WorldWideScience

Sample records for hybrid computer identification

  1. Analog and hybrid computing

    CERN Document Server

    Hyndman, D E

    2013-01-01

    Analog and Hybrid Computing focuses on the operations of analog and hybrid computers. The book first outlines the history of computing devices that influenced the creation of analog and digital computers. The types of problems to be solved on computers, computing systems, and digital computers are discussed. The text looks at the theory and operation of electronic analog computers, including linear and non-linear computing units and use of analog computers as operational amplifiers. The monograph examines the preparation of problems to be deciphered on computers. Flow diagrams, methods of ampl

  2. Hybrid quantum computation

    International Nuclear Information System (INIS)

    Sehrawat, Arun; Englert, Berthold-Georg; Zemann, Daniel

    2011-01-01

    We present a hybrid model of the unitary-evolution-based quantum computation model and the measurement-based quantum computation model. In the hybrid model, part of a quantum circuit is simulated by unitary evolution and the rest by measurements on star graph states, thereby combining the advantages of the two standard quantum computation models. In the hybrid model, a complicated unitary gate under simulation is decomposed in terms of a sequence of single-qubit operations, the controlled-z gates, and multiqubit rotations around the z axis. Every single-qubit and the controlled-z gate are realized by a respective unitary evolution, and every multiqubit rotation is executed by a single measurement on a required star graph state. The classical information processing in our model requires only an information flow vector and propagation matrices. We provide the implementation of multicontrol gates in the hybrid model. They are very useful for implementing Grover's search algorithm, which is studied as an illustrative example.

  3. Security in hybrid cloud computing

    OpenAIRE

    Koudelka, Ondřej

    2016-01-01

    This bachelor thesis deals with the area of hybrid cloud computing, specifically with its security. The major aim of the thesis is to analyze and compare the chosen hybrid cloud providers. For the minor aim this thesis compares the security challenges of hybrid cloud as opponent to other deployment models. In order to accomplish said aims, this thesis defines the terms cloud computing and hybrid cloud computing in its theoretical part. Furthermore the security challenges for cloud computing a...

  4. Hybrid computing - Generalities and bibliography

    International Nuclear Information System (INIS)

    Neel, Daniele

    1970-01-01

    This note presents the content of a research thesis. It describes the evolution of hybrid computing systems, discusses the benefits and shortcomings of analogue or hybrid systems, discusses the building up of an hybrid system (requires properties), comments different possible uses, addresses the issues of language and programming, discusses analysis methods and scopes of application. An appendix proposes a bibliography on these issues and notably the different scopes of application (simulation, fluid dynamics, biology, chemistry, electronics, energy, errors, space, programming languages, hardware, mechanics, and optimisation of equations or processes, physics) [fr

  5. Accurate Identification of Cancerlectins through Hybrid Machine Learning Technology.

    Science.gov (United States)

    Zhang, Jieru; Ju, Ying; Lu, Huijuan; Xuan, Ping; Zou, Quan

    2016-01-01

    Cancerlectins are cancer-related proteins that function as lectins. They have been identified through computational identification techniques, but these techniques have sometimes failed to identify proteins because of sequence diversity among the cancerlectins. Advanced machine learning identification methods, such as support vector machine and basic sequence features (n-gram), have also been used to identify cancerlectins. In this study, various protein fingerprint features and advanced classifiers, including ensemble learning techniques, were utilized to identify this group of proteins. We improved the prediction accuracy of the original feature extraction methods and classification algorithms by more than 10% on average. Our work provides a basis for the computational identification of cancerlectins and reveals the power of hybrid machine learning techniques in computational proteomics.

  6. Hybrid soft computing approaches research and applications

    CERN Document Server

    Dutta, Paramartha; Chakraborty, Susanta

    2016-01-01

    The book provides a platform for dealing with the flaws and failings of the soft computing paradigm through different manifestations. The different chapters highlight the necessity of the hybrid soft computing methodology in general with emphasis on several application perspectives in particular. Typical examples include (a) Study of Economic Load Dispatch by Various Hybrid Optimization Techniques, (b) An Application of Color Magnetic Resonance Brain Image Segmentation by ParaOptiMUSIG activation Function, (c) Hybrid Rough-PSO Approach in Remote Sensing Imagery Analysis,  (d) A Study and Analysis of Hybrid Intelligent Techniques for Breast Cancer Detection using Breast Thermograms, and (e) Hybridization of 2D-3D Images for Human Face Recognition. The elaborate findings of the chapters enhance the exhibition of the hybrid soft computing paradigm in the field of intelligent computing.

  7. Checkpointing for a hybrid computing node

    Science.gov (United States)

    Cher, Chen-Yong

    2016-03-08

    According to an aspect, a method for checkpointing in a hybrid computing node includes executing a task in a processing accelerator of the hybrid computing node. A checkpoint is created in a local memory of the processing accelerator. The checkpoint includes state data to restart execution of the task in the processing accelerator upon a restart operation. Execution of the task is resumed in the processing accelerator after creating the checkpoint. The state data of the checkpoint are transferred from the processing accelerator to a main processor of the hybrid computing node while the processing accelerator is executing the task.

  8. Generalised Computability and Applications to Hybrid Systems

    DEFF Research Database (Denmark)

    Korovina, Margarita V.; Kudinov, Oleg V.

    2001-01-01

    We investigate the concept of generalised computability of operators and functionals defined on the set of continuous functions, firstly introduced in [9]. By working in the reals, with equality and without equality, we study properties of generalised computable operators and functionals. Also we...... propose an interesting application to formalisation of hybrid systems. We obtain some class of hybrid systems, which trajectories are computable in the sense of computable analysis. This research was supported in part by the RFBR (grants N 99-01-00485, N 00-01- 00810) and by the Siberian Branch of RAS (a...... grant for young researchers, 2000)...

  9. Universal blind quantum computation for hybrid system

    Science.gov (United States)

    Huang, He-Liang; Bao, Wan-Su; Li, Tan; Li, Feng-Guang; Fu, Xiang-Qun; Zhang, Shuo; Zhang, Hai-Long; Wang, Xiang

    2017-08-01

    As progress on the development of building quantum computer continues to advance, first-generation practical quantum computers will be available for ordinary users in the cloud style similar to IBM's Quantum Experience nowadays. Clients can remotely access the quantum servers using some simple devices. In such a situation, it is of prime importance to keep the security of the client's information. Blind quantum computation protocols enable a client with limited quantum technology to delegate her quantum computation to a quantum server without leaking any privacy. To date, blind quantum computation has been considered only for an individual quantum system. However, practical universal quantum computer is likely to be a hybrid system. Here, we take the first step to construct a framework of blind quantum computation for the hybrid system, which provides a more feasible way for scalable blind quantum computation.

  10. Heterotic computing: exploiting hybrid computational devices.

    Science.gov (United States)

    Kendon, Viv; Sebald, Angelika; Stepney, Susan

    2015-07-28

    Current computational theory deals almost exclusively with single models: classical, neural, analogue, quantum, etc. In practice, researchers use ad hoc combinations, realizing only recently that they can be fundamentally more powerful than the individual parts. A Theo Murphy meeting brought together theorists and practitioners of various types of computing, to engage in combining the individual strengths to produce powerful new heterotic devices. 'Heterotic computing' is defined as a combination of two or more computational systems such that they provide an advantage over either substrate used separately. This post-meeting collection of articles provides a wide-ranging survey of the state of the art in diverse computational paradigms, together with reflections on their future combination into powerful and practical applications. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  11. Identification of computer graphics objects

    Directory of Open Access Journals (Sweden)

    Rossinskyi Yu.M.

    2016-04-01

    Full Text Available The article is devoted to the use of computer graphics methods in problems of creating drawings, charts, drafting, etc. The widespread use of these methods requires the development of efficient algorithms for the identification of objects of drawings. The article analyzes the model-making algorithms for this problem and considered the possibility of reducing the time using graphics editing operations. Editing results in such operations as copying, moving and deleting objects specified images. These operations allow the use of a reliable identification of images of objects methods. For information on the composition of the image of the object along with information about the identity and the color should include information about the spatial location and other characteristics of the object (the thickness and style of contour lines, fill style, and so on. In order to enable the pixel image analysis to structure the information it is necessary to enable the initial code image objects color. The article shows the results of the implementation of the algorithm of encoding object identifiers. To simplify the process of building drawings of any kind, and reduce time-consuming, method of drawing objects identification is proposed based on the use as the ID information of the object color.

  12. Hybrid computer modelling in plasma physics

    International Nuclear Information System (INIS)

    Hromadka, J; Ibehej, T; Hrach, R

    2016-01-01

    Our contribution is devoted to development of hybrid modelling techniques. We investigate sheath structures in the vicinity of solids immersed in low temperature argon plasma of different pressures by means of particle and fluid computer models. We discuss the differences in results obtained by these methods and try to propose a way to improve the results of fluid models in the low pressure area. There is a possibility to employ Chapman-Enskog method to find appropriate closure relations of fluid equations in a case when particle distribution function is not Maxwellian. We try to follow this way to enhance fluid model and to use it in hybrid plasma model further. (paper)

  13. Adaptation and hybridization in computational intelligence

    CERN Document Server

    Jr, Iztok

    2015-01-01

      This carefully edited book takes a walk through recent advances in adaptation and hybridization in the Computational Intelligence (CI) domain. It consists of ten chapters that are divided into three parts. The first part illustrates background information and provides some theoretical foundation tackling the CI domain, the second part deals with the adaptation in CI algorithms, while the third part focuses on the hybridization in CI. This book can serve as an ideal reference for researchers and students of computer science, electrical and civil engineering, economy, and natural sciences that are confronted with solving the optimization, modeling and simulation problems. It covers the recent advances in CI that encompass Nature-inspired algorithms, like Artificial Neural networks, Evolutionary Algorithms and Swarm Intelligence –based algorithms.  

  14. Identification of DNA viruses by membrane filter hybridization.

    OpenAIRE

    Stålhandske, P; Pettersson, U

    1982-01-01

    The use of membrane filter hybridization for the identification of DNA viruses is described. We designed and used a procedure for identification of herpes simplex virus. This method can discriminate between herpes simplex virus types 1 and 2 in a simple way.

  15. Accelerating Climate Simulations Through Hybrid Computing

    Science.gov (United States)

    Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

    2009-01-01

    Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

  16. HTTR plant dynamic simulation using a hybrid computer

    International Nuclear Information System (INIS)

    Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.

    1990-01-01

    A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)

  17. Modelling of data uncertainties on hybrid computers

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Anke (ed.)

    2016-06-15

    The codes d{sup 3}f and r{sup 3}t are well established for modelling density-driven flow and nuclide transport in the far field of repositories for hazardous material in deep geological formations. They are applicable in porous media as well as in fractured rock or mudstone, for modelling salt- and heat transport as well as a free groundwater surface. Development of the basic framework of d{sup 3}f and r{sup 3}t had begun more than 20 years ago. Since that time significant advancements took place in the requirements for safety assessment as well as for computer hardware development. The period of safety assessment for a repository of high-level radioactive waste was extended to 1 million years, and the complexity of the models is steadily growing. Concurrently, the demands on accuracy increase. Additionally, model and parameter uncertainties become more and more important for an increased understanding of prediction reliability. All this leads to a growing demand for computational power that requires a considerable software speed-up. An effective way to achieve this is the use of modern, hybrid computer architectures which requires basically the set-up of new data structures and a corresponding code revision but offers a potential speed-up by several orders of magnitude. The original codes d{sup 3}f and r{sup 3}t were applications of the software platform UG /BAS 94/ whose development had begun in the early nineteennineties. However, UG had recently been advanced to the C++ based, substantially revised version UG4 /VOG 13/. To benefit also in the future from state-of-the-art numerical algorithms and to use hybrid computer architectures, the codes d{sup 3}f and r{sup 3}t were transferred to this new code platform. Making use of the fact that coupling between different sets of equations is natively supported in UG4, d{sup 3}f and r{sup 3}t were combined to one conjoint code d{sup 3}f++. A direct estimation of uncertainties for complex groundwater flow models with the

  18. Computational botany methods for automated species identification

    CERN Document Server

    Remagnino, Paolo; Wilkin, Paul; Cope, James; Kirkup, Don

    2017-01-01

    This book discusses innovative methods for mining information from images of plants, especially leaves, and highlights the diagnostic features that can be implemented in fully automatic systems for identifying plant species. Adopting a multidisciplinary approach, it explores the problem of plant species identification, covering both the concepts of taxonomy and morphology. It then provides an overview of morphometrics, including the historical background and the main steps in the morphometric analysis of leaves together with a number of applications. The core of the book focuses on novel diagnostic methods for plant species identification developed from a computer scientist’s perspective. It then concludes with a chapter on the characterization of botanists' visions, which highlights important cognitive aspects that can be implemented in a computer system to more accurately replicate the human expert’s fixation process. The book not only represents an authoritative guide to advanced computational tools fo...

  19. Computing all hybridization networks for multiple binary phylogenetic input trees.

    Science.gov (United States)

    Albrecht, Benjamin

    2015-07-30

    The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events is the computation of hybridization networks. This work presents the first algorithm computing the hybridization number as well as a set of representative hybridization networks for multiple binary phylogenetic input trees on the same set of taxa. To improve its practical runtime, we show how this algorithm can be parallelized. Moreover, we demonstrate the efficiency of the software Hybroscale, containing an implementation of our algorithm, by comparing it to PIRNv2.0, which is so far the best available software computing the exact hybridization number for multiple binary phylogenetic trees on the same set of taxa. The algorithm is part of the software Hybroscale, which was developed specifically for the investigation of hybridization networks including their computation and visualization. Hybroscale is freely available(1) and runs on all three major operating systems. Our simulation study indicates that our approach is on average 100 times faster than PIRNv2.0. Moreover, we show how Hybroscale improves the interpretation of the reported hybridization networks by adding certain features to its graphical representation.

  20. Microcantilver-based DNA hybridization sensors for Salmonella identification

    Directory of Open Access Journals (Sweden)

    Carlo Ricciardi

    2012-02-01

    Full Text Available The detection of pathogenic microorganisms in foods remains a challenging since the safety of foodstuffs has to be ensured by the food producing companies. Conventional methods for the detection and identification of bacteria mainly rely on specific microbiological and biochemical identification. Biomolecular methods, are commonly used as a support for traditional techniques, thanks to their high sensitivity, specificity and not excessive costs. However, new methods like biosensors for example, can be an exciting alternative to the more traditional tecniques for the detection of pathogens in food. In this study we report Salmonella enterica serotype Enteritidis DNA detection through a novel class of label-free biosensors: microcantilevers (MCs. In general, MCs can operate as a microbalance and is used to detect the mass of the entities anchored to the cantilever surface using the decrease in the resonant frequency. We use DNA hybridization as model reaction system and for this reason, specific single stranded probe DNA of the pathogen and three different DNA targets (single-stranded complementary DNA, PCR product and serial dilutions of DNA extracted from S. Enteritidis strains were applied. Two protocols were reported in order to allow the probe immobilization on cantilever surface: i MC surface was functionalized with 3-aminopropyltriethoxysilane and glutaraldehyde and an amino-modified DNA probe was used; ii gold-coated sensors and thiolated DNA probes were used in order to generate a covalent bonding (Th-Au. For the first one, measures after hybridization with the PCR product showed related frequency shift 10 times higher than hybridization with complementary probe and detectable signals were obtained at the concentrations of 103 and 106 cfu/mL after hybridization with bacterial DNA. There are currently optimizations of the second protocol, where preliminary results have shown to be more uniform and therefore more precise within each of the

  1. Wireless Hybrid Identification and Sensing Platform for Equipment Recovery (WHISPER), Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Systems & Technologies proposed WHISPER (Wireless Hybrid Identification and Sensing Platform for Equipment Recovery) solution to NASA's need for...

  2. Wireless Hybrid Identification and Sensing Platform for Equipment Recovery (WHISPER), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Systems & Technologies proposed WHISPER (Wireless Hybrid Identification and Sensing Platform for Equipment Recovery) solution to NASA's need for...

  3. Concrete Crack Identification Using a UAV Incorporating Hybrid Image Processing.

    Science.gov (United States)

    Kim, Hyunjun; Lee, Junhwa; Ahn, Eunjong; Cho, Soojin; Shin, Myoungsu; Sim, Sung-Han

    2017-09-07

    Crack assessment is an essential process in the maintenance of concrete structures. In general, concrete cracks are inspected by manual visual observation of the surface, which is intrinsically subjective as it depends on the experience of inspectors. Further, it is time-consuming, expensive, and often unsafe when inaccessible structural members are to be assessed. Unmanned aerial vehicle (UAV) technologies combined with digital image processing have recently been applied to crack assessment to overcome the drawbacks of manual visual inspection. However, identification of crack information in terms of width and length has not been fully explored in the UAV-based applications, because of the absence of distance measurement and tailored image processing. This paper presents a crack identification strategy that combines hybrid image processing with UAV technology. Equipped with a camera, an ultrasonic displacement sensor, and a WiFi module, the system provides the image of cracks and the associated working distance from a target structure on demand. The obtained information is subsequently processed by hybrid image binarization to estimate the crack width accurately while minimizing the loss of the crack length information. The proposed system has shown to successfully measure cracks thicker than 0.1 mm with the maximum length estimation error of 7.3%.

  4. Creation of hybrid optoelectronic systems for document identification

    Science.gov (United States)

    Muravsky, Leonid I.; Voronyak, Taras I.; Kulynych, Yaroslav P.; Maksymenko, Olexander P.; Pogan, Ignat Y.

    2001-06-01

    Use of security devices based on a joint transform correlator (JTC) architecture for identification of credit cards and other products is very promising. The experimental demonstration of the random phase encoding technique for security verification shows that hybrid JTCs can be successfully utilized. The random phase encoding technique provides a very high protection level of products and things to be identified. However, the realization of this technique is connected with overcoming of the certain practical problems. To solve some of these problems and simultaneously to improve the security of documents and other products, we propose to use a transformed phase mask (TPM) as an input object in an optical correlator. This mask is synthesized from a random binary pattern (RBP), which is directly used to fabricate a reference phase mask (RPM). To obtain the TPM, we previously separate the RBP on a several parts (for example, K parts) of an arbitrary shape and further fabricate the TPM from this transformed RBP. The fabricated TPM can be bonded as the optical mark to any product or thing to be identified. If the RPM and the TPM are placed on the optical correlator input, the first diffracted order of the output correlation signal is containing the K narrow autocorrelation peaks. The distances between the peaks and the peak's intensities can be treated as the terms of the identification feature vector (FV) for the TPM identification.

  5. Hybrid Monte Carlo methods in computational finance

    NARCIS (Netherlands)

    Leitao Rodriguez, A.

    2017-01-01

    Monte Carlo methods are highly appreciated and intensively employed in computational finance in the context of financial derivatives valuation or risk management. The method offers valuable advantages like flexibility, easy interpretation and straightforward implementation. Furthermore, the

  6. Input/output routines for a hybrid computer

    International Nuclear Information System (INIS)

    Izume, Akitada; Yodo, Terutaka; Sakama, Iwao; Sakamoto, Akira; Miyake, Osamu

    1976-05-01

    This report is concerned with data processing programs for a hybrid computer system. Especially pre-data processing of magnetic tapes which are recorded during the dynamic experiment by FACOM 270/25 data logging system in the 50 MW steam generator test facility is described in detail. The magnetic tape is a most effective recording medium for data logging, but recording formats of the magnetic tape are different between data logging systems. In our section, the final data analyses are performed by data in the disk of EAI-690 hybrid computer system, and to transfer all required information in magnetic tapes to the disk, the magnetic tape editing and data transit are necessary by sub-computer NEAC-3200 system. This report is written for users as a manual and reference hand book of pre-data processing between different type computers. (auth.)

  7. Computer code MLCOSP for multiple-correlation and spectrum analysis with a hybrid computer

    International Nuclear Information System (INIS)

    Oguma, Ritsuo; Fujii, Yoshio; Usui, Hozumi; Watanabe, Koichi

    1975-10-01

    Usage of the computer code MLCOSP(Multiple Correlation and Spectrum) developed is described for a hybrid computer installed in JAERI Functions of the hybrid computer and its terminal devices are utilized ingeniously in the code to reduce complexity of the data handling which occurrs in analysis of the multivariable experimental data and to perform the analysis in perspective. Features of the code are as follows; Experimental data can be fed to the digital computer through the analog part of the hybrid computer by connecting with a data recorder. The computed results are displayed in figures, and hardcopies are taken when necessary. Series-messages to the code are shown on the terminal, so man-machine communication is possible. And further the data can be put in through a keyboard, so case study according to the results of analysis is possible. (auth.)

  8. Computational hybrid anthropometric paediatric phantom library for internal radiation dosimetry

    DEFF Research Database (Denmark)

    Xie, Tianwu; Kuster, Niels; Zaidi, Habib

    2017-01-01

    for children demonstrated that they follow the same trend when correlated with age. The constructed hybrid computational phantom library opens up the prospect of comprehensive radiation dosimetry calculations and risk assessment for the paediatric population of different age groups and diverse anthropometric...

  9. Hybrid computer optimization of systems with random parameters

    Science.gov (United States)

    White, R. C., Jr.

    1972-01-01

    A hybrid computer Monte Carlo technique for the simulation and optimization of systems with random parameters is presented. The method is applied to the simultaneous optimization of the means and variances of two parameters in the radar-homing missile problem treated by McGhee and Levine.

  10. Hybrid parallel computing architecture for multiview phase shifting

    Science.gov (United States)

    Zhong, Kai; Li, Zhongwei; Zhou, Xiaohui; Shi, Yusheng; Wang, Congjun

    2014-11-01

    The multiview phase-shifting method shows its powerful capability in achieving high resolution three-dimensional (3-D) shape measurement. Unfortunately, this ability results in very high computation costs and 3-D computations have to be processed offline. To realize real-time 3-D shape measurement, a hybrid parallel computing architecture is proposed for multiview phase shifting. In this architecture, the central processing unit can co-operate with the graphic processing unit (GPU) to achieve hybrid parallel computing. The high computation cost procedures, including lens distortion rectification, phase computation, correspondence, and 3-D reconstruction, are implemented in GPU, and a three-layer kernel function model is designed to simultaneously realize coarse-grained and fine-grained paralleling computing. Experimental results verify that the developed system can perform 50 fps (frame per second) real-time 3-D measurement with 260 K 3-D points per frame. A speedup of up to 180 times is obtained for the performance of the proposed technique using a NVIDIA GT560Ti graphics card rather than a sequential C in a 3.4 GHZ Inter Core i7 3770.

  11. Accelerating Climate and Weather Simulations through Hybrid Computing

    Science.gov (United States)

    Zhou, Shujia; Cruz, Carlos; Duffy, Daniel; Tucker, Robert; Purcell, Mark

    2011-01-01

    Unconventional multi- and many-core processors (e.g. IBM (R) Cell B.E.(TM) and NVIDIA (R) GPU) have emerged as effective accelerators in trial climate and weather simulations. Yet these climate and weather models typically run on parallel computers with conventional processors (e.g. Intel, AMD, and IBM) using Message Passing Interface. To address challenges involved in efficiently and easily connecting accelerators to parallel computers, we investigated using IBM's Dynamic Application Virtualization (TM) (IBM DAV) software in a prototype hybrid computing system with representative climate and weather model components. The hybrid system comprises two Intel blades and two IBM QS22 Cell B.E. blades, connected with both InfiniBand(R) (IB) and 1-Gigabit Ethernet. The system significantly accelerates a solar radiation model component by offloading compute-intensive calculations to the Cell blades. Systematic tests show that IBM DAV can seamlessly offload compute-intensive calculations from Intel blades to Cell B.E. blades in a scalable, load-balanced manner. However, noticeable communication overhead was observed, mainly due to IP over the IB protocol. Full utilization of IB Sockets Direct Protocol and the lower latency production version of IBM DAV will reduce this overhead.

  12. Identification of rice hybrids using microsatellite and RAPD markers

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-18

    May 18, 2009 ... presence of slower migrating heteroduplex DNA is, there- fore, useful for detection of heterozygous individuals. Maintenance of hybrid seeds conformity in high level is essential for exploitation of hybrid vigor. Therefore, test- ing the hybrid seed purity is necessarily required before its release into the market.

  13. Hybrid soft computing systems for electromyographic signals analysis: a review

    Science.gov (United States)

    2014-01-01

    Electromyographic (EMG) is a bio-signal collected on human skeletal muscle. Analysis of EMG signals has been widely used to detect human movement intent, control various human-machine interfaces, diagnose neuromuscular diseases, and model neuromusculoskeletal system. With the advances of artificial intelligence and soft computing, many sophisticated techniques have been proposed for such purpose. Hybrid soft computing system (HSCS), the integration of these different techniques, aims to further improve the effectiveness, efficiency, and accuracy of EMG analysis. This paper reviews and compares key combinations of neural network, support vector machine, fuzzy logic, evolutionary computing, and swarm intelligence for EMG analysis. Our suggestions on the possible future development of HSCS in EMG analysis are also given in terms of basic soft computing techniques, further combination of these techniques, and their other applications in EMG analysis. PMID:24490979

  14. Hybrid soft computing systems for electromyographic signals analysis: a review.

    Science.gov (United States)

    Xie, Hong-Bo; Guo, Tianruo; Bai, Siwei; Dokos, Socrates

    2014-02-03

    Electromyographic (EMG) is a bio-signal collected on human skeletal muscle. Analysis of EMG signals has been widely used to detect human movement intent, control various human-machine interfaces, diagnose neuromuscular diseases, and model neuromusculoskeletal system. With the advances of artificial intelligence and soft computing, many sophisticated techniques have been proposed for such purpose. Hybrid soft computing system (HSCS), the integration of these different techniques, aims to further improve the effectiveness, efficiency, and accuracy of EMG analysis. This paper reviews and compares key combinations of neural network, support vector machine, fuzzy logic, evolutionary computing, and swarm intelligence for EMG analysis. Our suggestions on the possible future development of HSCS in EMG analysis are also given in terms of basic soft computing techniques, further combination of these techniques, and their other applications in EMG analysis.

  15. Evaluation of a Compact Hybrid Brain-Computer Interface System

    Directory of Open Access Journals (Sweden)

    Jaeyoung Shin

    2017-01-01

    Full Text Available We realized a compact hybrid brain-computer interface (BCI system by integrating a portable near-infrared spectroscopy (NIRS device with an economical electroencephalography (EEG system. The NIRS array was located on the subjects’ forehead, covering the prefrontal area. The EEG electrodes were distributed over the frontal, motor/temporal, and parietal areas. The experimental paradigm involved a Stroop word-picture matching test in combination with mental arithmetic (MA and baseline (BL tasks, in which the subjects were asked to perform either MA or BL in response to congruent or incongruent conditions, respectively. We compared the classification accuracies of each of the modalities (NIRS or EEG with that of the hybrid system. We showed that the hybrid system outperforms the unimodal EEG and NIRS systems by 6.2% and 2.5%, respectively. Since the proposed hybrid system is based on portable platforms, it is not confined to a laboratory environment and has the potential to be used in real-life situations, such as in neurorehabilitation.

  16. On-line identification of hybrid systems using an adaptive growing and pruning RBF neural network

    DEFF Research Database (Denmark)

    Alizadeh, Tohid

    2008-01-01

    This paper introduces an adaptive growing and pruning radial basis function (GAP-RBF) neural network for on-line identification of hybrid systems. The main idea is to identify a global nonlinear model that can predict the continuous outputs of hybrid systems. In the proposed approach, GAP......-RBF neural network uses a modified unscented kalman filter (UKF) with forgetting factor scheme as the required on-line learning algorithm. The effectiveness of the resulting identification approach is tested and evaluated on a simulated benchmark hybrid system....

  17. CSP: A Multifaceted Hybrid Architecture for Space Computing

    Science.gov (United States)

    Rudolph, Dylan; Wilson, Christopher; Stewart, Jacob; Gauvin, Patrick; George, Alan; Lam, Herman; Crum, Gary Alex; Wirthlin, Mike; Wilson, Alex; Stoddard, Aaron

    2014-01-01

    Research on the CHREC Space Processor (CSP) takes a multifaceted hybrid approach to embedded space computing. Working closely with the NASA Goddard SpaceCube team, researchers at the National Science Foundation (NSF) Center for High-Performance Reconfigurable Computing (CHREC) at the University of Florida and Brigham Young University are developing hybrid space computers that feature an innovative combination of three technologies: commercial-off-the-shelf (COTS) devices, radiation-hardened (RadHard) devices, and fault-tolerant computing. Modern COTS processors provide the utmost in performance and energy-efficiency but are susceptible to ionizing radiation in space, whereas RadHard processors are virtually immune to this radiation but are more expensive, larger, less energy-efficient, and generations behind in speed and functionality. By featuring COTS devices to perform the critical data processing, supported by simpler RadHard devices that monitor and manage the COTS devices, and augmented with novel uses of fault-tolerant hardware, software, information, and networking within and between COTS devices, the resulting system can maximize performance and reliability while minimizing energy consumption and cost. NASA Goddard has adopted the CSP concept and technology with plans underway to feature flight-ready CSP boards on two upcoming space missions.

  18. Energy efficient hybrid computing systems using spin devices

    Science.gov (United States)

    Sharad, Mrigank

    Emerging spin-devices like magnetic tunnel junctions (MTJ's), spin-valves and domain wall magnets (DWM) have opened new avenues for spin-based logic design. This work explored potential computing applications which can exploit such devices for higher energy-efficiency and performance. The proposed applications involve hybrid design schemes, where charge-based devices supplement the spin-devices, to gain large benefits at the system level. As an example, lateral spin valves (LSV) involve switching of nanomagnets using spin-polarized current injection through a metallic channel such as Cu. Such spin-torque based devices possess several interesting properties that can be exploited for ultra-low power computation. Analog characteristic of spin current facilitate non-Boolean computation like majority evaluation that can be used to model a neuron. The magneto-metallic neurons can operate at ultra-low terminal voltage of ˜20mV, thereby resulting in small computation power. Moreover, since nano-magnets inherently act as memory elements, these devices can facilitate integration of logic and memory in interesting ways. The spin based neurons can be integrated with CMOS and other emerging devices leading to different classes of neuromorphic/non-Von-Neumann architectures. The spin-based designs involve `mixed-mode' processing and hence can provide very compact and ultra-low energy solutions for complex computation blocks, both digital as well as analog. Such low-power, hybrid designs can be suitable for various data processing applications like cognitive computing, associative memory, and currentmode on-chip global interconnects. Simulation results for these applications based on device-circuit co-simulation framework predict more than ˜100x improvement in computation energy as compared to state of the art CMOS design, for optimal spin-device parameters.

  19. Hybrid epidemics--a case study on computer worm conficker.

    Directory of Open Access Journals (Sweden)

    Changwang Zhang

    Full Text Available Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm's spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm's effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols.

  20. Hybrid epidemics--a case study on computer worm conficker.

    Science.gov (United States)

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M

    2015-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm's spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm's effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols.

  1. Hybrid Epidemics—A Case Study on Computer Worm Conficker

    Science.gov (United States)

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M.

    2015-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm’s spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore the tradeoff between spreading modes in determining the worm’s effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols. PMID:25978309

  2. Autonomic Management of Application Workflows on Hybrid Computing Infrastructure

    Directory of Open Access Journals (Sweden)

    Hyunjoo Kim

    2011-01-01

    Full Text Available In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical as computing infrastructures become increasingly heterogeneous, integrating different classes of resources from high-end HPC systems to commodity clusters and clouds. For example, the framework presented in this paper can be used to provision the appropriate mix of resources based on application requirements and constraints. The framework also monitors the system/application state and adapts the application and/or resources to respond to changing requirements or environment. To demonstrate the operation of the framework and to evaluate its ability, we employ a workflow used to characterize an oil reservoir executing on a hybrid infrastructure composed of TeraGrid nodes and Amazon EC2 instances of various types. Specifically, we show how different applications objectives such as acceleration, conservation and resilience can be effectively achieved while satisfying deadline and budget constraints, using an appropriate mix of dynamically provisioned resources. Our evaluations also demonstrate that public clouds can be used to complement and reinforce the scheduling and usage of traditional high performance computing infrastructure.

  3. Computational hybrid anthropometric paediatric phantom library for internal radiation dosimetry

    Science.gov (United States)

    Xie, Tianwu; Kuster, Niels; Zaidi, Habib

    2017-04-01

    Hybrid computational phantoms combine voxel-based and simplified equation-based modelling approaches to provide unique advantages and more realism for the construction of anthropomorphic models. In this work, a methodology and C++ code are developed to generate hybrid computational phantoms covering statistical distributions of body morphometry in the paediatric population. The paediatric phantoms of the Virtual Population Series (IT’IS Foundation, Switzerland) were modified to match target anthropometric parameters, including body mass, body length, standing height and sitting height/stature ratio, determined from reference databases of the National Centre for Health Statistics and the National Health and Nutrition Examination Survey. The phantoms were selected as representative anchor phantoms for the newborn, 1, 2, 5, 10 and 15 years-old children, and were subsequently remodelled to create 1100 female and male phantoms with 10th, 25th, 50th, 75th and 90th body morphometries. Evaluation was performed qualitatively using 3D visualization and quantitatively by analysing internal organ masses. Overall, the newly generated phantoms appear very reasonable and representative of the main characteristics of the paediatric population at various ages and for different genders, body sizes and sitting stature ratios. The mass of internal organs increases with height and body mass. The comparison of organ masses of the heart, kidney, liver, lung and spleen with published autopsy and ICRP reference data for children demonstrated that they follow the same trend when correlated with age. The constructed hybrid computational phantom library opens up the prospect of comprehensive radiation dosimetry calculations and risk assessment for the paediatric population of different age groups and diverse anthropometric parameters.

  4. OPTHYLIC: An Optimised Tool for Hybrid Limits Computation

    Science.gov (United States)

    Busato, Emmanuel; Calvet, David; Theveneaux-Pelzer, Timothée

    2018-05-01

    A software tool, computing observed and expected upper limits on Poissonian process rates using a hybrid frequentist-Bayesian CLs method, is presented. This tool can be used for simple counting experiments where only signal, background and observed yields are provided or for multi-bin experiments where binned distributions of discriminating variables are provided. It allows the combination of several channels and takes into account statistical and systematic uncertainties, as well as correlations of systematic uncertainties between channels. It has been validated against other software tools and analytical calculations, for several realistic cases.

  5. Identification of pine hybrids using SSR loci.: scientific paper | Doyle ...

    African Journals Online (AJOL)

    We have screened 11 microsatellite markers developed in other Pinus species for their ability to produce fingerprints in the Pinus elliottii x Pinus caribaea hybrid as well as their ability to determine gene flow and parental contribution in this hybrid. We found that cross-species amplification was possible with two thirds of the ...

  6. Computational methods for protein identification from mass spectrometry data.

    Directory of Open Access Journals (Sweden)

    Leo McHugh

    2008-02-01

    Full Text Available Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.

  7. A Review of Hybrid Brain-Computer Interface Systems

    Directory of Open Access Journals (Sweden)

    Setare Amiri

    2013-01-01

    Full Text Available Increasing number of research activities and different types of studies in brain-computer interface (BCI systems show potential in this young research area. Research teams have studied features of different data acquisition techniques, brain activity patterns, feature extraction techniques, methods of classifications, and many other aspects of a BCI system. However, conventional BCIs have not become totally applicable, due to the lack of high accuracy, reliability, low information transfer rate, and user acceptability. A new approach to create a more reliable BCI that takes advantage of each system is to combine two or more BCI systems with different brain activity patterns or different input signal sources. This type of BCI, called hybrid BCI, may reduce disadvantages of each conventional BCI system. In addition, hybrid BCIs may create more applications and possibly increase the accuracy and the information transfer rate. However, the type of BCIs and their combinations should be considered carefully. In this paper, after introducing several types of BCIs and their combinations, we review and discuss hybrid BCIs, different possibilities to combine them, and their advantages and disadvantages.

  8. Computational identification of mutually homologous Zika virus ...

    African Journals Online (AJOL)

    Ewen McLean

    2017-04-07

    Apr 7, 2017 ... of Computer Science & Mathematics, Claflin University, Orangeburg, SC, USA. ABSTRACT. Background .... It is still unclear how and at what time of gestation ZIKV infects fetal brain cells, ..... Soc Interface. 2012;9:2708-2717.

  9. Hybrid cloud and cluster computing paradigms for life science applications.

    Science.gov (United States)

    Qiu, Judy; Ekanayake, Jaliya; Gunarathne, Thilina; Choi, Jong Youl; Bae, Seung-Hee; Li, Hui; Zhang, Bingjing; Wu, Tak-Lon; Ruan, Yang; Ekanayake, Saliya; Hughes, Adam; Fox, Geoffrey

    2010-12-21

    Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas such as data mining because MapReduce has poor performance on problems with an iterative structure present in the linear algebra that underlies much data analysis. Such problems can be run efficiently on clusters using MPI leading to a hybrid cloud and cluster environment. This motivates the design and implementation of an open source Iterative MapReduce system Twister. Comparisons of Amazon, Azure, and traditional Linux and Windows environments on common applications have shown encouraging performance and usability comparisons in several important non iterative cases. These are linked to MPI applications for final stages of the data analysis. Further we have released the open source Twister Iterative MapReduce and benchmarked it against basic MapReduce (Hadoop) and MPI in information retrieval and life sciences applications. The hybrid cloud (MapReduce) and cluster (MPI) approach offers an attractive production environment while Twister promises a uniform programming environment for many Life Sciences applications. We used commercial clouds Amazon and Azure and the NSF resource FutureGrid to perform detailed comparisons and evaluations of different approaches to data intensive computing. Several applications were developed in MPI, MapReduce and Twister in these different environments.

  10. Genetic identification of F1 and post-F1 serrasalmid juvenile hybrids in Brazilian aquaculture.

    Directory of Open Access Journals (Sweden)

    Diogo Teruo Hashimoto

    Full Text Available Juvenile fish trade monitoring is an important task on Brazilian fish farms. However, the identification of juvenile fish through morphological analysis is not feasible, particularly between interspecific hybrids and pure species individuals, making the monitoring of these individuals difficult. Hybrids can be erroneously identified as pure species in breeding facilities, which might reduce production on farms and negatively affect native populations due to escapes or stocking practices. In the present study, we used a multi-approach analysis (molecular and cytogenetic markers to identify juveniles of three serrasalmid species (Colossoma macropomum, Piaractus mesopotamicus and Piaractus brachypomus and their hybrids in different stocks purchased from three seed producers in Brazil. The main findings of this study were the detection of intergenus backcrossing between the hybrid ♀ patinga (P. mesopotamicus×P. brachypomus×♂ C. macropomum and the occurrence of one hybrid triploid individual. This atypical specimen might result from automixis, a mechanism that produces unreduced gametes in some organisms. Moreover, molecular identification indicated that hybrid individuals are traded as pure species or other types of interspecific hybrids, particularly post-F1 individuals. These results show that serrasalmid fish genomes exhibit high genetic heterogeneity, and multi-approach methods and regulators could improve the surveillance of the production and trade of fish species and their hybrids, thereby facilitating the sustainable development of fish farming.

  11. Identification of chaotic systems by neural network with hybrid learning algorithm

    International Nuclear Information System (INIS)

    Pan, S.-T.; Lai, C.-C.

    2008-01-01

    Based on the genetic algorithm (GA) and steepest descent method (SDM), this paper proposes a hybrid algorithm for the learning of neural networks to identify chaotic systems. The systems in question are the logistic map and the Duffing equation. Different identification schemes are used to identify both the logistic map and the Duffing equation, respectively. Simulation results show that our hybrid algorithm is more efficient than that of other methods

  12. Identification of hybrid node and link communities in complex networks.

    Science.gov (United States)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-02

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  13. Identification of hybrid node and link communities in complex networks

    Science.gov (United States)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  14. Maze learning by a hybrid brain-computer system.

    Science.gov (United States)

    Wu, Zhaohui; Zheng, Nenggan; Zhang, Shaowu; Zheng, Xiaoxiang; Gao, Liqiang; Su, Lijuan

    2016-09-13

    The combination of biological and artificial intelligence is particularly driven by two major strands of research: one involves the control of mechanical, usually prosthetic, devices by conscious biological subjects, whereas the other involves the control of animal behaviour by stimulating nervous systems electrically or optically. However, to our knowledge, no study has demonstrated that spatial learning in a computer-based system can affect the learning and decision making behaviour of the biological component, namely a rat, when these two types of intelligence are wired together to form a new intelligent entity. Here, we show how rule operations conducted by computing components contribute to a novel hybrid brain-computer system, i.e., ratbots, exhibit superior learning abilities in a maze learning task, even when their vision and whisker sensation were blocked. We anticipate that our study will encourage other researchers to investigate combinations of various rule operations and other artificial intelligence algorithms with the learning and memory processes of organic brains to develop more powerful cyborg intelligence systems. Our results potentially have profound implications for a variety of applications in intelligent systems and neural rehabilitation.

  15. Maze learning by a hybrid brain-computer system

    Science.gov (United States)

    Wu, Zhaohui; Zheng, Nenggan; Zhang, Shaowu; Zheng, Xiaoxiang; Gao, Liqiang; Su, Lijuan

    2016-09-01

    The combination of biological and artificial intelligence is particularly driven by two major strands of research: one involves the control of mechanical, usually prosthetic, devices by conscious biological subjects, whereas the other involves the control of animal behaviour by stimulating nervous systems electrically or optically. However, to our knowledge, no study has demonstrated that spatial learning in a computer-based system can affect the learning and decision making behaviour of the biological component, namely a rat, when these two types of intelligence are wired together to form a new intelligent entity. Here, we show how rule operations conducted by computing components contribute to a novel hybrid brain-computer system, i.e., ratbots, exhibit superior learning abilities in a maze learning task, even when their vision and whisker sensation were blocked. We anticipate that our study will encourage other researchers to investigate combinations of various rule operations and other artificial intelligence algorithms with the learning and memory processes of organic brains to develop more powerful cyborg intelligence systems. Our results potentially have profound implications for a variety of applications in intelligent systems and neural rehabilitation.

  16. Genetic Identification of Hyalodaphnia Species and Interspecific Hybrids

    NARCIS (Netherlands)

    Billiones, R.; Brehm, G.M.; Klee, J.; Schwenk, K.

    2004-01-01

    Species of the genus Daphnia, in particular the subgenus Hyalodaphnia, represent a taxonomically problematic group due to their phenotypic plasticity, local races and the formation of interspecific hybrids and backcrosses. In this study, we present a genetic approach utilising nuclear DNA to

  17. Three-dimensional pseudo-random number generator for implementing in hybrid computer systems

    International Nuclear Information System (INIS)

    Ivanov, M.A.; Vasil'ev, N.P.; Voronin, A.V.; Kravtsov, M.Yu.; Maksutov, A.A.; Spiridonov, A.A.; Khudyakova, V.I.; Chugunkov, I.V.

    2012-01-01

    The algorithm for generating pseudo-random numbers oriented to implementation by using hybrid computer systems is considered. The proposed solution is characterized by a high degree of parallel computing [ru

  18. A hybrid computer simulation of reactor spatial dynamics

    International Nuclear Information System (INIS)

    Hinds, H.W.

    1977-08-01

    The partial differential equations describing the one-speed spatial dynamics of thermal neutron reactors were converted to a set of ordinary differential equations, using finite-difference approximations for the spatial derivatives. The variables were then normalized to a steady-state reference condition in a novel manner, to yield an equation set particularly suitable for implementation on a hybrid computer. One Applied Dynamics AD/FIVE analog-computer console is capable of solving, all in parallel, up to 30 simultaneous differential equations. This corresponds roughly to eight reactor nodes, each with two active delayed-neutron groups. To improve accuracy, an increase in the number of nodes is usually required. Using the Hsu-Howe multiplexing technique, an 8-node, one-dimensional module was switched back and forth between the left and right halves of the reactor, to simulate a 16-node model, also in one dimension. These two versions (8 or 16 nodes) of the model were tested on benchmark problems of the loss-of-coolant type, which were also solved using the digital code FORSIM, with two energy groups and 26 nodes. Good agreement was obtained between the two solution techniques. (author)

  19. Chromosome identification by new molecular markers and genomic in situ hybridization in the Triticum-Secale-Thinopyrum trigeneric hybrids.

    Science.gov (United States)

    Dai, Yi; Duan, Yamei; Chi, Dawn; Liu, Huiping; Huang, Shuai; Cao, Wenguang; Gao, Yong; Fedak, George; Chen, Jianmin

    2017-08-01

    It is very important to use chromosome-specific markers for identifying alien chromosomes in advanced generations of distant hybridization. The chromosome-specific markers of rye and Thinopyrum elongatum, as well as genomic in situ hybridization, were used to identify the alien chromosomes in eight lines that were derived from the crossing between Triticum trititrigia (AABBEE) and triticale (AABBRR). The results showed that four lines contained all rye chromosomes but no Th. elongatum chromosomes. The line RE36-1 contained all of the rye chromosomes except for chromosome 2R. The lines RE33-2 and RE62-1 contained all rye chromosomes and 1E and 5E translocated chromosome, respectively. The line RE24-4 contained 12 rye chromosomes plus a 7E chromosome or 12 rye chromosomes plus one R-E translocated chromosome. Chromosome identification in the above lines was consistent using chromosome-specific markers and genomic in situ hybridization. These chromosome-specific markers provide useful tools for detecting alien chromosomes in trigeneric hybrids, and these lines could be utilized as valuable germplasm in wheat improvement.

  20. A hybrid fingerprint identification system for immigration control ...

    African Journals Online (AJOL)

    Journal of Computer Science and Its Application. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 21, No 2 (2014) >. Log in or Register to get access to full text downloads.

  1. Molecular identification of hybrids from a former hot spot of Potamogeton hybrid diversity

    Czech Academy of Sciences Publication Activity Database

    Kaplan, Zdeněk; Fehrer, Judith

    2013-01-01

    Roč. 105, Feb 2013 (2013), s. 34-40 ISSN 0304-3770 R&D Projects: GA ČR GA206/09/0291 Institutional support: RVO:67985939 Keywords : hybridization * taxonomy * diversity Subject RIV: EF - Botanics Impact factor: 1.471, year: 2013

  2. Computational analysis on plug-in hybrid electric motorcycle chassis

    Science.gov (United States)

    Teoh, S. J.; Bakar, R. A.; Gan, L. M.

    2013-12-01

    Plug-in hybrid electric motorcycle (PHEM) is an alternative to promote sustainability lower emissions. However, the PHEM overall system packaging is constrained by limited space in a motorcycle chassis. In this paper, a chassis applying the concept of a Chopper is analysed to apply in PHEM. The chassis 3dimensional (3D) modelling is built with CAD software. The PHEM power-train components and drive-train mechanisms are intergraded into the 3D modelling to ensure the chassis provides sufficient space. Besides that, a human dummy model is built into the 3D modelling to ensure the rider?s ergonomics and comfort. The chassis 3D model then undergoes stress-strain simulation. The simulation predicts the stress distribution, displacement and factor of safety (FOS). The data are used to identify the critical point, thus suggesting the chassis design is applicable or need to redesign/ modify to meet the require strength. Critical points mean highest stress which might cause the chassis to fail. This point occurs at the joints at triple tree and bracket rear absorber for a motorcycle chassis. As a conclusion, computational analysis predicts the stress distribution and guideline to develop a safe prototype chassis.

  3. Carbon nanotube reinforced hybrid composites: Computational modeling of environmental fatigue and usability for wind blades

    DEFF Research Database (Denmark)

    Dai, Gaoming; Mishnaevsky, Leon

    2015-01-01

    The potential of advanced carbon/glass hybrid reinforced composites with secondary carbon nanotube reinforcement for wind energy applications is investigated here with the use of computational experiments. Fatigue behavior of hybrid as well as glass and carbon fiber reinforced composites...... with the secondary CNT reinforcements (especially, aligned tubes) present superior fatigue performances than those without reinforcements, also under combined environmental and cyclic mechanical loading. This effect is stronger for carbon composites, than for hybrid and glass composites....

  4. Identification of W chromosomes in Lepidoptera by comparative genome hybridization

    Czech Academy of Sciences Publication Activity Database

    Sahara, K.; Marec, František; Traut, W.

    1998-01-01

    Roč. 98, č. 6 (1998), s. 20 [International Symposium on Genomics and Proteomics - Functional and Computational Aspects and Annual Meeting of the GfG. 04.10.1998-07.10.1998, Heidelberg] Keywords : Galleria mellonella * DNA Subject RIV: EB - Genetics ; Molecular Biology

  5. Parameters identification and adaptive full state hybrid projective synchronization of chaotic (hyper-chaotic) systems

    International Nuclear Information System (INIS)

    Hu Manfeng; Xu Zhenyuan; Zhang Rong; Hu Aihua

    2007-01-01

    Based on the active control idea and the invariance principle of differential equations, a general scheme of adaptive full state hybrid projective synchronization (FSHPS) and parameters identification of a class of chaotic (hyper-chaotic) systems with linearly dependent uncertain parameters is proposed in this Letter. With this effective scheme parameters identification and FSHPS of chaotic and hyper-chaotic systems can be realized simultaneously. Numerical simulations on the chaotic Chen system and the hyper-chaotic Chen system are presented to verify the effectiveness of the proposed scheme

  6. Identification of formaldehyde-responsive genes by suppression subtractive hybridization

    International Nuclear Information System (INIS)

    Lee, Min-Ho; Kim, Young-Ae; Na, Tae-Young; Kim, Sung-Hye; Shin, Young Kee; Lee, Byung-Hoon; Shin, Ho-Sang; Lee, Mi-Ock

    2008-01-01

    Formaldehyde is frequently used in indoor household and occupational environments. Inhalation of formaldehyde invokes an inflammatory response, including a variety of allergic signs and symptoms. Therefore, formaldehyde has been considered as the most prevalent cause of sick building syndrome, which has become a major social problem, especially in developing urban areas. Further formaldehyde is classified as a genotoxicant in the respiratory tract of rats and humans. To better understand the molecular mechanisms involved in formaldehyde intoxication, we sought differentially regulated genes by formaldehyde exposure to Hs 680.Tr human trachea cells, using polymerase chain reaction (PCR)-based suppression subtractive hybridization. We identified 27 different formaldehyde-inducible genes, including those coding for the major histocompatibility complex, class IA, calcyclin, glutathione S-transferase pi, mouse double minute 2 (MDM2), platelet-derived growth factor receptor alpha, and which are known to be associated with cell proliferation and differentiation, immunity and inflammation, and detoxification. Induction of these genes by formaldehyde treatment was confirmed by reverse transcription PCR and western blot analysis. Further, the expression of calcyclin, glutathione S-transferase pi, PDGFRA and MDM2 were significantly induced in the tracheal epithelium of Sprague Dawley rats after formaldehyde inhalation. Our results suggest that the elevated levels of these genes may be associated with the formaldehyde-induced toxicity, and that they deserve evaluation as potential biomarkers for formaldehyde intoxication

  7. A hybrid approach to parameter identification of linear delay differential equations involving multiple delays

    Science.gov (United States)

    Marzban, Hamid Reza

    2018-05-01

    In this paper, we are concerned with the parameter identification of linear time-invariant systems containing multiple delays. The approach is based upon a hybrid of block-pulse functions and Legendre's polynomials. The convergence of the proposed procedure is established and an upper error bound with respect to the L2-norm associated with the hybrid functions is derived. The problem under consideration is first transformed into a system of algebraic equations. The least squares technique is then employed for identification of the desired parameters. Several multi-delay systems of varying complexity are investigated to evaluate the performance and capability of the proposed approximation method. It is shown that the proposed approach is also applicable to a class of nonlinear multi-delay systems. It is demonstrated that the suggested procedure provides accurate results for the desired parameters.

  8. Deterministic linear-optics quantum computing based on a hybrid approach

    International Nuclear Information System (INIS)

    Lee, Seung-Woo; Jeong, Hyunseok

    2014-01-01

    We suggest a scheme for all-optical quantum computation using hybrid qubits. It enables one to efficiently perform universal linear-optical gate operations in a simple and near-deterministic way using hybrid entanglement as off-line resources

  9. Deterministic linear-optics quantum computing based on a hybrid approach

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung-Woo; Jeong, Hyunseok [Center for Macroscopic Quantum Control, Department of Physics and Astronomy, Seoul National University, Seoul, 151-742 (Korea, Republic of)

    2014-12-04

    We suggest a scheme for all-optical quantum computation using hybrid qubits. It enables one to efficiently perform universal linear-optical gate operations in a simple and near-deterministic way using hybrid entanglement as off-line resources.

