptake use efficiency was 50% on average. Therefore, the CCE-P pool should be taken into account as an important component of a sound and reliable phosphorus balance. The instability of the yield prediction, based on the P(TI), was mainly due to an imbalanced management of both farmyard manure and phosphorus fertilizer. Oilseed rape plants provide a significant positive impact on the CCE-P pool after harvest, improving the productive stability of the entire cropping sequence. This phenomenon was documented by the P(TI) increase during wheat cultivation following oilseed rape. The Unit Phosphorus Uptake index also showed a higher stability in oilseed rape cropping systems compared to rotations based on maize. Cropping sequences are a primary factor impacting phosphorus management. Judicious implementation of crop rotations can improve soil P resources, efficiency of crop P use, and crop yield and yield stability. Use of cropping sequences can reduce the need for external P sources such as farmyard manure and chemical fertilizers.

Positive contrast high-resolution 3D-cine imaging of the cardiovascular system in small animals using a UTE sequence and iron nanoparticles at 4.7, 7 and 9.4 T.

PubMed

Trotier, Aurélien J; Lefrançois, William; Van Renterghem, Kris; Franconi, Jean-Michel; Thiaudière, Eric; Miraux, Sylvain

2015-07-07

To show that 3D sequences with ultra-short echo times (UTEs) can generate a positive contrast whatever the magnetic field (4.7, 7 or 9.4 T) and whatever Ultra Small Particles of Iron Oxide (USPIO) concentration injected and to use it for 3D time-resolved imaging of the murine cardiovascular system with high spatial and temporal resolutions. Three different concentrations (50, 200 and 500 μmol Fe/kg) of USPIO were injected in mice and static images of the middle part of the animals were acquired at 4.7, 7 and 9.4 T pre and post-contrast with UTE (TE/TR = 0.05/4.5 ms) sequences. Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) of blood and static tissus were evaluated before and after contrast agent injection. 3D-cine images (TE/TR = 0.05/3.5 ms, scan time < 12 min) at 156 μm isotropic resolution of the mouse cardiopulmonary system were acquired prospectively with the UTE sequence for the three magnetic fields and with an USPIO dose of 200 μmol Fe/kg. SNR, CNR and signal homogeneity of blood were measured. High spatial (104 μm) or temporal (3.5 ms) resolution 3D-cine imaging (scan time < 35 min) isotropic resolution were also performed at 7 T with a new sequence encoding scheme. UTE imaging generated positive contrast and higher SNR and CNR whatever the magnetic field and the USPIO concentration used compared to pre-contrast images. Time-resolved 3D acquisition enables high blood SNR (66.6 ± 4.5 at 7 T) and CNR (33.2 ± 4.2 at 7 T) without flow or motion artefact. Coronary arteries and aortic valve were visible on images acquired at 104 μm resolution. We have demonstrated that by combining the injection of iron nanoparticles with 3D-cine UTE sequences, it was possible to generate a strong positive contrast between blood and surrounding tissues. These properties were exploited to produce images of the cardiovascular system in small animals at high magnetic fields with a high spatial and temporal resolution. This approach might be useful to measure the functional cardiac parameters or to assess anatomical modifications to the blood vessels in cardio-vascular disease models.

Nanoplatforms for highly sensitive fluorescence detection of cancer-related proteases.

PubMed

Wang, Hongwang; Udukala, Dinusha N; Samarakoon, Thilani N; Basel, Matthew T; Kalita, Mausam; Abayaweera, Gayani; Manawadu, Harshi; Malalasekera, Aruni; Robinson, Colette; Villanueva, David; Maynez, Pamela; Bossmann, Leonie; Riedy, Elizabeth; Barriga, Jenny; Wang, Ni; Li, Ping; Higgins, Daniel A; Zhu, Gaohong; Troyer, Deryl L; Bossmann, Stefan H

2014-02-01

Numerous proteases are known to be necessary for cancer development and progression including matrix metalloproteinases (MMPs), tissue serine proteases, and cathepsins. The goal of this research is to develop an Fe/Fe3O4 nanoparticle-based system for clinical diagnostics, which has the potential to measure the activity of cancer-associated proteases in biospecimens. Nanoparticle-based "light switches" for measuring protease activity consist of fluorescent cyanine dyes and porphyrins that are attached to Fe/Fe3O4 nanoparticles via consensus sequences. These consensus sequences can be cleaved in the presence of the correct protease, thus releasing a fluorescent dye from the Fe/Fe3O4 nanoparticle, resulting in highly sensitive (down to 1 × 10(-16) mol l(-1) for 12 proteases), selective, and fast nanoplatforms (required time: 60 min).

Intrusion Detection in Control Systems using Sequence Characteristics

NASA Astrophysics Data System (ADS)

Kiuchi, Mai; Onoda, Takashi

Intrusion detection is considered effective in control systems. Sequences of the control application behavior observed in the communication, such as the order of the control device to be controlled, are important in control systems. However, most intrusion detection systems do not effectively reflect sequences in the application layer into the detection rules. In our previous work, we considered utilizing sequences for intrusion detection in control systems, and demonstrated the usefulness of sequences for intrusion detection. However, manually writing the detection rules for a large system can be difficult, so using machine learning methods becomes feasible. Also, in the case of control systems, there have been very few observed cyber attacks, so we have very little knowledge of the attack data that should be used to train the intrusion detection system. In this paper, we use an approach that combines CRF (Conditional Random Field) considering the sequence of the system, thus able to reflect the characteristics of control system sequences into the intrusion detection system, and also does not need the knowledge of attack data to construct the detection rules.

The "Motor" in Implicit Motor Sequence Learning: A Foot-stepping Serial Reaction Time Task.

PubMed

Du, Yue; Clark, Jane E

2018-05-03

This protocol describes a modified serial reaction time (SRT) task used to study implicit motor sequence learning. Unlike the classic SRT task that involves finger-pressing movements while sitting, the modified SRT task requires participants to step with both feet while maintaining a standing posture. This stepping task necessitates whole body actions that impose postural challenges. The foot-stepping task complements the classic SRT task in several ways. The foot-stepping SRT task is a better proxy for the daily activities that require ongoing postural control, and thus may help us better understand sequence learning in real-life situations. In addition, response time serves as an indicator of sequence learning in the classic SRT task, but it is unclear whether response time, reaction time (RT) representing mental process, or movement time (MT) reflecting the movement itself, is a key player in motor sequence learning. The foot-stepping SRT task allows researchers to disentangle response time into RT and MT, which may clarify how motor planning and movement execution are involved in sequence learning. Lastly, postural control and cognition are interactively related, but little is known about how postural control interacts with learning motor sequences. With a motion capture system, the movement of the whole body (e.g., the center of mass (COM)) can be recorded. Such measures allow us to reveal the dynamic processes underlying discrete responses measured by RT and MT, and may aid in elucidating the relationship between postural control and the explicit and implicit processes involved in sequence learning. Details of the experimental set-up, procedure, and data processing are described. The representative data are adopted from one of our previous studies. Results are related to response time, RT, and MT, as well as the relationship between the anticipatory postural response and the explicit processes involved in implicit motor sequence learning.

Sequential measurement of conjugate variables as an alternative quantum state tomography.

PubMed

Di Lorenzo, Antonio

2013-01-04

It is shown how it is possible to reconstruct the initial state of a one-dimensional system by sequentially measuring two conjugate variables. The procedure relies on the quasicharacteristic function, the Fourier transform of the Wigner quasiprobability. The proper characteristic function obtained by Fourier transforming the experimentally accessible joint probability of observing "position" then "momentum" (or vice versa) can be expressed as a product of the quasicharacteristic function of the two detectors and that unknown of the quantum system. This allows state reconstruction through the sequence (1) data collection, (2) Fourier transform, (3) algebraic operation, and (4) inverse Fourier transform. The strength of the measurement should be intermediate for the procedure to work.

HII 2407: AN ECLIPSING BINARY REVEALED BY K2 OBSERVATIONS OF THE PLEIADES

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

David, Trevor J.; Hillenbrand, Lynne A.; Zhang, Celia

2015-11-20

The star HII 2407 is a member of the relatively young Pleiades star cluster and was previously discovered to be a single-lined spectroscopic binary. It is newly identified here within Kepler/K2 photometric time series data as an eclipsing binary system. Mutual fitting of the radial velocity and photometric data leads to an orbital solution and constraints on fundamental stellar parameters. While the primary has arrived on the main sequence, the secondary is still pre-main sequence and we compare our results for the M/M{sub ⊙} and R/R{sub ⊙} values with stellar evolutionary models. We also demonstrate that the system is likelymore » to be tidally synchronized. Follow-up infrared spectroscopy is likely to reveal the lines of the secondary, allowing for dynamically measured masses and elevating the system to benchmark eclipsing binary status.« less

GHz Yb:KYW oscillators in time-resolved spectroscopy

NASA Astrophysics Data System (ADS)

Li, Changxiu; Krauß, Nico; Schäfer, Gerhard; Ebner, Lukas; Kliebisch, Oliver; Schmidt, Johannes; Winnerl, Stephan; Hettich, Mike; Dekorsy, Thomas

2018-02-01

A high-speed asynchronous optical sampling system (ASOPS) based on Yb:KYW oscillators with 1-GHz repetition rate is reported. Two frequency-offset-stabilized diode-pumped Yb:KYW oscillators are employed as pump and probe source, respectively. The temporal resolution of this system within 1-ns time window is limited to 500 fs and the noise floor around 10-6 (ΔR/R) close to the shot-noise level is obtained within an acquisition time of a few seconds. Coherent acoustic phonons are investigated by measuring multilayer semiconductor structures with multiple quantum wells and aluminum/silicon membranes in this ASOPS system. A wavepacket-like phonon sequence at 360 GHz range is detected in the semiconductor structures and a decaying sequence of acoustic oscillations up to 200 GHz is obtained in the aluminum/silicon membranes. Coherent acoustic phonons generated from semiconductor structures are further manipulated by a double pump scheme through pump time delay control.

Nicotine pharmacokinetic profiles of the Tobacco Heating System 2.2, cigarettes and nicotine gum in Japanese smokers.

PubMed

Brossard, Patrick; Weitkunat, Rolf; Poux, Valerie; Lama, Nicola; Haziza, Christelle; Picavet, Patrick; Baker, Gizelle; Lüdicke, Frank

2017-10-01

Two open-label randomized cross-over studies in Japanese smokers investigated the single-use nicotine pharmacokinetic profile of the Tobacco Heating System (THS) 2.2, cigarettes (CC) and nicotine replacement therapy (Gum). In each study, one on the regular and one on the menthol variants of the THS and CC, both using Gum as reference, 62 subjects were randomized to four sequences: Sequence 1: THS - CC (n = 22); Sequence 2: CC - THS (n = 22); Sequence 3: THS - Gum (n = 9); Sequence 4: Gum - THS (n = 9). Plasma nicotine concentrations were measured in 16 blood samples collected over 24 h after single use. Maximal nicotine concentration (C max ) and area under the curve from start of product use to time of last quantifiable concentration (AUC 0-last ) were similar between THS and CC in both studies, with ratios varying from 88 to 104% for C max and from 96 to 98% for AUC 0-last . Urge-to-smoke total scores were comparable between THS and CC. The THS nicotine pharmacokinetic profile was close to CC, with similar levels of urge-to-smoke. This suggests that THS can satisfy smokers and be a viable alternative to cigarettes for adult smokers who want to continue using tobacco. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A measurement of disorder in binary sequences

NASA Astrophysics Data System (ADS)

Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

2015-03-01

We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

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

NASA Astrophysics Data System (ADS)

Toh, Keat Beng; Tachikawa, Shin'ichi

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

Human body motion capture from multi-image video sequences

NASA Astrophysics Data System (ADS)

D'Apuzzo, Nicola

2003-01-01

In this paper is presented a method to capture the motion of the human body from multi image video sequences without using markers. The process is composed of five steps: acquisition of video sequences, calibration of the system, surface measurement of the human body for each frame, 3-D surface tracking and tracking of key points. The image acquisition system is currently composed of three synchronized progressive scan CCD cameras and a frame grabber which acquires a sequence of triplet images. Self calibration methods are applied to gain exterior orientation of the cameras, the parameters of internal orientation and the parameters modeling the lens distortion. From the video sequences, two kinds of 3-D information are extracted: a three-dimensional surface measurement of the visible parts of the body for each triplet and 3-D trajectories of points on the body. The approach for surface measurement is based on multi-image matching, using the adaptive least squares method. A full automatic matching process determines a dense set of corresponding points in the triplets. The 3-D coordinates of the matched points are then computed by forward ray intersection using the orientation and calibration data of the cameras. The tracking process is also based on least squares matching techniques. Its basic idea is to track triplets of corresponding points in the three images through the sequence and compute their 3-D trajectories. The spatial correspondences between the three images at the same time and the temporal correspondences between subsequent frames are determined with a least squares matching algorithm. The results of the tracking process are the coordinates of a point in the three images through the sequence, thus the 3-D trajectory is determined by computing the 3-D coordinates of the point at each time step by forward ray intersection. Velocities and accelerations are also computed. The advantage of this tracking process is twofold: it can track natural points, without using markers; and it can track local surfaces on the human body. In the last case, the tracking process is applied to all the points matched in the region of interest. The result can be seen as a vector field of trajectories (position, velocity and acceleration). The last step of the process is the definition of selected key points of the human body. A key point is a 3-D region defined in the vector field of trajectories, whose size can vary and whose position is defined by its center of gravity. The key points are tracked in a simple way: the position at the next time step is established by the mean value of the displacement of all the trajectories inside its region. The tracked key points lead to a final result comparable to the conventional motion capture systems: 3-D trajectories of key points which can be afterwards analyzed and used for animation or medical purposes.

Sequence-of-events-driven automation of the deep space network

NASA Technical Reports Server (NTRS)

Hill, R., Jr.; Fayyad, K.; Smyth, C.; Santos, T.; Chen, R.; Chien, S.; Bevan, R.

1996-01-01

In February 1995, sequence-of-events (SOE)-driven automation technology was demonstrated for a Voyager telemetry downlink track at DSS 13. This demonstration entailed automated generation of an operations procedure (in the form of a temporal dependency network) from project SOE information using artificial intelligence planning technology and automated execution of the temporal dependency network using the link monitor and control operator assistant system. This article describes the overall approach to SOE-driven automation that was demonstrated, identifies gaps in SOE definitions and project profiles that hamper automation, and provides detailed measurements of the knowledge engineering effort required for automation.

Sequence-of-Events-Driven Automation of the Deep Space Network

NASA Technical Reports Server (NTRS)

Hill, R., Jr.; Fayyad, K.; Smyth, C.; Santos, T.; Chen, R.; Chien, S.; Bevan, R.

1996-01-01

In February 1995, sequence-of-events (SOE)-driven automation technology was demonstrated for a Voyager telemetry downlink track at DSS 13. This demonstration entailed automated generation of an operations procedure (in the form of a temporal dependency network) from project SOE information using artificial intelligence planning technology and automated execution of the temporal dependency network using the link monitor and control operator assistant system. This article describes the overall approach to SOE-driven automation that was demonstrated, identifies gaps in SOE definitions and project profiles that hamper automation, and provides detailed measurements of the knowledge engineering effort required for automation.

Emerging Tools for Synthetic Genome Design

PubMed Central

Lee, Bo-Rahm; Cho, Suhyung; Song, Yoseb; Kim, Sun Chang; Cho, Byung-Kwan

2013-01-01

Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives. PMID:23708771

Predicting Protein-Protein Interactions by Combing Various Sequence-Derived.

PubMed

Zhao, Xiao-Wei; Ma, Zhi-Qiang; Yin, Ming-Hao

2011-09-20

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.

Single-molecule protein sequencing through fingerprinting: computational assessment

NASA Astrophysics Data System (ADS)

Yao, Yao; Docter, Margreet; van Ginkel, Jetty; de Ridder, Dick; Joo, Chirlmin

2015-10-01

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.

Quantum-Classical Hybrid for Information Processing

NASA Technical Reports Server (NTRS)

Zak, Michail

2011-01-01

Based upon quantum-inspired entanglement in quantum-classical hybrids, a simple algorithm for instantaneous transmissions of non-intentional messages (chosen at random) to remote distances is proposed. The idea is to implement instantaneous transmission of conditional information on remote distances via a quantum-classical hybrid that preserves superposition of random solutions, while allowing one to measure its state variables using classical methods. Such a hybrid system reinforces the advantages, and minimizes the limitations, of both quantum and classical characteristics. Consider n observers, and assume that each of them gets a copy of the system and runs it separately. Although they run identical systems, the outcomes of even synchronized runs may be different because the solutions of these systems are random. However, the global constrain must be satisfied. Therefore, if the observer #1 (the sender) made a measurement of the acceleration v(sub 1) at t =T, then the receiver, by measuring the corresponding acceleration v(sub 1) at t =T, may get a wrong value because the accelerations are random, and only their ratios are deterministic. Obviously, the transmission of this knowledge is instantaneous as soon as the measurements have been performed. In addition to that, the distance between the observers is irrelevant because the x-coordinate does not enter the governing equations. However, the Shannon information transmitted is zero. None of the senders can control the outcomes of their measurements because they are random. The senders cannot transmit intentional messages. Nevertheless, based on the transmitted knowledge, they can coordinate their actions based on conditional information. If the observer #1 knows his own measurements, the measurements of the others can be fully determined. It is important to emphasize that the origin of entanglement of all the observers is the joint probability density that couples their actions. There is no centralized source, or a sender of the signal, because each receiver can become a sender as well. An observer receives a signal by performing certain measurements synchronized with the measurements of the others. This means that the signal is uniformly and simultaneously distributed over the observers in a decentralized way. The signals transmit no intentional information that would favor one agent over another. All the sequence of signals received by different observers are not only statistically equivalent, but are also point-by-point identical. It is important to assume that each agent knows that the other agent simultaneously receives the identical signals. The sequences of the signals are true random, so that no agent could predict the next step with the probability different from those described by the density. Under these quite general assumptions, the entangled observers-agents can perform non-trivial tasks that include transmission of conditional information from one agent to another, simple paradigm of cooperation, etc. The problem of behavior of intelligent agents correlated by identical random messages in a decentralized way has its own significance: it simulates evolutionary behavior of biological and social systems correlated only via simultaneous sensoring sequences of unexpected events.

No scanning depth imaging system based on TOF

NASA Astrophysics Data System (ADS)

Sun, Rongchun; Piao, Yan; Wang, Yu; Liu, Shuo

2016-03-01

To quickly obtain a 3D model of real world objects, multi-point ranging is very important. However, the traditional measuring method usually adopts the principle of point by point or line by line measurement, which is too slow and of poor efficiency. In the paper, a no scanning depth imaging system based on TOF (time of flight) was proposed. The system is composed of light source circuit, special infrared image sensor module, processor and controller of image data, data cache circuit, communication circuit, and so on. According to the working principle of the TOF measurement, image sequence was collected by the high-speed CMOS sensor, and the distance information was obtained by identifying phase difference, and the amplitude image was also calculated. Experiments were conducted and the experimental results show that the depth imaging system can achieve no scanning depth imaging function with good performance.

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

NASA Astrophysics Data System (ADS)

Farzan Sabahi, Mohammad; Dehghanfard, Ali

2014-12-01

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

Isotachophoresis for fractionation and recovery of cytoplasmic RNA and nucleus from single cells.

PubMed

Kuriyama, Kentaro; Shintaku, Hirofumi; Santiago, Juan G

2015-07-01

There is a substantial need for simultaneous analyses of RNA and DNA from individual single cells. Such analysis provides unique evidence of cell-to-cell differences and the correlation between gene expression and genomic mutation in highly heterogeneous cell populations. We present a novel microfluidic system that leverages isotachophoresis to fractionate and isolate cytoplasmic RNA and genomic DNA (gDNA) from single cells. The system uniquely enables independent, sequence-specific analyses of these critical markers. Our system uses a microfluidic chip with a simple geometry and four end-channel electrodes, and completes the entire process in <5 min, including lysis, purification, fractionation, and delivery to DNA and RNA output reservoirs, each containing high quality and purity aliquots with no measurable cross-contamination of cytoplasmic RNA versus gDNA. We demonstrate our system with simultaneous, sequence-specific quantitation using off-chip RT-qPCR and qPCR for simultaneous cytoplasmic RNA and gDNA analyses, respectively. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

Walker, Ernest L.

1994-05-01

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

Simultaneous Measurement of Breathing and Heartbeat using Airborne Ultrasound in a Standing Position

NASA Astrophysics Data System (ADS)

Hoshiba, Kotaro; Hirata, Shinnosuke; Hachiya, Hiroyuki

We have been studied about non-contact measurement of respiration and heart rates. In previous papers, the measurement system of small velocity using the M-sequence-modulated signal and phase difference of reflected signals from the target has been proposed. In this paper, we describe measurement of breathing and heartbeat in a standing position using the proposed method. Body-surface velocities by breathing and heartbeat could be observed respectively when the volunteer was breathing and holding the breath. In addition, measured velocity of breathing volunteer includes the component by heartbeat. It is considered that it has possibility to measure breathing and heartbeat concurrently.

Impact Assessment of GNSS Spoofing Attacks on INS/GNSS Integrated Navigation System.

PubMed

Liu, Yang; Li, Sihai; Fu, Qiangwen; Liu, Zhenbo

2018-05-04

In the face of emerging Global Navigation Satellite System (GNSS) spoofing attacks, there is a need to give a comprehensive analysis on how the inertial navigation system (INS)/GNSS integrated navigation system responds to different kinds of spoofing attacks. A better understanding of the integrated navigation system’s behavior with spoofed GNSS measurements gives us valuable clues to develop effective spoofing defenses. This paper focuses on an impact assessment of GNSS spoofing attacks on the integrated navigation system Kalman filter’s error covariance, innovation sequence and inertial sensor bias estimation. A simple and straightforward measurement-level trajectory spoofing simulation framework is presented, serving as the basis for an impact assessment of both unsynchronized and synchronized spoofing attacks. Recommendations are given for spoofing detection and mitigation based on our findings in the impact assessment process.

Experimental Influences in the Accurate Measurement of Cartilage Thickness in MRI.

PubMed

Wang, Nian; Badar, Farid; Xia, Yang

2018-01-01

Objective To study the experimental influences to the measurement of cartilage thickness by magnetic resonance imaging (MRI). Design The complete thicknesses of healthy and trypsin-degraded cartilage were measured at high-resolution MRI under different conditions, using two intensity-based imaging sequences (ultra-short echo [UTE] and multislice-multiecho [MSME]) and 3 quantitative relaxation imaging sequences (T 1 , T 2 , and T 1 ρ). Other variables included different orientations in the magnet, 2 soaking solutions (saline and phosphate buffered saline [PBS]), and external loading. Results With cartilage soaked in saline, UTE and T 1 methods yielded complete and consistent measurement of cartilage thickness, while the thickness measurement by T 2 , T 1 ρ, and MSME methods were orientation dependent. The effect of external loading on cartilage thickness is also sequence and orientation dependent. All variations in cartilage thickness in MRI could be eliminated with the use of a 100 mM PBS or imaged by UTE sequence. Conclusions The appearance of articular cartilage and the measurement accuracy of cartilage thickness in MRI can be influenced by a number of experimental factors in ex vivo MRI, from the use of various pulse sequences and soaking solutions to the health of the tissue. T 2 -based imaging sequence, both proton-intensity sequence and quantitative relaxation sequence, similarly produced the largest variations. With adequate resolution, the accurate measurement of whole cartilage tissue in clinical MRI could be utilized to detect differences between healthy and osteoarthritic cartilage after compression.

An Adaptive Low-Cost INS/GNSS Tightly-Coupled Integration Architecture Based on Redundant Measurement Noise Covariance Estimation.

PubMed

Li, Zheng; Zhang, Hai; Zhou, Qifan; Che, Huan

2017-09-05

The main objective of the introduced study is to design an adaptive Inertial Navigation System/Global Navigation Satellite System (INS/GNSS) tightly-coupled integration system that can provide more reliable navigation solutions by making full use of an adaptive Kalman filter (AKF) and satellite selection algorithm. To achieve this goal, we develop a novel redundant measurement noise covariance estimation (RMNCE) theorem, which adaptively estimates measurement noise properties by analyzing the difference sequences of system measurements. The proposed RMNCE approach is then applied to design both a modified weighted satellite selection algorithm and a type of adaptive unscented Kalman filter (UKF) to improve the performance of the tightly-coupled integration system. In addition, an adaptive measurement noise covariance expanding algorithm is developed to mitigate outliers when facing heavy multipath and other harsh situations. Both semi-physical simulation and field experiments were conducted to evaluate the performance of the proposed architecture and were compared with state-of-the-art algorithms. The results validate that the RMNCE provides a significant improvement in the measurement noise covariance estimation and the proposed architecture can improve the accuracy and reliability of the INS/GNSS tightly-coupled systems. The proposed architecture can effectively limit positioning errors under conditions of poor GNSS measurement quality and outperforms all the compared schemes.

An Adaptive Low-Cost INS/GNSS Tightly-Coupled Integration Architecture Based on Redundant Measurement Noise Covariance Estimation

PubMed Central

Li, Zheng; Zhang, Hai; Zhou, Qifan; Che, Huan

2017-01-01

The main objective of the introduced study is to design an adaptive Inertial Navigation System/Global Navigation Satellite System (INS/GNSS) tightly-coupled integration system that can provide more reliable navigation solutions by making full use of an adaptive Kalman filter (AKF) and satellite selection algorithm. To achieve this goal, we develop a novel redundant measurement noise covariance estimation (RMNCE) theorem, which adaptively estimates measurement noise properties by analyzing the difference sequences of system measurements. The proposed RMNCE approach is then applied to design both a modified weighted satellite selection algorithm and a type of adaptive unscented Kalman filter (UKF) to improve the performance of the tightly-coupled integration system. In addition, an adaptive measurement noise covariance expanding algorithm is developed to mitigate outliers when facing heavy multipath and other harsh situations. Both semi-physical simulation and field experiments were conducted to evaluate the performance of the proposed architecture and were compared with state-of-the-art algorithms. The results validate that the RMNCE provides a significant improvement in the measurement noise covariance estimation and the proposed architecture can improve the accuracy and reliability of the INS/GNSS tightly-coupled systems. The proposed architecture can effectively limit positioning errors under conditions of poor GNSS measurement quality and outperforms all the compared schemes. PMID:28872629

ESIAC: A data products system for ERTS imagery (time-lapse viewing and measuring)

NASA Technical Reports Server (NTRS)

Evans, W. E.; Serebreny, S. M.

1974-01-01

An Electronic Satellite Image Analysis Console (ESIAC) has been developed for visual analysis and objective measurement of earth resources imagery. The system is being employed to process imagery for use by USGS investigators in several different disciplines studying dynamic hydrologic conditions. The ESIAC provides facilities for storing registered image sequences in a magnetic video disc memory for subsequent recall, enhancement, and animated display in monochrome or color. The unique feature of the system is the capability to time-lapse the ERTS imagery and/or analytic displays of the imagery. Data products have included quantitative measurements of distances and areas, brightness profiles, and movie loops of selected themes. The applications of these data products are identified and include such diverse problem areas as measurement of snowfield extent, sediment plumes from estuary dicharge, playa inventory, phreatophyte and other vegetation changes. A comparative ranking of the electronic system in terms of accuracy, cost effectiveness and data output shows it to be a viable means of data analysis.

Chain representations of Open Quantum Systems and Lieb-Robinson like bounds for the dynamics

NASA Astrophysics Data System (ADS)

Woods, Mischa

2013-03-01

This talk is concerned with the mapping of the Hamiltonian of open quantum systems onto chain representations, which forms the basis for a rigorous theory of the interaction of a system with its environment. This mapping progresses as an interaction which gives rise to a sequence of residual spectral densities of the system. The rigorous mathematical properties of this mapping have been unknown so far. Here we develop the theory of secondary measures to derive an analytic, expression for the sequence solely in terms of the initial measure and its associated orthogonal polynomials of the first and second kind. These mappings can be thought of as taking a highly nonlocal Hamiltonian to a local Hamiltonian. In the latter, a Lieb-Robinson like bound for the dynamics of the open quantum system makes sense. We develop analytical bounds on the error to observables of the system as a function of time when the semi-infinite chain in truncated at some finite length. The fact that this is possible shows that there is a finite ``Speed of sound'' in these chain representations. This has many implications of the simulatability of open quantum systems of this type and demonstrates that a truncated chain can faithfully reproduce the dynamics at shorter times. These results make a significant and mathematically rigorous contribution to the understanding of the theory of open quantum systems; and pave the way towards the efficient simulation of these systems, which within the standard methods, is often an intractable problem. EPSRC CDT in Controlled Quantum Dynamics, EU STREP project and Alexander von Humboldt Foundation

Using Sequence Diagrams to Detect Communication Problems Between Systems

NASA Technical Reports Server (NTRS)

Lindvall, Mikael; Ackermann, Chris; Stratton, William C.; Sibol, Deane E.; Ray, Arnab; Yonkwa, Lyly; Kresser, Jan; Godfrey, Sally H.; Knodel, Jens

2008-01-01

Many software systems are evolving complex system of systems (SoS) for which inter-system communication is both mission-critical and error-prone. Such communication problems ideally would be detected before deployment. In a NASA-supported Software Assurance Research Program (SARP) project, we are researching a new approach addressing such problems. In this paper, we show that problems in the communication between two systems can be detected by using sequence diagrams to model the planned communication and by comparing the planned sequence to the actual sequence. We identify different kinds of problems that can be addressed by modeling the planned sequence using different level of abstractions.

Cloud-based adaptive exon prediction for DNA analysis

PubMed Central

Putluri, Srinivasareddy; Fathima, Shaik Yasmeen

2018-01-01

Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing. True identification of exon regions in a DNA sequence is a key task in bioinformatics, which helps in disease identification and design drugs. Three base periodicity property of exons forms the basis of all exon identification techniques. Adaptive signal processing techniques found to be promising in comparison with several other methods. Several adaptive exon predictors (AEPs) are developed using variable normalised least mean square and its maximum normalised variants to reduce computational complexity. Finally, performance evaluation of various AEPs is done based on measures such as sensitivity, specificity and precision using various standard genomic datasets taken from National Center for Biotechnology Information genomic sequence database. PMID:29515813

Hemispheric asymmetries of a motor memory in a recognition test after learning a movement sequence.

PubMed

Leinen, Peter; Panzer, Stefan; Shea, Charles H

2016-11-01

Two experiments utilizing a spatial-temporal movement sequence were designed to determine if the memory of the sequence is lateralized in the left or right hemisphere. In Experiment 1, dominant right-handers were randomly assigned to one of two acquisition groups: a left-hand starter and a right-hand starter group. After an acquisition phase, reaction time (RT) was measured in a recognition test by providing the learned sequential pattern in the left or right visual half-field for 150ms. In a retention test and two transfer tests the dominant coordinate system for sequence production was evaluated. In Experiment 2 dominant left-handers and dominant right-handers had to acquire the sequence with their dominant limb. The results of Experiment 1 indicated that RT was significantly shorter when the acquired sequence was provided in the right visual field during the recognition test. The same results occurred in Experiment 2 for dominant right-handers and left-handers. These results indicated a right visual field left hemisphere advantage in the recognition test for the practiced stimulus for dominant left and right-handers, when the task was practiced with the dominant limb. Copyright © 2016 Elsevier B.V. All rights reserved.

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty.

PubMed

Mdluli, Thembi; Buzzard, Gregery T; Rundell, Ann E

2015-09-01

This model-based design of experiments (MBDOE) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study. The ideal global solution for this experiment design problem is generally computationally intractable because of parametric uncertainties in the mathematical model of the biological system. Others have addressed this issue by limiting the solution to a local estimate of the model parameters. Here we present an approach that is independent of the local parameter constraint. This approach is made computationally efficient and tractable by the use of: (1) sparse grid interpolation that approximates the biological system dynamics, (2) representative parameters that uniformly represent the data-consistent dynamical space, and (3) probability weights of the represented experimentally distinguishable dynamics. Our approach identifies data-consistent representative parameters using sparse grid interpolants, constructs the optimal input sequence from a greedy search, and defines the associated optimal measurements using a scenario tree. We explore the optimality of this MBDOE algorithm using a 3-dimensional Hes1 model and a 19-dimensional T-cell receptor model. The 19-dimensional T-cell model also demonstrates the MBDOE algorithm's scalability to higher dimensions. In both cases, the dynamical uncertainty region that bounds the trajectories of the target system states were reduced by as much as 86% and 99% respectively after completing the designed experiments in silico. Our results suggest that for resolving dynamical uncertainty, the ability to design an input sequence paired with its associated measurements is particularly important when limited by the number of measurements.

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty

PubMed Central

Mdluli, Thembi; Buzzard, Gregery T.; Rundell, Ann E.

2015-01-01

This model-based design of experiments (MBDOE) method determines the input magnitudes of an experimental stimuli to apply and the associated measurements that should be taken to optimally constrain the uncertain dynamics of a biological system under study. The ideal global solution for this experiment design problem is generally computationally intractable because of parametric uncertainties in the mathematical model of the biological system. Others have addressed this issue by limiting the solution to a local estimate of the model parameters. Here we present an approach that is independent of the local parameter constraint. This approach is made computationally efficient and tractable by the use of: (1) sparse grid interpolation that approximates the biological system dynamics, (2) representative parameters that uniformly represent the data-consistent dynamical space, and (3) probability weights of the represented experimentally distinguishable dynamics. Our approach identifies data-consistent representative parameters using sparse grid interpolants, constructs the optimal input sequence from a greedy search, and defines the associated optimal measurements using a scenario tree. We explore the optimality of this MBDOE algorithm using a 3-dimensional Hes1 model and a 19-dimensional T-cell receptor model. The 19-dimensional T-cell model also demonstrates the MBDOE algorithm’s scalability to higher dimensions. In both cases, the dynamical uncertainty region that bounds the trajectories of the target system states were reduced by as much as 86% and 99% respectively after completing the designed experiments in silico. Our results suggest that for resolving dynamical uncertainty, the ability to design an input sequence paired with its associated measurements is particularly important when limited by the number of measurements. PMID:26379275

Local alignment of two-base encoded DNA sequence

PubMed Central

Homer, Nils; Merriman, Barry; Nelson, Stanley F

2009-01-01

Background DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an encoded form, such as the two-base encoding considered here. In order to compare such data to a reference sequence, the data must be decoded into sequence. The decoding is deterministic, but the possibility of measurement errors requires searching among all possible error modes and resulting alignments to achieve an optimal balance of fewer errors versus greater sequence similarity. Results We present an extension of the standard dynamic programming method for local alignment, which simultaneously decodes the data and performs the alignment, maximizing a similarity score based on a weighted combination of errors and edits, and allowing an affine gap penalty. We also present simulations that demonstrate the performance characteristics of our two base encoded alignment method and contrast those with standard DNA sequence alignment under the same conditions. Conclusion The new local alignment algorithm for two-base encoded data has substantial power to properly detect and correct measurement errors while identifying underlying sequence variants, and facilitating genome re-sequencing efforts based on this form of sequence data. PMID:19508732

Internal control regions for transcription of eukaryotic tRNA genes.

PubMed Central

Sharp, S; DeFranco, D; Dingermann, T; Farrell, P; Söll, D

1981-01-01

We have identified the region within a eukaryotic tRNA gene required for initiation of transcription. These results were obtained by systematically constructing deletions extending from the 5' or the 3' flanking regions into a cloned Drosophila tRNAArg gene by using nuclease BAL 31. The ability of the newly generated deletion clones to direct the in vitro synthesis of tRNA precursors was measured in transcription systems from Xenopus laevis oocytes, Drosophila Kc cells, and HeLa cells. Two control regions within the coding sequence were identified. The first was essential for transcription and was contained between nucleotides 8 and 25 of the mature tRNA sequence. Genes devoid of the second control region, which was contained between nucleotides 50 and 58 of the mature tRNA sequence, could be transcribed but with reduced efficiency. Thus, the promoter regions within a tRNA gene encode the tRNA sequences of the D stem and D loop, the invariant uridine at position 8, and the semi-invariant G-T-psi-C sequence. Images PMID:6947245

Comparison of Dixon Sequences for Estimation of Percent Breast Fibroglandular Tissue

PubMed Central

Ledger, Araminta E. W.; Scurr, Erica D.; Hughes, Julie; Macdonald, Alison; Wallace, Toni; Thomas, Karen; Wilson, Robin; Leach, Martin O.; Schmidt, Maria A.

2016-01-01

Objectives To evaluate sources of error in the Magnetic Resonance Imaging (MRI) measurement of percent fibroglandular tissue (%FGT) using two-point Dixon sequences for fat-water separation. Methods Ten female volunteers (median age: 31 yrs, range: 23–50 yrs) gave informed consent following Research Ethics Committee approval. Each volunteer was scanned twice following repositioning to enable an estimation of measurement repeatability from high-resolution gradient-echo (GRE) proton-density (PD)-weighted Dixon sequences. Differences in measures of %FGT attributable to resolution, T1 weighting and sequence type were assessed by comparison of this Dixon sequence with low-resolution GRE PD-weighted Dixon data, and against gradient-echo (GRE) or spin-echo (SE) based T1-weighted Dixon datasets, respectively. Results %FGT measurement from high-resolution PD-weighted Dixon sequences had a coefficient of repeatability of ±4.3%. There was no significant difference in %FGT between high-resolution and low-resolution PD-weighted data. Values of %FGT from GRE and SE T1-weighted data were strongly correlated with that derived from PD-weighted data (r = 0.995 and 0.96, respectively). However, both sequences exhibited higher mean %FGT by 2.9% (p < 0.0001) and 12.6% (p < 0.0001), respectively, in comparison with PD-weighted data; the increase in %FGT from the SE T1-weighted sequence was significantly larger at lower breast densities. Conclusion Although measurement of %FGT at low resolution is feasible, T1 weighting and sequence type impact on the accuracy of Dixon-based %FGT measurements; Dixon MRI protocols for %FGT measurement should be carefully considered, particularly for longitudinal or multi-centre studies. PMID:27011312

Observation of Discrete-Time-Crystal Signatures in an Ordered Dipolar Many-Body System

NASA Astrophysics Data System (ADS)

Rovny, Jared; Blum, Robert L.; Barrett, Sean E.

2018-05-01

A discrete time crystal (DTC) is a robust phase of driven systems that breaks the discrete time translation symmetry of the driving Hamiltonian. Recent experiments have observed DTC signatures in two distinct systems. Here we show nuclear magnetic resonance observations of DTC signatures in a third, strikingly different system: an ordered spatial crystal. We use a novel DTC echo experiment to probe the coherence of the driven system. Finally, we show that interactions during the pulse of the DTC sequence contribute to the decay of the signal, complicating attempts to measure the intrinsic lifetime of the DTC.

Observation of Discrete-Time-Crystal Signatures in an Ordered Dipolar Many-Body System.

PubMed

Rovny, Jared; Blum, Robert L; Barrett, Sean E

2018-05-04

A discrete time crystal (DTC) is a robust phase of driven systems that breaks the discrete time translation symmetry of the driving Hamiltonian. Recent experiments have observed DTC signatures in two distinct systems. Here we show nuclear magnetic resonance observations of DTC signatures in a third, strikingly different system: an ordered spatial crystal. We use a novel DTC echo experiment to probe the coherence of the driven system. Finally, we show that interactions during the pulse of the DTC sequence contribute to the decay of the signal, complicating attempts to measure the intrinsic lifetime of the DTC.

Distortion-free diffusion MRI using an MRI-guided Tri-Cobalt 60 radiotherapy system: Sequence verification and preliminary clinical experience.

PubMed

Gao, Yu; Han, Fei; Zhou, Ziwu; Cao, Minsong; Kaprealian, Tania; Kamrava, Mitchell; Wang, Chenyang; Neylon, John; Low, Daniel A; Yang, Yingli; Hu, Peng

2017-10-01

Monitoring tumor response during the course of treatment and adaptively modifying treatment plan based on tumor biological feedback may represent a new paradigm for radiotherapy. Diffusion MRI has shown great promises in assessing and predicting tumor response to radiotherapy. However, the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) technique suffers from limited resolution, severe distortion, and possibly inaccurate ADC at low field strength. The purpose of this work was to develop a reliable, accurate and distortion-free diffusion MRI technique that is practicable for longitudinal tumor response evaluation and adaptive radiotherapy on a 0.35 T MRI-guided radiotherapy system. A diffusion-prepared turbo spin echo readout (DP-TSE) sequence was developed and compared with the conventional diffusion-weighted single-shot echo-planar-imaging sequence on a 0.35 T MRI-guided radiotherapy system (ViewRay). A spatial integrity phantom was used to quantitate and compare the geometric accuracy of the two diffusion sequences for three orthogonal orientations. The apparent diffusion coefficient (ADC) accuracy was evaluated on a diffusion phantom under both 0 °C and room temperature to cover a diffusivity range between 0.40 × 10 -3 and 2.10 × 10 -3 mm 2 /s. Ten room temperature measurements repeated on five different days were conducted to assess the ADC reproducibility of DP-TSE. Two glioblastoma (GBM) and six sarcoma patients were included to examine the in vivo feasibility. The target registration error (TRE) was calculated to quantitate the geometric accuracy where structural CT or MR images were co-registered to the diffusion images as references. ADC maps from DP-TSE and DW-ssEPI were calculated and compared. A tube phantom was placed next to patients not treated on ViewRay, and ADCs of this reference tube were also compared. The proposed DP-TSE passed the spatial integrity test (< 1 mm within 100 mm radius and < 2 mm within 175 mm radius) under the three orthogonal orientations. The detected errors were 0.474 ± 0.355 mm, 0.475 ± 0.287 mm, and 0.546 ± 0.336 mm in the axial, coronal, and sagittal plane. DW-ssEPI, however, failed the tests due to severe distortion and low signal intensity. Noise correction must be performed for the DW-ssEPI to avoid ADC quantitation errors, whereas it is optional for DP-TSE. At 0 °C, the two sequences provided accurate quantitation with < 3% variation with the reference. In the room temperature study, discrepancies between ADCs from DP-TSE and the reference were within 4%, but could be as high as 8% for DW-ssEPI after the noise correction. Excellent ADC reproducibility with a coefficient of variation < 5% was observed among the 10 measurements of DP-TSE, indicating desirable robustness for ADC-based tumor response assessment. In vivo TRE in DP-TSE was less than 1.6 mm overall, whereas it could be greater than 12 mm in DW-ssEPI. For GBM patients, the CSF and brain tissue ADCs from DP-TSE were within the ranges found in literature. ADC differences between the two techniques were within 8% among the six sarcoma patients. For the reference tube that had a relatively low diffusivity, the two diffusion sequences provided matched measurements. A diffusion technique with excellent geometric fidelity, accurate, and reproducible ADC measurement was demonstrated for longitudinal tumor response assessment using a low-field MRI-guided radiotherapy system. © 2017 American Association of Physicists in Medicine.

On the fallacy of quantitative segmentation for T1-weighted MRI

NASA Astrophysics Data System (ADS)

Plassard, Andrew J.; Harrigan, Robert L.; Newton, Allen T.; Rane, Swati; Pallavaram, Srivatsan; D'Haese, Pierre F.; Dawant, Benoit M.; Claassen, Daniel O.; Landman, Bennett A.