  10. Heart dosimetry in radiotherapy with hybrid computational phantoms

    International Nuclear Information System (INIS)

    Moignier, Cyril

    2014-01-01

    Cardiovascular diseases following radiotherapy are major secondary late effects raising questions among the scientific community, especially regarding the dose-effect relationship and confounding risk factors (chemotherapy, cholesterolemia, age at treatment, blood pressure,..). Post-radiation coronary diseases are one of the main causes of cardiac morbidity. Some approximations are made when coronary doses due to radiotherapy are estimated, especially regarding the morphology. For retrospective studies with old medical records, only radiographs are usually available with sometimes some contours made with a simulator. For recent medical records, CT scans displaying the anatomy in 3D are used for radiotherapy simulation but do not allow the coronary artery visualization due to low resolution and contrast. Currently, coronary doses are barely assessed in clinical practice, and when it is done, anatomical prior knowledge is generally used. This thesis proposes an original approach based on hybrid computational phantoms to study coronary artery doses following radiotherapy for left-side breast cancer and Hodgkin lymphoma. During the thesis, a method inserting hybrid computational phantoms in a DICOM format into the treatment planning system has been developed and validated. It has been adapted and tested in conditions where only radiographs provide anatomical information, as with old medical records for left side breast radiotherapy. The method has also been adapted to perform precise dose reconstructions to the coronary artery for patients treated for a mediastinal Hodgkin lymphoma and diagnosed with coronary stenosis through a coroscanner. A case-control study was carried out and the risk of coronary stenosis on a coronary artery segment was assessed to be multiplied by 1.049 at each additional gray on the median dose to the coronary artery segment. For recent medical records, coronary doses uncertainties related to an approach by anatomical prior knowledge

  11. Cardiovascular dosimetry using hybrid computational phantoms after external radiotherapy

    International Nuclear Information System (INIS)

    Moignier, Alexandra

    2014-01-01

    Cardiovascular diseases following radiotherapy are major secondary late effects raising questions among the scientific community, especially regarding the dose-effect relationship and confounding risk factors (chemotherapy, cholesterolemia, age at treatment, blood pressure,..). Post-radiation coronary diseases are one of the main causes of cardiac morbidity. Some approximations are made when coronary doses due to radiotherapy are estimated, especially regarding the morphology. For retrospective studies with old medical records, only radiographs are usually available with sometimes some contours made with a simulator. For recent medical records, CT scans displaying the anatomy in 3D are used for radiotherapy simulation but do not allow the coronary artery visualization due to low resolution and contrast. Currently, coronary doses are barely assessed in clinical practice, and when it is done, anatomical prior knowledge is generally used. This thesis proposes an original approach based on hybrid computational phantoms to study coronary artery doses following radiotherapy for left-side breast cancer and Hodgkin lymphoma. During the thesis, a method inserting hybrid computational phantoms in a DICOM format into the treatment planning system has been developed and validated. It has been adapted and tested in conditions where only radiographs provide anatomical information, as with old medical records for left side breast radiotherapy. The method has also been adapted to perform precise dose reconstructions to the coronary artery for patients treated for a mediastinal Hodgkin lymphoma and diagnosed with coronary stenosis through a coro-scanner. A case-control study was carried out and the risk of coronary stenosis on a coronary artery segment was assessed to be multiplied by 1.049 at each additional gray on the median dose to the coronary artery segment. For recent medical records, coronary doses uncertainties related to an approach by anatomical prior knowledge

  12. Hybrid Computational Model for High-Altitude Aeroassist Vehicles, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — A hybrid continuum/noncontinuum computational model will be developed for analyzing the aerodynamics and heating on aeroassist vehicles. Unique features of this...

  13. Hybrid NN/SVM Computational System for Optimizing Designs

    Science.gov (United States)

    Rai, Man Mohan

    2009-01-01

    A computational method and system based on a hybrid of an artificial neural network (NN) and a support vector machine (SVM) (see figure) has been conceived as a means of maximizing or minimizing an objective function, optionally subject to one or more constraints. Such maximization or minimization could be performed, for example, to optimize solve a data-regression or data-classification problem or to optimize a design associated with a response function. A response function can be considered as a subset of a response surface, which is a surface in a vector space of design and performance parameters. A typical example of a design problem that the method and system can be used to solve is that of an airfoil, for which a response function could be the spatial distribution of pressure over the airfoil. In this example, the response surface would describe the pressure distribution as a function of the operating conditions and the geometric parameters of the airfoil. The use of NNs to analyze physical objects in order to optimize their responses under specified physical conditions is well known. NN analysis is suitable for multidimensional interpolation of data that lack structure and enables the representation and optimization of a succession of numerical solutions of increasing complexity or increasing fidelity to the real world. NN analysis is especially useful in helping to satisfy multiple design objectives. Feedforward NNs can be used to make estimates based on nonlinear mathematical models. One difficulty associated with use of a feedforward NN arises from the need for nonlinear optimization to determine connection weights among input, intermediate, and output variables. It can be very expensive to train an NN in cases in which it is necessary to model large amounts of information. Less widely known (in comparison with NNs) are support vector machines (SVMs), which were originally applied in statistical learning theory. In terms that are necessarily

  14. Developing a personal computer based expert system for radionuclide identification

    International Nuclear Information System (INIS)

    Aarnio, P.A.; Hakulinen, T.T.

    1990-01-01

    Several expert system development tools are available for personal computers today. We have used one of the LISP-based high end tools for nearly two years in developing an expert system for identification of gamma sources. The system contains a radionuclide database of 2055 nuclides and 48000 gamma transitions with a knowledge base of about sixty rules. This application combines a LISP-based inference engine with database management and relatively heavy numerical calculations performed using C-language. The most important feature needed has been the possibility to use LISP and C together with the more advanced object oriented features of the development tool. Main difficulties have been long response times and the big amount (10-16 MB) of computer memory required

  15. A case of dual ectopy thyroid along the thyroglossal tract demonstrated on 99mTc-Pertechnatate hybrid single photon emission computed tomography/computed tomography

    International Nuclear Information System (INIS)

    Agarwal, Krishan Kant; Karunanithi, Sellam; Jain, Sachin; Tripathi, Madhavi

    2014-01-01

    Ectopic thyroid tissue (ETT) refers to the presence of thyroid tissue in locations other than the normal anterior neck region between the second and fourth tracheal cartilages. Multiple ectopia of the thyroid is extremely rare. Here we report a case of 10-year-old girl with anterior midline neck swelling and hypothyroidism with dual ectopia of thyroid gland without orthotopic thyroid gland. Planar 99 m-technetium pertechnatate scan identified ETT corresponding to the palpable neck swelling. Single photon emission computed tomography/computed tomography (SPECT/CT) demonstrated ETT in two locations, one corresponding to the palpable mass and another in the in the sublingual location. This case thus demonstrates the important role of hybrid SPECT/CT in the identification of dual ectopia along the thyroglossal tract

  16. A Hybrid Computational Intelligence Approach Combining Genetic Programming And Heuristic Classification for Pap-Smear Diagnosis

    DEFF Research Database (Denmark)

    Tsakonas, Athanasios; Dounias, Georgios; Jantzen, Jan

    2001-01-01

    The paper suggests the combined use of different computational intelligence (CI) techniques in a hybrid scheme, as an effective approach to medical diagnosis. Getting to know the advantages and disadvantages of each computational intelligence technique in the recent years, the time has come...

  17. MSM, an Efficient Workflow for Metabolite Identification Using Hybrid Linear Ion Trap Orbitrap Mass Spectrometer

    Science.gov (United States)

    Cho, Robert; Huang, Yingying; Schwartz, Jae C.; Chen, Yan; Carlson, Timothy J.; Ma, Ji

    2012-05-01

    Identification of drug metabolites can often yield important information regarding clearance mechanism, pharmacologic activity, or toxicity for drug candidate molecules. Additionally, the identification of metabolites can provide beneficial structure-activity insight to help guide lead optimization efforts towards molecules with optimal metabolic profiles. There are challenges associated with detecting and identifying metabolites in the presence of complex biological matrices, and new LC-MS technologies have been developed to meet these challenges. In this report, we describe the development of an experimental approach that applies unique features of the hybrid linear ion trap Orbitrap mass spectrometer to streamline in vitro and in vivo metabolite identification experiments. The approach, referred to as MSM, utilizes multiple collision cells, dissociation methods, mass analyzers, and detectors. With multiple scan types and different dissociation modes built into one experimental method, along with flexible post-acquisition analysis options, the MSM workflow offers an attractive option to fast and reliable identification of metabolites in different kinds of in vitro and in vivo samples. The MSM workflow was successfully applied to metabolite identification analysis of verapamil in both in vitro rat hepatocyte incubations and in vivo rat bile samples.

  18. 48 CFR 227.7203-10 - Contractor identification and marking of computer software or computer software documentation to...

    Science.gov (United States)

    2010-10-01

    ... operation of the software to display a restrictive rights legend or other license notice; and (2) Requires a... and marking of computer software or computer software documentation to be furnished with restrictive... Rights in Computer Software and Computer Software Documentation 227.7203-10 Contractor identification and...

  19. Phoneme-based speech segmentation using hybrid soft computing framework

    CERN Document Server

    Sarma, Mousmita

    2014-01-01

    The book discusses intelligent system design using soft computing and similar systems and their interdisciplinary applications. It also focuses on the recent trends to use soft computing as a versatile tool for designing a host of decision support systems.

  20. Identification of Enhancers In Human: Advances In Computational Studies

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2016-03-24

    Roughly ~50% of the human genome, contains noncoding sequences serving as regulatory elements responsible for the diverse gene expression of the cells in the body. One very well studied category of regulatory elements is the category of enhancers. Enhancers increase the transcriptional output in cells through chromatin remodeling or recruitment of complexes of binding proteins. Identification of enhancer using computational techniques is an interesting area of research and up to now several approaches have been proposed. However, the current state-of-the-art methods face limitations since the function of enhancers is clarified, but their mechanism of function is not well understood. This PhD thesis presents a bioinformatics/computer science study that focuses on the problem of identifying enhancers in different human cells using computational techniques. The dissertation is decomposed into four main tasks that we present in different chapters. First, since many of the enhancer’s functions are not well understood, we study the basic biological models by which enhancers trigger transcriptional functions and we survey comprehensively over 30 bioinformatics approaches for identifying enhancers. Next, we elaborate more on the availability of enhancer data as produced by different enhancer identification methods and experimental procedures. In particular, we analyze advantages and disadvantages of existing solutions and we report obstacles that require further consideration. To mitigate these problems we developed the Database of Integrated Human Enhancers (DENdb), a centralized online repository that archives enhancer data from 16 ENCODE cell-lines. The integrated enhancer data are also combined with many other experimental data that can be used to interpret the enhancers content and generate a novel enhancer annotation that complements the existing integrative annotation proposed by the ENCODE consortium. Next, we propose the first deep-learning computational

  1. Reducing the Digital Divide among Children Who Received Desktop or Hybrid Computers for the Home

    Directory of Open Access Journals (Sweden)

    Gila Cohen Zilka

    2016-06-01

    Full Text Available Researchers and policy makers have been exploring ways to reduce the digital divide. Parameters commonly used to examine the digital divide worldwide, as well as in this study, are: (a the digital divide in the accessibility and mobility of the ICT infrastructure and of the content infrastructure (e.g., sites used in school; and (b the digital divide in literacy skills. In the present study we examined the degree of effectiveness of receiving a desktop or hybrid computer for the home in reducing the digital divide among children of low socio-economic status aged 8-12 from various localities across Israel. The sample consisted of 1,248 respondents assessed in two measurements. As part of the mixed-method study, 128 children were also interviewed. Findings indicate that after the children received desktop or hybrid computers, changes occurred in their frequency of access, mobility, and computer literacy. Differences were found between the groups: hybrid computers reduce disparities and promote work with the computer and surfing the Internet more than do desktop computers. Narrowing the digital divide for this age group has many implications for the acquisition of skills and study habits, and consequently, for the realization of individual potential. The children spoke about self improvement as a result of exposure to the digital environment, about a sense of empowerment and of improvement in their advantage in the social fabric. Many children expressed a desire to continue their education and expand their knowledge of computer applications, the use of software, of games, and more. Therefore, if there is no computer in the home and it is necessary to decide between a desktop and a hybrid computer, a hybrid computer is preferable.

  2. Hybrid Computational Simulation and Study of Terahertz Pulsed Photoconductive Antennas

    Science.gov (United States)

    Emadi, R.; Barani, N.; Safian, R.; Nezhad, A. Zeidaabadi

    2016-11-01

    A photoconductive antenna (PCA) has been numerically investigated in the terahertz (THz) frequency band based on a hybrid simulation method. This hybrid method utilizes an optoelectronic solver, Silvaco TCAD, and a full-wave electromagnetic solver, CST. The optoelectronic solver is used to find the accurate THz photocurrent by considering realistic material parameters. Performance of photoconductive antennas and temporal behavior of the excited photocurrent for various active region geometries such as bare-gap electrode, interdigitated electrodes, and tip-to-tip rectangular electrodes are investigated. Moreover, investigations have been done on the center of the laser illumination on the substrate, substrate carrier lifetime, and diffusion photocurrent associated with the carriers temperature, to achieve efficient and accurate photocurrent. Finally, using the full-wave electromagnetic solver and the calculated photocurrent obtained from the optoelectronic solver, electromagnetic radiation of the antenna and its associated detected THz signal are calculated and compared with a measurement reference for verification.

  3. A computational model for lower hybrid current drive

    International Nuclear Information System (INIS)

    Englade, R.C.; Bonoli, P.T.; Porkolab, M.

    1983-01-01

    A detailed simulation model for lower hybrid (LH) current drive in toroidal devices is discussed. This model accounts reasonably well for the magnitude of radio frequency (RF) current observed in the PLT and Alcator C devices. It also reproduces the experimental dependencies of RF current generation on toroidal magnetic field and has provided insights about mechanisms which may underlie the observed density limit of current drive. (author)

  4. Energy Management Strategy for Hybrid Electric Vehicle Based on Driving Condition Identification Using KGA-Means

    Directory of Open Access Journals (Sweden)

    Shuxian Li

    2018-06-01

    Full Text Available In order to solve the problem related to adaptive energy management strategies based on driving condition identification being difficult to be applied to a real hybrid electric vehicle (HEV controller, this paper proposes an energy management strategy by combining the driving condition identification algorithm based on genetic optimized K-means clustering algorithm (KGA-means, and the equivalent consumption minimization strategy (ECMS. The simulation results show that compared with ECMS, the energy management strategy proposed in this article drives the engine working point closer to the best efficiency curve, and smooths out the state of charge (SOC change and better maintains the SOC in a highly efficient area. As a result, the vehicle fuel consumption reduces by 6.84%.

  5. Identification of double-yolked duck egg using computer vision.

    Directory of Open Access Journals (Sweden)

    Long Ma

    Full Text Available The double-yolked (DY egg is quite popular in some Asian countries because it is considered as a sign of good luck, however, the double yolk is one of the reasons why these eggs fail to hatch. The usage of automatic methods for identifying DY eggs can increase the efficiency in the poultry industry by decreasing egg loss during incubation or improving sale proceeds. In this study, two methods for DY duck egg identification were developed by using computer vision technology. Transmittance images of DY and single-yolked (SY duck eggs were acquired by a CCD camera to identify them according to their shape features. The Fisher's linear discriminant (FLD model equipped with a set of normalized Fourier descriptors (NFDs extracted from the acquired images and the convolutional neural network (CNN model using primary preprocessed images were built to recognize duck egg yolk types. The classification accuracies of the FLD model for SY and DY eggs were 100% and 93.2% respectively, while the classification accuracies of the CNN model for SY and DY eggs were 98% and 98.8% respectively. The CNN-based algorithm took about 0.12 s to recognize one sample image, which was slightly faster than the FLD-based (about 0.20 s. Finally, this work compared two classification methods and provided the better method for DY egg identification.

  6. Achieving a hybrid brain-computer interface with tactile selective attention and motor imagery

    Science.gov (United States)

    Ahn, Sangtae; Ahn, Minkyu; Cho, Hohyun; Jun, Sung Chan

    2014-12-01

    Objective. We propose a new hybrid brain-computer interface (BCI) system that integrates two different EEG tasks: tactile selective attention (TSA) using a vibro-tactile stimulator on the left/right finger and motor imagery (MI) of left/right hand movement. Event-related desynchronization (ERD) from the MI task and steady-state somatosensory evoked potential (SSSEP) from the TSA task are retrieved and combined into two hybrid senses. Approach. One hybrid approach is to measure two tasks simultaneously; the features of each task are combined for testing. Another hybrid approach is to measure two tasks consecutively (TSA first and MI next) using only MI features. For comparison with the hybrid approaches, the TSA and MI tasks are measured independently. Main results. Using a total of 16 subject datasets, we analyzed the BCI classification performance for MI, TSA and two hybrid approaches in a comparative manner; we found that the consecutive hybrid approach outperformed the others, yielding about a 10% improvement in classification accuracy relative to MI alone. It is understood that TSA may play a crucial role as a prestimulus in that it helps to generate earlier ERD prior to MI and thus sustains ERD longer and to a stronger degree; this ERD may give more discriminative information than ERD in MI alone. Significance. Overall, our proposed consecutive hybrid approach is very promising for the development of advanced BCI systems.

  7. A Hybrid Scheduler for Many Task Computing in Big Data Systems

    Directory of Open Access Journals (Sweden)

    Vasiliu Laura

    2017-06-01

    Full Text Available With the rapid evolution of the distributed computing world in the last few years, the amount of data created and processed has fast increased to petabytes or even exabytes scale. Such huge data sets need data-intensive computing applications and impose performance requirements to the infrastructures that support them, such as high scalability, storage, fault tolerance but also efficient scheduling algorithms. This paper focuses on providing a hybrid scheduling algorithm for many task computing that addresses big data environments with few penalties, taking into consideration the deadlines and satisfying a data dependent task model. The hybrid solution consists of several heuristics and algorithms (min-min, min-max and earliest deadline first combined in order to provide a scheduling algorithm that matches our problem. The experimental results are conducted by simulation and prove that the proposed hybrid algorithm behaves very well in terms of meeting deadlines.

  8. Identification of Cannabis sativa L. using the 1-kbTHCA synthase-fluorescence in situ hybridization probe.

    Science.gov (United States)

    Jeangkhwoa, Pattraporn; Bandhaya, Achirapa; Umpunjun, Puangpaka; Chuenboonngarm, Ngarmnij; Panvisavas, Nathinee

    2017-03-01

    This study reports a successful application of fluorescence in situ hybridization (FISH) technique in the identification of Cannabis sativa L. cells recovered from fresh and dried powdered plant materials. Two biotin-16-dUTP-labeled FISH probes were designed from the Cannabis-specific tetrahydrocannabinolic acid synthase (THCAS) gene and the ITS region of the 45S rRNA gene. Specificity of probe-target hybridization was tested against the target and 4 non-target plant species, i.e., Humulus lupulus, Mitragyna speciosa, Papaver sp., and Nicotiana tabacum. The 1-kb THCA synthase hybridization probe gave Cannabis-specific hybridization signals, unlike the 700-bp Cannabis-ITS hybridization probe. Probe-target hybridization was also confirmed against 20 individual Cannabis plant samples. The 1-kb THCA synthase and 700-bp Cannabis-ITS hybridization probes clearly showed 2 hybridization signals per cell with reproducibility. The 1-kb THCA synthase probe did not give any FISH signal when tested against H. lupulus, its closely related member of the Canabaceae family. It was also showed that 1-kb THCA synthase FISH probe can be applied to identify small amount of dried powdered Cannabis material with an addition of rehydration step prior to the experimental process. This study provided an alternative identification method for Cannabis trace. Copyright © 2016. Published by Elsevier B.V.

  9. Parameter identification of PEMFC model based on hybrid adaptive differential evolution algorithm

    International Nuclear Information System (INIS)

    Sun, Zhe; Wang, Ning; Bi, Yunrui; Srinivasan, Dipti

    2015-01-01

    In this paper, a HADE (hybrid adaptive differential evolution) algorithm is proposed for the identification problem of PEMFC (proton exchange membrane fuel cell). Inspired by biological genetic strategy, a novel adaptive scaling factor and a dynamic crossover probability are presented to improve the adaptive and dynamic performance of differential evolution algorithm. Moreover, two kinds of neighborhood search operations based on the bee colony foraging mechanism are introduced for enhancing local search efficiency. Through testing the benchmark functions, the proposed algorithm exhibits better performance in convergent accuracy and speed. Finally, the HADE algorithm is applied to identify the nonlinear parameters of PEMFC stack model. Through experimental comparison with other identified methods, the PEMFC model based on the HADE algorithm shows better performance. - Highlights: • We propose a hybrid adaptive differential evolution algorithm (HADE). • The search efficiency is enhanced in low and high dimension search space. • The effectiveness is confirmed by testing benchmark functions. • The identification of the PEMFC model is conducted by adopting HADE.

  10. A hybrid approach to automatic de-identification of psychiatric notes.

    Science.gov (United States)

    Lee, Hee-Jin; Wu, Yonghui; Zhang, Yaoyun; Xu, Jun; Xu, Hua; Roberts, Kirk

    2017-11-01

    De-identification, or identifying and removing protected health information (PHI) from clinical data, is a critical step in making clinical data available for clinical applications and research. This paper presents a natural language processing system for automatic de-identification of psychiatric notes, which was designed to participate in the 2016 CEGS N-GRID shared task Track 1. The system has a hybrid structure that combines machine leaning techniques and rule-based approaches. The rule-based components exploit the structure of the psychiatric notes as well as characteristic surface patterns of PHI mentions. The machine learning components utilize supervised learning with rich features. In addition, the system performance was boosted with integration of additional data to the training set through domain adaptation. The hybrid system showed overall micro-averaged F-score 90.74 on the test set, second-best among all the participants of the CEGS N-GRID task. Copyright © 2017. Published by Elsevier Inc.

  11. Study of an analog/logic processor for the design of an auto patch hybrid computer

    International Nuclear Information System (INIS)

    Koched, Hassen

    1976-01-01

    This paper presents the experimental study of an analog multiprocessor designed at SES/CEN-Saclay. An application of such a device as a basic component of an auto-patch hybrid computer is presented. First, the description of the processor, and a presentation of the theoretical concepts which governed the design of the processor are given. Experiments on an hybrid computer are then presented. Finally, different systems of automatic patching are presented, and conveniently modified, for the use of such a processor. (author) [fr

  12. A Hybrid Soft Computing Approach for Subset Problems

    Directory of Open Access Journals (Sweden)

    Broderick Crawford

    2013-01-01

    Full Text Available Subset problems (set partitioning, packing, and covering are formal models for many practical optimization problems. A set partitioning problem determines how the items in one set (S can be partitioned into smaller subsets. All items in S must be contained in one and only one partition. Related problems are set packing (all items must be contained in zero or one partitions and set covering (all items must be contained in at least one partition. Here, we present a hybrid solver based on ant colony optimization (ACO combined with arc consistency for solving this kind of problems. ACO is a swarm intelligence metaheuristic inspired on ants behavior when they search for food. It allows to solve complex combinatorial problems for which traditional mathematical techniques may fail. By other side, in constraint programming, the solving process of Constraint Satisfaction Problems can dramatically reduce the search space by means of arc consistency enforcing constraint consistencies either prior to or during search. Our hybrid approach was tested with set covering and set partitioning dataset benchmarks. It was observed that the performance of ACO had been improved embedding this filtering technique in its constructive phase.

  13. A hybrid method for the parallel computation of Green's functions

    DEFF Research Database (Denmark)

    Petersen, Dan Erik; Li, Song; Stokbro, Kurt

    2009-01-01

    of the large number of times this calculation needs to be performed, this is computationally very expensive even on supercomputers. The classical approach is based on recurrence formulas which cannot be efficiently parallelized. This practically prevents the solution of large problems with hundreds...... of thousands of atoms. We propose new recurrences for a general class of sparse matrices to calculate Green's and lesser Green's function matrices which extend formulas derived by Takahashi and others. We show that these recurrences may lead to a dramatically reduced computational cost because they only...... require computing a small number of entries of the inverse matrix. Then. we propose a parallelization strategy for block tridiagonal matrices which involves a combination of Schur complement calculations and cyclic reduction. It achieves good scalability even on problems of modest size....

  14. Hybrid computer simulation of the dynamics of the Hoger Onderwijs Reactor

    International Nuclear Information System (INIS)

    Moers, J.C.; Vries, J.W. de.

    1976-01-01

    A distributed parameter model for the dynamics of the Hoger Onderwijs Reactor (HOR) at Delft is presented. The neutronic and the thermodynamic part of this model have been separately implemented on the AD4-IBM1800 Hybrid Computer of the Delft University of Technology Computation Centre. A continuous Space/Discrete Time solution method has been employed. Some test results of the simulation are included

  15. A Cost–Effective Computer-Based, Hybrid Motorised and Gravity ...

    African Journals Online (AJOL)

    A Cost–Effective Computer-Based, Hybrid Motorised and Gravity-Driven Material Handling System for the Mauritian Apparel Industry. ... Thus, many companies are investing significantly in a Research & Development department in order to design new techniques to improve worker's efficiency, and to decrease the amount ...

  16. Computation of hybrid static potentials in SU(3 lattice gauge theory

    Directory of Open Access Journals (Sweden)

    Reisinger Christian

    2018-01-01

    Full Text Available We compute hybrid static potentials in SU(3 lattice gauge theory. We present a method to automatically generate a large set of suitable creation operators with defined quantum numbers from elementary building blocks. We show preliminary results for several channels and discuss, which structures of the gluonic flux tube seem to be realized by the ground states in these channels.

  17. Computational Identification of Novel Genes: Current and Future Perspectives.

    Science.gov (United States)

    Klasberg, Steffen; Bitard-Feildel, Tristan; Mallet, Ludovic

    2016-01-01

    While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and speciation events. Different techniques are available to identify genes and classify them as novel. Their classification as novel is usually based on their similarity to known genes, or lack thereof, detected by comparative genomics or against databases. Computational approaches are further prime methods that can be based on existing models or leveraging biological evidences from experiments. Identification of novel genes remains however a challenging task. With the constant software and technologies updates, no gold standard, and no available benchmark, evaluation and characterization of genomic novelty is a vibrant field. In this review, the classical and state-of-the-art tools for gene prediction are introduced. The current methods for novel gene detection are presented; the methodological strategies and their limits are discussed along with perspective approaches for further studies.

  18. Hybrid Epidemics - A Case Study on Computer Worm Conficker

    OpenAIRE

    Zhang, Changwang; Zhou, Shi; Chain, Benjamin M.

    2014-01-01

    Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading: local, neighbourhood, and global, to capture the worm's spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conficker epidemic. The model is then used to explore ...

  19. A hybrid method for the parallel computation of Green's functions

    International Nuclear Information System (INIS)

    Petersen, Dan Erik; Li Song; Stokbro, Kurt; Sorensen, Hans Henrik B.; Hansen, Per Christian; Skelboe, Stig; Darve, Eric

    2009-01-01

    Quantum transport models for nanodevices using the non-equilibrium Green's function method require the repeated calculation of the block tridiagonal part of the Green's and lesser Green's function matrices. This problem is related to the calculation of the inverse of a sparse matrix. Because of the large number of times this calculation needs to be performed, this is computationally very expensive even on supercomputers. The classical approach is based on recurrence formulas which cannot be efficiently parallelized. This practically prevents the solution of large problems with hundreds of thousands of atoms. We propose new recurrences for a general class of sparse matrices to calculate Green's and lesser Green's function matrices which extend formulas derived by Takahashi and others. We show that these recurrences may lead to a dramatically reduced computational cost because they only require computing a small number of entries of the inverse matrix. Then, we propose a parallelization strategy for block tridiagonal matrices which involves a combination of Schur complement calculations and cyclic reduction. It achieves good scalability even on problems of modest size.

  20. Hybrid computing using a neural network with dynamic external memory.

    Science.gov (United States)

    Graves, Alex; Wayne, Greg; Reynolds, Malcolm; Harley, Tim; Danihelka, Ivo; Grabska-Barwińska, Agnieszka; Colmenarejo, Sergio Gómez; Grefenstette, Edward; Ramalho, Tiago; Agapiou, John; Badia, Adrià Puigdomènech; Hermann, Karl Moritz; Zwols, Yori; Ostrovski, Georg; Cain, Adam; King, Helen; Summerfield, Christopher; Blunsom, Phil; Kavukcuoglu, Koray; Hassabis, Demis

    2016-10-27

    Artificial neural networks are remarkably adept at sensory processing, sequence learning and reinforcement learning, but are limited in their ability to represent variables and data structures and to store data over long timescales, owing to the lack of an external memory. Here we introduce a machine learning model called a differentiable neural computer (DNC), which consists of a neural network that can read from and write to an external memory matrix, analogous to the random-access memory in a conventional computer. Like a conventional computer, it can use its memory to represent and manipulate complex data structures, but, like a neural network, it can learn to do so from data. When trained with supervised learning, we demonstrate that a DNC can successfully answer synthetic questions designed to emulate reasoning and inference problems in natural language. We show that it can learn tasks such as finding the shortest path between specified points and inferring the missing links in randomly generated graphs, and then generalize these tasks to specific graphs such as transport networks and family trees. When trained with reinforcement learning, a DNC can complete a moving blocks puzzle in which changing goals are specified by sequences of symbols. Taken together, our results demonstrate that DNCs have the capacity to solve complex, structured tasks that are inaccessible to neural networks without external read-write memory.

  1. Identification of flooded area from satellite images using Hybrid Kohonen Fuzzy C-Means sigma classifier

    Directory of Open Access Journals (Sweden)

    Krishna Kant Singh

    2017-06-01

    Full Text Available A novel neuro fuzzy classifier Hybrid Kohonen Fuzzy C-Means-σ (HKFCM-σ is proposed in this paper. The proposed classifier is a hybridization of Kohonen Clustering Network (KCN with FCM-σ clustering algorithm. The network architecture of HKFCM-σ is similar to simple KCN network having only two layers, i.e., input and output layer. However, the selection of winner neuron is done based on FCM-σ algorithm. Thus, embedding the features of both, a neural network and a fuzzy clustering algorithm in the classifier. This hybridization results in a more efficient, less complex and faster classifier for classifying satellite images. HKFCM-σ is used to identify the flooding that occurred in Kashmir area in September 2014. The HKFCM-σ classifier is applied on pre and post flooding Landsat 8 OLI images of Kashmir to detect the areas that were flooded due to the heavy rainfalls of September, 2014. The classifier is trained using the mean values of the various spectral indices like NDVI, NDWI, NDBI and first component of Principal Component Analysis. The error matrix was computed to test the performance of the method. The method yields high producer’s accuracy, consumer’s accuracy and kappa coefficient value indicating that the proposed classifier is highly effective and efficient.

  2. Combination of microautoradiography and fluorescence in situ hybridization for identification of microorganisms degrading xenobiotic contaminants.

    Science.gov (United States)

    Yang, Yanru; Zarda, Annatina; Zeyer, Josef

    2003-12-01

    One of the central topics in environmental bioremediation research is to identify microorganisms that are capable of degrading the contaminants of interest. Here we report application of combined microautoradiography (MAR) and fluorescence in situ hybridization (FISH). The method has previously been used in a number of systems; however, here we demonstrate its feasibility in studying the degradation of xenobiotic compounds. With a model system (coculture of Pseudomonas putida B2 and Sphingomonas stygia incubated with [14C] o-nitrophenol), combination of MAR and FISH was shown to be able to successfully identify the microorganisms degrading o-nitrophenol. Compared with the conventional techniques, MAR-FISH allows fast and accurate identification of the microorganisms involved in environmental contaminant degradation.

  3. Computational identification of strain-, species- and genus-specific proteins

    Directory of Open Access Journals (Sweden)

    Thiagarajan Rathi

    2005-11-01

    Full Text Available Abstract Background The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets. Description A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Proteins encoded by a given strain are preliminarily considered to be unique if BLAST, using a comprehensive protein database, fails to retrieve (with an e-value better than 0.001 any protein not encoded by the query strain, species or genus (for strain-, species- and genus-specific proteins respectively, or if BLAST, using the best hit as the query (reverse BLAST, does not retrieve the initial query protein. Results are manually inspected for homology if the initial query is retrieved in the reverse BLAST but is not the best hit. Sequences unlikely to retrieve homologs using the default BLOSUM62 matrix (usually short sequences are re-tested using the PAM30 matrix, thereby increasing the number of retrieved homologs and increasing the stringency of the search for unique proteins. The above protocol was used to examine several food- and water-borne pathogens. We find that the reverse BLAST step filters out about 22% of proteins with homologs that would otherwise be considered unique at the genus and species levels. Analysis of the annotations of unique proteins reveals that many are remnants of prophage proteins, or may be involved in virulence. The data generated from this study can be accessed and further evaluated from the CUPID (Core and Unique Protein Identification system web site (updated semi-annually at http://pir.georgetown.edu/cupid. Conclusion CUPID

  4. An approach for identification of unknown viruses using sequencing-by-hybridization.

    Science.gov (United States)

    Katoski, Sarah E; Meyer, Hermann; Ibrahim, Sofi

    2015-09-01

    Accurate identification of biological threat agents, especially RNA viruses, in clinical or environmental samples can be challenging because the concentration of viral genomic material in a given sample is usually low, viral genomic RNA is liable to degradation, and RNA viruses are extremely diverse. A two-tiered approach was used for initial identification, then full genomic characterization of 199 RNA viruses belonging to virus families Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, and Togaviridae. A Sequencing-by-hybridization (SBH) microarray was used to tentatively identify a viral pathogen then, the identity is confirmed by guided next-generation sequencing (NGS). After optimization and evaluation of the SBH and NGS methodologies with various virus species and strains, the approach was used to test the ability to identify viruses in blinded samples. The SBH correctly identified two Ebola viruses in the blinded samples within 24 hr, and by using guided amplicon sequencing with 454 GS FLX, the identities of the viruses in both samples were confirmed. SBH provides at relatively low-cost screening of biological samples against a panel of viral pathogens that can be custom-designed on a microarray. Once the identity of virus is deduced from the highest hybridization signal on the SBH microarray, guided (amplicon) NGS sequencing can be used not only to confirm the identity of the virus but also to provide further information about the strain or isolate, including a potential genetic manipulation. This approach can be useful in situations where natural or deliberate biological threat incidents might occur and a rapid response is required. © 2015 Wiley Periodicals, Inc.

  5. Site-specific identification of heparan and chondroitin sulfate glycosaminoglycans in hybrid proteoglycans.

    Science.gov (United States)

    Noborn, Fredrik; Gomez Toledo, Alejandro; Green, Anders; Nasir, Waqas; Sihlbom, Carina; Nilsson, Jonas; Larson, Göran

    2016-10-03

    Heparan sulfate (HS) and chondroitin sulfate (CS) are complex polysaccharides that regulate important biological pathways in virtually all metazoan organisms. The polysaccharides often display opposite effects on cell functions with HS and CS structural motifs presenting unique binding sites for specific ligands. Still, the mechanisms by which glycan biosynthesis generates complex HS and CS polysaccharides required for the regulation of mammalian physiology remain elusive. Here we present a glycoproteomic approach that identifies and differentiates between HS and CS attachment sites and provides identity to the core proteins. Glycopeptides were prepared from perlecan, a complex proteoglycan known to be substituted with both HS and CS chains, further digested with heparinase or chondroitinase ABC to reduce the HS and CS chain lengths respectively, and thereafter analyzed by nLC-MS/MS. This protocol enabled the identification of three consensus HS sites and one hybrid site, carrying either a HS or a CS chain. Inspection of the amino acid sequence at the hybrid attachment locus indicates that certain peptide motifs may encode for the chain type selection process. This analytical approach will become useful when addressing fundamental questions in basic biology specifically in elucidating the functional roles of site-specific glycosylations of proteoglycans.

  6. Spatially hybrid computations for streamer discharges with generic features of pulled fronts: I. Planar fronts

    International Nuclear Information System (INIS)

    Li Chao; Ebert, Ute; Hundsdorfer, Willem

    2010-01-01

    Streamers are the first stage of sparks and lightning; they grow due to a strongly enhanced electric field at their tips; this field is created by a thin curved space charge layer. These multiple scales are already challenging when the electrons are approximated by densities. However, electron density fluctuations in the leading edge of the front and non-thermal stretched tails of the electron energy distribution (as a cause of X-ray emissions) require a particle model to follow the electron motion. But present computers cannot deal with all electrons in a fully developed streamer. Therefore, super-particle have to be introduced, which leads to wrong statistics and numerical artifacts. The method of choice is a hybrid computation in space where individual electrons are followed in the region of high electric field and low density while the bulk of the electrons is approximated by densities (or fluids). We here develop the hybrid coupling for planar fronts. First, to obtain a consistent flux at the interface between particle and fluid model in the hybrid computation, the widely used classical fluid model is replaced by an extended fluid model. Then the coupling algorithm and the numerical implementation of the spatially hybrid model are presented in detail, in particular, the position of the model interface and the construction of the buffer region. The method carries generic features of pulled fronts that can be applied to similar problems like large deviations in the leading edge of population fronts, etc.

  7. STAR - A computer language for hybrid AI applications

    Science.gov (United States)

    Borchardt, G. C.

    1986-01-01

    Constructing Artificial Intelligence application systems which rely on both symbolic and non-symbolic processing places heavy demands on the communication of data between dissimilar languages. This paper describes STAR (Simple Tool for Automated Reasoning), a computer language for the development of AI application systems which supports the transfer of data structures between a symbolic level and a non-symbolic level defined in languages such as FORTRAN, C and PASCAL. The organization of STAR is presented, followed by the description of an application involving STAR in the interpretation of airborne imaging spectrometer data.

  8. A Hybrid Verifiable and Delegated Cryptographic Model in Cloud Computing

    Directory of Open Access Journals (Sweden)

    Jaber Ibrahim Naser

    2018-02-01

    Full Text Available Access control is very important in cloud data sharing. Especially in the domains like healthcare, it is essential to have access control mechanisms in place for confidentiality and secure data access. Attribute based encryption has been around for many years to secure data and provide controlled access. In this paper, we proposed a framework that supports circuit and attributes based encryption mechanism that involves multiple parties. They are data owner, data user, cloud server and attribute authority. An important feature of the proposed system is the verifiable delegation of the decryption process to cloud server. Data owner encrypts data and delegates decryption process to cloud. Cloud server performs partial decryption and then the final decrypted data are shared for users as per the privileges. Data owner  thus reduces computational complexity by delegating decryption process cloud server. We built a prototype application using the Microsoft.NET platform for proof of the concept. The empirical results revealed that there is controlled access with multiple user roles and access control rights for secure and confidential data access in cloud computing.

  9. Modelling the WWER-type reactor dynamics using a hybrid computer. Part 1

    International Nuclear Information System (INIS)

    Karpeta, C.

    Results of simulation studies into reactor and steam generator dynamics of a WWER type power plant are presented. Spatial kinetics of the reactor core is described by a nodal approximation to diffusion equations, xenon poisoning equations and heat transfer equations. The simulation of the reactor model dynamics was performed on a hybrid computer. Models of both a horizontal and a vertical steam generator were developed. The dynamics was investigated over a large range of power by computing the transients on a digital computer. (author)

  10. Hybrid EEG—Eye Tracker: Automatic Identification and Removal of Eye Movement and Blink Artifacts from Electroencephalographic Signal

    Directory of Open Access Journals (Sweden)

    Malik M. Naeem Mannan

    2016-02-01

    Full Text Available Contamination of eye movement and blink artifacts in Electroencephalogram (EEG recording makes the analysis of EEG data more difficult and could result in mislead findings. Efficient removal of these artifacts from EEG data is an essential step in improving classification accuracy to develop the brain-computer interface (BCI. In this paper, we proposed an automatic framework based on independent component analysis (ICA and system identification to identify and remove ocular artifacts from EEG data by using hybrid EEG and eye tracker system. The performance of the proposed algorithm is illustrated using experimental and standard EEG datasets. The proposed algorithm not only removes the ocular artifacts from artifactual zone but also preserves the neuronal activity related EEG signals in non-artifactual zone. The comparison with the two state-of-the-art techniques namely ADJUST based ICA and REGICA reveals the significant improved performance of the proposed algorithm for removing eye movement and blink artifacts from EEG data. Additionally, results demonstrate that the proposed algorithm can achieve lower relative error and higher mutual information values between corrected EEG and artifact-free EEG data.

  11. Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

    Directory of Open Access Journals (Sweden)

    Huygens Flavia

    2007-08-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species. Results The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH data for Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile. Conclusion Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data.

  12. Innovative molecular approach to the identification of Colossoma macropomum and its hybrids

    Directory of Open Access Journals (Sweden)

    Fátima Gomes

    2012-06-01

    Full Text Available Tambaqui (Colossoma macropomum is the fish species most commonly raised in the Brazilian fish farms. The species is highly adaptable to captive conditions, and is both fast-growing and relatively fecund. In recent years, artificial breeding has produced hybrids with Characiform species, known as "Tambacu" and "Tambatinga". Identifying hybrids is a difficult process, given their morphological similarities with the parent species. This study presents an innovative molecular approach to the identification of hybrids based primarily on Multiplex PCR of a nuclear gene (α-Tropomyosin, which was tested on 93 specimens obtained from fish farms in northern Brazil. The sequencing of a 505-bp fragment of the Control Region (CR permitted the identification of the maternal lineage of the specimen, all of which corresponded to C. macropomum. Unexpectedly, only two CR haplotype were found in 93 samples, a very low genetic diversity for the pisciculture of Tambaqui. Multiplex PCR identified 42 hybrids, in contrast with 23 identified by the supplier on the basis of external morphology. This innovative tool has considerable potential for the development of the Brazilian aquaculture, given the possibility of the systematic identification of the genetic traits of both fry-producing stocks, and the fry and juveniles raised in farms.O Tambaqui (Colossoma macropomum é a espécie de peixe mais comumente cultivada em pisciculturas no Brasil. A espécie é altamente adaptada às condições de cativeiro, apresentando rápido crescimento e alta fecundidade. Nos últimos anos tem ocorrido o cruzamento artificial entre espécies de Characiformes, produzindo os híbridos "Tambacu" e "Tambatinga". A identificação de híbridos é uma tarefa difícil, em virtude da grande similaridade morfológica entre as espécies parentais. O presente estudo apresenta uma abordagem molecular inovadora para identificação de híbridos com base em PCR Multiplex de um gene nuclear (

  13. Fatigue of hybrid glass/carbon composites: 3D computational studies

    DEFF Research Database (Denmark)

    Dai, Gaoming; Mishnaevsky, Leon

    2014-01-01

    3D computational simulations of fatigue of hybrid carbon/glass fiber reinforced composites is carried out using X-FEM and multifiber unit cell models. A new software code for the automatic generation of unit cell multifiber models of composites with randomly misaligned fibers of various properties...... and geometrical parameters is developed. With the use of this program code and the X-FEM method, systematic investigations of the effect of microstructure of hybrid composites (fraction of carbon versus glass fibers, misalignment, and interface strength) and the loading conditions (tensile versus compression...... cyclic loading effects) on fatigue behavior of the materials are carried out. It was demonstrated that the higher fraction of carbon fibers in hybrid composites is beneficial for the fatigue lifetime of the composites under tension-tension cyclic loading, but might have negative effect on the lifetime...

  14. Hybrid VLSI/QCA Architecture for Computing FFTs

    Science.gov (United States)

    Fijany, Amir; Toomarian, Nikzad; Modarres, Katayoon; Spotnitz, Matthew

    2003-01-01

    A data-processor architecture that would incorporate elements of both conventional very-large-scale integrated (VLSI) circuitry and quantum-dot cellular automata (QCA) has been proposed to enable the highly parallel and systolic computation of fast Fourier transforms (FFTs). The proposed circuit would complement the QCA-based circuits described in several prior NASA Tech Briefs articles, namely Implementing Permutation Matrices by Use of Quantum Dots (NPO-20801), Vol. 25, No. 10 (October 2001), page 42; Compact Interconnection Networks Based on Quantum Dots (NPO-20855) Vol. 27, No. 1 (January 2003), page 32; and Bit-Serial Adder Based on Quantum Dots (NPO-20869), Vol. 27, No. 1 (January 2003), page 35. The cited prior articles described the limitations of very-large-scale integrated (VLSI) circuitry and the major potential advantage afforded by QCA. To recapitulate: In a VLSI circuit, signal paths that are required not to interact with each other must not cross in the same plane. In contrast, for reasons too complex to describe in the limited space available for this article, suitably designed and operated QCAbased signal paths that are required not to interact with each other can nevertheless be allowed to cross each other in the same plane without adverse effect. In principle, this characteristic could be exploited to design compact, coplanar, simple (relative to VLSI) QCA-based networks to implement complex, advanced interconnection schemes.

  15. Improved signal processing approaches in an offline simulation of a hybrid brain–computer interface

    Science.gov (United States)

    Brunner, Clemens; Allison, Brendan Z.; Krusienski, Dean J.; Kaiser, Vera; Müller-Putz, Gernot R.; Pfurtscheller, Gert; Neuper, Christa

    2012-01-01

    In a conventional brain–computer interface (BCI) system, users perform mental tasks that yield specific patterns of brain activity. A pattern recognition system determines which brain activity pattern a user is producing and thereby infers the user’s mental task, allowing users to send messages or commands through brain activity alone. Unfortunately, despite extensive research to improve classification accuracy, BCIs almost always exhibit errors, which are sometimes so severe that effective communication is impossible. We recently introduced a new idea to improve accuracy, especially for users with poor performance. In an offline simulation of a “hybrid” BCI, subjects performed two mental tasks independently and then simultaneously. This hybrid BCI could use two different types of brain signals common in BCIs – event-related desynchronization (ERD) and steady-state evoked potentials (SSEPs). This study suggested that such a hybrid BCI is feasible. Here, we re-analyzed the data from our initial study. We explored eight different signal processing methods that aimed to improve classification and further assess both the causes and the extent of the benefits of the hybrid condition. Most analyses showed that the improved methods described here yielded a statistically significant improvement over our initial study. Some of these improvements could be relevant to conventional BCIs as well. Moreover, the number of illiterates could be reduced with the hybrid condition. Results are also discussed in terms of dual task interference and relevance to protocol design in hybrid BCIs. PMID:20153371

  16. A hybrid source-driven method to compute fast neutron fluence in reactor pressure vessel - 017

    International Nuclear Information System (INIS)

    Ren-Tai, Chiang

    2010-01-01

    A hybrid source-driven method is developed to compute fast neutron fluence with neutron energy greater than 1 MeV in nuclear reactor pressure vessel (RPV). The method determines neutron flux by solving a steady-state neutron transport equation with hybrid neutron sources composed of peripheral fixed fission neutron sources and interior chain-reacted fission neutron sources. The relative rod-by-rod power distribution of the peripheral assemblies in a nuclear reactor obtained from reactor core depletion calculations and subsequent rod-by-rod power reconstruction is employed as the relative rod-by-rod fixed fission neutron source distribution. All fissionable nuclides other than U-238 (such as U-234, U-235, U-236, Pu-239 etc) are replaced with U-238 to avoid counting the fission contribution twice and to preserve fast neutron attenuation for heavy nuclides in the peripheral assemblies. An example is provided to show the feasibility of the method. Since the interior fuels only have a marginal impact on RPV fluence results due to rapid attenuation of interior fast fission neutrons, a generic set or one of several generic sets of interior fuels can be used as the driver and only the neutron sources in the peripheral assemblies will be changed in subsequent hybrid source-driven fluence calculations. Consequently, this hybrid source-driven method can simplify and reduce cost for fast neutron fluence computations. This newly developed hybrid source-driven method should be a useful and simplified tool for computing fast neutron fluence at selected locations of interest in RPV of contemporary nuclear power reactors. (authors)

  17. Identification of Learning Processes by Means of Computer Graphics.

    Science.gov (United States)

    Sorensen, Birgitte Holm

    1993-01-01

    Describes a development project for the use of computer graphics and video in connection with an inservice training course for primary education teachers in Denmark. Topics addressed include research approaches to computers; computer graphics in learning processes; activities relating to computer graphics; the role of the teacher; and student…

  18. Identification of natural images and computer-generated graphics based on statistical and textural features.

    Science.gov (United States)

    Peng, Fei; Li, Jiao-ting; Long, Min

    2015-03-01

    To discriminate the acquisition pipelines of digital images, a novel scheme for the identification of natural images and computer-generated graphics is proposed based on statistical and textural features. First, the differences between them are investigated from the view of statistics and texture, and 31 dimensions of feature are acquired for identification. Then, LIBSVM is used for the classification. Finally, the experimental results are presented. The results show that it can achieve an identification accuracy of 97.89% for computer-generated graphics, and an identification accuracy of 97.75% for natural images. The analyses also demonstrate the proposed method has excellent performance, compared with some existing methods based only on statistical features or other features. The method has a great potential to be implemented for the identification of natural images and computer-generated graphics. © 2014 American Academy of Forensic Sciences.

  19. Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

    International Nuclear Information System (INIS)

    Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.

    2011-01-01

    The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both many-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.

  20. Applications integration in a hybrid cloud computing environment: modelling and platform

    Science.gov (United States)

    Li, Qing; Wang, Ze-yuan; Li, Wei-hua; Li, Jun; Wang, Cheng; Du, Rui-yang

    2013-08-01

    With the development of application services providers and cloud computing, more and more small- and medium-sized business enterprises use software services and even infrastructure services provided by professional information service companies to replace all or part of their information systems (ISs). These information service companies provide applications, such as data storage, computing processes, document sharing and even management information system services as public resources to support the business process management of their customers. However, no cloud computing service vendor can satisfy the full functional IS requirements of an enterprise. As a result, enterprises often have to simultaneously use systems distributed in different clouds and their intra enterprise ISs. Thus, this article presents a framework to integrate applications deployed in public clouds and intra ISs. A run-time platform is developed and a cross-computing environment process modelling technique is also developed to improve the feasibility of ISs under hybrid cloud computing environments.

  1. An online hybrid brain-computer interface combining multiple physiological signals for webpage browse.

    Science.gov (United States)

    Long Chen; Zhongpeng Wang; Feng He; Jiajia Yang; Hongzhi Qi; Peng Zhou; Baikun Wan; Dong Ming

    2015-08-01

    The hybrid brain computer interface (hBCI) could provide higher information transfer rate than did the classical BCIs. It included more than one brain-computer or human-machine interact paradigms, such as the combination of the P300 and SSVEP paradigms. Research firstly constructed independent subsystems of three different paradigms and tested each of them with online experiments. Then we constructed a serial hybrid BCI system which combined these paradigms to achieve the functions of typing letters, moving and clicking cursor, and switching among them for the purpose of browsing webpages. Five subjects were involved in this study. They all successfully realized these functions in the online tests. The subjects could achieve an accuracy above 90% after training, which met the requirement in operating the system efficiently. The results demonstrated that it was an efficient system capable of robustness, which provided an approach for the clinic application.

  2. Hybrid and hierarchical nanoreinforced polymer composites: Computational modelling of structure–properties relationships

    DEFF Research Database (Denmark)

    Mishnaevsky, Leon; Dai, Gaoming

    2014-01-01

    by using computational micromechanical models. It is shown that while glass/carbon fibers hybrid composites clearly demonstrate higher stiffness and lower weight with increasing the carbon content, they can have lower strength as compared with usual glass fiber polymer composites. Secondary...... nanoreinforcement can drastically increase the fatigue lifetime of composites. Especially, composites with the nanoplatelets localized in the fiber/matrix interface layer (fiber sizing) ensure much higher fatigue lifetime than those with the nanoplatelets in the matrix....

  3. Solving Problems in Various Domains by Hybrid Models of High Performance Computations

    Directory of Open Access Journals (Sweden)

    Yurii Rogozhin

    2014-03-01

    Full Text Available This work presents a hybrid model of high performance computations. The model is based on membrane system (P~system where some membranes may contain quantum device that is triggered by the data entering the membrane. This model is supposed to take advantages of both biomolecular and quantum paradigms and to overcome some of their inherent limitations. The proposed approach is demonstrated through two selected problems: SAT, and image retrieving.

  4. Hybrid magic state distillation for universal fault-tolerant quantum computation

    OpenAIRE

    Zheng, Wenqiang; Yu, Yafei; Pan, Jian; Zhang, Jingfu; Li, Jun; Li, Zhaokai; Suter, Dieter; Zhou, Xianyi; Peng, Xinhua; Du, Jiangfeng

    2014-01-01

    A set of stabilizer operations augmented by some special initial states known as 'magic states', gives the possibility of universal fault-tolerant quantum computation. However, magic state preparation inevitably involves nonideal operations that introduce noise. The most common method to eliminate the noise is magic state distillation (MSD) by stabilizer operations. Here we propose a hybrid MSD protocol by connecting a four-qubit H-type MSD with a five-qubit T-type MSD, in order to overcome s...

  5. A Program for the Identification of the Enterobacteriaceae for Use in Teaching the Principles of Computer Identification of Bacteria.