2016-03-01

T1-weighted magnetic resonance imaging (MRI) generates contrasts with primary sensitivity to local T1 properties (with lesser T2 and PD contributions). The observed signal intensity is determined by these local properties and the sequence parameters of the acquisition. In common practice, a range of acceptable parameters is used to ensure "similar" contrast across scanners used for any particular study (e.g., the ADNI standard MPRAGE). However, different studies may use different ranges of parameters and report the derived data as simply "T1-weighted". Physics and imaging authors pay strong heed to the specifics of the imaging sequences, but image processing authors have historically been more lax. Herein, we consider three T1-weighted sequences acquired the same underlying protocol (MPRAGE) and vendor (Philips), but "normal study-to-study variation" in parameters. We show that the gray matter/white matter/cerebrospinal fluid contrast is subtly but systemically different between these images and yields systemically different measurements of brain volume. The problem derives from the visually apparent boundary shifts, which would also be seen by a human rater. We present and evaluate two solutions to produce consistent segmentation results across imaging protocols. First, we propose to acquire multiple sequences on a subset of the data and use the multi-modal imaging as atlases to segment target images any of the available sequences. Second (if additional imaging is not available), we propose to synthesize atlases of the target imaging sequence and use the synthesized atlases in place of atlas imaging data. Both approaches significantly improve consistency of target labeling.

Calibration of a Direct Detection Doppler Wind Lidar System using a Wind Tunnel

NASA Astrophysics Data System (ADS)

Rees, David

2012-07-01

As a critical stage of a Project to develop an airborne Direct-Detection Doppler Wind Lidar System, it was possible to exploit a Wind Tunnel of the VZLU, Prague, Czech Republic for a comprehensive series of tests against calibrated Air Speed generated by the Wind Tunnel. The initial results from these test sequences will be presented. The rms wind speed errors were of order 0.25 m/sec - very satisfactory for this class of Doppler Wind Lidar measurements. The next stage of this Project will exploit a more highly-developed laser and detection system for measurements of wind shear, wake vortex and other potentially hazardous meteorological phenomena at Airports. Following the end of this Project, key parts of the instrumentation will be used for routine ground-based Doppler Wind Lidar measurements of the troposphere and stratosphere.

Social and behavioral research in genomic sequencing: approaches from the Clinical Sequencing Exploratory Research Consortium Outcomes and Measures Working Group.

PubMed

Gray, Stacy W; Martins, Yolanda; Feuerman, Lindsay Z; Bernhardt, Barbara A; Biesecker, Barbara B; Christensen, Kurt D; Joffe, Steven; Rini, Christine; Veenstra, David; McGuire, Amy L

2014-10-01

The routine use of genomic sequencing in clinical medicine has the potential to dramatically alter patient care and medical outcomes. To fully understand the psychosocial and behavioral impact of sequencing integration into clinical practice, it is imperative that we identify the factors that influence sequencing-related decision making and patient outcomes. In an effort to develop a collaborative and conceptually grounded approach to studying sequencing adoption, members of the National Human Genome Research Institute's Clinical Sequencing Exploratory Research Consortium formed the Outcomes and Measures Working Group. Here we highlight the priority areas of investigation and psychosocial and behavioral outcomes identified by the Working Group. We also review some of the anticipated challenges to measurement in social and behavioral research related to genomic sequencing; opportunities for instrument development; and the importance of qualitative, quantitative, and mixed-method approaches. This work represents the early, shared efforts of multiple research teams as we strive to understand individuals' experiences with genomic sequencing. The resulting body of knowledge will guide recommendations for the optimal use of sequencing in clinical practice.

40 CFR 86.1330-90 - Test sequence; general requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... fuel and the point at which it is measured shall be specified by the manufacturer. (g) Pre-test engine...-fueled or methanol-fueled diesel engine fuel flows, etc.), pre-test engine performance checks (e.g., verification of actual rated rpm, etc.) and pre-test system calibrations (e.g., inlet and exhaust restrictions...

40 CFR 86.1330-90 - Test sequence; general requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... fuel and the point at which it is measured shall be specified by the manufacturer. (g) Pre-test engine...-fueled or methanol-fueled diesel engine fuel flows, etc.), pre-test engine performance checks (e.g., verification of actual rated rpm, etc.) and pre-test system calibrations (e.g., inlet and exhaust restrictions...

40 CFR 86.1330-90 - Test sequence; general requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... fuel and the point at which it is measured shall be specified by the manufacturer. (g) Pre-test engine...-fueled or methanol-fueled diesel engine fuel flows, etc.), pre-test engine performance checks (e.g., verification of actual rated rpm, etc.) and pre-test system calibrations (e.g., inlet and exhaust restrictions...

40 CFR 86.1330-90 - Test sequence; general requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... fuel and the point at which it is measured shall be specified by the manufacturer. (g) Pre-test engine...-fueled or methanol-fueled diesel engine fuel flows, etc.), pre-test engine performance checks (e.g., verification of actual rated rpm, etc.) and pre-test system calibrations (e.g., inlet and exhaust restrictions...

Potential Role of Lateral Gene Transfer in the Evolution of Biofilm Communities at the Lost City Hydrothermal Field and in the Earliest Stages of Cellular Evolution

NASA Astrophysics Data System (ADS)

Brazelton, W. J.; Mehta, M. P.; Baross, J. A.

2010-04-01

DNA sequencing and metabolic activity measurements show that lateral gene transfer promotes phenotypic diversity in single-species archaeal biofilms attached to hydrothermal chimneys. This system may be a useful model for early cellular evolution.

The Use of a Software-Assisted Method to Estimate Fetal Weight at and Near Term Using Magnetic Resonance Imaging.

PubMed

Kadji, Caroline; De Groof, Maxime; Camus, Margaux F; De Angelis, Riccardo; Fellas, Stéphanie; Klass, Magdalena; Cecotti, Vera; Dütemeyer, Vivien; Barakat, Elie; Cannie, Mieke M; Jani, Jacques C

2017-01-01

The aim of this study was to apply a semi-automated calculation method of fetal body volume and, thus, of magnetic resonance-estimated fetal weight (MR-EFW) prior to planned delivery and to evaluate whether the technique of measurement could be simplified while remaining accurate. MR-EFW was calculated using a semi-automated method at 38.6 weeks of gestation in 36 patients and compared to the picture archiving and communication system (PACS). Per patient, 8 sequences were acquired with a slice thickness of 4-8 mm and an intersection gap of 0, 4, 8, 12, 16, or 20 mm. The median absolute relative errors for MR-EFW and the time of planimetric measurements were calculated for all 8 sequences and for each method (assisted vs. PACS), and the difference between the methods was calculated. The median delivery weight was 3,280 g. The overall median relative error for all 288 MR-EFW calculations was 2.4% using the semi-automated method and 2.2% for the PACS method. Measurements did not differ between the 8 sequences using the assisted method (p = 0.313) or the PACS (p = 0.118), while the time of planimetric measurement decreased significantly with a larger gap (p < 0.001) and in the assisted method compared to the PACS method (p < 0.01). Our simplified MR-EFW measurement showed a dramatic decrease in time of planimetric measurement without a decrease in the accuracy of weight estimates. © 2017 S. Karger AG, Basel.

Searching for Partners of Cool Senior Citizens

NASA Astrophysics Data System (ADS)

Jao, Wei-Chun; Henry, T. J.

2012-01-01

Mass is one of the most fundamental parameters in stellar astronomy. In order to measure dynamical masses, one needs to find nearby binary systems that can be resolved and monitored, ideally with orbital periods that completely wrap in a reasonable amount of time. Many surveys have been made of nearby main sequence dwarfs, and their mass-luminosity relation is well established. As part of our Cool Subdwarf Investigations (CSI) program, we are searching for subdwarf binaries of spectral types K and M within 60 parsecs to measure their multiplicity rate and to reveal binaries appropriate for mass determinations. Here we present results of our CSI work using HST's Fine Guidance Sensors. When combined with previous CSI work and results in the literature, we find the multiplicity rate of subdwarfs, 21%, to be surprisingly low compared to that of similar main sequence K and M stars, 37%. This work has several implications, including that the star formation and/or evolution history of subdwarfs is different than for dwarfs, and that ideal systems for subdwarf mass determinations are difficult to find. This work is supported by HST grant GO-11943.

Photovoltaic System Modeling. Uncertainty and Sensitivity Analyses

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

Hansen, Clifford W.; Martin, Curtis E.

2015-08-01

We report an uncertainty and sensitivity analysis for modeling AC energy from ph otovoltaic systems . Output from a PV system is predicted by a sequence of models. We quantify u ncertainty i n the output of each model using empirical distribution s of each model's residuals. We propagate uncertainty through the sequence of models by sampli ng these distributions to obtain a n empirical distribution of a PV system's output. We consider models that: (1) translate measured global horizontal, direct and global diffuse irradiance to plane - of - array irradiance; (2) estimate effective irradiance; (3) predict cell temperature;more » (4) estimate DC voltage, current and power ; (5) reduce DC power for losses due to inefficient maximum power point tracking or mismatch among modules; and (6) convert DC to AC power . O ur analysis consider s a notional PV system com prising an array of FirstSolar FS - 387 modules and a 250 kW AC inverter ; we use measured irradiance and weather at Albuquerque, NM. We found the uncertainty in PV syste m output to be relatively small, on the order of 1% for daily energy. We found that unce rtainty in the models for POA irradiance and effective irradiance to be the dominant contributors to uncertainty in predicted daily energy. Our analysis indicates that efforts to reduce the uncertainty in PV system output predictions may yield the greatest improvements by focusing on the POA and effective irradiance models.« less

Operating characteristics of the implicit learning system supporting serial interception sequence learning.

PubMed

Sanchez, Daniel J; Reber, Paul J

2012-04-01

The memory system that supports implicit perceptual-motor sequence learning relies on brain regions that operate separately from the explicit, medial temporal lobe memory system. The implicit learning system therefore likely has distinct operating characteristics and information processing constraints. To attempt to identify the limits of the implicit sequence learning mechanism, participants performed the serial interception sequence learning (SISL) task with covertly embedded repeating sequences that were much longer than most previous studies: ranging from 30 to 60 (Experiment 1) and 60 to 90 (Experiment 2) items in length. Robust sequence-specific learning was observed for sequences up to 80 items in length, extending the known capacity of implicit sequence learning. In Experiment 3, 12-item repeating sequences were embedded among increasing amounts of irrelevant nonrepeating sequences (from 20 to 80% of training trials). Despite high levels of irrelevant trials, learning occurred across conditions. A comparison of learning rates across all three experiments found a surprising degree of constancy in the rate of learning regardless of sequence length or embedded noise. Sequence learning appears to be constant with the logarithm of the number of sequence repetitions practiced during training. The consistency in learning rate across experiments and conditions implies that the mechanisms supporting implicit sequence learning are not capacity-constrained by very long sequences nor adversely affected by high rates of irrelevant sequences during training.

Enhanced diffusion weighting generated by selective adiabatic pulse trains

NASA Astrophysics Data System (ADS)

Sun, Ziqi; Bartha, Robert

2007-09-01

A theoretical description and experimental validation of the enhanced diffusion weighting generated by selective adiabatic full passage (AFP) pulse trains is provided. Six phantoms (Ph-1-Ph-6) were studied on a 4 T Varian/Siemens whole body MRI system. Phantoms consisted of 2.8 cm diameter plastic tubes containing a mixture of 10 μm ORGASOL polymer beads and 2 mM Gd-DTPA dissolved in 5% agar (Ph-1) or nickel(II) ammonium sulphate hexahydrate doped (56.3-0.8 mM) water solutions (Ph-2-Ph-6). A customized localization by adiabatic selective refocusing (LASER) sequence containing slice selective AFP pulse trains and pulsed diffusion gradients applied in the phase encoding direction was used to measure 1H 2O diffusion. The b-value associated with the LASER sequence was derived using the Bloch-Torrey equation. The apparent diffusion coefficients measured by LASER were comparable to those measured by a conventional pulsed gradient spin-echo (PGSE) sequence for all phantoms. Image signal intensity increased in Ph-1 and decreased in Ph-2-Ph-6 as AFP pulse train length increased while maintaining a constant echo-time. These experimental results suggest that such AFP pulse trains can enhance contrast between regions containing microscopic magnetic susceptibility variations and homogeneous regions in which dynamic dephasing relaxation mechanisms are dominant.

SU-F-J-163: In Vivo Quantification of Sequence Parameter Effect On Geometric Distortion Caused by Implanted Titanium Brachytherapy Applicator

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

Sullivan, T; Diak, A; Surucu, M

Purpose: The use of MR to plan and evaluate brachytherapy treatment for cervical cancer is increasing given the availability of MR conditional or safe applicators and MRI’s proven superiority to CT for characterizing soft tissue lesions. The titanium applicators, however, cause geometric distortions or imaging artifacts, which reduce the utility of MRI for dosimetry. We sought to quantify the observed volume of the same applicator on a previously optimized T2 sequence in comparison to the conventional T2 sequence and CT obtained for brachytherapy planning. Methods: Prior work with testing in phantoms showed that increases in readout bandwidth yielded reductions inmore » artifact area and distortion measurements even with voxel increases. Following IRB approval, nine patients with titanium tandem & ovoid applicator (Varian Medical Systems) in place were scanned with a standard periprocedural protocol which included sagittal T2 fast spin echo (FSE) acquisition (res 0.98×0.78×4.0 mm{sup 3}; BW 200Hz). An additional T2-weighted FSE sequence (res 0.98×0.98×3–4 mm{sup 3}; BW500Hz) with increased readout bandwidth, readout voxel size, and echo train length was added to the protocol. Volume measurements of the applicator (from tip to cervical stop) were hand-segmented in Velocity AI 3.1 (Velocity Medical Solutions) for the two T2 FSE sequences and a planning CT obtained shortly after MRI. Differences were analyzed using a paired t-test. Results: Average apparent volumes of the applicator on standard T2 sequence, decreased bandwidth T2 sequence and CT were 5.922±1.283 cm{sup 3}, 4.544±1.524 cm3, and 2.304±0.509 cm{sup 3} respectively. Conclusion: Apparent volumes of a brachytherapy applicator can be compared in vivo. The modified sequence results in decreased apparent size of the cervical applicator. Both MR sequence volumes were larger than the planning CT, which was expected. Future work will focus on the diagnostic quality of the new sequence and quantifying any geometric shifts after CT to MRI registration based on anatomical landmarks.« less

TU-F-CAMPUS-I-04: Head-Only Asymmetric Gradient System Evaluation: ACR Image Quality and Acoustic Noise

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

Weavers, P; Shu, Y; Tao, S

Purpose: A high-performance head-only magnetic resonance imaging gradient system with an acquisition volume of 26 cm employing an asymmetric design for the transverse coils has been developed. It is able to reach a magnitude of 85 mT/m at a slew rate of 700 T/m/s, but operated at 80 mT/m and 500 T/m/s for this test. A challenge resulting from this asymmetric design is that the gradient nonlinearly exhibits both odd- and even-ordered terms, and as the full imaging field of view is often used, the nonlinearity is pronounced. The purpose of this work is to show the system can producemore » clinically useful images after an on-site gradient nonlinearity calibration and correction, and show that acoustic noise levels fall within non-significant risk (NSR) limits for standard clinical pulse sequences. Methods: The head-only gradient system was inserted into a standard 3T wide-bore scanner without acoustic damping. The ACR phantom was scanned in an 8-channel receive-only head coil and the standard American College of Radiology (ACR) MRI quality control (QC) test was performed. Acoustic noise levels were measured for several standard pulse sequences. Results: Images acquired with the head-only gradient system passed all ACR MR image quality tests; Both even and odd-order gradient distortion correction terms were required for the asymmetric gradients to pass. Acoustic noise measurements were within FDA NSR guidelines of 99 dBA (with assumed 20 dBA hearing protection) A-weighted and 140 dB for peak for all but one sequence. Note the gradient system was installed without any shroud or acoustic batting. We expect final system integration to greatly reduce noise experienced by the patient. Conclusion: A high-performance head-only asymmetric gradient system operating at 80 mT/m and 500 T/m/s conforms to FDA acoustic noise limits in all but one case, and passes all the ACR MR image quality control tests. This work was supported in part by the NIH grant 5R01EB010065.« less

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

PubMed

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

On irregularities of distribution of real sequences

PubMed Central

Chung, F. R. K.; Graham, R. L.

1981-01-01

A natural measure of the amount of unavoidable clustering that must occur in any bounded infinite sequence of real numbers is studied. We determine the extreme value for this measure and exhibit sequences that achieve this value. PMID:16593046

First experiment on LMJ facility: pointing and synchronisation qualification, sequences qualification

NASA Astrophysics Data System (ADS)

Henry, Olivier; Raffestin, Didier; Bretheau, Dominique; Luttmann, Michel; Graillot, Herve; Ferri, Michel; Seguineau, Frederic; Bar, Emmanuel; Patissou, Loic; Canal, Philippe; Sautarel, Françoise; Tranquille-Marques, Yves

2015-11-01

The LMJ (Laser mega Joule) facility at the CESTA site (Aquitaine, France) is a tool designed to deliver up to 1.2 MJ at 351 nm. The experiment system will include plasma diagnostics: UV and X energy balances, imagers (Streak and stripe camera, CCD), spectrometers, and a Visar/pyrometer. The facility must be able to deliver, within the hour following the shot, all the results of the plasma diagnostics, alignment images and laser diagnostic measurements. Part of the end of 2014 was devoted to the qualification of system pointing on target and synchronization within and between beams. The shots made with one chain (divided in 2 quads - 8 laser beams) have achieved 50 μm of misalignment accuracy and a synchronization accuracy in the order of 50 ps. The performances achieved for plasma diagnostic (in the order of less 100 μm of alignment and timing accuracy less than 150 ps) comply with expectations. At the same time the first automatic sequences were tested. They allowed a shot on target every 6h:30 and in some case twice a day by reducing preparation actions, leading to a sequence of 4h:00. These shooting sequences are managed by an operating team of 7 people helped by 3 people for security aspects.

Optimization of identity operation in NMR spectroscopy via genetic algorithm: Application to the TEDOR experiment

NASA Astrophysics Data System (ADS)

Manu, V. S.; Veglia, Gianluigi

2016-12-01

Identity operation in the form of π pulses is widely used in NMR spectroscopy. For an isolated single spin system, a sequence of even number of π pulses performs an identity operation, leaving the spin state essentially unaltered. For multi-spin systems, trains of π pulses with appropriate phases and time delays modulate the spin Hamiltonian to perform operations such as decoupling and recoupling. However, experimental imperfections often jeopardize the outcome, leading to severe losses in sensitivity. Here, we demonstrate that a newly designed Genetic Algorithm (GA) is able to optimize a train of π pulses, resulting in a robust identity operation. As proof-of-concept, we optimized the recoupling sequence in the transferred-echo double-resonance (TEDOR) pulse sequence, a key experiment in biological magic angle spinning (MAS) solid-state NMR for measuring multiple carbon-nitrogen distances. The GA modified TEDOR (GMO-TEDOR) experiment with improved recoupling efficiency results in a net gain of sensitivity up to 28% as tested on a uniformly 13C, 15N labeled microcrystalline ubiquitin sample. The robust identity operation achieved via GA paves the way for the optimization of several other pulse sequences used for both solid- and liquid-state NMR used for decoupling, recoupling, and relaxation experiments.

Designing Better Scaffolding in Teaching Complex Systems with Graphical Simulations

NASA Astrophysics Data System (ADS)

Li, Na

Complex systems are an important topic in science education today, but they are usually difficult for secondary-level students to learn. Although graphic simulations have many advantages in teaching complex systems, scaffolding is a critical factor for effective learning. This dissertation study was conducted around two complementary research questions on scaffolding: (1) How can we chunk and sequence learning activities in teaching complex systems? (2) How can we help students make connections among system levels across learning activities (level bridging)? With a sample of 123 seventh-graders, this study employed a 3x2 experimental design that factored sequencing methods (independent variable 1; three levels) with level-bridging scaffolding (independent variable 2; two levels) and compared the effectiveness of each combination. The study measured two dependent variables: (1) knowledge integration (i.e., integrating and connecting content-specific normative concepts and providing coherent scientific explanations); (2) understanding of the deep causal structure (i.e., being able to grasp and transfer the causal knowledge of a complex system). The study used a computer-based simulation environment as the research platform to teach the ideal gas law as a system. The ideal gas law is an emergent chemical system that has three levels: (1) experiential macro level (EM) (e.g., an aerosol can explodes when it is thrown into the fire); (2) abstract macro level (AM) (i.e., the relationships among temperature, pressure and volume); (3) micro level (Mi) (i.e., molecular activity). The sequencing methods of these levels were manipulated by changing the order in which they were delivered with three possibilities: (1) EM-AM-Mi; (2) Mi-AM-EM; (3) AM-Mi-EM. The level-bridging scaffolding variable was manipulated on two aspects: (1) inserting inter-level questions among learning activities; (2) two simulations dynamically linked in the final learning activity. Addressing the first research question, the Experiential macro-Abstract macro-Micro (EM-AM-Mi) sequencing method, following the "concrete to abstract" principle, produced better knowledge integration while the Micro-Abstract macro-Experiential macro (Mi-AM-EM) sequencing method, congruent with the causal direction of the emergent system, produced better understanding of the deep causal structure only when level-bridging scaffolding was provided. The Abstract macro-Micro-Experiential macro (AM-Mi-EM) sequencing method produced worse performance in general, because it did not follow the "concrete to abstract" principle, nor did it align with the causal structure of the emergent system. As to the second research question, the results showed that level-bridging scaffolding was important for both knowledge integration and understanding of the causal structure in learning the ideal gas law system.

Comparison of Next-Generation Sequencing Systems

PubMed Central

Liu, Lin; Li, Yinhu; Li, Siliang; Hu, Ni; He, Yimin; Pong, Ray; Lin, Danni; Lu, Lihua; Law, Maggie

2012-01-01

With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized. PMID:22829749

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, M.S.

1998-08-18

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device. 27 figs.

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.; Wang, Chunwei; Jevons, Luis C.; Bernhart, Derek H.; Lipshutz, Robert J.

2004-05-11

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

1998-08-18

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

2003-08-19

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

Real Time Apnoea Monitoring of Children Using the Microsoft Kinect Sensor: A Pilot Study

PubMed Central

Al-Naji, Ali; Gibson, Kim; Lee, Sang-Heon; Chahl, Javaan

2017-01-01

The objective of this study was to design a non-invasive system for the observation of respiratory rates and detection of apnoea using analysis of real time image sequences captured in any given sleep position and under any light conditions (even in dark environments). A Microsoft Kinect sensor was used to visualize the variations in the thorax and abdomen from the respiratory rhythm. These variations were magnified, analyzed and detected at a distance of 2.5 m from the subject. A modified motion magnification system and frame subtraction technique were used to identify breathing movements by detecting rapid motion areas in the magnified frame sequences. The experimental results on a set of video data from five subjects (3 h for each subject) showed that our monitoring system can accurately measure respiratory rate and therefore detect apnoea in infants and young children. The proposed system is feasible, accurate, safe and low computational complexity, making it an efficient alternative for non-contact home sleep monitoring systems and advancing health care applications. PMID:28165382

Knowledge-based decision support for Space Station assembly sequence planning

NASA Astrophysics Data System (ADS)

1991-04-01

A complete Personal Analysis Assistant (PAA) for Space Station Freedom (SSF) assembly sequence planning consists of three software components: the system infrastructure, intra-flight value added, and inter-flight value added. The system infrastructure is the substrate on which software elements providing inter-flight and intra-flight value-added functionality are built. It provides the capability for building representations of assembly sequence plans and specification of constraints and analysis options. Intra-flight value-added provides functionality that will, given the manifest for each flight, define cargo elements, place them in the National Space Transportation System (NSTS) cargo bay, compute performance measure values, and identify violated constraints. Inter-flight value-added provides functionality that will, given major milestone dates and capability requirements, determine the number and dates of required flights and develop a manifest for each flight. The current project is Phase 1 of a projected two phase program and delivers the system infrastructure. Intra- and inter-flight value-added were to be developed in Phase 2, which has not been funded. Based on experience derived from hundreds of projects conducted over the past seven years, ISX developed an Intelligent Systems Engineering (ISE) methodology that combines the methods of systems engineering and knowledge engineering to meet the special systems development requirements posed by intelligent systems, systems that blend artificial intelligence and other advanced technologies with more conventional computing technologies. The ISE methodology defines a phased program process that begins with an application assessment designed to provide a preliminary determination of the relative technical risks and payoffs associated with a potential application, and then moves through requirements analysis, system design, and development.

Knowledge-based decision support for Space Station assembly sequence planning

NASA Technical Reports Server (NTRS)

1991-01-01

A complete Personal Analysis Assistant (PAA) for Space Station Freedom (SSF) assembly sequence planning consists of three software components: the system infrastructure, intra-flight value added, and inter-flight value added. The system infrastructure is the substrate on which software elements providing inter-flight and intra-flight value-added functionality are built. It provides the capability for building representations of assembly sequence plans and specification of constraints and analysis options. Intra-flight value-added provides functionality that will, given the manifest for each flight, define cargo elements, place them in the National Space Transportation System (NSTS) cargo bay, compute performance measure values, and identify violated constraints. Inter-flight value-added provides functionality that will, given major milestone dates and capability requirements, determine the number and dates of required flights and develop a manifest for each flight. The current project is Phase 1 of a projected two phase program and delivers the system infrastructure. Intra- and inter-flight value-added were to be developed in Phase 2, which has not been funded. Based on experience derived from hundreds of projects conducted over the past seven years, ISX developed an Intelligent Systems Engineering (ISE) methodology that combines the methods of systems engineering and knowledge engineering to meet the special systems development requirements posed by intelligent systems, systems that blend artificial intelligence and other advanced technologies with more conventional computing technologies. The ISE methodology defines a phased program process that begins with an application assessment designed to provide a preliminary determination of the relative technical risks and payoffs associated with a potential application, and then moves through requirements analysis, system design, and development.

Software for Analyzing Sequences of Flow-Related Images

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2004-01-01

Spotlight is a computer program for analysis of sequences of images generated in combustion and fluid physics experiments. Spotlight can perform analysis of a single image in an interactive mode or a sequence of images in an automated fashion. The primary type of analysis is tracking of positions of objects over sequences of frames. Features and objects that are typically tracked include flame fronts, particles, droplets, and fluid interfaces. Spotlight automates the analysis of object parameters, such as centroid position, velocity, acceleration, size, shape, intensity, and color. Images can be processed to enhance them before statistical and measurement operations are performed. An unlimited number of objects can be analyzed simultaneously. Spotlight saves results of analyses in a text file that can be exported to other programs for graphing or further analysis. Spotlight is a graphical-user-interface-based program that at present can be executed on Microsoft Windows and Linux operating systems. A version that runs on Macintosh computers is being considered.

Anticipation measures of sequence learning: manual versus oculomotor versions of the serial reaction time task.

PubMed

Vakil, Eli; Bloch, Ayala; Cohen, Haggar

2017-03-01

The serial reaction time (SRT) task has generated a very large amount of research. Nevertheless the debate continues as to the exact cognitive processes underlying implicit sequence learning. Thus, the first goal of this study is to elucidate the underlying cognitive processes enabling sequence acquisition. We therefore compared reaction time (RT) in sequence learning in a standard manual activated (MA) to that in an ocular activated (OA) version of the task, within a single experimental setting. The second goal is to use eye movement measures to compare anticipation, as an additional indication of sequence learning, between the two versions of the SRT. Performance of the group given the MA version of the task (n = 29) was compared with that of the group given the OA version (n = 30). The results showed that although overall, RT was faster for the OA group, the rate of sequence learning was similar to that of the MA group performing the standard version of the SRT. Because the stimulus-response association is automatic and exists prior to training in the OA task, the decreased reaction time in this version of the task reflects a purer measure of the sequence learning that occurs in the SRT task. The results of this study show that eye tracking anticipation can be measured directly and can serve as a direct measure of sequence learning. Finally, using the OA version of the SRT to study sequence learning presents a significant methodological contribution by making sequence learning studies possible among populations that struggle to perform manual responses.

Design of an Optical System for Phase Retrieval based on a Spatial Light Modulator

NASA Astrophysics Data System (ADS)

Falldorf, Claas; Agour, Mostafa; von Kopylow, Christoph; Bergmann, Ralf B.

2010-04-01

We present an optical configuration for phase retrieval from a sequence of intensity measurements. The setup is based on a 4f-configuration with a phase modulating spatial light modulator (SLM) located in the Fourier domain. The SLM is used to modulate the incoming light with the transfer function of propagation, thus a sequence of propagated representations of the subjected wave field can be captured across a common sensor plane. The main advantage of this technique is the greatly reduced measurement time, since no mechanical adjustment of the camera sensor is required throughout the measurement process. The treatise is focused on the analysis of the wave field in the sensor domain. From the discussion a set of parameters is derived in order to minimize disturbing effects arising from the discrete nature of the SLM. Finally, the big potential of this approach is demonstrated by means of experimental investigations with regard to wave field sensing.

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Low noise charge ramp electrometer

DOEpatents

Morgan, John P.; Piper, Thomas C.

1992-01-01

An electrometer capable of measuring small currents without the use of a feedback resistor which tends to contribute a large noise factor to the measured data. The electrometer eliminates the feedback resistor through the use of a feedback capacitor located across the electrometer amplifier. The signal from the electrometer amplifier is transferred to a electrometer buffer amplifier which serves to transfer the signal to several receptors. If the electrometer amplifier is approaching saturation, the buffer amplifier signals a reset discriminator which energizes a coil whose magnetic field closes a magnetic relay switch which in turn resets or zeros the feedback capacitor. In turn, a reset complete discriminator restarts the measurement process when the electrometer amplifier approaches its initial condition. The buffer amplifier also transmits the voltage signal from the electrometer amplifier to a voltage-to-frequency converter. The signals from the voltage-to-frequency converter are counted over a fixed period of time and the information is relayed to a data processor. The timing and sequencing of the small current measuring system is under the control of a sequence control logic unit.

Low noise charge ramp electrometer

DOEpatents

Morgan, J.P.; Piper, T.C.

1992-10-06

An electrometer capable of measuring small currents without the use of a feedback resistor which tends to contribute a large noise factor to the measured data. The electrometer eliminates the feedback resistor through the use of a feedback capacitor located across the electrometer amplifier. The signal from the electrometer amplifier is transferred to a electrometer buffer amplifier which serves to transfer the signal to several receptors. If the electrometer amplifier is approaching saturation, the buffer amplifier signals a reset discriminator which energizes a coil whose magnetic field closes a magnetic relay switch which in turn resets or zeros the feedback capacitor. In turn, a reset complete discriminator restarts the measurement process when the electrometer amplifier approaches its initial condition. The buffer amplifier also transmits the voltage signal from the electrometer amplifier to a voltage-to-frequency converter. The signals from the voltage-to-frequency converter are counted over a fixed period of time and the information is relayed to a data processor. The timing and sequencing of the small current measuring system is under the control of a sequence control logic unit. 2 figs.

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.

Predicting protein-protein interactions by combing various sequence- derived features into the general form of Chou's Pseudo amino acid composition.

PubMed

Zhao, Xiao-Wei; Ma, Zhi-Qiang; Yin, Ming-Hao

2012-05-01

Knowledge of protein-protein interactions (PPIs) plays an important role in constructing protein interaction networks and understanding the general machineries of biological systems. In this study, a new method is proposed to predict PPIs using a comprehensive set of 930 features based only on sequence information, these features measure the interactions between residues a certain distant apart in the protein sequences from different aspects. To achieve better performance, the principal component analysis (PCA) is first employed to obtain an optimized feature subset. Then, the resulting 67-dimensional feature vectors are fed to Support Vector Machine (SVM). Experimental results on Drosophila melanogaster and Helicobater pylori datasets show that our method is very promising to predict PPIs and may at least be a useful supplement tool to existing methods.

Endogenous System Microbes as Treatment Process ...

EPA Pesticide Factsheets

Monitoring the efficacy of treatment strategies to remove pathogens in decentralized systems remains a challenge. Evaluating log reduction targets by measuring pathogen levels is hampered by their sporadic and low occurrence rates. Fecal indicator bacteria are used in centralized systems to indicate the presence of fecal pathogens, but are ineffective decentralized treatment process indicators as they generally occur at levels too low to assess log reduction targets. System challenge testing by spiking with high loads of fecal indicator organisms, like MS2 coliphage, has limitations, especially for large systems. Microbes that are endogenous to the decentralized system, occur in high abundances and mimic removal rates of bacterial, viral and/or parasitic protozoan pathogens during treatment could serve as alternative treatment process indicators to verify log reduction targets. To identify abundant microbes in wastewater, the bacterial and viral communities were examined using deep sequencing. Building infrastructure-associated bacteria, like Zoogloea, were observed as dominant members of the bacterial community in graywater. In blackwater, bacteriophage of the order Caudovirales constituted the majority of contiguous sequences from the viral community. This study identifies candidate treatment process indicators in decentralized systems that could be used to verify log removal during treatment. The association of the presence of treatment process indic

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

1999-10-26

A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

2001-06-05

A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Chaotic Behaviour of a Driven P-N Junction

NASA Astrophysics Data System (ADS)

Perez, Jose Maria

The chaotic behavior of a driven p-n junction is experimentally examined. Bifurcation diagrams for the system are measured, showing period doubling bifurcations up to f/32, onset of chaos, reverse bifurcations of chaotic bands, and periodic windows. Some of the measured bifurcation diagrams are similar to the bifurcation diagram of the logistic map x(,n+1) = (lamda)x(,n)(1 - x(,n)). A return map is also measured showing approximately a one-dimensional map with a single extremum at low driving voltages. The intermittency route to chaos is experimentally observed to occur near a tangent bifurcation as the system approaches a period 5 window at (lamda) = (lamda)(,5). Data are presented for the dependence of the average laminar length on (epsilon) = (lamda)(,5) - (lamda), and for the probability distribution P(l) vs. l. The effects of additive stochastic noise on period doubling, chaos, windows, and intermittency are examined and are found to agree with the logistic model and universal predictions. Three examples of crisis of the attractor are observed. The crises occur when an unstable orbit intersects the chaotic attractor. A period adding sequence is reported in which wide periodic windows of period 2, 3, 4, ... are observed for increasing driving voltage. The initial period doubling cascade and the period adding sequence are compared to two theoretical models, with reasonable success.

Uncertainty relations with quantum memory for the Wehrl entropy

NASA Astrophysics Data System (ADS)

De Palma, Giacomo

2018-03-01

We prove two new fundamental uncertainty relations with quantum memory for the Wehrl entropy. The first relation applies to the bipartite memory scenario. It determines the minimum conditional Wehrl entropy among all the quantum states with a given conditional von Neumann entropy and proves that this minimum is asymptotically achieved by a suitable sequence of quantum Gaussian states. The second relation applies to the tripartite memory scenario. It determines the minimum of the sum of the Wehrl entropy of a quantum state conditioned on the first memory quantum system with the Wehrl entropy of the same state conditioned on the second memory quantum system and proves that also this minimum is asymptotically achieved by a suitable sequence of quantum Gaussian states. The Wehrl entropy of a quantum state is the Shannon differential entropy of the outcome of a heterodyne measurement performed on the state. The heterodyne measurement is one of the main measurements in quantum optics and lies at the basis of one of the most promising protocols for quantum key distribution. These fundamental entropic uncertainty relations will be a valuable tool in quantum information and will, for example, find application in security proofs of quantum key distribution protocols in the asymptotic regime and in entanglement witnessing in quantum optics.

Automatic Human Movement Assessment With Switching Linear Dynamic System: Motion Segmentation and Motor Performance.

PubMed

de Souza Baptista, Roberto; Bo, Antonio P L; Hayashibe, Mitsuhiro

2017-06-01

Performance assessment of human movement is critical in diagnosis and motor-control rehabilitation. Recent developments in portable sensor technology enable clinicians to measure spatiotemporal aspects to aid in the neurological assessment. However, the extraction of quantitative information from such measurements is usually done manually through visual inspection. This paper presents a novel framework for automatic human movement assessment that executes segmentation and motor performance parameter extraction in time-series of measurements from a sequence of human movements. We use the elements of a Switching Linear Dynamic System model as building blocks to translate formal definitions and procedures from human movement analysis. Our approach provides a method for users with no expertise in signal processing to create models for movements using labeled dataset and later use it for automatic assessment. We validated our framework on preliminary tests involving six healthy adult subjects that executed common movements in functional tests and rehabilitation exercise sessions, such as sit-to-stand and lateral elevation of the arms and five elderly subjects, two of which with limited mobility, that executed the sit-to-stand movement. The proposed method worked on random motion sequences for the dual purpose of movement segmentation (accuracy of 72%-100%) and motor performance assessment (mean error of 0%-12%).

Time-of-flight radio location system

DOEpatents

McEwan, T.E.

1997-08-26

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. The sample signal in equivalent time is passed through an envelope detection circuit, formed of an absolute value circuit followed by a low pass filter, to convert the sample signal to a unipolar signal to eliminate effects of antenna misorientation. 8 figs.

Time-of-flight radio location system

DOEpatents

McEwan, Thomas E.

1997-01-01

A bi-static radar configuration measures the direct time-of-flight of a transmitted RF pulse and is capable of measuring this time-of-flight with a jitter on the order of about one pico-second, or about 0.01 inch of free space distance for an electromagnetic pulse over a range of about one to ten feet. A transmitter transmits a sequence of electromagnetic pulses in response to a transmit timing signal, and a receiver samples the sequence of electromagnetic pulses with controlled timing in response to a receive timing signal, and generates a sample signal in response to the samples. A timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the sequence of electromagnetic pulses such that the time between transmission of pulses in the sequence and sampling by the receiver sweeps over a range of delays. The receive timing signal sweeps over the range of delays in a sweep cycle such that pulses in the sequence are sampled at the pulse repetition rate, and with different delays in the range of delays to produce a sample signal representing magnitude of a received pulse in equivalent time. Automatic gain control circuitry in the receiver controls the magnitude of the equivalent time sample signal. A signal processor analyzes the sample signal to indicate the time-of-flight of the electromagnetic pulses in the sequence. The sample signal in equivalent time is passed through an envelope detection circuit, formed of an absolute value circuit followed by a low pass filter, to convert the sample signal to a unipolar signal to eliminate effects of antenna misorientation.

(Pea)nuts and bolts of visual narrative: Structure and meaning in sequential image comprehension

PubMed Central

Cohn, Neil; Paczynski, Martin; Jackendoff, Ray; Holcomb, Phillip J.; Kuperberg, Gina R.

2012-01-01

Just as syntax differentiates coherent sentences from scrambled word strings, the comprehension of sequential images must also use a cognitive system to distinguish coherent narrative sequences from random strings of images. We conducted experiments analogous to two classic studies of language processing to examine the contributions of narrative structure and semantic relatedness to processing sequential images. We compared four types of comic strips: 1) Normal sequences with both structure and meaning, 2) Semantic Only sequences (in which the panels were related to a common semantic theme, but had no narrative structure), 3) Structural Only sequences (narrative structure but no semantic relatedness), and 4) Scrambled sequences of randomly-ordered panels. In Experiment 1, participants monitored for target panels in sequences presented panel-by-panel. Reaction times were slowest to panels in Scrambled sequences, intermediate in both Structural Only and Semantic Only sequences, and fastest in Normal sequences. This suggests that both semantic relatedness and narrative structure offer advantages to processing. Experiment 2 measured ERPs to all panels across the whole sequence. The N300/N400 was largest to panels in both the Scrambled and Structural Only sequences, intermediate in Semantic Only sequences and smallest in the Normal sequences. This implies that a combination of narrative structure and semantic relatedness can facilitate semantic processing of upcoming panels (as reflected by the N300/N400). Also, panels in the Scrambled sequences evoked a larger left-lateralized anterior negativity than panels in the Structural Only sequences. This localized effect was distinct from the N300/N400, and appeared despite the fact that these two sequence types were matched on local semantic relatedness between individual panels. These findings suggest that sequential image comprehension uses a narrative structure that may be independent of semantic relatedness. Altogether, we argue that the comprehension of visual narrative is guided by an interaction between structure and meaning. PMID:22387723

Beryllium-10 dating of the duration and retreat of the last pinedale glacial sequence

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

Gosse, J.C.; Klein, J.; Evenson, E.B.

Accurate terrestrial glacial chronologies are needed for comparison with the marine record to establish the dynamics of global climate change during transitions from glacial to interglacial regimes. Cosmogenic beryllium-10 measurements in the Wind River Range indicate that the last glacial maximum (marine oxygen isotope stage 2) was achieved there by 21,700 {+-} 700 beryllium-10 years and lasted 5900 years. Ages of a sequence of recessional moraines and striated bedrock surfaces show that the initial deglaciation was rapid and that the entire glacial system retreated 33 kilometers to the cirque basin by 12,100 {+-} 500 beryllium-10 years.

Ensuring critical event sequences in high consequence computer based systems as inspired by path expressions

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

Kidd, M.E.C.

1997-02-01

The goal of our work is to provide a high level of confidence that critical software driven event sequences are maintained in the face of hardware failures, malevolent attacks and harsh or unstable operating environments. This will be accomplished by providing dynamic fault management measures directly to the software developer and to their varied development environments. The methodology employed here is inspired by previous work in path expressions. This paper discusses the perceived problems, a brief overview of path expressions, the proposed methods, and a discussion of the differences between the proposed methods and traditional path expression usage and implementation.

Performance and life cycle environmental benefits of recycling spent ion exchange brines by catalytic treatment of nitrate.

PubMed

Choe, Jong Kwon; Bergquist, Allison M; Jeong, Sangjo; Guest, Jeremy S; Werth, Charles J; Strathmann, Timothy J

2015-09-01

Salt used to make brines for regeneration of ion exchange (IX) resins is the dominant economic and environmental liability of IX treatment systems for nitrate-contaminated drinking water sources. To reduce salt usage, the applicability and environmental benefits of using a catalytic reduction technology to treat nitrate in spent IX brines and enable their reuse for IX resin regeneration were evaluated. Hybrid IX/catalyst systems were designed and life cycle assessment of process consumables are used to set performance targets for the catalyst reactor. Nitrate reduction was measured in a typical spent brine (i.e., 5000 mg/L NO3(-) and 70,000 mg/L NaCl) using bimetallic Pd-In hydrogenation catalysts with variable Pd (0.2-2.5 wt%) and In (0.0125-0.25 wt%) loadings on pelletized activated carbon support (Pd-In/C). The highest activity of 50 mgNO3(-)/(min - g(Pd)) was obtained with a 0.5 wt%Pd-0.1 wt%In/C catalyst. Catalyst longevity was demonstrated by observing no decrease in catalyst activity over more than 60 days in a packed-bed reactor. Based on catalyst activity measured in batch and packed-bed reactors, environmental impacts of hybrid IX/catalyst systems were evaluated for both sequencing-batch and continuous-flow packed-bed reactor designs and environmental impacts of the sequencing-batch hybrid system were found to be 38-81% of those of conventional IX. Major environmental impact contributors other than salt consumption include Pd metal, hydrogen (electron donor), and carbon dioxide (pH buffer). Sensitivity of environmental impacts of the sequencing-batch hybrid reactor system to sulfate and bicarbonate anions indicate the hybrid system is more sustainable than conventional IX when influent water contains <80 mg/L sulfate (at any bicarbonate level up to 100 mg/L) or <20 mg/L bicarbonate (at any sulfate level up to 100 mg/L) assuming 15 brine reuse cycles. The study showed that hybrid IX/catalyst reactor systems have potential to reduce resource consumption and improve environmental impacts associated with treating nitrate-contaminated water sources. Copyright © 2015 Elsevier Ltd. All rights reserved.

Neural-network-directed alignment of optical systems using the laser-beam spatial filter as an example

NASA Technical Reports Server (NTRS)

Decker, Arthur J.; Krasowski, Michael J.; Weiland, Kenneth E.

1993-01-01

This report describes an effort at NASA Lewis Research Center to use artificial neural networks to automate the alignment and control of optical measurement systems. Specifically, it addresses the use of commercially available neural network software and hardware to direct alignments of the common laser-beam-smoothing spatial filter. The report presents a general approach for designing alignment records and combining these into training sets to teach optical alignment functions to neural networks and discusses the use of these training sets to train several types of neural networks. Neural network configurations used include the adaptive resonance network, the back-propagation-trained network, and the counter-propagation network. This work shows that neural networks can be used to produce robust sequencers. These sequencers can learn by example to execute the step-by-step procedures of optical alignment and also can learn adaptively to correct for environmentally induced misalignment. The long-range objective is to use neural networks to automate the alignment and operation of optical measurement systems in remote, harsh, or dangerous aerospace environments. This work also shows that when neural networks are trained by a human operator, training sets should be recorded, training should be executed, and testing should be done in a manner that does not depend on intellectual judgments of the human operator.

Correlation time and diffusion coefficient imaging: application to a granular flow system.

PubMed

Caprihan, A; Seymour, J D

2000-05-01

A parametric method for spatially resolved measurements for velocity autocorrelation functions, R(u)(tau) = , expressed as a sum of exponentials, is presented. The method is applied to a granular flow system of 2-mm oil-filled spheres rotated in a half-filled horizontal cylinder, which is an Ornstein-Uhlenbeck process with velocity autocorrelation function R(u)(tau) = e(- ||tau ||/tau(c)), where tau(c) is the correlation time and D = tau(c) is the diffusion coefficient. The pulsed-field-gradient NMR method consists of applying three different gradient pulse sequences of varying motion sensitivity to distinguish the range of correlation times present for particle motion. Time-dependent apparent diffusion coefficients are measured for these three sequences and tau(c) and D are then calculated from the apparent diffusion coefficient images. For the cylinder rotation rate of 2.3 rad/s, the axial diffusion coefficient at the top center of the free surface was 5.5 x 10(-6) m(2)/s, the correlation time was 3 ms, and the velocity fluctuation or granular temperature was 1.8 x 10(-3) m(2)/s(2). This method is also applicable to study transport in systems involving turbulence and porous media flows. Copyright 2000 Academic Press.

Measuring the Mass of a Pre-Main Sequence Binary Star Through the Orbit of TWA 5A

NASA Astrophysics Data System (ADS)

Konopacky, Q. M.; Ghez, A. M.; McCabe, C.; Duchene, G.; Macintosh, B. A.

2005-12-01

We present the results of a five year monitoring campaign of the close binary TWA 5Aab in the TW Hydrae association, using speckle and adaptive optics on the W.M. Keck 10 m telescopes. These measurements were taken as part of our ongoing monitoring of pre-main sequence (PMS) binaries in an effort to increase the number of dynamically determined PMS masses and thereby calibrate the theoretical PMS evolutionary tracks. Our observations have allowed us to obtain the first determination of this system's astrometric orbit. We find an orbital period of 5.55 ± 0.07 years and a semi-major axis of 0.063 arcsec ± 0.004 arcsec. Combining these results with a kinematic distance, we calculate a total mass of 0.70 ± 0.24 M⊙ for this system. This mass measurement, as well as the estimated age of this system, are in best agreement with the model predictions of Baraffe et al. (1998), but are also consistent to within 1.6σ of all other models considered. Our formal significance is low due to our proper accounting of correlated uncertainties; these correlations are important and generally not accounted for in comparisons of this kind. Nonetheless, with only a few more years of observation, these models will be easily distinguished. Support for this work was provided by the NASA Astrobiology Institute, the NSF Science & Technology Center for AO, managed by UCSC (AST-9876783), and the Packard Foundation.

Working memory, short-term memory, and reading disabilities: a selective meta-analysis of the literature.

PubMed

Swanson, H Lee; Xinhua Zheng; Jerman, Olga

2009-01-01

The purpose of the present study was to synthesize research that compares children with and without reading disabilities (RD) on measures of short-term memory (STM) and working memory (WM). Across a broad age, reading, and IQ range, 578 effect sizes (ESs) were computed, yielding a mean ES across studies of -.89 (SD = 1.03). A total of 257 ESs were in the moderate range for STM measures (M = -.61, 95% confidence range of -.65 to -.58), and 320 ESs were in the moderate range for WM measures (M = -.67, 95% confidence range of -.68 to -.64). The results indicated that children with RD were distinctively disadvantaged compared with average readers on (a) STM measures requiring the recall of phonemes and digit sequences and (b) WM measures requiring the simultaneous processing and storage of digits within sentence sequences and final words from unrelated sentences. No significant moderating effects emerged for age, IQ, or reading level on memory ESs. The findings indicated that domain-specific STM and WM differences between ability groups persisted across age, suggesting that a verbal deficit model that fails to efficiently draw resources from both a phonological and executive system underlies RD.

Random digital encryption secure communication system

NASA Technical Reports Server (NTRS)

Doland, G. D. (Inventor)

1982-01-01

The design of a secure communication system is described. A product code, formed from two pseudorandom sequences of digital bits, is used to encipher or scramble data prior to transmission. The two pseudorandom sequences are periodically changed at intervals before they have had time to repeat. One of the two sequences is transmitted continuously with the scrambled data for synchronization. In the receiver portion of the system, the incoming signal is compared with one of two locally generated pseudorandom sequences until correspondence between the sequences is obtained. At this time, the two locally generated sequences are formed into a product code which deciphers the data from the incoming signal. Provision is made to ensure synchronization of the transmitting and receiving portions of the system.

Evaluation of Selected MR Pulse Sequences

NASA Astrophysics Data System (ADS)

Shin, Yong-Jin

1990-01-01

This research addressed four main areas of radiofrequency (rf) pulse programming: (1) correction of instrumentation errors in spin echo sequences by use of phase rolling of the rf pulses; (2) chemical shift imaging of water and lipid; (3) development of special pulse sequences for the measurement of phosphorus metabolites by ^ {31}P spectroscopy and lactate by ^1H spectroscopy; and (4) flow methods to measure and separate diffusion from perfusion. All experiments were performed on a horizontal 2.0T (superconducting magnet) 31-cm small-bore MR system. Computer programming and data analysis were performed on a PDP 11/84 computer system. 1. The effects of rf tips, dc and gain misadjustments in the rf spectrometer were evaluated for a series of MR images. Four different phase cycling schemes (FIXED, ALTERNATE, FORWARD, REVERSED) to suppress unwanted signal components such as mirror and ghost images were evaluated using two signal acquisitions. When the receiver phase factor is cycled counter-clockwise (REVERSED), these artifacts are completely removed. 2. A major problem common to all chemical shift imaging methods is static magnetic field non-uniformity. Four methods (Dixon's, CHESS, SECSI and modified CHESS-SECSI) were quantitatively evaluated for the measurement of water and fat content, which are separated by approximately 3.5 ppm, in in vivo biological tissues. It was demonstrated in phantoms that the modified CHESS+SECSI method gave superior results even without field shimming. 3. The development of new MR rf pulse sequences is essential in order to acquire specialized in vivo information concerning biologic metabolites. The time course of change in concentration of lactate and of phosphorus metabolites in human forearm muscle before and after exercise was determined. Lactate concentration returned to normal in 25 minutes after exercise. The Pi/PCr ratio was 0.25 before exercise, and increased to 0.5 at 4.5 minutes after exercise. 4. The fourth study involved the incorporation of a bipolar gradient pulse technique into a spin echo sequence; by varying the strength of the bipolar gradients, diffusion as well as perfusion can be quantitatively determined. The diffusion coefficient (D) for H_2O and acetone were 2.10 and 5.06 (times10 ^{-3} mm^2 /sec), respectively. The perfusion factor was linearly incremental for stepwise increases in flow velocities.

A TDM link with channel coding and digital voice.

NASA Technical Reports Server (NTRS)

Jones, M. W.; Tu, K.; Harton, P. L.

1972-01-01

The features of a TDM (time-division multiplexed) link model are described. A PCM telemetry sequence was coded for error correction and multiplexed with a digitized voice channel. An all-digital implementation of a variable-slope delta modulation algorithm was used to digitize the voice channel. The results of extensive testing are reported. The measured coding gain and the system performance over a Gaussian channel are compared with theoretical predictions and computer simulations. Word intelligibility scores are reported as a measure of voice channel performance.

Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

NASA Technical Reports Server (NTRS)

Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

2016-01-01

On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human Research Program investigations, and even life detection experiments for astrobiology missions.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

PubMed

Göke, Jonathan; Schulz, Marcel H; Lasserre, Julia; Vingron, Martin

2012-03-01

The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets. We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2. N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences. The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html. Supplementary data are available at Bioinformatics online.

Continuous blood pressure recordings simultaneously with functional brain imaging: studies of the glymphatic system

NASA Astrophysics Data System (ADS)

Zienkiewicz, Aleksandra; Huotari, Niko; Raitamaa, Lauri; Raatikainen, Ville; Ferdinando, Hany; Vihriälä, Erkki; Korhonen, Vesa; Myllylä, Teemu; Kiviniemi, Vesa

2017-03-01

The lymph system is responsible for cleaning the tissues of metabolic waste products, soluble proteins and other harmful fluids etc. Lymph flow in the body is driven by body movements and muscle contractions. Moreover, it is indirectly dependent on the cardiovascular system, where the heart beat and blood pressure maintain force of pressure in lymphatic channels. Over the last few years, studies revealed that the brain contains the so-called glymphatic system, which is the counterpart of the systemic lymphatic system in the brain. Similarly, the flow in the glymphatic system is assumed to be mostly driven by physiological pulsations such as cardiovascular pulses. Thus, continuous measurement of blood pressure and heart function simultaneously with functional brain imaging is of great interest, particularly in studies of the glymphatic system. We present our MRI compatible optics based sensing system for continuous blood pressure measurement and show our current results on the effects of blood pressure variations on cerebral brain dynamics, with a focus on the glymphatic system. Blood pressure was measured simultaneously with near-infrared spectroscopy (NIRS) combined with an ultrafast functional brain imaging (fMRI) sequence magnetic resonance encephalography (MREG, 3D brain 10 Hz sampling rate).

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

PubMed Central

2011-01-01

Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/. PMID:21385349

The writer independent online handwriting recognition system frog on hand and cluster generative statistical dynamic time warping.

PubMed

Bahlmann, Claus; Burkhardt, Hans

2004-03-01

In this paper, we give a comprehensive description of our writer-independent online handwriting recognition system frog on hand. The focus of this work concerns the presentation of the classification/training approach, which we call cluster generative statistical dynamic time warping (CSDTW). CSDTW is a general, scalable, HMM-based method for variable-sized, sequential data that holistically combines cluster analysis and statistical sequence modeling. It can handle general classification problems that rely on this sequential type of data, e.g., speech recognition, genome processing, robotics, etc. Contrary to previous attempts, clustering and statistical sequence modeling are embedded in a single feature space and use a closely related distance measure. We show character recognition experiments of frog on hand using CSDTW on the UNIPEN online handwriting database. The recognition accuracy is significantly higher than reported results of other handwriting recognition systems. Finally, we describe the real-time implementation of frog on hand on a Linux Compaq iPAQ embedded device.

Intensity inhomogeneity correction for magnetic resonance imaging of human brain at 7T.

PubMed

Uwano, Ikuko; Kudo, Kohsuke; Yamashita, Fumio; Goodwin, Jonathan; Higuchi, Satomi; Ito, Kenji; Harada, Taisuke; Ogawa, Akira; Sasaki, Makoto

2014-02-01

To evaluate the performance and efficacy for intensity inhomogeneity correction of various sequences of the human brain in 7T MRI using the extended version of the unified segmentation algorithm. Ten healthy volunteers were scanned with four different sequences (2D spin echo [SE], 3D fast SE, 2D fast spoiled gradient echo, and 3D time-of-flight) by using a 7T MRI system. Intensity inhomogeneity correction was performed using the "New Segment" module in SPM8 with four different values (120, 90, 60, and 30 mm) of full width at half maximum (FWHM) in Gaussian smoothness. The uniformity in signals in the entire white matter was evaluated using the coefficient of variation (CV); mean signal intensities between the subcortical and deep white matter were compared, and contrast between subcortical white matter and gray matter was measured. The length of the lenticulostriate (LSA) was measured on maximum intensity projection (MIP) images in the original and corrected images. In all sequences, the CV decreased as the FWHM value decreased. The differences of mean signal intensities between subcortical and deep white matter also decreased with smaller FWHM values. The contrast between white and gray matter was maintained at all FWHM values. LSA length was significantly greater in corrected MIP than in the original MIP images. Intensity inhomogeneity in 7T MRI can be successfully corrected using SPM8 for various scan sequences.

Molecular interaction networks in the analyses of sequence variation and proteomics data.

PubMed

Stelzl, Ulrich

2013-12-01

Protein-protein interaction networks are typically generated in standard cell lines or model organisms as it is prohibitively difficult to record large interaction datasets from specific tissues or disease models at a reasonable pace. Although the interaction data are of high confidence, they thus do not reflect in vivo relationships as such. A wealth of physiologically relevant protein information, obtained under different conditions and from different systems, is available including information on genetic variation, protein levels, and PTMs. However, these data are difficult to assess comprehensively because the relationships between the entities remain elusive from the measurements. Here, we exemplarily highlight recent studies that gained deeper insight from genetic variation, protein, and PTM measurements using interaction information pointing toward the importance and potential of interaction networks for the interpretation of sequencing and proteomics data. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sensitivity-enhanced IPAP experiments for measuring one-bond 13C '- 13C α and 13C α- 1H α residual dipolar couplings in proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2004-04-01

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C '- 13C α and 1H α- 13C α dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2 Δ. For cases of limited resolution in the 2D 15N- 1H N HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.

A single bout of high-intensity aerobic exercise facilitates response to paired associative stimulation and promotes sequence-specific implicit motor learning

PubMed Central

Mang, Cameron S.; Snow, Nicholas J.; Campbell, Kristin L.; Ross, Colin J. D.

2014-01-01

The objectives of the present study were to evaluate the impact of a single bout of high-intensity aerobic exercise on 1) long-term potentiation (LTP)-like neuroplasticity via response to paired associative stimulation (PAS) and 2) the temporal and spatial components of sequence-specific implicit motor learning. Additionally, relationships between exercise-induced increases in systemic brain-derived neurotrophic factor (BDNF) and response to PAS and motor learning were evaluated. Sixteen young healthy participants completed six experimental sessions, including the following: 1) rest followed by PAS; 2) aerobic exercise followed by PAS; 3) rest followed by practice of a continuous tracking (CT) task and 4) a no-exercise 24-h retention test; and 5) aerobic exercise followed by CT task practice and 6) a no-exercise 24-h retention test. The CT task included an embedded repeated sequence allowing for evaluation of sequence-specific implicit learning. Slope of motor-evoked potential recruitment curves generated with transcranial magnetic stimulation showed larger increases when PAS was preceded by aerobic exercise (59.8% increase) compared with rest (14.2% increase, P = 0.02). Time lag of CT task performance on the repeated sequence improved under the aerobic exercise condition from early (−100.8 ms) to late practice (−75.2 ms, P < 0.001) and was maintained at retention (−79.2 ms, P = 0.004) but did not change under the rest condition (P > 0.16). Systemic BDNF increased on average by 3.4-fold following aerobic exercise (P = 0.003), but the changes did not relate to neurophysiological or behavioral measures (P > 0.42). These results indicate that a single bout of high-intensity aerobic exercise can prime LTP-like neuroplasticity and promote sequence-specific implicit motor learning. PMID:25257866

Automated quantification of lumbar vertebral kinematics from dynamic fluoroscopic sequences

NASA Astrophysics Data System (ADS)

Camp, Jon; Zhao, Kristin; Morel, Etienne; White, Dan; Magnuson, Dixon; Gay, Ralph; An, Kai-Nan; Robb, Richard

2009-02-01

We hypothesize that the vertebra-to-vertebra patterns of spinal flexion and extension motion of persons with lower back pain will differ from those of persons who are pain-free. Thus, it is our goal to measure the motion of individual lumbar vertebrae noninvasively from dynamic fluoroscopic sequences. Two-dimensional normalized mutual information-based image registration was used to track frame-to-frame motion. Software was developed that required the operator to identify each vertebra on the first frame of the sequence using a four-point "caliper" placed at the posterior and anterior edges of the inferior and superior end plates of the target vertebrae. The program then resolved the individual motions of each vertebra independently throughout the entire sequence. To validate the technique, 6 cadaveric lumbar spine specimens were potted in polymethylmethacrylate and instrumented with optoelectric sensors. The specimens were then placed in a custom dynamic spine simulator and moved through flexion-extension cycles while kinematic data and fluoroscopic sequences were simultaneously acquired. We found strong correlation between the absolute flexionextension range of motion of each vertebra as recorded by the optoelectric system and as determined from the fluoroscopic sequence via registration. We conclude that this method is a viable way of noninvasively assessing twodimensional vertebral motion.

Eye vision system using programmable micro-optics and micro-electronics

NASA Astrophysics Data System (ADS)

Riza, Nabeel A.; Amin, M. Junaid; Riza, Mehdi N.

2014-02-01

Proposed is a novel eye vision system that combines the use of advanced micro-optic and microelectronic technologies that includes programmable micro-optic devices, pico-projectors, Radio Frequency (RF) and optical wireless communication and control links, energy harvesting and storage devices and remote wireless energy transfer capabilities. This portable light weight system can measure eye refractive powers, optimize light conditions for the eye under test, conduct color-blindness tests, and implement eye strain relief and eye muscle exercises via time sequenced imaging. Described is the basic design of the proposed system and its first stage system experimental results for vision spherical lens refractive error correction.

Recognising promoter sequences using an artificial immune system

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

Cooke, D.E.; Hunt, J.E.

1995-12-31

We have developed an artificial immune system (AIS) which is based on the human immune system. The AIS possesses an adaptive learning mechanism which enables antibodies to emerge which can be used for classification tasks. In this paper, we describe how the AIS has been used to evolve antibodies which can classify promoter containing and promoter negative DNA sequences. The DNA sequences used for teaching were 57 nucleotides in length and contained procaryotic promoters. The system classified previously unseen DNA sequences with an accuracy of approximately 90%.

Feasibility analysis on integration of luminous environment measuring and design based on exposure curve calibration

NASA Astrophysics Data System (ADS)

Zou, Yuan; Shen, Tianxing

2013-03-01

Besides illumination calculating during architecture and luminous environment design, to provide more varieties of photometric data, the paper presents combining relation between luminous environment design and SM light environment measuring system, which contains a set of experiment devices including light information collecting and processing modules, and can offer us various types of photometric data. During the research process, we introduced a simulation method for calibration, which mainly includes rebuilding experiment scenes in 3ds Max Design, calibrating this computer aid design software in simulated environment under conditions of various typical light sources, and fitting the exposure curves of rendered images. As analytical research went on, the operation sequence and points for attention during the simulated calibration were concluded, connections between Mental Ray renderer and SM light environment measuring system were established as well. From the paper, valuable reference conception for coordination between luminous environment design and SM light environment measuring system was pointed out.

The dynamics and optimal control of spinning spacecraft and movable telescoping appendages, part A. [two axis control with single offset boom

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Sellappan, R.

1977-01-01

The problem of optimal control with a minimum time criterion as applied to a single boom system for achieving two axis control is discussed. The special case where the initial conditions are such that the system can be driven to the equilibrium state with only a single switching maneuver in the bang-bang optimal sequence is analyzed. The system responses are presented. Application of the linear regulator problem for the optimal control of the telescoping system is extended to consider the effects of measurement and plant noises. The noise uncertainties are included with an application of the estimator - Kalman filter problem. Different schemes for measuring the components of the angular velocity are considered. Analytical results are obtained for special cases, and numerical results are presented for the general case.

Development of an electrochemical detection system for measuring DNA methylation levels using methyl CpG-binding protein and glucose dehydrogenase-fused zinc finger protein.

PubMed

Lee, Jinhee; Yoshida, Wataru; Abe, Koichi; Nakabayashi, Kazuhiko; Wakeda, Hironobu; Hata, Kenichiro; Marquette, Christophe A; Blum, Loïc J; Sode, Koji; Ikebukuro, Kazunori

2017-07-15

DNA methylation level at a certain gene region is considered as a new type of biomarker for diagnosis and its miniaturized and rapid detection system is required for diagnosis. Here we have developed a simple electrochemical detection system for DNA methylation using methyl CpG-binding domain (MBD) and a glucose dehydrogenase (GDH)-fused zinc finger protein. This analytical system consists of three steps: (1) methylated DNA collection by MBD, (2) PCR amplification of a target genomic region among collected methylated DNA, and (3) electrochemical detection of the PCR products using a GDH-fused zinc finger protein. With this system, we have successfully measured the methylation levels at the promoter region of the androgen receptor gene in 10 6 copies of genomic DNA extracted from PC3 and TSU-PR1 cancer cell lines. Since no sequence analysis or enzymatic digestion is required for this detection system, DNA methylation levels can be measured within 3h with a simple procedure. Copyright © 2016 Elsevier B.V. All rights reserved.

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile, and accurate RNA structure analysis

PubMed Central

Smola, Matthew J.; Rice, Greggory M.; Busan, Steven; Siegfried, Nathan A.; Weeks, Kevin M.

2016-01-01

SHAPE chemistries exploit small electrophilic reagents that react with the 2′-hydroxyl group to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues based on the ability of reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as for simple model RNAs. This protocol describes the experimental steps, implemented over three days, required to perform SHAPE probing and construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. These steps include RNA folding and SHAPE structure probing, mutational profiling by reverse transcription, library construction, and sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides useful troubleshooting information, often within an hour. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures, and visualize probable and alternative helices, often in under a day. We illustrate these algorithms with the E. coli thiamine pyrophosphate riboswitch, E. coli 16S rRNA, and HIV-1 genomic RNAs. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles, and entire transcriptomes. The straightforward MaP strategy greatly expands the number, length, and complexity of analyzable RNA structures. PMID:26426499

Discovery of Par 1802 as a Low-Mass, Pre-Main-Sequence Eclipsing Binary in the Orion Star-Forming Region

NASA Astrophysics Data System (ADS)

Cargile, P. A.; Stassun, K. G.; Mathieu, R. D.

2008-02-01

We report the discovery of a pre-main-sequence (PMS), low-mass, double-lined, spectroscopic, eclipsing binary in the Orion star-forming region. We present our observations, including radial velocities derived from optical high-resolution spectroscopy, and present an orbit solution that permits the determination of precise empirical masses for both components of the system. We find that Par 1802 is composed of two equal-mass (0.39 +/- 0.03, 0.40 +/- 0.03 M⊙) stars in a circular, 4.7 day orbit. There is strong evidence, such as the system exhibiting strong Li lines and a center-of-mass velocity consistent with cluster membership, that this system is a member of the Orion star-forming region and quite possibly the Orion Nebula Cluster, and therefore has an age of only a few million years. As there are currently only a few empirical mass and radius measurements for low-mass, PMS stars, this system presents an interesting test for the predictions of current theoretical models of PMS stellar evolution.

Rényi continuous entropy of DNA sequences.

PubMed

Vinga, Susana; Almeida, Jonas S

2004-12-07

Entropy measures of DNA sequences estimate their randomness or, inversely, their repeatability. L-block Shannon discrete entropy accounts for the empirical distribution of all length-L words and has convergence problems for finite sequences. A new entropy measure that extends Shannon's formalism is proposed. Renyi's quadratic entropy calculated with Parzen window density estimation method applied to CGR/USM continuous maps of DNA sequences constitute a novel technique to evaluate sequence global randomness without some of the former method drawbacks. The asymptotic behaviour of this new measure was analytically deduced and the calculation of entropies for several synthetic and experimental biological sequences was performed. The results obtained were compared with the distributions of the null model of randomness obtained by simulation. The biological sequences have shown a different p-value according to the kernel resolution of Parzen's method, which might indicate an unknown level of organization of their patterns. This new technique can be very useful in the study of DNA sequence complexity and provide additional tools for DNA entropy estimation. The main MATLAB applications developed and additional material are available at the webpage . Specialized functions can be obtained from the authors.

Sequence spaces [Formula: see text] and [Formula: see text] with application in clustering.

PubMed

Khan, Mohd Shoaib; Alamri, Badriah As; Mursaleen, M; Lohani, Qm Danish

2017-01-01

Distance measures play a central role in evolving the clustering technique. Due to the rich mathematical background and natural implementation of [Formula: see text] distance measures, researchers were motivated to use them in almost every clustering process. Beside [Formula: see text] distance measures, there exist several distance measures. Sargent introduced a special type of distance measures [Formula: see text] and [Formula: see text] which is closely related to [Formula: see text]. In this paper, we generalized the Sargent sequence spaces through introduction of [Formula: see text] and [Formula: see text] sequence spaces. Moreover, it is shown that both spaces are BK -spaces, and one is a dual of another. Further, we have clustered the two-moon dataset by using an induced [Formula: see text]-distance measure (induced by the Sargent sequence space [Formula: see text]) in the k-means clustering algorithm. The clustering result established the efficacy of replacing the Euclidean distance measure by the [Formula: see text]-distance measure in the k-means algorithm.

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

Li, Heng, E-mail: hengli@mdanderson.org; Zhu, X. Ronald; Zhang, Xiaodong

Purpose: To develop and validate a novel delivery strategy for reducing the respiratory motion–induced dose uncertainty of spot-scanning proton therapy. Methods and Materials: The spot delivery sequence was optimized to reduce dose uncertainty. The effectiveness of the delivery sequence optimization was evaluated using measurements and patient simulation. One hundred ninety-one 2-dimensional measurements using different delivery sequences of a single-layer uniform pattern were obtained with a detector array on a 1-dimensional moving platform. Intensity modulated proton therapy plans were generated for 10 lung cancer patients, and dose uncertainties for different delivery sequences were evaluated by simulation. Results: Without delivery sequence optimization,more » the maximum absolute dose error can be up to 97.2% in a single measurement, whereas the optimized delivery sequence results in a maximum absolute dose error of ≤11.8%. In patient simulation, the optimized delivery sequence reduces the mean of fractional maximum absolute dose error compared with the regular delivery sequence by 3.3% to 10.6% (32.5-68.0% relative reduction) for different patients. Conclusions: Optimizing the delivery sequence can reduce dose uncertainty due to respiratory motion in spot-scanning proton therapy, assuming the 4-dimensional CT is a true representation of the patients' breathing patterns.« less

Image-based computer-assisted diagnosis system for benign paroxysmal positional vertigo

NASA Astrophysics Data System (ADS)

Kohigashi, Satoru; Nakamae, Koji; Fujioka, Hiromu

2005-04-01

We develop the image based computer assisted diagnosis system for benign paroxysmal positional vertigo (BPPV) that consists of the balance control system simulator, the 3D eye movement simulator, and the extraction method of nystagmus response directly from an eye movement image sequence. In the system, the causes and conditions of BPPV are estimated by searching the database for record matching with the nystagmus response for the observed eye image sequence of the patient with BPPV. The database includes the nystagmus responses for simulated eye movement sequences. The eye movement velocity is obtained by using the balance control system simulator that allows us to simulate BPPV under various conditions such as canalithiasis, cupulolithiasis, number of otoconia, otoconium size, and so on. Then the eye movement image sequence is displayed on the CRT by the 3D eye movement simulator. The nystagmus responses are extracted from the image sequence by the proposed method and are stored in the database. In order to enhance the diagnosis accuracy, the nystagmus response for a newly simulated sequence is matched with that for the observed sequence. From the matched simulation conditions, the causes and conditions of BPPV are estimated. We apply our image based computer assisted diagnosis system to two real eye movement image sequences for patients with BPPV to show its validity.

Multilocus Sequence Typing Compared to Pulsed-Field Gel Electrophoresis for Molecular Typing of Pseudomonas aeruginosa▿

PubMed Central

Johnson, Jennifer K.; Arduino, Sonia M.; Stine, O. Colin; Johnson, Judith A.; Harris, Anthony D.

2007-01-01

For hospital epidemiologists, determining a system of typing that is discriminatory is essential for measuring the effectiveness of infection control measures. In situations in which the incidence of resistant Pseudomonas aeruginosa is increasing, the ability to discern whether it is due to patient-to-patient transmission versus an increase in patient endogenous strains is often made on the basis of molecular typing. The present study compared the discriminatory abilities of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for 90 P. aeruginosa isolates obtained from cultures of perirectal surveillance swabs from patients in an intensive care unit. PFGE identified 85 distinct types and 76 distinct groups when similarity cutoffs of 100% and 87%, respectively, were used. By comparison, MLST identified 60 sequence types that could be clustered into 11 clonal complexes and 32 singletons. By using the Simpson index of diversity (D), PFGE had a greater discriminatory ability than MLST for P. aeruginosa isolates (D values, 0.999 versus 0.975, respectively). Thus, while MLST was better for detecting genetic relatedness, we determined that PFGE was more discriminatory than MLST for determining genetic differences in P. aeruginosa. PMID:17881548

Software fault tolerance in computer operating systems

NASA Technical Reports Server (NTRS)

Iyer, Ravishankar K.; Lee, Inhwan

1994-01-01

This chapter provides data and analysis of the dependability and fault tolerance for three operating systems: the Tandem/GUARDIAN fault-tolerant system, the VAX/VMS distributed system, and the IBM/MVS system. Based on measurements from these systems, basic software error characteristics are investigated. Fault tolerance in operating systems resulting from the use of process pairs and recovery routines is evaluated. Two levels of models are developed to analyze error and recovery processes inside an operating system and interactions among multiple instances of an operating system running in a distributed environment. The measurements show that the use of process pairs in Tandem systems, which was originally intended for tolerating hardware faults, allows the system to tolerate about 70% of defects in system software that result in processor failures. The loose coupling between processors which results in the backup execution (the processor state and the sequence of events occurring) being different from the original execution is a major reason for the measured software fault tolerance. The IBM/MVS system fault tolerance almost doubles when recovery routines are provided, in comparison to the case in which no recovery routines are available. However, even when recovery routines are provided, there is almost a 50% chance of system failure when critical system jobs are involved.

Detection and interrogation of biomolecules via nanoscale probes: From fundamental physics to DNA sequencing

NASA Astrophysics Data System (ADS)

Zwolak, Michael

2013-03-01

A rapid and low-cost method to sequence DNA would revolutionize personalized medicine, where genetic information is used to diagnose, treat, and prevent diseases. There is a longstanding interest in nanopores as a platform for rapid interrogation of single DNA molecules. I will discuss a sequencing protocol based on the measurement of transverse electronic currents during the translocation of single-stranded DNA through nanopores. Using molecular dynamics simulations coupled to quantum mechanical calculations of the tunneling current, I will show that the DNA nucleotides are predicted to have distinguishable electronic signatures in experimentally realizable systems. Several recent experiments support our theoretical predictions. In addition to their possible impact in medicine and biology, the above methods offer ideal test beds to study open scientific issues in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. http://mike.zwolak.org

Quantifying Genome Editing Outcomes at Endogenous Loci using SMRT Sequencing

PubMed Central

Clark, Joseph; Punjya, Niraj; Sebastiano, Vittorio; Bao, Gang; Porteus, Matthew H

2014-01-01

SUMMARY Targeted genome editing with engineered nucleases has transformed the ability to introduce precise sequence modifications at almost any site within the genome. A major obstacle to probing the efficiency and consequences of genome editing is that no existing method enables the frequency of different editing events to be simultaneously measured across a cell population at any endogenous genomic locus. We have developed a novel method for quantifying individual genome editing outcomes at any site of interest using single molecule real time (SMRT) DNA sequencing. We show that this approach can be applied at various loci, using multiple engineered nuclease platforms including TALENs, RNA guided endonucleases (CRISPR/Cas9), and ZFNs, and in different cell lines to identify conditions and strategies in which the desired engineering outcome has occurred. This approach facilitates the evaluation of new gene editing technologies and permits sensitive quantification of editing outcomes in almost every experimental system used. PMID:24685129

An analysis of the uncertainty and bias in DCE-MRI measurements using the spoiled gradient-recalled echo pulse sequence.

PubMed

Subashi, Ergys; Choudhury, Kingshuk R; Johnson, G Allan

2014-03-01

The pharmacokinetic parameters derived from dynamic contrast-enhanced (DCE) MRI have been used in more than 100 phase I trials and investigator led studies. A comparison of the absolute values of these quantities requires an estimation of their respective probability distribution function (PDF). The statistical variation of the DCE-MRI measurement is analyzed by considering the fundamental sources of error in the MR signal intensity acquired with the spoiled gradient-echo (SPGR) pulse sequence. The variance in the SPGR signal intensity arises from quadrature detection and excitation flip angle inconsistency. The noise power was measured in 11 phantoms of contrast agent concentration in the range [0-1] mM (in steps of 0.1 mM) and in onein vivo acquisition of a tumor-bearing mouse. The distribution of the flip angle was determined in a uniform 10 mM CuSO4 phantom using the spin echo double angle method. The PDF of a wide range of T1 values measured with the varying flip angle (VFA) technique was estimated through numerical simulations of the SPGR equation. The resultant uncertainty in contrast agent concentration was incorporated in the most common model of tracer exchange kinetics and the PDF of the derived pharmacokinetic parameters was studied numerically. The VFA method is an unbiased technique for measuringT1 only in the absence of bias in excitation flip angle. The time-dependent concentration of the contrast agent measured in vivo is within the theoretically predicted uncertainty. The uncertainty in measuring K(trans) with SPGR pulse sequences is of the same order, but always higher than, the uncertainty in measuring the pre-injection longitudinal relaxation time (T10). The lowest achievable bias/uncertainty in estimating this parameter is approximately 20%-70% higher than the bias/uncertainty in the measurement of the pre-injection T1 map. The fractional volume parameters derived from the extended Tofts model were found to be extremely sensitive to the variance in signal intensity. The SNR of the pre-injection T1 map indicates the limiting precision with which K(trans) can be calculated. Current small-animal imaging systems and pulse sequences robust to motion artifacts have the capacity for reproducible quantitative acquisitions with DCE-MRI. In these circumstances, it is feasible to achieve a level of precision limited only by physiologic variability.

An innovative experimental sequence on electromagnetic induction and eddy currents based on video analysis and cheap data acquisition

NASA Astrophysics Data System (ADS)

Bonanno, A.; Bozzo, G.; Sapia, P.

2017-11-01

In this work, we present a coherent sequence of experiments on electromagnetic (EM) induction and eddy currents, appropriate for university undergraduate students, based on a magnet falling through a drilled aluminum disk. The sequence, leveraging on the didactical interplay between the EM and mechanical aspects of the experiments, allows us to exploit the students’ awareness of mechanics to elicit their comprehension of EM phenomena. The proposed experiments feature two kinds of measurements: (i) kinematic measurements (performed by means of high-speed video analysis) give information on the system’s kinematics and, via appropriate numerical data processing, allow us to get dynamic information, in particular on energy dissipation; (ii) induced electromagnetic field (EMF) measurements (by using a homemade multi-coil sensor connected to a cheap data acquisition system) allow us to quantitatively determine the inductive effects of the moving magnet on its neighborhood. The comparison between experimental results and the predictions from an appropriate theoretical model (of the dissipative coupling between the moving magnet and the conducting disk) offers many educational hints on relevant topics related to EM induction, such as Maxwell’s displacement current, magnetic field flux variation, and the conceptual link between induced EMF and induced currents. Moreover, the didactical activity gives students the opportunity to be trained in video analysis, data acquisition and numerical data processing.

Photovoltaic system criteria documents. Volume 6: Criteria for auditing photovoltaic system applications and experiments. Revision A

NASA Technical Reports Server (NTRS)

Koenig, John C.; Billitti, Joseph W.; Tallon, John M.

1980-01-01

The criteria is defined for auditing photovoltaic system applications and experiments. The purpose of the audit is twofold: to see if the application is meeting its stated objectives and to measure the application's progress in terms of the National Photovoltaic Program's goals of performance, cost, reliability, safety, and socio-environmental acceptance. The information obtained from an audit will be used to assess the status of an application and to provide the Department of Energy with recommendations on the future conduct of the application. Those aspects are covered of a site audit necessary to produce a systematic method for the gathering of qualitative and quantitative data to measure the success of an application. A sequence of audit events and guidelines for obtaining the required information is presented.

Coherent manipulation of non-thermal spin order in optical nuclear polarization experiments

NASA Astrophysics Data System (ADS)

Buntkowsky, Gerd; Ivanov, Konstantin L.; Zimmermann, Herbert; Vieth, Hans-Martin

2017-03-01

Time resolved measurements of Optical Nuclear Polarization (ONP) have been performed on hyperpolarized triplet states in molecular crystals created by light excitation. Transfer of the initial electron polarization to nuclear spins has been studied in the presence of radiofrequency excitation; the experiments have been performed with different pulse sequences using different doped molecular systems. The experimental results clearly demonstrate the dominant role of coherent mechanisms of spin order transfer, which manifest themselves in well pronounced oscillations. These oscillations are of two types, precessions and nutations, having characteristic frequencies, which are the same for the different molecular systems and the pulse sequences applied. Hence, precessions and nutations constitute a general feature of polarization transfer in ONP experiments. In general, coherent manipulation of spin order transfer creates a powerful resource for improving the performance of the ONP method, which paves the way to strong signal enhancement in nuclear magnetic resonance.

Prefire identification for pulse-power systems

DOEpatents

Longmire, J.L.; Thuot, M.E.; Warren, D.S.

1982-08-23

Prefires in a high-power, high-frequency, multi-stage pulse generator are detected by a system having an EMI shielded pulse timing transmitter associated with and tailored to each stage of the pulse generator. Each pulse timing transmitter upon detection of a pulse triggers a laser diode to send an optical signal through a high frequency fiber optic cable to a pulse timing receiver which converts the optical signal to an electrical pulse. The electrical pulses from all pulse timing receivers are fed through an OR circuit to start a time interval measuring device and each electrical pulse is used to stop an individual channel in the measuring device thereby recording the firing sequence of the multi-stage pulse generator.

Prefire identification for pulse power systems

DOEpatents

Longmire, Jerry L.; Thuot, Michael E.; Warren, David S.

1985-01-01

Prefires in a high-power, high-frequency, multi-stage pulse generator are detected by a system having an EMI shielded pulse timing transmitter associated with and tailored to each stage of the pulse generator. Each pulse timing transmitter upon detection of a pulse triggers a laser diode to send an optical signal through a high frequency fiber optic cable to a pulse timing receiver which converts the optical signal to an electrical pulse. The electrical pulses from all pulse timing receivers are fed through an OR circuit to start a time interval measuring device and each electrical pulse is used to stop an individual channel in the measuring device thereby recording the firing sequence of the multi-stage pulse generator.

Expanding the functionality and applications of nanopore sensors

NASA Astrophysics Data System (ADS)

Venta, Kimberly E.

Nanopore sensors have developed into powerful tools for single-molecule studies since their inception two decades ago. Nanopore sensors function as nanoscale Coulter counters, by monitoring ionic current modulations as particles pass through a nanopore. While nanopore sensors can be used to study any nanoscale particle, their most notable application is as a low cost, fast alternative to current DNA sequencing technologies. In recent years, signifcant progress has been made toward the goal of nanopore-based DNA sequencing, which requires an ambitious combination of a low-noise and high-bandwidth nanopore measurement system and spatial resolution. In this dissertation, nanopore sensors in thin membranes are developed to improve dimensional resolution, and these membranes are used in parallel with a high-bandwidth amplfier. Using this nanopore sensor system, the signals of three DNA homopolymers are differentiated for the first time in solid-state nanopores. The nanopore noise is also reduced through the addition of a layer of SU8, a spin-on polymer, to the supporting chip structure. By increasing the temporal and spatial resolution of nanopore sensors, studies of shorter molecules are now possible. Nanopore sensors are beginning to be used for the study and characterization of nanoparticles. Nanoparticles have found many uses from biomedical imaging to next-generation solar cells. However, further insights into the formation and characterization of nanoparticles would aid in developing improved synthesis methods leading to more effective and customizable nanoparticles. This dissertation presents two methods of employing nanopore sensors to benet nanoparticle characterization and fabrication. Nanopores were used to study the formation of individual nanoparticles and serve as nanoparticle growth templates that could be exploited to create custom nanoparticle arrays. Additionally, nanopore sensors were used to characterize the surface charge density of anisotropic nanopores, which previously could not be reliably measured. Current nanopore sensor resolution levels have facilitated innovative research on nanoscale systems, including studies of DNA and nanoparticle characterization. Further nanopore system improvements will enable vastly improved DNA sequencing capabilities and open the door to additional nanopore sensing applications.

Bearings Only Tracking with Fusion from Heterogenous Passive Sensors: ESM/EO and Acoustic

DTIC Science & Technology

2017-02-01

consists of an unscented Kalman filter (UKF) to handle in-sequence ESM/EO measurements and an OOSM unscented Gauss-Helmert filter (OOSM-UGHF) to handle out...bearings-only tracking, target motion analysis, unscented Gauss-Helmert filter , out-of-sequence measurement. I. INTRODUCTION The commonly used passive...proposed an unscented Gauss-Helmert filter (UGHF) [22] [21] to solve this problem. The existing UGHF works with in-sequence measurements. Further

Statistical complexity measure of pseudorandom bit generators

NASA Astrophysics Data System (ADS)

González, C. M.; Larrondo, H. A.; Rosso, O. A.

2005-08-01

Pseudorandom number generators (PRNG) are extensively used in Monte Carlo simulations, gambling machines and cryptography as substitutes of ideal random number generators (RNG). Each application imposes different statistical requirements to PRNGs. As L’Ecuyer clearly states “the main goal for Monte Carlo methods is to reproduce the statistical properties on which these methods are based whereas for gambling machines and cryptology, observing the sequence of output values for some time should provide no practical advantage for predicting the forthcoming numbers better than by just guessing at random”. In accordance with different applications several statistical test suites have been developed to analyze the sequences generated by PRNGs. In a recent paper a new statistical complexity measure [Phys. Lett. A 311 (2003) 126] has been defined. Here we propose this measure, as a randomness quantifier of a PRNGs. The test is applied to three very well known and widely tested PRNGs available in the literature. All of them are based on mathematical algorithms. Another PRNGs based on Lorenz 3D chaotic dynamical system is also analyzed. PRNGs based on chaos may be considered as a model for physical noise sources and important new results are recently reported. All the design steps of this PRNG are described, and each stage increase the PRNG randomness using different strategies. It is shown that the MPR statistical complexity measure is capable to quantify this randomness improvement. The PRNG based on the chaotic 3D Lorenz dynamical system is also evaluated using traditional digital signal processing tools for comparison.