    Science.gov (United States)

    Hammonds, S. J.

    1990-01-01

    A technique for the numerical identification of bacteria using normalized likelihoods calculated from a probabilistic database is described, and the principles of the technique are explained. The listing of the computer program is included. Specimen results from the program, and examples of how they should be interpreted, are given. (KR)

  6. Cloud computing-based energy optimization control framework for plug-in hybrid electric bus

    International Nuclear Information System (INIS)

    Yang, Chao; Li, Liang; You, Sixiong; Yan, Bingjie; Du, Xian

    2017-01-01

    Considering the complicated characteristics of traffic flow in city bus route and the nonlinear vehicle dynamics, optimal energy management integrated with clustering and recognition of driving conditions in plug-in hybrid electric bus is still a challenging problem. Motivated by this issue, this paper presents an innovative energy optimization control framework based on the cloud computing for plug-in hybrid electric bus. This framework, which includes offline part and online part, can realize the driving conditions clustering in offline part, and the energy management in online part. In offline part, utilizing the operating data transferred from a bus to the remote monitoring center, K-means algorithm is adopted to cluster the driving conditions, and then Markov probability transfer matrixes are generated to predict the possible operating demand of the bus driver. Next in online part, the current driving condition is real-time identified by a well-trained support vector machine, and Markov chains-based driving behaviors are accordingly selected. With the stochastic inputs, stochastic receding horizon control method is adopted to obtain the optimized energy management of hybrid powertrain. Simulations and hardware-in-loop test are carried out with the real-world city bus route, and the results show that the presented strategy could greatly improve the vehicle fuel economy, and as the traffic flow data feedback increases, the fuel consumption of every plug-in hybrid electric bus running in a specific bus route tends to be a stable minimum. - Highlights: • Cloud computing-based energy optimization control framework is proposed. • Driving cycles are clustered into 6 types by K-means algorithm. • Support vector machine is employed to realize the online recognition of driving condition. • Stochastic receding horizon control-based energy management strategy is designed for plug-in hybrid electric bus. • The proposed framework is verified by simulation and hard

  7. Computational modeling of electrically conductive networks formed by graphene nanoplatelet-carbon nanotube hybrid particles

    KAUST Repository

    Mora Cordova, Angel

    2018-01-30

    One strategy to ensure that nanofiller networks in a polymer composite percolate at low volume fractions is to promote segregation. In a segregated structure, the concentration of nanofillers is kept low in some regions of the sample. In turn, the concentration in remaining regions is much higher than the average concentration of the sample. This selective placement of the nanofillers ensures percolation at low average concentration. One original strategy to promote segregation is by tuning the shape of the nanofillers. We use a computational approach to study the conductive networks formed by hybrid particles obtained by growing carbon nanotubes (CNTs) on graphene nanoplatelets (GNPs). The objective of this study is (1) to show that the higher electrical conductivity of these composites is due to the hybrid particles forming a segregated structure and (2) to understand which parameters defining the hybrid particles determine the efficiency of the segregation. We construct a microstructure to observe the conducting paths and determine whether a segregated structure has indeed been formed inside the composite. A measure of efficiency is presented based on the fraction of nanofillers that contribute to the conductive network. Then, the efficiency of the hybrid-particle networks is compared to those of three other networks of carbon-based nanofillers in which no hybrid particles are used: only CNTs, only GNPs, and a mix of CNTs and GNPs. Finally, some parameters of the hybrid particle are studied: the CNT density on the GNPs, and the CNT and GNP geometries. We also present recommendations for the further improvement of a composite\\'s conductivity based on these parameters.

  8. Computational modeling of electrically conductive networks formed by graphene nanoplatelet-carbon nanotube hybrid particles

    Science.gov (United States)

    Mora, A.; Han, F.; Lubineau, G.

    2018-04-01

    One strategy to ensure that nanofiller networks in a polymer composite percolate at low volume fractions is to promote segregation. In a segregated structure, the concentration of nanofillers is kept low in some regions of the sample. In turn, the concentration in the remaining regions is much higher than the average concentration of the sample. This selective placement of the nanofillers ensures percolation at low average concentration. One original strategy to promote segregation is by tuning the shape of the nanofillers. We use a computational approach to study the conductive networks formed by hybrid particles obtained by growing carbon nanotubes (CNTs) on graphene nanoplatelets (GNPs). The objective of this study is (1) to show that the higher electrical conductivity of these composites is due to the hybrid particles forming a segregated structure and (2) to understand which parameters defining the hybrid particles determine the efficiency of the segregation. We construct a microstructure to observe the conducting paths and determine whether a segregated structure has indeed been formed inside the composite. A measure of efficiency is presented based on the fraction of nanofillers that contribute to the conductive network. Then, the efficiency of the hybrid-particle networks is compared to those of three other networks of carbon-based nanofillers in which no hybrid particles are used: only CNTs, only GNPs, and a mix of CNTs and GNPs. Finally, some parameters of the hybrid particle are studied: the CNT density on the GNPs, and the CNT and GNP geometries. We also present recommendations for the further improvement of a composite’s conductivity based on these parameters.

  9. Computational modeling of electrically conductive networks formed by graphene nanoplatelet-carbon nanotube hybrid particles

    KAUST Repository

    Mora Cordova, Angel; Han, Fei; Lubineau, Gilles

    2018-01-01

    One strategy to ensure that nanofiller networks in a polymer composite percolate at low volume fractions is to promote segregation. In a segregated structure, the concentration of nanofillers is kept low in some regions of the sample. In turn, the concentration in remaining regions is much higher than the average concentration of the sample. This selective placement of the nanofillers ensures percolation at low average concentration. One original strategy to promote segregation is by tuning the shape of the nanofillers. We use a computational approach to study the conductive networks formed by hybrid particles obtained by growing carbon nanotubes (CNTs) on graphene nanoplatelets (GNPs). The objective of this study is (1) to show that the higher electrical conductivity of these composites is due to the hybrid particles forming a segregated structure and (2) to understand which parameters defining the hybrid particles determine the efficiency of the segregation. We construct a microstructure to observe the conducting paths and determine whether a segregated structure has indeed been formed inside the composite. A measure of efficiency is presented based on the fraction of nanofillers that contribute to the conductive network. Then, the efficiency of the hybrid-particle networks is compared to those of three other networks of carbon-based nanofillers in which no hybrid particles are used: only CNTs, only GNPs, and a mix of CNTs and GNPs. Finally, some parameters of the hybrid particle are studied: the CNT density on the GNPs, and the CNT and GNP geometries. We also present recommendations for the further improvement of a composite's conductivity based on these parameters.

  10. 16th International Conference on Hybrid Intelligent Systems and the 8th World Congress on Nature and Biologically Inspired Computing

    CERN Document Server

    Haqiq, Abdelkrim; Alimi, Adel; Mezzour, Ghita; Rokbani, Nizar; Muda, Azah

    2017-01-01

    This book presents the latest research in hybrid intelligent systems. It includes 57 carefully selected papers from the 16th International Conference on Hybrid Intelligent Systems (HIS 2016) and the 8th World Congress on Nature and Biologically Inspired Computing (NaBIC 2016), held on November 21–23, 2016 in Marrakech, Morocco. HIS - NaBIC 2016 was jointly organized by the Machine Intelligence Research Labs (MIR Labs), USA; Hassan 1st University, Settat, Morocco and University of Sfax, Tunisia. Hybridization of intelligent systems is a promising research field in modern artificial/computational intelligence and is concerned with the development of the next generation of intelligent systems. The conference’s main aim is to inspire further exploration of the intriguing potential of hybrid intelligent systems and bio-inspired computing. As such, the book is a valuable resource for practicing engineers /scientists and researchers working in the field of computational intelligence and artificial intelligence.

  11. Attendance fingerprint identification system using arduino and single board computer

    Science.gov (United States)

    Muchtar, M. A.; Seniman; Arisandi, D.; Hasanah, S.

    2018-03-01

    Fingerprint is one of the most unique parts of the human body that distinguishes one person from others and is easily accessed. This uniqueness is supported by technology that can automatically identify or recognize a person called fingerprint sensor. Yet, the existing Fingerprint Sensor can only do fingerprint identification on one machine. For the mentioned reason, we need a method to be able to recognize each user in a different fingerprint sensor. The purpose of this research is to build fingerprint sensor system for fingerprint data management to be centralized so identification can be done in each Fingerprint Sensor. The result of this research shows that by using Arduino and Raspberry Pi, data processing can be centralized so that fingerprint identification can be done in each fingerprint sensor with 98.5 % success rate of centralized server recording.

  12. Hybrid Cloud Computing Environment for EarthCube and Geoscience Community

    Science.gov (United States)

    Yang, C. P.; Qin, H.

    2016-12-01

    The NSF EarthCube Integration and Test Environment (ECITE) has built a hybrid cloud computing environment to provides cloud resources from private cloud environments by using cloud system software - OpenStack and Eucalyptus, and also manages public cloud - Amazon Web Service that allow resource synchronizing and bursting between private and public cloud. On ECITE hybrid cloud platform, EarthCube and geoscience community can deploy and manage the applications by using base virtual machine images or customized virtual machines, analyze big datasets by using virtual clusters, and real-time monitor the virtual resource usage on the cloud. Currently, a number of EarthCube projects have deployed or started migrating their projects to this platform, such as CHORDS, BCube, CINERGI, OntoSoft, and some other EarthCube building blocks. To accomplish the deployment or migration, administrator of ECITE hybrid cloud platform prepares the specific needs (e.g. images, port numbers, usable cloud capacity, etc.) of each project in advance base on the communications between ECITE and participant projects, and then the scientists or IT technicians in those projects launch one or multiple virtual machines, access the virtual machine(s) to set up computing environment if need be, and migrate their codes, documents or data without caring about the heterogeneity in structure and operations among different cloud platforms.

  13. Contours identification of elements in a cone beam computed tomography for investigating maxillary cysts

    Science.gov (United States)

    Chioran, Doina; Nicoarǎ, Adrian; Roşu, Şerban; Cǎrligeriu, Virgil; Ianeş, Emilia

    2013-10-01

    Digital processing of two-dimensional cone beam computer tomography slicesstarts by identification of the contour of elements within. This paper deals with the collective work of specialists in medicine and applied mathematics in computer science on elaborating and implementation of algorithms in dental 2D imagery.

  14. Automatic Identification and Reconstruction of the Right Phrenic Nerve on Computed Tomography

    OpenAIRE

    Bamps, Kobe; Cuypers, Céline; Polmans, Pieter; Claesen, Luc; Koopman, Pieter

    2016-01-01

    An automatic computer algorithm was successfully constructed, enabling identification and reconstruction of the right phrenic nerve on high resolution coronary computed tomography scans. This could lead to a substantial reduction in the incidence of phrenic nerve paralysis during pulmonary vein isolation using ballon techniques.

  15. Preliminary Study on Hybrid Computational Phantom for Radiation Dosimetry Based on Subdivision Surface

    International Nuclear Information System (INIS)

    Jeong, Jong Hwi; Choi, Sang Hyoun; Cho, Sung Koo; Kim, Chan Hyeong

    2007-01-01

    The anthropomorphic computational phantoms are classified into two groups. One group is the stylized phantoms, or MIRD phantoms, which are based on mathematical representations of the anatomical structures. The shapes and positions of the organs and tissues in these phantoms can be adjusted by changing the coefficients of the equations in use. The other group is the voxel phantoms, which are based on tomographic images of a real person such as CT, MR and serially sectioned color slice images from a cadaver. Obviously, the voxel phantoms represent the anatomical structures of a human body much more realistically than the stylized phantoms. A realistic representation of anatomical structure is very important for an accurate calculation of radiation dose in the human body. Consequently, the ICRP recently has decided to use the voxel phantoms for the forthcoming update of the dose conversion coefficients. However, the voxel phantoms also have some limitations: (1) The topology and dimensions of the organs and tissues in a voxel model are extremely difficult to change, and (2) The thin organs, such as oral mucosa and skin, cannot be realistically modeled unless the voxel resolution is prohibitively high. Recently, a new approach has been implemented by several investigators. The investigators converted their voxel phantoms to hybrid computational phantoms based on NURBS (Non-Uniform Rational B-Splines) surface, which is smooth and deformable. It is claimed that these new phantoms have the flexibility of the stylized phantom along with the realistic representations of the anatomical structures. The topology and dimensions of the anatomical structures can be easily changed as necessary. Thin organs can be modeled without affecting computational speed or memory requirement. The hybrid phantoms can be also used for 4-D Monte Carlo simulations. In this preliminary study, the external shape of a voxel phantom (i.e., skin), HDRK-Man, was converted to a hybrid computational

  16. All-optical quantum computing with a hybrid solid-state processing unit

    International Nuclear Information System (INIS)

    Pei Pei; Zhang Fengyang; Li Chong; Song Heshan

    2011-01-01

    We develop an architecture of a hybrid quantum solid-state processing unit for universal quantum computing. The architecture allows distant and nonidentical solid-state qubits in distinct physical systems to interact and work collaboratively. All the quantum computing procedures are controlled by optical methods using classical fields and cavity QED. Our methods have a prominent advantage of the insensitivity to dissipation process benefiting from the virtual excitation of subsystems. Moreover, the quantum nondemolition measurements and state transfer for the solid-state qubits are proposed. The architecture opens promising perspectives for implementing scalable quantum computation in a broader sense that different solid-state systems can merge and be integrated into one quantum processor afterward.

  17. A novel hybrid approach with multidimensional-like effects for compressible flow computations

    Science.gov (United States)

    Kalita, Paragmoni; Dass, Anoop K.

    2017-07-01

    A multidimensional scheme achieves good resolution of strong and weak shocks irrespective of whether the discontinuities are aligned with or inclined to the grid. However, these schemes are computationally expensive. This paper achieves similar effects by hybridizing two schemes, namely, AUSM and DRLLF and coupling them through a novel shock switch that operates - unlike existing switches - on the gradient of the Mach number across the cell-interface. The schemes that are hybridized have contrasting properties. The AUSM scheme captures grid-aligned (and strong) shocks crisply but it is not so good for non-grid-aligned weaker shocks, whereas the DRLLF scheme achieves sharp resolution of non-grid-aligned weaker shocks, but is not as good for grid-aligned strong shocks. It is our experience that if conventional shock switches based on variables like density, pressure or Mach number are used to combine the schemes, the desired effect of crisp resolution of grid-aligned and non-grid-aligned discontinuities are not obtained. To circumvent this problem we design a shock switch based - for the first time - on the gradient of the cell-interface Mach number with very impressive results. Thus the strategy of hybridizing two carefully selected schemes together with the innovative design of the shock switch that couples them, affords a method that produces the effects of a multidimensional scheme with a lower computational cost. It is further seen that hybridization of the AUSM scheme with the recently developed DRLLFV scheme using the present shock switch gives another scheme that provides crisp resolution for both shocks and boundary layers. Merits of the scheme are established through a carefully selected set of numerical experiments.

  18. A hybrid model for the computationally-efficient simulation of the cerebellar granular layer

    Directory of Open Access Journals (Sweden)

    Anna eCattani

    2016-04-01

    Full Text Available The aim of the present paper is to efficiently describe the membrane potential dynamics of neural populations formed by species having a high density difference in specific brain areas. We propose a hybrid model whose main ingredients are a conductance-based model (ODE system and its continuous counterpart (PDE system obtained through a limit process in which the number of neurons confined in a bounded region of the brain tissue is sent to infinity. Specifically, in the discrete model, each cell is described by a set of time-dependent variables, whereas in the continuum model, cells are grouped into populations that are described by a set of continuous variables.Communications between populations, which translate into interactions among the discrete and the continuous models, are the essence of the hybrid model we present here. The cerebellum and cerebellum-like structures show in their granular layer a large difference in the relative density of neuronal species making them a natural testing ground for our hybrid model. By reconstructing the ensemble activity of the cerebellar granular layer network and by comparing our results to a more realistic computational network, we demonstrate that our description of the network activity, even though it is not biophysically detailed, is still capable of reproducing salient features of neural network dynamics. Our modeling approach yields a significant computational cost reduction by increasing the simulation speed at least $270$ times. The hybrid model reproduces interesting dynamics such as local microcircuit synchronization, traveling waves, center-surround and time-windowing.

  19. The UF family of hybrid phantoms of the developing human fetus for computational radiation dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Maynard, Matthew R; Geyer, John W; Bolch, Wesley [Department of Nuclear and Radiological Engineering, University of Florida, Gainesville, FL (United States); Aris, John P [Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL (United States); Shifrin, Roger Y, E-mail: wbolch@ufl.edu [Department of Radiology, University of Florida, Gainesville, FL (United States)

    2011-08-07

    Historically, the development of computational phantoms for radiation dosimetry has primarily been directed at capturing and representing adult and pediatric anatomy, with less emphasis devoted to models of the human fetus. As concern grows over possible radiation-induced cancers from medical and non-medical exposures of the pregnant female, the need to better quantify fetal radiation doses, particularly at the organ-level, also increases. Studies such as the European Union's SOLO (Epidemiological Studies of Exposed Southern Urals Populations) hope to improve our understanding of cancer risks following chronic in utero radiation exposure. For projects such as SOLO, currently available fetal anatomic models do not provide sufficient anatomical detail for organ-level dose assessment. To address this need, two fetal hybrid computational phantoms were constructed using high-quality magnetic resonance imaging and computed tomography image sets obtained for two well-preserved fetal specimens aged 11.5 and 21 weeks post-conception. Individual soft tissue organs, bone sites and outer body contours were segmented from these images using 3D-DOCTOR(TM) and then imported to the 3D modeling software package Rhinoceros(TM) for further modeling and conversion of soft tissue organs, certain bone sites and outer body contours to deformable non-uniform rational B-spline surfaces. The two specimen-specific phantoms, along with a modified version of the 38 week UF hybrid newborn phantom, comprised a set of base phantoms from which a series of hybrid computational phantoms was derived for fetal ages 8, 10, 15, 20, 25, 30, 35 and 38 weeks post-conception. The methodology used to construct the series of phantoms accounted for the following age-dependent parameters: (1) variations in skeletal size and proportion, (2) bone-dependent variations in relative levels of bone growth, (3) variations in individual organ masses and total fetal masses and (4) statistical percentile variations

  20. The UF family of hybrid phantoms of the developing human fetus for computational radiation dosimetry

    International Nuclear Information System (INIS)

    Maynard, Matthew R; Geyer, John W; Bolch, Wesley; Aris, John P; Shifrin, Roger Y

    2011-01-01

    Historically, the development of computational phantoms for radiation dosimetry has primarily been directed at capturing and representing adult and pediatric anatomy, with less emphasis devoted to models of the human fetus. As concern grows over possible radiation-induced cancers from medical and non-medical exposures of the pregnant female, the need to better quantify fetal radiation doses, particularly at the organ-level, also increases. Studies such as the European Union's SOLO (Epidemiological Studies of Exposed Southern Urals Populations) hope to improve our understanding of cancer risks following chronic in utero radiation exposure. For projects such as SOLO, currently available fetal anatomic models do not provide sufficient anatomical detail for organ-level dose assessment. To address this need, two fetal hybrid computational phantoms were constructed using high-quality magnetic resonance imaging and computed tomography image sets obtained for two well-preserved fetal specimens aged 11.5 and 21 weeks post-conception. Individual soft tissue organs, bone sites and outer body contours were segmented from these images using 3D-DOCTOR(TM) and then imported to the 3D modeling software package Rhinoceros(TM) for further modeling and conversion of soft tissue organs, certain bone sites and outer body contours to deformable non-uniform rational B-spline surfaces. The two specimen-specific phantoms, along with a modified version of the 38 week UF hybrid newborn phantom, comprised a set of base phantoms from which a series of hybrid computational phantoms was derived for fetal ages 8, 10, 15, 20, 25, 30, 35 and 38 weeks post-conception. The methodology used to construct the series of phantoms accounted for the following age-dependent parameters: (1) variations in skeletal size and proportion, (2) bone-dependent variations in relative levels of bone growth, (3) variations in individual organ masses and total fetal masses and (4) statistical percentile variations in

  1. Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.

    Science.gov (United States)

    Smukowski Heil, Caiti; Burton, Joshua N; Liachko, Ivan; Friedrich, Anne; Hanson, Noah A; Morris, Cody L; Schacherer, Joseph; Shendure, Jay; Thomas, James H; Dunham, Maitreya J

    2018-01-01

    Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method's application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute four bacterial and four yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed, yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  2. Data identification for improving gene network inference using computational algebra.

    Science.gov (United States)

    Dimitrova, Elena; Stigler, Brandilyn

    2014-11-01

    Identification of models of gene regulatory networks is sensitive to the amount of data used as input. Considering the substantial costs in conducting experiments, it is of value to have an estimate of the amount of data required to infer the network structure. To minimize wasted resources, it is also beneficial to know which data are necessary to identify the network. Knowledge of the data and knowledge of the terms in polynomial models are often required a priori in model identification. In applications, it is unlikely that the structure of a polynomial model will be known, which may force data sets to be unnecessarily large in order to identify a model. Furthermore, none of the known results provides any strategy for constructing data sets to uniquely identify a model. We provide a specialization of an existing criterion for deciding when a set of data points identifies a minimal polynomial model when its monomial terms have been specified. Then, we relax the requirement of the knowledge of the monomials and present results for model identification given only the data. Finally, we present a method for constructing data sets that identify minimal polynomial models.

  3. Identification of Enhancers In Human: Advances In Computational Studies

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2016-01-01

    Finally, we take a step further by developing a novel feature selection method suitable for defining a computational framework capable of analyzing the genomic content of enhancers and reporting cell-line specific predictive signatures.

  4. Identification of risk factors of computer information technologies in education

    Directory of Open Access Journals (Sweden)

    Hrebniak M.P.

    2014-03-01

    Full Text Available The basic direction of development of secondary school and vocational training is computer training of schoolchildren and students, including distance forms of education and widespread usage of world information systems. The purpose of the work is to determine risk factors for schoolchildren and students, when using modern information and computer technologies. Results of researches allowed to establish dynamics of formation of skills using computer information technologies in education and characteristics of mental ability among schoolchildren and students during training in high school. Common risk factors, while operating CIT, are: intensification and formalization of intellectual activity, adverse ergonomic parameters, unfavorable working posture, excess of hygiene standards by chemical and physical characteristics. The priority preventive directions in applying computer information technology in education are: improvement of optimal visual parameters of activity, rationalization of ergonomic parameters, minimizing of adverse effects of chemical and physical conditions, rationalization of work and rest activity.

  5. Morphological identification of Lucilia sericata, Lucilia cuprina and their hybrids (Diptera, Calliphoridae)

    Science.gov (United States)

    Williams, Kirstin A.; Villet, Martin H.

    2014-01-01

    Abstract Hybrids of Lucilia sericata and Lucilia cuprina have been shown to exist in previous studies using molecular methods, but no study has shown explicitly that these hybrids can be identified morphologically. Published morphological characters used to identify L. sericata and L. cuprina were reviewed, and then scored and tested using specimens of both species and known hybrids. Ordination by multi-dimensional scaling indicated that the species were separable, and that hybrids resembled L. cuprina, whatever their origin. Discriminant function analysis of the characters successfully separated the specimens into three unambiguous groups – L. sericata, L. cuprina and hybrids. The hybrids were morphologically similar irrespective of whether they were from an ancient introgressed lineage or more modern. This is the first evidence that hybrids of these two species can be identified from their morphology. The usefulness of the morphological characters is also discussed and photographs of several characters are included to facilitate their assessment. PMID:25061373

  6. Molecular identification and histopathological study of natural Streptococcus agalactiae infection in hybrid tilapia (Oreochromis niloticus).

    Science.gov (United States)

    Laith, A A; Ambak, Mohd Azmi; Hassan, Marina; Sheriff, Shahreza Md; Nadirah, Musa; Draman, Ahmad Shuhaimi; Wahab, Wahidah; Ibrahim, Wan Nurhafizah Wan; Aznan, Alia Syafiqah; Jabar, Amina; Najiah, Musa

    2017-01-01

    The main objective of this study was to emphasize on histopathological examinations and molecular identification of Streptococcus agalactiae isolated from natural infections in hybrid tilapia ( Oreochromis niloticus ) in Temerloh Pahang, Malaysia, as well as to determine the susceptibility of the pathogen strains to various currently available antimicrobial agents. The diseased fishes were observed for variable clinical signs including fin hemorrhages, alterations in behavior associated with erratic swimming, exophthalmia, and mortality. Tissue samples from the eyes, brain, kidney, liver, and spleen were taken for bacterial isolation. Identification of S. agalactiae was screened by biochemical methods and confirmed by VITEK 2 and 16S rRNA gene sequencing. The antibiogram profiling of the isolate was tested against 18 standard antibiotics included nitrofurantoin, flumequine, florfenicol, amoxylin, doxycycline, oleandomycin, tetracycline, ampicillin, lincomycin, colistin sulfate, oxolinic acid, novobiocin, spiramycin, erythromycin, fosfomycin, neomycin, gentamycin, and polymyxin B. The histopathological analysis of eyes, brain, liver, kidney, and spleen was observed for abnormalities related to S. agalactiae infection. The suspected colonies of S. agalactiae identified by biochemical methods was observed as Gram-positive chained cocci, β-hemolytic, and non-motile. The isolate was confirmed as S. agalactiae by VITEK 2 (99% similarity), reconfirmed by 16S rRNA gene sequencing (99% similarity) and deposited in GenBank with accession no. KT869025. The isolate was observed to be resistance to neomycin and gentamicin. The most consistent gross findings were marked hemorrhages, erosions of caudal fin, and exophthalmos. Microscopic examination confirmed the presence of marked congestion and infiltration of inflammatory cell in the eye, brain, kidney, liver, and spleen. Eye samples showed damage of the lens capsule, hyperemic and hemorrhagic choroid tissue, and retina

  7. Molecular identification and histopathological study of natural Streptococcus agalactiae infection in hybrid tilapia (Oreochromis niloticus

    Directory of Open Access Journals (Sweden)

    Laith Abdul Razzak

    2017-01-01

    Full Text Available Aim: The main objective of this study was to emphasize on histopathological examinations and molecular identification of Streptococcus agalactiae isolated from natural infections in hybrid tilapia (Oreochromis niloticus in Temerloh Pahang, Malaysia, as well as to determine the susceptibility of the pathogen strains to various currently available antimicrobial agents. Materials and Methods: The diseased fishes were observed for variable clinical signs including fin hemorrhages, alterations in behavior associated with erratic swimming, exophthalmia, and mortality. Tissue samples from the eyes, brain, kidney, liver, and spleen were taken for bacterial isolation. Identification of S. agalactiae was screened by biochemical methods and confirmed by VITEK 2 and 16S rRNA gene sequencing. The antibiogram profiling of the isolate was tested against 18 standard antibiotics included nitrofurantoin, flumequine, florfenicol, amoxylin, doxycycline, oleandomycin, tetracycline, ampicillin, lincomycin, colistin sulfate, oxolinic acid, novobiocin, spiramycin, erythromycin, fosfomycin, neomycin, gentamycin, and polymyxin B. The histopathological analysis of eyes, brain, liver, kidney, and spleen was observed for abnormalities related to S. agalactiae infection. Results: The suspected colonies of S. agalactiae identified by biochemical methods was observed as Gram-positive chained cocci, β-hemolytic, and non-motile. The isolate was confirmed as S. agalactiae by VITEK 2 (99% similarity, reconfirmed by 16S rRNA gene sequencing (99% similarity and deposited in GenBank with accession no. KT869025. The isolate was observed to be resistance to neomycin and gentamicin. The most consistent gross findings were marked hemorrhages, erosions of caudal fin, and exophthalmos. Microscopic examination confirmed the presence of marked congestion and infiltration of inflammatory cell in the eye, brain, kidney, liver, and spleen. Eye samples showed damage of the lens capsule

  8. ANIBAL - a Hybrid Computer Language for EAI 680-PDP 8/I, FPP 12

    DEFF Research Database (Denmark)

    Højberg, Kristian Søe

    1974-01-01

    and special hybrid computer commands. ANIBAL consists of a general-purpose analog interface subroutine ANI and the macro processor 8BAL (DECUS NO 8-497A.1). When a source program with FORTRAN and 8BAL statements is processed, the FORTRAN statements are transferred unchanged, while the 8BAL code is translated...... essentially to ANI sub-routine calls, which are defined in a macro library. The resulting code is translated by the standard FORTRAN compiler. The language is very flexible as the instructions can be changed and commands can be added to or excluded from the library ....

  9. Treatment of early and late reflections in a hybrid computer model for room acoustics

    DEFF Research Database (Denmark)

    Naylor, Graham

    1992-01-01

    The ODEON computer model for acoustics in large rooms is intended for use both in design (by predicting room acoustical indices quickly and easily) and in research (by forming the basis of an auralization system and allowing study of various room acoustical phenomena). These conflicting demands...... preclude the use of both ``pure'' image source and ``pure'' particle tracing methods. A hybrid model has been developed, in which rays discover potential image sources up to a specified order. Thereafter, the same ray tracing process is used in a different way to rapidly generate a dense reverberant decay...

  10. Identification of interspecific hybrids between loquat (eriobotrya japonica lindl.) and bengal loquat (e. bengalensis hook.)

    International Nuclear Information System (INIS)

    Wang, Y.; Deng, Q.; Zeng, J.; Zhang, J.

    2017-01-01

    Loquat (Eriobotrya japonica Lindl.) is an important subtropical fruit; however, loquat fruitlets are vulnerable to cold injury in winter, which significantly decreases loquat yield in most production regions. In the present study, two loquat cultivars ('Dawuxing' and '4-1-5') and one wild loquat (E. bengalensis Hook., Bengal loquat), were used for interspecific hybridization to produce hybrids with characteristics of spring blooming to avoid cold injury of fruitlets. Hybrid seedlings were derived from direct cross (loquat as female parent and Bengal loquat as male parent) and reciprocal cross. The authenticity of 47 hybrid seedlings was confirmed using inter-simple sequence repeat (ISSR) molecular markers; and leaf morphological characteristics of the hybrid offspring and parents were preliminarily studied and compared. The results suggested that 23 true direct cross hybrids and 12 true reciprocal cross hybrids were obtained, with hybrid authenticity rates of 100 and 50.0%, respectively. Thus, a novel method of distant hybridization for loquat breeding was developed, and with their various genetic and morphological characteristics these hybrids could be valuable germplasms for horticultural use. (author)

  11. Verification of a hybrid adjoint methodology in Titan for single photon emission computed tomography - 316

    International Nuclear Information System (INIS)

    Royston, K.; Haghighat, A.; Yi, C.

    2010-01-01

    The hybrid deterministic transport code TITAN is being applied to a Single Photon Emission Computed Tomography (SPECT) simulation of a myocardial perfusion study. The TITAN code's hybrid methodology allows the use of a discrete ordinates solver in the phantom region and a characteristics method solver in the collimator region. Currently we seek to validate the adjoint methodology in TITAN for this application using a SPECT model that has been created in the MCNP5 Monte Carlo code. The TITAN methodology was examined based on the response of a single voxel detector placed in front of the heart with and without collimation. For the case without collimation, the TITAN response for single voxel-sized detector had a -9.96% difference relative to the MCNP5 response. To simulate collimation, the adjoint source was specified in directions located within the collimator acceptance angle. For a single collimator hole with a diameter matching the voxel dimension, a difference of -0.22% was observed. Comparisons to groupings of smaller collimator holes of two different sizes resulted in relative differences of 0.60% and 0.12%. The number of adjoint source directions within an acceptance angle was increased and showed no significant change in accuracy. Our results indicate that the hybrid adjoint methodology of TITAN yields accurate solutions greater than a factor of two faster than MCNP5. (authors)

  12. EEG Classification for Hybrid Brain-Computer Interface Using a Tensor Based Multiclass Multimodal Analysis Scheme.

    Science.gov (United States)

    Ji, Hongfei; Li, Jie; Lu, Rongrong; Gu, Rong; Cao, Lei; Gong, Xiaoliang

    2016-01-01

    Electroencephalogram- (EEG-) based brain-computer interface (BCI) systems usually utilize one type of changes in the dynamics of brain oscillations for control, such as event-related desynchronization/synchronization (ERD/ERS), steady state visual evoked potential (SSVEP), and P300 evoked potentials. There is a recent trend to detect more than one of these signals in one system to create a hybrid BCI. However, in this case, EEG data were always divided into groups and analyzed by the separate processing procedures. As a result, the interactive effects were ignored when different types of BCI tasks were executed simultaneously. In this work, we propose an improved tensor based multiclass multimodal scheme especially for hybrid BCI, in which EEG signals are denoted as multiway tensors, a nonredundant rank-one tensor decomposition model is proposed to obtain nonredundant tensor components, a weighted fisher criterion is designed to select multimodal discriminative patterns without ignoring the interactive effects, and support vector machine (SVM) is extended to multiclass classification. Experiment results suggest that the proposed scheme can not only identify the different changes in the dynamics of brain oscillations induced by different types of tasks but also capture the interactive effects of simultaneous tasks properly. Therefore, it has great potential use for hybrid BCI.

  13. Hybrid simulation of scatter intensity in industrial cone-beam computed tomography

    International Nuclear Information System (INIS)

    Thierry, R.; Miceli, A.; Hofmann, J.; Flisch, A.; Sennhauser, U.

    2009-01-01

    A cone-beam computed tomography (CT) system using a 450 kV X-ray tube has been developed to challenge the three-dimensional imaging of parts of the automotive industry in short acquisition time. Because the probability of detecting scattered photons is high regarding the energy range and the area of detection, a scattering correction becomes mandatory for generating reliable images with enhanced contrast detectability. In this paper, we present a hybrid simulator for the fast and accurate calculation of the scattering intensity distribution. The full acquisition chain, from the generation of a polyenergetic photon beam, its interaction with the scanned object and the energy deposit in the detector is simulated. Object phantoms can be spatially described in form of voxels, mathematical primitives or CAD models. Uncollided radiation is treated with a ray-tracing method and scattered radiation is split into single and multiple scattering. The single scattering is calculated with a deterministic approach accelerated with a forced detection method. The residual noisy signal is subsequently deconvoluted with the iterative Richardson-Lucy method. Finally the multiple scattering is addressed with a coarse Monte Carlo (MC) simulation. The proposed hybrid method has been validated on aluminium phantoms with varying size and object-to-detector distance, and found in good agreement with the MC code Geant4. The acceleration achieved by the hybrid method over the standard MC on a single projection is approximately of three orders of magnitude.

  14. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus).

    Science.gov (United States)

    Moody, Michael L; Rieseberg, Loren H

    2012-07-01

    The annual sunflowers (Helianthus sect. Helianthus) present a formidable challenge for phylogenetic inference because of ancient hybrid speciation, recent introgression, and suspected issues with deep coalescence. Here we analyze sequence data from 11 nuclear DNA (nDNA) genes for multiple genotypes of species within the section to (1) reconstruct the phylogeny of this group, (2) explore the utility of nDNA gene trees for detecting hybrid speciation and introgression; and (3) test an empirical method of hybrid identification based on the phylogenetic congruence of nDNA gene trees from tightly linked genes. We uncovered considerable topological heterogeneity among gene trees with or without three previously identified hybrid species included in the analyses, as well as a general lack of reciprocal monophyly of species. Nonetheless, partitioned Bayesian analyses provided strong support for the reciprocal monophyly of all species except H. annuus (0.89 PP), the most widespread and abundant annual sunflower. Previous hypotheses of relationships among taxa were generally strongly supported (1.0 PP), except among taxa typically associated with H. annuus, apparently due to the paraphyly of the latter in all gene trees. While the individual nDNA gene trees provided a useful means for detecting recent hybridization, identification of ancient hybridization was problematic for all ancient hybrid species, even when linkage was considered. We discuss biological factors that affect the efficacy of phylogenetic methods for hybrid identification.

  15. A Semiactive and Adaptive Hybrid Control System for a Tracked Vehicle Hydropneumatic Suspension Based on Disturbance Identification

    Directory of Open Access Journals (Sweden)

    Shousong Han

    2017-01-01

    Full Text Available The riding conditions for a high-speed tracked vehicle are quite complex. To enhance the adaptability of suspension systems to different riding conditions, a semiactive and self-adaptive hybrid control strategy based on disturbance velocity and frequency identification was proposed. A mathematical model of the semiactive, self-adaptive hybrid suspension control system, along with a performance evaluation function, was established. Based on a two-degree-of-freedom (DOF suspension system, the kinematic relations and frequency zero-crossing detection method were defined, and expressions for the disturbance velocity and disturbance frequency of the road were obtained. Optimal scheduling of the semiactive hybrid damping control gain (csky, cground, chybrid and self-adaptive control gain (cv under different disturbances were realized by exploiting the particle swarm multiobjective optimization algorithm. An experimental study using a carefully designed test rig was performed under a number of typical riding conditions of tracked vehicles, and the results showed that the proposed control strategy is capable of accurately recognizing different disturbances, shifting between control modes (semiactive/self-adaptive, and scheduling the damping control gain according to the disturbance identification outcomes; hence, the proposed strategy could achieve a good trade-off between ride comfort and ride safety and efficiently increase the overall performance of the suspension under various riding conditions.

  16. General hybrid projective complete dislocated synchronization with non-derivative and derivative coupling based on parameter identification in several chaotic and hyperchaotic systems

    International Nuclear Information System (INIS)

    Sun Jun-Wei; Shen Yi; Zhang Guo-Dong; Wang Yan-Feng; Cui Guang-Zhao

    2013-01-01

    According to the Lyapunov stability theorem, a new general hybrid projective complete dislocated synchronization scheme with non-derivative and derivative coupling based on parameter identification is proposed under the framework of drive-response systems. Every state variable of the response system equals the summation of the hybrid drive systems in the previous hybrid synchronization. However, every state variable of the drive system equals the summation of the hybrid response systems while evolving with time in our method. Complete synchronization, hybrid dislocated synchronization, projective synchronization, non-derivative and derivative coupling, and parameter identification are included as its special item. The Lorenz chaotic system, Rössler chaotic system, memristor chaotic oscillator system, and hyperchaotic Lü system are discussed to show the effectiveness of the proposed methods. (general)

  17. Computational identification of putative cytochrome P450 genes in ...

    African Journals Online (AJOL)

    In this work, a computational study of expressed sequence tags (ESTs) of soybean was performed by data mining methods and bio-informatics tools and as a result 78 putative P450 genes were identified, including 57 new ones. These genes were classified into five clans and 20 families by sequence similarities and among ...

  18. Genome-wide Studies of Mycolic Acid Bacteria: Computational Identification and Analysis of a Minimal Genome

    KAUST Repository

    Kamanu, Frederick Kinyua

    2012-12-01

    The mycolic acid bacteria are a distinct suprageneric group of asporogenous Grampositive, high GC-content bacteria, distinguished by the presence of mycolic acids in their cell envelope. They exhibit great diversity in their cell and morphology; although primarily non-pathogens, this group contains three major pathogens Mycobacterium leprae, Mycobacterium tuberculosis complex, and Corynebacterium diphtheria. Although the mycolic acid bacteria are a clearly defined group of bacteria, the taxonomic relationships between its constituent genera and species are less well defined. Two approaches were tested for their suitability in describing the taxonomy of the group. First, a Multilocus Sequence Typing (MLST) experiment was assessed and found to be superior to monophyletic (16S small ribosomal subunit) in delineating a total of 52 mycolic acid bacterial species. Phylogenetic inference was performed using the neighbor-joining method. To further refine phylogenetic analysis and to take advantage of the widespread availability of bacterial genome data, a computational framework that simulates DNA-DNA hybridisation was developed and validated using multiscale bootstrap resampling. The tool classifies microbial genomes based on whole genome DNA, and was deployed as a web-application using PHP and Javascript. It is accessible online at http://cbrc.kaust.edu.sa/dna_hybridization/ A third study was a computational and statistical methods in the identification and analysis of a putative minimal mycolic acid bacterial genome so as to better understand (1) the genomic requirements to encode a mycolic acid bacterial cell and (2) the role and type of genes and genetic elements that lead to the massive increase in genome size in environmental mycolic acid bacteria. Using a reciprocal comparison approach, a total of 690 orthologous gene clusters forming a putative minimal genome were identified across 24 mycolic acid bacterial species. In order to identify new potential drug

  19. Hybrid Single Photon Emission Computed Tomography/Computed Tomography Sulphur Colloid Scintigraphy in Focal Nodular Hyperplasia

    International Nuclear Information System (INIS)

    Bhoil, Amit; Gayana, Shankramurthy; Sood, Ashwani; Bhattacharya, Anish; Mittal, Bhagwant Rai

    2013-01-01

    It is important to differentiate focal nodular hyperplasia (FNH), a benign condition of liver most commonly affecting women, from other neoplasm such as hepatic adenoma and metastasis. The functional reticuloendothelial features of FNH can be demonstrated by scintigraphy. We present a case of breast cancer in whom fluorodeoxyglucose positron emission tomography/computerized tomography (CT) showed a homogenous hyperdense lesion in liver, which on Tc99m sulfur colloid single-photon emission computed tomography/CT was found to have increased focal tracer uptake suggestive of FNH

  20. Symmetric and asymmetric hybrid cryptosystem based on compressive sensing and computer generated holography

    Science.gov (United States)

    Ma, Lihong; Jin, Weimin

    2018-01-01

    A novel symmetric and asymmetric hybrid optical cryptosystem is proposed based on compressive sensing combined with computer generated holography. In this method there are six encryption keys, among which two decryption phase masks are different from the two random phase masks used in the encryption process. Therefore, the encryption system has the feature of both symmetric and asymmetric cryptography. On the other hand, because computer generated holography can flexibly digitalize the encrypted information and compressive sensing can significantly reduce data volume, what is more, the final encryption image is real function by phase truncation, the method favors the storage and transmission of the encryption data. The experimental results demonstrate that the proposed encryption scheme boosts the security and has high robustness against noise and occlusion attacks.

  1. PWR hybrid computer model for assessing the safety implications of control systems

    International Nuclear Information System (INIS)

    Smith, O.L.; Renier, J.P.; Difilippo, F.C.; Clapp, N.E.; Sozer, A.; Booth, R.S.; Craddick, W.G.; Morris, D.G.

    1986-03-01

    The ORNL study of safety-related aspects of nuclear power plant control systems consists of two interrelated tasks: (1) failure mode and effects analysis (FMEA) that identified single and multiple component failures that might lead to significant plant upsets and (2) computer models that used these failures as initial conditions and traced the dynamic impact on the control system and remainder of the plant. This report describes the simulation of Oconee Unit 1, the first plant analyzed. A first-principles, best-estimate model was developed and implemented on a hybrid computer consisting of AD-4 analog and PDP-10 digital machines. Controls were placed primarily on the analog to use its interactive capability to simulate operator action. 48 refs., 138 figs., 15 tabs

  2. Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

    Science.gov (United States)

    Wu, Xin; Koslowski, Axel; Thiel, Walter

    2012-07-10

    In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

  3. The UF family of reference hybrid phantoms for computational radiation dosimetry

    International Nuclear Information System (INIS)

    Lee, Choonsik; Lodwick, Daniel; Hurtado, Jorge; Pafundi, Deanna; Williams, Jonathan L; Bolch, Wesley E

    2010-01-01

    Computational human phantoms are computer models used to obtain dose distributions within the human body exposed to internal or external radiation sources. In addition, they are increasingly used to develop detector efficiencies for in vivo whole-body counters. Two classes of computational human phantoms have been widely utilized for dosimetry calculation: stylized and voxel phantoms that describe human anatomy through mathematical surface equations and 3D voxel matrices, respectively. Stylized phantoms are flexible in that changes to organ position and shape are possible given avoidance of region overlap, while voxel phantoms are typically fixed to a given patient anatomy, yet can be proportionally scaled to match individuals of larger or smaller stature, but of equivalent organ anatomy. Voxel phantoms provide much better anatomical realism as compared to stylized phantoms which are intrinsically limited by mathematical surface equations. To address the drawbacks of these phantoms, hybrid phantoms based on non-uniform rational B-spline (NURBS) surfaces have been introduced wherein anthropomorphic flexibility and anatomic realism are both preserved. Researchers at the University of Florida have introduced a series of hybrid phantoms representing the ICRP Publication 89 reference newborn, 15 year, and adult male and female. In this study, six additional phantoms are added to the UF family of hybrid phantoms-those of the reference 1 year, 5 year and 10 year child. Head and torso CT images of patients whose ages were close to the targeted ages were obtained under approved protocols. Major organs and tissues were segmented from these images using an image processing software, 3D-DOCTOR(TM). NURBS and polygon mesh surfaces were then used to model individual organs and tissues after importing the segmented organ models to the 3D NURBS modeling software, Rhinoceros(TM). The phantoms were matched to four reference datasets: (1) standard anthropometric data, (2) reference

  4. Computational identification of candidate nucleotide cyclases in higher plants

    KAUST Repository

    Wong, Aloysius Tze

    2013-09-03

    In higher plants guanylyl cyclases (GCs) and adenylyl cyclases (ACs) cannot be identified using BLAST homology searches based on annotated cyclic nucleotide cyclases (CNCs) of prokaryotes, lower eukaryotes, or animals. The reason is that CNCs are often part of complex multifunctional proteins with different domain organizations and biological functions that are not conserved in higher plants. For this reason, we have developed CNC search strategies based on functionally conserved amino acids in the catalytic center of annotated and/or experimentally confirmed CNCs. Here we detail this method which has led to the identification of >25 novel candidate CNCs in Arabidopsis thaliana, several of which have been experimentally confirmed in vitro and in vivo. We foresee that the application of this method can be used to identify many more members of the growing family of CNCs in higher plants. © Springer Science+Business Media New York 2013.

  5. A simplified computational fluid-dynamic approach to the oxidizer injector design in hybrid rockets

    Science.gov (United States)

    Di Martino, Giuseppe D.; Malgieri, Paolo; Carmicino, Carmine; Savino, Raffaele

    2016-12-01

    Fuel regression rate in hybrid rockets is non-negligibly affected by the oxidizer injection pattern. In this paper a simplified computational approach developed in an attempt to optimize the oxidizer injector design is discussed. Numerical simulations of the thermo-fluid-dynamic field in a hybrid rocket are carried out, with a commercial solver, to investigate into several injection configurations with the aim of increasing the fuel regression rate and minimizing the consumption unevenness, but still favoring the establishment of flow recirculation at the motor head end, which is generated with an axial nozzle injector and has been demonstrated to promote combustion stability, and both larger efficiency and regression rate. All the computations have been performed on the configuration of a lab-scale hybrid rocket motor available at the propulsion laboratory of the University of Naples with typical operating conditions. After a preliminary comparison between the two baseline limiting cases of an axial subsonic nozzle injector and a uniform injection through the prechamber, a parametric analysis has been carried out by varying the oxidizer jet flow divergence angle, as well as the grain port diameter and the oxidizer mass flux to study the effect of the flow divergence on heat transfer distribution over the fuel surface. Some experimental firing test data are presented, and, under the hypothesis that fuel regression rate and surface heat flux are proportional, the measured fuel consumption axial profiles are compared with the predicted surface heat flux showing fairly good agreement, which allowed validating the employed design approach. Finally an optimized injector design is proposed.

  6. Workflow Scheduling Using Hybrid GA-PSO Algorithm in Cloud Computing

    Directory of Open Access Journals (Sweden)

    Ahmad M. Manasrah

    2018-01-01

    Full Text Available Cloud computing environment provides several on-demand services and resource sharing for clients. Business processes are managed using the workflow technology over the cloud, which represents one of the challenges in using the resources in an efficient manner due to the dependencies between the tasks. In this paper, a Hybrid GA-PSO algorithm is proposed to allocate tasks to the resources efficiently. The Hybrid GA-PSO algorithm aims to reduce the makespan and the cost and balance the load of the dependent tasks over the heterogonous resources in cloud computing environments. The experiment results show that the GA-PSO algorithm decreases the total execution time of the workflow tasks, in comparison with GA, PSO, HSGA, WSGA, and MTCT algorithms. Furthermore, it reduces the execution cost. In addition, it improves the load balancing of the workflow application over the available resources. Finally, the obtained results also proved that the proposed algorithm converges to optimal solutions faster and with higher quality compared to other algorithms.

  7. Autumn Algorithm-Computation of Hybridization Networks for Realistic Phylogenetic Trees.

    Science.gov (United States)

    Huson, Daniel H; Linz, Simone

    2018-01-01

    A minimum hybridization network is a rooted phylogenetic network that displays two given rooted phylogenetic trees using a minimum number of reticulations. Previous mathematical work on their calculation has usually assumed the input trees to be bifurcating, correctly rooted, or that they both contain the same taxa. These assumptions do not hold in biological studies and "realistic" trees have multifurcations, are difficult to root, and rarely contain the same taxa. We present a new algorithm for computing minimum hybridization networks for a given pair of "realistic" rooted phylogenetic trees. We also describe how the algorithm might be used to improve the rooting of the input trees. We introduce the concept of "autumn trees", a nice framework for the formulation of algorithms based on the mathematics of "maximum acyclic agreement forests". While the main computational problem is hard, the run-time depends mainly on how different the given input trees are. In biological studies, where the trees are reasonably similar, our parallel implementation performs well in practice. The algorithm is available in our open source program Dendroscope 3, providing a platform for biologists to explore rooted phylogenetic networks. We demonstrate the utility of the algorithm using several previously studied data sets.

  8. COMPUTER-AIDED IDENTIFICATION OF ENVIRONMENTAL IMPACTS OF BUSINESSES

    Directory of Open Access Journals (Sweden)

    Halina Marczak

    2015-11-01

    Full Text Available Discussed elements of the computer databases used in “input-output” analysis method to identify enterprise impact on the environment. Presented “input-output” database parameters essential for a company performing road transport of finished products. Presented a method for determining parameters: energy consumption by means of road transport and the emissions amount with exhaust fumes from vehicles. Discussed parameters of the computer databases needed to calculate the amount of fees for use of the environment. These data and amount of fees for environment usage may be useful in assessing the scale of the impact on environment by businesses. Described a method for determining the fee for gases and dust emitted into the air from combustion of fuels in internal combustion engines.

  9. Hybrid Brain–Computer Interface Techniques for Improved Classification Accuracy and Increased Number of Commands: A Review

    OpenAIRE

    Hong, Keum-Shik; Khan, Muhammad Jawad

    2017-01-01

    In this article, non-invasive hybrid brain–computer interface (hBCI) technologies for improving classification accuracy and increasing the number of commands are reviewed. Hybridization combining more than two modalities is a new trend in brain imaging and prosthesis control. Electroencephalography (EEG), due to its easy use and fast temporal resolution, is most widely utilized in combination with other brain/non-brain signal acquisition modalities, for instance, functional near infrared spec...

  10. Cloth-based hybridization array system for expanded identification of the animal species origin of derived materials in feeds.

    Science.gov (United States)

    Murphy, Johanna; Armour, Jennifer; Blais, Burton W

    2007-12-01

    A cloth-based hybridization array system (CHAS) previously developed for the detection of animal species for which prohibited materials have been specified (cattle, sheep, goat, elk, and deer) has been expanded to include the detection of animal species for which there are no prohibitions (pig and horse) in Canadian and American animal feeds. Animal species were identified by amplification of mitochondrial DNA sequences by PCR and subsequent hybridization of the amplicons with an array of species-specific oligonucleotide capture probes immobilized on a polyester cloth support, followed by an immunoenzymatic assay of the bound PCR products. The CHAS permitted sensitive and specific detection of meat meals from different animal species blended in a grain-based feed and should provide a useful adjunct to microscopic examination for the identification of prohibited materials in animal feeds.

  11. Computational identification of MoRFs in protein sequences.

    Science.gov (United States)

    Malhis, Nawar; Gsponer, Jörg

    2015-06-01

    Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge. In this study, we introduce MoRFCHiBi, a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRFCHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVMS, is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVMT, is used to identify similarities between regions in a query sequence and MoRFs of the training set. We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRFCHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRFCHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools. http://www.chibi.ubc.ca/morf/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Cloud identification using genetic algorithms and massively parallel computation

    Science.gov (United States)

    Buckles, Bill P.; Petry, Frederick E.