Multi-sensor Array for High Altitude Balloon Missions to the Stratosphere

NASA Astrophysics Data System (ADS)

Davis, Tim; McClurg, Bryce; Sohl, John

2008-10-01

We have designed and built a microprocessor controlled and expandable multi-sensor array for data collection on near space missions. Weber State University has started a high altitude research balloon program called HARBOR. This array has been designed to data log a base set of measurements for every flight and has room for six guest instruments. The base measurements are absolute pressure, on-board temperature, 3-axis accelerometer for attitude measurement, and 2-axis compensated magnetic compass. The system also contains a real time clock and circuitry for logging data directly to a USB memory stick. In typical operation the measurements will be cycled through in sequence and saved to the memory stick along with the clock's time stamp. The microprocessor can be reprogrammed to adapt to guest experiments with either analog or digital interfacing. This system will fly with every mission and will provide backup data collection for other instrumentation for which the primary task is measuring atmospheric pressure and temperature. The attitude data will be used to determine the orientation of the onboard camera systems to aid in identifying features in the images. This will make these images easier to use for any future GIS (geographic information system) remote sensing missions.

System for Measuring Flexing of a Large Spaceborne Structure

NASA Technical Reports Server (NTRS)

Scharf, Daniel; Kuhnert, Andreas; Kovalik, Joseph; Hadaegh, Fred; Shaddock, Daniel

2008-01-01

An optoelectronic metrology system is used for determining the attitude and flexing of a large spaceborne radar antenna or similar structure. The measurements are needed for accurate pointing of the antenna and correction and control of the phase of the radar signal wavefront. The system includes a dual-field-of-view star tracker; a laser ranging unit (LRU) and a position-sensitive-detector (PSD)-based camera mounted on an optical bench; and fiducial targets at various locations on the structure. The fiducial targets are illuminated in sequence by laser light coupled via optical fibers. The LRU and the PSD provide measurements of the position of each fiducial target in a reference frame attached to the optical bench. During routine operation, the star tracker utilizes one field of view and functions conventionally to determine the orientation of the optical bench. During operation in a calibration mode, the star tracker also utilizes its second field of view, which includes stars that are imaged alongside some of the fiducial targets in the PSD; in this mode, the PSD measurements are traceable to star measurements.

Using FRET to Measure the Angle at Which a Protein Bends DNA: TBP Binding a TATA Box as a Model System

ERIC Educational Resources Information Center

Kugel, Jennifer F.

2008-01-01

An undergraduate biochemistry laboratory experiment that will teach the technique of fluorescence resonance energy transfer (FRET) while analyzing protein-induced DNA bending is described. The experiment uses the protein TATA binding protein (TBP), which is a general transcription factor that recognizes and binds specific DNA sequences known as…

Minimizing structural vibrations with Input Shaping (TM)

NASA Technical Reports Server (NTRS)

Singhose, Bill; Singer, Neil

1995-01-01

A new method for commanding machines to move with increased dynamic performance was developed. This method is an enhanced version of input shaping, a patented vibration suppression algorithm. This technique intercepts a command input to a system command that moves the mechanical system with increased performance and reduced residual vibration. This document describes many advanced methods for generating highly optimized shaping sequences which are tuned to particular systems. The shaping sequence is important because it determines the trade off between move/settle time of the system and the insensitivity of the input shaping algorithm to variations or uncertainties in the machine which can be controlled. For example, a system with a 5 Hz resonance that takes 1 second to settle can be improved to settle instantaneously using a 0.2 shaping sequence (thus improving settle time by a factor of 5). This system could vary by plus or minus 15% in its natural frequency and still have no apparent vibration. However, the same system shaped with a 0.3 second shaping sequence could tolerate plus or minus 40% or more variation in natural frequency. This document describes how to generate sequences that maximize performance, sequences that maximize insensitivity, and sequences that trade off between the two. Several software tools are documented and included.

Distribution of injected wastewater in the saline-lava aquifer, Wailuku-Kahului wastewater treatment facility, Kahului, Maui, Hawaii

USGS Publications Warehouse

Burnham, Willis L.; Larson, S.P.; Cooper, Hilton Hammond

1977-01-01

Field studies and digital modeling of a lava rock aquifer system near Kahului, Maui, Hawaii, describe the distribution of planned injected wastewater from a secondary treatment facility. The aquifer contains water that is almost as saline as seawater. The saline water is below a seaward-discharging freshwater lens, and separated from it by a transition zone of varying salinity. Injection of wastewater at an average rate of 6.2 cubic feet per second is planned through wells open only to the aquifer deep within the saline water zone. The lava rock aquifer is overlain by a sequence of residual soil, clay, coral reef deposits, and marine sand that form a low-permeability caprock which semiconfines the lava rock aquifer. Under conditions measured and assumed without significant change. After reaching a new steady state, the wastewater will discharge into and through the caprock sequence within an area measuring approximately 1,000 feet inland, 1,000 feet laterally on either side of the injection site, and about 2,000 feet seaward. Little, if any, of the injected wastewater may be expected to reach the upper part of the caprock flow system landward of the treatment plant facility. (Woodard-USGS)

Prophylaxis against the systemic hypotension induced by propofol during rapid-sequence intubation.

PubMed

el-Beheiry, H; Kim, J; Milne, B; Seegobin, R

1995-10-01

The objective of this study was to determine the effectiveness of two prophylactic approaches against the anticipated hypotension induced by propofol during rapid-sequence intubation. Thirty-six male or female nonpremedicated ASA class I-II patients aged 21-60 yr undergoing elective outpatient surgery were included in the study. Patients were randomly allocated to receive pre-induction ephedrine sulphate (70 micrograms x kg(-1)iv), pre-induction volume loading (12 ml x kg(-1) Ringer's lactate) or no treatment. Rapid-sequence intubation with cricoid pressure was then performed with propofol (2.5 mg. x kg(-1)) and succinylcholine (1.5 mg x kg(-1). The lungs were subsequently ventilated with 0.25-0.5% isoflurane in a 2:1 N2O/O2 mixture. Vecuronium was given once neuromuscular function had recovered from the succinylcholine. Heart rate and systemic arterial blood pressure were measured non-invasively before induction, after propofol administration and every minute for ten minutes after intubation. Pre-induction volume loading prevented the hypotension observed before surgical stimulation in control and ephedrine groups. Moreover, pre-induction volume loading was not associated with increases in heart rate after intubation as was ephedrine administration. The intubating conditions were excellent to satisfactory in most patients and the overall incidence of adverse events during intubation was mainly due to pain during injection of propofol. The present study showed that preoperative volume loading is more efficacious than pre-induction administration of ephedrine sulphate in maintaining haemodynamic stability during rapid-sequence induction with propofol and succinylcholine. In addition, propofol in combination with succinylcholine provides excellent conditions for rapid-sequence intubation.

Pathfinder Photogrammetry Research for Ultra-Lightweight and Inflatable Space Structures

NASA Technical Reports Server (NTRS)

Giersch, Louis Roy Miller

2001-01-01

The defining characteristic of ultra-lightweight and inflatable space structures is that they are both very large and very low mass. This makes standard contacting methods of measurement (e.g. attaching accelerometers) impractical because the dynamics of the structure would be changed by the mass of the contacting instrument. Optical measurements are therefore more appropriate. Photogrammetry is a leading candidate for the optical analysis of gossamer structures because it allows for the measurement of a large number of points, is amenable to time sequences, and offers the potential for a high degree of accuracy. The purpose of this thesis is to develop the methodology and determine the effectiveness of a photogrammetry system in measuring ultra-lightweight and inflatable space structures. The results of this thesis will be considered in the design of an automated photogrammetry system for the l6m-diameter vacuum chamber at the NASA Langley Research Center.

High-resolution motion compensated MRA in patients with congenital heart disease using extracellular contrast agent at 3 Tesla.

PubMed

Dabir, Darius; Naehle, Claas Philip; Clauberg, Ralf; Gieseke, Juergen; Schild, Hans H; Thomas, Daniel

2012-10-29

Using first-pass MRA (FP-MRA) spatial resolution is limited by breath-hold duration. In addition, image quality may be hampered by respiratory and cardiac motion artefacts. In order to overcome these limitations an ECG- and navigator-gated high-resolution-MRA sequence (HR-MRA) with slow infusion of extracellular contrast agent was implemented at 3 Tesla for the assessment of congenital heart disease and compared to standard first-pass-MRA (FP-MRA). 34 patients (median age: 13 years) with congenital heart disease (CHD) were prospectively examined on a 3 Tesla system. The CMR-protocol comprised functional imaging, FP- and HR-MRA, and viability imaging. After the acquisition of the FP-MRA sequence using a single dose of extracellular contrast agent the motion compensated HR-MRA sequence with isotropic resolution was acquired while injecting the second single dose, utilizing the timeframe before viability imaging. Qualitative scores for image quality (two independent reviewers) as well as quantitative measurements of vessel sharpness and relative contrast were compared using the Wilcoxon signed-rank test. Quantitative measurements of vessel diameters were compared using the Bland-Altman test. The mean image quality score revealed significantly better image quality of the HR-MRA sequence compared to the FP-MRA sequence in all vessels of interest (ascending aorta (AA), left pulmonary artery (LPA), left superior pulmonary vein (LSPV), coronary sinus (CS), and coronary ostia (CO); all p < 0.0001). In comparison to FP-MRA, HR-MRA revealed significantly better vessel sharpness for all considered vessels (AA, LSPV and LPA; all p < 0.0001). The relative contrast of the HR-MRA sequence was less compared to the FP-MRA sequence (AA: p <0.028, main pulmonary artery: p <0.004, LSPV: p <0.005). Both, the results of the intra- and interobserver measurements of the vessel diameters revealed closer correlation and closer 95 % limits of agreement for the HR-MRA. HR-MRA revealed one additional clinical finding, missed by FP-MRA. An ECG- and navigator-gated HR-MRA-protocol with infusion of extracellular contrast agent at 3 Tesla is feasible. HR-MRA delivers significantly better image quality and vessel sharpness compared to FP-MRA. It may be integrated into a standard CMR-protocol for patients with CHD without the need for additional contrast agent injection and without any additional examination time.

Using string alignment in a query-by-humming system for real world applications

NASA Astrophysics Data System (ADS)

Sailer, Christian

2005-09-01

Though query by humming (i.e., retrieving music or information about music by singing a characteristic melody) has been a popular research topic during the past decade, few approaches have reached a level of usefulness beyond mere scientific interest. One of the main problems is the inherent contradiction between error tolerance and dicriminative power in conventional melody matching algorithms that rely on a melody contour approach to handle intonation or transcription errors. Adopting the string matching/alignment techniques from bioinformatics to melody sequences allows to directly assess the similarity between two melodies. This method takes an MPEG-7 compliant melody sequence (i.e., a list of note intervals and length ratios) as query and evaluates the steps necessary to transform it into the reference sequence. By introducing a musically founded cost-of-replace function and an adequate post processing, this method yields a measure for melodic similarity. Thus it is possible to construct a query by humming system that can properly discriminate between thousands of melodies and still be sufficiently error tolerant to be used by untrained singers. The robustness has been verified in extensive tests and real world applications.

Phase-based motion magnification video for monitoring of vital signals using the Hermite transform

NASA Astrophysics Data System (ADS)

Brieva, Jorge; Moya-Albor, Ernesto

2017-11-01

In this paper we present a new Eulerian phase-based motion magnification technique using the Hermite Transform (HT) decomposition that is inspired in the Human Vision System (HVS). We test our method in one sequence of the breathing of a newborn baby and on a video sequence that shows the heartbeat on the wrist. We detect and magnify the heart pulse applying our technique. Our motion magnification approach is compared to the Laplacian phase based approach by means of quantitative metrics (based on the RMS error and the Fourier transform) to measure the quality of both reconstruction and magnification. In addition a noise robustness analysis is performed for the two methods.

Cortical Sensitivity to Guitar Note Patterns: EEG Entrainment to Repetition and Key.

PubMed

Bridwell, David A; Leslie, Emily; McCoy, Dakarai Q; Plis, Sergey M; Calhoun, Vince D

2017-01-01

Music is ubiquitous throughout recent human culture, and many individual's have an innate ability to appreciate and understand music. Our appreciation of music likely emerges from the brain's ability to process a series of repeated complex acoustic patterns. In order to understand these processes further, cortical responses were measured to a series of guitar notes presented with a musical pattern or without a pattern. ERP responses to individual notes were measured using a 24 electrode Bluetooth mobile EEG system (Smarting mBrainTrain) while 13 healthy non-musicians listened to structured (i.e., within musical keys and with repetition) or random sequences of guitar notes for 10 min each. We demonstrate an increased amplitude to the ERP that appears ~200 ms to notes presented within the musical sequence. This amplitude difference between random notes and patterned notes likely reflects individual's cortical sensitivity to guitar note patterns. These amplitudes were compared to ERP responses to a rare note embedded within a stream of frequent notes to determine whether the sensitivity to complex musical structure overlaps with the sensitivity to simple irregularities reflected in traditional auditory oddball experiments. Response amplitudes to the negative peak at ~175 ms are statistically correlated with the mismatch negativity (MMN) response measured to a rare note presented among a series of frequent notes (i.e., in a traditional oddball sequence), but responses to the subsequent positive peak at ~200 do not show a statistical relationship with the P300 response. Thus, the sensitivity to musical structure identified to 4 Hz note patterns appears somewhat distinct from the sensitivity to statistical regularities reflected in the traditional "auditory oddball" sequence. Overall, we suggest that this is a promising approach to examine individual's sensitivity to complex acoustic patterns, which may overlap with higher level cognitive processes, including language.

Microbes in mercury-enriched geothermal springs in western North America.

PubMed

Geesey, Gill G; Barkay, Tamar; King, Sue

2016-11-01

Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea. Copyright © 2016 Elsevier B.V. All rights reserved.

A method of measuring three-dimensional scapular attitudes using the optotrak probing system.

PubMed

Hébert, L J; Moffet, H; McFadyen, B J; St-Vincent, G

2000-01-01

To develop a method to obtain accurate three-dimensional scapular attitudes and to assess their concurrent validity and reliability. In this methodological study, the three-dimensional scapular attitudes were calculated in degrees, using a rotation matrix (cyclic Cardanic sequence), from spatial coordinates obtained with the probing of three non colinear landmarks first on an anatomical model and second on a healthy subject. Although abnormal movement of the scapula is related to shoulder impingement syndrome, it is not clearly understood whether or not scapular motion impairment is a predisposing factor. Characterization of three-dimensional scapular attitudes in planes and at joint angles for which sub-acromial impingement is more likely to occur is not known. The Optotrak probing system was used. An anatomical model of the scapula was built and allowed us to impose scapular attitudes of known direction and magnitude. A local coordinate reference system was defined with three non colinear anatomical landmarks to assess accuracy and concurrent validity of the probing method with fixed markers. Axial rotation angles were calculated from a rotation matrix using a cyclic Cardanic sequence of rotations. The same three non colinear body landmarks were digitized on one healthy subject and the three dimensional scapular attitudes obtained were compared between sessions in order to assess the reliability. The measure of three dimensional scapular attitudes calculated from data using the Optotrak probing system was accurate with means of the differences between imposed and calculated rotation angles ranging from 1.5 degrees to 4.2 degrees. Greatest variations were observed around the third axis of the Cardanic sequence associated with posterior-anterior transverse rotations. The mean difference between the Optotrak probing system method and fixed markers was 1.73 degrees showing a good concurrent validity. Differences between the two methods were generally very low for one and two direction displacements and the largest discrepancies were observed for imposed displacements combining movement about the three axes. The between sessions variation of three dimensional scapular attitudes was less than 10% for most of the arm positions adopted by a healthy subject suggesting a good reliability. The Optotrak probing system used with a standardized protocol lead to accurate, valid and reliable measures of scapular attitudes. Although abnormal range of motion of the scapula is often related to shoulder pathologies, reliable outcome measures to quantify three-dimensional scapular motion on subjects are not available. It is important to establish a standardized protocol to characterize three-dimensional scapular motion on subjects using a method for which the accuracy and validity are known. The method used in the present study has provided such a protocol and will now allow to verify to what extent, scapular motion impairment is linked to the development of specific shoulder pathologies.

Tidal-bundle sequences in the Jordan Sandstone (Upper Cambrian), southeastern Minnesota, U.S.A.: Evidence for tides along inboard shorelines of the Sauk Epicontinental Sea

USGS Publications Warehouse

Tape, C.H.; Cowan, Clinton A.; Runkel, Anthony C.

2003-01-01

This study documents for the first time tidal bundling in a lower Paleozoic sheet sandstone from the cratonic interior of North America, providing insights into the hydrodynamics of ancient epicontinental seas. The Jordan Sandstone (Upper Cambrian) in the Upper Mississippi Valley contains large-scale planar tabular cross-sets with tidal-bundle sequences, which were analyzed in detail at an exceptional exposure. Tidal-bundle sequences (neap-spring-neap cycles) were delineated by foreset thickening-thinning patterns and composite shale drapes, the latter of which represent accumulations of mud during the neap tides of neap-spring-neap tidal cycles. Fourier analysis of the bundle thickness data from the 26 measurable bundle sequences revealed cycles ranging from 15 to 34 bundles per sequence, which suggests a semidiurnal or mixed tidal system along this part of the Late Cambrian shoreline. We extend the tidal interpretation to widespread occurrences of the same facies in outcrops of lesser quality, where the facies is recognizable but too few bundles are exposed for tidal cycles to be measured. By doing so, this study shows that tidally generated deposits have a significant geographic and temporal extent in Upper Cambrian strata of central mid-continent North America. The deposition and preservation of tidal facies was related to the intermittent development of shoreline embayments during transgressions. The tidally dominated deposits filled ravined topographies that were repeatedly developed on the updip parts of the shoreface. Resulting coastal geomorphologies, accompanied perhaps by larger-scale changes in basinal conditions and/or configuration, led to changes in depositional conditions from wave-dominated to tide-dominated. Outcrops of the Jordan Sandstone tidal facies in the Upper Mississippi Valley represent the farthest inboard recorded transmission of ocean-generated tides in the Laurentian epicontinental seas, demonstrating that tidal currents were significant agents in the transport of sand along the far cratonic interior shorelines of Cambrian North America. The results of this study improve the facies-level understanding of the genesis of sheet sandstones. Furthermore, tidalites documented here occur in a specific position within a sequence stratigraphic architecture for the Jordan Sandstone. This provides a framework to compare these ancient deposits and processes to younger (e.g., Carboniferous) epicontinental systems where stratal and sediment dynamics are better documented. ?? 2003, SEPM (Society for Sedimentary Geology).

A general model for memory interference in a multiprocessor system with memory hierarchy

NASA Technical Reports Server (NTRS)

Taha, Badie A.; Standley, Hilda M.

1989-01-01

The problem of memory interference in a multiprocessor system with a hierarchy of shared buses and memories is addressed. The behavior of the processors is represented by a sequence of memory requests with each followed by a determined amount of processing time. A statistical queuing network model for determining the extent of memory interference in multiprocessor systems with clusters of memory hierarchies is presented. The performance of the system is measured by the expected number of busy memory clusters. The results of the analytic model are compared with simulation results, and the correlation between them is found to be very high.

Automatic prediction of protein domains from sequence information using a hybrid learning system.

PubMed

Nagarajan, Niranjan; Yona, Golan

2004-06-12

We describe a novel method for detecting the domain structure of a protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence and are combined into a single predictor using a neural network. The output is further smoothed and post-processed using a probabilistic model to predict the most likely transition positions between domains. The method was assessed using the domain definitions in SCOP and CATH for proteins of known structure and was compared with several other existing methods. Our method performs well both in terms of accuracy and sensitivity. It improves significantly over the best methods available, even some of the semi-manual ones, while being fully automatic. Our method can also be used to suggest and verify domain partitions based on structural data. A few examples of predicted domain definitions and alternative partitions, as suggested by our method, are also discussed. An online domain-prediction server is available at http://biozon.org/tools/domains/

High-rep-rate Thomson scattering for LHD

NASA Astrophysics Data System (ADS)

den Hartog, D. J.; Borchardt, M. T.; Holly, D. J.; Schmitz, O.; Yasuhara, R.; Yamada, I.; Funaba, H.; Osakabe, M.; Morisaki, T.

2017-10-01

A high-rep-rate pulse-burst laser system is being built for the LHD Thomson scattering (TS) diagnostic. This laser will have two operating scenarios, a fast-burst sequence of 15 kHz rep rate for at least 15 ms, and a slow-burst sequence of 1 kHz for at least 50 ms. There will be substantial flexibility in burst sequences for tailoring to experimental requirements. This new laser system will operate alongside the existing lasers in the LHD TS diagnostic, and will use the same beamline. This increase in temporal resolution capability complements the high spatial resolution (144 points) of the LHD TS diagnostic, providing unique measurement capability unmatched on any other fusion experiment. The new pulse-burst laser is a straightforward application of technology developed at UW-Madison, consisting of a Nd:YAG laser head with modular flashlamp drive units and a customized control system. Variable pulse-width drive of the flashlamps is accomplished by IGBT (insulated gate bipolar transistor) switching of electrolytic capacitor banks. Direct control of the laser Pockels cell drive enables optimal pulse energy extraction, producing >1.5 J q-switched pulses with 20 ns FWHM. Burst operation of this laser system will be used to capture fast time evolution of the electron temperature and density profiles during events such as ELMs, RMP perturbations, and various MHD modes. This work is supported by the U. S. Department of Energy and the National Institute for Fusion Science (Japan).

Clinical application of a light-pen computer system for quantitative angiography

NASA Technical Reports Server (NTRS)

Alderman, E. L.

1975-01-01

The paper describes an angiographic analysis system which uses a video disk for recording and playback, a light-pen for data input, minicomputer processing, and an electrostatic printer/plotter for hardcopy output. The method is applied to quantitative analysis of ventricular volumes, sequential ventriculography for assessment of physiologic and pharmacologic interventions, analysis of instantaneous time sequence of ventricular systolic and diastolic events, and quantitation of segmental abnormalities. The system is shown to provide the capability for computation of ventricular volumes and other measurements from operator-defined margins by greatly reducing the tedium and errors associated with manual planimetry.

[Microbial air purity in hospitals. Operating theatres with air conditioning system].

PubMed

Krogulski, Adam; Szczotko, Maciej

2010-01-01

The aim of this study was to show the influence of air conditioning control for microbial contamination of air inside the operating theatres equipped with correctly working air-conditioning system. This work was based on the results of bacteria and fungi concentration in hospital air obtained since 2001. Assays of microbial air purity conducted on atmospheric air in parallel with indoor air demonstrated that air filters applied in air-conditioning systems worked correctly in every case. To show the problem of fluctuation of bacteria concentration more precisely, every sequences of single results from successive measure series were examined independently.

Wideband Arrhythmia-Insensitive-Rapid (AIR) Pulse Sequence for Cardiac T1 mapping without Image Artifacts induced by ICD

PubMed Central

Hong, KyungPyo; Jeong, Eun-Kee; Wall, T. Scott; Drakos, Stavros G.; Kim, Daniel

2015-01-01

Purpose To develop and evaluate a wideband arrhythmia-insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by implantable-cardioverter-defibrillator (ICD). Methods We developed a wideband AIR pulse sequence by incorporating a saturation pulse with wide frequency bandwidth (8.9 kHz), in order to achieve uniform T1 weighting in the heart with ICD. We tested the performance of original and “wideband” AIR cardiac T1 mapping pulse sequences in phantom and human experiments at 1.5T. Results In 5 phantoms representing native myocardium and blood and post-contrast blood/tissue T1 values, compared with the control T1 values measured with an inversion-recovery pulse sequence without ICD, T1 values measured with original AIR with ICD were considerably lower (absolute percent error >29%), whereas T1 values measured with wideband AIR with ICD were similar (absolute percent error <5%). Similarly, in 11 human subjects, compared with the control T1 values measured with original AIR without ICD, T1 measured with original AIR with ICD was significantly lower (absolute percent error >10.1%), whereas T1 measured with wideband AIR with ICD was similar (absolute percent error <2.0%). Conclusion This study demonstrates the feasibility of a wideband pulse sequence for cardiac T1 mapping without significant image artifacts induced by ICD. PMID:25975192

Utility of 16S rDNA Sequencing for Identification of Rare Pathogenic Bacteria.

PubMed

Loong, Shih Keng; Khor, Chee Sieng; Jafar, Faizatul Lela; AbuBakar, Sazaly

2016-11-01

Phenotypic identification systems are established methods for laboratory identification of bacteria causing human infections. Here, the utility of phenotypic identification systems was compared against 16S rDNA identification method on clinical isolates obtained during a 5-year study period, with special emphasis on isolates that gave unsatisfactory identification. One hundred and eighty-seven clinical bacteria isolates were tested with commercial phenotypic identification systems and 16S rDNA sequencing. Isolate identities determined using phenotypic identification systems and 16S rDNA sequencing were compared for similarity at genus and species level, with 16S rDNA sequencing as the reference method. Phenotypic identification systems identified ~46% (86/187) of the isolates with identity similar to that identified using 16S rDNA sequencing. Approximately 39% (73/187) and ~15% (28/187) of the isolates showed different genus identity and could not be identified using the phenotypic identification systems, respectively. Both methods succeeded in determining the species identities of 55 isolates; however, only ~69% (38/55) of the isolates matched at species level. 16S rDNA sequencing could not determine the species of ~20% (37/187) of the isolates. The 16S rDNA sequencing is a useful method over the phenotypic identification systems for the identification of rare and difficult to identify bacteria species. The 16S rDNA sequencing method, however, does have limitation for species-level identification of some bacteria highlighting the need for better bacterial pathogen identification tools. © 2016 Wiley Periodicals, Inc.

Combined measurement system for double shield tunnel boring machine guidance based on optical and visual methods.

PubMed

Lin, Jiarui; Gao, Kai; Gao, Yang; Wang, Zheng

2017-10-01

In order to detect the position of the cutting shield at the head of a double shield tunnel boring machine (TBM) during the excavation, this paper develops a combined measurement system which is mainly composed of several optical feature points, a monocular vision sensor, a laser target sensor, and a total station. The different elements of the combined system are mounted on the TBM in suitable sequence, and the position of the cutting shield in the reference total station frame is determined by coordinate transformations. Subsequently, the structure of the feature points and matching technique for them are expounded, the position measurement method based on monocular vision is presented, and the calibration methods for the unknown relationships among different parts of the system are proposed. Finally, a set of experimental platforms to simulate the double shield TBM is established, and accuracy verification experiments are conducted. Experimental results show that the mean deviation of the system is 6.8 mm, which satisfies the requirements of double shield TBM guidance.

Localization of Non-Linearly Modeled Autonomous Mobile Robots Using Out-of-Sequence Measurements

PubMed Central

Besada-Portas, Eva; Lopez-Orozco, Jose A.; Lanillos, Pablo; de la Cruz, Jesus M.

2012-01-01

This paper presents a state of the art of the estimation algorithms dealing with Out-of-Sequence (OOS) measurements for non-linearly modeled systems. The state of the art includes a critical analysis of the algorithm properties that takes into account the applicability of these techniques to autonomous mobile robot navigation based on the fusion of the measurements provided, delayed and OOS, by multiple sensors. Besides, it shows a representative example of the use of one of the most computationally efficient approaches in the localization module of the control software of a real robot (which has non-linear dynamics, and linear and non-linear sensors) and compares its performance against other approaches. The simulated results obtained with the selected OOS algorithm shows the computational requirements that each sensor of the robot imposes to it. The real experiments show how the inclusion of the selected OOS algorithm in the control software lets the robot successfully navigate in spite of receiving many OOS measurements. Finally, the comparison highlights that not only is the selected OOS algorithm among the best performing ones of the comparison, but it also has the lowest computational and memory cost. PMID:22736962

Localization of non-linearly modeled autonomous mobile robots using out-of-sequence measurements.

PubMed

Besada-Portas, Eva; Lopez-Orozco, Jose A; Lanillos, Pablo; de la Cruz, Jesus M

2012-01-01

This paper presents a state of the art of the estimation algorithms dealing with Out-of-Sequence (OOS) measurements for non-linearly modeled systems. The state of the art includes a critical analysis of the algorithm properties that takes into account the applicability of these techniques to autonomous mobile robot navigation based on the fusion of the measurements provided, delayed and OOS, by multiple sensors. Besides, it shows a representative example of the use of one of the most computationally efficient approaches in the localization module of the control software of a real robot (which has non-linear dynamics, and linear and non-linear sensors) and compares its performance against other approaches. The simulated results obtained with the selected OOS algorithm shows the computational requirements that each sensor of the robot imposes to it. The real experiments show how the inclusion of the selected OOS algorithm in the control software lets the robot successfully navigate in spite of receiving many OOS measurements. Finally, the comparison highlights that not only is the selected OOS algorithm among the best performing ones of the comparison, but it also has the lowest computational and memory cost.

A new complexity measure for time series analysis and classification

NASA Astrophysics Data System (ADS)

Nagaraj, Nithin; Balasubramanian, Karthi; Dey, Sutirth

2013-07-01

Complexity measures are used in a number of applications including extraction of information from data such as ecological time series, detection of non-random structure in biomedical signals, testing of random number generators, language recognition and authorship attribution etc. Different complexity measures proposed in the literature like Shannon entropy, Relative entropy, Lempel-Ziv, Kolmogrov and Algorithmic complexity are mostly ineffective in analyzing short sequences that are further corrupted with noise. To address this problem, we propose a new complexity measure ETC and define it as the "Effort To Compress" the input sequence by a lossless compression algorithm. Here, we employ the lossless compression algorithm known as Non-Sequential Recursive Pair Substitution (NSRPS) and define ETC as the number of iterations needed for NSRPS to transform the input sequence to a constant sequence. We demonstrate the utility of ETC in two applications. ETC is shown to have better correlation with Lyapunov exponent than Shannon entropy even with relatively short and noisy time series. The measure also has a greater rate of success in automatic identification and classification of short noisy sequences, compared to entropy and a popular measure based on Lempel-Ziv compression (implemented by Gzip).

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

NASA Technical Reports Server (NTRS)

Ni, Jianjun (David)

2012-01-01

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

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes.

PubMed

Fredlake, Christopher P; Hert, Daniel G; Kan, Cheuk-Wai; Chiesl, Thomas N; Root, Brian E; Forster, Ryan E; Barron, Annelise E

2008-01-15

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

PubMed Central

Fredlake, Christopher P.; Hert, Daniel G.; Kan, Cheuk-Wai; Chiesl, Thomas N.; Root, Brian E.; Forster, Ryan E.; Barron, Annelise E.

2008-01-01

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require ≈70 min to deliver ≈650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered “hybrid” mechanism of DNA electromigration, in which DNA molecules alternate rapidly between reptating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs. PMID:18184818

Do Close-in Giant Planets Orbiting Evolved Stars Prefer Eccentric Orbits?

NASA Astrophysics Data System (ADS)

Grunblatt, Samuel K.; Huber, Daniel; Gaidos, Eric; Lopez, Eric D.; Barclay, Thomas; Chontos, Ashley; Sinukoff, Evan; Van Eylen, Vincent; Howard, Andrew W.; Isaacson, Howard T.

2018-07-01

The NASA Kepler and K2 Missions have recently revealed a population of transiting giant planets orbiting moderately evolved, low-luminosity red giant branch stars. Here, we present radial velocity (RV) measurements of three of these systems, revealing significantly non-zero orbital eccentricities in each case. Comparing these systems with the known planet population suggests that close-in giant planets around evolved stars tend to have more eccentric orbits than those around main sequence stars. We interpret this as tentative evidence that the orbits of these planets pass through a transient, moderately eccentric phase where they shrink faster than they circularize due to tides raised on evolved host stars. Additional RV measurements of currently known systems, along with new systems discovered by the recently launched NASA Transiting Exoplanet Survey Satellite (TESS) mission, may constrain the timescale and mass dependence of this process.

An Intelligent Computerized Stretch Reflex Measurement System For Clinical And Investigative Neurology

NASA Astrophysics Data System (ADS)

Flanagan, P. M.; Chutkow, J. G.; Riggs, M. T.; Cristiano, V. D.

1987-05-01

We describe the design of a reliable, user-friendly preprototype system for quantifying the tendon stretch reflexes in humans and large mammals. A hand-held, instrumented reflex gun, the impactor of which contains a single force sensor, interfaces with a computer. The resulting test system can deliver sequences of reproducible stimuli at graded intensities and adjustable durations to a muscle's tendon ("tendon taps"), measure the impacting force of each tap, and record the subsequent reflex muscle contraction from the same tendon -- all automatically. The parameters of the reflex muscle contraction include latency; mechanical threshold; and peak time, peak magnitude, and settling time. The results of clinical tests presented in this paper illustrate the system's potential usefulness in detecting neurologic dysfunction affecting the tendon stretch reflexes, in documenting the course of neurologic illnesses and their response to therapy, and in clinical and laboratory neurologic research.

The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets.

PubMed

Droege, Marcus; Hill, Brendon

2008-08-31

The Genome Sequencer FLX System (GS FLX), powered by 454 Sequencing, is a next-generation DNA sequencing technology featuring a unique mix of long reads, exceptional accuracy, and ultra-high throughput. It has been proven to be the most versatile of all currently available next-generation sequencing technologies, supporting many high-profile studies in over seven applications categories. GS FLX users have pursued innovative research in de novo sequencing, re-sequencing of whole genomes and target DNA regions, metagenomics, and RNA analysis. 454 Sequencing is a powerful tool for human genetics research, having recently re-sequenced the genome of an individual human, currently re-sequencing the complete human exome and targeted genomic regions using the NimbleGen sequence capture process, and detected low-frequency somatic mutations linked to cancer.

Functional MR imaging of the cervical spinal cord by use of electrical stimulation at LI4 (Hegu).

PubMed

Wang, W D; Kong, K M; Xiao, Y Y; Wang, X J; Liang, B; Qi, W L; Wu, R H

2006-01-01

The purpose is to investigate the cervical spinal cord mapping on electrical stimulation at LI4 (Hegu) by using 'signal enhancement by extravascular water protons' (SEEP)-fMRI, and to establish the response of acupoint-stimulation in spinal cord. Three healthy volunteers were underwent low-frequency electrical stimulation at LI4. Meanwhile, a single-shot fast spin-echo (SSFSE) sequence was used to perform functional MR imaging on a 1.5 T GE Signa MR system. Cord activation was measured both in the sagittal and transverse imaging planes and then analyzed by AFNI (analysis of functional neuroimages) system. In the sagittal view, two subjects had an fMRI response in the cervical spinal cord upon electrical stimulation at LI4. The localizations of the segmental fMRI activation are both at C6 through T1 and C2/3 cervical spinal cord level. In the transverse imaging plane, significant fMRI responses could be measured in the last subjects locating at C6/7 segment, the cross-sectional localization of the activity measured in the spinal cord was most in terms of the ipsilateral posterior direction. It is concluded that the fMRI technique can be used for detecting with activity in the human cervical spinal cord by a single-shot fast spin-echo sequence on a 1.5 T GE clinical system. Investigating the acupoint-stimulation response in the spinal cord using the spinal fMRI will be helpful for the further discussion on the mechanisms of acupuncture to spinal cord diseases.

Random sequences generation through optical measurements by phase-shifting interferometry

NASA Astrophysics Data System (ADS)

François, M.; Grosges, T.; Barchiesi, D.; Erra, R.; Cornet, A.

2012-04-01

The development of new techniques for producing random sequences with a high level of security is a challenging topic of research in modern cryptographics. The proposed method is based on the measurement by phase-shifting interferometry of the speckle signals of the interaction between light and structures. We show how the combination of amplitude and phase distributions (maps) under a numerical process can produce random sequences. The produced sequences satisfy all the statistical requirements of randomness and can be used in cryptographic schemes.

White dwarf-main sequence binaries from LAMOST: the DR5 catalogue

NASA Astrophysics Data System (ADS)

Ren, J.-J.; Rebassa-Mansergas, A.; Parsons, S. G.; Liu, X.-W.; Luo, A.-L.; Kong, X.; Zhang, H.-T.

2018-07-01

We present the data release (DR) 5 catalogue of white dwarf-main sequence (WDMS) binaries from the Large sky Area Multi-Object fibre Spectroscopic Telescope (LAMOST). The catalogue contains 876 WDMS binaries, of which 757 are additions to our previous LAMOST DR1 sample and 357 are systems that have not been published before. We also describe a LAMOST-dedicated survey that aims at obtaining spectra of photometrically selected WDMS binaries from the Sloan Digital Sky Survey (SDSS) that are expected to contain cool white dwarfs and/or early-type M dwarf companions. This is a population under-represented in previous SDSS WDMS binary catalogues. We determine the stellar parameters (white dwarf effective temperatures, surface gravities and masses, and M dwarf spectral types) of the LAMOST DR5 WDMS binaries and make use of the parameter distributions to analyse the properties of the sample. We find that, despite our efforts, systems containing cool white dwarfs remain under-represented. Moreover, we make use of LAMOST DR5 and SDSS DR14 (when available) spectra to measure the Na I λλ 8183.27, 8194.81 absorption doublet and/or Hα emission radial velocities of our systems. This allows identifying 128 binaries displaying significant radial velocity variations, 76 of which are new. Finally, we cross-match our catalogue with the Catalina Surveys and identify 57 systems displaying light-curve variations. These include 16 eclipsing systems, two of which are new, and nine binaries that are new eclipsing candidates. We calculate periodograms from the photometric data and measure (estimate) the orbital periods of 30 (15) WDMS binaries.

White dwarf-main sequence binaries from LAMOST: the DR5 catalogue

NASA Astrophysics Data System (ADS)

Ren, J.-J.; Rebassa-Mansergas, A.; Parsons, S. G.; Liu, X.-W.; Luo, A.-L.; Kong, X.; Zhang, H.-T.

2018-03-01

We present the data release (DR) 5 catalogue of white dwarf-main sequence (WDMS) binaries from the Large Area Multi-Object fiber Spectroscopic Telescope (LAMOST). The catalogue contains 876 WDMS binaries, of which 757 are additions to our previous LAMOST DR1 sample and 357 are systems that have not been published before. We also describe a LAMOST-dedicated survey that aims at obtaining spectra of photometrically-selected WDMS binaries from the Sloan Digital Sky Survey (SDSS) that are expected to contain cool white dwarfs and/or early type M dwarf companions. This is a population under-represented in previous SDSS WDMS binary catalogues. We determine the stellar parameters (white dwarf effective temperatures, surface gravities and masses, and M dwarf spectral types) of the LAMOST DR5 WDMS binaries and make use of the parameter distributions to analyse the properties of the sample. We find that, despite our efforts, systems containing cool white dwarfs remain under-represented. Moreover, we make use of LAMOST DR5 and SDSS DR14 (when available) spectra to measure the Na I λλ 8183.27, 8194.81 absorption doublet and/or Hα emission radial velocities of our systems. This allows identifying 128 binaries displaying significant radial velocity variations, 76 of which are new. Finally, we cross-match our catalogue with the Catalina Surveys and identify 57 systems displaying light curve variations. These include 16 eclipsing systems, two of which are new, and nine binaries that are new eclipsing candidates. We calculate periodograms from the photometric data and measure (estimate) the orbital periods of 30 (15) WDMS binaries.

Detecting and Characterizing Repeating Earthquake Sequences During Volcanic Eruptions

NASA Astrophysics Data System (ADS)

Tepp, G.; Haney, M. M.; Wech, A.

2017-12-01

A major challenge in volcano seismology is forecasting eruptions. Repeating earthquake sequences often precede volcanic eruptions or lava dome activity, providing an opportunity for short-term eruption forecasting. Automatic detection of these sequences can lead to timely eruption notification and aid in continuous monitoring of volcanic systems. However, repeating earthquake sequences may also occur after eruptions or along with magma intrusions that do not immediately lead to an eruption. This additional challenge requires a better understanding of the processes involved in producing these sequences to distinguish those that are precursory. Calculation of the inverse moment rate and concepts from the material failure forecast method can lead to such insights. The temporal evolution of the inverse moment rate is observed to differ for precursory and non-precursory sequences, and multiple earthquake sequences may occur concurrently. These observations suggest that sequences may occur in different locations or through different processes. We developed an automated repeating earthquake sequence detector and near real-time alarm to send alerts when an in-progress sequence is identified. Near real-time inverse moment rate measurements can further improve our ability to forecast eruptions by allowing for characterization of sequences. We apply the detector to eruptions of two Alaskan volcanoes: Bogoslof in 2016-2017 and Redoubt Volcano in 2009. The Bogoslof eruption produced almost 40 repeating earthquake sequences between its start in mid-December 2016 and early June 2017, 21 of which preceded an explosive eruption, and 2 sequences in the months before eruptive activity. Three of the sequences occurred after the implementation of the alarm in late March 2017 and successfully triggered alerts. The nearest seismometers to Bogoslof are over 45 km away, requiring a detector that can work with few stations and a relatively low signal-to-noise ratio. During the Redoubt eruption, earthquake sequences were observed in the months leading up to the eruptive activity beginning in March 2009 as well as immediately preceding 7 of the 19 explosive events. In contrast to Bogoslof, Redoubt has a local monitoring network which allows for better detection and more detailed analysis of the repeating earthquake sequences.

Design and preliminary accuracy studies of an MRI-guided transrectal prostate intervention system.

PubMed

Krieger, Axel; Csoma, Csaba; Iordachital, Iulian I; Guion, Peter; Singh, Anurag K; Fichtinger, Gabor; Whitcomb, Louis L

2007-01-01

This paper reports a novel system for magnetic resonance imaging (MRI) guided transrectal prostate interventions, such as needle biopsy, fiducial marker placement, and therapy delivery. The system utilizes a hybrid tracking method, comprised of passive fiducial tracking for initial registration and subsequent incremental motion measurement along the degrees of freedom using fiber-optical encoders and mechanical scales. Targeting accuracy of the system is evaluated in prostate phantom experiments. Achieved targeting accuracy and procedure times were found to compare favorably with existing systems using passive and active tracking methods. Moreover, the portable design of the system using only standard MRI image sequences and minimal custom scanner interfacing allows the system to be easily used on different MRI scanners.

The influence of pH adjustment on kinetics parameters in tapioca wastewater treatment using aerobic sequencing batch reactor system

NASA Astrophysics Data System (ADS)

Mulyani, Happy; Budianto, Gregorius Prima Indra; Margono, Kaavessina, Mujtahid

2018-02-01

The present investigation deals with the aerobic sequencing batch reactor system of tapioca wastewater treatment with varying pH influent conditions. This project was carried out to evaluate the effect of pH on kinetics parameters of system. It was done by operating aerobic sequencing batch reactor system during 8 hours in many tapioca wastewater conditions (pH 4.91, pH 7, pH 8). The Chemical Oxygen Demand (COD) and Mixed Liquor Volatile Suspended Solids (MLVSS) of the aerobic sequencing batch reactor system effluent at steady state condition were determined at interval time of two hours to generate data for substrate inhibition kinetics parameters. Values of the kinetics constants were determined using Monod and Andrews models. There was no inhibition constant (Ki) detected in all process variation of aerobic sequencing batch reactor system for tapioca wastewater treatment in this study. Furthermore, pH 8 was selected as the preferred aerobic sequencing batch reactor system condition in those ranging pH investigated due to its achievement of values of kinetics parameters such µmax = 0.010457/hour and Ks = 255.0664 mg/L COD.

Vision-based overlay of a virtual object into real scene for designing room interior

NASA Astrophysics Data System (ADS)

Harasaki, Shunsuke; Saito, Hideo

2001-10-01

In this paper, we introduce a geometric registration method for augmented reality (AR) and an application system, interior simulator, in which a virtual (CG) object can be overlaid into a real world space. Interior simulator is developed as an example of an AR application of the proposed method. Using interior simulator, users can visually simulate the location of virtual furniture and articles in the living room so that they can easily design the living room interior without placing real furniture and articles, by viewing from many different locations and orientations in real-time. In our system, two base images of a real world space are captured from two different views for defining a projective coordinate of object 3D space. Then each projective view of a virtual object in the base images are registered interactively. After such coordinate determination, an image sequence of a real world space is captured by hand-held camera with tracking non-metric measured feature points for overlaying a virtual object. Virtual objects can be overlaid onto the image sequence by taking each relationship between the images. With the proposed system, 3D position tracking device, such as magnetic trackers, are not required for the overlay of virtual objects. Experimental results demonstrate that 3D virtual furniture can be overlaid into an image sequence of the scene of a living room nearly at video rate (20 frames per second).

Polyfluorophore Labels on DNA: Dramatic Sequence Dependence of Quenching

PubMed Central

Teo, Yin Nah; Wilson, James N.

2010-01-01

We describe studies carried out in the DNA context to test how a common fluorescence quencher, dabcyl, interacts with oligodeoxynu-cleoside fluorophores (ODFs)—a system of stacked, electronically interacting fluorophores built on a DNA scaffold. We tested twenty different tetrameric ODF sequences containing varied combinations and orderings of pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and spacer (S) monomers conjugated to the 3′ end of a DNA oligomer. Hybridization of this probe sequence to a dabcyl-labeled complementary strand resulted in strong quenching of fluorescence in 85% of the twenty ODF sequences. The high efficiency of quenching was also established by their large Stern–Volmer constants (KSV) of between 2.1 × 104 and 4.3 × 105M−1, measured with a free dabcyl quencher. Interestingly, quenching of ODFs displayed strong sequence dependence. This was particularly evident in anagrams of ODF sequences; for example, the sequence BYDS had a KSV that was approximately two orders of magnitude greater than that of BSDY, which has the same dye composition. Other anagrams, for example EDSY and ESYD, also displayed different responses upon quenching by dabcyl. Analysis of spectra showed that apparent excimer and exciplex emission bands were quenched with much greater efficiency compared to monomer emission bands by at least an order of magnitude. This suggests an important role played by delocalized excited states of the π stack of fluorophores in the amplified quenching of fluorescence. PMID:19780115

Competing streams at the cocktail party: Exploring the mechanisms of attention and temporal integration

PubMed Central

Xiang, Juanjuan; Simon, Jonathan; Elhilali, Mounya

2010-01-01

Processing of complex acoustic scenes depends critically on the temporal integration of sensory information as sounds evolve naturally over time. It has been previously speculated that this process is guided by both innate mechanisms of temporal processing in the auditory system, as well as top-down mechanisms of attention, and possibly other schema-based processes. In an effort to unravel the neural underpinnings of these processes and their role in scene analysis, we combine Magnetoencephalography (MEG) with behavioral measures in humans in the context of polyrhythmic tone sequences. While maintaining unchanged sensory input, we manipulate subjects’ attention to one of two competing rhythmic streams in the same sequence. The results reveal that the neural representation of the attended rhythm is significantly enhanced both in its steady-state power and spatial phase coherence relative to its unattended state, closely correlating with its perceptual detectability for each listener. Interestingly, the data reveals a differential efficiency of rhythmic rates of the order of few hertz during the streaming process, closely following known neural and behavioral measures of temporal modulation sensitivity in the auditory system. These findings establish a direct link between known temporal modulation tuning in the auditory system (particularly at the level of auditory cortex) and the temporal integration of perceptual features in a complex acoustic scene, while mediated by processes of attention. PMID:20826671

A novel anthropomorphic flow phantom for the quantitative evaluation of prostate DCE-MRI acquisition techniques

NASA Astrophysics Data System (ADS)

Knight, Silvin P.; Browne, Jacinta E.; Meaney, James F.; Smith, David S.; Fagan, Andrew J.

2016-10-01

A novel anthropomorphic flow phantom device has been developed, which can be used for quantitatively assessing the ability of magnetic resonance imaging (MRI) scanners to accurately measure signal/concentration time-intensity curves (CTCs) associated with dynamic contrast-enhanced (DCE) MRI. Modelling of the complex pharmacokinetics of contrast agents as they perfuse through the tumour capillary network has shown great promise for cancer diagnosis and therapy monitoring. However, clinical adoption has been hindered by methodological problems, resulting in a lack of consensus regarding the most appropriate acquisition and modelling methodology to use and a consequent wide discrepancy in published data. A heretofore overlooked source of such discrepancy may arise from measurement errors of tumour CTCs deriving from the imaging pulse sequence itself, while the effects on the fidelity of CTC measurement of using rapidly-accelerated sequences such as parallel imaging and compressed sensing remain unknown. The present work aimed to investigate these features by developing a test device in which ‘ground truth’ CTCs were generated and presented to the MRI scanner for measurement, thereby allowing for an assessment of the DCE-MRI protocol to accurately measure this curve shape. The device comprised a four-pump flow system wherein CTCs derived from prior patient prostate data were produced in measurement chambers placed within the imaged volume. The ground truth was determined as the mean of repeat measurements using an MRI-independent, custom-built optical imaging system. In DCE-MRI experiments, significant discrepancies between the ground truth and measured CTCs were found for both tumorous and healthy tissue-mimicking curve shapes. Pharmacokinetic modelling revealed errors in measured K trans, v e and k ep values of up to 42%, 31%, and 50% respectively, following a simple variation of the parallel imaging factor and number of signal averages in the acquisition protocol. The device allows for the quantitative assessment and standardisation of DCE-MRI protocols (both existing and emerging).

A micro-rheological method for determination of blood type.

PubMed

Makulska, Sylwia; Jakiela, Slawomir; Garstecki, Piotr

2013-07-21

The measurement of time and distance can be used for determining agglutination in small (nL) samples of liquid. We demonstrate the use of this new scheme of detection in typing and subtyping blood in a simple microfluidic system that monitors the speed of flow of microdroplets. The system (i) accepts small samples of liquids deposited directly onto the chip, (ii) forms droplets on demand from these samples, (iii) merges the droplets, and (iv) measures their speed in a microchannel. A sequence of measurements on different combinations of blood and antibodies can thus be used to determine blood type with the estimated probability of mistyping being less than 1 in a million tests. In addition, in the agglutinated samples, red blood cells concentrate at the rear of the droplets yielding an additional vista for detection and suggesting a possible mechanism for separations.

cyclostratigraphy, sequence stratigraphy and organic matter accumulation mechanism

NASA Astrophysics Data System (ADS)

Cong, F.; Li, J.

2016-12-01

The first member of Maokou Formation of Sichuan basin is composed of well preserved carbonate ramp couplets of limestone and marlstone/shale. It acts as one of the potential shale gas source rock, and is suitable for time-series analysis. We conducted time-series analysis to identify high-frequency sequences, reconstruct high-resolution sedimentation rate, estimate detailed primary productivity for the first time in the study intervals and discuss organic matter accumulation mechanism of source rock under sequence stratigraphic framework.Using the theory of cyclostratigraphy and sequence stratigraphy, the high-frequency sequences of one outcrop profile and one drilling well are identified. Two third-order sequences and eight fourth-order sequences are distinguished on outcrop profile based on the cycle stacking patterns. For drilling well, sequence boundary and four system tracts is distinguished by "integrated prediction error filter analysis" (INPEFA) of Gamma-ray logging data, and eight fourth-order sequences is identified by 405ka long eccentricity curve in depth domain which is quantified and filtered by integrated analysis of MTM spectral analysis, evolutive harmonic analysis (EHA), evolutive average spectral misfit (eASM) and band-pass filtering. It suggests that high-frequency sequences correlate well with Milankovitch orbital signals recorded in sediments, and it is applicable to use cyclostratigraphy theory in dividing high-frequency(4-6 orders) sequence stratigraphy.High-resolution sedimentation rate is reconstructed through the study interval by tracking the highly statistically significant short eccentricity component (123ka) revealed by EHA. Based on sedimentation rate, measured TOC and density data, the burial flux, delivery flux and primary productivity of organic carbon was estimated. By integrating redox proxies, we can discuss the controls on organic matter accumulation by primary production and preservation under the high-resolution sequence stratigraphic framework. Results show that high average organic carbon contents in the study interval are mainly attributed to high primary production. The results also show a good correlation between high organic carbon accumulation and intervals of transgression.

Learning Quantitative Sequence-Function Relationships from Massively Parallel Experiments

NASA Astrophysics Data System (ADS)

Atwal, Gurinder S.; Kinney, Justin B.

2016-03-01

A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships—functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques for effectively measuring these relationships been developed. The advent of such "massively parallel" experiments presents an exciting opportunity for the concepts and methods of statistical physics to inform the study of biological systems. After reviewing these recent experimental advances, we focus on the problem of how to infer parametric models of sequence-function relationships from the data produced by these experiments. Specifically, we retrace and extend recent theoretical work showing that inference based on mutual information, not the standard likelihood-based approach, is often necessary for accurately learning the parameters of these models. Closely connected with this result is the emergence of "diffeomorphic modes"—directions in parameter space that are far less constrained by data than likelihood-based inference would suggest. Analogous to Goldstone modes in physics, diffeomorphic modes arise from an arbitrarily broken symmetry of the inference problem. An analytically tractable model of a massively parallel experiment is then described, providing an explicit demonstration of these fundamental aspects of statistical inference. This paper concludes with an outlook on the theoretical and computational challenges currently facing studies of quantitative sequence-function relationships.

Molecular and Morphological Characterization of Fasciola spp. Isolated from Different Host Species in a Newly Emerging Focus of Human Fascioliasis in Iran

PubMed Central

Shafiei, Reza; Sarkari, Bahador; Sadjjadi, Seyed Mahmuod; Mowlavi, Gholam Reza; Moshfe, Abdolali

2014-01-01

The current study aimed to find out the morphometric and genotypic divergences of the flukes isolated from different hosts in a newly emerging focus of human fascioliasis in Iran. Adult Fasciola spp. were collected from 34 cattle, 13 sheep, and 11 goats from Kohgiluyeh and Boyer-Ahmad province, southwest of Iran. Genomic DNA was extracted from the flukes and PCR-RFLP was used to characterize the isolates. The ITS1, ITS2, and mitochondrial genes (mtDNA) of NDI and COI from individual liver flukes were amplified and the amplicons were sequenced. Genetic variation within and between the species was evaluated by comparing the sequences. Moreover, morphometric characteristics of flukes were measured through a computer image analysis system. Based on RFLP profile, from the total of 58 isolates, 41 isolates (from cattle, sheep, and goat) were identified as Fasciola hepatica, while 17 isolates from cattle were identified as Fasciola gigantica. Comparison of the ITS1 and ITS2 sequences showed six and seven single-base substitutions, resulting in segregation of the specimens into two different genotypes. The sequences of COI markers showed seven DNA polymorphic sites for F. hepatica and 35 DNA polymorphic sites for F. gigantica. Morphological diversity of the two species was observed in linear, ratios, and areas measurements. The findings have implications for studying the population genetics, epidemiology, and control of the disease. PMID:25018891

Volumetric dispenser for small particles from plural sources

DOEpatents

Bradley, R.A.; Miller, W.H.; Sease, J.D.

1975-12-16

Apparatus is described for rapidly and accurately dispensing measured volumes of small particles from a supply hopper. The apparatus includes an adjustable, vertically oriented measuring tube and orifice member defining the volume to be dispensed, a ball plug valve for selectively closing the bottom end of the orifice member, and a compression valve for selectively closing the top end of the measuring tube. A supply hopper is disposed above and in gravity flow communication with the measuring tube. Properly sequenced opening and closing of the two valves provides accurate volumetric discharge through the ball plug valve. A dispensing system is described wherein several appropriately sized measuring tubes, orifice members, and associated valves are arranged to operate contemporaneously to facilitate blending of different particles.

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

PubMed Central

Oberstrass, Florian C.; Fernandes, Louis E.; Bryant, Zev

2012-01-01

B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)n sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context. PMID:22474350

SSh versus TSE sequence protocol in rapid MR examination of pediatric patients with programmable drainage system.

PubMed

Brichtová, Eva; Šenkyřík, J

2017-05-01

A low radiation burden is essential during diagnostic procedures in pediatric patients due to their high tissue sensitivity. Using MR examination instead of the routinely used CT reduces the radiation exposure and the risk of adverse stochastic effects. Our retrospective study evaluated the possibility of using ultrafast single-shot (SSh) sequences and turbo spin echo (TSE) sequences in rapid MR brain imaging in pediatric patients with hydrocephalus and a programmable ventriculoperitoneal drainage system. SSh sequences seem to be suitable for examining pediatric patients due to the speed of using this technique, but significant susceptibility artifacts due to the programmable drainage valve degrade the image quality. Therefore, a rapid MR examination protocol based on TSE sequences, less sensitive to artifacts due to ferromagnetic components, has been developed. Of 61 pediatric patients who were examined using MR and the SSh sequence protocol, a group of 15 patients with hydrocephalus and a programmable drainage system also underwent TSE sequence MR imaging. The susceptibility artifact volume in both rapid MR protocols was evaluated using a semiautomatic volumetry system. A statistically significant decrease in the susceptibility artifact volume has been demonstrated in TSE sequence imaging in comparison with SSh sequences. Using TSE sequences reduced the influence of artifacts from the programmable valve, and the image quality in all cases was rated as excellent. In all patients, rapid MR examinations were performed without any need for intravenous sedation or general anesthesia. Our study results strongly suggest the superiority of the TSE sequence MR protocol compared to the SSh sequence protocol in pediatric patients with a programmable ventriculoperitoneal drainage system due to a significant reduction of susceptibility artifact volume. Both rapid sequence MR protocols provide quick and satisfactory brain imaging with no ionizing radiation and a reduced need for intravenous or general anesthesia.

Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.

PubMed

Hayat, Maqsood; Khan, Asifullah

2011-02-21

Membrane proteins are vital type of proteins that serve as channels, receptors, and energy transducers in a cell. Prediction of membrane protein types is an important research area in bioinformatics. Knowledge of membrane protein types provides some valuable information for predicting novel example of the membrane protein types. However, classification of membrane protein types can be both time consuming and susceptible to errors due to the inherent similarity of membrane protein types. In this paper, neural networks based membrane protein type prediction system is proposed. Composite protein sequence representation (CPSR) is used to extract the features of a protein sequence, which includes seven feature sets; amino acid composition, sequence length, 2 gram exchange group frequency, hydrophobic group, electronic group, sum of hydrophobicity, and R-group. Principal component analysis is then employed to reduce the dimensionality of the feature vector. The probabilistic neural network (PNN), generalized regression neural network, and support vector machine (SVM) are used as classifiers. A high success rate of 86.01% is obtained using SVM for the jackknife test. In case of independent dataset test, PNN yields the highest accuracy of 95.73%. These classifiers exhibit improved performance using other performance measures such as sensitivity, specificity, Mathew's correlation coefficient, and F-measure. The experimental results show that the prediction performance of the proposed scheme for classifying membrane protein types is the best reported, so far. This performance improvement may largely be credited to the learning capabilities of neural networks and the composite feature extraction strategy, which exploits seven different properties of protein sequences. The proposed Mem-Predictor can be accessed at http://111.68.99.218/Mem-Predictor. Copyright © 2010 Elsevier Ltd. All rights reserved.

In vitro induction of T regulatory cells by a methylated CpG DNA sequence in humans: Potential therapeutic applications in allergic and autoimmune diseases.

PubMed

Lawless, Oliver J; Bellanti, Joseph A; Brown, Milton L; Sandberg, Kathryn; Umans, Jason G; Zhou, Li; Chen, Weiqian; Wang, Julie; Wang, Kan; Zheng, Song Guo

2018-03-01

Allergic and autoimmune diseases comprise a group of inflammatory disorders caused by aberrant immune responses in which CD25+ Forkhead box P3-positive (FOXP3+) T regulatory (Treg) cells that normally suppress inflammatory events are often poorly functioning. This has stimulated an intensive investigative effort to find ways of increasing Tregs as a method of therapy for these conditions. One such line of investigation includes the study of how ligation of Toll-like receptors (TLRs) by CpG oligonucleotides (ODN) results in an immunostimulatory cascade that leads to induction of T-helper (Th) type 1 and Treg-type immune responses. The present study investigated the mechanisms by which calf thymus mammalian double-stranded DNA (CT-DNA) and a synthetic methylated DNA CpG ODN sequence suppress in vitro lymphoproliferative responses to antigens, mitogens, and alloantigens when measured by [3H]-thymidine incorporation and promote FoxP3 expression in human CD4+ T cells in the presence of transforming growth factor (TGF) beta and interleukin-2 (IL-2). Lymphoproliferative responses of peripheral blood mononuclear cells from four healthy subjects or nine subjects with systemic lupus erythematosus to CT-DNA or phytohemagglutinin (PHA) was measured by tritiated thymidine ([3H]-TdR) incorporation expressed as a stimulation index. Mechanisms of immunosuppressive effects of CT-DNA were evaluated by measurement of the degree of inhibition to lymphoproliferative responses to streptokinase-streptodornase, phytohemagglutinin (PHA), concanavalin A (Con A), pokeweed mitogen (PWM), or alloantigens by a Con A suppressor assay. The effects of CpG methylation on induction of FoxP3 expression in human T cells were measured by comparing inhibitory responses of synthetic methylated and nonmethylated 8-mer CpG ODN sequences by using cell sorting, in vitro stimulation, and suppressor assay. Here, we showed that CT-DNA and a synthetic methylated DNA 8-mer sequence could suppress antigen-, mitogen-, and alloantigen-induced lymphoproliferation in vitro when measured by [3H]-thymidine. The synthetic methylated DNA CpG ODN but not an unmethylated CpG ODN sequence was shown to promote FoxP3 expression in human CD4+ T cells in the presence of TGF beta and IL-2. The induction of FoxP3+ suppressor cells is dose dependent and offers a potential clinical therapeutic application in allergic and autoimmune and inflammatory diseases. The use of this methylated CpG ODN offers a broad clinical application as a novel therapeutic method for Treg induction and, because of its low cost and small size, should facilitate delivery via nasal, respiratory, gastrointestinal routes, and/or by injection, routes of administration important for vaccine delivery to target sites responsible for respiratory, gastrointestinal, and systemic forms of allergic and autoimmune disease.

Transgressive systems tract development and incised-valley fills within a quaternary estuary-shelf system: Virginia inner shelf, USA

USGS Publications Warehouse

Foyle, A.M.; Oertel, G.F.

1997-01-01

High-frequency Quaternary glacioeustasy resulted in the incision of six moderate- to high-relief fluvial erosion surfaces beneath the Virginia inner shelf and coastal zone along the updip edges of the Atlantic continental margin. Fluvial valleys up to 5 km wide, with up to 37 m of relief and thalweg depths of up to 72 m below modern mean sea level, cut through underlying Pleistocene and Mio-Pliocene strata in response to drops in baselevel on the order of 100 m. Fluvially incised valleys were significantly modified during subsequent marine transgressions as fluvial drainage basins evolved into estuarine embayments (ancestral generations of the Chesapeake Bay). Complex incised-valley fill successions are bounded by, or contain, up to four stacked erosional surfaces (basal fluvial erosion surface, bay ravinement, tidal ravinement, and ebb-flood channel-base diastem) in vertical succession. These surfaces, combined with the transgressive oceanic ravinement that generally caps incised-valley fills, control the lateral and vertical development of intervening seismic facies (depositional systems). Transgressive stratigraphy characterizes the Quaternary section beneath the Virginia inner shelf where six depositional sequences (Sequences I-VI) are identified. Depositional sequences consist primarily of estuarine depositional systems (subjacent to the transgressive oceanic ravinement) and shoreface-shelf depositional systems; highstand systems tract coastal systems are thinly developed. The Quaternary section can be broadly subdivided into two parts. The upper part contains sequences consisting predominantly of inner shelf facies, whereas sequences in the lower part of the section consist predominantly of estuarine facies. Three styles of sequence preservation are identified. Style 1, represented by Sequences VI and V, is characterized by large estuarine systems (ancestral generations of the Chesapeake Bay) that are up to 40 m thick, have hemicylindrical wedge geometries, and occur within large, coast-oblique trending depressions (paleo-estuaries). Style 1 is dominated by fluvial through estuary-mouth depositional systems (Seismic Facies 1-4). Style 2 sequence preservation, represented by Sequences III and II, is dominantly an inner shelf and shoreface succession with a seaward-thickening tabular wedge geometry that does not exceed 15 m in thickness. These shoreface and inner shelf depositional systems of the upper transgressive systems tract (Seismic Facies 9) and highstand systems tract (Seismic Facies 7 and 11) are not associated with paleo-estuaries. Style 3 sequence preservation is represented by Sequence 1, the Holocene Sequence. It consists of lower transgressive systems tract fluvial-estuarine, lagoonal, and tidal-inlet fill deposits (Seismic Facies 1-6, and 8) overlain by upper transgressive systems tract shelf and shoreface sands (Seismic Facies 9). Style 3 has a crenulated wedge geometry, and is thickest beneath and seaward of the modern Chesapeake Bay mouth. It thins northward and landward onto Late Pleistocene interfluvial highs on the basinward side of the southern Delmarva Peninsula.

Studies and simulations of the DigiCipher system

NASA Technical Reports Server (NTRS)

Sayood, K.; Chen, Y. C.; Kipp, G.

1993-01-01

During this period the development of simulators for the various high definition television (HDTV) systems proposed to the FCC was continued. The FCC has indicated that it wants the various proposers to collaborate on a single system. Based on all available information this system will look very much like the advanced digital television (ADTV) system with major contributions only from the DigiCipher system. The results of our simulations of the DigiCipher system are described. This simulator was tested using test sequences from the MPEG committee. The results are extrapolated to HDTV video sequences. Once again, some caveats are in order. The sequences used for testing the simulator and generating the results are those used for testing the MPEG algorithm. The sequences are of much lower resolution than the HDTV sequences would be, and therefore the extrapolations are not totally accurate. One would expect to get significantly higher compression in terms of bits per pixel with sequences that are of higher resolution. However, the simulator itself is a valid one, and should HDTV sequences become available, they could be used directly with the simulator. A brief overview of the DigiCipher system is given. Some coding results obtained using the simulator are looked at. These results are compared to those obtained using the ADTV system. These results are evaluated in the context of the CCSDS specifications and make some suggestions as to how the DigiCipher system could be implemented in the NASA network. Simulations such as the ones reported can be biased depending on the particular source sequence used. In order to get more complete information about the system one needs to obtain a reasonable set of models which mirror the various kinds of sources encountered during video coding. A set of models which can be used to effectively model the various possible scenarios is provided. As this is somewhat tangential to the other work reported, the results are included as an appendix.

Interlocking Nailing Versus Interlocking Plating in Intra-articular Calcaneal Fractures: A Biomechanical Study.

PubMed

Reinhardt, Sophia; Martin, Heiner; Ulmar, Benjamin; Döbele, Stefan; Zwipp, Hans; Rammelt, Stefan; Richter, Martinus; Pompach, Martin; Mittlmeier, Thomas

2016-08-01

Open reduction and internal fixation with a plate is deemed to represent the gold standard of surgical treatment for displaced intra-articular calcaneal fractures. Standard plate fixation is usually placed through an extended lateral approach with high risk for wound complications. Minimally invasive techniques might avoid wound complications but provide limited construct stability. Therefore, 2 different types of locking nails were developed to allow for minimally invasive technique with sufficient stability. The aim of this study was to quantify primary stability of minimally invasive calcaneal interlocking nail systems in comparison to a variable-angle interlocking plate. After quantitative CT analysis, a standardized Sanders type IIB fracture model was created in 21 fresh-frozen cadavers. For osteosynthesis, 2 different interlocking nail systems (C-Nail; Medin, Nov. Město n. Moravě, Czech Republic; Calcanail; FH Orthopedics SAS; Heimsbrunn, France) as well as a polyaxial interlocking plate (Rimbus; Intercus GmbH; Rudolstadt, Germany) were used. Biomechanical testing consisted of a dynamic load sequence (preload 20 N, 1000 N up to 2500 N, stepwise increase of 100 N every 100 cycles, 0.5 mm/s) and a load to failure sequence (max. load 5000 N, 0.5 mm/s). Interfragmentary movement was detected via a 3-D optical measurement system. Boehler angle was measured after osteosynthesis and after failure occurred. No significant difference regarding load to failure, stiffness, Boehler angle, or interfragmentary motion was found between the different fixation systems. A significant difference was found with the dynamic failure testing sequence where 87.5% of the Calcanail implants failed in contrast to 14% of the C-Nail group (P < .01) and 66% of the Rimbus plate. The highest load to failure was observed for the C-Nail. Boehler angle showed physiologic range with all implants before and after the biomechanical tests. Both minimally invasive interlocking nail systems displayed a high primary stability that was not inferior to an interlocking plate. Based on our results, both interlocking nails appear to represent a viable option for treating displaced intra-articular calcaneal fractures. © The Author(s) 2016.

Project Report: Automatic Sequence Processor Software Analysis

NASA Technical Reports Server (NTRS)

Benjamin, Brandon

2011-01-01

The Mission Planning and Sequencing (MPS) element of Multi-Mission Ground System and Services (MGSS) provides space missions with multi-purpose software to plan spacecraft activities, sequence spacecraft commands, and then integrate these products and execute them on spacecraft. Jet Propulsion Laboratory (JPL) is currently is flying many missions. The processes for building, integrating, and testing the multi-mission uplink software need to be improved to meet the needs of the missions and the operations teams that command the spacecraft. The Multi-Mission Sequencing Team is responsible for collecting and processing the observations, experiments and engineering activities that are to be performed on a selected spacecraft. The collection of these activities is called a sequence and ultimately a sequence becomes a sequence of spacecraft commands. The operations teams check the sequence to make sure that no constraints are violated. The workflow process involves sending a program start command, which activates the Automatic Sequence Processor (ASP). The ASP is currently a file-based system that is comprised of scripts written in perl, c-shell and awk. Once this start process is complete, the system checks for errors and aborts if there are any; otherwise the system converts the commands to binary, and then sends the resultant information to be radiated to the spacecraft.

Probabilistic metrology or how some measurement outcomes render ultra-precise estimates

NASA Astrophysics Data System (ADS)

Calsamiglia, J.; Gendra, B.; Muñoz-Tapia, R.; Bagan, E.

2016-10-01

We show on theoretical grounds that, even in the presence of noise, probabilistic measurement strategies (which have a certain probability of failure or abstention) can provide, upon a heralded successful outcome, estimates with a precision that exceeds the deterministic bounds for the average precision. This establishes a new ultimate bound on the phase estimation precision of particular measurement outcomes (or sequence of outcomes). For probe systems subject to local dephasing, we quantify such precision limit as a function of the probability of failure that can be tolerated. Our results show that the possibility of abstaining can set back the detrimental effects of noise.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

PubMed

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-11-23

Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.

Guidance on Nanomaterial Hazards and Risks

DTIC Science & Technology

2015-05-21

and at room temperature and 37 C°– solid separation by centrifugation, filtration , or chemical techniques (more experimental techniques combining...members in this potency sequence using bolus in vivo testing, verify the bolus results with selective inhalation testing. The potency of members of...measures in in vitro and limited in vivo experimental systems would facilitate the characterization of dose-response relationships across a set of ENMs

Object tracking using plenoptic image sequences

NASA Astrophysics Data System (ADS)

Kim, Jae Woo; Bae, Seong-Joon; Park, Seongjin; Kim, Do Hyung

2017-05-01

Object tracking is a very important problem in computer vision research. Among the difficulties of object tracking, partial occlusion problem is one of the most serious and challenging problems. To address the problem, we proposed novel approaches to object tracking on plenoptic image sequences. Our approaches take advantage of the refocusing capability that plenoptic images provide. Our approaches input the sequences of focal stacks constructed from plenoptic image sequences. The proposed image selection algorithms select the sequence of optimal images that can maximize the tracking accuracy from the sequence of focal stacks. Focus measure approach and confidence measure approach were proposed for image selection and both of the approaches were validated by the experiments using thirteen plenoptic image sequences that include heavily occluded target objects. The experimental results showed that the proposed approaches were satisfactory comparing to the conventional 2D object tracking algorithms.

Photometric binary stars in Praesepe and the search for globular cluster binaries

NASA Technical Reports Server (NTRS)

Bolte, Michael

1991-01-01

A radial velocity study of the stars which are located on a second sequence above the single-star zero-age main sequence at a given color in the color-magnitude diagram of the open cluster Praesepe, (NGC 2632) shows that 10, and possibly 11, of 17 are binary systems. Of the binary systems, five have full amplitudes for their velocity variations that are greater than 50 km/s. To the extent that they can be applied to globular clusters, these results suggests that (1) observations of 'second-sequence' stars in globular clusters would be an efficient way of finding main-sequence binary systems in globulars, and (2) current instrumentation on large telescopes is sufficient for establishing unambiguously the existence of main-sequence binary systems in nearby globular clusters.

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

Curry, J J; Gallagher, D W; Modarres, M

Appendices are presented concerning isolation condenser makeup; vapor suppression system; station air system; reactor building closed cooling water system; turbine building secondary closed water system; service water system; emergency service water system; fire protection system; emergency ac power; dc power system; event probability estimation; methodology of accident sequence quantification; and assignment of dominant sequences to release categories.

[Sequences and expression pattern of mce gene in Leptospira interrogans of different serogroups].

PubMed

Zhang, Lei; Xue, Feng; Yan, Jie; Mao, Ya-fei; Li, Li-wei

2008-11-01

To determine the frequency of mce gene in Leptospira interrogans, and to investigate the gene transcription levels of L. interrogans before and after infecting cells. The segments of entire mce genes from 13 L.interrogans strains and 1 L.biflexa strain were amplified by PCR and then sequenced after T-A cloning. A prokaryotic expression system of mce gene was constructed; the expression and output of the target recombinant protein rMce were examined by SDS-PAGE and Western Blot assay. Rabbits were intradermally immunized with rMce to prepare the antiserum, the titer of antiserum was measured by immunodiffusion test. The transcription levels of mce gene in L.interrogans serogroup Icterohaemorrhagiae serovar lai strain 56601 before and after infecting J774A.1 cells were monitored by real-time fluorescence quantitative RT-PCR. mce gene was carried in all tested L.interrogans strains, but not in L.biflexa serogroup Semaranga serovar patoc strain Patoc I. The similarities of nucleotide and putative amino acid sequences of the cloned mce genes to the reported sequences (GenBank accession No: NP712236) were 99.02%-100% and 97.91%-100%, respectively. The constructed prokaryotic expression system of mce gene expressed rMce and the output of rMce was about 5% of the total bacterial proteins. The antiserum against whole cell of L.interrogans strain 56601 efficiently recognized rMce. After infecting J774A.1 cells, transcription levels of the mce gene in L.interrogans strain 56601 were remarkably up-regulated. The constructed prokaryotic expression system of mce gene and the prepared antiserum against rMce provide useful tools for further study of the gene function.

Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems

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

Samudrala, Ram; Heffron, Fred; McDermott, Jason E.

2009-04-24

The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates, effector proteins, are not. We have used a machine learning approach to identify new secreted effectors. The method integrates evolutionary measures, such as the pattern of homologs in a range of other organisms, and sequence-based features, such as G+C content, amino acid composition and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from Salmonella typhimurium and validated on a corresponding set of effectors from Pseudomonas syringae, aftermore » eliminating effectors with detectable sequence similarity. The method was able to identify all of the known effectors in P. syringae with a specificity of 84% and sensitivity of 82%. The reciprocal validation, training on P. syringae and validating on S. typhimurium, gave similar results with a specificity of 86% when the sensitivity level was 87%. These results show that type III effectors in disparate organisms share common features. We found that maximal performance is attained by including an N-terminal sequence of only 30 residues, which agrees with previous studies indicating that this region contains the secretion signal. We then used the method to define the most important residues in this putative secretion signal. Finally, we present novel predictions of secreted effectors in S. typhimurium, some of which have been experimentally validated, and apply the method to predict secreted effectors in the genetically intractable human pathogen Chlamydia trachomatis. This approach is a novel and effective way to identify secreted effectors in a broad range of pathogenic bacteria for further experimental characterization and provides insight into the nature of the type III secretion signal.« less

Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition.

PubMed

Lee, Jessica A; Francis, Christopher A

2017-12-01

Denitrification is a dominant nitrogen loss process in the sediments of San Francisco Bay. In this study, we sought to understand the ecology of denitrifying bacteria by using next-generation sequencing (NGS) to survey the diversity of a denitrification functional gene, nirS (encoding cytchrome-cd 1 nitrite reductase), along the salinity gradient of San Francisco Bay over the course of a year. We compared our dataset to a library of nirS sequences obtained previously from the same samples by standard PCR cloning and Sanger sequencing, and showed that both methods similarly demonstrated geography, salinity and, to a lesser extent, nitrogen, to be strong determinants of community composition. Furthermore, the depth afforded by NGS enabled novel techniques for measuring the association between environment and community composition. We used Random Forests modelling to demonstrate that the site and salinity of a sample could be predicted from its nirS sequences, and to identify indicator taxa associated with those environmental characteristics. This work contributes significantly to our understanding of the distribution and dynamics of denitrifying communities in San Francisco Bay, and provides valuable tools for the further study of this key N-cycling guild in all estuarine systems. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Demonstrating real-time feedback that enhances the performance of measurement sequence with cat states in a cavity

NASA Astrophysics Data System (ADS)

Ofek, N.; Petrenko, A.; Liu, Y.; Vlastakis, B.; Sun, L.; Leghtas, Z.; Heeres, R.; Sliwa, K. M.; Mirrahimi, M.; Jiang, L.; Devoret, M. H.; Schoelkopf, R. J.

2015-03-01

Real-time feedback offers not just the convenience of streamlined data acquisition, but is an essential element in any quantum computational architecture that requires branching based on measurement outcomes. State-preparation, mitigating the effects of qubit decoherence, and recording the trajectories of quantum systems are just a few of the many potential applications of real-time feedback. Photon number parity measurements of cat states in superconducting resonators are a particularly useful platform for demonstrating the clear advantages of having sophisticated feedback schemes to enhance the performance a proposed error-correction protocol [Leghtas et.al. PRL 2013]. In a cQED architecture, where a transmon qubit is coupled to two superconducting cavities, we present a field-programmable gate array (FPGA) device capable of making decisions and calculations with latency times far shorter than the lifetimes of any of the system's constituents. This level of performance opens the door to realizing many complex, previously unfeasible, experiments in superconducting qubit systems.

Dynamical complexity of short and noisy time series. Compression-Complexity vs. Shannon entropy

NASA Astrophysics Data System (ADS)

Nagaraj, Nithin; Balasubramanian, Karthi

2017-07-01

Shannon entropy has been extensively used for characterizing complexity of time series arising from chaotic dynamical systems and stochastic processes such as Markov chains. However, for short and noisy time series, Shannon entropy performs poorly. Complexity measures which are based on lossless compression algorithms are a good substitute in such scenarios. We evaluate the performance of two such Compression-Complexity Measures namely Lempel-Ziv complexity (LZ) and Effort-To-Compress (ETC) on short time series from chaotic dynamical systems in the presence of noise. Both LZ and ETC outperform Shannon entropy (H) in accurately characterizing the dynamical complexity of such systems. For very short binary sequences (which arise in neuroscience applications), ETC has higher number of distinct complexity values than LZ and H, thus enabling a finer resolution. For two-state ergodic Markov chains, we empirically show that ETC converges to a steady state value faster than LZ. Compression-Complexity measures are promising for applications which involve short and noisy time series.

Real-time chirp-coded imaging with a programmable ultrasound biomicroscope.

PubMed

Bosisio, Mattéo R; Hasquenoph, Jean-Michel; Sandrin, Laurent; Laugier, Pascal; Bridal, S Lori; Yon, Sylvain

2010-03-01

Ultrasound biomicroscopy (UBM) of mice can provide a testing ground for new imaging strategies. The UBM system presented in this paper facilitates the development of imaging and measurement methods with programmable design, arbitrary waveform coding, broad bandwidth (2-80 MHz), digital filtering, programmable processing, RF data acquisition, multithread/multicore real-time display, and rapid mechanical scanning (

The search for extra-solar planetary systems.

PubMed

Paresce, F

1992-01-01

I review the observational evidence for planetary systems around nearby stars and, using our own solar system as a guide, assess the stringent requirements that new searches need to meet in order to unambiguously establish the presence of another planetary system. Basically, these requirements are: 1 milliarcsecond or better positional accuracy for astrometric techniques, 9 orders of magnitude or better star to planet luminosity ratio discrimination at 0.5 to 1" separation in the optical for direct imaging techniques, 10 meters sec-1 or better radial velocity accuracy for reflex motion techniques and +/-1% or better brightness fluctuation accuracy for planet/star occultation measurements. The astrometric accuracy is in reach of HST, direct imaging will require much larger telescopes and/or a 50 times smoother mirror than HST while the reflex motion and occultation techniques best performed on the ground are just becoming viable and promise exciting new discoveries. On the other band, new indirect evidence on the existence of other planetary systems also comes from the observation of large dusty disks around nearby main sequence stars not too dissimilar from our sun. In one particular case, that of Beta Pictoris, a flattened disk seen nearly edge-on has been imaged in the optical and near IR down to almost 70 AU of the star. It probably represents a young planetary system in its clearing out phase as planetesimals collide, erode and are swept out of the inner system by radiation pressure. The hypothesized Kuiper belt around our solar system may be the analogous structure in a later evolutionary stage. Features of this type have been detected in the far IR and sub-millimeter wavelength regions around 50-100 nearby main sequence and pre-main sequence stars. I discuss a battery of new accurate observations planned in the near future of these objects some of which may actually harbour planets or planetesimals that will certainly dramatically improve our knowledge of planetary system formation processes and our peculiar position in this scheme.

Robo-AO Kepler Asteroseismic Survey. I. Adaptive Optics Imaging of 99 Asteroseismic Kepler Dwarfs and Subgiants

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

Schonhut-Stasik, Jessica S.; Baranec, Christoph; Huber, Daniel

We used the Robo-AO laser adaptive optics (AOs) system to image 99 main sequence and subgiant stars that have Kepler -detected asteroseismic signals. Robo-AO allows us to resolve blended secondary sources at separations as close as ∼0.″15 that may contribute to the measured Kepler light curves and affect asteroseismic analysis and interpretation. We report eight new secondary sources within 4.″0 of these Kepler asteroseismic stars. We used Subaru and Keck AOs to measure differential infrared photometry for these candidate companion systems. Two of the secondary sources are likely foreground objects, while the remaining six are background sources; however, we cannotmore » exclude the possibility that three of the objects may be physically associated. We measured a range of i ′-band amplitude dilutions for the candidate companion systems from 0.43% to 15.4%. We find that the measured amplitude dilutions are insufficient to explain the previously identified excess scatter in the relationship between asteroseismic oscillation amplitude and the frequency of maximum power.« less

Embedded 3D shape measurement system based on a novel spatio-temporal coding method

NASA Astrophysics Data System (ADS)

Xu, Bin; Tian, Jindong; Tian, Yong; Li, Dong

2016-11-01

Structured light measurement has been wildly used since 1970s in industrial component detection, reverse engineering, 3D molding, robot navigation, medical and many other fields. In order to satisfy the demand for high speed, high precision and high resolution 3-D measurement for embedded system, a new patterns combining binary and gray coding principle in space are designed and projected onto the object surface orderly. Each pixel corresponds to the designed sequence of gray values in time - domain, which is treated as a feature vector. The unique gray vector is then dimensionally reduced to a scalar which could be used as characteristic information for binocular matching. In this method, the number of projected structured light patterns is reduced, and the time-consuming phase unwrapping in traditional phase shift methods is avoided. This algorithm is eventually implemented on DM3730 embedded system for 3-D measuring, which consists of an ARM and a DSP core and has a strong capability of digital signal processing. Experimental results demonstrated the feasibility of the proposed method.

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

PubMed Central

Andersen, Malin C; Engström, Pär G; Lithwick, Stuart; Arenillas, David; Eriksson, Per; Lenhard, Boris; Wasserman, Wyeth W; Odeberg, Jacob

2008-01-01

Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression. For genes linked to genetic diseases, most identified causal mutations alter an encoded protein sequence. Technological advances for measuring RNA abundance suggest that a significant number of undiscovered causal mutations may alter the regulation of gene transcription. However, it remains a challenge to separate causal genetic variations from linked neutral variations. Here we present an in silico driven approach to identify possible genetic variation in regulatory sequences. The approach combines phylogenetic footprinting and transcription factor binding site prediction to identify variation in candidate cis-regulatory elements. The bioinformatics approach has been tested on a set of SNPs that are reported to have a regulatory function, as well as background SNPs. In the absence of additional information about an analyzed gene, the poor specificity of binding site prediction is prohibitive to its application. However, when additional data is available that can give guidance on which transcription factor is involved in the regulation of the gene, the in silico binding site prediction improves the selection of candidate regulatory polymorphisms for further analyses. The bioinformatics software generated for the analysis has been implemented as a Web-based application system entitled RAVEN (regulatory analysis of variation in enhancers). The RAVEN system is available at http://www.cisreg.ca for all researchers interested in the detection and characterization of regulatory sequence variation. PMID:18208319

1D and 2D diffusion pore imaging on a preclinical MR system using adaptive rephasing: Feasibility and pulse sequence comparison

NASA Astrophysics Data System (ADS)

Bertleff, Marco; Domsch, Sebastian; Laun, Frederik B.; Kuder, Tristan A.; Schad, Lothar R.