    1996-01-01

    As a Guest Computational Investigator under the NASA administered component of the High Performance Computing and Communication Program, we implemented a massively parallel genetic algorithm on the MasPar SIMD computer. Experiments were conducted using Earth Science data in the domains of meteorology and oceanography. Results obtained in these domains are competitive with, and in most cases better than, similar problems solved using other methods. In the meteorological domain, we chose to identify clouds using AVHRR spectral data. Four cloud speciations were used although most researchers settle for three. Results were remarkedly consistent across all tests (91% accuracy). Refinements of this method may lead to more timely and complete information for Global Circulation Models (GCMS) that are prevalent in weather forecasting and global environment studies. In the oceanographic domain, we chose to identify ocean currents from a spectrometer having similar characteristics to AVHRR. Here the results were mixed (60% to 80% accuracy). Given that one is willing to run the experiment several times (say 10), then it is acceptable to claim the higher accuracy rating. This problem has never been successfully automated. Therefore, these results are encouraging even though less impressive than the cloud experiment. Successful conclusion of an automated ocean current detection system would impact coastal fishing, naval tactics, and the study of micro-climates. Finally we contributed to the basic knowledge of GA (genetic algorithm) behavior in parallel environments. We developed better knowledge of the use of subpopulations in the context of shared breeding pools and the migration of individuals. Rigorous experiments were conducted based on quantifiable performance criteria. While much of the work confirmed current wisdom, for the first time we were able to submit conclusive evidence. The software developed under this grant was placed in the public domain. An extensive user

  13. Computational identification of antigen-binding antibody fragments.

    Science.gov (United States)

    Burkovitz, Anat; Leiderman, Olga; Sela-Culang, Inbal; Byk, Gerardo; Ofran, Yanay

    2013-03-01

    Determining which parts of the Ab are essential for Ag recognition and binding is crucial for understanding B cell-mediated immunity. Identification of fragments of Abs that maintain specificity to the Ag will also allow for the development of improved Ab-based therapy and diagnostics. In this article, we show that structural analysis of Ab-Ag complexes reveals which fragments of the Ab may bind the Ag on their own. In particular, it is possible to predict whether a given CDR is likely to bind the Ag as a peptide by analyzing the energetic contribution of each CDR to Ag binding and by assessing to what extent the interaction between that CDR and the Ag depends on other CDRs. To demonstrate this, we analyzed five Ab-Ag complexes and predicted for each of them which of the CDRs may bind the Ag on its own as a peptide. We then show that these predictions are in agreement with our experimental analysis and with previously published experimental results. These findings promote our understanding of the modular nature of Ab-Ag interactions and lay the foundation for the rational design of active CDR-derived peptides.

  14. PWR hybrid computer model for assessing the safety implications of control systems

    International Nuclear Information System (INIS)

    Smith, O.L.; Booth, R.S.; Clapp, N.E.; DiFilippo, F.C.; Renier, J.P.; Sozer, A.

    1985-01-01

    The ORNL study of safety-related aspects of control systems consists of two interrelated tasks, (1) a failure mode and effects analysis that, in part, identifies single and multiple component failures that may lead to significant plant upsets, and (2) a hybrid computer model that uses these failures as initial conditions and traces the dynamic impact on the control system and remainder of the plant. The second task is reported here. The initial step in model development was to define a suitable interface between the FMEA and computer simulation tasks. This involved identifying primary plant components that must be simulated in dynamic detail and secondary components that can be treated adequately by the FMEA alone. The FMEA in general explores broader spectra of initiating events that may collapse into a reduced number of computer runs. A portion of the FMEA includes consideration of power supply failures. Consequences of the transients may feedback on the initiating causes, and there may be an interactive relationship between the FMEA and the computer simulation. Since the thrust of this program is to investigate control system behavior, the controls are modeled in detail to accurately reproduce characteristic response under normal and off-normal transients. The balance of the model, including neutronics, thermohydraulics and component submodels, is developed in sufficient detail to provide a suitable support for the control system

  15. Computer-Aided Identification and Validation of Privacy Requirements

    Directory of Open Access Journals (Sweden)

    Rene Meis

    2016-05-01

    Full Text Available Privacy is a software quality that is closely related to security. The main difference is that security properties aim at the protection of assets that are crucial for the considered system, and privacy aims at the protection of personal data that are processed by the system. The identification of privacy protection needs in complex systems is a hard and error prone task. Stakeholders whose personal data are processed might be overlooked, or the sensitivity and the need of protection of the personal data might be underestimated. The later personal data and the needs to protect them are identified during the development process, the more expensive it is to fix these issues, because the needed changes of the system-to-be often affect many functionalities. In this paper, we present a systematic method to identify the privacy needs of a software system based on a set of functional requirements by extending the problem-based privacy analysis (ProPAn method. Our method is tool-supported and automated where possible to reduce the effort that has to be spent for the privacy analysis, which is especially important when considering complex systems. The contribution of this paper is a semi-automatic method to identify the relevant privacy requirements for a software-to-be based on its functional requirements. The considered privacy requirements address all dimensions of privacy that are relevant for software development. As our method is solely based on the functional requirements of the system to be, we enable users of our method to identify the privacy protection needs that have to be addressed by the software-to-be at an early stage of the development. As initial evaluation of our method, we show its applicability on a small electronic health system scenario.

  16. Species delineation and hybrid identification using diagnostic nuclear markers for Plectropomus leopardus and Plectropomus maculatus

    KAUST Repository

    He, Song

    2018-06-01

    Diagnostic molecular markers are an essential tool in the study of species’ ecology and evolution, particularly in closely related and sympatric species. Furthermore, the increasing awareness of wild-hybrids has led to a renewed interest in rapid diagnostic assays. Here, we test the ability of two mitochondrial (Cytb and COI) and two nuclear markers (ETS2 and TMO-4c4) to confidently discriminate purebred P. leopardus and P. maculatus and their first-generation hybrids. A sample of 48 purebred individuals and 91 interspecific hybrids were used in this study and their delineation confirmed using a set of microsatellite markers. Our results indicate mitochondrial markers could not distinguish even between species but both nuclear markers confidently identified species and first-generation hybrids. However, later-generation hybrids could not always be confidently identified due to on-going introgression between species. Our findings provide a robust tool to distinguish purebred individuals and interspecific hybrids in a pair of species with an unexpectedly high incidence of hybridization. The quick species discrimination abilities provided by these diagnostic markers are important for stock assessment and recruitment studies of these important fishery species.

  17. Species delineation and hybrid identification using diagnostic nuclear markers for Plectropomus leopardus and Plectropomus maculatus

    KAUST Repository

    He, Song; Harrison, Hugo B.; Berumen, Michael L.

    2018-01-01

    Diagnostic molecular markers are an essential tool in the study of species’ ecology and evolution, particularly in closely related and sympatric species. Furthermore, the increasing awareness of wild-hybrids has led to a renewed interest in rapid diagnostic assays. Here, we test the ability of two mitochondrial (Cytb and COI) and two nuclear markers (ETS2 and TMO-4c4) to confidently discriminate purebred P. leopardus and P. maculatus and their first-generation hybrids. A sample of 48 purebred individuals and 91 interspecific hybrids were used in this study and their delineation confirmed using a set of microsatellite markers. Our results indicate mitochondrial markers could not distinguish even between species but both nuclear markers confidently identified species and first-generation hybrids. However, later-generation hybrids could not always be confidently identified due to on-going introgression between species. Our findings provide a robust tool to distinguish purebred individuals and interspecific hybrids in a pair of species with an unexpectedly high incidence of hybridization. The quick species discrimination abilities provided by these diagnostic markers are important for stock assessment and recruitment studies of these important fishery species.

  18. Identification of warm day and cool night conditions induced flowering-related genes in a Phalaenopsis orchid hybrid by suppression subtractive hybridization.

    Science.gov (United States)

    Li, D M; Lü, F B; Zhu, G F; Sun, Y B; Xu, Y C; Jiang, M D; Liu, J W; Wang, Z

    2014-02-14

    The influence of warm day and cool night conditions on induction of spikes in Phalaenopsis orchids has been studied with respect to photosynthetic efficiency, metabolic cycles and physiology. However, molecular events involved in spike emergence induced by warm day and cool night conditions are not clearly understood. We examined gene expression induced by warm day and cool night conditions in the Phalaenopsis hybrid Fortune Saltzman through suppression subtractive hybridization, which allowed identification of flowering-related genes in warm day and cool night conditions in spikes and leaves at vegetative phase grown under warm daily temperatures. In total, 450 presumably regulated expressed sequence tags (ESTs) were identified and classified into functional categories, including metabolism, development, transcription factor, signal transduction, transportation, cell defense, and stress. Furthermore, database comparisons revealed a notable number of Phalaenopsis hybrid Fortune Saltzman ESTs that matched genes with unknown function. The expression profiles of 24 genes (from different functional categories) have been confirmed by quantitative real-time PCR in induced spikes and juvenile apical leaves. The results of the real-time PCR showed that, compared to the vegetative apical leaves, the transcripts of genes encoding flowering locus T, AP1, AP2, KNOX1, knotted1-like homeobox protein, R2R3-like MYB, adenosine kinase 2, S-adenosylmethionine synthetase, dihydroflavonol 4-reductase, and naringenin 3-dioxygenase accumulated significantly higher levels, and genes encoding FCA, retrotransposon protein Ty3 and C3HC4-type RING finger protein accumulated remarkably lower levels in spikes of early developmental stages. These results suggested that the genes of two expression changing trends may play positive and negative roles in the early floral transition of Phalaenopsis orchids. In conclusion, spikes induced by warm day and cool night conditions were complex in

  19. Near-term hybrid vehicle program, phase 1. Appendix B: Design trade-off studies report. Volume 3: Computer program listings

    Science.gov (United States)

    1979-01-01

    A description and listing is presented of two computer programs: Hybrid Vehicle Design Program (HYVELD) and Hybrid Vehicle Simulation Program (HYVEC). Both of the programs are modifications and extensions of similar programs developed as part of the Electric and Hybrid Vehicle System Research and Development Project.

  20. Apps for Angiosperms: The Usability of Mobile Computers and Printed Field Guides for UK Wild Flower and Winter Tree Identification

    Science.gov (United States)

    Stagg, Bethan C.; Donkin, Maria E.

    2017-01-01

    We investigated usability of mobile computers and field guide books with adult botanical novices, for the identification of wildflowers and deciduous trees in winter. Identification accuracy was significantly higher for wildflowers using a mobile computer app than field guide books but significantly lower for deciduous trees. User preference…

  1. Parallel Computing Characteristics of CUPID code under MPI and Hybrid environment

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Ryong; Yoon, Han Young [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Jeon, Byoung Jin; Choi, Hyoung Gwon [Seoul National Univ. of Science and Technology, Seoul (Korea, Republic of)

    2014-05-15

    In this paper, a characteristic of parallel algorithm is presented for solving an elliptic type equation of CUPID via domain decomposition method using the MPI and the parallel performance is estimated in terms of a scalability which shows the speedup ratio. In addition, the time-consuming pattern of major subroutines is studied. Two different grid systems are taken into account: 40,000 meshes for coarse system and 320,000 meshes for fine system. Since the matrix of the CUPID code differs according to whether the flow is single-phase or two-phase, the effect of matrix shape is evaluated. Finally, the effect of the preconditioner for matrix solver is also investigated. Finally, the hybrid (OpenMP+MPI) parallel algorithm is introduced and discussed in detail for solving pressure solver. Component-scale thermal-hydraulics code, CUPID has been developed for two-phase flow analysis, which adopts a three-dimensional, transient, three-field model, and parallelized to fulfill a recent demand for long-transient and highly resolved multi-phase flow behavior. In this study, the parallel performance of the CUPID code was investigated in terms of scalability. The CUPID code was parallelized with domain decomposition method. The MPI library was adopted to communicate the information at the neighboring domain. For managing the sparse matrix effectively, the CSR storage format is used. To take into account the characteristics of the pressure matrix which turns to be asymmetric for two-phase flow, both single-phase and two-phase calculations were run. In addition, the effect of the matrix size and preconditioning was also investigated. The fine mesh calculation shows better scalability than the coarse mesh because the number of coarse mesh does not need to decompose the computational domain excessively. The fine mesh can be present good scalability when dividing geometry with considering the ratio between computation and communication time. For a given mesh, single-phase flow

  2. Hybrid Donor-Dot Devices made using Top-down Ion Implantation for Quantum Computing

    Science.gov (United States)

    Bielejec, Edward; Bishop, Nathan; Carroll, Malcolm

    2012-02-01

    We present progress towards fabricating hybrid donor -- quantum dots (QD) for quantum computing. These devices will exploit the long coherence time of the donor system and the surface state manipulation associated with a QD. Fabrication requires detection of single ions implanted with 10's of nanometer precision. We show in this talk, 100% detection efficiency for single ions using a single ion Geiger mode avalanche (SIGMA) detector integrated into a Si MOS QD process flow. The NanoImplanter (nI) a focused ion beam system is used for precision top-down placement of the implanted ion. This machine has a 10 nm resolution combined with a mass velocity filter, allowing for the use of multi-species liquid metal ion sources (LMIS) to implant P and Sb ions, and a fast blanking and chopping system for single ion implants. The combination of the nI and integration of the SIGMA with the MOS QD process flow establishes a path to fabricate hybrid single donor-dot devices. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  3. Intelligent Soft Computing on Forex: Exchange Rates Forecasting with Hybrid Radial Basis Neural Network.

    Science.gov (United States)

    Falat, Lukas; Marcek, Dusan; Durisova, Maria

    2016-01-01

    This paper deals with application of quantitative soft computing prediction models into financial area as reliable and accurate prediction models can be very helpful in management decision-making process. The authors suggest a new hybrid neural network which is a combination of the standard RBF neural network, a genetic algorithm, and a moving average. The moving average is supposed to enhance the outputs of the network using the error part of the original neural network. Authors test the suggested model on high-frequency time series data of USD/CAD and examine the ability to forecast exchange rate values for the horizon of one day. To determine the forecasting efficiency, they perform a comparative statistical out-of-sample analysis of the tested model with autoregressive models and the standard neural network. They also incorporate genetic algorithm as an optimizing technique for adapting parameters of ANN which is then compared with standard backpropagation and backpropagation combined with K-means clustering algorithm. Finally, the authors find out that their suggested hybrid neural network is able to produce more accurate forecasts than the standard models and can be helpful in eliminating the risk of making the bad decision in decision-making process.

  4. Intelligent Soft Computing on Forex: Exchange Rates Forecasting with Hybrid Radial Basis Neural Network

    Directory of Open Access Journals (Sweden)

    Lukas Falat

    2016-01-01

    Full Text Available This paper deals with application of quantitative soft computing prediction models into financial area as reliable and accurate prediction models can be very helpful in management decision-making process. The authors suggest a new hybrid neural network which is a combination of the standard RBF neural network, a genetic algorithm, and a moving average. The moving average is supposed to enhance the outputs of the network using the error part of the original neural network. Authors test the suggested model on high-frequency time series data of USD/CAD and examine the ability to forecast exchange rate values for the horizon of one day. To determine the forecasting efficiency, they perform a comparative statistical out-of-sample analysis of the tested model with autoregressive models and the standard neural network. They also incorporate genetic algorithm as an optimizing technique for adapting parameters of ANN which is then compared with standard backpropagation and backpropagation combined with K-means clustering algorithm. Finally, the authors find out that their suggested hybrid neural network is able to produce more accurate forecasts than the standard models and can be helpful in eliminating the risk of making the bad decision in decision-making process.

  5. Requirements for Control Room Computer-Based Procedures for use in Hybrid Control Rooms

    Energy Technology Data Exchange (ETDEWEB)

    Le Blanc, Katya Lee [Idaho National Lab. (INL), Idaho Falls, ID (United States); Oxstrand, Johanna Helene [Idaho National Lab. (INL), Idaho Falls, ID (United States); Joe, Jeffrey Clark [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-05-01

    Many plants in the U.S. are currently undergoing control room modernization. The main drivers for modernization are the aging and obsolescence of existing equipment, which typically results in a like-for-like replacement of analogue equipment with digital systems. However, the modernization efforts present an opportunity to employ advanced technology that would not only extend the life, but enhance the efficiency and cost competitiveness of nuclear power. Computer-based procedures (CBPs) are one example of near-term advanced technology that may provide enhanced efficiencies above and beyond like for like replacements of analog systems. Researchers in the LWRS program are investigating the benefits of advanced technologies such as CBPs, with the goal of assisting utilities in decision making during modernization projects. This report will describe the existing research on CBPs, discuss the unique issues related to using CBPs in hybrid control rooms (i.e., partially modernized analog control rooms), and define the requirements of CBPs for hybrid control rooms.

  6. Optimization of a Continuous Hybrid Impeller Mixer via Computational Fluid Dynamics

    Directory of Open Access Journals (Sweden)

    N. Othman

    2014-01-01

    Full Text Available This paper presents the preliminary steps required for conducting experiments to obtain the optimal operating conditions of a hybrid impeller mixer and to determine the residence time distribution (RTD using computational fluid dynamics (CFD. In this paper, impeller speed and clearance parameters are examined. The hybrid impeller mixer consists of a single Rushton turbine mounted above a single pitched blade turbine (PBT. Four impeller speeds, 50, 100, 150, and 200 rpm, and four impeller clearances, 25, 50, 75, and 100 mm, were the operation variables used in this study. CFD was utilized to initially screen the parameter ranges to reduce the number of actual experiments needed. Afterward, the residence time distribution (RTD was determined using the respective parameters. Finally, the Fluent-predicted RTD and the experimentally measured RTD were compared. The CFD investigations revealed that an impeller speed of 50 rpm and an impeller clearance of 25 mm were not viable for experimental investigations and were thus eliminated from further analyses. The determination of RTD using a k-ε turbulence model was performed using CFD techniques. The multiple reference frame (MRF was implemented and a steady state was initially achieved followed by a transient condition for RTD determination.

  7. Optimization of a continuous hybrid impeller mixer via computational fluid dynamics.

    Science.gov (United States)

    Othman, N; Kamarudin, S K; Takriff, M S; Rosli, M I; Engku Chik, E M F; Meor Adnan, M A K

    2014-01-01

    This paper presents the preliminary steps required for conducting experiments to obtain the optimal operating conditions of a hybrid impeller mixer and to determine the residence time distribution (RTD) using computational fluid dynamics (CFD). In this paper, impeller speed and clearance parameters are examined. The hybrid impeller mixer consists of a single Rushton turbine mounted above a single pitched blade turbine (PBT). Four impeller speeds, 50, 100, 150, and 200 rpm, and four impeller clearances, 25, 50, 75, and 100 mm, were the operation variables used in this study. CFD was utilized to initially screen the parameter ranges to reduce the number of actual experiments needed. Afterward, the residence time distribution (RTD) was determined using the respective parameters. Finally, the Fluent-predicted RTD and the experimentally measured RTD were compared. The CFD investigations revealed that an impeller speed of 50 rpm and an impeller clearance of 25 mm were not viable for experimental investigations and were thus eliminated from further analyses. The determination of RTD using a k-ε turbulence model was performed using CFD techniques. The multiple reference frame (MRF) was implemented and a steady state was initially achieved followed by a transient condition for RTD determination.

  8. Intelligent Soft Computing on Forex: Exchange Rates Forecasting with Hybrid Radial Basis Neural Network

    Science.gov (United States)

    Marcek, Dusan; Durisova, Maria

    2016-01-01

    This paper deals with application of quantitative soft computing prediction models into financial area as reliable and accurate prediction models can be very helpful in management decision-making process. The authors suggest a new hybrid neural network which is a combination of the standard RBF neural network, a genetic algorithm, and a moving average. The moving average is supposed to enhance the outputs of the network using the error part of the original neural network. Authors test the suggested model on high-frequency time series data of USD/CAD and examine the ability to forecast exchange rate values for the horizon of one day. To determine the forecasting efficiency, they perform a comparative statistical out-of-sample analysis of the tested model with autoregressive models and the standard neural network. They also incorporate genetic algorithm as an optimizing technique for adapting parameters of ANN which is then compared with standard backpropagation and backpropagation combined with K-means clustering algorithm. Finally, the authors find out that their suggested hybrid neural network is able to produce more accurate forecasts than the standard models and can be helpful in eliminating the risk of making the bad decision in decision-making process. PMID:26977450

  9. Computational identification and analysis of novel sugarcane microRNAs

    Directory of Open Access Journals (Sweden)

    Thiebaut Flávia

    2012-07-01

    Full Text Available Abstract Background MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. Results A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species and DNA methylation (24-nt-species, respectively. Conclusions A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.

  10. A hybrid computational method for the discovery of novel reproduction-related genes.

    Science.gov (United States)

    Chen, Lei; Chu, Chen; Kong, Xiangyin; Huang, Guohua; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Uncovering the molecular mechanisms underlying reproduction is of great importance to infertility treatment and to the generation of healthy offspring. In this study, we discovered novel reproduction-related genes with a hybrid computational method, integrating three different types of method, which offered new clues for further reproduction research. This method was first executed on a weighted graph, constructed based on known protein-protein interactions, to search the shortest paths connecting any two known reproduction-related genes. Genes occurring in these paths were deemed to have a special relationship with reproduction. These newly discovered genes were filtered with a randomization test. Then, the remaining genes were further selected according to their associations with known reproduction-related genes measured by protein-protein interaction score and alignment score obtained by BLAST. The in-depth analysis of the high confidence novel reproduction genes revealed hidden mechanisms of reproduction and provided guidelines for further experimental validations.

  11. A hybrid computation method for determining fluctuations of temperature in branched structures

    International Nuclear Information System (INIS)

    Czomber, L.

    1982-01-01

    A hybrid computation method for determining temperature fluctuations at discrete points of slab like geometries is developed on the basis of a new formulation of the finite difference method. For this purpose, a new finite difference method is combined with an exact solution of the heat equation within the range of values of the Laplace transformation. Whereas the exact solution can be applied to arbitraryly large ranges, the finite difference formulation is given for structural ranges which need finer discretization. The boundary conditions of the exact solution are substituted by finite difference terms for the boundary residual flow or an internal heat source, depending on the problem. The resulting system of conditional equations contains only the node parameters of the finite difference method. (orig.) [de

  12. A Hybrid Soft-computing Method for Image Analysis of Digital Plantar Scanners

    Science.gov (United States)

    Razjouyan, Javad; Khayat, Omid; Siahi, Mehdi; Mansouri, Ali Alizadeh

    2013-01-01

    Digital foot scanners have been developed in recent years to yield anthropometrists digital image of insole with pressure distribution and anthropometric information. In this paper, a hybrid algorithm containing gray level spatial correlation (GLSC) histogram and Shanbag entropy is presented for analysis of scanned foot images. An evolutionary algorithm is also employed to find the optimum parameters of GLSC and transform function of the membership values. Resulting binary images as the thresholded images are undergone anthropometric measurements taking in to account the scale factor of pixel size to metric scale. The proposed method is finally applied to plantar images obtained through scanning feet of randomly selected subjects by a foot scanner system as our experimental setup described in the paper. Running computation time and the effects of GLSC parameters are investigated in the simulation results. PMID:24083133

  13. Hybrid automata models of cardiac ventricular electrophysiology for real-time computational applications.

    Science.gov (United States)

    Andalam, Sidharta; Ramanna, Harshavardhan; Malik, Avinash; Roop, Parthasarathi; Patel, Nitish; Trew, Mark L

    2016-08-01

    Virtual heart models have been proposed for closed loop validation of safety-critical embedded medical devices, such as pacemakers. These models must react in real-time to off-the-shelf medical devices. Real-time performance can be obtained by implementing models in computer hardware, and methods of compiling classes of Hybrid Automata (HA) onto FPGA have been developed. Models of ventricular cardiac cell electrophysiology have been described using HA which capture the complex nonlinear behavior of biological systems. However, many models that have been used for closed-loop validation of pacemakers are highly abstract and do not capture important characteristics of the dynamic rate response. We developed a new HA model of cardiac cells which captures dynamic behavior and we implemented the model in hardware. This potentially enables modeling the heart with over 1 million dynamic cells, making the approach ideal for closed loop testing of medical devices.

  14. A Hybrid Soft-computing Method for Image Analysis of Digital Plantar Scanners.

    Science.gov (United States)

    Razjouyan, Javad; Khayat, Omid; Siahi, Mehdi; Mansouri, Ali Alizadeh

    2013-01-01

    Digital foot scanners have been developed in recent years to yield anthropometrists digital image of insole with pressure distribution and anthropometric information. In this paper, a hybrid algorithm containing gray level spatial correlation (GLSC) histogram and Shanbag entropy is presented for analysis of scanned foot images. An evolutionary algorithm is also employed to find the optimum parameters of GLSC and transform function of the membership values. Resulting binary images as the thresholded images are undergone anthropometric measurements taking in to account the scale factor of pixel size to metric scale. The proposed method is finally applied to plantar images obtained through scanning feet of randomly selected subjects by a foot scanner system as our experimental setup described in the paper. Running computation time and the effects of GLSC parameters are investigated in the simulation results.

  15. Insect-computer hybrid legged robot with user-adjustable speed, step length and walking gait.

    Science.gov (United States)

    Cao, Feng; Zhang, Chao; Choo, Hao Yu; Sato, Hirotaka

    2016-03-01

    We have constructed an insect-computer hybrid legged robot using a living beetle (Mecynorrhina torquata; Coleoptera). The protraction/retraction and levation/depression motions in both forelegs of the beetle were elicited by electrically stimulating eight corresponding leg muscles via eight pairs of implanted electrodes. To perform a defined walking gait (e.g., gallop), different muscles were individually stimulated in a predefined sequence using a microcontroller. Different walking gaits were performed by reordering the applied stimulation signals (i.e., applying different sequences). By varying the duration of the stimulation sequences, we successfully controlled the step frequency and hence the beetle's walking speed. To the best of our knowledge, this paper presents the first demonstration of living insect locomotion control with a user-adjustable walking gait, step length and walking speed. © 2016 The Author(s).

  16. Fluorescence In Situ Hybridization with Peptide Nucleic Acid Probes for Rapid Identification of Candida albicans Directly from Blood Culture Bottles

    Science.gov (United States)

    Rigby, Susan; Procop, Gary W.; Haase, Gerhard; Wilson, Deborah; Hall, Geraldine; Kurtzman, Cletus; Oliveira, Kenneth; Von Oy, Sabina; Hyldig-Nielsen, Jens J.; Coull, James; Stender, Henrik

    2002-01-01

    A new fluorescence in situ hybridization (FISH) method that uses peptide nucleic acid (PNA) probes for identification of Candida albicans directly from positive-blood-culture bottles in which yeast was observed by Gram staining (herein referred to as yeast-positive blood culture bottles) is described. The test (the C. albicans PNA FISH method) is based on a fluorescein-labeled PNA probe that targets C. albicans 26S rRNA. The PNA probe is added to smears made directly from the contents of the blood culture bottle and hybridized for 90 min at 55°C. Unhybridized PNA probe is removed by washing of the mixture (30 min), and the smears are examined by fluorescence microscopy. The specificity of the method was confirmed with 23 reference strains representing phylogenetically related yeast species and 148 clinical isolates covering the clinically most significant yeast species, including C. albicans (n = 72), C. dubliniensis (n = 58), C. glabrata (n = 5), C. krusei (n = 2), C. parapsilosis (n = 4), and C. tropicalis (n = 3). The performance of the C. albicans PNA FISH method as a diagnostic test was evaluated with 33 routine and 25 simulated yeast-positive blood culture bottles and showed 100% sensitivity and 100% specificity. It is concluded that this 2.5-h method for the definitive identification of C. albicans directly from yeast-positive blood culture bottles provides important information for optimal antifungal therapy and patient management. PMID:12037084

  17. An Efficient Framework for EEG Analysis with Application to Hybrid Brain Computer Interfaces Based on Motor Imagery and P300

    Directory of Open Access Journals (Sweden)

    Jinyi Long

    2017-01-01

    Full Text Available The hybrid brain computer interface (BCI based on motor imagery (MI and P300 has been a preferred strategy aiming to improve the detection performance through combining the features of each. However, current methods used for combining these two modalities optimize them separately, which does not result in optimal performance. Here, we present an efficient framework to optimize them together by concatenating the features of MI and P300 in a block diagonal form. Then a linear classifier under a dual spectral norm regularizer is applied to the combined features. Under this framework, the hybrid features of MI and P300 can be learned, selected, and combined together directly. Experimental results on the data set of hybrid BCI based on MI and P300 are provided to illustrate competitive performance of the proposed method against other conventional methods. This provides an evidence that the method used here contributes to the discrimination performance of the brain state in hybrid BCI.

  18. Identification of superior parents and hybrids from diallel crosses of bread wheat (triticum aestivum l.)

    International Nuclear Information System (INIS)

    Baloch, M.J.; Rajper, T.A.; Jatoi, W.A.

    2013-01-01

    Five parents of bread wheat (Triticum aestivum L.) viz. TD-1, SKD-1, Marvi, Moomal and Mehran were crossed in a half diallel design; hence 10 F 1 hybrids were developed. Parents alongwith hybrids were evaluated for combining ability and heterosis for tillers/plant, spike length, spike density, grains/spike, grain yield/plant and seed index. The experiment was conducted in a randomized complete block design with four replications at Botanical Garden, Department of Plant Breeding and Genetics, Sindh Agriculture University,Tandojam, during 2010. The analysis of variance due to genotypes, parents, hybrids and parents vs. hybrids was significant for all the characters which revealed presence of significant amount of genetic variability in the material. The results also indicated significant differences among the parents for their general combining ability (GCA) and hybrids for specific combining ability (SCA) suggesting the importance of both additive and non-additive genes in the expression of traits studied. The greater magnitude of SCA variances over GCA were recorded for tillers/plant, grains/spike and grain yield/plant which indicated the importance of additive gene action while the involvement of non-additive genes was evident in the inheritance of spike length, spike density and seed index. Among the parents, generally TD-I, Mehran, Moomal and Marvi were the best general combiners for tillers/plant, spike length, spike density, grains/spike, grain yield/plant and seed index. Whereas, the hybrids like SKD-1 x Mehran, Marvi x Mehran, Marvix Moomal and TD-I x SKD-I were the best specific combiners for majority of yield traits. Positive heterosis was expressed by the hybrid SKD-1 x Moomal for tillers per plant; TD-I x Moomal for spike length; TD-1 x SKD-I for grains per spike; Marvi x Mehran for spike density and Marvi x Moomal for seed index. The best parents and hybrids could be effectively utilized in hybridization and selection programmes and also for hybrid crop

  19. A hybrid method for the computation of quasi-3D seismograms.

    Science.gov (United States)

    Masson, Yder; Romanowicz, Barbara

    2013-04-01

    The development of powerful computer clusters and efficient numerical computation methods, such as the Spectral Element Method (SEM) made possible the computation of seismic wave propagation in a heterogeneous 3D earth. However, the cost of theses computations is still problematic for global scale tomography that requires hundreds of such simulations. Part of the ongoing research effort is dedicated to the development of faster modeling methods based on the spectral element method. Capdeville et al. (2002) proposed to couple SEM simulations with normal modes calculation (C-SEM). Nissen-Meyer et al. (2007) used 2D SEM simulations to compute 3D seismograms in a 1D earth model. Thanks to these developments, and for the first time, Lekic et al. (2011) developed a 3D global model of the upper mantle using SEM simulations. At the local and continental scale, adjoint tomography that is using a lot of SEM simulation can be implemented on current computers (Tape, Liu et al. 2009). Due to their smaller size, these models offer higher resolution. They provide us with images of the crust and the upper part of the mantle. In an attempt to teleport such local adjoint tomographic inversions into the deep earth, we are developing a hybrid method where SEM computation are limited to a region of interest within the earth. That region can have an arbitrary shape and size. Outside this region, the seismic wavefield is extrapolated to obtain synthetic data at the Earth's surface. A key feature of the method is the use of a time reversal mirror to inject the wavefield induced by distant seismic source into the region of interest (Robertsson and Chapman 2000). We compute synthetic seismograms as follow: Inside the region of interest, we are using regional spectral element software RegSEM to compute wave propagation in 3D. Outside this region, the wavefield is extrapolated to the surface by convolution with the Green's functions from the mirror to the seismic stations. For now, these

  20. COED Transactions, Vol. X, No. 9, September 1978. Use of the Analog/Hybrid Computer in Boundary Layer and Convection Studies.

    Science.gov (United States)

    Mitchell, Eugene E., Ed.

    In certain boundary layer or natural convection work, where a similarity transformation is valid, the equations can be reduced to a set of nonlinear ordinary differential equations. They are therefore well-suited to a fast solution on an analog/hybrid computer. This paper illustrates such usage of the analog/hybrid computer by a set of…

  1. Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment.

    Science.gov (United States)

    Abdullahi, Mohammed; Ngadi, Md Asri

    2016-01-01

    Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS) has been shown to perform competitively with Particle Swarm Optimization (PSO). The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA) based SOS (SASOS) in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs) which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan.

  2. Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment.

    Directory of Open Access Journals (Sweden)

    Mohammed Abdullahi

    Full Text Available Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS has been shown to perform competitively with Particle Swarm Optimization (PSO. The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA based SOS (SASOS in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan.

  3. COED Transactions, Vol. X, No. 10, October 1978. Simulation of a Sampled-Data System on a Hybrid Computer.

    Science.gov (United States)

    Mitchell, Eugene E., Ed.

    The simulation of a sampled-data system is described that uses a full parallel hybrid computer. The sampled data system simulated illustrates the proportional-integral-derivative (PID) discrete control of a continuous second-order process representing a stirred-tank. The stirred-tank is simulated using continuous analog components, while PID…

  4. Two molecular markers based on mitochondrial genomes for varieties identification of the northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids.

    Science.gov (United States)

    Xincheng, Zhang; Kunci, Chen; Xinping, Zhu; Jian, Zhao; Qing, Luo; Xiaoyou, Hong; Wei, Li; Fengfang, Xiao

    2015-08-01

    The northern snakehead (Channa argus) and blotched snakehead (Channa maculata) and their reciprocal hybrids have played important roles in the Chinese freshwater aquaculture industry, with an annual production in China exceeding 400 thousand tons. While these are popular aquaculture breeds in China, it is not easy to identify northern snakehead, blotched snakehead, and their hybrids. Thus, a method should be developed to identify these varieties. To distinguish between the reciprocal hybrids (C. argus ♀ × C. maculata ♂ and C. maculata ♀ × C. argus ♂), the mitochondrial genome sequences of northern snakehead and blotched snakehead and their reciprocal hybrids were compared. Following the alignment and analysis of mtDNA sequences of northern snakehead, blotched snakehead and their hybrids, two pairs of specific primers were designed based on identified differences ranging from 12S rRNA to 16S rRNA gene. The BY1 primers amplified the same bands in the blotched snakehead and the hybrid (C. maculata ♀ × C. argus ♂), while producing no products in northern snakehead and the hybrid (C. argus ♀ × C. maculata ♂). Amplification with WY1 yielded the opposite results. Then, 30 individuals per fish were randomized to verify the primers, and the results showed that the primers were specific for breeds, as intended. The specific primers can not only simply distinguish between two kinds of hybrids, but also rapidly identify the two parents. This study provides a method of molecular marker identification to identify reciprocal hybrids.

  5. A Hybrid Scheme for Fine-Grained Search and Access Authorization in Fog Computing Environment

    Science.gov (United States)

    Xiao, Min; Zhou, Jing; Liu, Xuejiao; Jiang, Mingda

    2017-01-01

    In the fog computing environment, the encrypted sensitive data may be transferred to multiple fog nodes on the edge of a network for low latency; thus, fog nodes need to implement a search over encrypted data as a cloud server. Since the fog nodes tend to provide service for IoT applications often running on resource-constrained end devices, it is necessary to design lightweight solutions. At present, there is little research on this issue. In this paper, we propose a fine-grained owner-forced data search and access authorization scheme spanning user-fog-cloud for resource constrained end users. Compared to existing schemes only supporting either index encryption with search ability or data encryption with fine-grained access control ability, the proposed hybrid scheme supports both abilities simultaneously, and index ciphertext and data ciphertext are constructed based on a single ciphertext-policy attribute based encryption (CP-ABE) primitive and share the same key pair, thus the data access efficiency is significantly improved and the cost of key management is greatly reduced. Moreover, in the proposed scheme, the resource constrained end devices are allowed to rapidly assemble ciphertexts online and securely outsource most of decryption task to fog nodes, and mediated encryption mechanism is also adopted to achieve instantaneous user revocation instead of re-encrypting ciphertexts with many copies in many fog nodes. The security and the performance analysis show that our scheme is suitable for a fog computing environment. PMID:28629131

  6. A Hybrid Scheme for Fine-Grained Search and Access Authorization in Fog Computing Environment.

    Science.gov (United States)

    Xiao, Min; Zhou, Jing; Liu, Xuejiao; Jiang, Mingda

    2017-06-17

    In the fog computing environment, the encrypted sensitive data may be transferred to multiple fog nodes on the edge of a network for low latency; thus, fog nodes need to implement a search over encrypted data as a cloud server. Since the fog nodes tend to provide service for IoT applications often running on resource-constrained end devices, it is necessary to design lightweight solutions. At present, there is little research on this issue. In this paper, we propose a fine-grained owner-forced data search and access authorization scheme spanning user-fog-cloud for resource constrained end users. Compared to existing schemes only supporting either index encryption with search ability or data encryption with fine-grained access control ability, the proposed hybrid scheme supports both abilities simultaneously, and index ciphertext and data ciphertext are constructed based on a single ciphertext-policy attribute based encryption (CP-ABE) primitive and share the same key pair, thus the data access efficiency is significantly improved and the cost of key management is greatly reduced. Moreover, in the proposed scheme, the resource constrained end devices are allowed to rapidly assemble ciphertexts online and securely outsource most of decryption task to fog nodes, and mediated encryption mechanism is also adopted to achieve instantaneous user revocation instead of re-encrypting ciphertexts with many copies in many fog nodes. The security and the performance analysis show that our scheme is suitable for a fog computing environment.

  7. A hybrid computational strategy to address WGS variant analysis in >5000 samples.

    Science.gov (United States)

    Huang, Zhuoyi; Rustagi, Navin; Veeraraghavan, Narayanan; Carroll, Andrew; Gibbs, Richard; Boerwinkle, Eric; Venkata, Manjunath Gorentla; Yu, Fuli

    2016-09-10

    The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies. We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms. Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low

  8. Accident identification system with automatic detection of abnormal condition using quantum computation

    International Nuclear Information System (INIS)

    Nicolau, Andressa dos Santos; Schirru, Roberto; Lima, Alan Miranda Monteiro de

    2011-01-01

    Transient identification systems have been proposed in order to maintain the plant operating in safe conditions and help operators in make decisions in emergency short time interval with maximum certainty associated. This article presents a system, time independent and without the use of an event that can be used as a starting point for t = 0 (reactor scram, for instance), for transient/accident identification of a pressurized water nuclear reactor (PWR). The model was developed in order to be able to recognize the normal condition and three accidents of the design basis list of the Nuclear Power Plant Angra 2, postulated in the Final Safety Analysis Report (FSAR). Were used several sets of process variables in order to establish a minimum set of variables considered necessary and sufficient. The optimization step of the identification algorithm is based upon the paradigm of Quantum Computing. In this case, the optimization metaheuristic Quantum Inspired Evolutionary Algorithm (QEA) was implemented and works as a data mining tool. The results obtained with the QEA without the time variable are compatible to the techniques in the reference literature, for the transient identification problem, with less computational effort (number of evaluations). This system allows a solution that approximates the ideal solution, the Voronoi Vectors with only one partition for the classes of accidents with robustness. (author)

  9. Molecular identification and genetic diversity analysis of Chinese sugarcane (Saccharum spp. hybrids) varieties using SSR markers

    Science.gov (United States)

    Sugarcane (Saccharum spp. hybrids) is an important sugar and renewable bioenergy crop. However, its complex aneupolyploidy genome and vegetative mode of propagation often cause difficulty in selection and some variety identity issues in a breeding program. Therefore, the present study was set up to ...

  10. Control of a nursing bed based on a hybrid brain-computer interface.

    Science.gov (United States)

    Nengneng Peng; Rui Zhang; Haihua Zeng; Fei Wang; Kai Li; Yuanqing Li; Xiaobin Zhuang

    2016-08-01

    In this paper, we propose an intelligent nursing bed system which is controlled by a hybrid brain-computer interface (BCI) involving steady-state visual evoked potential (SSVEP) and P300. Specifically, the hybrid BCI includes an asynchronous brain switch based on SSVEP and P300, and a P300-based BCI. The brain switch is used to turn on/off the control system of the electric nursing bed through idle/control state detection, whereas the P300-based BCI is for operating the nursing bed. At the beginning, the user may focus on one group of flashing buttons in the graphic user interface (GUI) of the brain switch, which can simultaneously evoke SSVEP and P300, to switch on the control system. Here, the combination of SSVEP and P300 is used for improving the performance of the brain switch. Next, the user can control the nursing bed using the P300-based BCI. The GUI of the P300-based BCI includes 10 flashing buttons, which correspond to 10 functional operations, namely, left-side up, left-side down, back up, back down, bedpan open, bedpan close, legs up, legs down, right-side up, and right-side down. For instance, he/she can focus on the flashing button "back up" in the GUI of the P300-based BCI to activate the corresponding control such that the nursing bed is adjusted up. Eight healthy subjects participated in our experiment, and obtained an average accuracy of 93.75% and an average false positive rate (FPR) of 0.15 event/min. The effectiveness of our system was thus demonstrated.

  11. Computational lymphatic node models in pediatric and adult hybrid phantoms for radiation dosimetry

    International Nuclear Information System (INIS)

    Lee, Choonsik; Lamart, Stephanie; Moroz, Brian E

    2013-01-01

    We developed models of lymphatic nodes for six pediatric and two adult hybrid computational phantoms to calculate the lymphatic node dose estimates from external and internal radiation exposures. We derived the number of lymphatic nodes from the recommendations in International Commission on Radiological Protection (ICRP) Publications 23 and 89 at 16 cluster locations for the lymphatic nodes: extrathoracic, cervical, thoracic (upper and lower), breast (left and right), mesentery (left and right), axillary (left and right), cubital (left and right), inguinal (left and right) and popliteal (left and right), for different ages (newborn, 1-, 5-, 10-, 15-year-old and adult). We modeled each lymphatic node within the voxel format of the hybrid phantoms by assuming that all nodes have identical size derived from published data except narrow cluster sites. The lymph nodes were generated by the following algorithm: (1) selection of the lymph node site among the 16 cluster sites; (2) random sampling of the location of the lymph node within a spherical space centered at the chosen cluster site; (3) creation of the sphere or ovoid of tissue representing the node based on lymphatic node characteristics defined in ICRP Publications 23 and 89. We created lymph nodes until the pre-defined number of lymphatic nodes at the selected cluster site was reached. This algorithm was applied to pediatric (newborn, 1-, 5-and 10-year-old male, and 15-year-old males) and adult male and female ICRP-compliant hybrid phantoms after voxelization. To assess the performance of our models for internal dosimetry, we calculated dose conversion coefficients, called S values, for selected organs and tissues with Iodine-131 distributed in six lymphatic node cluster sites using MCNPX2.6, a well validated Monte Carlo radiation transport code. Our analysis of the calculations indicates that the S values were significantly affected by the location of the lymph node clusters and that the values increased for

  12. Computation of the Lyapunov exponents in the compass-gait model under OGY control via a hybrid Poincaré map

    International Nuclear Information System (INIS)

    Gritli, Hassène; Belghith, Safya

    2015-01-01

    Highlights: • A numerical calculation method of the Lyapunov exponents in the compass-gait model under OGY control is proposed. • A new linearization method of the impulsive hybrid dynamics around a one-periodic hybrid limit cycle is achieved. • We develop a simple analytical expression of a controlled hybrid Poincaré map. • A dimension reduction of the hybrid Poincaré map is realized. • We describe the numerical computation procedure of the Lyapunov exponents via the designed hybrid Poincaré map. - Abstract: This paper aims at providing a numerical calculation method of the spectrum of Lyapunov exponents in a four-dimensional impulsive hybrid nonlinear dynamics of a passive compass-gait model under the OGY control approach by means of a controlled hybrid Poincaré map. We present a four-dimensional simplified analytical expression of such hybrid map obtained by linearizing the uncontrolled impulsive hybrid nonlinear dynamics around a desired one-periodic passive hybrid limit cycle. In order to compute the spectrum of Lyapunov exponents, a dimension reduction of the controlled hybrid Poincaré map is realized. The numerical calculation of the spectrum of Lyapunov exponents using the reduced-dimension controlled hybrid Poincaré map is given in detail. In order to show the effectiveness of the developed method, the spectrum of Lyapunov exponents is calculated as the slope (bifurcation) parameter varies and hence used to predict the walking dynamics behavior of the compass-gait model under the OGY control.

  13. Hybridization relics complicate barcode-based identification of species in earthworms.

    Science.gov (United States)

    Dupont, L; Porco, D; Symondson, W O C; Roy, V

    2016-07-01

    Introgressive hybridization results in mito-nuclear discordance which could obscure the delimitation of closely related taxa. Although such events are increasingly reported, they have been poorly studied in earthworms. Here, we propose a method for investigating the degree of introgressive hybridization between three taxa of the Allolobophora chlorotica aggregate within two field populations (N = 67 and N = 105) using a reference data set including published DNA barcoding and microsatellite data of all known A. chlorotica lineages (N = 85). For this, we used both molecular phylogenetic and population genetic approaches. The test of correspondence between mitochondrial cytochrome c oxidase I (COI) lineages and clusters of nuclear microsatellite genotypes allowed individuals to be sorted in three categories (matching, admixed and nonmatching) and additional markers (mitochondrial NADH dehydrogenase subunit 1, nuclear Histone 3 and Internal transcribed Spacer Region 2) were used for phylogenetic reconstructions in order to check assignments. Although 15 admixed individuals were observed, no early-generation hybrids were detected within the two populations. Interestingly, 14 nonmatching individuals (i.e. with a mtDNA haplotype that did not correspond to their nuclear cluster) were detected, a pattern that would result after multiple generations of unidirectional hybridization of female from one taxon to male of the other taxon. Because earthworms are simultaneous hermaphrodites, these events of unidirectional hybridization suggest sterility of the male function in several crosses and highlight that some individuals can be misidentified if reliance is placed on COI barcodes alone. These findings could improve the use of these barcodes in earthworms for species delineation. © 2016 John Wiley & Sons Ltd.

  14. UPTF test instrumentation. Measurement system identification, engineering units and computed parameters

    International Nuclear Information System (INIS)

    Sarkar, J.; Liebert, J.; Laeufer, R.

    1992-11-01

    This updated version of the previous report /1/ contains, besides additional instrumentation needed for 2D/3D Programme, the supplementary instrumentation in the inlet plenum of SG simulator and hot and cold leg of broken loop, the cold leg of intact loops and the upper plenum to meet the requirements (Test Phase A) of the UPTF Programme, TRAM, sponsored by the Federal Minister of Research and Technology (BMFT) of the Federal Republic of Germany. For understanding, the derivation and the description of the identification codes for the entire conventional and advanced measurement systems classifying the function, and the equipment unit, key, as adopted in the conventional power plants, have been included. Amendments have also been made to the appendices. In particular, the list of measurement systems covering the measurement identification code, instrument, measured quantity, measuring range, band width, uncertainty and sensor location has been updated and extended to include the supplementary instrumentation. Beyond these amendments, the uncertainties of measurements have been precisely specified. The measurement identification codes which also stand for the identification of the corresponding measured quantities in engineering units and the identification codes derived therefrom for the computed parameters have been adequately detailed. (orig.)

  15. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Ávila Robledillo, Laura; Koblížková, Andrea; Vrbová, Iva; Neumann, Pavel; Macas, Jiří

    2017-01-01

    Roč. 45, č. 12 (2017), č. článku e111. ISSN 0305-1048 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LM2015047 Institutional support: RVO:60077344 Keywords : in-situ hybridization * repetitive sequences * tandem repeats * vicia-faba Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 10.162, year: 2016

  16. Evaluation of a polymerase chain reaction reverse hybridization line probe assay for the detection and identification of medically important fungi in bronchoalveolar lavage fluids.

    NARCIS (Netherlands)

    Meletiadis, J.; Melchers, W.J.G.; Meis, J.F.G.M.; Hurk, P.J.J.C. van den; Jannes, G.; Verweij, P.E.

    2003-01-01

    An assay system in which polymerase chain reaction (PCR) amplification of the ITS-1 region of ribosomal DNA (rDNA) is combined with a reverse-hybridization line probe assay (LiPA) was used for the identification of six Candida species and four Aspergillus species in pure cultures of clinical

  17. Identification of bester hybrid and its parental species (♀ Huso huso Linnaeus, 1758 and ♂ Acipenser ruthenus Linnaeus, 1758 by nuclear markers

    Directory of Open Access Journals (Sweden)

    Andreea Dudu

    2015-05-01

    Full Text Available In Romania, sturgeon farming is gaining advance, different species being raised for commercial purposes and for restocking activities. A correct identification of individuals is imposed since severe ecological damages might occur if non-native species or hybrids are used for restocking. Such identification is required also for commercial reasons, the meat and caviar from different species having different prices. The aim of our study was to analyze two sturgeon species, Huso huso and Acipenser ruthenus and their interspecific hybrid - bester, using nuclear markers, in order to set up a molecular method for their accurate identification. The genetic pattern of the species was inferred from the analysis of nine microsatellite loci (LS19, LS34, LS39, LS54, AoxD234, AnacC11, LS68, Aox45 and Aox27 amplified by multiplex PCR reactions. The genotype data were analyzed with GENETIX v4.05 and STRUCTURE. The FCA analysis grouped the individuals in three distinct clusters corresponding to each of the pure species and to the interspecific hybrids. The admixture analysis performed in STRUCTURE also assigned three groups, confirming the results highlighted by FCA. We can conclude that the selected microsatellite markers allow the unambiguously identification of the bester hybrid and its genitor species from Romanian farms.

  18. A Hybrid of Deep Network and Hidden Markov Model for MCI Identification with Resting-State fMRI.

    Science.gov (United States)

    Suk, Heung-Il; Lee, Seong-Whan; Shen, Dinggang

    2015-10-01

    In this paper, we propose a novel method for modelling functional dynamics in resting-state fMRI (rs-fMRI) for Mild Cognitive Impairment (MCI) identification. Specifically, we devise a hybrid architecture by combining Deep Auto-Encoder (DAE) and Hidden Markov Model (HMM). The roles of DAE and HMM are, respectively, to discover hierarchical non-linear relations among features, by which we transform the original features into a lower dimension space, and to model dynamic characteristics inherent in rs-fMRI, i.e. , internal state changes. By building a generative model with HMMs for each class individually, we estimate the data likelihood of a test subject as MCI or normal healthy control, based on which we identify the clinical label. In our experiments, we achieved the maximal accuracy of 81.08% with the proposed method, outperforming state-of-the-art methods in the literature.

  19. Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

    Science.gov (United States)

    Jin, Lian-Qun; Li, Jun-Wen; Wang, Sheng-Qi; Chao, Fu-Huan; Wang, Xin-Wei; Yuan, Zheng-Quan

    2005-01-01

    AIM: To detect the common intestinal pathogenic bacteria quickly and accurately. METHODS: A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays. RESULTS: One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified. CONCLUSION: Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost. PMID:16437687

  20. Identification of transformer fault based on dissolved gas analysis using hybrid support vector machine-modified evolutionary particle swarm optimisation

    Science.gov (United States)

    2018-01-01

    Early detection of power transformer fault is important because it can reduce the maintenance cost of the transformer and it can ensure continuous electricity supply in power systems. Dissolved Gas Analysis (DGA) technique is commonly used to identify oil-filled power transformer fault type but utilisation of artificial intelligence method with optimisation methods has shown convincing results. In this work, a hybrid support vector machine (SVM) with modified evolutionary particle swarm optimisation (EPSO) algorithm was proposed to determine the transformer fault type. The superiority of the modified PSO technique with SVM was evaluated by comparing the results with the actual fault diagnosis, unoptimised SVM and previous reported works. Data reduction was also applied using stepwise regression prior to the training process of SVM to reduce the training time. It was found that the proposed hybrid SVM-Modified EPSO (MEPSO)-Time Varying Acceleration Coefficient (TVAC) technique results in the highest correct identification percentage of faults in a power transformer compared to other PSO algorithms. Thus, the proposed technique can be one of the potential solutions to identify the transformer fault type based on DGA data on site. PMID:29370230

  1. A novel hybrid method of beta-turn identification in protein using binary logistic regression and neural network.

    Science.gov (United States)

    Asghari, Mehdi Poursheikhali; Hayatshahi, Sayyed Hamed Sadat; Abdolmaleki, Parviz

    2012-01-01

    From both the structural and functional points of view, β-turns play important biological roles in proteins. In the present study, a novel two-stage hybrid procedure has been developed to identify β-turns in proteins. Binary logistic regression was initially used for the first time to select significant sequence parameters in identification of β-turns due to a re-substitution test procedure. Sequence parameters were consisted of 80 amino acid positional occurrences and 20 amino acid percentages in sequence. Among these parameters, the most significant ones which were selected by binary logistic regression model, were percentages of Gly, Ser and the occurrence of Asn in position i+2, respectively, in sequence. These significant parameters have the highest effect on the constitution of a β-turn sequence. A neural network model was then constructed and fed by the parameters selected by binary logistic regression to build a hybrid predictor. The networks have been trained and tested on a non-homologous dataset of 565 protein chains. With applying a nine fold cross-validation test on the dataset, the network reached an overall accuracy (Qtotal) of 74, which is comparable with results of the other β-turn prediction methods. In conclusion, this study proves that the parameter selection ability of binary logistic regression together with the prediction capability of neural networks lead to the development of more precise models for identifying β-turns in proteins.