2017-05-01

Diffusion pore imaging (DPI) has recently been proposed as a means to acquire images of the average pore shape in an image voxel or region of interest. The highly asymmetric gradient scheme of its sequence makes it substantially demanding in terms of the hardware of the NMR system. The aim of this work is to show the feasibility of DPI on a preclinical 9.4 T animal scanner. Using water-filled capillaries with an inner radius of 10 μm, four different variants of the DPI sequence were compared in 1D and 2D measurements. The pulse sequences applied cover the basic implementation using one long and one temporally narrow gradient pulse, a CPMG-like variant with multiple refocusing RF pulses as well as two variants splitting up the long gradient and distributing it on either side of the refocusing pulse. Substantial differences between the methods were found in terms of signal-to-noise ratio, contrast, blurring, deviations from the expected results and sensitivity to gradient imperfections. Each of the tested sequences was found to produce characteristic gradient mismatches dependent on the absolute value, direction and sign of the applied q-value. Read gradients were applied to compensate these mismatches translating them into time shifts, which enabled 1D DPI yielding capillary radius estimations within the tolerances specified by the manufacturer. For a successful DPI application in 2D, a novel gradient amplitude adaption scheme was implemented to correct for the occurring time shifts. Using this adaption, higher conformity to the expected pore shape, reduced blurring and enhanced contrast were achieved. Images of the phantom's pore shape could be acquired with a nominal resolution of 2.2 μm.

Characterization and expression analysis of Toll-like receptor 3 cDNA from Atlantic salmon (Salmo salar).

PubMed

Vidal, R; González, R; Gil, F

2015-06-10

Innate pathway activation is fundamental for early anti-viral defense in fish, but currently there is insufficient understanding of how salmonid fish identify viral molecules and activate these pathways. The Toll-like receptor (TLR) is believed to play a crucial role in host defense of pathogenic microbes in the innate immune system. In the present study, the full-length cDNA of Salmo salar TLR3 (ssTLR3) was cloned. The ssTLR3 cDNA sequence was 6071 bp long, containing an open reading frame of 2754 bp and encoding 971 amino acids. The TLR group motifs, such as leucine-rich repeat (LRR) domains and Toll-interleukin-1 receptor (TIR) domains, were maintained in ssTLR3, with sixteen LRR domains and one TIR domain. In contrast to descriptions of the TLR3 in rainbow trout and the murine (TATA-less), we found a putative TATA box in the proximal promoter region 29 bp upstream of the transcription start point of ssTLR3. Multiple-sequence alignment analysis of the ssTLR3 protein-coding sequence with other known TLR3 sequences showed the sequence to be conserved among all species analyzed, implying that the function of the TLR3 had been sustained throughout evolution. The ssTLR3 mRNA expression patterns were measured using real-time PCR. The results revealed that TLR3 is widely expressed in various healthy tissues. Individuals challenged with infectious pancreatic necrosis virus and immunostimulated with polyinosinic:polycytidylic acid exhibited increased expression of TLR3 at the mRNA level, indicating that ssTLR3 may be involved in pathogen recognition in the early innate immune system.

Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Patel, Kamlesh D.

2018-01-22

Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Patel, Kamlesh D.

2012-06-01

Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

The in-plant evaluation of a uranium NDA system

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

Sprinkle, J.K. Jr.; Baxman, H.R.; Langner, D.G.

1979-12-31

The Los Alamos Scientific Laboratory has an unirradiated enriched uranium reprocessing facility. Various types of solutions are generated in this facility, including distillates and raffinates containing ppm of uranium and concentrated solutions with up to 400 grams U/t. In addition to uranyl nitrate and HNO{sub 3}, the solutions may also contain zirconium, niobium, fluoride, and small amounts of many metals. A uranium solution assay system (USAS) has been installed to allow accurate and more timely process control, accountability, and criticality data to be obtained. The USAS assays are made by a variety of techniques that depend upon state-of-the-art high-resolution Ge(Li)more » gamma-ray spectroscopy integrated with an interactive, user-oriented computer software package. Tight control of the system`s performance is maintained by constantly monitoring the USAS status. Daily measurement control sequences are required, and the user is forced by the software to perform these sequences. Routine assays require 400 or 1000 seconds for a precision of 0.5% over the concentration range of 5--400 g/t. A comparison of the USAS precision and accuracy with that obtained by traditional destructive analytical chemistry techniques (colorimetric and volumetric) is presented.« less

Self-propelled in-tube shuttle and control system for automated measurements of magnetic field alignment

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

Boroski, W.N.; Nicol, T.H.; Pidcoe, S.V.

1990-03-01

A magnetic field alignment gauge is used to measure the field angle as a function of axial position in each of the magnets for the Superconducting Super Collider (SSC). Present measurements are made by manually pushing the through the magnet bore tube and stopping at intervals to record field measurements. Gauge location is controlled through graduation marks and alignment pins on the push rods. Field measurements are recorded on a logging multimeter with tape output. Described is a computerized control system being developed to replace the manual procedure for field alignment measurements. The automated system employs a pneumatic walking devicemore » to move the measurement gauge through the bore tube. Movement of the device, called the Self-Propelled In-Tube Shuttle (SPITS), is accomplished through an integral, gas driven, double-acting cylinder. The motion of the SPITS is transferred to the bore tube by means of a pair of controlled, retractable support feet. Control of the SPITS is accomplished through an RS-422 interface from an IBM-compatible computer to a series of solenoid-actuated air valves. Direction of SPITS travel is determined by the air-valve sequence, and is managed through the control software. Precise axial position of the gauge within the magnet is returned to the control system through an optically-encoded digital position transducer attached to the shuttle. Discussed is the performance of the transport device and control system during preliminary testing of the first prototype shuttle. 1 ref., 7 figs.« less

Spreading Sequence System for Full Connectivity Relay Network

NASA Technical Reports Server (NTRS)

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

2018-01-01

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

Variation in promiscuity and sexual selection drives avian rate of Faster-Z evolution.

PubMed

Wright, Alison E; Harrison, Peter W; Zimmer, Fabian; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

2015-03-01

Higher rates of coding sequence evolution have been observed on the Z chromosome relative to the autosomes across a wide range of species. However, despite a considerable body of theory, we lack empirical evidence explaining variation in the strength of the Faster-Z Effect. To assess the magnitude and drivers of Faster-Z Evolution, we assembled six de novo transcriptomes, spanning 90 million years of avian evolution. Our analysis combines expression, sequence and polymorphism data with measures of sperm competition and promiscuity. In doing so, we present the first empirical evidence demonstrating the positive relationship between Faster-Z Effect and measures of promiscuity, and therefore variance in male mating success. Our results from multiple lines of evidence indicate that selection is less effective on the Z chromosome, particularly in promiscuous species, and that Faster-Z Evolution in birds is due primarily to genetic drift. Our results reveal the power of mating system and sexual selection in shaping broad patterns in genome evolution. © 2015 John Wiley & Sons Ltd.

Study of time-lapse processing for dynamic hydrologic conditions. [electronic satellite image analysis console for Earth Resources Technology Satellites imagery

NASA Technical Reports Server (NTRS)

Serebreny, S. M.; Evans, W. E.; Wiegman, E. J.

1974-01-01

The usefulness of dynamic display techniques in exploiting the repetitive nature of ERTS imagery was investigated. A specially designed Electronic Satellite Image Analysis Console (ESIAC) was developed and employed to process data for seven ERTS principal investigators studying dynamic hydrological conditions for diverse applications. These applications include measurement of snowfield extent and sediment plumes from estuary discharge, Playa Lake inventory, and monitoring of phreatophyte and other vegetation changes. The ESIAC provides facilities for storing registered image sequences in a magnetic video disc memory for subsequent recall, enhancement, and animated display in monochrome or color. The most unique feature of the system is the capability to time lapse the imagery and analytic displays of the imagery. Data products included quantitative measurements of distances and areas, binary thematic maps based on monospectral or multispectral decisions, radiance profiles, and movie loops. Applications of animation for uses other than creating time-lapse sequences are identified. Input to the ESIAC can be either digital or via photographic transparencies.

Quantum and classical noise in practical quantum-cryptography systems based on polarization-entangled photons

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

Castelletto, S.; Degiovanni, I.P.; Rastello, M.L.

2003-02-01

Quantum-cryptography key distribution (QCKD) experiments have been recently reported using polarization-entangled photons. However, in any practical realization, quantum systems suffer from either unwanted or induced interactions with the environment and the quantum measurement system, showing up as quantum and, ultimately, statistical noise. In this paper, we investigate how an ideal polarization entanglement in spontaneous parametric down-conversion (SPDC) suffers quantum noise in its practical implementation as a secure quantum system, yielding errors in the transmitted bit sequence. Since all SPDC-based QCKD schemes rely on the measurement of coincidence to assert the bit transmission between the two parties, we bundle up themore » overall quantum and statistical noise in an exhaustive model to calculate the accidental coincidences. This model predicts the quantum-bit error rate and the sifted key and allows comparisons between different security criteria of the hitherto proposed QCKD protocols, resulting in an objective assessment of performances and advantages of different systems.« less

Joint Europa Mission (JEM) : A multi-scale study of Europa to characterize its habitability and search for life.

NASA Astrophysics Data System (ADS)

Blanc, Michel; Prieto Ballesteros, Olga; Andre, Nicolas; Cooper, John F.

2017-04-01

Europa is the closest and probably the most promising target to perform a comprehensive characterization of habitability and search for extant life. We propose that NASA and ESA join forces to design an ambitious planetary mission we call JEM (for Joint Europa Mission) to reach this objective. JEM will be assigned the following overarching goal: Understand Europa as a complex system responding to Jupiter system forcing, characterize the habitability of its potential biosphere, and search for life in its surface, sub-surface and exosphere. Our observation strategy to address these goals will combine three scientific measurement sequences: measurements on a high-latitude, low-latitude Europan orbit providing a continuous and global mapping of planetary fields (magnetic and gravity) and of the neutral and charged environment during a period of three months; in-situ measurements at the surface, using a soft lander operating during 35 days, to search for bio-signatures at the surface and sub-surface and operate a geophysical station; measurements of the chemical composition of the very low exosphere and plumes in search for biomolecules. The implementation of these three observation sequences will rest on the combination of two science platforms equipped with the most advanced instrumentation: a soft lander to perform all scientific measurements at the surface and sub-surface at a selected landing site, and a carrier/relay/orbiter to perform the orbital survey and descent sequences. In this concept, the orbiter will perform science operations during the relay phase on a carefully optimized halo orbit of the Europa-Jupiter system before moving to its final Europan orbit. The design of both orbiter and lander instruments will have to accommodate the very challenging radiation mitigation and Planetary Protection issues. The proposed lander science platform is composed of a geophysical station and of two complementary astrobiology facilities dedicated to bio-signature characterization experiments operating respectively in the solid and in the liquid phases, fed by a common articulated arm. The "Astrobiology Wet Laboratory" will be a specific European contribution. We propose an innovative distribution of roles to make JEM an appealing and affordable joint venture for the two agencies: while NASA would provide an SLS launcher, the lander stack and mission operations, ESA would provide the carrier-orbiter-relay platform. The delivery of the orbiter by ESA could take advantage of a double European heritage: an adaptation of the ORION ESM bus to JEM, complemented by avionics derived from JUICE.

Single stars in the Hyades open cluster. Fiducial sequence for testing stellar and atmospheric models

NASA Astrophysics Data System (ADS)

Kopytova, Taisiya G.; Brandner, Wolfgang; Tognelli, Emanuele; Prada Moroni, Pier Giorgio; Da Rio, Nicola; Röser, Siegfried; Schilbach, Elena

2016-01-01

Context. Age and mass determinations for isolated stellar objects remain model-dependent. While stellar interior and atmospheric theoretical models are rapidly evolving, we need a powerful tool to test them. Open clusters are good candidates for this role. Aims: We aim to create a fiducial sequence of stellar objects for testing stellar and atmospheric models. Methods: We complement previous studies on the Hyades multiplicity by Lucky Imaging observations with the AstraLux Norte camera. This allows us to exclude possible binary and multiple systems with companions outside a 2-7 AU separation and to create a single-star sequence for the Hyades. The sequence encompasses 250 main-sequence stars ranging from A5V to M6V. Using the Tool for Astrophysical Data Analysis (TA-DA), we create various theoretical isochrones applying different combinations of interior and atmospheric models. We compare the isochrones with the observed Hyades single-star sequence on J vs. J-Ks, J vs. J-H, and Ks vs. H-Ks color-magnitude diagrams. As a reference we also compute absolute fluxes and magnitudes for all stars from X-ray to mid-infrared based on photometric measurements available in the literature(ROSAT X-ray, GALEX UV, APASS gri, 2MASS JHKs, and WISE W1 to W4). Results: We find that combinations of both PISA and DARTMOUTH stellar interior models with BT-Settl 2010 atmospheric models describe the observed sequence well. We use PISA in combination with BT-Settl 2010 models to derive theoretical predictions for physical parameters (Teff, mass, log g) of 250 single stars in the Hyades. The full sequence covers the mass range of 0.13-2.30 M⊙, and effective temperatures between 3060 K and 8200 K. Conclusions: Within the measurement uncertainties, the current generation of models agree well with the single-star sequence. The primary limitations are the uncertainties in the measurement of the distances to individual Hyades members, and uncertainties in the photometry. Gaia parallaxes, photometry, and spectroscopy will greatly reduce the uncertainties in particular at the lowest mass range, and will enable us to test model predictions with greater confidence. Additionally, a small (~0.05 mag) systematic offset can be noted in J vs. J-K and K vs. H-K diagrams - the observed sequence is shifted to redder colors than the theoretical predictions. Based on observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).Full Table 2 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/585/A7

Ultrafast Pulse Sequencing for Fast Projective Measurements of Atomic Hyperfine Qubits

NASA Astrophysics Data System (ADS)

Ip, Michael; Ransford, Anthony; Campbell, Wesley

2015-05-01

Projective readout of quantum information stored in atomic hyperfine structure typically uses state-dependent CW laser-induced fluorescence. This method requires an often sophisticated imaging system to spatially filter out the background CW laser light. We present an alternative approach that instead uses simple pulse sequences from a mode-locked laser to affect the same state-dependent excitations in less than 1 ns. The resulting atomic fluorescence occurs in the dark, allowing the placement of non-imaging detectors right next to the atom to improve the qubit state detection efficiency and speed. We also discuss methods of Doppler cooling with mode-locked lasers for trapped ions, where the creation of the necessary UV light is often difficult with CW lasers.

A Rapid Whole Genome Sequencing and Analysis System Supporting Genomic Epidemiology (7th Annual SFAF Meeting, 2012)

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

FitzGerald, Michael

2012-06-01

Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

A Rapid Whole Genome Sequencing and Analysis System Supporting Genomic Epidemiology (7th Annual SFAF Meeting, 2012)

ScienceCinema

FitzGerald, Michael

2018-01-11

Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

Generalized energy measurements and modified transient quantum fluctuation theorems

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Venkatesh, B. Prasanna; Talkner, Peter

2014-05-01

Determining the work which is supplied to a system by an external agent provides a crucial step in any experimental realization of transient fluctuation relations. This, however, poses a problem for quantum systems, where the standard procedure requires the projective measurement of energy at the beginning and the end of the protocol. Unfortunately, projective measurements, which are preferable from the point of view of theory, seem to be difficult to implement experimentally. We demonstrate that, when using a particular type of generalized energy measurements, the resulting work statistics is simply related to that of projective measurements. This relation between the two work statistics entails the existence of modified transient fluctuation relations. The modifications are exclusively determined by the errors incurred in the generalized energy measurements. They are universal in the sense that they do not depend on the force protocol. Particularly simple expressions for the modified Crooks relation and Jarzynski equality are found for Gaussian energy measurements. These can be obtained by a sequence of sufficiently many generalized measurements which need not be Gaussian. In accordance with the central limit theorem, this leads to an effective error reduction in the individual measurements and even yields a projective measurement in the limit of infinite repetitions.

Efficient measurement of large light source near-field color and luminance distributions for optical design and simulation

NASA Astrophysics Data System (ADS)

Kostal, Hubert; Kreysar, Douglas; Rykowski, Ronald

2009-08-01

The color and luminance distributions of large light sources are difficult to measure because of the size of the source and the physical space required for the measurement. We describe a method for the measurement of large light sources in a limited space that efficiently overcomes the physical limitations of traditional far-field measurement techniques. This method uses a calibrated, high dynamic range imaging colorimeter and a goniometric system to move the light source through an automated measurement sequence in the imaging colorimeter's field-of-view. The measurement is performed from within the near-field of the light source, enabling a compact measurement set-up. This method generates a detailed near-field color and luminance distribution model that can be directly converted to ray sets for optical design and that can be extrapolated to far-field distributions for illumination design. The measurements obtained show excellent correlation to traditional imaging colorimeter and photogoniometer measurement methods. The near-field goniometer approach that we describe is broadly applicable to general lighting systems, can be deployed in a compact laboratory space, and provides full near-field data for optical design and simulation.

Sequence and facies architecture of the upper Blackhawk Formation and the Lower Castlegate Sandstone (Upper Cretaceous), Book Cliffs, Utah, USA

NASA Astrophysics Data System (ADS)

Yoshida, S.

2000-11-01

High-frequency stratigraphic sequences that comprise the Desert Member of the Blackhawk Formation, the Lower Castlegate Sandstone, and the Buck Tongue in the Green River area of Utah display changes in sequence architecture from marine deposits to marginal marine deposits to an entirely nonmarine section. Facies and sequence architecture differ above and below the regionally extensive Castlegate sequence boundary, which separates two low-frequency (106-year cyclicity) sequences. Below this surface, high-frequency sequences are identified and interpreted as comprising the highstand systems tract of the low-frequency Blackhawk sequence. Each high-frequency sequence has a local incised valley system on top of the wave-dominated delta, and coastal plain to shallow marine deposits are preserved. Above the Castlegate sequence boundary, in contrast, a regionally extensive sheet sandstone of fluvial to estuarine origin with laterally continuous internal erosional surfaces occurs. These deposits above the Castlegate sequence boundary are interpreted as the late lowstand to early transgressive systems tracts of the low-frequency Castlegate sequence. The base-level changes that generated both the low- and high-frequency sequences are attributed to crustal response to fluctuations in compressive intraplate stress on two different time scales. The low-frequency stratigraphic sequences are attributed to changes in the long-term regional subsidence rate and regional tilting of foreland basin fill. High-frequency sequences probably reflect the response of anisotropic basement to tectonism. Sequence architecture changes rapidly across the faulted margin of the underlying Paleozoic Paradox Basin. The high-frequency sequences are deeply eroded and stack above the Paradox Basin, but display less relief and become conformable updip. These features indicate that the area above the Paradox Basin was more prone to vertical structural movements during formation of the Blackhawk-Lower Castlegate succession.

Continuous- and discrete-time stimulus sequences for high stimulus rate paradigm in evoked potential studies.

PubMed

Wang, Tao; Huang, Jiang-hua; Lin, Lin; Zhan, Chang'an A

2013-01-01

To obtain reliable transient auditory evoked potentials (AEPs) from EEGs recorded using high stimulus rate (HSR) paradigm, it is critical to design the stimulus sequences of appropriate frequency properties. Traditionally, the individual stimulus events in a stimulus sequence occur only at discrete time points dependent on the sampling frequency of the recording system and the duration of stimulus sequence. This dependency likely causes the implementation of suboptimal stimulus sequences, sacrificing the reliability of resulting AEPs. In this paper, we explicate the use of continuous-time stimulus sequence for HSR paradigm, which is independent of the discrete electroencephalogram (EEG) recording system. We employ simulation studies to examine the applicability of the continuous-time stimulus sequences and the impacts of sampling frequency on AEPs in traditional studies using discrete-time design. Results from these studies show that the continuous-time sequences can offer better frequency properties and improve the reliability of recovered AEPs. Furthermore, we find that the errors in the recovered AEPs depend critically on the sampling frequencies of experimental systems, and their relationship can be fitted using a reciprocal function. As such, our study contributes to the literature by demonstrating the applicability and advantages of continuous-time stimulus sequences for HSR paradigm and by revealing the relationship between the reliability of AEPs and sampling frequencies of the experimental systems when discrete-time stimulus sequences are used in traditional manner for the HSR paradigm.

An analysis of the uncertainty and bias in DCE-MRI measurements using the spoiled gradient-recalled echo pulse sequence

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

Subashi, Ergys; Choudhury, Kingshuk R.; Johnson, G. Allan, E-mail: gjohnson@duke.edu

2014-03-15

Purpose: The pharmacokinetic parameters derived from dynamic contrast-enhanced (DCE) MRI have been used in more than 100 phase I trials and investigator led studies. A comparison of the absolute values of these quantities requires an estimation of their respective probability distribution function (PDF). The statistical variation of the DCE-MRI measurement is analyzed by considering the fundamental sources of error in the MR signal intensity acquired with the spoiled gradient-echo (SPGR) pulse sequence. Methods: The variance in the SPGR signal intensity arises from quadrature detection and excitation flip angle inconsistency. The noise power was measured in 11 phantoms of contrast agentmore » concentration in the range [0–1] mM (in steps of 0.1 mM) and in onein vivo acquisition of a tumor-bearing mouse. The distribution of the flip angle was determined in a uniform 10 mM CuSO{sub 4} phantom using the spin echo double angle method. The PDF of a wide range of T1 values measured with the varying flip angle (VFA) technique was estimated through numerical simulations of the SPGR equation. The resultant uncertainty in contrast agent concentration was incorporated in the most common model of tracer exchange kinetics and the PDF of the derived pharmacokinetic parameters was studied numerically. Results: The VFA method is an unbiased technique for measuringT1 only in the absence of bias in excitation flip angle. The time-dependent concentration of the contrast agent measured in vivo is within the theoretically predicted uncertainty. The uncertainty in measuring K{sup trans} with SPGR pulse sequences is of the same order, but always higher than, the uncertainty in measuring the pre-injection longitudinal relaxation time (T1{sub 0}). The lowest achievable bias/uncertainty in estimating this parameter is approximately 20%–70% higher than the bias/uncertainty in the measurement of the pre-injection T1 map. The fractional volume parameters derived from the extended Tofts model were found to be extremely sensitive to the variance in signal intensity. The SNR of the pre-injection T1 map indicates the limiting precision with which K{sup trans} can be calculated. Conclusions: Current small-animal imaging systems and pulse sequences robust to motion artifacts have the capacity for reproducible quantitative acquisitions with DCE-MRI. In these circumstances, it is feasible to achieve a level of precision limited only by physiologic variability.« less

Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding.

PubMed

Ma, Eddie Y T; Ratnasingham, Sujeevan; Kremer, Stefan C

2018-01-01

This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label. KB must also rate the replacement with quality value of in the additional read. Corrections are only available during system training. Developing the system, nearly 850,000 N-labels are obtained from Barcode of Life Datasystems, the premier database of genetic markers called DNA Barcodes. Increasing the number of correct bases improves reference sequence reliability, increases sequence identification accuracy, and assures analysis correctness. Keeping with barcoding standards, our system maintains an error rate of percent. Our system only applies corrections when it estimates low rate of error. Tested on this data, our automation selects and recovers: 79 percent of N-labels from COI (animal barcode); 80 percent from matK and rbcL (plant barcodes); and 58 percent from non-protein-coding sequences (across eukaryotes).

Exploring Dance Movement Data Using Sequence Alignment Methods

PubMed Central

Chavoshi, Seyed Hossein; De Baets, Bernard; Neutens, Tijs; De Tré, Guy; Van de Weghe, Nico

2015-01-01

Despite the abundance of research on knowledge discovery from moving object databases, only a limited number of studies have examined the interaction between moving point objects in space over time. This paper describes a novel approach for measuring similarity in the interaction between moving objects. The proposed approach consists of three steps. First, we transform movement data into sequences of successive qualitative relations based on the Qualitative Trajectory Calculus (QTC). Second, sequence alignment methods are applied to measure the similarity between movement sequences. Finally, movement sequences are grouped based on similarity by means of an agglomerative hierarchical clustering method. The applicability of this approach is tested using movement data from samba and tango dancers. PMID:26181435

SU-E-J-223: A BOLD Contrast Imaging Sequence to Evaluate Oxygenation Changes Due to Breath Holding for Breast Radiotherapy: A Pilot Study

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

Adamson, J; Chang, Z; Cai, J

Purpose: To develop a robust MRI sequence to measure BOLD breath hold induced contrast in context of breast radiotherapy. Methods: Two sequences were selected from prior studies as candidates to measure BOLD contrast attributable to breath holding within the breast: (1) T2* based Gradient Echo EPI (TR/TE = 500/41ms, flip angle = 60°), and (2) T2 based Single Shot Fast Spin Echo (SSFSE) (TR/TE = 3000/60ms). We enrolled ten women post-lumpectomy for breast cancer who were undergoing treatment planning for whole breast radiotherapy. Each session utilized a 1.5T GE MRI and 4 channel breast coil with the subject immobilized pronemore » on a custom board. For each sequence, 1–3 planes of the lumpectomy breast were imaged continuously during a background measurement (1min) and intermittent breath holds (20–40s per breath hold, 3–5 holds per sequence). BOLD contrast was quantified as correlation of changes in per-pixel intensity with the breath hold schedule convolved with a hemodynamic response function. Subtle motion was corrected using a deformable registration algorithm. Correlation with breath-holding was considered significant if p<0.001. Results: The percentage of the breast ROI with positive BOLD contrast measured by the two sequences were in agreement with a correlation coefficient of R=0.72 (p=0.02). While both sequences demonstrated areas with strong BOLD response, the response was more systematic throughout the breast for the SSFSE (T2) sequence (% breast with response in the same direction: 51.2%±0.7% for T2* vs. 68.1%±16% for T2). In addition, the T2 sequence was less prone to magnetic susceptibility artifacts, especially in presence of seroma, and provided a more robust image with little distortion or artifacts. Conclusion: A T2 SSFSE sequence shows promise for measuring BOLD contrast in the context of breast radiotherapy utilizing a breath hold technique. Further study in a larger patient cohort is warranted to better refine this novel technique.« less

RNA Interference towards the Potato Psyllid, Bactericera cockerelli, Is Induced in Plants Infected with Recombinant Tobacco mosaic virus (TMV)

PubMed Central

Wuriyanghan, Hada; Falk, Bryce W.

2013-01-01

The potato/tomato psyllid, Bactericera cockerelli (B. cockerelli), is an important plant pest and the vector of the phloem-limited bacterium Candidatus Liberibacter psyllaurous (solanacearum), which is associated with the zebra chip disease of potatoes. Previously, we reported induction of RNA interference effects in B. cockerelli via in vitro-prepared dsRNA/siRNAs after intrathoracic injection, and after feeding of artificial diets containing these effector RNAs. In order to deliver RNAi effectors via plant hosts and to rapidly identify effective target sequences in plant-feeding B. cockerelli, here we developed a plant virus vector-based in planta system for evaluating candidate sequences. We show that recombinant Tobacco mosaic virus (TMV) containing B. cockerelli sequences can efficiently infect and generate small interfering RNAs in tomato (Solanum lycopersicum), tomatillo (Physalis philadelphica) and tobacco (Nicotiana tabacum) plants, and more importantly delivery of interfering sequences via TMV induces RNAi effects, as measured by actin and V-ATPase mRNA reductions, in B. cockerelli feeding on these plants. RNAi effects were primarily detected in the B. cockerelli guts. In contrast to our results with TMV, recombinant Potato virus X (PVX) and Tobacco rattle virus (TRV) did not give robust infections in all plants and did not induce detectable RNAi effects in B. cockerelli. The greatest RNA interference effects were observed when B. cockerelli nymphs were allowed to feed on leaf discs collected from inoculated or lower expanded leaves from corresponding TMV-infected plants. Tomatillo plants infected with recombinant TMV containing B. cockerelli actin or V-ATPase sequences also showed phenotypic effects resulting in decreased B. cockerelli progeny production as compared to plants infected by recombinant TMV containing GFP. These results showed that RNAi effects can be achieved in plants against the phloem feeder, B. cockerelli, and the TMV-plant system will provide a faster and more convenient method for screening of suitable RNAi target sequences in planta. PMID:23824081

Accuracy and Reproducibility of Adipose Tissue Measurements in Young Infants by Whole Body Magnetic Resonance Imaging

PubMed Central

Bauer, Jan Stefan; Noël, Peter Benjamin; Vollhardt, Christiane; Much, Daniela; Degirmenci, Saliha; Brunner, Stefanie; Rummeny, Ernst Josef; Hauner, Hans

2015-01-01

Purpose MR might be well suited to obtain reproducible and accurate measures of fat tissues in infants. This study evaluates MR-measurements of adipose tissue in young infants in vitro and in vivo. Material and Methods MR images of ten phantoms simulating subcutaneous fat of an infant’s torso were obtained using a 1.5T MR scanner with and without simulated breathing. Scans consisted of a cartesian water-suppression turbo spin echo (wsTSE) sequence, and a PROPELLER wsTSE sequence. Fat volume was quantified directly and by MR imaging using k-means clustering and threshold-based segmentation procedures to calculate accuracy in vitro. Whole body MR was obtained in sleeping young infants (average age 67±30 days). This study was approved by the local review board. All parents gave written informed consent. To obtain reproducibility in vivo, cartesian and PROPELLER wsTSE sequences were repeated in seven and four young infants, respectively. Overall, 21 repetitions were performed for the cartesian sequence and 13 repetitions for the PROPELLER sequence. Results In vitro accuracy errors depended on the chosen segmentation procedure, ranging from 5.4% to 76%, while the sequence showed no significant influence. Artificial breathing increased the minimal accuracy error to 9.1%. In vivo reproducibility errors for total fat volume of the sleeping infants ranged from 2.6% to 3.4%. Neither segmentation nor sequence significantly influenced reproducibility. Conclusion With both cartesian and PROPELLER sequences an accurate and reproducible measure of body fat was achieved. Adequate segmentation was mandatory for high accuracy. PMID:25706876

Accuracy and reproducibility of adipose tissue measurements in young infants by whole body magnetic resonance imaging.

PubMed

Bauer, Jan Stefan; Noël, Peter Benjamin; Vollhardt, Christiane; Much, Daniela; Degirmenci, Saliha; Brunner, Stefanie; Rummeny, Ernst Josef; Hauner, Hans

2015-01-01

MR might be well suited to obtain reproducible and accurate measures of fat tissues in infants. This study evaluates MR-measurements of adipose tissue in young infants in vitro and in vivo. MR images of ten phantoms simulating subcutaneous fat of an infant's torso were obtained using a 1.5T MR scanner with and without simulated breathing. Scans consisted of a cartesian water-suppression turbo spin echo (wsTSE) sequence, and a PROPELLER wsTSE sequence. Fat volume was quantified directly and by MR imaging using k-means clustering and threshold-based segmentation procedures to calculate accuracy in vitro. Whole body MR was obtained in sleeping young infants (average age 67±30 days). This study was approved by the local review board. All parents gave written informed consent. To obtain reproducibility in vivo, cartesian and PROPELLER wsTSE sequences were repeated in seven and four young infants, respectively. Overall, 21 repetitions were performed for the cartesian sequence and 13 repetitions for the PROPELLER sequence. In vitro accuracy errors depended on the chosen segmentation procedure, ranging from 5.4% to 76%, while the sequence showed no significant influence. Artificial breathing increased the minimal accuracy error to 9.1%. In vivo reproducibility errors for total fat volume of the sleeping infants ranged from 2.6% to 3.4%. Neither segmentation nor sequence significantly influenced reproducibility. With both cartesian and PROPELLER sequences an accurate and reproducible measure of body fat was achieved. Adequate segmentation was mandatory for high accuracy.

An MRI-Compatible Robotic System With Hybrid Tracking for MRI-Guided Prostate Intervention

PubMed Central

Krieger, Axel; Iordachita, Iulian I.; Guion, Peter; Singh, Anurag K.; Kaushal, Aradhana; Ménard, Cynthia; Pinto, Peter A.; Camphausen, Kevin; Fichtinger, Gabor

2012-01-01

This paper reports the development, evaluation, and first clinical trials of the access to the prostate tissue (APT) II system—a scanner independent system for magnetic resonance imaging (MRI)-guided transrectal prostate interventions. The system utilizes novel manipulator mechanics employing a steerable needle channel and a novel six degree-of-freedom hybrid tracking method, comprising passive fiducial tracking for initial registration and subsequent incremental motion measurements. Targeting accuracy of the system in prostate phantom experiments and two clinical human-subject procedures is shown to compare favorably with existing systems using passive and active tracking methods. The portable design of the APT II system, using only standard MRI image sequences and minimal custom scanner interfacing, allows the system to be easily used on different MRI scanners. PMID:22009867

Diversity of microbial communities correlated to physiochemical parameters in a digestion basin of a zero-discharge mariculture system.

PubMed

Cytryn, Eddie; Gelfand, Ilya; Barak, Yoram; van Rijn, Jaap; Minz, Dror

2003-01-01

Bacterial community structure and physiochemical parameters were examined in a sedimentation basin of a zero-discharge mariculture system. The system consisted of an intensively stocked fish basin from which water was recirculated through two separate treatment loops. Surface water from the basin was pumped over a trickling filter in one loop while bottom-water was recirculated through a sedimentation basin followed by a fluidized bed reactor in the other. Ammonia oxidation to nitrate in the trickling filter and organic matter digestion together with nitrate reduction in the sedimentation basin and fluidized bed reactor, allowed zero-discharge operation of the system. Relatively high concentrations of oxygen, nitrate, sulphate and organic matter detected simultaneously in the digestion basin suggested the potential for a wide range of microbially-mediated transformation processes. In this study, physiochemical parameters were correlated to bacterial diversity and distribution in horizontal and vertical profiles within this basin in an effort to obtain a basic understanding of the chemical and microbial processes in this system. Chemical activity and microbial diversity, the latter measured by denaturing gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction (PCR) amplified 16S rDNA fragments, were higher in the sludge layer than in the overlying aqueous layer of the basin. Chemical parameters in sludge samples close to the basin inlet suggested enhanced microbial activity relative to other sampling areas with evidence of both nitrate and sulphate reduction. Four of the nine DGGE bands identified in this zone were affiliated with the Bacteroidetes phylum. Detected sequences closely related to sequences of organisms involved in the sulphur cycle included Desulfovibrio, Dethiosulfovibrio and apparent sulphur oxidizers from the gamma-proteobacteria. In addition, a number of sequences from the beta and alpha-proteobacteria were identified.

Method and apparatus for automated assembly

DOEpatents

Jones, Rondall E.; Wilson, Randall H.; Calton, Terri L.

1999-01-01

A process and apparatus generates a sequence of steps for assembly or disassembly of a mechanical system. Each step in the sequence is geometrically feasible, i.e., the part motions required are physically possible. Each step in the sequence is also constraint feasible, i.e., the step satisfies user-definable constraints. Constraints allow process and other such limitations, not usually represented in models of the completed mechanical system, to affect the sequence.

Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models.

PubMed

Park, Byungkyu; Im, Jinyong; Tuvshinjargal, Narankhuu; Lee, Wook; Han, Kyungsook

2014-11-01

As many structures of protein-DNA complexes have been known in the past years, several computational methods have been developed to predict DNA-binding sites in proteins. However, its inverse problem (i.e., predicting protein-binding sites in DNA) has received much less attention. One of the reasons is that the differences between the interaction propensities of nucleotides are much smaller than those between amino acids. Another reason is that DNA exhibits less diverse sequence patterns than protein. Therefore, predicting protein-binding DNA nucleotides is much harder than predicting DNA-binding amino acids. We computed the interaction propensity (IP) of nucleotide triplets with amino acids using an extensive dataset of protein-DNA complexes, and developed two support vector machine (SVM) models that predict protein-binding nucleotides from sequence data alone. One SVM model predicts protein-binding nucleotides using DNA sequence data alone, and the other SVM model predicts protein-binding nucleotides using both DNA and protein sequences. In a 10-fold cross-validation with 1519 DNA sequences, the SVM model that uses DNA sequence data only predicted protein-binding nucleotides with an accuracy of 67.0%, an F-measure of 67.1%, and a Matthews correlation coefficient (MCC) of 0.340. With an independent dataset of 181 DNAs that were not used in training, it achieved an accuracy of 66.2%, an F-measure 66.3% and a MCC of 0.324. Another SVM model that uses both DNA and protein sequences achieved an accuracy of 69.6%, an F-measure of 69.6%, and a MCC of 0.383 in a 10-fold cross-validation with 1519 DNA sequences and 859 protein sequences. With an independent dataset of 181 DNAs and 143 proteins, it showed an accuracy of 67.3%, an F-measure of 66.5% and a MCC of 0.329. Both in cross-validation and independent testing, the second SVM model that used both DNA and protein sequence data showed better performance than the first model that used DNA sequence data. To the best of our knowledge, this is the first attempt to predict protein-binding nucleotides in a given DNA sequence from the sequence data alone. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Spatial analysis of extension fracture systems: A process modeling approach

USGS Publications Warehouse

Ferguson, C.C.

1985-01-01

Little consensus exists on how best to analyze natural fracture spacings and their sequences. Field measurements and analyses published in geotechnical literature imply fracture processes radically different from those assumed by theoretical structural geologists. The approach adopted in this paper recognizes that disruption of rock layers by layer-parallel extension results in two spacing distributions, one representing layer-fragment lengths and another separation distances between fragments. These two distributions and their sequences reflect mechanics and history of fracture and separation. Such distributions and sequences, represented by a 2 ?? n matrix of lengthsL, can be analyzed using a method that is history sensitive and which yields also a scalar estimate of bulk extension, e (L). The method is illustrated by a series of Monte Carlo experiments representing a variety of fracture-and-separation processes, each with distinct implications for extension history. Resulting distributions of e (L)are process-specific, suggesting that the inverse problem of deducing fracture-and-separation history from final structure may be tractable. ?? 1985 Plenum Publishing Corporation.

Measures of Working Memory, Sequence Learning, and Speech Recognition in the Elderly.

ERIC Educational Resources Information Center

Humes, Larry E.; Floyd, Shari S.

2005-01-01

This study describes the measurement of 2 cognitive functions, working-memory capacity and sequence learning, in 2 groups of listeners: young adults with normal hearing and elderly adults with impaired hearing. The measurement of these 2 cognitive abilities with a unique, nonverbal technique capable of auditory, visual, and auditory-visual…

Precise Ionosphere Monitoring via a DSFH Satellite TT&C Link

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Direct Measurement of the Density Matrix of a Quantum System

NASA Astrophysics Data System (ADS)

Thekkadath, G. S.; Giner, L.; Chalich, Y.; Horton, M. J.; Banker, J.; Lundeen, J. S.

2016-09-01

One drawback of conventional quantum state tomography is that it does not readily provide access to single density matrix elements since it requires a global reconstruction. Here, we experimentally demonstrate a scheme that can be used to directly measure individual density matrix elements of general quantum states. The scheme relies on measuring a sequence of three observables, each complementary to the last. The first two measurements are made weak to minimize the disturbance they cause to the state, while the final measurement is strong. We perform this joint measurement on polarized photons in pure and mixed states to directly measure their density matrix. The weak measurements are achieved using two walk-off crystals, each inducing a polarization-dependent spatial shift that couples the spatial and polarization degrees of freedom of the photons. This direct measurement method provides an operational meaning to the density matrix and promises to be especially useful for large dimensional states.

Direct Measurement of the Density Matrix of a Quantum System.

PubMed

Thekkadath, G S; Giner, L; Chalich, Y; Horton, M J; Banker, J; Lundeen, J S

2016-09-16

One drawback of conventional quantum state tomography is that it does not readily provide access to single density matrix elements since it requires a global reconstruction. Here, we experimentally demonstrate a scheme that can be used to directly measure individual density matrix elements of general quantum states. The scheme relies on measuring a sequence of three observables, each complementary to the last. The first two measurements are made weak to minimize the disturbance they cause to the state, while the final measurement is strong. We perform this joint measurement on polarized photons in pure and mixed states to directly measure their density matrix. The weak measurements are achieved using two walk-off crystals, each inducing a polarization-dependent spatial shift that couples the spatial and polarization degrees of freedom of the photons. This direct measurement method provides an operational meaning to the density matrix and promises to be especially useful for large dimensional states.

Further improvement of an intraocular lens holder for more physiological measurements within a mechanical eye model

NASA Astrophysics Data System (ADS)

Reutterer, Bernd; Traxler, Lukas; Bayer, Natascha; Drauschke, Andreas

2017-04-01

To evaluate the performance of intraocular lenses to treat cataract, an optomechanical eye model was developed. One of the most crucial components is the IOL holder, which should guarantee a physiological representation of the capsular bag and a stable position during measurement sequences. Individual holders are required due to the fact that every IOL has different geometric parameters. A method which allows obtaining the correct dimensions for the holder of a special IOL was developed and tested, by verifying the position of the IOL before and after a measurement sequence. Results of telecentric measurements and MTF measurements show that the IOL position does not change during the displacement sequence induced by the stepper motors of the eye model.

Understanding the dynamics of sustainable social-ecological systems: human behavior, institutions, and regulatory feedback networks.

PubMed

Anderies, John M

2015-02-01

I present a general mathematical modeling framework that can provide a foundation for the study of sustainability in social- ecological systems (SESs). Using basic principles from feedback control and a sequence of specific models from bioeconomics and economic growth, I outline several mathematical and empirical challenges associated with the study of sustainability of SESs. These challenges are categorized into three classes: (1) the social choice of performance measures, (2) uncertainty, and (3) collective action. Finally, I present some opportunities for combining stylized dynamical systems models with empirical data on human behavior and biophysical systems to address practical challenges for the design of effective governance regimes (policy feedbacks) for highly uncertain natural resource systems.

Nanostructure Control of Biologically Inspired Polymers

NASA Astrophysics Data System (ADS)

Rosales, Adrianne Marie

Biological polymers, such as polypeptides, are responsible for many of life's most sophisticated functions due to precisely evolved hierarchical structures. These protein structures are the result of monodisperse sequences of amino acids that fold into well-defined chain shapes and tertiary structures. Recently, there has been much interest in the design of such sequence-specific polymers for materials applications in fields ranging from biotechnology to separations membranes. Non-natural polymers offer the stability and robustness necessary for materials applications; however, our ability to control monomer sequence in non-natural polymers has traditionally operated on a much simpler level. In addition, the relationship between monomer sequence and self-assembly is not well understood for biological molecules, much less synthetic polymers. Thus, there is a need to explore self-assembly phase space with sequence using a model system. Polypeptoids are non-natural, sequence-specific polymers that offer the opportunity to probe the effect of sequence on self-assembly. A variety of monomer interactions have an impact on polymer properties, such as chirality, hydrophobicity, and electrostatic interactions. Thus, a necessary starting point for this project was to investigate monomer sequence effects on the bulk properties of polypeptoid homopolymers. It was found that several polypeptoids have experimentally accessible melting transitions that are dependent on the choice of side chains, and it was shown that this transition is tuned by the incorporation of "defects" or a comonomer. The polypeptoid chain shape is also controlled with the choice of monomer and monomer sequence. By using at least 50% monomers with bulky, chiral side chains, the polypeptoid backbone is sterically twisted into a helix, and as found for the first time in this work, the persistence length is increased. However, this persistence length, which is a measure of the stiffness of the polymer, is small compared to other folded helices, indicating the conformational flexibility of polypeptoid chains. With a firmer understanding of how monomer sequence and composition influence polypeptoid bulk properties, we designed block copolymer systems for self-assembly. Because the governing parameters of block copolymer self-assembly are well understood, this architecture provides a convenient starting point for probing the effect of changing polymer sequence. We found that polystyrene-polypeptoid block copolymers readily self-assemble into hexagonally-packed and lamellar morphologies with long range order, and furthermore, sequence control of the polypeptoid block enables us to tune the strength of segregation (and therefore the order-disorder transition) of the block copolymer. Polypeptoid chain shape also affects self-assembly. In classical synthetic block copolymers, it has typically been difficult to change chain shape without also changing polymer chemistry and therefore other factors affecting self-assembly. The advantage of the polypeptoid system is that it is modular, as the side chain chemistry (and therefore polymer properties) can easily be changed without changing the backbone chemistry. Thus, we have decoupled conformational effects from chemical composition by comparing the self-assembly of block copolymers containing either a helical peptoid block or its racemic, non-helical analog. The increase in the persistence length of the peptoid block due to helicity translates to an increase in the morphological domain spacing. In this work, we further the understanding of the effect of monomer sequence on bulk polypeptoid properties and self-assembly. Our findings pave the way for the rational design of structured synthetic polymers with tunable, sequence-specific properties.