  2. Identification of transformer fault based on dissolved gas analysis using hybrid support vector machine-modified evolutionary particle swarm optimisation.

    Directory of Open Access Journals (Sweden)

    Hazlee Azil Illias

    Full Text Available Early detection of power transformer fault is important because it can reduce the maintenance cost of the transformer and it can ensure continuous electricity supply in power systems. Dissolved Gas Analysis (DGA technique is commonly used to identify oil-filled power transformer fault type but utilisation of artificial intelligence method with optimisation methods has shown convincing results. In this work, a hybrid support vector machine (SVM with modified evolutionary particle swarm optimisation (EPSO algorithm was proposed to determine the transformer fault type. The superiority of the modified PSO technique with SVM was evaluated by comparing the results with the actual fault diagnosis, unoptimised SVM and previous reported works. Data reduction was also applied using stepwise regression prior to the training process of SVM to reduce the training time. It was found that the proposed hybrid SVM-Modified EPSO (MEPSO-Time Varying Acceleration Coefficient (TVAC technique results in the highest correct identification percentage of faults in a power transformer compared to other PSO algorithms. Thus, the proposed technique can be one of the potential solutions to identify the transformer fault type based on DGA data on site.

  3. Identification of transformer fault based on dissolved gas analysis using hybrid support vector machine-modified evolutionary particle swarm optimisation.

    Science.gov (United States)

    Illias, Hazlee Azil; Zhao Liang, Wee

    2018-01-01

    Early detection of power transformer fault is important because it can reduce the maintenance cost of the transformer and it can ensure continuous electricity supply in power systems. Dissolved Gas Analysis (DGA) technique is commonly used to identify oil-filled power transformer fault type but utilisation of artificial intelligence method with optimisation methods has shown convincing results. In this work, a hybrid support vector machine (SVM) with modified evolutionary particle swarm optimisation (EPSO) algorithm was proposed to determine the transformer fault type. The superiority of the modified PSO technique with SVM was evaluated by comparing the results with the actual fault diagnosis, unoptimised SVM and previous reported works. Data reduction was also applied using stepwise regression prior to the training process of SVM to reduce the training time. It was found that the proposed hybrid SVM-Modified EPSO (MEPSO)-Time Varying Acceleration Coefficient (TVAC) technique results in the highest correct identification percentage of faults in a power transformer compared to other PSO algorithms. Thus, the proposed technique can be one of the potential solutions to identify the transformer fault type based on DGA data on site.

  4. Identification of bacteria used for microbial enhanced oil recovery process by fluorescence in situ hybridization technique

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, K.; Tanaka, S.; Otsuka, M. [Kansai Research Institute, Kyoto (Japan). Lifescience Lab.; Yonebayashi, H. [Japan National Oil Corp., Chiba (Japan). Tech. Research Center; Enomoto, H. [Tohoku University, Sendai (Japan). Dept. of Geoscience and Tech.

    2000-01-01

    A fluorescence in situ hybridization (FISH) technique using 16S rRNA-targeted oligonucleotide probes was developed for rapid detection of microorganisms for use in the microbial enhancement of oil recovery (MEOR) process. Two microorganisms, Enterobacter cloacae TRC-322 and Bacillus licheniformis TRC-18-2-a, were selected from a collection of Enterobacter sp. and Bacillus sp. which were screened in previous studies as candidate microorganisms for injection, and were used for this experiment. Oligonucleotide probes, design based on specific sequences in the 16S rRNA gene were labeled with either fluorescein isothiocyanate (FITC), or 6-car-boxy-X-rhodamine (ROX), and were allowed to hybridize with fixed cells of the two microorganisms noted above. The fluorescence signal emitted from each microorganism cells could clearly be detected by an epifluorescence microscope. Moreover, E. cloacae TRC-322 and B, licheniformis TRC-18-2-a, suspended in actual reservoir brine, including inorganic salts, oil and aboriginal cells of the reservoir brine, could be detected directly by this hybridization method, without the need for cultivation and isolation. (author)

  5. The identification of genes specific to Prevotella intermedia and Prevotella nigrescens using genomic subtractive hybridization.

    Science.gov (United States)

    Masakiyo, Yoshiaki; Yoshida, Akihiro; Shintani, Yasuyuki; Takahashi, Yusuke; Ansai, Toshihiro; Takehara, Tadamichi

    2010-06-01

    Prevotella intermedia and Prevotella nigrescens, which are often isolated from periodontal sites, were once considered two different genotypes of P. intermedia. Although the genomic sequence of P. intermedia was determined recently, little is known about the genetic differences between P. intermedia and P. nigrescens. The subtractive hybridization technique is a powerful method for generating a set of DNA fragments differing between two closely related bacterial strains or species. We used subtractive hybridization to identify the DNA regions specific to P. intermedia ATCC 25611 and P. nigrescens ATCC 25261. Using this method, four P. intermedia ATCC 25611-specific and three P. nigrescens ATCC 25261-specific regions were determined. From the species-specific regions, insertion sequence (IS) elements were isolated for P. intermedia. IS elements play an important role in the pathogenicity of bacteria. For the P. intermedia-specific regions, the genes adenine-specific DNA-methyltransferase and 8-amino-7-oxononanoate synthase were isolated. The P. nigrescens-specific region contained a Flavobacterium psychrophilum SprA homologue, a cell-surface protein involved in gliding motility, Prevotella melaninogenica ATCC 25845 glutathione peroxide, and Porphyromonas gingivalis ATCC 33277 leucyl-tRNA synthetase. The results demonstrate that the subtractive hybridization technique was useful for distinguishing between the two closely related species. Furthermore, this technique will contribute to our understanding of the virulence of these species. 2009 Elsevier Ltd. All rights reserved.

  6. Performance dependence of hybrid x-ray computed tomography/fluorescence molecular tomography on the optical forward problem.

    Science.gov (United States)

    Hyde, Damon; Schulz, Ralf; Brooks, Dana; Miller, Eric; Ntziachristos, Vasilis

    2009-04-01

    Hybrid imaging systems combining x-ray computed tomography (CT) and fluorescence tomography can improve fluorescence imaging performance by incorporating anatomical x-ray CT information into the optical inversion problem. While the use of image priors has been investigated in the past, little is known about the optimal use of forward photon propagation models in hybrid optical systems. In this paper, we explore the impact on reconstruction accuracy of the use of propagation models of varying complexity, specifically in the context of these hybrid imaging systems where significant structural information is known a priori. Our results demonstrate that the use of generically known parameters provides near optimal performance, even when parameter mismatch remains.

  7. Potential of Hybrid Computational Phantoms for Retrospective Heart Dosimetry After Breast Radiation Therapy: A Feasibility Study

    Energy Technology Data Exchange (ETDEWEB)

    Moignier, Alexandra, E-mail: alexandra.moignier@irsn.fr [Institut de Radioprotection et de Surete Nucleaire, Fontenay-aux-Roses (France); Derreumaux, Sylvie; Broggio, David; Beurrier, Julien [Institut de Radioprotection et de Surete Nucleaire, Fontenay-aux-Roses (France); Chea, Michel; Boisserie, Gilbert [Groupe Hospitalier Pitie Salpetriere, Service de Radiotherapie, Paris (France); Franck, Didier; Aubert, Bernard [Institut de Radioprotection et de Surete Nucleaire, Fontenay-aux-Roses (France); Mazeron, Jean-Jacques [Groupe Hospitalier Pitie Salpetriere, Service de Radiotherapie, Paris (France)

    2013-02-01

    Purpose: Current retrospective cardiovascular dosimetry studies are based on a representative patient or simple mathematic phantoms. Here, a process of patient modeling was developed to personalize the anatomy of the thorax and to include a heart model with coronary arteries. Methods and Materials: The patient models were hybrid computational phantoms (HCPs) with an inserted detailed heart model. A computed tomography (CT) acquisition (pseudo-CT) was derived from HCP and imported into a treatment planning system where treatment conditions were reproduced. Six current patients were selected: 3 were modeled from their CT images (A patients) and the others were modelled from 2 orthogonal radiographs (B patients). The method performance and limitation were investigated by quantitative comparison between the initial CT and the pseudo-CT, namely, the morphology and the dose calculation were compared. For the B patients, a comparison with 2 kinds of representative patients was also conducted. Finally, dose assessment was focused on the whole coronary artery tree and the left anterior descending coronary. Results: When 3-dimensional anatomic information was available, the dose calculations performed on the initial CT and the pseudo-CT were in good agreement. For the B patients, comparison of doses derived from HCP and representative patients showed that the HCP doses were either better or equivalent. In the left breast radiation therapy context and for the studied cases, coronary mean doses were at least 5-fold higher than heart mean doses. Conclusions: For retrospective dose studies, it is suggested that HCP offers a better surrogate, in terms of dose accuracy, than representative patients. The use of a detailed heart model eliminates the problem of identifying the coronaries on the patient's CT.

  8. Prediction of monthly regional groundwater levels through hybrid soft-computing techniques

    Science.gov (United States)

    Chang, Fi-John; Chang, Li-Chiu; Huang, Chien-Wei; Kao, I.-Feng

    2016-10-01

    Groundwater systems are intrinsically heterogeneous with dynamic temporal-spatial patterns, which cause great difficulty in quantifying their complex processes, while reliable predictions of regional groundwater levels are commonly needed for managing water resources to ensure proper service of water demands within a region. In this study, we proposed a novel and flexible soft-computing technique that could effectively extract the complex high-dimensional input-output patterns of basin-wide groundwater-aquifer systems in an adaptive manner. The soft-computing models combined the Self Organized Map (SOM) and the Nonlinear Autoregressive with Exogenous Inputs (NARX) network for predicting monthly regional groundwater levels based on hydrologic forcing data. The SOM could effectively classify the temporal-spatial patterns of regional groundwater levels, the NARX could accurately predict the mean of regional groundwater levels for adjusting the selected SOM, the Kriging was used to interpolate the predictions of the adjusted SOM into finer grids of locations, and consequently the prediction of a monthly regional groundwater level map could be obtained. The Zhuoshui River basin in Taiwan was the study case, and its monthly data sets collected from 203 groundwater stations, 32 rainfall stations and 6 flow stations during 2000 and 2013 were used for modelling purpose. The results demonstrated that the hybrid SOM-NARX model could reliably and suitably predict monthly basin-wide groundwater levels with high correlations (R2 > 0.9 in both training and testing cases). The proposed methodology presents a milestone in modelling regional environmental issues and offers an insightful and promising way to predict monthly basin-wide groundwater levels, which is beneficial to authorities for sustainable water resources management.

  9. Evaluation of External Memory Access Performance on a High-End FPGA Hybrid Computer

    Directory of Open Access Journals (Sweden)

    Konstantinos Kalaitzis

    2016-10-01

    Full Text Available The motivation of this research was to evaluate the main memory performance of a hybrid super computer such as the Convey HC-x, and ascertain how the controller performs in several access scenarios, vis-à-vis hand-coded memory prefetches. Such memory patterns are very useful in stencil computations. The theoretical bandwidth of the memory of the Convey is compared with the results of our measurements. The accurate study of the memory subsystem is particularly useful for users when they are developing their application-specific personality. Experiments were performed to measure the bandwidth between the coprocessor and the memory subsystem. The experiments aimed mainly at measuring the reading access speed of the memory from Application Engines (FPGAs. Different ways of accessing data were used in order to find the most efficient way to access memory. This way was proposed for future work in the Convey HC-x. When performing a series of accesses to memory, non-uniform latencies occur. The Memory Controller of the Convey HC-x in the coprocessor attempts to cover this latency. We measure memory efficiency as a ratio of the number of memory accesses and the number of execution cycles. The result of this measurement converges to one in most cases. In addition, we performed experiments with hand-coded memory accesses. The analysis of the experimental results shows how the memory subsystem and Memory Controllers work. From this work we conclude that the memory controllers do an excellent job, largely because (transparently to the user they seem to cache large amounts of data, and hence hand-coding is not needed in most situations.

  10. Adaptive hybrid brain-computer interaction: ask a trainer for assistance!

    Science.gov (United States)

    Müller-Putz, Gernot R; Steyrl, David; Faller, Josef

    2014-01-01

    In applying mental imagery brain-computer interfaces (BCIs) to end users, training is a key part for novice users to get control. In general learning situations, it is an established concept that a trainer assists a trainee to improve his/her aptitude in certain skills. In this work, we want to evaluate whether we can apply this concept in the context of event-related desynchronization (ERD) based, adaptive, hybrid BCIs. Hence, in a first session we merged the features of a high aptitude BCI user, a trainer, and a novice user, the trainee, in a closed-loop BCI feedback task and automatically adapted the classifier over time. In a second session the trainees operated the system unassisted. Twelve healthy participants ran through this protocol. Along with the trainer, the trainees achieved a very high overall peak accuracy of 95.3 %. In the second session, where users operated the BCI unassisted, they still achieved a high overall peak accuracy of 83.6%. Ten of twelve first time BCI users successfully achieved significantly better than chance accuracy. Concluding, we can say that this trainer-trainee approach is very promising. Future research should investigate, whether this approach is superior to conventional training approaches. This trainer-trainee concept could have potential for future application of BCIs to end users.

  11. Tools for Brain-Computer Interaction: a general concept for a hybrid BCI (hBCI

    Directory of Open Access Journals (Sweden)

    Gernot R. Mueller-Putz

    2011-11-01

    Full Text Available The aim of this work is to present the development of a hybrid Brain-Computer Interface (hBCI which combines existing input devices with a BCI. Thereby, the BCI should be available if the user wishes to extend the types of inputs available to an assistive technology system, but the user can also choose not to use the BCI at all; the BCI is active in the background. The hBCI might decide on the one hand which input channel(s offer the most reliable signal(s and switch between input channels to improve information transfer rate, usability, or other factors, or on the other hand fuse various input channels. One major goal therefore is to bring the BCI technology to a level where it can be used in a maximum number of scenarios in a simple way. To achieve this, it is of great importance that the hBCI is able to operate reliably for long periods, recognizing and adapting to changes as it does so. This goal is only possible if many different subsystems in the hBCI can work together. Since one research institute alone cannot provide such different functionality, collaboration between institutes is necessary. To allow for such a collaboration, a common software framework was investigated.

  12. Hybrid setup for micro- and nano-computed tomography in the hard X-ray range

    Science.gov (United States)

    Fella, Christian; Balles, Andreas; Hanke, Randolf; Last, Arndt; Zabler, Simon

    2017-12-01

    With increasing miniaturization in industry and medical technology, non-destructive testing techniques are an area of ever-increasing importance. In this framework, X-ray microscopy offers an efficient tool for the analysis, understanding, and quality assurance of microscopic samples, in particular as it allows reconstructing three-dimensional data sets of the whole sample's volume via computed tomography (CT). The following article describes a compact X-ray microscope in the hard X-ray regime around 9 keV, based on a highly brilliant liquid-metal-jet source. In comparison to commercially available instruments, it is a hybrid that works in two different modes. The first one is a micro-CT mode without optics, which uses a high-resolution detector to allow scans of samples in the millimeter range with a resolution of 1 μm. The second mode is a microscope, which contains an X-ray optical element to magnify the sample and allows resolving 150 nm features. Changing between the modes is possible without moving the sample. Thus, the instrument represents an important step towards establishing high-resolution laboratory-based multi-mode X-ray microscopy as a standard investigation method.

  13. sBCI-Headset—Wearable and Modular Device for Hybrid Brain-Computer Interface

    Directory of Open Access Journals (Sweden)

    Tatsiana Malechka

    2015-02-01

    Full Text Available Severely disabled people, like completely paralyzed persons either with tetraplegia or similar disabilities who cannot use their arms and hands, are often considered as a user group of Brain Computer Interfaces (BCI. In order to achieve high acceptance of the BCI by this user group and their supporters, the BCI system has to be integrated into their support infrastructure. Critical disadvantages of a BCI are the time consuming preparation of the user for the electroencephalography (EEG measurements and the low information transfer rate of EEG based BCI. These disadvantages become apparent if a BCI is used to control complex devices. In this paper, a hybrid BCI is described that enables research for a Human Machine Interface (HMI that is optimally adapted to requirements of the user and the tasks to be carried out. The solution is based on the integration of a Steady-state visual evoked potential (SSVEP-BCI, an Event-related (de-synchronization (ERD/ERS-BCI, an eye tracker, an environmental observation camera, and a new EEG head cap for wearing comfort and easy preparation. The design of the new fast multimodal BCI (called sBCI system is described and first test results, obtained in experiments with six healthy subjects, are presented. The sBCI concept may also become useful for healthy people in cases where a “hands-free” handling of devices is necessary.

  14. Hybrid computational phantoms of the male and female newborn patient: NURBS-based whole-body models

    International Nuclear Information System (INIS)

    Lee, Choonsik; Lodwick, Daniel; Hasenauer, Deanna; Williams, Jonathan L; Lee, Choonik; Bolch, Wesley E

    2007-01-01

    Anthropomorphic computational phantoms are computer models of the human body for use in the evaluation of dose distributions resulting from either internal or external radiation sources. Currently, two classes of computational phantoms have been developed and widely utilized for organ dose assessment: (1) stylized phantoms and (2) voxel phantoms which describe the human anatomy via mathematical surface equations or 3D voxel matrices, respectively. Although stylized phantoms based on mathematical equations can be very flexible in regard to making changes in organ position and geometrical shape, they are limited in their ability to fully capture the anatomic complexities of human internal anatomy. In turn, voxel phantoms have been developed through image-based segmentation and correspondingly provide much better anatomical realism in comparison to simpler stylized phantoms. However, they themselves are limited in defining organs presented in low contrast within either magnetic resonance or computed tomography images-the two major sources in voxel phantom construction. By definition, voxel phantoms are typically constructed via segmentation of transaxial images, and thus while fine anatomic features are seen in this viewing plane, slice-to-slice discontinuities become apparent in viewing the anatomy of voxel phantoms in the sagittal or coronal planes. This study introduces the concept of a hybrid computational newborn phantom that takes full advantage of the best features of both its stylized and voxel counterparts: flexibility in phantom alterations and anatomic realism. Non-uniform rational B-spline (NURBS) surfaces, a mathematical modeling tool traditionally applied to graphical animation studies, was adopted to replace the limited mathematical surface equations of stylized phantoms. A previously developed whole-body voxel phantom of the newborn female was utilized as a realistic anatomical framework for hybrid phantom construction. The construction of a hybrid

  15. A hybrid NIRS-EEG system for self-paced brain computer interface with online motor imagery.

    Science.gov (United States)

    Koo, Bonkon; Lee, Hwan-Gon; Nam, Yunjun; Kang, Hyohyeong; Koh, Chin Su; Shin, Hyung-Cheul; Choi, Seungjin

    2015-04-15

    For a self-paced motor imagery based brain-computer interface (BCI), the system should be able to recognize the occurrence of a motor imagery, as well as the type of the motor imagery. However, because of the difficulty of detecting the occurrence of a motor imagery, general motor imagery based BCI studies have been focusing on the cued motor imagery paradigm. In this paper, we present a novel hybrid BCI system that uses near infrared spectroscopy (NIRS) and electroencephalography (EEG) systems together to achieve online self-paced motor imagery based BCI. We designed a unique sensor frame that records NIRS and EEG simultaneously for the realization of our system. Based on this hybrid system, we proposed a novel analysis method that detects the occurrence of a motor imagery with the NIRS system, and classifies its type with the EEG system. An online experiment demonstrated that our hybrid system had a true positive rate of about 88%, a false positive rate of 7% with an average response time of 10.36 s. As far as we know, there is no report that explored hemodynamic brain switch for self-paced motor imagery based BCI with hybrid EEG and NIRS system. From our experimental results, our hybrid system showed enough reliability for using in a practical self-paced motor imagery based BCI. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Rapid Identification of Staphylococcus aureus Directly from Blood Cultures by Fluorescence In Situ Hybridization with Peptide Nucleic Acid Probes

    Science.gov (United States)

    Oliveira, Kenneth; Procop, Gary W.; Wilson, Deborah; Coull, James; Stender, Henrik

    2002-01-01

    A new fluorescence in situ hybridization (FISH) method with peptide nucleic acid (PNA) probes for identification of Staphylococcus aureus directly from positive blood culture bottles that contain gram-positive cocci in clusters (GPCC) is described. The test (the S. aureus PNA FISH assay) is based on a fluorescein-labeled PNA probe that targets a species-specific sequence of the 16S rRNA of S. aureus. Evaluations with 17 reference strains and 48 clinical isolates, including methicillin-resistant and methicillin-susceptible S. aureus species, coagulase-negative Staphylococcus species, and other clinically relevant and phylogenetically related bacteria and yeast species, showed that the assay had 100% sensitivity and 96% specificity. Clinical trials with 87 blood cultures positive for GPCC correctly identified 36 of 37 (97%) of the S. aureus-positive cultures identified by standard microbiological methods. The positive and negative predictive values were 100 and 98%, respectively. It is concluded that this rapid method (2.5 h) for identification of S. aureus directly from blood culture bottles that contain GPCC offers important information for optimal antibiotic therapy. PMID:11773123

  17. Computer-assisted photo identification outperforms visible implant elastomers in an endangered salamander, Eurycea tonkawae.

    Directory of Open Access Journals (Sweden)

    Nathan F Bendik

    Full Text Available Despite recognition that nearly one-third of the 6300 amphibian species are threatened with extinction, our understanding of the general ecology and population status of many amphibians is relatively poor. A widely-used method for monitoring amphibians involves injecting captured individuals with unique combinations of colored visible implant elastomer (VIE. We compared VIE identification to a less-invasive method - computer-assisted photographic identification (photoID - in endangered Jollyville Plateau salamanders (Eurycea tonkawae, a species with a known range limited to eight stream drainages in central Texas. We based photoID on the unique pigmentation patterns on the dorsal head region of 1215 individual salamanders using identification software Wild-ID. We compared the performance of photoID methods to VIEs using both 'high-quality' and 'low-quality' images, which were taken using two different camera types and technologies. For high-quality images, the photoID method had a false rejection rate of 0.76% compared to 1.90% for VIEs. Using a comparable dataset of lower-quality images, the false rejection rate was much higher (15.9%. Photo matching scores were negatively correlated with time between captures, suggesting that evolving natural marks could increase misidentification rates in longer term capture-recapture studies. Our study demonstrates the utility of large-scale capture-recapture using photo identification methods for Eurycea and other species with stable natural marks that can be reliably photographed.

  18. Computational identification of 18 micrornas and their targets in three species of rose

    International Nuclear Information System (INIS)

    Baloch, I.A.; Barozai, M.Y.K.; Achakzai, A.K.K.

    2015-01-01

    MicroRNAs (miRNAs) are non-protein coding, small endogenous RNAs. Their length ranges from 18-26 nucleotides (nt). The miRNAs convergence property becomes a rational approach for the hunt of novel miRNAs in other organisms by homology search. As presently very little miRNAs are reported for rose species, so this study deals with the identification of miRNAs in different species of rose. Consequently 18 miRNA belonging to 17 miRNA families were identified in 3 species of rose (Rosa hybrid, Rosa chinensis and Rosa virginiana). All of the identified miRNA families (miR156, 160, 164, 166, 398, 482, 831, 837, 838, 841, 847, 3436, 3627, 6135, 6285, 6287 and 6288) are being reported for the first time in rose. Precursors of the identified miRNAs form stable minimum free energy (MFE) stem-loop structures and the mature miRNAs are found in the stem portions of their corresponding precursors. 11 putative targets of the miRNAs have also been identified. The identified targets are various proteins including transcription factors. Identification of 18 miRNAs will be supportive to explore the gene regulation phenomenon in various species of roses and it will be a good contribution for understanding the post transcriptional gene regulation in various stages of the life cycles of roses. (author)

  19. Proposing Hybrid Architecture to Implement Cloud Computing in Higher Education Institutions Using a Meta-synthesis Appro

    Directory of Open Access Journals (Sweden)

    hamid reza bazi

    2017-12-01

    Full Text Available Cloud computing is a new technology that considerably helps Higher Education Institutions (HEIs to develop and create competitive advantage with inherent characteristics such as flexibility, scalability, accessibility, reliability, fault tolerant and economic efficiency. Due to the numerous advantages of cloud computing, and in order to take advantage of cloud computing infrastructure, services of universities and HEIs need to migrate to the cloud. However, this transition involves many challenges, one of which is lack or shortage of appropriate architecture for migration to the technology. Using a reliable architecture for migration ensures managers to mitigate risks in the cloud computing technology. Therefore, organizations always search for suitable cloud computing architecture. In previous studies, these important features have received less attention and have not been achieved in a comprehensive way. The aim of this study is to use a meta-synthesis method for the first time to analyze the previously published studies and to suggest appropriate hybrid cloud migration architecture (IUHEC. We reviewed many papers from relevant journals and conference proceedings. The concepts extracted from these papers are classified to related categories and sub-categories. Then, we developed our proposed hybrid architecture based on these concepts and categories. The proposed architecture was validated by a panel of experts and Lawshe’s model was used to determine the content validity. Due to its innovative yet user-friendly nature, comprehensiveness, and high security, this architecture can help HEIs have an effective migration to cloud computing environment.

  20. Dynamic provisioning of a HEP computing infrastructure on a shared hybrid HPC system

    International Nuclear Information System (INIS)

    Meier, Konrad; Fleig, Georg; Hauth, Thomas; Quast, Günter; Janczyk, Michael; Von Suchodoletz, Dirk; Wiebelt, Bernd

    2016-01-01

    Experiments in high-energy physics (HEP) rely on elaborate hardware, software and computing systems to sustain the high data rates necessary to study rare physics processes. The Institut fr Experimentelle Kernphysik (EKP) at KIT is a member of the CMS and Belle II experiments, located at the LHC and the Super-KEKB accelerators, respectively. These detectors share the requirement, that enormous amounts of measurement data must be processed and analyzed and a comparable amount of simulated events is required to compare experimental results with theoretical predictions. Classical HEP computing centers are dedicated sites which support multiple experiments and have the required software pre-installed. Nowadays, funding agencies encourage research groups to participate in shared HPC cluster models, where scientist from different domains use the same hardware to increase synergies. This shared usage proves to be challenging for HEP groups, due to their specialized software setup which includes a custom OS (often Scientific Linux), libraries and applications. To overcome this hurdle, the EKP and data center team of the University of Freiburg have developed a system to enable the HEP use case on a shared HPC cluster. To achieve this, an OpenStack-based virtualization layer is installed on top of a bare-metal cluster. While other user groups can run their batch jobs via the Moab workload manager directly on bare-metal, HEP users can request virtual machines with a specialized machine image which contains a dedicated operating system and software stack. In contrast to similar installations, in this hybrid setup, no static partitioning of the cluster into a physical and virtualized segment is required. As a unique feature, the placement of the virtual machine on the cluster nodes is scheduled by Moab and the job lifetime is coupled to the lifetime of the virtual machine. This allows for a seamless integration with the jobs sent by other user groups and honors the fairshare

  1. Large-Scale, Multi-Sensor Atmospheric Data Fusion Using Hybrid Cloud Computing

    Science.gov (United States)

    Wilson, B. D.; Manipon, G.; Hua, H.; Fetzer, E. J.

    2015-12-01

    NASA's Earth Observing System (EOS) is an ambitious facility for studying global climate change. The mandate now is to combine measurements from the instruments on the "A-Train" platforms (AIRS, MODIS, MLS, and CloudSat) and other Earth probes to enable large-scale studies of climate change over decades. Moving to multi-sensor, long-duration presents serious challenges for large-scale data mining and fusion. For example, one might want to compare temperature and water vapor retrievals from one instrument (AIRS) to another (MODIS), and to a model (ECMWF), stratify the comparisons using a classification of the "cloud scenes" from CloudSat, and repeat the entire analysis over 10 years of data. HySDS is a Hybrid-Cloud Science Data System that has been developed and applied under NASA AIST, MEaSUREs, and ACCESS grants. HySDS uses the SciFlow workflow engine to partition analysis workflows into parallel tasks (e.g. segmenting by time or space) that are pushed into a durable job queue. The tasks are "pulled" from the queue by worker Virtual Machines (VM's) and executed in an on-premise Cloud (Eucalyptus or OpenStack) or at Amazon in the public Cloud or govCloud. In this way, years of data (millions of files) can be processed in a massively parallel way. Input variables (arrays) are pulled on-demand into the Cloud using OPeNDAP URLs or other subsetting services, thereby minimizing the size of the transferred data. We are using HySDS to automate the production of multiple versions of a ten-year A-Train water vapor climatology under a MEASURES grant. We will present the architecture of HySDS, describe the achieved "clock time" speedups in fusing datasets on our own nodes and in the Amazon Cloud, and discuss the Cloud cost tradeoffs for storage, compute, and data transfer. Our system demonstrates how one can pull A-Train variables (Levels 2 & 3) on-demand into the Amazon Cloud, and cache only those variables that are heavily used, so that any number of compute jobs can be

  2. Dynamic provisioning of a HEP computing infrastructure on a shared hybrid HPC system

    Science.gov (United States)

    Meier, Konrad; Fleig, Georg; Hauth, Thomas; Janczyk, Michael; Quast, Günter; von Suchodoletz, Dirk; Wiebelt, Bernd

    2016-10-01

    Experiments in high-energy physics (HEP) rely on elaborate hardware, software and computing systems to sustain the high data rates necessary to study rare physics processes. The Institut fr Experimentelle Kernphysik (EKP) at KIT is a member of the CMS and Belle II experiments, located at the LHC and the Super-KEKB accelerators, respectively. These detectors share the requirement, that enormous amounts of measurement data must be processed and analyzed and a comparable amount of simulated events is required to compare experimental results with theoretical predictions. Classical HEP computing centers are dedicated sites which support multiple experiments and have the required software pre-installed. Nowadays, funding agencies encourage research groups to participate in shared HPC cluster models, where scientist from different domains use the same hardware to increase synergies. This shared usage proves to be challenging for HEP groups, due to their specialized software setup which includes a custom OS (often Scientific Linux), libraries and applications. To overcome this hurdle, the EKP and data center team of the University of Freiburg have developed a system to enable the HEP use case on a shared HPC cluster. To achieve this, an OpenStack-based virtualization layer is installed on top of a bare-metal cluster. While other user groups can run their batch jobs via the Moab workload manager directly on bare-metal, HEP users can request virtual machines with a specialized machine image which contains a dedicated operating system and software stack. In contrast to similar installations, in this hybrid setup, no static partitioning of the cluster into a physical and virtualized segment is required. As a unique feature, the placement of the virtual machine on the cluster nodes is scheduled by Moab and the job lifetime is coupled to the lifetime of the virtual machine. This allows for a seamless integration with the jobs sent by other user groups and honors the fairshare

  3. Computational Acoustic Beamforming for Noise Source Identification for Small Wind Turbines.

    Science.gov (United States)

    Ma, Ping; Lien, Fue-Sang; Yee, Eugene

    2017-01-01

    This paper develops a computational acoustic beamforming (CAB) methodology for identification of sources of small wind turbine noise. This methodology is validated using the case of the NACA 0012 airfoil trailing edge noise. For this validation case, the predicted acoustic maps were in excellent conformance with the results of the measurements obtained from the acoustic beamforming experiment. Following this validation study, the CAB methodology was applied to the identification of noise sources generated by a commercial small wind turbine. The simulated acoustic maps revealed that the blade tower interaction and the wind turbine nacelle were the two primary mechanisms for sound generation for this small wind turbine at frequencies between 100 and 630 Hz.

  4. Identification and Prediction of Large Pedestrian Flow in Urban Areas Based on a Hybrid Detection Approach

    Directory of Open Access Journals (Sweden)

    Kaisheng Zhang

    2016-12-01

    Full Text Available Recently, population density has grown quickly with the increasing acceleration of urbanization. At the same time, overcrowded situations are more likely to occur in populous urban areas, increasing the risk of accidents. This paper proposes a synthetic approach to recognize and identify the large pedestrian flow. In particular, a hybrid pedestrian flow detection model was constructed by analyzing real data from major mobile phone operators in China, including information from smartphones and base stations (BS. With the hybrid model, the Log Distance Path Loss (LDPL model was used to estimate the pedestrian density from raw network data, and retrieve information with the Gaussian Progress (GP through supervised learning. Temporal-spatial prediction of the pedestrian data was carried out with Machine Learning (ML approaches. Finally, a case study of a real Central Business District (CBD scenario in Shanghai, China using records of millions of cell phone users was conducted. The results showed that the new approach significantly increases the utility and capacity of the mobile network. A more reasonable overcrowding detection and alert system can be developed to improve safety in subway lines and other hotspot landmark areas, such as the Bundle, People’s Square or Disneyland, where a large passenger flow generally exists.

  5. Learning Support Assessment Study of a Computer Simulation for the Development of Microbial Identification Strategies

    Directory of Open Access Journals (Sweden)

    Tristan E. Johnson

    2009-12-01

    Full Text Available This paper describes a study that examined how microbiology students construct knowledge of bacterial identification while using a computer simulation. The purpose of this study was to understand how the simulation affects the cognitive processing of students during thinking, problem solving, and learning about bacterial identification and to determine how the simulation facilitates the learning of a domain-specific problem-solving strategy. As part of an upper-division microbiology course, five students participated in several simulation assignments. The data were collected using think-aloud protocol and video action logs as the students used the simulation. The analysis revealed two major themes that determined the performance of the students: Simulation Usage—how the students used the software features and Problem-Solving Strategy Development—the strategy level students started with and the skill level they achieved when they completed their use of the simulation. Several conclusions emerged from the analysis of the data: (i The simulation affects various aspects of cognitive processing by creating an environment that makes it possible to practice the application of a problem-solving strategy. The simulation was used as an environment that allowed students to practice the cognitive skills required to solve an unknown. (ii Identibacter (the computer simulation may be considered to be a cognitive tool to facilitate the learning of a bacterial identification problem-solving strategy. (iii The simulation characteristics did support student learning of a problem-solving strategy. (iv Students demonstrated problem-solving strategy development specific to bacterial identification. (v Participants demonstrated an improved performance from their repeated use of the simulation.

  6. A quadratic kernel for computing the hybridization number of multiple trees

    NARCIS (Netherlands)

    L.J.J. van Iersel (Leo); S. Linz

    2012-01-01

    htmlabstractIt has recently been shown that the NP-hard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixed-parameter tractable if an instance of the problem consists of

  7. Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

    Science.gov (United States)

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  8. Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

    International Nuclear Information System (INIS)

    Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

    2014-01-01

    Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

  9. Hybrid MPI/OpenMP parallelization of the explicit Volterra integral equation solver for multi-core computer architectures

    KAUST Repository

    Al Jarro, Ahmed

    2011-08-01

    A hybrid MPI/OpenMP scheme for efficiently parallelizing the explicit marching-on-in-time (MOT)-based solution of the time-domain volume (Volterra) integral equation (TD-VIE) is presented. The proposed scheme equally distributes tested field values and operations pertinent to the computation of tested fields among the nodes using the MPI standard; while the source field values are stored in all nodes. Within each node, OpenMP standard is used to further accelerate the computation of the tested fields. Numerical results demonstrate that the proposed parallelization scheme scales well for problems involving three million or more spatial discretization elements. © 2011 IEEE.

  10. Impact of PECS tablet computer app on receptive identification of pictures given a verbal stimulus.

    Science.gov (United States)

    Ganz, Jennifer B; Hong, Ee Rea; Goodwyn, Fara; Kite, Elizabeth; Gilliland, Whitney

    2015-04-01

    The purpose of this brief report was to determine the effect on receptive identification of photos of a tablet computer-based augmentative and alternative communication (AAC) system with voice output. A multiple baseline single-case experimental design across vocabulary words was implemented. One participant, a preschool-aged boy with autism and little intelligible verbal language, was included in the study. Although a functional relation between the intervention and the dependent variable was not established, the intervention did appear to result in mild improvement for two of the three vocabulary words selected. The authors recommend further investigations of the collateral impacts of AAC on skills other than expressive language.

  11. A hybrid three-class brain-computer interface system utilizing SSSEPs and transient ERPs

    Science.gov (United States)

    Breitwieser, Christian; Pokorny, Christoph; Müller-Putz, Gernot R.

    2016-12-01

    Objective. This paper investigates the fusion of steady-state somatosensory evoked potentials (SSSEPs) and transient event-related potentials (tERPs), evoked through tactile simulation on the left and right-hand fingertips, in a three-class EEG based hybrid brain-computer interface. It was hypothesized, that fusing the input signals leads to higher classification rates than classifying tERP and SSSEP individually. Approach. Fourteen subjects participated in the studies, consisting of a screening paradigm to determine person dependent resonance-like frequencies and a subsequent online paradigm. The whole setup of the BCI system was based on open interfaces, following suggestions for a common implementation platform. During the online experiment, subjects were instructed to focus their attention on the stimulated fingertips as indicated by a visual cue. The recorded data were classified during runtime using a multi-class shrinkage LDA classifier and the outputs were fused together applying a posterior probability based fusion. Data were further analyzed offline, involving a combined classification of SSSEP and tERP features as a second fusion principle. The final results were tested for statistical significance applying a repeated measures ANOVA. Main results. A significant classification increase was achieved when fusing the results with a combined classification compared to performing an individual classification. Furthermore, the SSSEP classifier was significantly better in detecting a non-control state, whereas the tERP classifier was significantly better in detecting control states. Subjects who had a higher relative band power increase during the screening session also achieved significantly higher classification results than subjects with lower relative band power increase. Significance. It could be shown that utilizing SSSEP and tERP for hBCIs increases the classification accuracy and also that tERP and SSSEP are not classifying control- and non

  12. A hybrid agent-based computational economics and optimization approach for supplier selection problem

    Directory of Open Access Journals (Sweden)

    Zahra Pourabdollahi

    2017-12-01

    Full Text Available Supplier evaluation and selection problem is among the most important of logistics decisions that have been addressed extensively in supply chain management. The same logistics decision is also important in freight transportation since it identifies trade relationships between business establishments and determines commodity flows between production and consumption points. The commodity flows are then used as input to freight transportation models to determine cargo movements and their characteristics including mode choice and shipment size. Various approaches have been proposed to explore this latter problem in previous studies. Traditionally, potential suppliers are evaluated and selected using only price/cost as the influential criteria and the state-of-practice methods. This paper introduces a hybrid agent-based computational economics and optimization approach for supplier selection. The proposed model combines an agent-based multi-criteria supplier evaluation approach with a multi-objective optimization model to capture both behavioral and economical aspects of the supplier selection process. The model uses a system of ordered response models to determine importance weights of the different criteria in supplier evaluation from a buyers’ point of view. The estimated weights are then used to calculate a utility for each potential supplier in the market and rank them. The calculated utilities are then entered into a mathematical programming model in which best suppliers are selected by maximizing the total accrued utility for all buyers and minimizing total shipping costs while balancing the capacity of potential suppliers to ensure market clearing mechanisms. The proposed model, herein, was implemented under an operational agent-based supply chain and freight transportation framework for the Chicago Metropolitan Area.

  13. A hybrid computational model to explore the topological characteristics of epithelial tissues.

    Science.gov (United States)

    González-Valverde, Ismael; García-Aznar, José Manuel

    2017-11-01

    Epithelial tissues show a particular topology where cells resemble a polygon-like shape, but some biological processes can alter this tissue topology. During cell proliferation, mitotic cell dilation deforms the tissue and modifies the tissue topology. Additionally, cells are reorganized in the epithelial layer and these rearrangements also alter the polygon distribution. We present here a computer-based hybrid framework focused on the simulation of epithelial layer dynamics that combines discrete and continuum numerical models. In this framework, we consider topological and mechanical aspects of the epithelial tissue. Individual cells in the tissue are simulated by an off-lattice agent-based model, which keeps the information of each cell. In addition, we model the cell-cell interaction forces and the cell cycle. Otherwise, we simulate the passive mechanical behaviour of the cell monolayer using a material that approximates the mechanical properties of the cell. This continuum approach is solved by the finite element method, which uses a dynamic mesh generated by the triangulation of cell polygons. Forces generated by cell-cell interaction in the agent-based model are also applied on the finite element mesh. Cell movement in the agent-based model is driven by the displacements obtained from the deformed finite element mesh of the continuum mechanical approach. We successfully compare the results of our simulations with some experiments about the topology of proliferating epithelial tissues in Drosophila. Our framework is able to model the emergent behaviour of the cell monolayer that is due to local cell-cell interactions, which have a direct influence on the dynamics of the epithelial tissue. Copyright © 2017 John Wiley & Sons, Ltd.

  14. Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

    International Nuclear Information System (INIS)

    Flores, J.; Sears, J.; Schael, I.P.; White, L.; Garcia, D.; Lanata, C.; Kapikian, A.Z.

    1990-01-01

    We have synthesized 32 P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated from field studies

  15. Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

    Energy Technology Data Exchange (ETDEWEB)

    Flores, J.; Sears, J.; Schael, I.P.; White, L.; Garcia, D.; Lanata, C.; Kapikian, A.Z. (National Institutes of Health, Bethesda, MD (USA))

    1990-08-01

    We have synthesized {sup 32}P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated from field studies.

  16. Mode identification using stochastic hybrid models with applications to conflict detection and resolution

    Science.gov (United States)

    Naseri Kouzehgarani, Asal

    2009-12-01

    Most models of aircraft trajectories are non-linear and stochastic in nature; and their internal parameters are often poorly defined. The ability to model, simulate and analyze realistic air traffic management conflict detection scenarios in a scalable, composable, multi-aircraft fashion is an extremely difficult endeavor. Accurate techniques for aircraft mode detection are critical in order to enable the precise projection of aircraft conflicts, and for the enactment of altitude separation resolution strategies. Conflict detection is an inherently probabilistic endeavor; our ability to detect conflicts in a timely and accurate manner over a fixed time horizon is traded off against the increased human workload created by false alarms---that is, situations that would not develop into an actual conflict, or would resolve naturally in the appropriate time horizon-thereby introducing a measure of probabilistic uncertainty in any decision aid fashioned to assist air traffic controllers. The interaction of the continuous dynamics of the aircraft, used for prediction purposes, with the discrete conflict detection logic gives rise to the hybrid nature of the overall system. The introduction of the probabilistic element, common to decision alerting and aiding devices, places the conflict detection and resolution problem in the domain of probabilistic hybrid phenomena. A hidden Markov model (HMM) has two stochastic components: a finite-state Markov chain and a finite set of output probability distributions. In other words an unobservable stochastic process (hidden) that can only be observed through another set of stochastic processes that generate the sequence of observations. The problem of self separation in distributed air traffic management reduces to the ability of aircraft to communicate state information to neighboring aircraft, as well as model the evolution of aircraft trajectories between communications, in the presence of probabilistic uncertain dynamics as well

  17. Identification of supernumerary ring chromosome 1 mosaicism using fluorescence in situ hybridization.

    Science.gov (United States)

    Chen, H; Tuck-Muller, C M; Batista, D A; Wertelecki, W

    1995-03-27

    We report on a 15-year-old black boy with severe mental retardation, multiple congenital anomalies, and a supernumerary ring chromosome mosaicism. Fluorescence in situ hybridization with a chromosome 1 painting probe (pBS1) identified the ring as derived from chromosome 1. The karyotype was 46,XY/47,XY,+r(1)(p13q23). A review showed 8 reports of ring chromosome 1. In 5 cases, the patients had a non-supernumerary ring chromosome 1 resulting in partial monosomies of the short and/or long arm of chromosome 1. In 3 cases, the presence of a supernumerary ring resulted in partial trisomy of different segments of chromosome 1. In one of these cases the supernumerary ring was composed primarily of the centromere and the heterochromatic region of chromosome 1, resulting in normal phenotype. Our patient represents the third report of a supernumerary ring chromosome 1 resulting in abnormal phenotype.

  18. Identification and biosynthesis of a novel xanthomonadin-dialkylresorcinol-hybrid from Azoarcus sp. BH72.

    Directory of Open Access Journals (Sweden)

    Tim A Schöner

    Full Text Available A novel xanthomonadin-dialkylresorcinol hybrid named arcuflavin was identified in Azoarcus sp. BH72 by a combination of feeding experiments, HPLC-MS and MALDI-MS and gene clusters encoding the biosynthesis of this non-isoprenoid aryl-polyene containing pigment are reported. A chorismate-utilizing enzyme from the XanB2-type producing 3- and 4-hydroxybenzoic acid and an AMP-ligase encoded by these gene clusters were characterized, that might perform the first two steps of the polyene biosynthesis. Furthermore, a detailed analysis of the already known or novel biosynthesis gene clusters involved in the biosynthesis of polyene containing pigments like arcuflavin, flexirubin and xanthomonadin revealed the presence of similar gene clusters in a wide range of bacterial taxa, suggesting that polyene and polyene-dialkylresorcinol pigments are more widespread than previously realized.

  19. Hybrid Wing Body Model Identification Using Forced-Oscillation Water Tunnel Data

    Science.gov (United States)

    Murphy, Patrick C.; Vicroy, Dan D.; Kramer, Brian; Kerho, Michael

    2014-01-01

    Static and dynamic testing of the NASA 0.7 percent scale Hybrid Wing Body (HWB) configuration was conducted in the Rolling Hills Research Corporation water tunnel to investigate aerodynamic behavior over a large range of angle-of-attack and to develop models that can predict aircraft response in nonlinear unsteady flight regimes. This paper reports primarily on the longitudinal axis results. Flow visualization tests were also performed. These tests provide additional static data and new dynamic data that complement tests conducted at NASA Langley 14- by 22-Foot Subsonic Tunnel. HWB was developed to support the NASA Environmentally Responsible Aviation Project goals of lower noise, emissions, and fuel burn. This study also supports the NASA Aviation Safety Program efforts to model and control advanced transport configurations in loss-of-control conditions.

  20. [Identification of C(2)M interacting proteins by yeast two-hybrid screening].

    Science.gov (United States)

    Yue, Shan-shan; Xia, Lai-xin

    2015-11-01

    The synaptonemal complex (SC) is a huge structure which assembles between the homologous chromosomes during meiotic prophase I. Drosophila germ cell-specific nucleoprotein C(2)M clustering at chromosomes can induce SC formation. To further study the molecular function and mechanism of C(2)M in meiosis, we constructed a bait vector for C(2)M and used the yeast two-hybrid system to identify C(2)M interacting proteins. Forty interacting proteins were obtained, including many DNA and histone binding proteins, ATP synthases and transcription factors. Gene silencing assays in Drosophila showed that two genes, wech and Psf1, may delay the disappearance of SC. These results indicate that Wech and Psf1 may form a complex with C(2)M to participate in the formation or stabilization of the SC complex.

  1. Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

    Science.gov (United States)

    Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

    2004-01-01

    A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

  2. Noise Threshold and Resource Cost of Fault-Tolerant Quantum Computing with Majorana Fermions in Hybrid Systems.

    Science.gov (United States)

    Li, Ying

    2016-09-16

    Fault-tolerant quantum computing in systems composed of both Majorana fermions and topologically unprotected quantum systems, e.g., superconducting circuits or quantum dots, is studied in this Letter. Errors caused by topologically unprotected quantum systems need to be corrected with error-correction schemes, for instance, the surface code. We find that the error-correction performance of such a hybrid topological quantum computer is not superior to a normal quantum computer unless the topological charge of Majorana fermions is insusceptible to noise. If errors changing the topological charge are rare, the fault-tolerance threshold is much higher than the threshold of a normal quantum computer and a surface-code logical qubit could be encoded in only tens of topological qubits instead of about 1,000 normal qubits.

  3. CERPI and CEREL, two computer codes for the automatic identification and determination of gamma emitters in thermal neutron activated samples

    International Nuclear Information System (INIS)

    Giannini, M.; Oliva, P.R.; Ramorino, C.

    1978-01-01

    A description is given of a computer code which automatically analyses gamma-ray spectra obtained with Ge(Li) detectors. The program contains features as automatic peak location and fitting, determination of peak energies and intensities, nuclide identification and calculation of masses and errors. Finally the results obtained with our computer code for a lunar sample are reported and briefly discussed

  4. Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization.

    Directory of Open Access Journals (Sweden)

    Marjolein Meijerink

    Full Text Available BACKGROUND: Probiotics can be used to stimulate or regulate epithelial and immune cells of the intestinal mucosa and generate beneficial mucosal immunomodulatory effects. Beneficial effects of specific strains of probiotics have been established in the treatment and prevention of various intestinal disorders, including allergic diseases and diarrhea. However, the precise molecular mechanisms and the strain-dependent factors involved are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we aimed to identify gene loci in the model probiotic organism Lactobacillus plantarum WCFS1 that modulate the immune response of host dendritic cells. The amounts of IL-10 and IL-12 secreted by dendritic cells (DCs after stimulation with 42 individual L. plantarum strains were measured and correlated with the strain-specific genomic composition using comparative genome hybridisation and the Random Forest algorithm. This in silico "gene-trait matching" approach led to the identification of eight candidate genes in the L. plantarum genome that might modulate the DC cytokine response to L. plantarum. Six of these genes were involved in bacteriocin production or secretion, one encoded a bile salt hydrolase and one encoded a transcription regulator of which the exact function is unknown. Subsequently, gene deletions mutants were constructed in L. plantarum WCFS1 and compared to the wild-type strain in DC stimulation assays. All three bacteriocin mutants as well as the transcription regulator (lp_2991 had the predicted effect on cytokine production confirming their immunomodulatory effect on the DC response to L. plantarum. Transcriptome analysis and qPCR data showed that transcript level of gtcA3, which is predicted to be involved in glycosylation of cell wall teichoic acids, was substantially increased in the lp_2991 deletion mutant (44 and 29 fold respectively. CONCLUSION: Comparative genome hybridization led to the identification of gene loci in L

  5. Simultaneous detection of P300 and steady-state visually evoked potentials for hybrid brain-computer interface.

    Science.gov (United States)

    Combaz, Adrien; Van Hulle, Marc M

    2015-01-01

    We study the feasibility of a hybrid Brain-Computer Interface (BCI) combining simultaneous visual oddball and Steady-State Visually Evoked Potential (SSVEP) paradigms, where both types of stimuli are superimposed on a computer screen. Potentially, such a combination could result in a system being able to operate faster than a purely P300-based BCI and encode more targets than a purely SSVEP-based BCI. We analyse the interactions between the brain responses of the two paradigms, and assess the possibility to detect simultaneously the brain activity evoked by both paradigms, in a series of 3 experiments where EEG data are analysed offline. Despite differences in the shape of the P300 response between pure oddball and hybrid condition, we observe that the classification accuracy of this P300 response is not affected by the SSVEP stimulation. We do not observe either any effect of the oddball stimulation on the power of the SSVEP response in the frequency of stimulation. Finally results from the last experiment show the possibility of detecting both types of brain responses simultaneously and suggest not only the feasibility of such hybrid BCI but also a gain over pure oddball- and pure SSVEP-based BCIs in terms of communication rate.

  6. Identification of control targets in Boolean molecular network models via computational algebra.

    Science.gov (United States)

    Murrugarra, David; Veliz-Cuba, Alan; Aguilar, Boris; Laubenbacher, Reinhard

    2016-09-23

    Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other therapeutic treatment. The identification of such strategies is typically based on a mathematical model of the process to be altered through targeted control inputs. This paper focuses on processes at the molecular level that determine the state of an individual cell, involving signaling or gene regulation. The mathematical model type considered is that of Boolean networks. The potential control targets can be represented by a set of nodes and edges that can be manipulated to produce a desired effect on the system. This paper presents a method for the identification of potential intervention targets in Boolean molecular network models using algebraic techniques. The approach exploits an algebraic representation of Boolean networks to encode the control candidates in the network wiring diagram as the solutions of a system of polynomials equations, and then uses computational algebra techniques to find such controllers. The control methods in this paper are validated through the identification of combinatorial interventions in the signaling pathways of previously reported control targets in two well studied systems, a p53-mdm2 network and a blood T cell lymphocyte granular leukemia survival signaling network. Supplementary data is available online and our code in Macaulay2 and Matlab are available via http://www.ms.uky.edu/~dmu228/ControlAlg . This paper presents a novel method for the identification of intervention targets in Boolean network models. The results in this paper show that the proposed methods are useful and efficient for moderately large networks.

  7. Combined fluorescent-chromogenic in situ hybridization for identification and laser microdissection of interphase chromosomes.