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

NASA Astrophysics Data System (ADS)

Wong, Hon Lun; Smith, Daniela-Lee; Visscher, Pieter T.; Burns, Brendan P.

2015-10-01

Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.

First experiment on LMJ facility: pointing and synchronisation qualification

NASA Astrophysics Data System (ADS)

Henry, Olivier; Raffestin, Didier; Bretheau, Dominique; Luttmann, Michel; Graillot, Herve; Ferri, Michel; Seguineau, Frederic; Bar, Emmanuel; Patissou, Loic; Canal, Philippe; Sautarel, Franöise; Tranquille-Marques, Yves

2017-10-01

The LMJ (Laser mega Joule) facility at the CESTA site (Aquitaine, France) is a tool designed to deliver up to 1.2 MJ at 351 nm for plasma experiments. The experiment system will include 11 diagnostics: UV and X energy balances, imagers (Streak and stripe camera, CCD), spectrometers, and a Visar/pyrometer. The facility must be able to deliver, within the hour following the shot, all the results of the plasma diagnostics, alignment images and laser diagnostic measurements. These results have to be guaranteed in terms of conformity to the request and quality of measurement. The end of 2016 was devoted to the qualification of system pointing on target and synchronization within and between beams. The shots made with two chains (divided in 4 quads - 8 laser beams) have achieved 50 µm of misalignment accuracy (chain and quad channel) and a synchronization accuracy in the order of 50 ps . The performances achieved for plasma diagnostic (in the order of less 100 µm of alignment and timing accuracy less than 150 ps) comply with expectations. At the same time the first automatic sequences were tested. They allowed a shot on target every 6h:30 and in some case twice a day by reducing preparation actions, leading to a sequence of 4h:00.

Dry, portable calorimeter for nondestructive measurement of the activity of nuclear fuel

DOEpatents

Beyer, Norman S.; Lewis, Robert N.; Perry, Ronald B.

1976-01-01

The activity of a quantity of heat-producing nuclear fuel is measured rapidly, accurately and nondestructively by a portable dry calorimeter comprising a preheater, an array of temperature-controlled structures comprising a thermally guarded temperature-controlled oven, and a calculation and control unit. The difference between the amounts of electric power required to maintain the oven temperature with and without nuclear fuel in the oven is measured to determine the power produced by radioactive disintegration and hence the activity of the fuel. A portion of the electronic control system is designed to terminate a continuing sequence of measurements when the standard deviation of the variations of the amount of electric power required to maintain oven temperature is within a predetermined value.

Causality, Measurement, and Elementary Interactions

NASA Astrophysics Data System (ADS)

Gillis, Edward J.

2011-12-01

Signal causality, the prohibition of superluminal information transmission, is the fundamental property shared by quantum measurement theory and relativity, and it is the key to understanding the connection between nonlocal measurement effects and elementary interactions. To prevent those effects from transmitting information between the generating and observing process, they must be induced by the kinds of entangling interactions that constitute measurements, as implied in the Projection Postulate. They must also be nondeterministic as reflected in the Born Probability Rule. The nondeterminism of entanglement-generating processes explains why the relevant types of information cannot be instantiated in elementary systems, and why the sequencing of nonlocal effects is, in principle, unobservable. This perspective suggests a simple hypothesis about nonlocal transfers of amplitude during entangling interactions, which yields straightforward experimental consequences.

gr-MRI: A software package for magnetic resonance imaging using software defined radios

NASA Astrophysics Data System (ADS)

Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

2016-09-01

The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

PubMed Central

Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

2014-01-01

Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

Real-time micro-vibration multi-spot synchronous measurement within a region based on heterodyne interference

NASA Astrophysics Data System (ADS)

Lan, Ma; Xiao, Wen; Chen, Zonghui; Hao, Hongliang; Pan, Feng

2018-01-01

Real-time micro-vibration measurement is widely used in engineering applications. It is very difficult for traditional optical detection methods to achieve real-time need in a relatively high frequency and multi-spot synchronous measurement of a region at the same time,especially at the nanoscale. Based on the method of heterodyne interference, an experimental system of real-time measurement of micro - vibration is constructed to satisfy the demand in engineering applications. The vibration response signal is measured by combing optical heterodyne interferometry and a high-speed CMOS-DVR image acquisition system. Then, by extracting and processing multiple pixels at the same time, four digital demodulation technique are implemented to simultaneously acquire the vibrating velocity of the target from the recorded sequences of images. Different kinds of demodulation algorithms are analyzed and the results show that these four demodulation algorithms are suitable for different interference signals. Both autocorrelation algorithm and cross-correlation algorithm meet the needs of real-time measurements. The autocorrelation algorithm demodulates the frequency more accurately, while the cross-correlation algorithm is more accurate in solving the amplitude.

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

Genomic Sequencing: Assessing The Health Care System, Policy, And Big-Data Implications

PubMed Central

Phillips, Kathryn A.; Trosman, Julia; Kelley, Robin K.; Pletcher, Mark J.; Douglas, Michael P.; Weldon, Christine B.

2014-01-01

New genomic sequencing technologies enable the high-speed analysis of multiple genes simultaneously, including all of those in a person's genome. Sequencing is a prominent example of a “big data” technology because of the massive amount of information it produces and its complexity, diversity, and timeliness. Our objective in this article is to provide a policy primer on sequencing and illustrate how it can affect health care system and policy issues. Toward this end, we developed an easily applied classification of sequencing based on inputs, methods, and outputs. We used it to examine the implications of sequencing for three health care system and policy issues: making care more patient-centered, developing coverage and reimbursement policies, and assessing economic value. We conclude that sequencing has great promise but that policy challenges include how to optimize patient engagement as well as privacy, develop coverage policies that distinguish research from clinical uses and account for bioinformatics costs, and determine the economic value of sequencing through complex economic models that take into account multiple findings and downstream costs. PMID:25006153

Genomic sequencing: assessing the health care system, policy, and big-data implications.

PubMed

Phillips, Kathryn A; Trosman, Julia R; Kelley, Robin K; Pletcher, Mark J; Douglas, Michael P; Weldon, Christine B

2014-07-01

New genomic sequencing technologies enable the high-speed analysis of multiple genes simultaneously, including all of those in a person's genome. Sequencing is a prominent example of a "big data" technology because of the massive amount of information it produces and its complexity, diversity, and timeliness. Our objective in this article is to provide a policy primer on sequencing and illustrate how it can affect health care system and policy issues. Toward this end, we developed an easily applied classification of sequencing based on inputs, methods, and outputs. We used it to examine the implications of sequencing for three health care system and policy issues: making care more patient-centered, developing coverage and reimbursement policies, and assessing economic value. We conclude that sequencing has great promise but that policy challenges include how to optimize patient engagement as well as privacy, develop coverage policies that distinguish research from clinical uses and account for bioinformatics costs, and determine the economic value of sequencing through complex economic models that take into account multiple findings and downstream costs. Project HOPE—The People-to-People Health Foundation, Inc.

Pose Self-Calibration of Stereo Vision Systems for Autonomous Vehicle Applications.

PubMed

Musleh, Basam; Martín, David; Armingol, José María; de la Escalera, Arturo

2016-09-14

Nowadays, intelligent systems applied to vehicles have grown very rapidly; their goal is not only the improvement of safety, but also making autonomous driving possible. Many of these intelligent systems are based on making use of computer vision in order to know the environment and act accordingly. It is of great importance to be able to estimate the pose of the vision system because the measurement matching between the perception system (pixels) and the vehicle environment (meters) depends on the relative position between the perception system and the environment. A new method of camera pose estimation for stereo systems is presented in this paper, whose main contribution regarding the state of the art on the subject is the estimation of the pitch angle without being affected by the roll angle. The validation of the self-calibration method is accomplished by comparing it with relevant methods of camera pose estimation, where a synthetic sequence is used in order to measure the continuous error with a ground truth. This validation is enriched by the experimental results of the method in real traffic environments.

Pose Self-Calibration of Stereo Vision Systems for Autonomous Vehicle Applications

PubMed Central

Musleh, Basam; Martín, David; Armingol, José María; de la Escalera, Arturo

2016-01-01

Nowadays, intelligent systems applied to vehicles have grown very rapidly; their goal is not only the improvement of safety, but also making autonomous driving possible. Many of these intelligent systems are based on making use of computer vision in order to know the environment and act accordingly. It is of great importance to be able to estimate the pose of the vision system because the measurement matching between the perception system (pixels) and the vehicle environment (meters) depends on the relative position between the perception system and the environment. A new method of camera pose estimation for stereo systems is presented in this paper, whose main contribution regarding the state of the art on the subject is the estimation of the pitch angle without being affected by the roll angle. The validation of the self-calibration method is accomplished by comparing it with relevant methods of camera pose estimation, where a synthetic sequence is used in order to measure the continuous error with a ground truth. This validation is enriched by the experimental results of the method in real traffic environments. PMID:27649178

Viral morphogenesis is the dominant source of sequence censorship in M13 combinatorial peptide phage display.

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

Rodi, D. J.; Soares, A. S.; Makowski, L.

Novel statistical methods have been developed and used to quantitate and annotate the sequence diversity within combinatorial peptide libraries on the basis of small numbers (1-200) of sequences selected at random from commercially available M13 p3-based phage display libraries. These libraries behave statistically as though they correspond to populations containing roughly 4.0{+-}1.6% of the random dodecapeptides and 7.9{+-}2.6% of the random constrained heptapeptides that are theoretically possible within the phage populations. Analysis of amino acid residue occurrence patterns shows no demonstrable influence on sequence censorship by Escherichia coli tRNA isoacceptor profiles or either overall codon or Class II codon usagemore » patterns, suggesting no metabolic constraints on recombinant p3 synthesis. There is an overall depression in the occurrence of cysteine, arginine and glycine residues and an overabundance of proline, threonine and histidine residues. The majority of position-dependent amino acid sequence bias is clustered at three positions within the inserted peptides of the dodecapeptide library, +1, +3 and +12 downstream from the signal peptidase cleavage site. Conformational tendency measures of the peptides indicate a significant preference for inserts favoring a {beta}-turn conformation. The observed protein sequence limitations can primarily be attributed to genetic codon degeneracy and signal peptidase cleavage preferences. These data suggest that for applications in which maximal sequence diversity is essential, such as epitope mapping or novel receptor identification, combinatorial peptide libraries should be constructed using codon-corrected trinucleotide cassettes within vector-host systems designed to minimize morphogenesis-related censorship.« less

Robust object tracking techniques for vision-based 3D motion analysis applications

NASA Astrophysics Data System (ADS)

Knyaz, Vladimir A.; Zheltov, Sergey Y.; Vishnyakov, Boris V.

2016-04-01

Automated and accurate spatial motion capturing of an object is necessary for a wide variety of applications including industry and science, virtual reality and movie, medicine and sports. For the most part of applications a reliability and an accuracy of the data obtained as well as convenience for a user are the main characteristics defining the quality of the motion capture system. Among the existing systems for 3D data acquisition, based on different physical principles (accelerometry, magnetometry, time-of-flight, vision-based), optical motion capture systems have a set of advantages such as high speed of acquisition, potential for high accuracy and automation based on advanced image processing algorithms. For vision-based motion capture accurate and robust object features detecting and tracking through the video sequence are the key elements along with a level of automation of capturing process. So for providing high accuracy of obtained spatial data the developed vision-based motion capture system "Mosca" is based on photogrammetric principles of 3D measurements and supports high speed image acquisition in synchronized mode. It includes from 2 to 4 technical vision cameras for capturing video sequences of object motion. The original camera calibration and external orientation procedures provide the basis for high accuracy of 3D measurements. A set of algorithms as for detecting, identifying and tracking of similar targets, so for marker-less object motion capture is developed and tested. The results of algorithms' evaluation show high robustness and high reliability for various motion analysis tasks in technical and biomechanics applications.

Adaptive Learning Resources Sequencing in Educational Hypermedia Systems

ERIC Educational Resources Information Center

Karampiperis, Pythagoras; Sampson, Demetrios

2005-01-01

Adaptive learning resources selection and sequencing is recognized as among the most interesting research questions in adaptive educational hypermedia systems (AEHS). In order to adaptively select and sequence learning resources in AEHS, the definition of adaptation rules contained in the Adaptation Model, is required. Although, some efforts have…

All-to-all sequenced fault detection system

DOEpatents

Archer, Charles Jens; Pinnow, Kurt Walter; Ratterman, Joseph D.; Smith, Brian Edward

2010-11-02

An apparatus, program product and method enable nodal fault detection by sequencing communications between all system nodes. A master node may coordinate communications between two slave nodes before sequencing to and initiating communications between a new pair of slave nodes. The communications may be analyzed to determine the nodal fault.

Theoretical and experimental study of the electronic states and spectra of KBi and KSb

NASA Astrophysics Data System (ADS)

Setzer, K. D.; Fink, E. H.; Alekseyev, A. B.; Liebermann, H.-P.; Buenker, R. J.

2017-03-01

Gas phase emission spectra of the hitherto unknown free radicals KBi and KSb were measured in the NIR range with a Fourier-transform spectrometer. The emissions were observed from a fast-flow system in which bismuth or antimony vapor in argon carrier gas was passed through a microwave discharge and mixed with potassium vapor in an observation tube. For KBi, two systems of blue-degraded bands observed in the range 5800-7700 cm-1 are assigned to the transitions A3Π (A20+) → X3Σ-(X10+, X21). Nine bands of the A20+ → X10+ and three bands of the A20+ → X21 system were measured at high spectral resolution and rotationally analysed. The rotational and vibrational analyses yielded the spectroscopic parameters of the X10+, X21, and A20+ states. For KSb, in the range of the sensitive Ge detector, only one sequence of bands was measured near 6880 cm-1. By analogy with the previously observed spectra of NaSb and NaAs these bands were identified to be the Δv = 0 sequence of the a2 → X21 transition of KSb. Some very weak bands observed at low resolution in the range 3800-5200 cm-1 are assigned to the transitions A3Π (A21) → X3Σ -(X10+, X21). To aid in the analysis of the experimental data, a series of relativistic configuration interaction calculations has been carried out to obtain potential energy curves for the low-lying states of KBi and KSb, vibrational constants, equilibrium internuclear distances, and also electric dipole transition moments connecting the states.

A multigenerational family study of oral and hand motor sequencing ability provides evidence for a familial speech sound disorder subtype

PubMed Central

Peter, Beate; Raskind, Wendy H.

2011-01-01

Purpose To evaluate phenotypic expressions of speech sound disorder (SSD) in multigenerational families with evidence of familial forms of SSD. Method Members of five multigenerational families (N = 36) produced rapid sequences of monosyllables and disyllables and tapped computer keys with repetitive and alternating movements. Results Measures of repetitive and alternating motor speed were correlated within and between the two motor systems. Repetitive and alternating motor speeds increased in children and decreased in adults as a function of age. In two families with children who had severe speech deficits consistent with disrupted praxis, slowed alternating, but not repetitive, oral movements characterized most of the affected children and adults with a history of SSD, and slowed alternating hand movements were seen in some of the biologically related participants as well. Conclusion Results are consistent with a familial motor-based SSD subtype with incomplete penetrance, motivating new clinical questions about motor-based intervention not only in the oral but also the limb system. PMID:21909176

Short-read, high-throughput sequencing technology for STR genotyping

PubMed Central

Bornman, Daniel M.; Hester, Mark E.; Schuetter, Jared M.; Kasoji, Manjula D.; Minard-Smith, Angela; Barden, Curt A.; Nelson, Scott C.; Godbold, Gene D.; Baker, Christine H.; Yang, Boyu; Walther, Jacquelyn E.; Tornes, Ivan E.; Yan, Pearlly S.; Rodriguez, Benjamin; Bundschuh, Ralf; Dickens, Michael L.; Young, Brian A.; Faith, Seth A.

2013-01-01

DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples. PMID:25621315

The infinitesimal operator for the semigroup of the Frobenius-Perron operator from image sequence data: vector fields and transport barriers from movies.

PubMed

Santitissadeekorn, N; Bollt, E M

2007-06-01

In this paper, we present an approach to approximate the Frobenius-Perron transfer operator from a sequence of time-ordered images, that is, a movie dataset. Unlike time-series data, successive images do not provide a direct access to a trajectory of a point in a phase space; more precisely, a pixel in an image plane. Therefore, we reconstruct the velocity field from image sequences based on the infinitesimal generator of the Frobenius-Perron operator. Moreover, we relate this problem to the well-known optical flow problem from the computer vision community and we validate the continuity equation derived from the infinitesimal operator as a constraint equation for the optical flow problem. Once the vector field and then a discrete transfer operator are found, then, in addition, we present a graph modularity method as a tool to discover basin structure in the phase space. Together with a tool to reconstruct a velocity field, this graph-based partition method provides us with a way to study transport behavior and other ergodic properties of measurable dynamical systems captured only through image sequences.

Evaluation of targeted exome sequencing for 28 protein-based blood group systems, including the homologous gene systems, for blood group genotyping.

PubMed

Schoeman, Elizna M; Lopez, Genghis H; McGowan, Eunike C; Millard, Glenda M; O'Brien, Helen; Roulis, Eileen V; Liew, Yew-Wah; Martin, Jacqueline R; McGrath, Kelli A; Powley, Tanya; Flower, Robert L; Hyland, Catherine A

2017-04-01

Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform. Genes for 28 protein-based blood group systems, GATA1, and KLF1 were analyzed. Copy number variation analysis was used to characterize complex structural variants in the GYPC and RH systems. The average sequencing depth per target region was 66.2 ± 39.8. Each sample harbored on average 43 ± 9 variants, of which 10 ± 3 were used for genotyping. For the 28 samples, massively parallel sequencing variant sequences correctly matched expected sequences based on single nucleotide polymorphism genotyping data. Copy number variation analysis defined the Rh C/c alleles and complex RHD hybrids. Hybrid RHD*D-CE-D variants were correctly identified, but copy number variation analysis did not confidently distinguish between D and CE exon deletion versus rearrangement. The targeted exome sequencing strategy employed extended the range of blood group genotypes detected compared with single nucleotide polymorphism typing. This single-test format included detection of complex MNS hybrid cases and, with copy number variation analysis, defined RH hybrid genes along with the RHCE*C allele hitherto difficult to resolve by variant detection. The approach is economical compared with whole-genome sequencing and is suitable for a red blood cell reference laboratory setting. © 2017 AABB.

Integrative network alignment reveals large regions of global network similarity in yeast and human.

PubMed

Kuchaiev, Oleksii; Przulj, Natasa

2011-05-15

High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment heuristics is currently a foremost challenge in computational biology. We introduce a novel network alignment algorithm, called Matching-based Integrative GRAph ALigner (MI-GRAAL), which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity and structural similarity. Hence, we resolve the ties in similarity measures and find a combination of similarity measures yielding the largest contiguous (i.e. connected) and biologically sound alignments. MI-GRAAL exposes the largest functional, connected regions of protein-protein interaction (PPI) network similarity to date: surprisingly, it reveals that 77.7% of proteins in the baker's yeast high-confidence PPI network participate in such a subnetwork that is fully contained in the human high-confidence PPI network. This is the first demonstration that species as diverse as yeast and human contain so large, continuous regions of global network similarity. We apply MI-GRAAL's alignments to predict functions of un-annotated proteins in yeast, human and bacteria validating our predictions in the literature. Furthermore, using network alignment scores for PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship. This is the first time that phylogeny is exactly reconstructed from purely topological alignments of PPI networks. Supplementary files and MI-GRAAL executables: http://bio-nets.doc.ic.ac.uk/MI-GRAAL/.

High-resolution motion compensated MRA in patients with congenital heart disease using extracellular contrast agent at 3 Tesla

PubMed Central

2012-01-01

Background Using first-pass MRA (FP-MRA) spatial resolution is limited by breath-hold duration. In addition, image quality may be hampered by respiratory and cardiac motion artefacts. In order to overcome these limitations an ECG- and navigator-gated high-resolution-MRA sequence (HR-MRA) with slow infusion of extracellular contrast agent was implemented at 3 Tesla for the assessment of congenital heart disease and compared to standard first-pass-MRA (FP-MRA). Methods 34 patients (median age: 13 years) with congenital heart disease (CHD) were prospectively examined on a 3 Tesla system. The CMR-protocol comprised functional imaging, FP- and HR-MRA, and viability imaging. After the acquisition of the FP-MRA sequence using a single dose of extracellular contrast agent the motion compensated HR-MRA sequence with isotropic resolution was acquired while injecting the second single dose, utilizing the timeframe before viability imaging. Qualitative scores for image quality (two independent reviewers) as well as quantitative measurements of vessel sharpness and relative contrast were compared using the Wilcoxon signed-rank test. Quantitative measurements of vessel diameters were compared using the Bland-Altman test. Results The mean image quality score revealed significantly better image quality of the HR-MRA sequence compared to the FP-MRA sequence in all vessels of interest (ascending aorta (AA), left pulmonary artery (LPA), left superior pulmonary vein (LSPV), coronary sinus (CS), and coronary ostia (CO); all p < 0.0001). In comparison to FP-MRA, HR-MRA revealed significantly better vessel sharpness for all considered vessels (AA, LSPV and LPA; all p < 0.0001). The relative contrast of the HR-MRA sequence was less compared to the FP-MRA sequence (AA: p <0.028, main pulmonary artery: p <0.004, LSPV: p <0.005). Both, the results of the intra- and interobserver measurements of the vessel diameters revealed closer correlation and closer 95 % limits of agreement for the HR-MRA. HR-MRA revealed one additional clinical finding, missed by FP-MRA. Conclusions An ECG- and navigator-gated HR-MRA-protocol with infusion of extracellular contrast agent at 3 Tesla is feasible. HR-MRA delivers significantly better image quality and vessel sharpness compared to FP-MRA. It may be integrated into a standard CMR-protocol for patients with CHD without the need for additional contrast agent injection and without any additional examination time. PMID:23107424

Compensating for magnetic field inhomogeneity in multigradient-echo-based MR thermometry.

PubMed

Simonis, Frank F J; Petersen, Esben T; Bartels, Lambertus W; Lagendijk, Jan J W; van den Berg, Cornelis A T

2015-03-01

MR thermometry (MRT) is a noninvasive method for measuring temperature that can potentially be used for radio frequency (RF) safety monitoring. This application requires measuring absolute temperature. In this study, a multigradient-echo (mGE) MRT sequence was used for that purpose. A drawback of this sequence, however, is that its accuracy is affected by background gradients. In this article, we present a method to minimize this effect and to improve absolute temperature measurements using MRI. By determining background gradients using a B0 map or by combining data acquired with two opposing readout directions, the error can be removed in a homogenous phantom, thus improving temperature maps. All scans were performed on a 3T system using ethylene glycol-filled phantoms. Background gradients were varied, and one phantom was uniformly heated to validate both compensation approaches. Independent temperature recordings were made with optical probes. Errors correlated closely to the background gradients in all experiments. Temperature distributions showed a much smaller standard deviation when the corrections were applied (0.21°C vs. 0.45°C) and correlated well with thermo-optical probes. The corrections offer the possibility to measure RF heating in phantoms more precisely. This allows mGE MRT to become a valuable tool in RF safety assessment. © 2014 Wiley Periodicals, Inc.

[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.

Joint Sequence Analysis: Association and Clustering

ERIC Educational Resources Information Center

Piccarreta, Raffaella

2017-01-01

In its standard formulation, sequence analysis aims at finding typical patterns in a set of life courses represented as sequences. Recently, some proposals have been introduced to jointly analyze sequences defined on different domains (e.g., work career, partnership, and parental histories). We introduce measures to evaluate whether a set of…

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

PubMed Central

Inskeep, William P.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Rusch, Douglas B.; Tringe, Susannah G.; Macur, Richard E.; Jennings, Ryan deM.; Boyd, Eric S.; Spear, John R.; Roberto, Francisco F.

2013-01-01

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP. PMID:23720654

Comparative analysis of the feline immunoglobulin repertoire.

PubMed

Steiniger, Sebastian C J; Glanville, Jacob; Harris, Douglas W; Wilson, Thomas L; Ippolito, Gregory C; Dunham, Steven A

2017-03-01

Next-Generation Sequencing combined with bioinformatics is a powerful tool for analyzing the large number of DNA sequences present in the expressed antibody repertoire and these data sets can be used to advance a number of research areas including antibody discovery and engineering. The accurate measurement of the immune repertoire sequence composition, diversity and abundance is important for understanding the repertoire response in infections, vaccinations and cancer immunology and could also be useful for elucidating novel molecular targets. In this study 4 individual domestic cats (Felis catus) were subjected to antibody repertoire sequencing with total number of sequences generated 1079863 for VH for IgG, 1050824 VH for IgM, 569518 for VK and 450195 for VL. Our analysis suggests that a similar VDJ expression patterns exists across all cats. Similar to the canine repertoire, the feline repertoire is dominated by a single subgroup, namely VH3. The antibody paratope of felines showed similar amino acid variation when compared to human, mouse and canine counterparts. All animals show a similarly skewed VH CDR-H3 profile and, when compared to canine, human and mouse, distinct differences are observed. Our study represents the first attempt to characterize sequence diversity in the expressed feline antibody repertoire and this demonstrates the utility of using NGS to elucidate entire antibody repertoires from individual animals. These data provide significant insight into understanding the feline immune system function. Copyright © 2017 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models

PubMed Central

2017-01-01

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder–decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis. PMID:29104927

Comparison of Macroscopic Pathology Measurements With Magnetic Resonance Imaging and Assessment of Microscopic Pathology Extension for Colorectal Liver Metastases

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

Mendez Romero, Alejandra, E-mail: a.mendezromero@erasmusmc.nl; Verheij, Joanne; Dwarkasing, Roy S.

2012-01-01

Purpose: To compare pathology macroscopic tumor dimensions with magnetic resonance imaging (MRI) measurements and to establish the microscopic tumor extension of colorectal liver metastases. Methods and Materials: In a prospective pilot study we included patients with colorectal liver metastases planned for surgery and eligible for MRI. A liver MRI was performed within 48 hours before surgery. Directly after surgery, an MRI of the specimen was acquired to measure the degree of tumor shrinkage. The specimen was fixed in formalin for 48 hours, and another MRI was performed to assess the specimen/tumor shrinkage. All MRI sequences were imported into our radiotherapymore » treatment planning system, where the tumor and the specimen were delineated. For the macroscopic pathology analyses, photographs of the sliced specimens were used to delineate and reconstruct the tumor and the specimen volumes. Microscopic pathology analyses were conducted to assess the infiltration depth of tumor cell nests. Results: Between February 2009 and January 2010 we included 13 patients for analysis with 21 colorectal liver metastases. Specimen and tumor shrinkage after resection and fixation was negligible. The best tumor volume correlations between MRI and pathology were found for T1-weighted (w) echo gradient sequence (r{sub s} = 0.99, slope = 1.06), and the T2-w fast spin echo (FSE) single-shot sequence (r{sub s} = 0.99, slope = 1.08), followed by the T2-w FSE fat saturation sequence (r{sub s} = 0.99, slope = 1.23), and the T1-w gadolinium-enhanced sequence (r{sub s} = 0.98, slope = 1.24). We observed 39 tumor cell nests beyond the tumor border in 12 metastases. Microscopic extension was found between 0.2 and 10 mm from the main tumor, with 90% of the cases within 6 mm. Conclusions: MRI tumor dimensions showed a good agreement with the macroscopic pathology suggesting that MRI can be used for accurate tumor delineation. However, microscopic extensions found beyond the tumor border indicate that caution is needed in selecting appropriate tumor margins.« less

Scheduling with genetic algorithms

NASA Technical Reports Server (NTRS)

Fennel, Theron R.; Underbrink, A. J., Jr.; Williams, George P. W., Jr.

1994-01-01

In many domains, scheduling a sequence of jobs is an important function contributing to the overall efficiency of the operation. At Boeing, we develop schedules for many different domains, including assembly of military and commercial aircraft, weapons systems, and space vehicles. Boeing is under contract to develop scheduling systems for the Space Station Payload Planning System (PPS) and Payload Operations and Integration Center (POIC). These applications require that we respect certain sequencing restrictions among the jobs to be scheduled while at the same time assigning resources to the jobs. We call this general problem scheduling and resource allocation. Genetic algorithms (GA's) offer a search method that uses a population of solutions and benefits from intrinsic parallelism to search the problem space rapidly, producing near-optimal solutions. Good intermediate solutions are probabalistically recombined to produce better offspring (based upon some application specific measure of solution fitness, e.g., minimum flowtime, or schedule completeness). Also, at any point in the search, any intermediate solution can be accepted as a final solution; allowing the search to proceed longer usually produces a better solution while terminating the search at virtually any time may yield an acceptable solution. Many processes are constrained by restrictions of sequence among the individual jobs. For a specific job, other jobs must be completed beforehand. While there are obviously many other constraints on processes, it is these on which we focussed for this research: how to allocate crews to jobs while satisfying job precedence requirements and personnel, and tooling and fixture (or, more generally, resource) requirements.

SMITH: a LIMS for handling next-generation sequencing workflows

PubMed Central

2014-01-01

Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. Conclusions SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis. PMID:25471934

SMITH: a LIMS for handling next-generation sequencing workflows.

PubMed

Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

2014-01-01

Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc. SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis.

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

PubMed

Leung, Kaston; Klaus, Anders; Lin, Bill K; Laks, Emma; Biele, Justina; Lai, Daniel; Bashashati, Ali; Huang, Yi-Fei; Aniba, Radhouane; Moksa, Michelle; Steif, Adi; Mes-Masson, Anne-Marie; Hirst, Martin; Shah, Sohrab P; Aparicio, Samuel; Hansen, Carl L

2016-07-26

The genomes of large numbers of single cells must be sequenced to further understanding of the biological significance of genomic heterogeneity in complex systems. Whole genome amplification (WGA) of single cells is generally the first step in such studies, but is prone to nonuniformity that can compromise genomic measurement accuracy. Despite recent advances, robust performance in high-throughput single-cell WGA remains elusive. Here, we introduce droplet multiple displacement amplification (MDA), a method that uses commercially available liquid dispensing to perform high-throughput single-cell MDA in nanoliter volumes. The performance of droplet MDA is characterized using a large dataset of 129 normal diploid cells, and is shown to exceed previously reported single-cell WGA methods in amplification uniformity, genome coverage, and/or robustness. We achieve up to 80% coverage of a single-cell genome at 5× sequencing depth, and demonstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA product to achieve a median allelic dropout of 15%, and using whole genome sequencing to achieve false and true positive rates of 9.66 × 10(-6) and 68.8%, respectively, in a G1-phase cell. We further show that droplet MDA allows for the detection of copy number variants (CNVs) as small as 30 kb in single cells of an ovarian cancer cell line and as small as 9 Mb in two high-grade serous ovarian cancer samples using only 0.02× depth. Droplet MDA provides an accessible and scalable method for performing robust and accurate CNV and SNV measurements on large numbers of single cells.

Quantum random bit generation using energy fluctuations in stimulated Raman scattering.

PubMed

Bustard, Philip J; England, Duncan G; Nunn, Josh; Moffatt, Doug; Spanner, Michael; Lausten, Rune; Sussman, Benjamin J

2013-12-02

Random number sequences are a critical resource in modern information processing systems, with applications in cryptography, numerical simulation, and data sampling. We introduce a quantum random number generator based on the measurement of pulse energy quantum fluctuations in Stokes light generated by spontaneously-initiated stimulated Raman scattering. Bright Stokes pulse energy fluctuations up to five times the mean energy are measured with fast photodiodes and converted to unbiased random binary strings. Since the pulse energy is a continuous variable, multiple bits can be extracted from a single measurement. Our approach can be generalized to a wide range of Raman active materials; here we demonstrate a prototype using the optical phonon line in bulk diamond.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow

PubMed Central

Latorre, Mariano; Silva, Herman; Saba, Juan; Guziolowski, Carito; Vizoso, Paula; Martinez, Veronica; Maldonado, Jonathan; Morales, Andrea; Caroca, Rodrigo; Cambiazo, Veronica; Campos-Vargas, Reinaldo; Gonzalez, Mauricio; Orellana, Ariel; Retamales, Julio; Meisel, Lee A

2006-01-01

Background Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. Results In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. Conclusion JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from or . PMID:17123449

HLA genotyping by next-generation sequencing of complementary DNA.

PubMed

Segawa, Hidenobu; Kukita, Yoji; Kato, Kikuya

2017-11-28

Genotyping of the human leucocyte antigen (HLA) is indispensable for various medical treatments. However, unambiguous genotyping is technically challenging due to high polymorphism of the corresponding genomic region. Next-generation sequencing is changing the landscape of genotyping. In addition to high throughput of data, its additional advantage is that DNA templates are derived from single molecules, which is a strong merit for the phasing problem. Although most currently developed technologies use genomic DNA, use of cDNA could enable genotyping with reduced costs in data production and analysis. We thus developed an HLA genotyping system based on next-generation sequencing of cDNA. Each HLA gene was divided into 3 or 4 target regions subjected to PCR amplification and subsequent sequencing with Ion Torrent PGM. The sequence data were then subjected to an automated analysis. The principle of the analysis was to construct candidate sequences generated from all possible combinations of variable bases and arrange them in decreasing order of the number of reads. Upon collecting candidate sequences from all target regions, 2 haplotypes were usually assigned. Cases not assigned 2 haplotypes were forwarded to 4 additional processes: selection of candidate sequences applying more stringent criteria, removal of artificial haplotypes, selection of candidate sequences with a relaxed threshold for sequence matching, and countermeasure for incomplete sequences in the HLA database. The genotyping system was evaluated using 30 samples; the overall accuracy was 97.0% at the field 3 level and 98.3% at the G group level. With one sample, genotyping of DPB1 was not completed due to short read size. We then developed a method for complete sequencing of individual molecules of the DPB1 gene, using the molecular barcode technology. The performance of the automatic genotyping system was comparable to that of systems developed in previous studies. Thus, next-generation sequencing of cDNA is a viable option for HLA genotyping.

Three-dimensional T1rho-weighted MRI at 1.5 Tesla.

PubMed

Borthakur, Arijitt; Wheaton, Andrew; Charagundla, Sridhar R; Shapiro, Erik M; Regatte, Ravinder R; Akella, Sarma V S; Kneeland, J Bruce; Reddy, Ravinder

2003-06-01

To design and implement a magnetic resonance imaging (MRI) pulse sequence capable of performing three-dimensional T(1rho)-weighted MRI on a 1.5-T clinical scanner, and determine the optimal sequence parameters, both theoretically and experimentally, so that the energy deposition by the radiofrequency pulses in the sequence, measured as the specific absorption rate (SAR), does not exceed safety guidelines for imaging human subjects. A three-pulse cluster was pre-encoded to a three-dimensional gradient-echo imaging sequence to create a three-dimensional, T(1rho)-weighted MRI pulse sequence. Imaging experiments were performed on a GE clinical scanner with a custom-built knee-coil. We validated the performance of this sequence by imaging articular cartilage of a bovine patella and comparing T(1rho) values measured by this sequence to those obtained with a previously tested two-dimensional imaging sequence. Using a previously developed model for SAR calculation, the imaging parameters were adjusted such that the energy deposition by the radiofrequency pulses in the sequence did not exceed safety guidelines for imaging human subjects. The actual temperature increase due to the sequence was measured in a phantom by a MRI-based temperature mapping technique. Following these experiments, the performance of this sequence was demonstrated in vivo by obtaining T(1rho)-weighted images of the knee joint of a healthy individual. Calculated T(1rho) of articular cartilage in the specimen was similar for both and three-dimensional and two-dimensional methods (84 +/- 2 msec and 80 +/- 3 msec, respectively). The temperature increase in the phantom resulting from the sequence was 0.015 degrees C, which is well below the established safety guidelines. Images of the human knee joint in vivo demonstrate a clear delineation of cartilage from surrounding tissues. We developed and implemented a three-dimensional T(1rho)-weighted pulse sequence on a 1.5-T clinical scanner. Copyright 2003 Wiley-Liss, Inc.

Jitter Correction

NASA Technical Reports Server (NTRS)

Waegell, Mordecai J.; Palacios, David M.

2011-01-01

Jitter_Correct.m is a MATLAB function that automatically measures and corrects inter-frame jitter in an image sequence to a user-specified precision. In addition, the algorithm dynamically adjusts the image sample size to increase the accuracy of the measurement. The Jitter_Correct.m function takes an image sequence with unknown frame-to-frame jitter and computes the translations of each frame (column and row, in pixels) relative to a chosen reference frame with sub-pixel accuracy. The translations are measured using a Cross Correlation Fourier transformation method in which the relative phase of the two transformed images is fit to a plane. The measured translations are then used to correct the inter-frame jitter of the image sequence. The function also dynamically expands the image sample size over which the cross-correlation is measured to increase the accuracy of the measurement. This increases the robustness of the measurement to variable magnitudes of inter-frame jitter

Effect of echo spacing and readout bandwidth on basic performances of EPI-fMRI acquisition sequences implemented on two 1.5 T MR scanner systems.

PubMed

Giannelli, Marco; Diciotti, Stefano; Tessa, Carlo; Mascalchi, Mario

2010-01-01

Although in EPI-fMRI analyses typical acquisition parameters (TR, TE, matrix, slice thickness, etc.) are generally employed, various readout bandwidth (BW) values are used as a function of gradients characteristics of the MR scanner. Echo spacing (ES) is another fundamental parameter of EPI-fMRI acquisition sequences but the employed ES value is not usually reported in fMRI studies. In the present work, the authors investigated the effect of ES and BW on basic performances of EPI-fMRI sequences in terms of temporal stability and overall image quality of time series acquisition. EPI-fMRI acquisitions of the same water phantom were performed using two clinical MR scanner systems (scanners A and B) with different gradient characteristics and functional designs of radiofrequency coils. For both scanners, the employed ES values ranged from 0.75 to 1.33 ms. The used BW values ranged from 125.0 to 250.0 kHz/64pixels and from 78.1 to 185.2 kHz/64pixels for scanners A and B, respectively. The temporal stability of EPI-fMRI sequence was assessed measuring the signal-to-fluctuation noise ratio (SFNR) and signal drift (DR), while the overall image quality was assessed evaluating the signal-to-noise ratio (SNR(ts)) and nonuniformity (NU(ts)) of the time series acquisition. For both scanners, no significant effect of ES and BW on signal drift was revealed. The SFNR, NU(ts) and SNR(ts) values of scanner A did not significantly vary with ES. On the other hand, the SFNR, NU(ts), and SNR(ts) values of scanner B significantly varied with ES. SFNR (5.8%) and SNR(ts) (5.9%) increased with increasing ES. SFNR (25% scanner A, 32% scanner B) and SNR(ts) (26.2% scanner A, 30.1% scanner B) values of both scanners significantly decreased with increasing BW. NU(ts) values of scanners A and B were less than 3% for all BW and ES values. Nonetheless, scanner A was characterized by a significant upward trend (3% percentage of variation) of time series nonuniformity with increasing BW while NU(ts) of scanner B significantly increased (19% percentage of variation) with increasing ES. Temporal stability (SFNR and DR) and overall image quality (NU(ts) and SNR(ts)) of EPI-fMRI time series can significantly vary with echo spacing and readout bandwidth. The specific pattern of variation may depend on the performance of each single MR scanner system in terms of gradients characteristics, EPI sequence calibrations (eddy currents, shimming, etc.), and functional design of radiofrequency coil. Our results indicate that the employment of low BW improves not only the signal-to-noise ratio of EPI-fMRI time series but also the temporal stability of functional acquisitions. The use of minimum ES values is not entirely advantageous when the MR scanner system is characterized by gradients with low performances and suboptimal EPI sequence calibration. Since differences in basic performances of MR scanner system are potential source of variability for fMRI activation, phantom measurements of SFNR, DR, NU(ts), and SNR(ts) can be executed before subjects acquisitions to monitor the stability of MR scanner performances in clinical group comparison and longitudinal studies.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

Direct method for measuring and witnessing quantum entanglement of arbitrary two-qubit states through Hong-Ou-Mandel interference

NASA Astrophysics Data System (ADS)

Bartkiewicz, Karol; Chimczak, Grzegorz; Lemr, Karel

2017-02-01

We describe a direct method for experimental determination of the negativity of an arbitrary two-qubit state with 11 measurements performed on multiple copies of the two-qubit system. Our method is based on the experimentally accessible sequences of singlet projections performed on up to four qubit pairs. In particular, our method permits the application of the Peres-Horodecki separability criterion to an arbitrary two-qubit state. We explicitly demonstrate that measuring entanglement in terms of negativity requires three measurements more than detecting two-qubit entanglement. The reported minimal set of interferometric measurements provides a complete description of bipartite quantum entanglement in terms of two-photon interference. This set is smaller than the set of 15 measurements needed to perform a complete quantum state tomography of an arbitrary two-qubit system. Finally, we demonstrate that the set of nine Makhlin's invariants needed to express the negativity can be measured by performing 13 multicopy projections. We demonstrate both that these invariants are a useful theoretical concept for designing specialized quantum interferometers and that their direct measurement within the framework of linear optics does not require performing complete quantum state tomography.

A Constant-Field Interrupted Resonance System for Percutaneous Electromagnetic Measurement of Blood Flow

PubMed Central

Kolin, Alexander; Steele, James R.; Imai, James S.; Macalpin, Rex N.

1974-01-01

A combination of deformable flow probes of negligible lateral dimensions with an electronic circuit capable of providing a prolonged plateau of dB/dt = 0 and of sampling the flow signal at the end of this interval permits electromagnetic measurement of blood flow with a reliable zero base line secured by switching off the magnet. An extracorporeal magnet provides the magnetic field. The flow transducer is introduced into the vascular system percutaneously through a standard angiographic catheter by conventional technique. The idea of the current generator can be described as “principle of interrupted resonance.” The current wave form can be described as a sequence of disconnected bisected sine waves joined at the apices by horizontal current plateaus where di/dt is strictly zero. Images PMID:4275395

Bridge deck surface temperature monitoring by infrared thermography and inner structure identification using PPT and PCT analysis methods

NASA Astrophysics Data System (ADS)

Dumoulin, Jean

2013-04-01

One of the objectives of ISTIMES project was to evaluate the potentialities offered by the integration of different electromagnetic techniques able to perform non-invasive diagnostics for surveillance and monitoring of transport infrastructures. Among the EM methods investigated, we focused our research and development efforts on uncooled infrared camera techniques due to their promising potential level of dissemination linked to their relative low cost on the market. On the other hand, works were also carried out to identify well adapted implementation protocols and key limits of Pulse Phase Thermography (PPT) and Principal Component Thermography (PCT) processing methods to analyse thermal image sequence and retrieve information about the inner structure. So the first part of this research works addresses infrared thermography measurement when it is used in quantitative mode (not in laboratory conditions) and not in qualitative mode (vision applied to survey). In such context, it requires to process in real time thermal radiative corrections on raw data acquired to take into account influences of natural environment evolution with time, thanks to additional measurements. But, camera sensor has to be enough smart to apply in real time calibration law and radiometric corrections in a varying atmosphere. So, a complete measurement system was studied and developed [1] with low cost infrared cameras available on the market. In the system developed, infrared camera is coupled with other sensors to feed simplified radiative models running, in real time, on GPU available on small PC. The whole measurement system was implemented on the "Musmeci" bridge located in Potenza (Italy). No traffic interruption was required during the mounting of our measurement system. The infrared camera was fixed on top of a mast at 6 m elevation from the surface of the bridge deck. A small weather station was added on the same mast at 1 m under the camera. A GPS antenna was also fixed at the basis of the mast and at a same elevation than the bridge deck surface. This trial took place during 4 days, but our system was leaved in stand alone acquisition mode only during 3 days. Thanks to the software developed and the small computer hardware used, thermal image were acquired at a frame rate of 0.1 Hz by averaging 50 thermal images leaving the original camera frame rate fixed at 5 Hz. Each hour, a thermal image sequence was stored on the internal hard drive and data were also retrieved, on demand, by using a wireless connection and a tablet PC. In the second part of this work, thermal image sequences analysis was carried out. Two analysis approaches were studied: one based on the use of the Fast Fourier Transform [2] and the second one based on the Principal Component Analysis [3-4]. Results obtained show that the inner structure of the deck was identified though thermal images were affected by the fact that the bridge was open to traffic during the whole experiments duration. ACKNOWLEDGEMENT - The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant Agreement n° 225663. References [1] Dumoulin J. and Averty R., « Development of an infrared system coupled with a weather station for real time atmospheric corrections using GPU computing: Application to bridge monitoring", QIRT 2012, Naples, Italy, June 2012. [2] Cooley J.W., Tukey J.W., "An algorithm for the machine calculation of complex Fourier series", Mathematics of Computation, vol. 19, n° 90, 1965, p. 297-301. [3] Rajic N., "Principal component thermography for flaw contrast enhancement and flaw depth characterization in composite structures", Composite Structures, vol 58, pp 521-528, 2002. [4] Marinetti S., Grinzato E., Bison P. G., Bozzi E., Chimenti M., Pieri G. and Salvetti O. "Statistical analysis of IR thermographic sequences by PCA," Infrared Physics & Technology vol 46 pp 85-91, 2004.

Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces

PubMed Central

Partha, Raghavendran; Raman, Karthik

2014-01-01

Robustness and evolvability are highly intertwined properties of biological systems. The relationship between these properties determines how biological systems are able to withstand mutations and show variation in response to them. Computational studies have explored the relationship between these two properties using neutral networks of RNA sequences (genotype) and their secondary structures (phenotype) as a model system. However, these studies have assumed every mutation to a sequence to be equally likely; the differences in the likelihood of the occurrence of various mutations, and the consequence of probabilistic nature of the mutations in such a system have previously been ignored. Associating probabilities to mutations essentially results in the weighting of genotype space. We here perform a comparative analysis of weighted and unweighted neutral networks of RNA sequences, and subsequently explore the relationship between robustness and evolvability. We show that assuming an equal likelihood for all mutations (as in an unweighted network), underestimates robustness and overestimates evolvability of a system. In spite of discarding this assumption, we observe that a negative correlation between sequence (genotype) robustness and sequence evolvability persists, and also that structure (phenotype) robustness promotes structure evolvability, as observed in earlier studies using unweighted networks. We also study the effects of base composition bias on robustness and evolvability. Particularly, we explore the association between robustness and evolvability in a sequence space that is AU-rich – sequences with an AU content of 80% or higher, compared to a normal (unbiased) sequence space. We find that evolvability of both sequences and structures in an AU-rich space is lesser compared to the normal space, and robustness higher. We also observe that AU-rich populations evolving on neutral networks of phenotypes, can access less phenotypic variation compared to normal populations evolving on neutral networks. PMID:25390641

Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity

PubMed Central

Cousins, Matthew M.; Ou, San-San; Wawer, Maria J.; Munshaw, Supriya; Swan, David; Magaret, Craig A.; Mullis, Caroline E.; Serwadda, David; Porcella, Stephen F.; Gray, Ronald H.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

2012-01-01

Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution. PMID:22785188

Colorstratigraphy; A New Stratigraphic Correlation Technique

NASA Astrophysics Data System (ADS)

Nanayakkara, N. U.; Ranasinghage, P. N.; Priyantha, C.; Abillapitiya, T.

2016-12-01

Here we introduce a novel stratigraphic technique namely colorstratigraphy for correlating sedimentary sequences. Minihagalkanda is about 1 km long amphitheater like sedimentary terrain, situated at the southeastern coast of Sri Lanka. It has Miocene sedimentary sequences, separated in to 10-12 m high small hillocks by erosion, and bounded by about 30 m high escarpment. Sandstone, yellowish sandy clay, greenish silty clay sequences are capped by 4-5 m limestone bed in these hillocks but not at the boundary escarpment. Stratigraphic profiles at two hillocks and the boundary escarpment, separated each other by 200-300 m, were selected to test the new colorstartigraphic correlation technique. Color reflectance (DSR) was measured at four samples in each sequence at every profile and hence altogether 36 reflectance measurements were taken using Minolta 2500D hand-held color spectrophotometer. The first-derivative of the reflectance spectra (dR/dλ) defines the "spectral shape" of the sample. Therefore, DSR data (360-740 nm) measured at 10 nm resolution were used to calculate a center-weighted, first-derivative spectra for each reflectance sample consisting of 39 channels. Particle size of each sequence was measured at all 03 profiles using laser particle size analyzer to verify the stratigraphic correlation. Mean reflectance spectrum for each sequence at all 03 profiles were plotted on the same graph for comparison. Same was done for the grain size spectrums. Discriminant function analysis was performed separately for dsr data and grain size data using a number assigned to each sedimentary sequence as the grouping variable Color spectrums of sandstone, yellowish sandy clay, and greenish silty clay sequences at all three profiles perfectly match showing clear stratigraphic correlation among these three stratigraphic profiles. Matching grain size distribution curves of the three sequence at the three profiles verify the stratigraphic correlation. Perfect 100 % discrimination of the three sequences with color reflectance data proves the accuracy of the correlation. Similar 100 % discrimination resulted with grain size data further verifies the results. Therefore, colorstratigraphy based on DSR can be introduced as a quick and easy technique for stratigraphic correlation of sedimentary sequences.

Robust QKD-based private database queries based on alternative sequences of single-qubit measurements

NASA Astrophysics Data System (ADS)

Yang, YuGuang; Liu, ZhiChao; Chen, XiuBo; Zhou, YiHua; Shi, WeiMin

2017-12-01

Quantum channel noise may cause the user to obtain a wrong answer and thus misunderstand the database holder for existing QKD-based quantum private query (QPQ) protocols. In addition, an outside attacker may conceal his attack by exploiting the channel noise. We propose a new, robust QPQ protocol based on four-qubit decoherence-free (DF) states. In contrast to existing QPQ protocols against channel noise, only an alternative fixed sequence of single-qubit measurements is needed by the user (Alice) to measure the received DF states. This property makes it easy to implement the proposed protocol by exploiting current technologies. Moreover, to retain the advantage of flexible database queries, we reconstruct Alice's measurement operators so that Alice needs only conditioned sequences of single-qubit measurements.

Constraining tidal dissipation in F-type main-sequence stars: the case of CoRoT-11

NASA Astrophysics Data System (ADS)

Lanza, A. F.; Damiani, C.; Gandolfi, D.

2011-05-01

Context. Tidal dissipation in late-type stars is presently poorly understood and the study of planetary systems hosting hot Jupiters can provide new observational constraints to test proposed theories. Aims: We focus on systems with F-type main-sequence stars and find that the recently discovered system CoRoT-11 is presently the best suited for this kind of investigation. Methods: A classic constant tidal lag model is applied to reproduce the evolution of the system from a plausible nearly synchronous state on the zero-age main sequence (ZAMS) to the present state, thus putting constraints on the average modified tidal quality factor < Q_s' > of its F6V star.Initial conditions with the stellar rotation period longer than the orbital period of the planet can be excluded on the basis of the presently observed state in which the star spins faster than the planet orbit. Results: It is found that 4 × 106 ≲ < Q_s' > ≲ 2 × 107, if the system started its evolution on the ZAMS close to synchronization, with an uncertainty related to the constant tidal lag hypothesis and the estimated stellar magnetic braking within a factor of ≈5-6.For a non-synchronous initial state of the system, < Qs' > ≲ 4 × 106 implies an age younger than ~1 Gyr, while < Q_s' > ≳ 2 × 107 may be tested by comparing the theoretically derived initial orbital and stellar rotation periods with those of a sample of observed systems. Moreover, we discuss how the present value of Qs' can be measured by a timing of the mid-epoch and duration of the transits as well as of the planetary eclipses to be observed in the infrared with an accuracy of ~0.5-1 s over a time baseline of ~25 yr. Conclusions: CoRoT-11 is a highly interesting system that potentially allows us a direct measure of the tidal dissipation in an F-type star as well as the detection of the precession of the orbital plane of the planet that provides us with an accurate upper limit for the obliquity of the stellar equator. If the planetary orbit has a significant eccentricity (e ≳ 0.05), it will be possible to also detect the precession of the line of the apsides and derive information on the Love number of the planet and its tidal quality factor.

Optical resolution of phenylthiohydantoin-amino acids by capillary electrophoresis and identification of the phenylthiohydantoin-D-amino acid residue of [D-Ala2]-methionine enkephalin.

PubMed

Kurosu, Y; Murayama, K; Shindo, N; Shisa, Y; Ishioka, N

1996-11-01

This is an initial report to propose a protein sequence analysis system with DL differentiation using capillary electrophoresis (CE). This system consists of a protein sequencer and a CE system. After fractionation of phenyl-thiohydantoin (PTH)-amino acids using a protein sequencer, optical resolution for each PTH-amino acid is performed by CE using some chiral selectors such as digitonin, beta-escin and others. As a model peptide, [D-Ala2]-methionine enkephalin (L-Tyr-D-Ala-Gly-L-Phe-L-Met), was used and the sequence with DL differentiation was determined, with the exception of the fourth amino acid, L-Phe, using our proposed system.

Can We Improve Structured Sequence Processing? Exploring the Direct and Indirect Effects of Computerized Training Using a Mediational Model

PubMed Central

Smith, Gretchen N. L.; Conway, Christopher M.; Bauernschmidt, Althea; Pisoni, David B.

2015-01-01

Recent research suggests that language acquisition may rely on domain-general learning abilities, such as structured sequence processing, which is the ability to extract, encode, and represent structured patterns in a temporal sequence. If structured sequence processing supports language, then it may be possible to improve language function by enhancing this foundational learning ability. The goal of the present study was to use a novel computerized training task as a means to better understand the relationship between structured sequence processing and language function. Participants first were assessed on pre-training tasks to provide baseline behavioral measures of structured sequence processing and language abilities. Participants were then quasi-randomly assigned to either a treatment group involving adaptive structured visuospatial sequence training, a treatment group involving adaptive non-structured visuospatial sequence training, or a control group. Following four days of sequence training, all participants were assessed with the same pre-training measures. Overall comparison of the post-training means revealed no group differences. However, in order to examine the potential relations between sequence training, structured sequence processing, and language ability, we used a mediation analysis that showed two competing effects. In the indirect effect, adaptive sequence training with structural regularities had a positive impact on structured sequence processing performance, which in turn had a positive impact on language processing. This finding not only identifies a potential novel intervention to treat language impairments but also may be the first demonstration that structured sequence processing can be improved and that this, in turn, has an impact on language processing. However, in the direct effect, adaptive sequence training with structural regularities had a direct negative impact on language processing. This unexpected finding suggests that adaptive training with structural regularities might potentially interfere with language processing. Taken together, these findings underscore the importance of pursuing designs that promote a better understanding of the mechanisms underlying training-related changes, so that regimens can be developed that help reduce these types of negative effects while simultaneously maximizing the benefits to outcome measures of interest. PMID:25946222

Can we improve structured sequence processing? Exploring the direct and indirect effects of computerized training using a mediational model.

PubMed

Smith, Gretchen N L; Conway, Christopher M; Bauernschmidt, Althea; Pisoni, David B

2015-01-01

Recent research suggests that language acquisition may rely on domain-general learning abilities, such as structured sequence processing, which is the ability to extract, encode, and represent structured patterns in a temporal sequence. If structured sequence processing supports language, then it may be possible to improve language function by enhancing this foundational learning ability. The goal of the present study was to use a novel computerized training task as a means to better understand the relationship between structured sequence processing and language function. Participants first were assessed on pre-training tasks to provide baseline behavioral measures of structured sequence processing and language abilities. Participants were then quasi-randomly assigned to either a treatment group involving adaptive structured visuospatial sequence training, a treatment group involving adaptive non-structured visuospatial sequence training, or a control group. Following four days of sequence training, all participants were assessed with the same pre-training measures. Overall comparison of the post-training means revealed no group differences. However, in order to examine the potential relations between sequence training, structured sequence processing, and language ability, we used a mediation analysis that showed two competing effects. In the indirect effect, adaptive sequence training with structural regularities had a positive impact on structured sequence processing performance, which in turn had a positive impact on language processing. This finding not only identifies a potential novel intervention to treat language impairments but also may be the first demonstration that structured sequence processing can be improved and that this, in turn, has an impact on language processing. However, in the direct effect, adaptive sequence training with structural regularities had a direct negative impact on language processing. This unexpected finding suggests that adaptive training with structural regularities might potentially interfere with language processing. Taken together, these findings underscore the importance of pursuing designs that promote a better understanding of the mechanisms underlying training-related changes, so that regimens can be developed that help reduce these types of negative effects while simultaneously maximizing the benefits to outcome measures of interest.

Providers' perceptions of the implementation of a performance measurement system for substance abuse treatment: A process evaluation of the Service Quality Measures initiative.

PubMed

Myers, Bronwyn; Williams, Petal Petersen; Johnson, Kim; Govender, Rajen; Manderscheid, Ron; Koch, J Randy

2016-02-22

In South Africa, concerns exist about the quality of substance abuse treatment. We developed a performance measurement system, known as the Service Quality Measures (SQM) initiative, to monitor the quality of treatment and assess efforts to improve quality of care. In 2014, the SQM system was implemented at six treatment sites to evaluate how implementation protocols could be improved in preparation for wider roll-out. To describe providers' perceptions of the feasibility and acceptability of implementing the SQM system, including barriers to and facilitators of implementation. We conducted 15 in-depth interviews (IDIs) with treatment providers from six treatment sites (two sites in KwaZulu-Natal and four in the Western Cape). Providers were asked about their experiences in implementing the system, the perceived feasibility of the system, and barriers to implementation. All IDIs were audio-recorded and transcribed verbatim. A framework approach was used to analyse the data. Providers reported that the SQM system was feasible to implement and acceptable to patients and providers. Issues identified through the IDIs included a perceived lack of clarity about sequencing of key elements in the implementation of the SQM system, questions on integration of the system into clinical care pathways, difficulties in tracking patients through the system, and concerns about maximising patient participation in the process. Findings suggest that the SQM system is feasible to implement and acceptable to providers, but that some refinements to the implementation protocols are needed to maximise patient participation and the likelihood of sustained implementation.

Graph determined symbolic dynamics and hybrid systems

NASA Astrophysics Data System (ADS)

Ayers, Kimberly Danielle

In this paper we explore the concept of symbolic dynamical systems whose structure is determined by a directed graph, and then discrete-continuous hybrid systems that arise from such dynamical systems. Typically, symbolic dynamics involve the study of a left shift of a bi-infinite sequence. We examine the case when the bi-infinite system is dictated by a graph; that is, the sequence is a bi-infinite path of a directed graph. We then use the concept to study a system of dynamical systems all on the same compact space M, where "switching" between the systems occurs as given by the bi-infinite sequence in question. The concepts of limit sets, chain recurrent sets, chaos, and Morse sets for these systems are explored.

Speech and Nonspeech Sequence Skill Learning in Adults Who Stutter

ERIC Educational Resources Information Center

Smits-Bandstra, Sarah; De Nil, Luc; Saint-Cyr, Jean A.

2006-01-01

Two studies compared the speech and nonspeech sequence skill learning of nine persons who stutter (PWS) and nine matched fluent speakers (PNS). Sequence skill learning was defined as a continuing process of stable improvement in speed and/or accuracy of sequencing performance over practice and was measured by comparing PWS's and PNS's performance…

Reduction of Left Visual Field Lexical Decision Accuracy as a Result of Concurrent Nonverbal Auditory Stimulation

ERIC Educational Resources Information Center

Van Strien, Jan W.

2004-01-01

To investigate whether concurrent nonverbal sound sequences would affect visual-hemifield lexical processing, lexical-decision performance of 24 strongly right-handed students (12 men, 12 women) was measured in three conditions: baseline, concurrent neutral sound sequence, and concurrent emotional sound sequence. With the neutral sequence,…

BONSAI Garden: Parallel knowledge discovery system for amino acid sequences

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

Shoudai, T.; Miyano, S.; Shinohara, A.

1995-12-31

We have developed a machine discovery system BON-SAI which receives positive and negative examples as inputs and produces as a hypothesis a pair of a decision tree over regular patterns and an alphabet indexing. This system has succeeded in discovering reasonable knowledge on transmembrane domain sequences and signal peptide sequences by computer experiments. However, when several kinds of sequences axe mixed in the data, it does not seem reasonable for a single BONSAI system to find a hypothesis of a reasonably small size with high accuracy. For this purpose, we have designed a system BONSAI Garden, in which several BONSAI`smore » and a program called Gardener run over a network in parallel, to partition the data into some number of classes together with hypotheses explaining these classes accurately.« less

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

PubMed Central

Meyer, Pablo; Siwo, Geoffrey; Zeevi, Danny; Sharon, Eilon; Norel, Raquel; Segal, Eran; Stolovitzky, Gustavo; Siwo, Geoffrey; Rider, Andrew K.; Tan, Asako; Pinapati, Richard S.; Emrich, Scott; Chawla, Nitesh; Ferdig, Michael T.; Tung, Yi-An; Chen, Yong-Syuan; Chen, Mei-Ju May; Chen, Chien-Yu; Knight, Jason M.; Sahraeian, Sayed Mohammad Ebrahim; Esfahani, Mohammad Shahrokh; Dreos, Rene; Bucher, Philipp; Maier, Ezekiel; Saeys, Yvan; Szczurek, Ewa; Myšičková, Alena; Vingron, Martin; Klein, Holger; Kiełbasa, Szymon M.; Knisley, Jeff; Bonnell, Jeff; Knisley, Debra; Kursa, Miron B.; Rudnicki, Witold R.; Bhattacharjee, Madhuchhanda; Sillanpää, Mikko J.; Yeung, James; Meysman, Pieter; Rodríguez, Aminael Sánchez; Engelen, Kristof; Marchal, Kathleen; Huang, Yezhou; Mordelet, Fantine; Hartemink, Alexander; Pinello, Luca; Yuan, Guo-Cheng

2013-01-01

The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. The challenge was presented to the community in the framework of the sixth Dialogue for Reverse Engineering Assessments and Methods (DREAM6), a community effort to evaluate the status of systems biology modeling methodologies. Nucleotide-specific promoter activity was obtained by measuring fluorescence from promoter sequences fused upstream of a gene for yellow fluorescence protein and inserted in the same genomic site of yeast Saccharomyces cerevisiae. Twenty-one teams submitted results predicting the expression levels of 53 different promoters from yeast ribosomal protein genes. Analysis of participant predictions shows that accurate values for low-expressed and mutated promoters were difficult to obtain, although in the latter case, only when the mutation induced a large change in promoter activity compared to the wild-type sequence. As in previous DREAM challenges, we found that aggregation of participant predictions provided robust results, but did not fare better than the three best algorithms. Finally, this study not only provides a benchmark for the assessment of methods predicting activity of a specific set of promoters from their sequence, but it also shows that the top performing algorithm, which used machine-learning approaches, can be improved by the addition of biological features such as transcription factor binding sites. PMID:23950146

HIV-1 envelope sequence-based diversity measures for identifying recent infections

PubMed Central

Kafando, Alexis; Fournier, Eric; Serhir, Bouchra; Martineau, Christine; Doualla-Bell, Florence; Sangaré, Mohamed Ndongo; Sylla, Mohamed; Chamberland, Annie; El-Far, Mohamed; Charest, Hugues

2017-01-01

Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC) of the receiver operating characteristic (ROC). Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001). Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806), gp120 C2_3 (AUC = 0.805) and gp120 V3 (AUC = 0.812). Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency. PMID:29284009

HIV-1 envelope sequence-based diversity measures for identifying recent infections.

PubMed

Kafando, Alexis; Fournier, Eric; Serhir, Bouchra; Martineau, Christine; Doualla-Bell, Florence; Sangaré, Mohamed Ndongo; Sylla, Mohamed; Chamberland, Annie; El-Far, Mohamed; Charest, Hugues; Tremblay, Cécile L

2017-01-01

Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC) of the receiver operating characteristic (ROC). Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001). Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806), gp120 C2_3 (AUC = 0.805) and gp120 V3 (AUC = 0.812). Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.

Application of binomial-edited CPMG to shale characterization

USGS Publications Warehouse

Washburn, Kathryn E.; Birdwell, Justin E.

2014-01-01

Unconventional shale resources may contain a significant amount of hydrogen in organic solids such as kerogen, but it is not possible to directly detect these solids with many NMR systems. Binomial-edited pulse sequences capitalize on magnetization transfer between solids, semi-solids, and liquids to provide an indirect method of detecting solid organic materials in shales. When the organic solids can be directly measured, binomial-editing helps distinguish between different phases. We applied a binomial-edited CPMG pulse sequence to a range of natural and experimentally-altered shale samples. The most substantial signal loss is seen in shales rich in organic solids while fluids associated with inorganic pores seem essentially unaffected. This suggests that binomial-editing is a potential method for determining fluid locations, solid organic content, and kerogen–bitumen discrimination.

Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing.

PubMed

Olvera, Alex; Busquets, Núria; Cortey, Marti; de Deus, Nilsa; Ganges, Llilianne; Núñez, José Ignacio; Peralta, Bibiana; Toskano, Jennifer; Dolz, Roser

2010-05-01

Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases. Copyright 2009 Elsevier Ltd. All rights reserved.

Surface and Subsurface Fault Displacements from the September 2010 Darfield (Canterbury) Earthquake

NASA Astrophysics Data System (ADS)

Meyers, B.; Furlong, K. P.; Hayes, G. P.; Herman, M. W.; Quigley, M.

2012-12-01

On September 3, 2010 a Magnitude 7.1 earthquake struck near Darfield, New Zealand. This was to be the first earthquake in an ongoing, damaging sequence near the city of Christchurch. The earthquake produced a surface rupture with measurable offsets of up to 5.3m along a 30km surface fault system. The spatial pattern of slip during this rupture has been determined by various groups using a range of approaches and several independent data sets. Surface fault rupture was measured in the field and fault slip at depth has been inferred from a seismologic finite fault model (FFM) and various geodetic observations including GPS and InSAR. Here we compare the observed segmented surface displacements with fault slip inferred from the other data. Measurements of the surface rupture show segmented faulting consistent with subsurface slip in the FFM. In the FFM, the main slip patch near the hypocenter can be directly correlated to the region of maximum surface displacement. The FFM and some evidence in the InSAR data also indicate that the Greendale fault system, the structure responsible for the bulk of the rupture, continues at depth closer towards Christchurch than is seen in surface rupture patterns. There is an additional 20km long patch with up to 3m of modeled slip seen in the eastern end of the inverted fault, offset to the south from the Greendale fault trace. This additional fault segment is consistent with a zone of aftershock activity of the main Darfield event, and with local patterns of strong motion. It thus appears that slip recorded at the surface does not describe the entire fault system. This eastward extension of the September rupture means that there is only a short segment of unruptured crust remaining along the entire fault system involved in the Canterbury earthquake sequence.

The Automatic Meteorological Station System AN/TMQ-30 ( ).

DTIC Science & Technology

1982-08-01

network, the station electronics initiate the above operating sequence. 3.2.1 Meteorological Parameters Vindspeed. Windspeed measurements are made over a...much like a pocket calculator. Provision has been made to enable the operator to set or read the clock of the master station and to * set, modify, or...conditions is occuring during a regular cycle period. A normal report is not made under these conditions. Control is passed to the read data module under

Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

PubMed Central

Shaw, Jennifer L. A.; Weyrich, Laura S.; Sawade, Emma; Drikas, Mary; Cooper, Alan J.

2015-01-01

Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. PMID:26162884

Development of the Computerized Model of Performance-Based Measurement System to Measure Nurses' Clinical Competence.

PubMed

Liou, Shwu-Ru; Liu, Hsiu-Chen; Tsai, Shu-Ling; Cheng, Ching-Yu; Yu, Wei-Chieh; Chu, Tsui-Ping

2016-04-01

Critical thinking skills and clinical competence are for providing quality patient care. The purpose of this study is to develop the Computerized Model of Performance-Based Measurement system based on the Clinical Reasoning Model. The system can evaluate and identify learning needs for clinical competency and be used as a learning tool to increase clinical competency by using computers. The system includes 10 high-risk, high-volume clinical case scenarios coupled with questions testing clinical reasoning, interpersonal, and technical skills. Questions were sequenced to reflect patients' changing condition and arranged by following the process of collecting and managing information, diagnosing and differentiating urgency of problems, and solving problems. The content validity and known-groups validity was established. The Kuder-Richardson Formula 20 was 0.90 and test-retest reliability was supported (r = 0.78). Nursing educators can use the system to understand students' needs for achieving clinical competence, and therefore, educational plans can be made to better prepare students and facilitate their smooth transition to a future clinical environment. Clinical nurses can use the system to evaluate their performance-based abilities and weakness in clinical reasoning. Appropriate training programs can be designed and implemented to practically promote nurses' clinical competence and quality of patient care.

Lunar impact basins: Stratigraphy, sequence and ages from superposed impact crater populations measured from Lunar Orbiter Laser Altimeter (LOLA) data

NASA Astrophysics Data System (ADS)

Fassett, C. I.; Head, J. W.; Kadish, S. J.; Mazarico, E.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.

2012-02-01

Impact basin formation is a fundamental process in the evolution of the Moon and records the history of impactors in the early solar system. In order to assess the stratigraphy, sequence, and ages of impact basins and the impactor population as a function of time, we have used topography from the Lunar Orbiter Laser Altimeter (LOLA) on the Lunar Reconnaissance Orbiter (LRO) to measure the superposed impact crater size-frequency distributions for 30 lunar basins (D ≥ 300 km). These data generally support the widely used Wilhelms sequence of lunar basins, although we find significantly higher densities of superposed craters on many lunar basins than derived by Wilhelms (50% higher densities). Our data also provide new insight into the timing of the transition between distinct crater populations characteristic of ancient and young lunar terrains. The transition from a lunar impact flux dominated by Population 1 to Population 2 occurred before the mid-Nectarian. This is before the end of the period of rapid cratering, and potentially before the end of the hypothesized Late Heavy Bombardment. LOLA-derived crater densities also suggest that many Pre-Nectarian basins, such as South Pole-Aitken, have been cratered to saturation equilibrium. Finally, both crater counts and stratigraphic observations based on LOLA data are applicable to specific basin stratigraphic problems of interest; for example, using these data, we suggest that Serenitatis is older than Nectaris, and Humboldtianum is younger than Crisium. Sample return missions to specific basins can anchor these measurements to a Pre-Imbrian absolute chronology.

Lunar Impact Basins: Stratigraphy, Sequence and Ages from Superposed Impact Crater Populations Measured from Lunar Orbiter Laser Altimeter (LOLA) Data

NASA Technical Reports Server (NTRS)

Fassett, C. I.; Head, J. W.; Kadish, S. J.; Mazarico, E.; Neumann, G. A.; Smith, D. E.; Zuber, M. T.

2012-01-01

Impact basin formation is a fundamental process in the evolution of the Moon and records the history of impactors in the early solar system. In order to assess the stratigraphy, sequence, and ages of impact basins and the impactor population as a function of time, we have used topography from the Lunar Orbiter Laser Altimeter (LOLA) on the Lunar Reconnaissance Orbiter (LRO) to measure the superposed impact crater size-frequency distributions for 30 lunar basins (D = 300 km). These data generally support the widely used Wilhelms sequence of lunar basins, although we find significantly higher densities of superposed craters on many lunar basins than derived by Wilhelms (50% higher densities). Our data also provide new insight into the timing of the transition between distinct crater populations characteristic of ancient and young lunar terrains. The transition from a lunar impact flux dominated by Population 1 to Population 2 occurred before the mid-Nectarian. This is before the end of the period of rapid cratering, and potentially before the end of the hypothesized Late Heavy Bombardment. LOLA-derived crater densities also suggest that many Pre-Nectarian basins, such as South Pole-Aitken, have been cratered to saturation equilibrium. Finally, both crater counts and stratigraphic observations based on LOLA data are applicable to specific basin stratigraphic problems of interest; for example, using these data, we suggest that Serenitatis is older than Nectaris, and Humboldtianum is younger than Crisium. Sample return missions to specific basins can anchor these measurements to a Pre-Imbrian absolute chronology.

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

PubMed

Quick, Joshua; Quinlan, Aaron R; Loman, Nicholas J

2014-01-01

The MinION™ is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies. It measures four inches in length and is powered from the USB 3.0 port of a laptop computer. The MinION™ measures the change in current resulting from DNA strands interacting with a charged protein nanopore. These measurements can then be used to deduce the underlying nucleotide sequence. We present a read dataset from whole-genome shotgun sequencing of the model organism Escherichia coli K-12 substr. MG1655 generated on a MinION™ device during the early-access MinION™ Access Program (MAP). Sequencing runs of the MinION™ are presented, one generated using R7 chemistry (released in July 2014) and one using R7.3 (released in September 2014). Base-called sequence data are provided to demonstrate the nature of data produced by the MinION™ platform and to encourage the development of customised methods for alignment, consensus and variant calling, de novo assembly and scaffolding. FAST5 files containing event data within the HDF5 container format are provided to assist with the development of improved base-calling methods.

CAFE: aCcelerated Alignment-FrEe sequence analysis.

PubMed

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

2017-07-03

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

PubMed

Haiminen, Niina; Feltus, F Alex; Parida, Laxmi

2011-04-15

We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.

Digit-color synaesthesia only enhances memory for colors in a specific context: A new method of duration thresholds to measure serial recall.

PubMed

Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

2017-08-01

For digit-color synaesthetes, digits elicit vivid experiences of color that are highly consistent for each individual. The conscious experience of synaesthesia is typically unidirectional: Digits evoke colors but not vice versa. There is an ongoing debate about whether synaesthetes have a memory advantage over non-synaesthetes. One key question in this debate is whether synaesthetes have a general superiority or whether any benefit is specific to a certain type of material. Here, we focus on immediate serial recall and ask digit-color synaesthetes and controls to memorize digit and color sequences. We developed a sensitive staircase method manipulating presentation duration to measure participants' serial recall of both overlearned and novel sequences. Our results show that synaesthetes can activate digit information to enhance serial memory for color sequences. When color sequences corresponded to ascending or descending digit sequences, synaesthetes encoded these sequences at a faster rate than their non-synaesthetes counterparts and faster than non-structured color sequences. However, encoding color sequences is approximately 200 ms slower than encoding digit sequences directly, independent of group and condition, which shows that the translation process is time consuming. These results suggest memory advantages in synaesthesia require a modified dual-coding account, in which secondary (synaesthetically linked) information is useful only if it is more memorable than the primary information to be recalled. Our study further shows that duration thresholds are a sensitive method to measure subtle differences in serial recall performance. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Multimodal navigated skull base tumor resection using image-based vascular and cranial nerve segmentation: A prospective pilot study

PubMed Central

Dolati, Parviz; Gokoglu, Abdulkerim; Eichberg, Daniel; Zamani, Amir; Golby, Alexandra; Al-Mefty, Ossama

2015-01-01

Background: Skull base tumors frequently encase or invade adjacent normal neurovascular structures. For this reason, optimal tumor resection with incomplete knowledge of patient anatomy remains a challenge. Methods: To determine the accuracy and utility of image-based preoperative segmentation in skull base tumor resections, we performed a prospective study. Ten patients with skull base tumors underwent preoperative 3T magnetic resonance imaging, which included thin section three-dimensional (3D) space T2, 3D time of flight, and magnetization-prepared rapid acquisition gradient echo sequences. Imaging sequences were loaded in the neuronavigation system for segmentation and preoperative planning. Five different neurovascular landmarks were identified in each case and measured for accuracy using the neuronavigation system. Each segmented neurovascular element was validated by manual placement of the navigation probe, and errors of localization were measured. Results: Strong correspondence between image-based segmentation and microscopic view was found at the surface of the tumor and tumor-normal brain interfaces in all cases. The accuracy of the measurements was 0.45 ± 0.21 mm (mean ± standard deviation). This information reassured the surgeon and prevented vascular injury intraoperatively. Preoperative segmentation of the related cranial nerves was possible in 80% of cases and helped the surgeon localize involved cranial nerves in all cases. Conclusion: Image-based preoperative vascular and neural element segmentation with 3D reconstruction is highly informative preoperatively and could increase the vigilance of neurosurgeons for preventing neurovascular injury during skull base surgeries. Additionally, the accuracy found in this study is superior to previously reported measurements. This novel preliminary study is encouraging for future validation with larger numbers of patients. PMID:26674155

Multimodal navigated skull base tumor resection using image-based vascular and cranial nerve segmentation: A prospective pilot study.

PubMed

Dolati, Parviz; Gokoglu, Abdulkerim; Eichberg, Daniel; Zamani, Amir; Golby, Alexandra; Al-Mefty, Ossama

2015-01-01

Skull base tumors frequently encase or invade adjacent normal neurovascular structures. For this reason, optimal tumor resection with incomplete knowledge of patient anatomy remains a challenge. To determine the accuracy and utility of image-based preoperative segmentation in skull base tumor resections, we performed a prospective study. Ten patients with skull base tumors underwent preoperative 3T magnetic resonance imaging, which included thin section three-dimensional (3D) space T2, 3D time of flight, and magnetization-prepared rapid acquisition gradient echo sequences. Imaging sequences were loaded in the neuronavigation system for segmentation and preoperative planning. Five different neurovascular landmarks were identified in each case and measured for accuracy using the neuronavigation system. Each segmented neurovascular element was validated by manual placement of the navigation probe, and errors of localization were measured. Strong correspondence between image-based segmentation and microscopic view was found at the surface of the tumor and tumor-normal brain interfaces in all cases. The accuracy of the measurements was 0.45 ± 0.21 mm (mean ± standard deviation). This information reassured the surgeon and prevented vascular injury intraoperatively. Preoperative segmentation of the related cranial nerves was possible in 80% of cases and helped the surgeon localize involved cranial nerves in all cases. Image-based preoperative vascular and neural element segmentation with 3D reconstruction is highly informative preoperatively and could increase the vigilance of neurosurgeons for preventing neurovascular injury during skull base surgeries. Additionally, the accuracy found in this study is superior to previously reported measurements. This novel preliminary study is encouraging for future validation with larger numbers of patients.

Operating Characteristics of the Implicit Learning System Supporting Serial Interception Sequence Learning

ERIC Educational Resources Information Center

Sanchez, Daniel J.; Reber, Paul J.

2012-01-01

The memory system that supports implicit perceptual-motor sequence learning relies on brain regions that operate separately from the explicit, medial temporal lobe memory system. The implicit learning system therefore likely has distinct operating characteristics and information processing constraints. To attempt to identify the limits of the…

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Not all (possibly) “random” sequences are created equal

PubMed Central

Pincus, Steve; Kalman, Rudolf E.

1997-01-01

The need to assess the randomness of a single sequence, especially a finite sequence, is ubiquitous, yet is unaddressed by axiomatic probability theory. Here, we assess randomness via approximate entropy (ApEn), a computable measure of sequential irregularity, applicable to single sequences of both (even very short) finite and infinite length. We indicate the novelty and facility of the multidimensional viewpoint taken by ApEn, in contrast to classical measures. Furthermore and notably, for finite length, finite state sequences, one can identify maximally irregular sequences, and then apply ApEn to quantify the extent to which given sequences differ from maximal irregularity, via a set of deficit (defm) functions. The utility of these defm functions which we show allows one to considerably refine the notions of probabilistic independence and normality, is featured in several studies, including (i) digits of e, π, √2, and √3, both in base 2 and in base 10, and (ii) sequences given by fractional parts of multiples of irrationals. We prove companion analytic results, which also feature in a discussion of the role and validity of the almost sure properties from axiomatic probability theory insofar as they apply to specified sequences and sets of sequences (in the physical world). We conclude by relating the present results and perspective to both previous and subsequent studies. PMID:11038612

Development of Rapid, Continuous Calibration Techniques and Implementation as a Prototype System for Civil Engineering Materials Evaluation

NASA Astrophysics Data System (ADS)

Scott, M. L.; Gagarin, N.; Mekemson, J. R.; Chintakunta, S. R.

2011-06-01

Until recently, civil engineering material calibration data could only be obtained from material sample cores or via time consuming, stationary calibration measurements in a limited number of locations. Calibration data are used to determine material propagation velocities of electromagnetic waves in test materials for use in layer thickness measurements and subsurface imaging. Limitations these calibration methods impose have been a significant impediment to broader use of nondestructive evaluation methods such as ground-penetrating radar (GPR). In 2006, a new rapid, continuous calibration approach was designed using simulation software to address these measurement limitations during a Federal Highway Administration (FHWA) research and development effort. This continuous calibration method combines a digitally-synthesized step-frequency (SF)-GPR array and a data collection protocol sequence for the common midpoint (CMP) method. Modeling and laboratory test results for various data collection protocols and materials are presented in this paper. The continuous-CMP concept was finally implemented for FHWA in a prototype demonstration system called the Advanced Pavement Evaluation (APE) system in 2009. Data from the continuous-CMP protocol is processed using a semblance/coherency analysis to determine material propagation velocities. Continuously calibrated pavement thicknesses measured with the APE system in 2009 are presented. This method is efficient, accurate, and cost-effective.

Development of rapid, continuous calibration techniques and implementation as a prototype system for civil engineering materials evaluation

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

Scott, M. L.; Gagarin, N.; Mekemson, J. R.

Until recently, civil engineering material calibration data could only be obtained from material sample cores or via time consuming, stationary calibration measurements in a limited number of locations. Calibration data are used to determine material propagation velocities of electromagnetic waves in test materials for use in layer thickness measurements and subsurface imaging. Limitations these calibration methods impose have been a significant impediment to broader use of nondestructive evaluation methods such as ground-penetrating radar (GPR). In 2006, a new rapid, continuous calibration approach was designed using simulation software to address these measurement limitations during a Federal Highway Administration (FHWA) research andmore » development effort. This continuous calibration method combines a digitally-synthesized step-frequency (SF)-GPR array and a data collection protocol sequence for the common midpoint (CMP) method. Modeling and laboratory test results for various data collection protocols and materials are presented in this paper. The continuous-CMP concept was finally implemented for FHWA in a prototype demonstration system called the Advanced Pavement Evaluation (APE) system in 2009. Data from the continuous-CMP protocol is processed using a semblance/coherency analysis to determine material propagation velocities. Continuously calibrated pavement thicknesses measured with the APE system in 2009 are presented. This method is efficient, accurate, and cost-effective.« less

AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES

EPA Science Inventory

This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods

PubMed Central

Wu, Yuhua; Wang, Yulei; Li, Jun; Li, Wei; Zhang, Li; Li, Yunjing; Li, Xiaofei; Li, Jun; Zhu, Li; Wu, Gang

2014-01-01

The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods. PMID:25483893

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

Sequence stratigraphy of the Kingak Shale (Jurassic-Lower Cretaceous), National Petroleum Reserve in Alaska

USGS Publications Warehouse

Houseknecht, D.W.; Bird, K.J.

2004-01-01

Beaufortian strata (Jurassic-Lower Cretaceous) in the National Petroleum Reserve in Alaska (NPRA) are a focus of exploration since the 1994 discovery of the nearby Alpine oil field (>400 MMBO). These strata include the Kingak Shale, a succession of depositional sequences influenced by rift opening of the Arctic Ocean Basin. Interpretation of sequence stratigraphy and depositional facies from a regional two-dimensional seismic grid and well data allows the definition of four sequence sets that each displays unique stratal geometries and thickness trends across NPRA. A Lower to Middle Jurassic sequence set includes numerous transgressive-regressive sequences that collectively built a clastic shelf in north-central NPRA. Along the south-facing, lobate shelf margin, condensed shales in transgressive systems tracts downlap and coalesce into a basinal condensed section that is likely an important hydrocarbon source rock. An Oxfordian-Kimmeridgian sequence set, deposited during pulses of uplift on the Barrow arch, includes multiple transgressive-regressive sequences that locally contain well-winnowed, shoreface sandstones at the base of transgressive systems tracts. These shoreface sandstones and overlying shales, deposited during maximum flooding, form stratigraphic traps that are the main objective of exploration in the Alpine play in NPRA. A Valanginian sequence set includes at least two transgressive-regressive sequences that display relatively distal characteristics, suggesting high relative sea level. An important exception is the presence of a basal transgressive systems tract that locally contains shoreface sandstones of reservoir quality. A Hauterivian sequence set includes two transgressive-regressive sequences that constitute a shelf-margin wedge developed as the result of tectonic uplift along the Barrow arch during rift opening of the Arctic Ocean Basin. This sequence set displays stratal geometries suggesting incision and synsedimentary collapse of the shelf margin. ?? 2004. The American Association of Petroleum Geologists. All rights reserved.

A General Conditional Large Deviation Principle

DOE PAGES

La Cour, Brian R.; Schieve, William C.

2015-07-18

Given a sequence of Borel probability measures on a Hausdorff space which satisfy a large deviation principle (LDP), we consider the corresponding sequence of measures formed by conditioning on a set B. If the large deviation rate function I is good and effectively continuous, and the conditioning set has the property that (1)more » $$\\overline{B°}$$=$$\\overline{B}$$ and (2) I(x)<∞ for all xε$$\\overline{B}$$, then the sequence of conditional measures satisfies a LDP with the good, effectively continuous rate function I B, where I B(x)=I(x)-inf I(B) if xε$$\\overline{B}$$ and I B(x)=∞ otherwise.« less