    Directory of Open Access Journals (Sweden)

    Nerea Paz

    Full Text Available Chromosome territories constitute the most conspicuous feature of nuclear architecture, and they exhibit non-random distribution patterns in the interphase nucleus. We observed that in cell nuclei from humans with Down Syndrome two chromosomes 21 frequently localize proximal to one another and distant from the third chromosome. To systematically investigate whether the proximally positioned chromosomes were always the same in all cells, we developed an approach consisting of sequential FISH and CISH combined with laser-microdissection of chromosomes from the interphase nucleus and followed by subsequent chromosome identification by microsatellite allele genotyping. This approach identified proximally positioned chromosomes from cultured cells, and the analysis showed that the identity of the chromosomes proximally positioned varies. However, the data suggest that there may be a tendency of the same chromosomes to be positioned close to each other in the interphase nucleus of trisomic cells. The protocol described here represents a powerful new method for genome analysis.

  8. Hybrid Swarm Intelligence Optimization Approach for Optimal Data Storage Position Identification in Wireless Sensor Networks

    Science.gov (United States)

    Mohanasundaram, Ranganathan; Periasamy, Pappampalayam Sanmugam

    2015-01-01

    The current high profile debate with regard to data storage and its growth have become strategic task in the world of networking. It mainly depends on the sensor nodes called producers, base stations, and also the consumers (users and sensor nodes) to retrieve and use the data. The main concern dealt here is to find an optimal data storage position in wireless sensor networks. The works that have been carried out earlier did not utilize swarm intelligence based optimization approaches to find the optimal data storage positions. To achieve this goal, an efficient swam intelligence approach is used to choose suitable positions for a storage node. Thus, hybrid particle swarm optimization algorithm has been used to find the suitable positions for storage nodes while the total energy cost of data transmission is minimized. Clustering-based distributed data storage is utilized to solve clustering problem using fuzzy-C-means algorithm. This research work also considers the data rates and locations of multiple producers and consumers to find optimal data storage positions. The algorithm is implemented in a network simulator and the experimental results show that the proposed clustering and swarm intelligence based ODS strategy is more effective than the earlier approaches. PMID:25734182

  9. Identification of Bacillus anthracis specific chromosomal sequences by suppressive subtractive hybridization

    Directory of Open Access Journals (Sweden)

    Redkar Rajendra

    2004-02-01

    Full Text Available Abstract Background Bacillus anthracis, Bacillus thuringiensis and Bacillus cereus are closely related members of the B. cereus-group of bacilli. Suppressive subtractive hybridization (SSH was used to identify specific chromosomal sequences unique to B. anthracis. Results Two SSH libraries were generated. Genomic DNA from plasmid-cured B. anthracis was used as the tester DNA in both libraries, while genomic DNA from either B. cereus or B. thuringiensis served as the driver DNA. Progressive screening of the libraries by colony filter and Southern blot analyses identified 29 different clones that were specific for the B. anthracis chromosome relative not only to the respective driver DNAs, but also to seven other different strains of B. cereus and B. thuringiensis included in the process. The nucleotide sequences of the clones were compared with those found in genomic databases, revealing that over half of the clones were located into 2 regions on the B. anthracis chromosome. Conclusions Genes encoding potential cell wall synthesis proteins dominated one region, while bacteriophage-related sequences dominated the other region. The latter supports the hypothesis that acquisition of these bacteriophage sequences occurred during or after speciation of B. anthracis relative to B. cereus and B. thuringiensis. This study provides insight into the chromosomal differences between B. anthracis and its closest phylogenetic relatives.

  10. Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization.

    Science.gov (United States)

    Zhang, Zongying; Jiang, Shenghui; Wang, Nan; Li, Min; Ji, Xiaohao; Sun, Shasha; Liu, Jingxuan; Wang, Deyun; Xu, Haifeng; Qi, Sumin; Wu, Shujing; Fei, Zhangjun; Feng, Shouqian; Chen, Xuesen

    2015-01-01

    Apple is one of the most economically important horticultural fruit crops worldwide. It is critical to gain insights into fruit ripening and softening to improve apple fruit quality and extend shelf life. In this study, forward and reverse suppression subtractive hybridization libraries were generated from 'Taishanzaoxia' apple fruits sampled around the ethylene climacteric to isolate ripening- and softening-related genes. A set of 648 unigenes were derived from sequence alignment and cluster assembly of 918 expressed sequence tags. According to gene ontology functional classification, 390 out of 443 unigenes (88%) were assigned to the biological process category, 356 unigenes (80%) were classified in the molecular function category, and 381 unigenes (86%) were allocated to the cellular component category. A total of 26 unigenes differentially expressed during fruit development period were analyzed by quantitative RT-PCR. These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated. Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'. Some of the identified unigenes associated with fruit ripening and softening have not been characterized in public databases. The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

  11. Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

    Energy Technology Data Exchange (ETDEWEB)

    Gan, Yangzhou; Zhao, Qunfei [Department of Automation, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240 (China); Xia, Zeyang, E-mail: zy.xia@siat.ac.cn, E-mail: jing.xiong@siat.ac.cn; Hu, Ying [Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, and The Chinese University of Hong Kong, Shenzhen 518055 (China); Xiong, Jing, E-mail: zy.xia@siat.ac.cn, E-mail: jing.xiong@siat.ac.cn [Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 510855 (China); Zhang, Jianwei [TAMS, Department of Informatics, University of Hamburg, Hamburg 22527 (Germany)

    2015-01-15

    Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0

  12. Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

    International Nuclear Information System (INIS)

    Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang; Hu, Ying; Xiong, Jing; Zhang, Jianwei

    2015-01-01

    Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slice and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm 3 ) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm 3 , 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm 3 , 91.57 ± 0.82%, 0.27 ± 0.02 mm, 0.28 ± 0.03 mm

  13. Bridging Social and Semantic Computing - Design and Evaluation of User Interfaces for Hybrid Systems

    Science.gov (United States)

    Bostandjiev, Svetlin Alex I.

    2012-01-01

    The evolution of the Web brought new interesting problems to computer scientists that we loosely classify in the fields of social and semantic computing. Social computing is related to two major paradigms: computations carried out by a large amount of people in a collective intelligence fashion (i.e. wikis), and performing computations on social…

  14. Integration of Computed Tomography and Three-Dimensional Echocardiography for Hybrid Three-Dimensional Printing in Congenital Heart Disease.

    Science.gov (United States)

    Gosnell, Jordan; Pietila, Todd; Samuel, Bennett P; Kurup, Harikrishnan K N; Haw, Marcus P; Vettukattil, Joseph J

    2016-12-01

    Three-dimensional (3D) printing is an emerging technology aiding diagnostics, education, and interventional, and surgical planning in congenital heart disease (CHD). Three-dimensional printing has been derived from computed tomography, cardiac magnetic resonance, and 3D echocardiography. However, individually the imaging modalities may not provide adequate visualization of complex CHD. The integration of the strengths of two or more imaging modalities has the potential to enhance visualization of cardiac pathomorphology. We describe the feasibility of hybrid 3D printing from two imaging modalities in a patient with congenitally corrected transposition of the great arteries (L-TGA). Hybrid 3D printing may be useful as an additional tool for cardiologists and cardiothoracic surgeons in planning interventions in children and adults with CHD.

  15. A novel methodology for non-linear system identification of battery cells used in non-road hybrid electric vehicles

    Science.gov (United States)

    Unger, Johannes; Hametner, Christoph; Jakubek, Stefan; Quasthoff, Marcus

    2014-12-01

    An accurate state of charge (SoC) estimation of a traction battery in hybrid electric non-road vehicles, which possess higher dynamics and power densities than on-road vehicles, requires a precise battery cell terminal voltage model. This paper presents a novel methodology for non-linear system identification of battery cells to obtain precise battery models. The methodology comprises the architecture of local model networks (LMN) and optimal model based design of experiments (DoE). Three main novelties are proposed: 1) Optimal model based DoE, which aims to high dynamically excite the battery cells at load ranges frequently used in operation. 2) The integration of corresponding inputs in the LMN to regard the non-linearities SoC, relaxation, hysteresis as well as temperature effects. 3) Enhancements to the local linear model tree (LOLIMOT) construction algorithm, to achieve a physical appropriate interpretation of the LMN. The framework is applicable for different battery cell chemistries and different temperatures, and is real time capable, which is shown on an industrial PC. The accuracy of the obtained non-linear battery model is demonstrated on cells with different chemistries and temperatures. The results show significant improvement due to optimal experiment design and integration of the battery non-linearities within the LMN structure.

  16. A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection

    Directory of Open Access Journals (Sweden)

    Simeone Marino

    2016-10-01

    Full Text Available Tuberculosis (TB is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB. The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs is the formation of spherical structures, primarily in lungs, called granulomas. Infection occurs after inhalation of bacteria into lungs, where resident antigen-presenting cells (APCs, take up bacteria and initiate the immune response to Mtb infection. APCs traffic from the site of infection (lung to lung-draining lymph nodes (LNs where they prime T cells to recognize Mtb. These T cells, circulating back through blood, migrate back to lungs to perform their immune effector functions. We have previously developed a hybrid agent-based model (ABM, labeled GranSim describing in silico immune cell, bacterial (Mtb and molecular behaviors during tuberculosis infection and recently linked that model to operate across three physiological compartments: lung (infection site where granulomas form, lung draining lymph node (LN, site of generation of adaptive immunity and blood (a measurable compartment. Granuloma formation and function is captured by a spatio-temporal model (i.e., ABM, while LN and blood compartments represent temporal dynamics of the whole body in response to infection and are captured with ordinary differential equations (ODEs. In order to have a more mechanistic representation of APC trafficking from the lung to the lymph node, and to better capture antigen presentation in a draining LN, this current study incorporates the role of dendritic cells (DCs in a computational fashion into GranSim. Results: The model was calibrated using experimental data from the lungs and blood of NHPs. The addition of DCs allowed us to investigate in greater detail mechanisms of recruitment, trafficking and antigen presentation and their role in tuberculosis infection. Conclusion: The main conclusion of this study is

  17. Identification of Genes Associated with Morphology in Aspergillus Niger by Using Suppression Subtractive Hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Ziyu; Mao, Xingxue; Magnuson, Jon K.; Lasure, Linda L.

    2004-04-01

    The morphology of citric acid production strains of Aspergillus niger is sensitive to a variety of factors including the concentration of manganese (Mn2+). Upon increasing the Mn2+ concentration in A. niger (ATCC 11414) cultures to 14 ppb or higher, the morphology switches from pelleted to filamentous, accompanied by a rapid decline in citric acid production. Molecular mechanisms through which Mn2+ exerts effects on morphology and citric acid production in A. niger have not been well defined, but our use of suppression subtractive hybridization has identified 22 genes responsive to Mn2+. Fifteen genes were differentially expressed when A. niger was grown in media containing 1000 ppb Mn2+ (filamentous form) and seven genes in 10 ppb Mn2+ (pelleted form). Of the fifteen filamentous-associated genes, seven are novel and eight share 47-100% identity to genes from other organisms. Five of the pellet-associated genes are novel, and the other two genes encode a pepsin-type protease and polyubiquitin. All ten genes with deduced functions are either involved in amino acid metabolism/protein catabolism or cell regulatory processes. Northern-blot analysis showed that the transcripts of all 22 genes were rapidly enhanced or suppressed by Mn2+. Steady-state mRNA levels of six selected filamentous associated genes remained high during five days of culture in a filamentous state and low under pelleted growth conditions. The opposite behavior was observed for four selected pellet-associated genes. The full-length cDNA of the filamentous-associated clone, Brsa-25 was isolated. Antisense expression of Brsa-25 permitted pelleted growth and increased citrate production at higher concentrations of Mn2+ than could be tolerated by the parent strain. The results suggest the involvement of the newly isolated genes in regulation of A. niger morphology.

  18. Data of NODDI diffusion metrics in the brain and computer simulation of hybrid diffusion imaging (HYDI acquisition scheme

    Directory of Open Access Journals (Sweden)

    Chandana Kodiweera

    2016-06-01

    Full Text Available This article provides NODDI diffusion metrics in the brains of 52 healthy participants and computer simulation data to support compatibility of hybrid diffusion imaging (HYDI, “Hybrid diffusion imaging” [1] acquisition scheme in fitting neurite orientation dispersion and density imaging (NODDI model, “NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain” [2]. HYDI is an extremely versatile diffusion magnetic resonance imaging (dMRI technique that enables various analyzes methods using a single diffusion dataset. One of the diffusion data analysis methods is the NODDI computation, which models the brain tissue with three compartments: fast isotropic diffusion (e.g., cerebrospinal fluid, anisotropic hindered diffusion (e.g., extracellular space, and anisotropic restricted diffusion (e.g., intracellular space. The NODDI model produces microstructural metrics in the developing brain, aging brain or human brain with neurologic disorders. The first dataset provided here are the means and standard deviations of NODDI metrics in 48 white matter region-of-interest (ROI averaging across 52 healthy participants. The second dataset provided here is the computer simulation with initial conditions guided by the first dataset as inputs and gold standard for model fitting. The computer simulation data provide a direct comparison of NODDI indices computed from the HYDI acquisition [1] to the NODDI indices computed from the originally proposed acquisition [2]. These data are related to the accompanying research article “Age Effects and Sex Differences in Human Brain White Matter of Young to Middle-Aged Adults: A DTI, NODDI, and q-Space Study” [3].

  19. Identification of genes differentially regulated in rat alveolar bone wound healing by subtractive hybridization.

    Science.gov (United States)

    Ohira, T; Myokai, F; Shiomi, N; Yamashiro, K; Yamamoto, T; Murayama, Y; Arai, H; Nishimura, F; Takashiba, S

    2004-07-01

    Periodontal healing requires the participation of regulatory molecules, cells, and scaffold or matrix. Here, we hypothesized that a certain set of genes is expressed in alveolar bone wound healing. Reciprocal subtraction gave 400 clones from the injured alveolar bone of Wistar rats. Identification of 34 genes and analysis of their expression in injured tissue revealed several clusters of unique gene regulation patterns, including the up-regulation at 1 wk of cytochrome c oxidase regulating electron transfer and energy metabolism, presumably occurring at the site of inflammation; up-regulation at 2.5 wks of pro-alpha-2 type I collagen involving the formation of a connective tissue structure; and up-regulation at 1 and 2 wks and down-regulation at 2.5 and 4 wks of ubiquitin carboxyl-terminal hydrolase l3 involving cell cycle, DNA repair, and stress response. The differential expression of genes may be associated with the processes of inflammation, wound contraction, and formation of a connective tissue structure.

  20. DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes.

    Science.gov (United States)

    Vanhaecke, Delphine; Garcia de Leaniz, Carlos; Gajardo, Gonzalo; Young, Kyle; Sanzana, Jose; Orellana, Gabriel; Fowler, Daniel; Howes, Paul; Monzon-Arguello, Catalina; Consuegra, Sofia

    2012-01-01

    The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.

  1. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.

    Science.gov (United States)

    Novák, Petr; Ávila Robledillo, Laura; Koblížková, Andrea; Vrbová, Iva; Neumann, Pavel; Macas, Jirí

    2017-07-07

    Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Hybrid incompatibilities in the parasitic wasp genus Nasonia : Negative effects of hemizygosity and the identification of transmission ratio distortion loci

    NARCIS (Netherlands)

    Koevoets, T.; Niehuis, O.; van de Zande, L.; Beukeboom, L. W.

    The occurrence of hybrid incompatibilities forms an important stage during the evolution of reproductive isolation. In early stages of speciation, males and females often respond differently to hybridization. Haldane's rule states that the heterogametic sex suffers more from hybridization than the

  3. Identification of proteins involved in the functioning of Riftia pachyptila symbiosis by Subtractive Suppression Hybridization

    Directory of Open Access Journals (Sweden)

    Lallier François H

    2007-09-01

    Full Text Available Abstract Background Since its discovery around deep sea hydrothermal vents of the Galapagos Rift about 30 years ago, the chemoautotrophic symbiosis between the vestimentiferan tubeworm Riftia pachyptila and its symbiotic sulfide-oxidizing γ-proteobacteria has been extensively studied. However, studies on the tubeworm host were essentially targeted, biochemical approaches. We decided to use a global molecular approach to identify new proteins involved in metabolite exchanges and assimilation by the host. We used a Subtractive Suppression Hybridization approach (SSH in an unusual way, by comparing pairs of tissues from a single individual. We chose to identify the sequences preferentially expressed in the branchial plume tissue (the only organ in contact with the sea water and in the trophosome (the organ housing the symbiotic bacteria using the body wall as a reference tissue because it is supposedly not involved in metabolite exchanges in this species. Results We produced four cDNA libraries: i body wall-subtracted branchial plume library (BR-BW, ii and its reverse library, branchial plume-subtracted body wall library (BW-BR, iii body wall-subtracted trophosome library (TR-BW, iv and its reverse library, trophosome-subtracted body wall library (BW-TR. For each library, we sequenced about 200 clones resulting in 45 different sequences on average in each library (58 and 59 cDNAs for BR-BW and TR-BW libraries respectively. Overall, half of the contigs matched records found in the databases with good E-values. After quantitative PCR analysis, it resulted that 16S, Major Vault Protein, carbonic anhydrase (RpCAbr, cathepsin and chitinase precursor transcripts were highly represented in the branchial plume tissue compared to the trophosome and the body wall tissues, whereas carbonic anhydrase (RpCAtr, myohemerythrin, a putative T-Cell receptor and one non identified transcript were highly specific of the trophosome tissue. Conclusion Quantitative PCR

  4. Identification of proteins involved in the functioning of Riftia pachyptila symbiosis by Subtractive Suppression Hybridization.

    Science.gov (United States)

    Sanchez, Sophie; Hourdez, Stéphane; Lallier, François H

    2007-09-24

    Since its discovery around deep sea hydrothermal vents of the Galapagos Rift about 30 years ago, the chemoautotrophic symbiosis between the vestimentiferan tubeworm Riftia pachyptila and its symbiotic sulfide-oxidizing gamma-proteobacteria has been extensively studied. However, studies on the tubeworm host were essentially targeted, biochemical approaches. We decided to use a global molecular approach to identify new proteins involved in metabolite exchanges and assimilation by the host. We used a Subtractive Suppression Hybridization approach (SSH) in an unusual way, by comparing pairs of tissues from a single individual. We chose to identify the sequences preferentially expressed in the branchial plume tissue (the only organ in contact with the sea water) and in the trophosome (the organ housing the symbiotic bacteria) using the body wall as a reference tissue because it is supposedly not involved in metabolite exchanges in this species. We produced four cDNA libraries: i) body wall-subtracted branchial plume library (BR-BW), ii) and its reverse library, branchial plume-subtracted body wall library (BW-BR), iii) body wall-subtracted trophosome library (TR-BW), iv) and its reverse library, trophosome-subtracted body wall library (BW-TR). For each library, we sequenced about 200 clones resulting in 45 different sequences on average in each library (58 and 59 cDNAs for BR-BW and TR-BW libraries respectively). Overall, half of the contigs matched records found in the databases with good E-values. After quantitative PCR analysis, it resulted that 16S, Major Vault Protein, carbonic anhydrase (RpCAbr), cathepsin and chitinase precursor transcripts were highly represented in the branchial plume tissue compared to the trophosome and the body wall tissues, whereas carbonic anhydrase (RpCAtr), myohemerythrin, a putative T-Cell receptor and one non identified transcript were highly specific of the trophosome tissue. Quantitative PCR analyses were congruent with our libraries

  5. Computationally Probing the Performance of Hybrid, Heterogeneous, and Homogeneous Iridium-Based Catalysts for Water Oxidation

    Energy Technology Data Exchange (ETDEWEB)

    García-Melchor, Max [SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford CA (United States); Vilella, Laia [Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST),Tarragona (Spain); Departament de Quimica, Universitat Autonoma de Barcelona, Barcelona (Spain); López, Núria [Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Tarragona (Spain); Vojvodic, Aleksandra [SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, Menlo Park CA (United States)

    2016-04-29

    An attractive strategy to improve the performance of water oxidation catalysts would be to anchor a homogeneous molecular catalyst on a heterogeneous solid surface to create a hybrid catalyst. The idea of this combined system is to take advantage of the individual properties of each of the two catalyst components. We use Density Functional Theory to determine the stability and activity of a model hybrid water oxidation catalyst consisting of a dimeric Ir complex attached on the IrO2(110) surface through two oxygen atoms. We find that homogeneous catalysts can be bound to its matrix oxide without losing significant activity. Hence, designing hybrid systems that benefit from both the high tunability of activity of homogeneous catalysts and the stability of heterogeneous systems seems feasible.

  6. Leptospira borgpetersenii hybrid leucine-rich repeat protein: Cloning and expression, immunogenic identification and molecular docking evaluation.

    Science.gov (United States)

    Sritrakul, Tepyuda; Nitipan, Supachai; Wajjwalku, Worawidh; La-Ard, Anchalee; Suphatpahirapol, Chattip; Petkarnjanapong, Wimol; Ongphiphadhanakul, Boonsong; Prapong, Siriwan

    2017-11-01

    Leptospirosis is an important zoonotic disease, and the major outbreak of this disease in Thailand in 1999 was due largely to the Leptospira borgpetersenii serovar Sejroe. Identification of the leucine-rich repeat (LRR) LBJ_2271 protein containing immunogenic epitopes and the discovery of the LBJ_2271 ortholog in Leptospira serovar Sejroe, KU_Sej_R21_2271, led to further studies of the antigenic immune properties of KU_Sej_LRR_2271. The recombinant hybrid (rh) protein was created and expressed from a hybrid PCR fragment of KU_Sej_R21_2271 fused with DNA encoding the LBJ_2271 signal sequence for targeting protein as a membrane-anchoring protein. The fusion DNA was cloned into pET160/GW/D-TOPO® to form the pET160_hKU_R21_2271 plasmid. The plasmid was used to express the rhKU_Sej_LRR_2271 protein in Escherichia coli BL21 Star™ (DE3). The expressed protein was immunologically detected by Western blotting and immunoreactivity detection with hyperimmune sera, T cell epitope prediction by HLA allele and epitope peptide binding affinity, and potential T cell reactivity analysis. The immunogenic epitopes of the protein were evaluated and verified by HLA allele and epitope peptide complex structure molecular docking. Among fourteen best allele epitopes of this protein, binding affinity values of 12 allele epitopes remained unchanged compared to LBJ_2271. Two epitopes for alleles HLA-A0202 and -A0301 had higher IC 50 values, while T cell reactivity values of these peptides were better than values from LBJ_2271 epitopes. Eight of twelve epitope peptides had positive T-cell reactivity scores. Although the molecular docking of two epitopes, 3FPLLKEFLV11/47FPLLKEFLV55 and 50KLSTVPEGV58, into an HLA-A0202 model revealed a good fit in the docked structures, 50KLSTVPEGV58 and 94KLSTVPEEV102 are still considered as the proteins' best epitopes for allele HLA-A0202. The results of this study showed that rhKU_Sej_LRR_2271 protein contained natural immunological properties that should

  7. Computer identification of symptomatic deep venous thrombosis associated with peripherally inserted venous catheters.

    Science.gov (United States)

    Evans, R Scott; Linford, Lorraine H; Sharp, Jamie H; White, Gayle; Lloyd, James F; Weaver, Lindell K

    2007-10-11

    Peripherally inserted central catheters (PICCs) are considered a safe method to provide long-term antibiotic therapy, chemotherapy and nutrition support. Deep venous thrombosis (DVT) is a complication that requires early PICC removal, may extend hospitalization and can result in pulmonary embolism. PICC insertion teams strive to understand risk factors and develop methods to prevent DVTs. However, they can only manage what they can measure. At LDS Hospital, identification of PICC associated DVTs was dependent on verbal notification or manual surveillance of more than a thousand free-text vascular reports. Accurate DVT rates were not known which hindered prevention. We describe the development of a computer application (PICC-DVT monitor) to identify PICC associated DVTs each day. A one-year evaluation of the monitor by the PICC team and a review of 445 random vascular reports found a positive predictive value of 98%, sensitivity of 94%, specificity of 100% and a PICC team associated DVT rate of 2.8%.

  8. Computer game as a tool for training the identification of phonemic length.

    Science.gov (United States)

    Pennala, Riitta; Richardson, Ulla; Ylinen, Sari; Lyytinen, Heikki; Martin, Maisa

    2014-12-01

    Computer-assisted training of Finnish phonemic length was conducted with 7-year-old Russian-speaking second-language learners of Finnish. Phonemic length plays a different role in these two languages. The training included game activities with two- and three-syllable word and pseudo-word minimal pairs with prototypical vowel durations. The lowest accuracy scores were recorded for two-syllable words. Accuracy scores were higher for the minimal pairs with larger rather than smaller differences in duration. Accuracy scores were lower for long duration than for short duration. The ability to identify quantity degree was generalized to stimuli used in the identification test in two of the children. Ideas for improving the game are introduced.

  9. Hybrid incompatibilities in the parasitic wasp genus Nasonia: negative effects of hemizygosity and the identification of transmission ratio distortion loci.

    Science.gov (United States)

    Koevoets, T; Niehuis, O; van de Zande, L; Beukeboom, L W

    2012-03-01

    The occurrence of hybrid incompatibilities forms an important stage during the evolution of reproductive isolation. In early stages of speciation, males and females often respond differently to hybridization. Haldane's rule states that the heterogametic sex suffers more from hybridization than the homogametic sex. Although haplodiploid reproduction (haploid males, diploid females) does not involve sex chromosomes, sex-specific incompatibilities are predicted to be prevalent in haplodiploid species. Here, we evaluate the effect of sex/ploidy level on hybrid incompatibilities and locate genomic regions that cause increased mortality rates in hybrid males of the haplodiploid wasps Nasonia vitripennis and Nasonia longicornis. Our data show that diploid F(1) hybrid females suffer less from hybridization than haploid F(2) hybrid males. The latter not only suffer from an increased mortality rate, but also from behavioural and spermatogenic sterility. Genetic mapping in recombinant F(2) male hybrids revealed that the observed hybrid mortality is most likely due to a disruption of cytonuclear interactions. As these sex-specific hybrid incompatibilities follow predictions based on Haldane's rule, our data accentuate the need to broaden the view of Haldane's rule to include species with haplodiploid sex determination, consistent with Haldane's original definition.

  10. The photon identification loophole in EPRB experiments: computer models with single-wing selection

    Science.gov (United States)

    De Raedt, Hans; Michielsen, Kristel; Hess, Karl

    2017-11-01

    Recent Einstein-Podolsky-Rosen-Bohm experiments [M. Giustina et al. Phys. Rev. Lett. 115, 250401 (2015); L. K. Shalm et al. Phys. Rev. Lett. 115, 250402 (2015)] that claim to be loophole free are scrutinized. The combination of a digital computer and discrete-event simulation is used to construct a minimal but faithful model of the most perfected realization of these laboratory experiments. In contrast to prior simulations, all photon selections are strictly made, as they are in the actual experiments, at the local station and no other "post-selection" is involved. The simulation results demonstrate that a manifestly non-quantum model that identifies photons in the same local manner as in these experiments can produce correlations that are in excellent agreement with those of the quantum theoretical description of the corresponding thought experiment, in conflict with Bell's theorem which states that this is impossible. The failure of Bell's theorem is possible because of our recognition of the photon identification loophole. Such identification measurement-procedures are necessarily included in all actual experiments but are not included in the theory of Bell and his followers.

  11. The photon identification loophole in EPRB experiments: computer models with single-wing selection

    Directory of Open Access Journals (Sweden)

    De Raedt Hans

    2017-11-01

    Full Text Available Recent Einstein-Podolsky-Rosen-Bohm experiments [M. Giustina et al. Phys. Rev. Lett. 115, 250401 (2015; L. K. Shalm et al. Phys. Rev. Lett. 115, 250402 (2015] that claim to be loophole free are scrutinized. The combination of a digital computer and discrete-event simulation is used to construct a minimal but faithful model of the most perfected realization of these laboratory experiments. In contrast to prior simulations, all photon selections are strictly made, as they are in the actual experiments, at the local station and no other “post-selection” is involved. The simulation results demonstrate that a manifestly non-quantum model that identifies photons in the same local manner as in these experiments can produce correlations that are in excellent agreement with those of the quantum theoretical description of the corresponding thought experiment, in conflict with Bell’s theorem which states that this is impossible. The failure of Bell’s theorem is possible because of our recognition of the photon identification loophole. Such identification measurement-procedures are necessarily included in all actual experiments but are not included in the theory of Bell and his followers.

  12. A hyperspectral X-ray computed tomography system for enhanced material identification

    Science.gov (United States)

    Wu, Xiaomei; Wang, Qian; Ma, Jinlei; Zhang, Wei; Li, Po; Fang, Zheng

    2017-08-01

    X-ray computed tomography (CT) can distinguish different materials according to their absorption characteristics. The hyperspectral X-ray CT (HXCT) system proposed in the present work reconstructs each voxel according to its X-ray absorption spectral characteristics. In contrast to a dual-energy or multi-energy CT system, HXCT employs cadmium telluride (CdTe) as the x-ray detector, which provides higher spectral resolution and separate spectral lines according to the material's photon-counter working principle. In this paper, a specimen containing ten different polymer materials randomly arranged was adopted for material identification by HXCT. The filtered back-projection algorithm was applied for image and spectral reconstruction. The first step was to sort the individual material components of the specimen according to their cross-sectional image intensity. The second step was to classify materials with similar intensities according to their reconstructed spectral characteristics. The results demonstrated the feasibility of the proposed material identification process and indicated that the proposed HXCT system has good prospects for a wide range of biomedical and industrial nondestructive testing applications.

  13. Contribute to quantitative identification of casting defects based on computer analysis of X-ray images

    Directory of Open Access Journals (Sweden)

    Z. Ignaszak

    2007-12-01

    Full Text Available The forecast of structure and properties of casting is based on results of computer simulation of physical processes which are carried out during the casting processes. For the effective using of simulation system it is necessary to validate mathematica-physical models describing process of casting formation and the creation of local discontinues, witch determinate the casting properties.In the paper the proposition for quantitative validation of VP system using solidification casting defects by information sources of II group (methods of NDT was introduced. It was named the VP/RT validation (virtual prototyping/radiographic testing validation. Nowadays identification of casting defects noticeable on X-ray images bases on comparison of X-ray image of casting with relates to the ASTM. The results of this comparison are often not conclusive because based on operator’s subjective assessment. In the paper the system of quantitative identification of iron casting defects on X-ray images and classification this defects to ASTM class is presented. The methods of pattern recognition and machine learning were applied.

  14. Possibilities of the new hybrid technology single photon emission computer technology/computer tomography (SPECT/CT) and the first impressions of its application

    International Nuclear Information System (INIS)

    Kostadinova, I.

    2010-01-01

    With the help of the new hybrid technique SPECT/ CT it is possible, using the only investigation, to acquire a combine image of the investigated organ, visualizing its function and structure. Combining the possibilities of the new multimodality method, which combines the possibilities of the Single Photon Emission Computer Tomography - SPECT and Computer Tomography - CT, it is possible to precisely localize the pathologically changed organs function. With the further combination of the tomographic gamma camera with diagnostic CT, a detailed morphological evaluation of the finding was possible. The main clinical application of the new hybrid diagnostic is in the fields of cardiology, oncology, orthopedics with more and more extension of those, not connected with oncology, such as - thyroid, parathyroid, brain (especially localization of the epileptic foci), visualization of local infection and recently for the purposes of the radiotherapy planning. According to the literature data, around 35% of SPECT-investigations have to be combined with CT in order to increase the specificity of the diagnosis, which changes the interpretation of the result in 56% of the cases. After installation of the SPECT/CT camera in the University hospital 'Alexandrovska' in January 2009, the following changes have been done: the number of the investigated patients have increased, including number of heart, thyroid (especially scintigraphy with 131I), bones and parathyroid glands. As a result of the application of the hybrid technique, a shortage of the investigated time was realized and a decrease prize in comparison with the individual application of the investigations. Summarizing the literature data and the preliminary impression of the first multimodality scanner in our country in the University hospital 'Alexandrovska' it could be said, that there is continuously increasing information for the new clinical applications of SPECT/CT. It is now accepted, that its usage will increase in

  15. FMT-XCT: in vivo animal studies with hybrid fluorescence molecular tomography-X-ray computed tomography.

    Science.gov (United States)

    Ale, Angelique; Ermolayev, Vladimir; Herzog, Eva; Cohrs, Christian; de Angelis, Martin Hrabé; Ntziachristos, Vasilis

    2012-06-01

    The development of hybrid optical tomography methods to improve imaging performance has been suggested over a decade ago and has been experimentally demonstrated in animals and humans. Here we examined in vivo performance of a camera-based hybrid fluorescence molecular tomography (FMT) system for 360° imaging combined with X-ray computed tomography (XCT). Offering an accurately co-registered, information-rich hybrid data set, FMT-XCT has new imaging possibilities compared to stand-alone FMT and XCT. We applied FMT-XCT to a subcutaneous 4T1 tumor mouse model, an Aga2 osteogenesis imperfecta model and a Kras lung cancer mouse model, using XCT information during FMT inversion. We validated in vivo imaging results against post-mortem planar fluorescence images of cryoslices and histology data. Besides offering concurrent anatomical and functional information, FMT-XCT resulted in the most accurate FMT performance to date. These findings indicate that addition of FMT optics into the XCT gantry may be a potent upgrade for small-animal XCT systems.

  16. Error compensation for hybrid-computer solution of linear differential equations

    Science.gov (United States)

    Kemp, N. H.

    1970-01-01

    Z-transform technique compensates for digital transport delay and digital-to-analog hold. Method determines best values for compensation constants in multi-step and Taylor series projections. Technique also provides hybrid-calculation error compared to continuous exact solution, plus system stability properties.

  17. Application of soft computing based hybrid models in hydrological variables modeling: a comprehensive review

    Science.gov (United States)

    Fahimi, Farzad; Yaseen, Zaher Mundher; El-shafie, Ahmed

    2017-05-01

    Since the middle of the twentieth century, artificial intelligence (AI) models have been used widely in engineering and science problems. Water resource variable modeling and prediction are the most challenging issues in water engineering. Artificial neural network (ANN) is a common approach used to tackle this problem by using viable and efficient models. Numerous ANN models have been successfully developed to achieve more accurate results. In the current review, different ANN models in water resource applications and hydrological variable predictions are reviewed and outlined. In addition, recent hybrid models and their structures, input preprocessing, and optimization techniques are discussed and the results are compared with similar previous studies. Moreover, to achieve a comprehensive view of the literature, many articles that applied ANN models together with other techniques are included. Consequently, coupling procedure, model evaluation, and performance comparison of hybrid models with conventional ANN models are assessed, as well as, taxonomy and hybrid ANN models structures. Finally, current challenges and recommendations for future researches are indicated and new hybrid approaches are proposed.

  18. Hybrid brain-computer interfaces and hybrid neuroprostheses for restoration of upper limb functions in individuals with high-level spinal cord injury.

    Science.gov (United States)

    Rohm, Martin; Schneiders, Matthias; Müller, Constantin; Kreilinger, Alex; Kaiser, Vera; Müller-Putz, Gernot R; Rupp, Rüdiger

    2013-10-01

    The bilateral loss of the grasp function associated with a lesion of the cervical spinal cord severely limits the affected individuals' ability to live independently and return to gainful employment after sustaining a spinal cord injury (SCI). Any improvement in lost or limited grasp function is highly desirable. With current neuroprostheses, relevant improvements can be achieved in end users with preserved shoulder and elbow, but missing hand function. The aim of this single case study is to show that (1) with the support of hybrid neuroprostheses combining functional electrical stimulation (FES) with orthoses, restoration of hand, finger and elbow function is possible in users with high-level SCI and (2) shared control principles can be effectively used to allow for a brain-computer interface (BCI) control, even if only moderate BCI performance is achieved after extensive training. The individual in this study is a right-handed 41-year-old man who sustained a traumatic SCI in 2009 and has a complete motor and sensory lesion at the level of C4. He is unable to generate functionally relevant movements of the elbow, hand and fingers on either side. He underwent extensive FES training (30-45min, 2-3 times per week for 6 months) and motor imagery (MI) BCI training (415 runs in 43 sessions over 12 months). To meet individual needs, the system was designed in a modular fashion including an intelligent control approach encompassing two input modalities, namely an MI-BCI and shoulder movements. After one year of training, the end user's MI-BCI performance ranged from 50% to 93% (average: 70.5%). The performance of the hybrid system was evaluated with different functional assessments. The user was able to transfer objects of the grasp-and-release-test and he succeeded in eating a pretzel stick, signing a document and eating an ice cream cone, which he was unable to do without the system. This proof-of-concept study has demonstrated that with the support of hybrid FES

  19. Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis

    Directory of Open Access Journals (Sweden)

    Jolly Emmitt R

    2005-11-01

    Full Text Available Abstract Background A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. Results Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. Conclusion We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation.

  20. Hybrid Brain–Computer Interface Techniques for Improved Classification Accuracy and Increased Number of Commands: A Review

    Science.gov (United States)

    Hong, Keum-Shik; Khan, Muhammad Jawad

    2017-01-01

    In this article, non-invasive hybrid brain–computer interface (hBCI) technologies for improving classification accuracy and increasing the number of commands are reviewed. Hybridization combining more than two modalities is a new trend in brain imaging and prosthesis control. Electroencephalography (EEG), due to its easy use and fast temporal resolution, is most widely utilized in combination with other brain/non-brain signal acquisition modalities, for instance, functional near infrared spectroscopy (fNIRS), electromyography (EMG), electrooculography (EOG), and eye tracker. Three main purposes of hybridization are to increase the number of control commands, improve classification accuracy and reduce the signal detection time. Currently, such combinations of EEG + fNIRS and EEG + EOG are most commonly employed. Four principal components (i.e., hardware, paradigm, classifiers, and features) relevant to accuracy improvement are discussed. In the case of brain signals, motor imagination/movement tasks are combined with cognitive tasks to increase active brain–computer interface (BCI) accuracy. Active and reactive tasks sometimes are combined: motor imagination with steady-state evoked visual potentials (SSVEP) and motor imagination with P300. In the case of reactive tasks, SSVEP is most widely combined with P300 to increase the number of commands. Passive BCIs, however, are rare. After discussing the hardware and strategies involved in the development of hBCI, the second part examines the approaches used to increase the number of control commands and to enhance classification accuracy. The future prospects and the extension of hBCI in real-time applications for daily life scenarios are provided. PMID:28790910

  1. Hybrid Brain-Computer Interface Techniques for Improved Classification Accuracy and Increased Number of Commands: A Review.

    Science.gov (United States)

    Hong, Keum-Shik; Khan, Muhammad Jawad

    2017-01-01

    In this article, non-invasive hybrid brain-computer interface (hBCI) technologies for improving classification accuracy and increasing the number of commands are reviewed. Hybridization combining more than two modalities is a new trend in brain imaging and prosthesis control. Electroencephalography (EEG), due to its easy use and fast temporal resolution, is most widely utilized in combination with other brain/non-brain signal acquisition modalities, for instance, functional near infrared spectroscopy (fNIRS), electromyography (EMG), electrooculography (EOG), and eye tracker. Three main purposes of hybridization are to increase the number of control commands, improve classification accuracy and reduce the signal detection time. Currently, such combinations of EEG + fNIRS and EEG + EOG are most commonly employed. Four principal components (i.e., hardware, paradigm, classifiers, and features) relevant to accuracy improvement are discussed. In the case of brain signals, motor imagination/movement tasks are combined with cognitive tasks to increase active brain-computer interface (BCI) accuracy. Active and reactive tasks sometimes are combined: motor imagination with steady-state evoked visual potentials (SSVEP) and motor imagination with P300. In the case of reactive tasks, SSVEP is most widely combined with P300 to increase the number of commands. Passive BCIs, however, are rare. After discussing the hardware and strategies involved in the development of hBCI, the second part examines the approaches used to increase the number of control commands and to enhance classification accuracy. The future prospects and the extension of hBCI in real-time applications for daily life scenarios are provided.

  2. Hybrid Brain–Computer Interface Techniques for Improved Classification Accuracy and Increased Number of Commands: A Review

    Directory of Open Access Journals (Sweden)

    Keum-Shik Hong

    2017-07-01

    Full Text Available In this article, non-invasive hybrid brain–computer interface (hBCI technologies for improving classification accuracy and increasing the number of commands are reviewed. Hybridization combining more than two modalities is a new trend in brain imaging and prosthesis control. Electroencephalography (EEG, due to its easy use and fast temporal resolution, is most widely utilized in combination with other brain/non-brain signal acquisition modalities, for instance, functional near infrared spectroscopy (fNIRS, electromyography (EMG, electrooculography (EOG, and eye tracker. Three main purposes of hybridization are to increase the number of control commands, improve classification accuracy and reduce the signal detection time. Currently, such combinations of EEG + fNIRS and EEG + EOG are most commonly employed. Four principal components (i.e., hardware, paradigm, classifiers, and features relevant to accuracy improvement are discussed. In the case of brain signals, motor imagination/movement tasks are combined with cognitive tasks to increase active brain–computer interface (BCI accuracy. Active and reactive tasks sometimes are combined: motor imagination with steady-state evoked visual potentials (SSVEP and motor imagination with P300. In the case of reactive tasks, SSVEP is most widely combined with P300 to increase the number of commands. Passive BCIs, however, are rare. After discussing the hardware and strategies involved in the development of hBCI, the second part examines the approaches used to increase the number of control commands and to enhance classification accuracy. The future prospects and the extension of hBCI in real-time applications for daily life scenarios are provided.

  3. Automated oral cancer identification using histopathological images: a hybrid feature extraction paradigm.

    Science.gov (United States)

    Krishnan, M Muthu Rama; Venkatraghavan, Vikram; Acharya, U Rajendra; Pal, Mousumi; Paul, Ranjan Rashmi; Min, Lim Choo; Ray, Ajoy Kumar; Chatterjee, Jyotirmoy; Chakraborty, Chandan

    2012-02-01

    Oral cancer (OC) is the sixth most common cancer in the world. In India it is the most common malignant neoplasm. Histopathological images have widely been used in the differential diagnosis of normal, oral precancerous (oral sub-mucous fibrosis (OSF)) and cancer lesions. However, this technique is limited by subjective interpretations and less accurate diagnosis. The objective of this work is to improve the classification accuracy based on textural features in the development of a computer assisted screening of OSF. The approach introduced here is to grade the histopathological tissue sections into normal, OSF without Dysplasia (OSFWD) and OSF with Dysplasia (OSFD), which would help the oral onco-pathologists to screen the subjects rapidly. The biopsy sections are stained with H&E. The optical density of the pixels in the light microscopic images is recorded and represented as matrix quantized as integers from 0 to 255 for each fundamental color (Red, Green, Blue), resulting in a M×N×3 matrix of integers. Depending on either normal or OSF condition, the image has various granular structures which are self similar patterns at different scales termed "texture". We have extracted these textural changes using Higher Order Spectra (HOS), Local Binary Pattern (LBP), and Laws Texture Energy (LTE) from the histopathological images (normal, OSFWD and OSFD). These feature vectors were fed to five different classifiers: Decision Tree (DT), Sugeno Fuzzy, Gaussian Mixture Model (GMM), K-Nearest Neighbor (K-NN), Radial Basis Probabilistic Neural Network (RBPNN) to select the best classifier. Our results show that combination of texture and HOS features coupled with Fuzzy classifier resulted in 95.7% accuracy, sensitivity and specificity of 94.5% and 98.8% respectively. Finally, we have proposed a novel integrated index called Oral Malignancy Index (OMI) using the HOS, LBP, LTE features, to diagnose benign or malignant tissues using just one number. We hope that this OMI can

  4. Resource-Efficient, Hierarchical Auto-Tuning of a Hybrid Lattice Boltzmann Computation on the Cray XT4

    International Nuclear Information System (INIS)

    Williams, Samuel; Carter, Jonathan; Oliker, Leonid; Shalf, John; Yelick, Katherine

    2009-01-01

    We apply auto-tuning to a hybrid MPI-pthreads lattice Boltzmann computation running on the Cray XT4 at National Energy Research Scientific Computing Center (NERSC). Previous work showed that multicore-specific auto-tuning can improve the performance of lattice Boltzmann magnetohydrodynamics (LBMHD) by a factor of 4x when running on dual- and quad-core Opteron dual-socket SMPs. We extend these studies to the distributed memory arena via a hybrid MPI/pthreads implementation. In addition to conventional auto-tuning at the local SMP node, we tune at the message-passing level to determine the optimal aspect ratio as well as the correct balance between MPI tasks and threads per MPI task. Our study presents a detailed performance analysis when moving along an isocurve of constant hardware usage: fixed total memory, total cores, and total nodes. Overall, our work points to approaches for improving intra- and inter-node efficiency on large-scale multicore systems for demanding scientific applications

  5. A hybrid FDTD-Rayleigh integral computational method for the simulation of the ultrasound measurement of proximal femur.

    Science.gov (United States)

    Cassereau, Didier; Nauleau, Pierre; Bendjoudi, Aniss; Minonzio, Jean-Gabriel; Laugier, Pascal; Bossy, Emmanuel; Grimal, Quentin

    2014-07-01

    The development of novel quantitative ultrasound (QUS) techniques to measure the hip is critically dependent on the possibility to simulate the ultrasound propagation. One specificity of hip QUS is that ultrasounds propagate through a large thickness of soft tissue, which can be modeled by a homogeneous fluid in a first approach. Finite difference time domain (FDTD) algorithms have been widely used to simulate QUS measurements but they are not adapted to simulate ultrasonic propagation over long distances in homogeneous media. In this paper, an hybrid numerical method is presented to simulate hip QUS measurements. A two-dimensional FDTD simulation in the vicinity of the bone is coupled to the semi-analytic calculation of the Rayleigh integral to compute the wave propagation between the probe and the bone. The method is used to simulate a setup dedicated to the measurement of circumferential guided waves in the cortical compartment of the femoral neck. The proposed approach is validated by comparison with a full FDTD simulation and with an experiment on a bone phantom. For a realistic QUS configuration, the computation time is estimated to be sixty times less with the hybrid method than with a full FDTD approach. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Identification of rounded atelectasis in workers exposed to asbestos by contrast helical computed tomography

    International Nuclear Information System (INIS)

    Terra-Filho, M.; Kavakama, J.; Bagatin, E.; Capelozzi, V.L.; Nery, L.E.; Tavares, R.

    2003-01-01

    Rounded atelectasis (RA) is a benign and unusual form of sub pleural lung collapse that has been described mostly in asbestos-exposed workers. This form of atelectasis manifests as a lung nodule and can be confused with bronchogenic carcinoma upon conventional radiologic examination. The objective of the present study was to evaluate the variation in contrast uptake in computed tomography for the identification of asbestos-related RA in Brazil. Between January 1998 and December 2000, high-resolution computed tomography (HRCT) was performed in 1658 asbestos-exposed workers. The diagnosis was made in nine patients based on a history of prior asbestos exposure, the presence of characteristic (HRCT) findings and lesions unchanged in size over 2 years or more. In three of them the diagnosis was confirmed during surgery. The dynamic contrast enhancement study was modified to evaluate nodules and pulmonary masses. All nine patients with R A received iodide contrast according to weight. The average enhancement after iodide contrast was infused, reported as Hounsfield units (HU), increased from 62.5±9.7 to 125.4±20.7 (P < 0.05), with a mean enhancement of 62.5±19.7 (range 40 to 89) and with a uniform dense opacification. In conclusion, in this study all patients with R A showed contrast enhancement with uniform dense opacification. The main clinical implication of this finding is that this procedure does not permit differentiation between RA and malignant pulmonary neoplasm. (author)

  7. Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach.

    Science.gov (United States)

    Pan, Yuliang; Wang, Zixiang; Zhan, Weihua; Deng, Lei

    2018-05-01

    Identifying RNA-binding residues, especially energetically favored hot spots, can provide valuable clues for understanding the mechanisms and functional importance of protein-RNA interactions. Yet, limited availability of experimentally recognized energy hot spots in protein-RNA crystal structures leads to the difficulties in developing empirical identification approaches. Computational prediction of RNA-binding hot spot residues is still in its infant stage. Here, we describe a computational method, PrabHot (Prediction of protein-RNA binding hot spots), that can effectively detect hot spot residues on protein-RNA binding interfaces using an ensemble of conceptually different machine learning classifiers. Residue interaction network features and new solvent exposure characteristics are combined together and selected for classification with the Boruta algorithm. In particular, two new reference datasets (benchmark and independent) have been generated containing 107 hot spots from 47 known protein-RNA complex structures. In 10-fold cross-validation on the training dataset, PrabHot achieves promising performances with an AUC score of 0.86 and a sensitivity of 0.78, which are significantly better than that of the pioneer RNA-binding hot spot prediction method HotSPRing. We also demonstrate the capability of our proposed method on the independent test dataset and gain a competitive advantage as a result. The PrabHot webserver is freely available at http://denglab.org/PrabHot/. leideng@csu.edu.cn. Supplementary data are available at Bioinformatics online.

  8. Computer Modeling of Radiative Transfer in Hybrid-Stabilized Argon–Water Electric Arc

    Czech Academy of Sciences Publication Activity Database

    Jeništa, Jiří; Takana, H.; Nishiyama, H.; Křenek, Petr; Bartlová, M.; Aubrecht, V.

    2011-01-01

    Roč. 39, č. 11 (2011), s. 2892-2893 ISSN 0093-3813 Institutional research plan: CEZ:AV0Z20430508 Keywords : Divergence of radiation flux * hybrid-stabilized electric arc * mass flow rate * partial characteristics * radiation flux Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.174, year: 2011 http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=27

  9. Computational analysis of electrical conduction in hybrid nanomaterials with embedded non-penetrating conductive particles

    Science.gov (United States)

    Cai, Jizhe; Naraghi, Mohammad

    2016-08-01

    In this work, a comprehensive multi-resolution two-dimensional (2D) resistor network model is proposed to analyze the electrical conductivity of hybrid nanomaterials made of insulating matrix with conductive particles such as CNT reinforced nanocomposites and thick film resistors. Unlike existing approaches, our model takes into account the impenetrability of the particles and their random placement within the matrix. Moreover, our model presents a detailed description of intra-particle conductivity via finite element analysis, which to the authors’ best knowledge has not been addressed before. The inter-particle conductivity is assumed to be primarily due to electron tunneling. The model is then used to predict the electrical conductivity of electrospun carbon nanofibers as a function of microstructural parameters such as turbostratic domain alignment and aspect ratio. To simulate the microstructure of single CNF, randomly positioned nucleation sites were seeded and grown as turbostratic particles with anisotropic growth rates. Particle growth was in steps and growth of each particle in each direction was stopped upon contact with other particles. The study points to the significant contribution of both intra-particle and inter-particle conductivity to the overall conductivity of hybrid composites. Influence of particle alignment and anisotropic growth rate ratio on electrical conductivity is also discussed. The results show that partial alignment in contrast to complete alignment can result in maximum electrical conductivity of whole CNF. High degrees of alignment can adversely affect conductivity by lowering the probability of the formation of a conductive path. The results demonstrate approaches to enhance electrical conductivity of hybrid materials through controlling their microstructure which is applicable not only to carbon nanofibers, but also many other types of hybrid composites such as thick film resistors.

  10. Development of the method of aggregation to determine the current storage area using computer vision and radiofrequency identification

    Science.gov (United States)

    Astafiev, A.; Orlov, A.; Privezencev, D.

    2018-01-01

    The article is devoted to the development of technology and software for the construction of positioning and control systems in industrial plants based on aggregation to determine the current storage area using computer vision and radiofrequency identification. It describes the developed of the project of hardware for industrial products positioning system in the territory of a plant on the basis of radio-frequency grid. It describes the development of the project of hardware for industrial products positioning system in the plant on the basis of computer vision methods. It describes the development of the method of aggregation to determine the current storage area using computer vision and radiofrequency identification. Experimental studies in laboratory and production conditions have been conducted and described in the article.

  11. Automatic Identification of the Repolarization Endpoint by Computing the Dominant T-wave on a Reduced Number of Leads.

    Science.gov (United States)

    Giuliani, C; Agostinelli, A; Di Nardo, F; Fioretti, S; Burattini, L

    2016-01-01

    Electrocardiographic (ECG) T-wave endpoint (Tend) identification suffers lack of reliability due to the presence of noise and variability among leads. Tend identification can be improved by using global repolarization waveforms obtained by combining several leads. The dominant T-wave (DTW) is a global repolarization waveform that proved to improve Tend identification when computed using the 15 (I to III, aVr, aVl, aVf, V1 to V6, X, Y, Z) leads usually available in clinics, of which only 8 (I, II, V1 to V6) are independent. The aim of the present study was to evaluate if the 8 independent leads are sufficient to obtain a DTW which allows a reliable Tend identification. To this aim Tend measures automatically identified from 15-dependent-lead DTWs of 46 control healthy subjects (CHS) and 103 acute myocardial infarction patients (AMIP) were compared with those obtained from 8-independent-lead DTWs. Results indicate that Tend distributions have not statistically different median values (CHS: 340 ms vs. 340 ms, respectively; AMIP: 325 ms vs. 320 ms, respectively), besides being strongly correlated (CHS: ρ=0.97, AMIP: 0.88; Pautomatic Tend identification from DTW, the 8 independent leads can be used without a statistically significant loss of accuracy but with a significant decrement of computational effort. The lead dependence of 7 out of 15 leads does not introduce a significant bias in the Tend determination from 15 dependent lead DTWs.

  12. Developing a computationally efficient dynamic multilevel hybrid optimization scheme using multifidelity model interactions.

    Energy Technology Data Exchange (ETDEWEB)

    Hough, Patricia Diane (Sandia National Laboratories, Livermore, CA); Gray, Genetha Anne (Sandia National Laboratories, Livermore, CA); Castro, Joseph Pete Jr. (; .); Giunta, Anthony Andrew

    2006-01-01

    Many engineering application problems use optimization algorithms in conjunction with numerical simulators to search for solutions. The formulation of relevant objective functions and constraints dictate possible optimization algorithms. Often, a gradient based approach is not possible since objective functions and constraints can be nonlinear, nonconvex, non-differentiable, or even discontinuous and the simulations involved can be computationally expensive. Moreover, computational efficiency and accuracy are desirable and also influence the choice of solution method. With the advent and increasing availability of massively parallel computers, computational speed has increased tremendously. Unfortunately, the numerical and model complexities of many problems still demand significant computational resources. Moreover, in optimization, these expenses can be a limiting factor since obtaining solutions often requires the completion of numerous computationally intensive simulations. Therefore, we propose a multifidelity optimization algorithm (MFO) designed to improve the computational efficiency of an optimization method for a wide range of applications. In developing the MFO algorithm, we take advantage of the interactions between multi fidelity models to develop a dynamic and computational time saving optimization algorithm. First, a direct search method is applied to the high fidelity model over a reduced design space. In conjunction with this search, a specialized oracle is employed to map the design space of this high fidelity model to that of a computationally cheaper low fidelity model using space mapping techniques. Then, in the low fidelity space, an optimum is obtained using gradient or non-gradient based optimization, and it is mapped back to the high fidelity space. In this paper, we describe the theory and implementation details of our MFO algorithm. We also demonstrate our MFO method on some example problems and on two applications: earth penetrators and

  13. Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

    Science.gov (United States)

    Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

    2013-10-31

    Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

  14. Hybrid-PIC Computer Simulation of the Plasma and Erosion Processes in Hall Thrusters

    Science.gov (United States)

    Hofer, Richard R.; Katz, Ira; Mikellides, Ioannis G.; Gamero-Castano, Manuel

    2010-01-01

    HPHall software simulates and tracks the time-dependent evolution of the plasma and erosion processes in the discharge chamber and near-field plume of Hall thrusters. HPHall is an axisymmetric solver that employs a hybrid fluid/particle-in-cell (Hybrid-PIC) numerical approach. HPHall, originally developed by MIT in 1998, was upgraded to HPHall-2 by the Polytechnic University of Madrid in 2006. The Jet Propulsion Laboratory has continued the development of HPHall-2 through upgrades to the physical models employed in the code, and the addition of entirely new ones. Primary among these are the inclusion of a three-region electron mobility model that more accurately depicts the cross-field electron transport, and the development of an erosion sub-model that allows for the tracking of the erosion of the discharge chamber wall. The code is being developed to provide NASA science missions with a predictive tool of Hall thruster performance and lifetime that can be used to validate Hall thrusters for missions.

  15. Short term load forecasting of anomalous load using hybrid soft computing methods

    Science.gov (United States)

    Rasyid, S. A.; Abdullah, A. G.; Mulyadi, Y.

    2016-04-01

    Load forecast accuracy will have an impact on the generation cost is more economical. The use of electrical energy by consumers on holiday, show the tendency of the load patterns are not identical, it is different from the pattern of the load on a normal day. It is then defined as a anomalous load. In this paper, the method of hybrid ANN-Particle Swarm proposed to improve the accuracy of anomalous load forecasting that often occur on holidays. The proposed methodology has been used to forecast the half-hourly electricity demand for power systems in the Indonesia National Electricity Market in West Java region. Experiments were conducted by testing various of learning rate and learning data input. Performance of this methodology will be validated with real data from the national of electricity company. The result of observations show that the proposed formula is very effective to short-term load forecasting in the case of anomalous load. Hybrid ANN-Swarm Particle relatively simple and easy as a analysis tool by engineers.

  16. A hybrid computational approach to estimate solar global radiation: An empirical evidence from Iran

    International Nuclear Information System (INIS)

    Mostafavi, Elham Sadat; Ramiyani, Sara Saeidi; Sarvar, Rahim; Moud, Hashem Izadi; Mousavi, Seyyed Mohammad

    2013-01-01

    This paper presents an innovative hybrid approach for the estimation of the solar global radiation. New prediction equations were developed for the global radiation using an integrated search method of genetic programming (GP) and simulated annealing (SA), called GP/SA. The solar radiation was formulated in terms of several climatological and meteorological parameters. Comprehensive databases containing monthly data collected for 6 years in two cities of Iran were used to develop GP/SA-based models. Separate models were established for each city. The generalization of the models was verified using a separate testing database. A sensitivity analysis was conducted to investigate the contribution of the parameters affecting the solar radiation. The derived models make accurate predictions of the solar global radiation and notably outperform the existing models. -- Highlights: ► A hybrid approach is presented for the estimation of the solar global radiation. ► The proposed method integrates the capabilities of GP and SA. ► Several climatological and meteorological parameters are included in the analysis. ► The GP/SA models make accurate predictions of the solar global radiation.

  17. Prototype of an auto-calibrating, context-aware, hybrid brain-computer interface.

    Science.gov (United States)

    Faller, J; Torrellas, S; Miralles, F; Holzner, C; Kapeller, C; Guger, C; Bund, J; Müller-Putz, G R; Scherer, R

    2012-01-01

    We present the prototype of a context-aware framework that allows users to control smart home devices and to access internet services via a Hybrid BCI system of an auto-calibrating sensorimotor rhythm (SMR) based BCI and another assistive device (Integra Mouse mouth joystick). While there is extensive literature that describes the merit of Hybrid BCIs, auto-calibrating and co-adaptive ERD BCI training paradigms, specialized BCI user interfaces, context-awareness and smart home control, there is up to now, no system that includes all these concepts in one integrated easy-to-use framework that can truly benefit individuals with severe functional disabilities by increasing independence and social inclusion. Here we integrate all these technologies in a prototype framework that does not require expert knowledge or excess time for calibration. In a first pilot-study, 3 healthy volunteers successfully operated the system using input signals from an ERD BCI and an Integra Mouse and reached average positive predictive values (PPV) of 72 and 98% respectively. Based on what we learned here we are planning to improve the system for a test with a larger number of healthy volunteers so we can soon bring the system to benefit individuals with severe functional disability.

  18. Computer simulations of upper-hybrid and electron cyclotron resonance heating

    International Nuclear Information System (INIS)

    Lin, A.T.; Lin, C.C.

    1983-01-01

    A 2 1/2 -dimensional relativistic electromagnetic particle code is used to investigate the dynamic behavior of electron heating around the electron cyclotron and upper-hybrid layers when an extraordinary wave is obliquely launched from the high-field side into a magnetized plasma. With a large angle of incidence most of the radiation wave energy converts into electrostatic electron Bernstein waves at the upper-hybrid layer. These mode-converted waves propagate back to the cyclotron layer and deposit their energy in the electrons through resonant interactions dominated first by the Doppler broadening and later by the relativistic mass correction. The line shape for both mechanisms has been observed in the simulations. At a later stage, the relativistic resonance effects shift the peak of the temperature profile to the high-field side. The heating ultimately causes the extraordinary wave to be substantially absorbed by the high-energy electrons. The steep temperature gradient created by the electron cyclotron heating eventually reflects a substantial part of the incident wave energy. The diamagnetic effects due to the gradient of the mode-converted Bernstein wave pressure enhance the spreading of the electron heating from the original electron cyclotron layer

  19. Hybrid brain-computer interface for biomedical cyber-physical system application using wireless embedded EEG systems.

    Science.gov (United States)

    Chai, Rifai; Naik, Ganesh R; Ling, Sai Ho; Nguyen, Hung T

    2017-01-07

    One of the key challenges of the biomedical cyber-physical system is to combine cognitive neuroscience with the integration of physical systems to assist people with disabilities. Electroencephalography (EEG) has been explored as a non-invasive method of providing assistive technology by using brain electrical signals. This paper presents a unique prototype of a hybrid brain computer interface (BCI) which senses a combination classification of mental task, steady state visual evoked potential (SSVEP) and eyes closed detection using only two EEG channels. In addition, a microcontroller based head-mounted battery-operated wireless EEG sensor combined with a separate embedded system is used to enhance portability, convenience and cost effectiveness. This experiment has been conducted with five healthy participants and five patients with tetraplegia. Generally, the results show comparable classification accuracies between healthy subjects and tetraplegia patients. For the offline artificial neural network classification for the target group of patients with tetraplegia, the hybrid BCI system combines three mental tasks, three SSVEP frequencies and eyes closed, with average classification accuracy at 74% and average information transfer rate (ITR) of the system of 27 bits/min. For the real-time testing of the intentional signal on patients with tetraplegia, the average success rate of detection is 70% and the speed of detection varies from 2 to 4 s.

  20. Computer Identification of Symptomatic Deep Venous Thrombosis Associated with Peripherally Inserted Central Catheters

    Science.gov (United States)

    Evans, R. Scott; Linford, Lorraine H.; Sharp, Jamie H.; White, Gayle; Lloyd, James F.; Weaver, Lindell K.

    2007-01-01

    Peripherally inserted central catheters (PICCs) are considered a safe method to provide long-term antibiotic therapy, chemotherapy and nutrition support. Deep venous thrombosis (DVT) is a complication that requires early PICC removal, may extend hospitalization and can result in pulmonary embolism. PICC insertion teams strive to understand risk factors and develop methods to prevent DVTs. However, they can only manage what they can measure. At LDS Hospital, identification of PICC associated DVTs was dependent on verbal notification or manual surveillance of more than a thousand free-text vascular reports. Accurate DVT rates were not known which hindered prevention. We describe the development of a computer application (PICC-DVT monitor) to identify PICC associated DVTs each day. A one-year evaluation of the monitor by the PICC team and a review of 445 random vascular reports found a positive predictive value of 98%, sensitivity of 94%, specificity of 100% and a PICC team associated DVT rate of 2.8%. PMID:18693831

  1. Validation of DNA-based identification software by computation of pedigree likelihood ratios.

    Science.gov (United States)

    Slooten, K

    2011-08-01

    Disaster victim identification (DVI) can be aided by DNA-evidence, by comparing the DNA-profiles of unidentified individuals with those of surviving relatives. The DNA-evidence is used optimally when such a comparison is done by calculating the appropriate likelihood ratios. Though conceptually simple, the calculations can be quite involved, especially with large pedigrees, precise mutation models etc. In this article we describe a series of test cases designed to check if software designed to calculate such likelihood ratios computes them correctly. The cases include both simple and more complicated pedigrees, among which inbred ones. We show how to calculate the likelihood ratio numerically and algebraically, including a general mutation model and possibility of allelic dropout. In Appendix A we show how to derive such algebraic expressions mathematically. We have set up these cases to validate new software, called Bonaparte, which performs pedigree likelihood ratio calculations in a DVI context. Bonaparte has been developed by SNN Nijmegen (The Netherlands) for the Netherlands Forensic Institute (NFI). It is available free of charge for non-commercial purposes (see www.dnadvi.nl for details). Commercial licenses can also be obtained. The software uses Bayesian networks and the junction tree algorithm to perform its calculations. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  2. Early detection and identification of anomalies in chemical regime based on computational intelligence techniques

    International Nuclear Information System (INIS)

    Figedy, Stefan; Smiesko, Ivan

    2012-01-01

    This article provides brief information about the fundamental features of a newly-developed diagnostic system for early detection and identification of anomalies being generated in water chemistry regime of the primary and secondary circuit of the VVER-440 reactor. This system, which is called SACHER (System of Analysis of CHEmical Regime), was installed within the major modernization project at the NPP-V2 Bohunice in the Slovak Republic. The SACHER system has been fully developed on MATLAB environment. It is based on computational intelligence techniques and inserts various elements of intelligent data processing modules for clustering, diagnosing, future prediction, signal validation, etc, into the overall chemical information system. The application of SACHER would essentially assist chemists to identify the current situation regarding anomalies being generated in the primary and secondary circuit water chemistry. This system is to be used for diagnostics and data handling, however it is not intended to fully replace the presence of experienced chemists to decide upon corrective actions. (author)

  3. Hybrid Computational Model for High-Altitude Aeroassist Vehicles, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed effort addresses a need for accurate computational models to support aeroassist and entry vehicle system design over a broad range of flight conditions...

  4. Hybrid GPU-CPU adaptive precision ray-triangle intersection tests for robust high-performance GPU dosimetry computations

    International Nuclear Information System (INIS)

    Perrotte, Lancelot; Bodin, Bruno; Chodorge, Laurent

    2011-01-01

    Before an intervention on a nuclear site, it is essential to study different scenarios to identify the less dangerous one for the operator. Therefore, it is mandatory to dispose of an efficient dosimetry simulation code with accurate results. One classical method in radiation protection is the straight-line attenuation method with build-up factors. In the case of 3D industrial scenes composed of meshes, the computation cost resides in the fast computation of all of the intersections between the rays and the triangles of the scene. Efficient GPU algorithms have already been proposed, that enable dosimetry calculation for a huge scene (800000 rays, 800000 triangles) in a fraction of second. But these algorithms are not robust: because of the rounding caused by floating-point arithmetic, the numerical results of the ray-triangle intersection tests can differ from the expected mathematical results. In worst case scenario, this can lead to a computed dose rate dramatically inferior to the real dose rate to which the operator is exposed. In this paper, we present a hybrid GPU-CPU algorithm to manage adaptive precision floating-point arithmetic. This algorithm allows robust ray-triangle intersection tests, with very small loss of performance (less than 5 % overhead), and without any need for scene-dependent tuning. (author)

  5. Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR.

    Science.gov (United States)

    Kaufmann, P; Pfefferkorn, A; Teuber, M; Meile, L

    1997-04-01

    A Bifidobacterium genus-specific target sequence in the V9 variable region of the 16S rRNA has been elaborated and was used to develop a hybridization probe. The specificity of this probe, named lm3 (5'-CGGGTGCTI*CCCACTTTCATG-3'), was used to identify all known type strains and distinguish them from other bacteria. All of the 30 type strains of Bifidobacterium which are available at the German culture collection Deutsche Sammlung von Mikroorganismen und Zellkulturen, 6 commercially available production strains, and 34 closely related relevant strains (as negative controls) were tested. All tested bifidobacteria showed distinct positive signals by colony hybridization, whereas all negative controls showed no distinct dots except Gardnerella vaginalis DSM4944 and Propionibacterium freudenreichii subsp. shermanii DSM4902, which gave slight signals. Furthermore, we established a method for isolation and identification of bifidobacteria from food by using a PCR assay without prior isolation of DNA but breaking the cells with proteinase K. By this method, all Bifidobacterium strains lead to a DNA product of the expected size. We also established a quick assay to quantitatively measure Bifidobacterium counts in food and feces by dilution plating and colony hybridization. We were able to demonstrate that 2.1 x 10(6) to 2.3 x 10(7) colonies/g of sour milk containing bifidobacteria hybridized with the specific nucleotide probe. With these two methods, genus-specific colony hybridization and genus-specific PCR, it is now possible to readily and accurately detect any bifidobacteria in food and fecal samples and to discriminate between them and members of other genera.

  6. Compression of Born ratio for fluorescence molecular tomography/x-ray computed tomography hybrid imaging: methodology and in vivo validation.

    Science.gov (United States)

    Mohajerani, Pouyan; Ntziachristos, Vasilis

    2013-07-01

    The 360° rotation geometry of the hybrid fluorescence molecular tomography/x-ray computed tomography modality allows for acquisition of very large datasets, which pose numerical limitations on the reconstruction. We propose a compression method that takes advantage of the correlation of the Born-normalized signal among sources in spatially formed clusters to reduce the size of system model. The proposed method has been validated using an ex vivo study and an in vivo study of a nude mouse with a subcutaneous 4T1 tumor, with and without inclusion of a priori anatomical information. Compression rates of up to two orders of magnitude with minimum distortion of reconstruction have been demonstrated, resulting in large reduction in weight matrix size and reconstruction time.

  7. A hybrid solution using computational prediction and measured data to accurately determine process corrections with reduced overlay sampling

    Science.gov (United States)

    Noyes, Ben F.; Mokaberi, Babak; Mandoy, Ram; Pate, Alex; Huijgen, Ralph; McBurney, Mike; Chen, Owen

    2017-03-01

    Reducing overlay error via an accurate APC feedback system is one of the main challenges in high volume production of the current and future nodes in the semiconductor industry. The overlay feedback system directly affects the number of dies meeting overlay specification and the number of layers requiring dedicated exposure tools through the fabrication flow. Increasing the former number and reducing the latter number is beneficial for the overall efficiency and yield of the fabrication process. An overlay feedback system requires accurate determination of the overlay error, or fingerprint, on exposed wafers in order to determine corrections to be automatically and dynamically applied to the exposure of future wafers. Since current and future nodes require correction per exposure (CPE), the resolution of the overlay fingerprint must be high enough to accommodate CPE in the overlay feedback system, or overlay control module (OCM). Determining a high resolution fingerprint from measured data requires extremely dense overlay sampling that takes a significant amount of measurement time. For static corrections this is acceptable, but in an automated dynamic correction system this method creates extreme bottlenecks for the throughput of said system as new lots have to wait until the previous lot is measured. One solution is using a less dense overlay sampling scheme and employing computationally up-sampled data to a dense fingerprint. That method uses a global fingerprint model over the entire wafer; measured localized overlay errors are therefore not always represented in its up-sampled output. This paper will discuss a hybrid system shown in Fig. 1 that combines a computationally up-sampled fingerprint with the measured data to more accurately capture the actual fingerprint, including local overlay errors. Such a hybrid system is shown to result in reduced modelled residuals while determining the fingerprint, and better on-product overlay performance.

  8. Identification of hybrids of painted and milky storks using FTA card-collected blood, molecular markers, and morphologies.

    Science.gov (United States)

    Yee, Elsie Yoke Sim; Zainuddin, Zainal Zahari; Ismail, Ahmad; Yap, Chee Kong; Tan, Soon Guan

    2013-10-01

    Suspicious hybrids of painted storks and milky storks were found in a Malaysian zoo. Blood of these birds was sampled on FTA cards for DNA fingerprinting. Of 44 optimized primers, 6 produced diagnostic markers that could identify hybrids. The markers were based on simple, direct PCR-generated multilocus banding patterns that provided two sets of genetic data, one for each of the two stork species and another for the hybrids. It also revealed that large DNA fragments (3,000 bp) could be amplified from blood collected on FTA cards. When the results of each individual bird's DNA fingerprint were compared with plumage characters, the hybrids were found to express a range of intermediate phenotypic traits of the pure breeds with no dominant plumage characteristic from either parental species.

  9. The “Chimera”: An Off-The-Shelf CPU/GPGPU/FPGA Hybrid Computing Platform

    Directory of Open Access Journals (Sweden)

    Ra Inta

    2012-01-01

    Full Text Available The nature of modern astronomy means that a number of interesting problems exhibit a substantial computational bound and this situation is gradually worsening. Scientists, increasingly fighting for valuable resources on conventional high-performance computing (HPC facilities—often with a limited customizable user environment—are increasingly looking to hardware acceleration solutions. We describe here a heterogeneous CPU/GPGPU/FPGA desktop computing system (the “Chimera”, built with commercial-off-the-shelf components. We show that this platform may be a viable alternative solution to many common computationally bound problems found in astronomy, however, not without significant challenges. The most significant bottleneck in pipelines involving real data is most likely to be the interconnect (in this case the PCI Express bus residing on the CPU motherboard. Finally, we speculate on the merits of our Chimera system on the entire landscape of parallel computing, through the analysis of representative problems from UC Berkeley’s “Thirteen Dwarves.”

  10. Identification of single nucleotide polymorphisms (SNPs) at candidate genes involved in abiotic stress in two Prosopis species of hybrids

    OpenAIRE

    Maria F. Pomponio; Susana Marcucci Poltri; Diego Lopez Lauenstein; Susana Torales

    2014-01-01

    Aim of the study: Identify and compare SNPs on candidate genes related to abiotic stress in Prosopis chilensis, Prosopis flexuosa and interspecific hybridsArea of the study: Chaco árido, Argentina. Material and Methods: Fragments from 6 candidate genes were sequenced in 60 genotypes. DNA polymorphisms were analyzed.Main Results: The analysis revealed that the hybrids had the highest rate of polymorphism, followed by P. flexuosa and P. chilensis, the values found are comparable to other forest...

  11. A hybrid optical switch architecture to integrate IP into optical networks to provide flexible and intelligent bandwidth on demand for cloud computing

    Science.gov (United States)

    Yang, Wei; Hall, Trevor J.

    2013-12-01

    The Internet is entering an era of cloud computing to provide more cost effective, eco-friendly and reliable services to consumer and business users. As a consequence, the nature of the Internet traffic has been fundamentally transformed from a pure packet-based pattern to today's predominantly flow-based pattern. Cloud computing has also brought about an unprecedented growth in the Internet traffic. In this paper, a hybrid optical switch architecture is presented to deal with the flow-based Internet traffic, aiming to offer flexible and intelligent bandwidth on demand to improve fiber capacity utilization. The hybrid optical switch is capable of integrating IP into optical networks for cloud-based traffic with predictable performance, for which the delay performance of the electronic module in the hybrid optical switch architecture is evaluated through simulation.

  12. Solving difficult problems creatively: A role for energy optimised deterministic/stochastic hybrid computing

    Directory of Open Access Journals (Sweden)

    Tim ePalmer

    2015-10-01

    Full Text Available How is the brain configured for creativity? What is the computational substrate for ‘eureka’ moments of insight? Here we argue that creative thinking arises ultimately from a synergy between low-energy stochastic and energy-intensive deterministic processing, and is a by-product of a nervous system whose signal-processing capability per unit of available energy has become highly energy optimised. We suggest that the stochastic component has its origin in thermal noise affecting the activity of neurons. Without this component, deterministic computational models of the brain are incomplete.

  13. Solving difficult problems creatively: a role for energy optimised deterministic/stochastic hybrid computing.

    Science.gov (United States)

    Palmer, Tim N; O'Shea, Michael

    2015-01-01

    How is the brain configured for creativity? What is the computational substrate for 'eureka' moments of insight? Here we argue that creative thinking arises ultimately from a synergy between low-energy stochastic and energy-intensive deterministic processing, and is a by-product of a nervous system whose signal-processing capability per unit of available energy has become highly energy optimised. We suggest that the stochastic component has its origin in thermal (ultimately quantum decoherent) noise affecting the activity of neurons. Without this component, deterministic computational models of the brain are incomplete.

  14. Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics

    International Nuclear Information System (INIS)

    Villarreal, Oscar D.; Yu, Lili; Rodriguez, Roberto A.; Chen, Liao Y.

    2017-01-01

    Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity- -pulling out the ligand- -closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by

  15. A Hybrid Computing Testbed for Mobile Threat Detection and Enhanced Research and Education in Information

    Science.gov (United States)

    2014-11-20

    after by the cloud computing and cybersecurity industry. By participating in this project, the students gain strong competitiveness in the job market ...team in May 2013 and another Ph.D. student, Michael Grace, has been helping Samsung Mobile on the KNOX team to better ensure OS kernel integrity since January 2014. 2

  16. A hybrid approach to the computational aeroacoustics of human voice production

    Czech Academy of Sciences Publication Activity Database

    Šidlof, Petr; Zörner, S.; Huppe, A.

    2015-01-01

    Roč. 14, č. 3 (2015), s. 473-488 ISSN 1617-7959 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional support: RVO:61388998 Keywords : computational aeroacoustics * parallel CFD * human voice * vocal folds * ventricular folds Subject RIV: BI - Acoustics Impact factor: 3.032, year: 2015

  17. Identification and Endodontic Management of Middle Mesial Canal in Mandibular Second Molar Using Cone Beam Computed Tomography

    Directory of Open Access Journals (Sweden)

    Bonny Paul

    2015-01-01

    Full Text Available Endodontic treatments are routinely done with the help of radiographs. However, radiographs represent only a two-dimensional image of an object. Failure to identify aberrant anatomy can lead to endodontic failure. This case report presents the use of three-dimensional imaging with cone beam computed tomography (CBCT as an adjunct to digital radiography in identification and management of mandibular second molar with three mesial canals.

  18. Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

    Directory of Open Access Journals (Sweden)

    Laurent Gautier

    Full Text Available Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet, perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.

  19. Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

    Science.gov (United States)

    Gautier, Laurent; Lund, Ole

    2013-01-01

    Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc. PMID:24391826

  20. A hybrid computational-experimental approach for automated crystal structure solution

    Science.gov (United States)

    Meredig, Bryce; Wolverton, C.

    2013-02-01

    Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li-air batteries; and high-pressure silane, SiH4.

  1. A hybrid model for computing nonthermal ion distributions in a long mean-free-path plasma

    Science.gov (United States)

    Tang, Xianzhu; McDevitt, Chris; Guo, Zehua; Berk, Herb

    2014-10-01

    Non-thermal ions, especially the suprathermal ones, are known to make a dominant contribution to a number of important physics such as the fusion reactivity in controlled fusion, the ion heat flux, and in the case of a tokamak, the ion bootstrap current. Evaluating the deviation from a local Maxwellian distribution of these non-thermal ions can be a challenging task in the context of a global plasma fluid model that evolves the plasma density, flow, and temperature. Here we describe a hybrid model for coupling such constrained kinetic calculation to global plasma fluid models. The key ingredient is a non-perturbative treatment of the tail ions where the ion Knudsen number approaches or surpasses order unity. This can be sharply constrasted with the standard Chapman-Enskog approach which relies on a perturbative treatment that is frequently invalidated. The accuracy of our coupling scheme is controlled by the precise criteria for matching the non-perturbative kinetic model to perturbative solutions in both configuration space and velocity space. Although our specific application examples will be drawn from laboratory controlled fusion experiments, the general approach is applicable to space and astrophysical plasmas as well. Work supported by DOE.

  2. A Hybrid Autonomic Computing-Based Approach to Distributed Constraint Satisfaction Problems

    Directory of Open Access Journals (Sweden)

    Abhishek Bhatia

    2015-03-01

    Full Text Available Distributed constraint satisfaction problems (DisCSPs are among the widely endeavored problems using agent-based simulation. Fernandez et al. formulated sensor and mobile tracking problem as a DisCSP, known as SensorDCSP In this paper, we adopt a customized ERE (environment, reactive rules and entities algorithm for the SensorDCSP, which is otherwise proven as a computationally intractable problem. An amalgamation of the autonomy-oriented computing (AOC-based algorithm (ERE and genetic algorithm (GA provides an early solution of the modeled DisCSP. Incorporation of GA into ERE facilitates auto-tuning of the simulation parameters, thereby leading to an early solution of constraint satisfaction. This study further contributes towards a model, built up in the NetLogo simulation environment, to infer the efficacy of the proposed approach.

  3. The development of an oscilloscope visualization system for the hybrid computer E.A.I. 8900

    International Nuclear Information System (INIS)

    Djukanovic, Radojka

    1970-01-01

    This report was the first subject of a thesis submitted to the Faculte des Sciences in Paris, on the 30 of June 1970 by Mistress Radojka Djukanovic-Remsak, in order to obtain the grade of doctor engineer. A visualization system was studied and developed, whereby various figures could be displayed on an oscilloscope screen without a memory by means of points and segments. This system was realized by the utilisation of the analog and logic elements of an analog computer E.A.I. 8800 and a series of programs intended to be used in conjunction with the E.A.I. 8400 digital computer. The second subject: 'The evolution of multiprogramming' was dealt with in a note CEA-N-1346. (author) [fr

  4. The top-transmon: a hybrid superconducting qubit for parity-protected quantum computation

    International Nuclear Information System (INIS)

    Hassler, F; Akhmerov, A R; Beenakker, C W J

    2011-01-01

    Qubits constructed from uncoupled Majorana fermions are protected from decoherence, but to perform a quantum computation this topological protection needs to be broken. Parity-protected quantum computation breaks the protection in a minimally invasive way, by coupling directly to the fermion parity of the system-irrespective of any quasiparticle excitations. Here, we propose to use a superconducting charge qubit in a transmission line resonator (the so-called transmon) to perform parity-protected rotations and read-out of a topological (top) qubit. The advantage over an earlier proposal using a flux qubit is that the coupling can be switched on and off with exponential accuracy, promising a reduced sensitivity to charge noise.

  5. Cloned polynucleotide and synthetic oligonucleotide probes used in colony hybridization are equally efficient in the identification of enterotoxigenic Escherichia coli

    International Nuclear Information System (INIS)

    Sommerfelt, H.; Kalland, K.H.; Raj, P.; Moseley, S.L.; Bhan, M.K.; Bjorvatn, B.

    1988-01-01

    Restriction endonuclease-generated polynucleotide and synthetically produced oligonucleotide gene probes used in colony hybridization assays proved to be efficient for the detection and differentiation of enterotoxigenic Escherichia coli. To compare their relative efficiencies, these two sets of probes were radiolabeled with 32 P and were applied to 74 strains of E. coli with known enterotoxin profiles and to 156 previously unexamined E. coli isolates. The enterotoxigenic bacteria Vibrio cholerae O1, Vibrio cholerae non-O1 (NAG), Yersinia enterocolitica, and E. coli harboring the plasmid vectors of the polynucleotide gene probes were examined for further evaluation of probe specificity. The two classes of probes showed a perfect concordance in their specific detection and differentiation of enterotoxigenic E. coli. In the analysis of six strains, the signal strength on autoradiography after hybridization with oligonucleotides was weaker than that obtained after hybridization with polynucleotide probes. The probes did not hybridize with DNA from V. cholerae O1, V. cholerae non-O1 (NAG), or Y. enterocolitica. The strains of E. coli harboring the plasmid vectors of the polynucleotide gene probes were, likewise, negative in the hybridization assays

  6. Cloned polynucleotide and synthetic oligonucleotide probes used in colony hybridization are equally efficient in the identification of enterotoxigenic Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Sommerfelt, H.; Kalland, K.H.; Raj, P.; Moseley, S.L.; Bhan, M.K.; Bjorvatn, B.

    1988-11-01

    Restriction endonuclease-generated polynucleotide and synthetically produced oligonucleotide gene probes used in colony hybridization assays proved to be efficient for the detection and differentiation of enterotoxigenic Escherichia coli. To compare their relative efficiencies, these two sets of probes were radiolabeled with /sup 32/P and were applied to 74 strains of E. coli with known enterotoxin profiles and to 156 previously unexamined E. coli isolates. The enterotoxigenic bacteria Vibrio cholerae O1, Vibrio cholerae non-O1 (NAG), Yersinia enterocolitica, and E. coli harboring the plasmid vectors of the polynucleotide gene probes were examined for further evaluation of probe specificity. The two classes of probes showed a perfect concordance in their specific detection and differentiation of enterotoxigenic E. coli. In the analysis of six strains, the signal strength on autoradiography after hybridization with oligonucleotides was weaker than that obtained after hybridization with polynucleotide probes. The probes did not hybridize with DNA from V. cholerae O1, V. cholerae non-O1 (NAG), or Y. enterocolitica. The strains of E. coli harboring the plasmid vectors of the polynucleotide gene probes were, likewise, negative in the hybridization assays.

  7. Efficient Adjoint Computation of Hybrid Systems of Differential Algebraic Equations with Applications in Power Systems

    Energy Technology Data Exchange (ETDEWEB)

    Abhyankar, Shrirang [Argonne National Lab. (ANL), Argonne, IL (United States); Anitescu, Mihai [Argonne National Lab. (ANL), Argonne, IL (United States); Constantinescu, Emil [Argonne National Lab. (ANL), Argonne, IL (United States); Zhang, Hong [Argonne National Lab. (ANL), Argonne, IL (United States)

    2016-03-31

    Sensitivity analysis is an important tool to describe power system dynamic behavior in response to parameter variations. It is a central component in preventive and corrective control applications. The existing approaches for sensitivity calculations, namely, finite-difference and forward sensitivity analysis, require a computational effort that increases linearly with the number of sensitivity parameters. In this work, we investigate, implement, and test a discrete adjoint sensitivity approach whose computational effort is effectively independent of the number of sensitivity parameters. The proposed approach is highly efficient for calculating trajectory sensitivities of larger systems and is consistent, within machine precision, with the function whose sensitivity we are seeking. This is an essential feature for use in optimization applications. Moreover, our approach includes a consistent treatment of systems with switching, such as DC exciters, by deriving and implementing the adjoint jump conditions that arise from state and time-dependent discontinuities. The accuracy and the computational efficiency of the proposed approach are demonstrated in comparison with the forward sensitivity analysis approach.

  8. Degradation of ciprofloxacin antibiotic by Homogeneous Fenton oxidation: Hybrid AHP-PROMETHEE method, optimization, biodegradability improvement and identification of oxidized by-products.

    Science.gov (United States)

    Salari, Marjan; Rakhshandehroo, Gholam Reza; Nikoo, Mohammad Reza

    2018-09-01

    The main purpose of this experimental study was to optimize Homogeneous Fenton oxidation (HFO) and identification of oxidized by-products from degradation of Ciprofloxacin (CIP) using hybrid AHP-PROMETHEE, Response Surface Methodology (RSM) and High Performance Liquid Chromatography coupled with Mass Spectrometry (HPLC-MS). At the first step, an assessment was made for performances of two catalysts (FeSO 4 ·7H 2 O and FeCl 2 ·4H 2 O) based on hybrid AHP-PROMETHEE decision making method. Then, RSM was utilized to examine and optimize the influence of different variables including initial CIP concentration, Fe 2+ concentration, [H 2 O 2 ]/[ Fe 2+ ] mole ratio and initial pH as independent variables on CIP removal, COD removal, and sludge to iron (SIR) as the response functions in a reaction time of 25 min. Weights of the mentioned responses as well as cost criteria were determined by AHP model based on pairwise comparison and then used as inputs to PROMETHEE method to develop hybrid AHP-PROMETHEE. Based on net flow results of this hybrid model, FeCl 2 ·4H 2 O was more efficient because of its less environmental stability as well as lower SIR production. Then, optimization of experiments using Central Composite Design (CCD) under RSM was performed with the FeCl 2 ·4H 2 O catalyst. Biodegradability of wastewater was determined in terms of BOD 5 /COD ratio, showing that HFO process is able to improve wastewater biodegradability from zero to 0.42. Finally, the main intermediaries of degradation and degradation pathways of CIP were investigated with (HPLC-MS). Major degradation pathways from hydroxylation of both piperazine and quinolonic rings, oxidation and cleavage of the piperazine ring, and defluorination (OH/F substitution) were suggested. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Circular-detector array hybrid emission computed tomograph, HEADTOME-II

    Energy Technology Data Exchange (ETDEWEB)

    Uemura, Kazuo; Kanno, Iwao; Miura, Yuko; Miura, Syuichi [Research Inst. of Brain and Blood Vessels, Akita (Japan); Hattori, Hiroyuki; Hirose, Yoshiharu; Nagata, Takashi; Higashi, Yoshihumi

    1982-08-01

    The HEADTOME-II is a successor of the original hybrid ECT, the HEADTOME-I, which was built and used in Research Institute of Brain and Blood Vessels, Akita. The new machine has three detector rings comprising 64 Nal crystals each, the axial length of which is 30 mm, 100 mm in total for three rings including 5 mm lead shield between the rings, and is long enough to examine most of the brain at a given time. The system sensitivity for positrons is 27.5 kcps/..mu..Ci/ml for intra-ring coincidence and 36.5 kcps for inter-ring coincidence. Spatial resolution is 10 mm FWHM at the center of the field of view. For single photon ECT study, new ''Turbofan'' rotating collimators, high sensitivity H.S. and high resolution H.R., are adopted. The collimators for single photons and positrons can be selected by manual operation. The system sensitivity for sup(99m)Tc is, 52.5 kcps/..mu..Ci/ml by H.S. and 13.8 kcps by H.R. collimator. Spatial resolution at the center of the field of view is 20 mm for H.S. and 11 mm for H.R. respectively. High quality images have been obtained by sup(99m)Tc, /sup 81/mKr, /sup 111/In and /sup 11/C. The regional cerebral blood flow study by /sup 133/Xe inhalation or intra-venous injection has been tried and good results are obtained.

  10. A circular-detector array hybrid emission computed tomograph, HEADTOME-II

    International Nuclear Information System (INIS)

    Uemura, Kazuo; Kanno, Iwao; Miura, Yuko; Miura, Syuichi; Hattori, Hiroyuki; Hirose, Yoshiharu; Nagata, Takashi; Higashi, Yoshihumi.

    1982-01-01

    The HEADTOME-II is a successor of the original hybrid ECT, the HEADTOME-I, which was built and used in Research Institute of Brain and Blood Vessels, Akita. The new machine has three detector rings comprising 64 Nal crystals each, the axial length of which is 30 mm, 100 mm in total for three rings including 5 mm lead shield between the rings, and is long enought to examine the most part of the brain at a time. The system sensitivity for positrons is 27.5 kcps/μCi/ml for intra-ring coincidence and 36.5 kcps for inter-ring coincidence. Spatial resolution is 10 mm FWHM at the center of the field of view. For single photon ECT study, new ''Turbofan'' rotaing collimators, high sensitivity H.S. and high resolution H.R., are adopted. The collimators for single photons and positrons can be selected by manual operation. The system sensitivity for sup(99m)Tc is, 52.5 kcps/μCi/ml by H.S. and 13.8 kcps by H.R. collimator. Spatial resolution at the center of the field of view is 20 mm for H.S. and 11 mm for H.R. respectively. High quality images have been obtained by sup(99m)Tc, 81 mKr, 111 In and 11 C. The regional cerebral blood flow study by 133 Xe inhalation or intra-venous injection has been tried and good results are obtained. (author)

  11. Identification of novel CYP2D7-2D6 hybrids: non-functional and functional variants

    Directory of Open Access Journals (Sweden)

    Andrea Gaedigk

    2010-10-01

    Full Text Available Polymorphic expression of CYP2D6 contributes to the wide range of activity observed for this clinically important drug metabolizing enzyme. In this report we describe novel CYP2D7/2D6 hybrid genes encoding non-functional and functional CYP2D6 protein and a CYP2D7 variant that mimics a CYP2D7/2D6 hybrid gene. Five kb long PCR products encompassing the novel genes were entirely sequenced. A quantitative assay probing in different gene regions was employed to determine CYP2D6 and 2D7 copy number variations and the relative position of the hybrid genes within the locus was assessed by long-range PCR. In addition to the previously known CYP2D6*13 and *66 hybrids, we describe three novel non-functional CYP2D7-2D6 hybrids with gene switching in exon 2 (CYP2D6*79, intron 2 (CYP2D6*80 and intron 5 (CYP2D6*67. A CYP2D7-specific T-ins in exon 1 causes a detrimental frame shift. One subject revealed a CYP2D7 conversion in the 5’-flanking region of a CYP2D6*35 allele, was otherwise unaffected (designated CYP2D6*35B. Finally, three DNAs revealed a CYP2D7 gene with a CYP2D6-like region downstream of exon 9 (designated CYP2D7[REP6]. Quantitative copy number determination, sequence analyses and long-range PCR mapping were in agreement and excluded the presence of additional gene units. Undetected hybrid genes may cause over-estimation of CYP2D6 activity (CYP2D6*1/*1 vs *1/hybrid, etc, but may also cause results that may interfere with the genotype determination. Detection of hybrid events, ‘single’ and tandem, will contribute to more accurate phenotype prediction from genotype data.

  12. Hybrid Cloud Computing Architecture Optimization by Total Cost of Ownership Criterion

    Directory of Open Access Journals (Sweden)

    Elena Valeryevna Makarenko

    2014-12-01

    Full Text Available Achieving the goals of information security is a key factor in the decision to outsource information technology and, in particular, to decide on the migration of organizational data, applications, and other resources to the infrastructure, based on cloud computing. And the key issue in the selection of optimal architecture and the subsequent migration of business applications and data to the cloud organization information environment is the question of the total cost of ownership of IT infrastructure. This paper focuses on solving the problem of minimizing the total cost of ownership cloud.

  13. Hybrid spin and valley quantum computing with singlet-triplet qubits.

    Science.gov (United States)

    Rohling, Niklas; Russ, Maximilian; Burkard, Guido

    2014-10-24

    The valley degree of freedom in the electronic band structure of silicon, graphene, and other materials is often considered to be an obstacle for quantum computing (QC) based on electron spins in quantum dots. Here we show that control over the valley state opens new possibilities for quantum information processing. Combining qubits encoded in the singlet-triplet subspace of spin and valley states allows for universal QC using a universal two-qubit gate directly provided by the exchange interaction. We show how spin and valley qubits can be separated in order to allow for single-qubit rotations.

  14. A boundary integral method for numerical computation of radar cross section of 3D targets using hybrid BEM/FEM with edge elements

    Science.gov (United States)

    Dodig, H.

    2017-11-01

    This contribution presents the boundary integral formulation for numerical computation of time-harmonic radar cross section for 3D targets. Method relies on hybrid edge element BEM/FEM to compute near field edge element coefficients that are associated with near electric and magnetic fields at the boundary of the computational domain. Special boundary integral formulation is presented that computes radar cross section directly from these edge element coefficients. Consequently, there is no need for near-to-far field transformation (NTFFT) which is common step in RCS computations. By the end of the paper it is demonstrated that the formulation yields accurate results for canonical models such as spheres, cubes, cones and pyramids. Method has demonstrated accuracy even in the case of dielectrically coated PEC sphere at interior resonance frequency which is common problem for computational electromagnetic codes.

  15. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples

    International Nuclear Information System (INIS)

    Voordouw, G.; Voordouw, J.K.; Karkhoff-Schweizer, R.R.; Fedorak, P.M.; Westlake, D.W.S.

    1991-01-01

    A novel method for identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a standard) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples

  16. Identification of parental chromosomes in hybridogenetic water frog Pelophylax esculentus (Rana esculenta) by genomic in situ hybridization (GISH)

    Czech Academy of Sciences Publication Activity Database

    Zalésna, A.; Choleva, Lukáš; Ogielska, M.; Rábová, Marie; Marec, František; Ráb, Petr

    2010-01-01

    Roč. 18, č. 16 (2010), s. 754-755 ISSN 0967-3849. [19th International Colloquium on animal cytogenetics and gene mapping. 06.06.-09.06.2010, Krakow] Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50070508 Keywords : parental chromosomes * Pelophylax esculentus * hybridization Subject RIV: EB - Genetics ; Molecular Biology

  17. Chromosomal regions involved in hybrid performance and heterosis : their AFLP-based identification and practical use in prediction models

    NARCIS (Netherlands)

    Vuylsteke, M.; Kuiper, M.; Stam, P.

    2000-01-01

    In this paper, a novel approach towards the prediction of hybrid performance and heterosis is presented. Here, we describe an approach based on: (i) the assessment of associations between AFLPÒ22 AFLPÒ is a registered trademark of Keygene N.V. ,33 The methylation AFLPÒ method is subject to a patent

  18. Identification of environmental issues: Hybrid wood-geothermal power plant, Wendel-Amedee KGRA, Lassen County, California: First phase report

    Energy Technology Data Exchange (ETDEWEB)

    1981-08-14

    The development of a 55 MWe power plant in Lassen County, California, has been proposed. The proposed power plant is unique in that it will utilize goethermal heat and wood fuel to generate electrical power. This report identifies environmental issues and constraints which may impact the proposed hybrid wood-geothermal power plant. (ACR)

  19. Identification of chromosome aberrations in sporadic microsatellite stable and unstable colorectal cancers using array comparative genomic hybridization

    DEFF Research Database (Denmark)

    Jensen, Thomas Dyrsø; Li, Jian; Wang, Kai

    2011-01-01

    cancers constitute approximately 85% of sporadic cases, whereas microsatellite unstable (MSI) cases constitute the remaining 15%. In this study, we used array comparative genomic hybridization (aCGH) to identify genomic hotspot regions that harbor recurrent copy number changes. The study material...

  20. Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis

    Directory of Open Access Journals (Sweden)

    Chen Jiun-Ching

    2007-05-01

    Full Text Available Abstract Background Genome-wide identification of specific oligonucleotides (oligos is a computationally-intensive task and is a requirement for designing microarray probes, primers, and siRNAs. An artificial neural network (ANN is a machine learning technique that can effectively process complex and high noise data. Here, ANNs are applied to process the unique subsequence distribution for prediction of specific oligos. Results We present a novel and efficient algorithm, named the integration of ANN and BLAST (IAB algorithm, to identify specific oligos. We establish the unique marker database for human and rat gene index databases using the hash table algorithm. We then create the input vectors, via the unique marker database, to train and test the ANN. The trained ANN predicted the specific oligos with high efficiency, and these oligos were subsequently verified by BLAST. To improve the prediction performance, the ANN over-fitting issue was avoided by early stopping with the best observed error and a k-fold validation was also applied. The performance of the IAB algorithm was about 5.2, 7.1, and 6.7 times faster than the BLAST search without ANN for experimental results of 70-mer, 50-mer, and 25-mer specific oligos, respectively. In addition, the results of polymerase chain reactions showed that the primers predicted by the IAB algorithm could specifically amplify the corresponding genes. The IAB algorithm has been integrated into a previously published comprehensive web server to support microarray analysis and genome-wide iterative enrichment analysis, through which users can identify a group of desired genes and then discover the specific oligos of these genes. Conclusion The IAB algorithm has been developed to construct SpecificDB, a web server that provides a specific and valid oligo database of the probe, siRNA, and primer design for the human genome. We also demonstrate the ability of the IAB algorithm to predict specific oligos through

  1. Design Patterns for Sparse-Matrix Computations on Hybrid CPU/GPU Platforms

    Directory of Open Access Journals (Sweden)

    Valeria Cardellini

    2014-01-01

    Full Text Available We apply object-oriented software design patterns to develop code for scientific software involving sparse matrices. Design patterns arise when multiple independent developments produce similar designs which converge onto a generic solution. We demonstrate how to use design patterns to implement an interface for sparse matrix computations on NVIDIA GPUs starting from PSBLAS, an existing sparse matrix library, and from existing sets of GPU kernels for sparse matrices. We also compare the throughput of the PSBLAS sparse matrix–vector multiplication on two platforms exploiting the GPU with that obtained by a CPU-only PSBLAS implementation. Our experiments exhibit encouraging results regarding the comparison between CPU and GPU executions in double precision, obtaining a speedup of up to 35.35 on NVIDIA GTX 285 with respect to AMD Athlon 7750, and up to 10.15 on NVIDIA Tesla C2050 with respect to Intel Xeon X5650.

  2. Evaluation of the reliability concerning the identification of human factors as contributing factors by a computer supported event analysis (CEA)

    International Nuclear Information System (INIS)

    Wilpert, B.; Maimer, H.; Loroff, C.

    2000-01-01

    The project's objectives are the evaluation of the reliability concerning the identification of Human Factors as contributing factors by a computer supported event analysis (CEA). CEA is a computer version of SOL (Safety through Organizational Learning). Parts of the first step were interviews with experts from the nuclear power industry and the evaluation of existing computer supported event analysis methods. This information was combined to a requirement profile for the CEA software. The next step contained the implementation of the software in an iterative process of evaluation. The completion of this project was the testing of the CEA software. As a result the testing demonstrated that it is possible to identify contributing factors with CEA validly. In addition, CEA received a very positive feedback from the experts. (orig.) [de

  3. Computerized nipple identification for multiple image analysis in computer-aided diagnosis

    International Nuclear Information System (INIS)

    Zhou Chuan; Chan Heangping; Paramagul, Chintana; Roubidoux, Marilyn A.; Sahiner, Berkman; Hadjiiski, Labomir M.; Petrick, Nicholas

    2004-01-01

    Correlation of information from multiple-view mammograms (e.g., MLO and CC views, bilateral views, or current and prior mammograms) can improve the performance of breast cancer diagnosis by radiologists or by computer. The nipple is a reliable and stable landmark on mammograms for the registration of multiple mammograms. However, accurate identification of nipple location on mammograms is challenging because of the variations in image quality and in the nipple projections, resulting in some nipples being nearly invisible on the mammograms. In this study, we developed a computerized method to automatically identify the nipple location on digitized mammograms. First, the breast boundary was obtained using a gradient-based boundary tracking algorithm, and then the gray level profiles along the inside and outside of the boundary were identified. A geometric convergence analysis was used to limit the nipple search to a region of the breast boundary. A two-stage nipple detection method was developed to identify the nipple location using the gray level information around the nipple, the geometric characteristics of nipple shapes, and the texture features of glandular tissue or ducts which converge toward the nipple. At the first stage, a rule-based method was designed to identify the nipple location by detecting significant changes of intensity along the gray level profiles inside and outside the breast boundary and the changes in the boundary direction. At the second stage, a texture orientation-field analysis was developed to estimate the nipple location based on the convergence of the texture pattern of glandular tissue or ducts towards the nipple. The nipple location was finally determined from the detected nipple candidates by a rule-based confidence analysis. In this study, 377 and 367 randomly selected digitized mammograms were used for training and testing the nipple detection algorithm, respectively. Two experienced radiologists identified the nipple locations

  4. Detecting number processing and mental calculation in patients with disorders of consciousness using a hybrid brain-computer interface system.

    Science.gov (United States)

    Li, Yuanqing; Pan, Jiahui; He, Yanbin; Wang, Fei; Laureys, Steven; Xie, Qiuyou; Yu, Ronghao

    2015-12-15

    For patients with disorders of consciousness such as coma, a vegetative state or a minimally conscious state, one challenge is to detect and assess the residual cognitive functions in their brains. Number processing and mental calculation are important brain functions but are difficult to detect in patients with disorders of consciousness using motor response-based clinical assessment scales such as the Coma Recovery Scale-Revised due to the patients' motor impairments and inability to provide sufficient motor responses for number- and calculation-based communication. In this study, we presented a hybrid brain-computer interface that combines P300 and steady state visual evoked potentials to detect number processing and mental calculation in Han Chinese patients with disorders of consciousness. Eleven patients with disorders of consciousness who were in a vegetative state (n = 6) or in a minimally conscious state (n = 3) or who emerged from a minimally conscious state (n = 2) participated in the brain-computer interface-based experiment. During the experiment, the patients with disorders of consciousness were instructed to perform three tasks, i.e., number recognition, number comparison, and mental calculation, including addition and subtraction. In each experimental trial, an arithmetic problem was first presented. Next, two number buttons, only one of which was the correct answer to the problem, flickered at different frequencies to evoke steady state visual evoked potentials, while the frames of the two buttons flashed in a random order to evoke P300 potentials. The patients needed to focus on the target number button (the correct answer). Finally, the brain-computer interface system detected P300 and steady state visual evoked potentials to determine the button to which the patients attended, further presenting the results as feedback. Two of the six patients who were in a vegetative state, one of the three patients who were in a minimally conscious state, and

  5. Usability Studies in Virtual and Traditional Computer Aided Design Environments for Fault Identification

    Science.gov (United States)

    2017-08-08

    communicate their subjective opinions. Keywords: Usability Analysis; CAVETM (Cave Automatic Virtual Environments); Human Computer Interface (HCI...the differences in interaction when compared with traditional human computer interfaces. This paper provides analysis via usability study methods

  6. Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

    Science.gov (United States)

    Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

    2010-05-01

    The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

  7. GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

    Science.gov (United States)

    Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

    2017-09-30

    GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  8. Hybrid EEG-fNIRS Asynchronous Brain-Computer Interface for Multiple Motor Tasks.

    Directory of Open Access Journals (Sweden)

    Alessio Paolo Buccino

    Full Text Available Non-invasive Brain-Computer Interfaces (BCI have demonstrated great promise for neuroprosthetics and assistive devices. Here we aim to investigate methods to combine Electroencephalography (EEG and functional Near-Infrared Spectroscopy (fNIRS in an asynchronous Sensory Motor rhythm (SMR-based BCI. We attempted to classify 4 different executed movements, namely, Right-Arm-Left-Arm-Right-Hand-Left-Hand tasks. Previous studies demonstrated the benefit of EEG-fNIRS combination. However, since normally fNIRS hemodynamic response shows a long delay, we investigated new features, involving slope indicators, in order to immediately detect changes in the signals. Moreover, Common Spatial Patterns (CSPs have been applied to both EEG and fNIRS signals. 15 healthy subjects took part in the experiments and since 25 trials per class were available, CSPs have been regularized with information from the entire population of participants and optimized using genetic algorithms. The different features have been compared in terms of performance and the dynamic accuracy over trials shows that the introduced methods diminish the fNIRS delay in the detection of changes.

  9. Analysis and identification of time-invariant systems, time-varying systems, and multi-delay systems using orthogonal hybrid functions theory and algorithms with Matlab

    CERN Document Server

    Deb, Anish; Sarkar, Gautam

    2016-01-01

    This book introduces a new set of orthogonal hybrid functions (HF) which approximates time functions in a piecewise linear manner which is very suitable for practical applications. The book presents an analysis of different systems namely, time-invariant system, time-varying system, multi-delay systems---both homogeneous and non-homogeneous type- and the solutions are obtained in the form of discrete samples. The book also investigates system identification problems for many of the above systems. The book is spread over 15 chapters and contains 180 black and white figures, 18 colour figures, 85 tables and 56 illustrative examples. MATLAB codes for many such examples are included at the end of the book.

  10. Unambiguous Metabolite Identification in High-Throughput Metabolomics by Hybrid 1H-NMR/ESI-MS1 Approach

    Energy Technology Data Exchange (ETDEWEB)

    2016-10-18

    The invention improves accuracy of metabolite identification by combining direct infusion ESI-MS with one-dimensional 1H-NMR spectroscopy. First, we apply a standard 1H-NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in a metabolomics reference libraries. This generates a list of candidate metabolites. The list contains both false positive and ambiguous identifications. The software tool (the invention) takes the list of candidate metabolites, generated from NMRbased metabolite identification, and then calculates, for each of the candidate metabolites, the monoisotopic mass-tocharge (m/z) ratios for each commonly observed ion, fragment and adduct feature. These are then used to assign m/z ratios in experimental ESI-MS spectra of the same sample. Detection of the signals of a given metabolite in both NMR and MS spectra resolves the ambiguities, and therefore, significantly improves the confidence of the identification.

  11. Man-Computer Symbiosis Through Interactive Graphics: A Survey and Identification of Critical Research Areas.

    Science.gov (United States)

    Knoop, Patricia A.

    The purpose of this report was to determine the research areas that appear most critical to achieving man-computer symbiosis. An operational definition of man-computer symbiosis was developed by: (1) reviewing and summarizing what others have said about it, and (2) attempting to distinguish it from other types of man-computer relationships. From…

  12. Reshaping Computer Literacy Teaching in Higher Education: Identification of Critical Success Factors

    Science.gov (United States)

    Taylor, Estelle; Goede, Roelien; Steyn, Tjaart

    2011-01-01

    Purpose: Acquiring computer skills is more important today than ever before, especially in a developing country. Teaching of computer skills, however, has to adapt to new technology. This paper aims to model factors influencing the success of the learning of computer literacy by means of an e-learning environment. The research question for this…

  13. Utilization of the computational technique to improve the thermophysical performance in the transportation of an electrically conducting Al2O3 - Ag/H2O hybrid nanofluid

    Science.gov (United States)

    Iqbal, Z.; Azhar, Ehtsham; Maraj, E. N.

    2017-12-01

    In this study, we analyzed the induced magnetic field effect on stagnation-point flow of a Al2O3-Ag/water hybrid nanofluid over a stretching sheet. Hybrid nanofluid, a new type of conventional fluid has been used for enhancement of heat transfer within boundary layer flow. It is notable here that only 1% to 5% contribution of nanoparticles enhance thermal conductivity of water. Nonlinear governing equations are simplified into boundary layer equations under boundary layer approximation assumption. A coupled system of nonlinear partial differential equation is transformed into a nonlinear system of ordinary differential equation by implementing suitable similarity conversions. Numerical analysis is performed by means of Keller box scheme. Effects of different non-dimensional governing parameters on velocity, induced magnetic field and temperature profiles, along with skinfriction coefficient and local Nusselt number, are discussed and presented through graphs and tables. Hybrid nanofluid is considered by keeping the 0.1% volumetric fraction of silver. From this study it is observed that the heat transfer rate of hybrid nanofluid (Al2O3-Ag/water) is higher than nanofluid (Ag/water). Novel results computed are useful in academic studies of hybrid nanofluids in engineering and industry.

  14. Identification of single nucleotide polymorphisms (SNPs at candidate genes involved in abiotic stress in two Prosopis species of hybrids

    Directory of Open Access Journals (Sweden)

    Maria F. Pomponio

    2014-12-01

    Full Text Available Aim of the study: Identify and compare SNPs on candidate genes related to abiotic stress in Prosopis chilensis, Prosopis flexuosa and interspecific hybridsArea of the study: Chaco árido, Argentina. Material and Methods: Fragments from 6 candidate genes were sequenced in 60 genotypes. DNA polymorphisms were analyzed.Main Results: The analysis revealed that the hybrids had the highest rate of polymorphism, followed by P. flexuosa and P. chilensis, the values found are comparable to other forest tree species.Research highlights: This approach will help to study genetic diversity variation on natural populations for assessing the effects of environmental changes.Keywords: SNPs; abiotic stress; interspecific variation; molecular markers. 

  15. [Feasibility and acceptance of computer-based assessment for the identification of psychosocially distressed patients in routine clinical care].

    Science.gov (United States)

    Sehlen, Susanne; Ott, Martin; Marten-Mittag, Birgitt; Haimerl, Wolfgang; Dinkel, Andreas; Duehmke, Eckhart; Klein, Christian; Schaefer, Christof; Herschbach, Peter

    2012-07-01

    This study investigated feasibility and acceptance of computer-based assessment for the identification of psychosocial distress in routine radiotherapy care. 155 cancer patients were assessed using QSC-R10, PO-Bado-SF and Mach-9. The congruence between computerized tablet PC and conventional paper assessment was analysed in 50 patients. The agreement between the 2 modes was high (ICC 0.869-0.980). Acceptance of computer-based assessment was very high (>95%). Sex, age, education, distress and Karnofsky performance status (KPS) did not influence acceptance. Computerized assessment was rated more difficult by older patients (p = 0.039) and patients with low KPS (p = 0.020). 75.5% of the respondents supported referral for psycho-social intervention for distressed patients. The prevalence of distress was 27.1% (QSC-R10). Computer-based assessment allows easy identification of distressed patients. Level of staff involvement is low, and the results are quickly available for care providers. © Georg Thieme Verlag KG Stuttgart · New York.

  16. Identification of MYCN gene amplification in neuroblastoma using chromogenic in situ hybridization (CISH): an alternative and practical method.

    Science.gov (United States)

    Bhargava, Rohit; Oppenheimer, Orit; Gerald, William; Jhanwar, Suresh C; Chen, Beiyun

    2005-06-01

    Chromogenic in situ hybridization (CISH) is a recently developed technique, which utilizes the general principles of in situ hybridization and a detection system similar to immunohistochemistry. To assess the utility of CISH for analysis of MYCN gene amplification, we compared this assay with established diagnostic assays such as Southern blot analysis (SB) and fluorescent in situ hybridization (FISH). CISH was performed on 67 cases of neuroblastoma using tissue microarray (65 cases) and whole tissue sections (2 cases). Unequivocal, high-level amplification (> or =10 gene copies per tumor nucleus) was identified in 19 of 67 (28.4%) tumors. Two (3%) tumors showed low-level amplification (6-9 gene copies per tumor nucleus). No amplification was seen in 46 of 67 (68.6%) tumors. SB data were available in 44 tumors. Forty-one of the 44 tumors (93%) showed concordant results between CISH and SB. Three tumors showed MYCN amplification by CISH but no amplification by SB, most likely due to dilution effect of nonneoplastic tissue in the test samples. Two of these three tumors also showed MYCN amplification by FISH, and the third tumor was not analyzed by FISH. FISH data were available in total of 30 tumors. All 30 tumors showed concordant results between CISH and FISH for classifying a tumor as MYCN amplified or not amplified. We conclude that CISH is an accurate method for determining MYCN gene amplification, with added advantages that make it a more practically useful method.

  17. Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content.

    Science.gov (United States)

    Fazi, Stefano; Amalfitano, Stefano; Pizzetti, Ilaria; Pernthaler, Jakob

    2007-09-01

    We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes (FISH) significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of (3)H leucine. FISH and signal amplification by catalyzed reporter deposition (CARD-FISH) could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD-FISH showed comparable values in dry and wet conditions. This approach was unrelated to (3)H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram-positive Actinobacteria in the studied samples. CARD-FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems.

  18. Screening and identification of male-specific DNA fragments in common carps Cyprinus carpio using suppression subtractive hybridization.

    Science.gov (United States)

    Chen, J J; Du, Q Y; Yue, Y Y; Dang, B J; Chang, Z J

    2010-08-01

    In this study, a sex subtractive genomic DNA library was constructed using suppression subtractive hybridization (SSH) between male and female Cyprinus carpio. Twenty-two clones with distinguishable hybridization signals were selected and sequenced. The specific primers were designed based on the sequence data. Those primers were then used to amplify the sex-specific fragments from the genomic DNA of male and female carp. The amplified fragments from two clones showed specificity to males but not to females, which were named as Ccmf2 [387 base pairs (bp)] and Ccmf3 (183 bp), respectively. The sex-specific pattern was analysed in a total of 40 individuals from three other different C. carpio. stocks and grass carp Ctenopharyngodon idella using Ccmf2 and Ccmf3 as dot-blotting probes. The results revealed that the molecular diversity exists on the Y chromosome of C. carpio. No hybridization signals, however, were detected from individuals of C. idella, suggesting that the two sequences are specific to C. carpio. No significant homologous sequences of Ccmf2 and Ccmf3 were found in GenBank. Therefore, it was interpreted that the results as that Ccmf2 and Ccmf3 are two novel male-specific sequences; and both fragments could be used as markers to rapidly and accurately identify the genetic sex of part of C. carpio. This may provide a very efficient selective tool for practically breeding monosex female populations in aquacultural production.

  19. Computer system for identification of tool wear model in hot forging

    Directory of Open Access Journals (Sweden)

    Wilkus Marek

    2016-01-01

    Full Text Available The aim of the research was to create a methodology that will enable effective and reliable prediction of the tool wear. The idea of the hybrid model, which accounts for various mechanisms of tool material deterioration, is proposed in the paper. The mechanisms, which were considered, include abrasive wear, adhesive wear, thermal fatigue, mechanical fatigue, oxidation and plastic deformation. Individual models of various complexity were used for separate phenomena and strategy of combination of these models in one hybrid system was developed to account for the synergy of various mechanisms. The complex hybrid model was built on the basis of these individual models for various wear mechanisms. The individual models expanded from phenomenological ones for abrasive wear to multi-scale methods for modelling micro cracks initiation and propagation utilizing virtual representations of granular microstructures. The latter have been intensively developed recently and they form potentially a powerful tool that allows modelling of thermal and mechanical fatigue, accounting explicitly for the tool material microstructure.

  20. Linear equations and rap battles: how students in a wired classroom utilized the computer as a resource to coordinate personal and mathematical positional identities in hybrid spaces

    Science.gov (United States)

    Langer-Osuna, Jennifer

    2015-03-01

    This paper draws on the constructs of hybridity, figured worlds, and cultural capital to examine how a group of African-American students in a technology-driven, project-based algebra classroom utilized the computer as a resource to coordinate personal and mathematical positional identities during group work. Analyses of several vignettes of small group dynamics highlight how hybridity was established as the students engaged in multiple on-task and off-task computer-based activities, each of which drew on different lived experiences and forms of cultural capital. The paper ends with a discussion on how classrooms that make use of student-led collaborative work, and where students are afforded autonomy, have the potential to support the academic engagement of students from historically marginalized communities.

  1. Stability and economy analysis based on computational fluid dynamics and field testing of hybrid-driven underwater glider with the water quality sensor in Danjiangkou Reservoir

    Directory of Open Access Journals (Sweden)

    Chao Li

    2015-12-01

    Full Text Available Hybrid-driven underwater glider is a new kind of unmanned platform for water quality monitoring. It has advantages such as high controllability and maneuverability, low cost, easy operation, and ability to carry multiple sensors. This article develops a hybrid-driven underwater glider, PETRELII, and integrates a water quality monitoring sensor. Considering stability and economy, an optimal layout scheme is selected from four candidates by simulation using computational fluid dynamics method. Trials were carried out in Danjiangkou Reservoir—important headwaters of the Middle Route of the South-to-North Water Diversion Project. In the trials, a monitoring strategy with polygonal mixed-motion was adopted to make full use of the advantages of the unmanned platform. The measuring data, including temperature, dissolved oxygen, conductivity, pH, turbidity, chlorophyll, and ammonia nitrogen, are obtained. These data validate the practicability of the theoretical layout obtained using computational fluid dynamics method and the practical performance of PETRELII with sensor.

  2. Identification of High-Risk Plaques Destined to Cause Acute Coronary Syndrome Using Coronary Computed Tomographic Angiography and Computational Fluid Dynamics.

    Science.gov (United States)

    Lee, Joo Myung; Choi, Gilwoo; Koo, Bon-Kwon; Hwang, Doyeon; Park, Jonghanne; Zhang, Jinlong; Kim, Kyung-Jin; Tong, Yaliang; Kim, Hyun Jin; Grady, Leo; Doh, Joon-Hyung; Nam, Chang-Wook; Shin, Eun-Seok; Cho, Young-Seok; Choi, Su-Yeon; Chun, Eun Ju; Choi, Jin-Ho; Nørgaard, Bjarne L; Christiansen, Evald H; Niemen, Koen; Otake, Hiromasa; Penicka, Martin; de Bruyne, Bernard; Kubo, Takashi; Akasaka, Takashi; Narula, Jagat; Douglas, Pamela S; Taylor, Charles A; Kim, Hyo-Soo

    2018-03-14

    We investigated the utility of noninvasive hemodynamic assessment in the identification of high-risk plaques that caused subsequent acute coronary syndrome (ACS). ACS is a critical event that impacts the prognosis of patients with coronary artery disease. However, the role of hemodynamic factors in the development of ACS is not well-known. Seventy-two patients with clearly documented ACS and available coronary computed tomographic angiography (CTA) acquired between 1 month and 2 years before the development of ACS were included. In 66 culprit and 150 nonculprit lesions as a case-control design, the presence of adverse plaque characteristics (APC) was assessed and hemodynamic parameters (fractional flow reserve derived by coronary computed tomographic angiography [FFR CT ], change in FFR CT across the lesion [△FFR CT ], wall shear stress [WSS], and axial plaque stress) were analyzed using computational fluid dynamics. The best cut-off values for FFR CT , △FFR CT , WSS, and axial plaque stress were used to define the presence of adverse hemodynamic characteristics (AHC). The incremental discriminant and reclassification abilities for ACS prediction were compared among 3 models (model 1: percent diameter stenosis [%DS] and lesion length, model 2: model 1 + APC, and model 3: model 2 + AHC). The culprit lesions showed higher %DS (55.5 ± 15.4% vs. 43.1 ± 15.0%; p stress than nonculprit lesions (all p values statistic [c-index] 0.789 vs. 0.747; p = 0.014) and reclassification abilities (category-free net reclassification index 0.287; p = 0.047; relative integrated discrimination improvement 0.368; p < 0.001) than model 2. Lesions with both APC and AHC showed significantly higher risk of the culprit for subsequent ACS than those with no APC/AHC (hazard ratio: 11.75; 95% confidence interval: 2.85 to 48.51; p = 0.001) and with either APC or AHC (hazard ratio: 3.22; 95% confidence interval: 1.86 to 5.55; p < 0.001). Noninvasive hemodynamic assessment enhanced

  3. The Use of Computer-Assisted Identification of ARIMA Time-Series.

    Science.gov (United States)

    Brown, Roger L.

    This study was conducted to determine the effects of using various levels of tutorial statistical software for the tentative identification of nonseasonal ARIMA models, a statistical technique proposed by Box and Jenkins for the interpretation of time-series data. The Box-Jenkins approach is an iterative process encompassing several stages of…

  4. Validation of DNA-based identification software by computation of pedigree likelihood ratios

    NARCIS (Netherlands)

    Slooten, K.

    Disaster victim identification (DVI) can be aided by DNA-evidence, by comparing the DNA-profiles of unidentified individuals with those of surviving relatives. The DNA-evidence is used optimally when such a comparison is done by calculating the appropriate likelihood ratios. Though conceptually

  5. Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions.

    Science.gov (United States)

    Xiao, Meng; Kong, Fanrong; Sorrell, Tania C; Cao, Yongyan; Lee, Ok Cha; Liu, Ying; Sintchenko, Vitali; Chen, Sharon C A

    2010-02-01

    Although 16S rRNA gene sequence analysis is employed most often for the definitive identification of Nocardia species, alternate molecular methods and polymorphisms in other gene targets have also enabled species determinations. We evaluated a combined Nocardia PCR-based reverse line blot (RLB) hybridization assay based on 16S and 16S-23S rRNA gene spacer region polymorphisms to identify 12 American Type Culture Collection and 123 clinical Nocardia isolates representing 14 species; results were compared with results from 16S rRNA gene sequencing. Thirteen 16S rRNA gene-based (two group-specific and 11 species-specific) and five 16S-23S spacer-targeted (two taxon-specific and three species-specific) probes were utilized. 16S rRNA gene-based probes correctly identified 124 of 135 isolates (sensitivity, 92%) but were unable to identify Nocardia paucivorans strains (n = 10 strains) and a Nocardia asteroides isolate with a novel 16S rRNA gene sequence. Nocardia farcinica and Nocardia cyriacigeorgica strains were identified by the sequential use of an N. farcinica-"negative" probe and a combined N. farcinica/N. cyriacigeorgica probe. The assay specificity was high (99%) except for weak cross-reactivity between the Nocardia brasiliensis probe with the Nocardia thailandica DNA product; however, cross-hybridization with closely related nontarget species may occur. The incorporation of 16S-23S rRNA gene spacer-based probes enabled the identification of all N. paucivorans strains. The overall sensitivity using both probe sets was >99%. Both N. farcinica-specific 16S-23S rRNA gene spacer-directed probes were required to identify all N. farcinica stains by using this probe set. The study demonstrates the utility of a combined PCR/RLB assay for the identification of clinically relevant Nocardia species and its potential for studying subtypes of N. farcinica. Where species assignment is ambiguous or not possible, 16S rRNA gene sequencing is recommended.

  6. CERPI and CEREL, two computer codes for the automatic identification and determination of gamma emitters in thermal-neutron-activated samples

    International Nuclear Information System (INIS)

    Giannini, M.; Oliva, P.R.; Ramorino, M.C.

    1979-01-01

    A computer code that automatically analyzes gamma-ray spectra obtained with Ge(Li) detectors is described. The program contains such features as automatic peak location and fitting, determination of peak energies and intensities, nuclide identification, and calculation of masses and errors. Finally, the results obtained with this computer code for a lunar sample are reported and briefly discussed

  7. Small supernumerary marker chromosome derived from proximal p-arm of chromosome 2: identification by fluorescent in situ hybridization.

    Science.gov (United States)

    Lasan Trcić, Ruzica; Hitrec, Vlasta; Letica, Ljiljana; Cuk, Mario; Begović, Davor

    2003-08-01

    Conventional cytogenetics detected an interstitial deletion of proximal region of p-arm of chromosome 2 in a 6-month-old boy with a phenotype slightly resembling Down's syndrome. The deletion was inherited from the father, whose karyotype revealed a small ring-shaped marker chromosome, in addition to interstitial deletion. Fluorescence in situ hybridization identified the marker, which consisted of the proximal region of the p-arm of chromosome 2, including a part of its centromere. This case shows that molecular cytogenetic analysis can reveal the mechanism of the formation of the marker chromosome.

  8. A Hybrid Computer-aided-diagnosis System for Prediction of Breast Cancer Recurrence (HPBCR Using Optimized Ensemble Learning

    Directory of Open Access Journals (Sweden)

    Mohammad R. Mohebian

    Full Text Available Cancer is a collection of diseases that involves growing abnormal cells with the potential to invade or spread to the body. Breast cancer is the second leading cause of cancer death among women. A method for 5-year breast cancer recurrence prediction is presented in this manuscript. Clinicopathologic characteristics of 579 breast cancer patients (recurrence prevalence of 19.3% were analyzed and discriminative features were selected using statistical feature selection methods. They were further refined by Particle Swarm Optimization (PSO as the inputs of the classification system with ensemble learning (Bagged Decision Tree: BDT. The proper combination of selected categorical features and also the weight (importance of the selected interval-measurement-scale features were identified by the PSO algorithm. The performance of HPBCR (hybrid predictor of breast cancer recurrence was assessed using the holdout and 4-fold cross-validation. Three other classifiers namely as supported vector machines, DT, and multilayer perceptron neural network were used for comparison. The selected features were diagnosis age, tumor size, lymph node involvement ratio, number of involved axillary lymph nodes, progesterone receptor expression, having hormone therapy and type of surgery. The minimum sensitivity, specificity, precision and accuracy of HPBCR were 77%, 93%, 95% and 85%, respectively in the entire cross-validation folds and the hold-out test fold. HPBCR outperformed the other tested classifiers. It showed excellent agreement with the gold standard (i.e. the oncologist opinion after blood tumor marker and imaging tests, and tissue biopsy. This algorithm is thus a promising online tool for the prediction of breast cancer recurrence. Keywords: Breast cancer, Cancer recurrence, Computer-assisted diagnosis, Machine learning, Prognosis

  9. Integrating Remote Sensing Data, Hybrid-Cloud Computing, and Event Notifications for Advanced Rapid Imaging & Analysis (Invited)

    Science.gov (United States)

    Hua, H.; Owen, S. E.; Yun, S.; Lundgren, P.; Fielding, E. J.; Agram, P.; Manipon, G.; Stough, T. M.; Simons, M.; Rosen, P. A.; Wilson, B. D.; Poland, M. P.; Cervelli, P. F.; Cruz, J.

    2013-12-01

    Space-based geodetic measurement techniques such as Interferometric Synthetic Aperture Radar (InSAR) and Continuous Global Positioning System (CGPS) are now important elements in our toolset for monitoring earthquake-generating faults, volcanic eruptions, hurricane damage, landslides, reservoir subsidence, and other natural and man-made hazards. Geodetic imaging's unique ability to capture surface deformation with high spatial and temporal resolution has revolutionized both earthquake science and volcanology. Continuous monitoring of surface deformation and surface change before, during, and after natural hazards improves decision-making from better forecasts, increased situational awareness, and more informed recovery. However, analyses of InSAR and GPS data sets are currently handcrafted following events and are not generated rapidly and reliably enough for use in operational response to natural disasters. Additionally, the sheer data volumes needed to handle a continuous stream of InSAR data sets also presents a bottleneck. It has been estimated that continuous processing of InSAR coverage of California alone over 3-years would reach PB-scale data volumes. Our Advanced Rapid Imaging and Analysis for Monitoring Hazards (ARIA-MH) science data system enables both science and decision-making communities to monitor areas of interest with derived geodetic data products via seamless data preparation, processing, discovery, and access. We will present our findings on the use of hybrid-cloud computing to improve the timely processing and delivery of geodetic data products, integrating event notifications from USGS to improve the timely processing for response, as well as providing browse results for quick looks with other tools for integrative analysis.

  10. Contrasting molecular and morphological evidence for the identification of an anomalous Buteo: a cautionary tale for hybrid diagnosis

    Directory of Open Access Journals (Sweden)

    William S. Clark

    2017-01-01

    Full Text Available An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus;. It is now a specimen in the Museum of Wildlife and Fisheries Biology (WFB 4816 at the University of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus and Red-shouldered Hawk (ssp elegans, leading us to hypothesize that the bird was a hybrid. However, mtDNA sequences and nuDNA microsatellites proved definitively that the bird was a Red-shouldered Hawk, most likely of eastern origin. This case illustrates that apparent hybrids or apparent vagrants could be individuals with anomalous phenotypes caused by rare genetic variation or novel epigenetic effects.

  11. Design and construction the identification of nitriding plasma process parameters using personal computer based on serial communication

    International Nuclear Information System (INIS)

    Frida Iswinning Diah; Slamet Santosa

    2012-01-01

    Design and construction the identification of process parameters using personal computer based on serial communication PLC M-series has been done. The function of this device is to identify the process parameters of a system (plan), to which then be analyzed and conducted a follow-up given to the plan by the user. The main component of this device is the M-Series T100MD1616 PLC and personal computer (PC). In this device the data plan parameters obtained from the corresponding sensor outputs in the form of voltage or current. While the analog parameter data is adjusted to the ADC analog input of the PLC using a signal conditioning system. Then, as the parameter is processed by the PLC then sent to a PC via RS232 to be displayed in the form of graphs or tables and stored in the database. Software to program the database is created using Visual Basic Programming V-6. The device operation test is performed for the measurement of temperature parameter and vacuum level on the plasma nitriding machine. The results indicate that the device has functioning as an identification device parameters process of plasma nitriding machine. (author)

  12. Use of 99mTc-sestamibi Single-photon Emission Computed Tomography / X-ray Computed Tomography in the Diagnosis of Hybrid Oncocytic / Chromophobe Tumor in a Pediatric Patient.

    Science.gov (United States)

    Almassi, Nima; Gorin, Michael A; Purysko, Andrei S; Rowe, Steven P; Kaouk, Jihad; Allaf, Mohamad E; Campbell, Steven C; Rhee, Audrey

    2018-03-01

    The differential diagnosis of solid renal neoplasms in adolescence includes aggressive malignancy and indolent oncocytic tumors, which are typically indistinguishable using conventional imaging. We report the use of 99m Tc-sestamibi single-photon emission computed tomography / x-ray computed tomography (SPECT/CT) in characterizing enhancing renal neoplasms in a pediatric patient. Genetic testing suggested a hereditary syndrome associated with aggressive malignancy, whereas renal mass biopsy suggested an oncocytic tumor. 99m Tc-sestamibi SPECT/CT indicated probable oncocytomas or hybrid oncocytic / chomophobe tumors. Enucleative resection was performed with final pathology demonstrating hybrid oncocytic / chomophobe tumors. This case highlights the potential utility of 99m Tc-sestamibi SPECT/CT in characterizing indeterminate enhancing renal neoplasm in pediatric patients. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Identification and ranking of the risk factors of cloud computing in State-Owned organizations

    Directory of Open Access Journals (Sweden)

    Noor Mohammad Yaghoubi

    2015-05-01

    Full Text Available Rapid development of processing and storage technologies and the success of the Internet have made computing resources cheaper, more powerful and more available than before. This technological trend has enabled the realization of a new computing model called cloud computing. Recently, the State-Owned organizations have begun to utilize cloud computing architectures, platforms, and applications to deliver services and meet constituents’ needs. Despite all of the advantages and opportunities of cloud computing technology, there are so many risks that State-Owned organizations need to know about before their migration to cloud environment. The purpose of this study is to identify and rank the risks factors of cloud computing in State-Owned organizations by making use of IT experts’ opinion. Firstly, by reviewing key articles, a comprehensive list of risks factors were extracted and classified into two categories: tangible and intangible. Then, six experts were interviewed about these risks and their classifications, and 10 risks were identified. After that, process of ranking the risks was done by seeking help from 52 experts and by fuzzy analytic hierarchy process. The results show that experts have identified intangible risks as the most important risks in cloud computing usage by State-Owned organizations. As the results indicate, "data confidentiality" risk has the highest place among the other risks.

  14. Identification of unknown contaminants in surface water : combination of analytical and computer-based approaches

    OpenAIRE

    Hu, Meng

    2017-01-01

    Thousands of different chemicals are used in our daily life for household, industry, agriculture and medical purpose, and many of them are discharged into water bodies by direct or indirect ways. Thus, monitoring and identification of organic pollutants in aquatic ecosystem is one of the most essential concerns with respects to human health and aquatic life. Althrough liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) has made huge advancements in recent years, allow...

  15. Comments and Criticism: Comment on "Identification of Student Misconceptions in Genetics Problem Solving via Computer Program."

    Science.gov (United States)

    Smith, Mike U.

    1991-01-01

    Criticizes an article by Browning and Lehman (1988) for (1) using "gene" instead of allele, (2) misusing the word "misconception," and (3) the possible influences of the computer environment on the results of the study. (PR)

  16. Computer-aided modeling framework for efficient model development, analysis and identification

    DEFF Research Database (Denmark)

    Heitzig, Martina; Sin, Gürkan; Sales Cruz, Mauricio

    2011-01-01

    Model-based computer aided product-process engineering has attained increased importance in a number of industries, including pharmaceuticals, petrochemicals, fine chemicals, polymers, biotechnology, food, energy, and water. This trend is set to continue due to the substantial benefits computer-aided...... methods introduce. The key prerequisite of computer-aided product-process engineering is however the availability of models of different types, forms, and application modes. The development of the models required for the systems under investigation tends to be a challenging and time-consuming task....... The methodology has been implemented into a computer-aided modeling framework, which combines expert skills, tools, and database connections that are required for the different steps of the model development work-flow with the goal to increase the efficiency of the modeling process. The framework has two main...

  17. Structure and weights optimisation of a modified Elman network emotion classifier using hybrid computational intelligence algorithms: a comparative study

    Science.gov (United States)

    Sheikhan, Mansour; Abbasnezhad Arabi, Mahdi; Gharavian, Davood

    2015-10-01

    Artificial neural networks are efficient models in pattern recognition applications, but their performance is dependent on employing suitable structure and connection weights. This study used a hybrid method for obtaining the optimal weight set and architecture of a recurrent neural emotion classifier based on gravitational search algorithm (GSA) and its binary version (BGSA), respectively. By considering the features of speech signal that were related to prosody, voice quality, and spectrum, a rich feature set was constructed. To select more efficient features, a fast feature selection method was employed. The performance of the proposed hybrid GSA-BGSA method was compared with similar hybrid methods based on particle swarm optimisation (PSO) algorithm and its binary version, PSO and discrete firefly algorithm, and hybrid of error back-propagation and genetic algorithm that were used for optimisation. Experimental tests on Berlin emotional database demonstrated the superior performance of the proposed method using a lighter network structure.

  18. Identification of derlin-1 as a novel growth factor-responsive endothelial antigen by suppression subtractive hybridization

    International Nuclear Information System (INIS)

    Ran Yuliang; Jiang Yangfu; Zhong Xing; Zhou Zhuan; Liu Haiyan; Hu Hai; Lou Jinning; Yang Zhihua

    2006-01-01

    Endothelial cells play an important regulatory role in embryonic development, reproductive functions, tumor growth and progression. In the present study, the suppression subtractive hybridization (SSH) method was employed to identify differentially expressed genes between non-stimulated endothelial cells and activated endothelial cells. Following mRNA isolation of non-stimulated and hepatocellular carcinoma homogenate-stimulated cells, cDNAs of both populations were prepared and subtracted by suppressive PCR. Sequencing of the enriched cDNAs identified a couple of genes differentially expressed, including derlin-1. Derlin-1 was significantly up-regulated by tumor homogenates, VEGF, and endothelial growth supplements in a dose-dependent manner. Knock-down of derlin-1 triggered endothelial cell apoptosis, inhibited endothelial cell proliferation, and blocked the formation of a network of tubular-like structures. Our data reveal that derlin-1 is a novel growth factor-responsive endothelial antigen that promotes endothelial cell survival and growth

  19. Implementation of a cell-wise block-Gauss-Seidel iterative method for SN transport on a hybrid parallel computer architecture

    International Nuclear Information System (INIS)

    Rosa, Massimiliano; Warsa, James S.; Perks, Michael

    2011-01-01

    We have implemented a cell-wise, block-Gauss-Seidel (bGS) iterative algorithm, for the solution of the S_n transport equations on the Roadrunner hybrid, parallel computer architecture. A compute node of this massively parallel machine comprises AMD Opteron cores that are linked to a Cell Broadband Engine™ (Cell/B.E.)"1. LAPACK routines have been ported to the Cell/B.E. in order to make use of its parallel Synergistic Processing Elements (SPEs). The bGS algorithm is based on the LU factorization and solution of a linear system that couples the fluxes for all S_n angles and energy groups on a mesh cell. For every cell of a mesh that has been parallel decomposed on the higher-level Opteron processors, a linear system is transferred to the Cell/B.E. and the parallel LAPACK routines are used to compute a solution, which is then transferred back to the Opteron, where the rest of the computations for the S_n transport problem take place. Compared to standard parallel machines, a hundred-fold speedup of the bGS was observed on the hybrid Roadrunner architecture. Numerical experiments with strong and weak parallel scaling demonstrate the bGS method is viable and compares favorably to full parallel sweeps (FPS) on two-dimensional, unstructured meshes when it is applied to optically thick, multi-material problems. As expected, however, it is not as efficient as FPS in optically thin problems. (author)

  20. Identification of strain fields in pure Al and hybrid Ni/Al metal foams using X-ray micro-tomography under loading

    International Nuclear Information System (INIS)

    Fíla, T.; Jiroušek, O.; Jung, A.; Kumpová, I.

    2016-01-01

    Hybrid foams are materials formed by a core from a standard open cell metal foam that is during the process of electrodeposition coated by a thin layer of different nanocrystalline metals. The material properties of the base metal foam are in this way modified resulting in higher plateau stress and, more importantly, by introduction of strain-rate dependence to its deformation response. In this paper, we used time-lapse X-ray micro-tomography for the mechanical characterization of Ni/Al hybrid foams (aluminium open cell foams with nickel coating layer). To fully understand the effects of the coating layer on the material's effective properties, we compared the compressive response of the base uncoated foam to the response of the material with coating thickness of 50 and 75 μm. Digital volume correlation (DVC) was applied to obtain volumetric strain fields of the deforming micro-structure up to the densification region of the deforming cellular structure. The analysis was performed as a compressive mechanical test with simultaneous observation using X-ray radiography and tomography. A custom design experimental device was used for compression of the foam specimens in several deformation states directly in the X-ray setup. Planar X-ray images were taken during the loading phases and a X-ray tomography was performed at the end of each loading phase (up to engineering strain 22%). The samples were irradiated using micro-focus reflection type X-ray tube and images were taken using a large area flat panel detector. Tomography reconstructions were used for an identification of a strain distribution in the foam using digital volumetric correlation. A comparison of the deformation response of the coated and the uncoated foam in uniaxial quasi-static compression is summarized in the paper.

  1. The utility of including pathology reports in improving the computational identification of patients

    Directory of Open Access Journals (Sweden)

    Wei Chen

    2016-01-01

    Full Text Available Background: Celiac disease (CD is a common autoimmune disorder. Efficient identification of patients may improve chronic management of the disease. Prior studies have shown searching International Classification of Diseases-9 (ICD-9 codes alone is inaccurate for identifying patients with CD. In this study, we developed automated classification algorithms leveraging pathology reports and other clinical data in Electronic Health Records (EHRs to refine the subset population preselected using ICD-9 code (579.0. Materials and Methods: EHRs were searched for established ICD-9 code (579.0 suggesting CD, based on which an initial identification of cases was obtained. In addition, laboratory results for tissue transglutaminse were extracted. Using natural language processing we analyzed pathology reports from upper endoscopy. Twelve machine learning classifiers using different combinations of variables related to ICD-9 CD status, laboratory result status, and pathology reports were experimented to find the best possible CD classifier. Ten-fold cross-validation was used to assess the results. Results: A total of 1498 patient records were used including 363 confirmed cases and 1135 false positive cases that served as controls. Logistic model based on both clinical and pathology report features produced the best results: Kappa of 0.78, F1 of 0.92, and area under the curve (AUC of 0.94, whereas in contrast using ICD-9 only generated poor results: Kappa of 0.28, F1 of 0.75, and AUC of 0.63. Conclusion: Our automated classification system presented an efficient and reliable way to improve the performance of CD patient identification.

  2. Construction, implementation and testing of an image identification system using computer vision methods for fruit flies with economic importance (Diptera: Tephritidae).

    Science.gov (United States)

    Wang, Jiang-Ning; Chen, Xiao-Lin; Hou, Xin-Wen; Zhou, Li-Bing; Zhu, Chao-Dong; Ji, Li-Qiang

    2017-07-01

    Many species of Tephritidae are damaging to fruit, which might negatively impact international fruit trade. Automatic or semi-automatic identification of fruit flies are greatly needed for diagnosing causes of damage and quarantine protocols for economically relevant insects. A fruit fly image identification system named AFIS1.0 has been developed using 74 species belonging to six genera, which include the majority of pests in the Tephritidae. The system combines automated image identification and manual verification, balancing operability and accuracy. AFIS1.0 integrates image analysis and expert system into a content-based image retrieval framework. In the the automatic identification module, AFIS1.0 gives candidate identification results. Afterwards users can do manual selection based on comparing unidentified images with a subset of images corresponding to the automatic identification result. The system uses Gabor surface features in automated identification and yielded an overall classification success rate of 87% to the species level by Independent Multi-part Image Automatic Identification Test. The system is useful for users with or without specific expertise on Tephritidae in the task of rapid and effective identification of fruit flies. It makes the application of computer vision technology to fruit fly recognition much closer to production level. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  3. Course on hybrid calculation

    International Nuclear Information System (INIS)

    Weill, J.; Tellier; Bonnemay; Craigne; Chareton; Di Falco

    1969-02-01

    After a definition of hybrid calculation (combination of analogue and digital calculation) with a distinction between series and parallel hybrid computing, and a description of a hybrid computer structure and of task sharing between computers, this course proposes a description of hybrid hardware used in Saclay and Cadarache computing centres, and of operations performed by these systems. The next part addresses issues related to programming languages and software. The fourth part describes how a problem is organised for its processing on these computers. Methods of hybrid analysis are then addressed: resolution of optimisation problems, of partial differential equations, and of integral equations by means of different methods (gradient, maximum principle, characteristics, functional approximation, time slicing, Monte Carlo, Neumann iteration, Fischer iteration)

  4. A hybrid LIBS-Raman system combined with chemometrics: an efficient tool for plastic identification and sorting.

    Science.gov (United States)

    Shameem, K M Muhammed; Choudhari, Khoobaram S; Bankapur, Aseefhali; Kulkarni, Suresh D; Unnikrishnan, V K; George, Sajan D; Kartha, V B; Santhosh, C

    2017-05-01

    Classification of plastics is of great importance in the recycling industry as the littering of plastic wastes increases day by day as a result of its extensive use. In this paper, we demonstrate the efficacy of a combined laser-induced breakdown spectroscopy (LIBS)-Raman system for the rapid identification and classification of post-consumer plastics. The atomic information and molecular information of polyethylene terephthalate, polyethylene, polypropylene, and polystyrene were studied using plasma emission spectra and scattered signal obtained in the LIBS and Raman technique, respectively. The collected spectral features of the samples were analyzed using statistical tools (principal component analysis, Mahalanobis distance) to categorize the plastics. The analyses of the data clearly show that elemental information and molecular information obtained from these techniques are efficient for classification of plastics. In addition, the molecular information collected via Raman spectroscopy exhibits clearly distinct features for the transparent plastics (100% discrimination), whereas the LIBS technique shows better spectral feature differences for the colored samples. The study shows that the information obtained from these complementary techniques allows the complete classification of the plastic samples, irrespective of the color or additives. This work further throws some light on the fact that the potential limitations of any of these techniques for sample identification can be overcome by the complementarity of these two techniques. Graphical Abstract ᅟ.

  5. Modal–Physical Hybrid System Identification of High-rise Building via Subspace and Inverse-Mode Methods

    Directory of Open Access Journals (Sweden)

    Kohei Fujita

    2017-08-01

    Full Text Available A system identification (SI problem of high-rise buildings is investigated under restricted data environments. The shear and bending stiffnesses of a shear-bending model (SB model representing the high-rise buildings are identified via the smart combination of the subspace and inverse-mode methods. Since the shear and bending stiffnesses of the SB model can be identified in the inverse-mode method by using the lowest mode of horizontal displacements and floor rotation angles, the lowest mode of the objective building is identified first by using the subspace method. Identification of the lowest mode is performed by using the amplitude of transfer functions derived in the subspace method. Considering the resolution in measuring the floor rotation angles in lower stories, floor rotation angles in most stories are predicted from the floor rotation angle at the top floor. An empirical equation of floor rotation angles is proposed by investigating those for various building models. From the viewpoint of application of the present SI method to practical situations, a non-simultaneous measurement system is also proposed. In order to investigate the reliability and accuracy of the proposed SI method, a 10-story building frame subjected to micro-tremor is examined.

  6. The program system for the automatic graphical representation, on the Calcomp recorder, of the results of numerical or hybrid simulations on the E.A.I. 8900 Computer

    International Nuclear Information System (INIS)

    Neel, Daniele

    1970-01-01

    This report was the first subject of a thesis submitted by Madame Daniele NEEL, on the 25 of May 1970, to the Faculte des Sciences in Paris in order to obtain the grade of doctor engineer. The differential equations, treated by hybrid calculations, were solved continuously by the analog machine; at the same time the digital computer sampled the results at different times. The program system was divided Into two parts. A card index system was developed progressively from the results (even if they were in real time); the results were displayed graphically directly on an oscilloscope screen with a memory as a curve or a series of curves or, by a delayed system using a digital tracer. The graphs obtained were ready to be inserted in a report and contained all the relevant information. The second subject 'The hybrid calculation - Generalities and Bibliography' was covered by a note CEA-N-1345. (author) [fr

  7. TPASS: a gamma-ray spectrum analysis and isotope identification computer code

    International Nuclear Information System (INIS)

    Dickens, J.K.

    1981-03-01

    The gamma-ray spectral data-reduction and analysis computer code TPASS is described. This computer code is used to analyze complex Ge(Li) gamma-ray spectra to obtain peak areas corrected for detector efficiencies, from which are determined gamma-ray yields. These yields are compared with an isotope gamma-ray data file to determine the contributions to the observed spectrum from decay of specific radionuclides. A complete FORTRAN listing of the code and a complex test case are given

  8. Identification of Streptococcus agalactiae by fluorescent in situ hybridization compared to culturing and the determination of prevalence of Streptococcus agalactiae colonization among pregnant women in Bushehr, Iran.

    Science.gov (United States)

    Tajbakhsh, Saeed; Norouzi Esfahani, Marjan; Emaneini, Mohammad; Motamed, Niloofar; Rahmani, Elham; Gharibi, Somayyeh

    2013-09-08

    Pregnant women colonized by Streptococcus agalactiae (group B streptococci [GBS]) may transfer this microorganism to their newborns. S. agalactiae is an important cause of pneumonia, sepsis, and meningitis in newborns. Fluorescent in situ hybridization (FISH) is considered as a method of identification in the field of diagnostic microbiology. In this paper, we have designed a study to compare the DNA FISH after 7 h Lim broth enrichment and culturing for the identification of S. agalactiae and to determine the prevalence of vaginal colonization by S. agalactiae among pregnant women in Bushehr, Iran. Vaginal swab specimens were obtained from 285 pregnant women at 35 weeks or more than 35 weeks of gestation. The specimens were inoculated into Lim broth. In order to evaluate the sensitivity and specificity of GBS DNA FISH after 7 h Lim broth enrichment, the specimens were tested using both FISH and conventional culture methods. In addition, the prevalence of GBS colonization was determined. Based on the results of this study, both the sensitivity and specificity of FISH were 100%. S. agalactiae was detected by both culture and FISH in 27 of the 285 pregnant women. Thus, the prevalence of GBS colonization was 9.5%. Since short-term (7 h) Lim broth enrichment followed by FISH using oligonucleotide probes showed a high sensitivity and specificity, this protocol is therefore a highly accurate and relatively rapid method for the detection of S. agalactiae. Our analysis suggests that the use of DNA FISH to screen for S. agalactiae colonization in pregnant women may be considered in the absence of GBS culture availability.

  9. Evaluation of the UF/NCI hybrid computational phantoms for use in organ dosimetry of pediatric patients undergoing fluoroscopically guided cardiac procedures

    Science.gov (United States)

    Marshall, Emily L.; Borrego, David; Tran, Trung; Fudge, James C.; Bolch, Wesley E.

    2018-03-01

    Epidemiologic data demonstrate that pediatric patients face a higher relative risk of radiation induced cancers than their adult counterparts at equivalent exposures. Infants and children with congenital heart defects are a critical patient population exposed to ionizing radiation during life-saving procedures. These patients will likely incur numerous procedures throughout their lifespan, each time increasing their cumulative radiation absorbed dose. As continued improvements in long-term prognosis of congenital heart defect patients is achieved, a better understanding of organ radiation dose following treatment becomes increasingly vital. Dosimetry of these patients can be accomplished using Monte Carlo radiation transport simulations, coupled with modern anatomical patient models. The aim of this study was to evaluate the performance of the University of Florida/National Cancer Institute (UF/NCI) pediatric hybrid computational phantom library for organ dose assessment of patients that have undergone fluoroscopically guided cardiac catheterizations. In this study, two types of simulations were modeled. A dose assessment was performed on 29 patient-specific voxel phantoms (taken as representing the patient’s true anatomy), height/weight-matched hybrid library phantoms, and age-matched reference phantoms. Two exposure studies were conducted for each phantom type. First, a parametric study was constructed by the attending pediatric interventional cardiologist at the University of Florida to model the range of parameters seen clinically. Second, four clinical cardiac procedures were simulated based upon internal logfiles captured by a Toshiba Infinix-i Cardiac Bi-Plane fluoroscopic unit. Performance of the phantom library was quantified by computing both the percent difference in individual organ doses, as well as the organ dose root mean square values for overall phantom assessment between the matched phantoms (UF/NCI library or reference) and the patient

  10. Identification of Requirements for Computer-Supported Matching of Food Consumption Data with Food Composition Data.

    NARCIS (Netherlands)

    Koroušić Seljak, Barbara; Korošec, Peter; Eftimov, Tome; Ocke, Marga; van der Laan, Jan; Roe, Mark; Berry, Rachel; Crispim, Sandra Patricia; Turrini, Aida; Krems, Carolin; Slimani, Nadia; Finglas, Paul

    2018-01-01

    This paper identifies the requirements for computer-supported food matching, in order to address not only national and European but also international current related needs and represents an integrated research contribution of the FP7 EuroDISH project. The available classification and coding systems

  11. A computer-aided framework for development, identification andmanagement of physiologically-based pharmacokinetic models

    DEFF Research Database (Denmark)

    Heitzig, Martina; Linninger, Andreas; Sin, Gürkan

    2014-01-01

    The objective of this work is the development of a generic computer-aided modelling framework to support the development of physiologically-based pharmacokinetic models thereby increasing the efficiency and quality of the modelling process. In particular, the framework systematizes the modelling...

  12. Identification of waves by RF magnetic probes during lower hybrid wave injection experiments on the TST-2 spherical tokamak

    International Nuclear Information System (INIS)

    Shinya, Takahiro; Ejiri, Akira; Takase, Yuichi

    2014-01-01

    RF magnetic probes can be used to measure not only the wavevector, but also the polarization of waves in plasmas. A 5-channel RF magnetic probe (5ch-RFMP) was installed in the TST-2 spherical tokamak and the waves were studied in detail during lower hybrid wave injection experiments. From the polarization measurements, the poloidal RF magnetic field is found to be dominant. In addition to polarization, components of k perpendicular to the major radial direction were obtained from phase differences among the five channels. The radial wavenumber was obtained by scanning the radial position of the 5ch-RFMP on a shot by shot basis. The measured wavevector and polarization in the plasma edge region were consistent with those calculated from the wave equation for the slow wave branch. While the waves with small and large k ∥ were excited by the antenna, only the small k ∥ component was measured by the 5ch-RFMP; this suggests that the waves with larger k ∥ were absorbed by the plasma. (author)

  13. Identification of immune response-related genes in the Chinese oak silkworm, Antheraea pernyi by suppression subtractive hybridization.

    Science.gov (United States)

    Liu, Qiu-Ning; Zhu, Bao-Jian; Wang, Lei; Wei, Guo-Qing; Dai, Li-Shang; Lin, Kun-Zhang; Sun, Yu; Qiu, Jian-Feng; Fu, Wei-Wei; Liu, Chao-Liang

    2013-11-01

    Insects possess an innate immune system that responds to invading microorganisms. In this study, a subtractive cDNA library was constructed to screen for immune response-related genes in the fat bodies of Antheraea pernyi (Lepidoptera: Saturniidae) pupa challenged with Escherichia coli. Four hundred putative EST clones were identified by suppression subtractive hybridization (SSH), including 50 immune response-related genes, three cytoskeleton genes, eight cell cycle and apoptosis genes, five respiration and energy metabolism genes, five transport genes, 40 metabolism genes, ten stress response genes, four transcription and translation regulation genes and 77 unknown genes. To verify the reliability of the SSH data, the transcription of a set of randomly selected immune response-related genes were confirmed by semi-quantitative reverse transcription-PCR (RT-PCR) and real-time quantitative reverse transcription-PCR (qRT-PCR). These identified immune response-related genes provide insight into understanding the innate immunity in A. pernyi. Copyright © 2013 Elsevier Inc. All rights reserved.

  14. Identification of differential gene expression in in vitro FSH treated pig granulosa cells using suppression subtractive hybridization

    Directory of Open Access Journals (Sweden)

    Tosser-Klopp G

    2006-07-01

    Full Text Available Abstract FSH, which binds to specific receptors on granulosa cells in mammals, plays a key role in folliculogenesis. Its biological activity involves stimulation of intercellular communication and upregulation of steroidogenesis, but the entire spectrum of the genes regulated by FSH has yet to be fully characterized. In order to find new regulated transcripts, however rare, we have used a Suppression Subtractive Hybridization approach (SSH on pig granulosa cells in primary culture treated or not with FSH. Two SSH libraries were generated and 76 clones were sequenced after selection by differential screening. Sixty four different sequences were identified, including 3 novel sequences. Experiments demonstrated the presence of 25 regulated transcripts. A gene ontology analysis of these 25 genes revealed (1 catalytic; (2 transport; (3 signal transducer; (4 binding; (5 anti-oxidant and (6 structural activities. These findings may deepen our understanding of FSH's effects. Particularly, they suggest that FSH is involved in the modulation of peroxidase activity and remodelling of chromatin.

  15. Identification and Cloning of Differentially Expressed SOUL and ELIP Genes in Saffron Stigmas Using a Subtractive Hybridization Approach.

    Directory of Open Access Journals (Sweden)

    Oussama Ahrazem

    Full Text Available Using a subtractive hybridization approach, differentially expressed genes involved in the light response in saffron stigmas were identified. Twenty-two differentially expressed transcript-derived fragments were cloned and sequenced. Two of them were highly induced by light and had sequence similarity to early inducible proteins (ELIP and SOUL heme-binding proteins. Using these sequences, we searched for other family members expressed in saffron stigma. ELIP and SOUL are represented by small gene families in saffron, with four and five members, respectively. The expression of these genes was analyzed during the development of the stigma and in light and dark conditions. ELIP transcripts were detected in all the developmental stages showing much higher expression levels in the developed stigmas of saffron and all were up-regulated by light but at different levels. By contrast, only one SOUL gene was up-regulated by light and was highly expressed in the stigma at anthesis. Both the ELIP and SOUL genes induced by light in saffron stigmas might be associated with the structural changes affecting the chromoplast of the stigma, as a result of light exposure, which promotes the development and increases the number of plastoglobules, specialized in the recruitment of specific proteins, which enables them to act in metabolite synthesis and disposal under changing environmental conditions and developmental stages.

  16. Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana).

    Science.gov (United States)

    Usha, S; Jyothi, M N; Suchithra, B; Dixit, Rekha; Rai, D V; Nagesh Babu, R

    2017-03-01

    MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.

  17. Modeling and identification of ARMG models for stochastic processes: application to on-line computation of the power spectral density

    International Nuclear Information System (INIS)

    Zwingelstein, Gilles; Thabet, Gabriel.

    1977-01-01

    Control algorithms for components of nuclear power plants are currently based on external diagnostic methods. Modeling and identification techniques for autoregressive moving average models (ARMA) for stochastic processes are described. The identified models provide a means of estimating the power spectral density with improved accuracy and computer time compared with the classical methods. They are particularly will suited for on-line estimation of the power spectral density. The observable stochastic process y (t) is modeled assuming that it is the output of a linear filter driven by Gaussian while noise w (t). Two identification schemes were tested to find the orders m and n of the ARMA (m,n) models and to estimate the parameters of the recursion equation relating the input and output signals. The first scheme consists in transforming the ARMA model to an autoregressive model. The parameters of this AR model are obtained using least squares estimation techniques. The second scheme consists in finding the parameters of the ARMA by nonlinear programming techniques. The power spectral density of y(t) is instantaneously deduced from these ARMA models [fr

  18. Comparison between ultrasound and noncontrast helical computed tomography for identification of acute ureterolithiasis in a teaching hospital setting

    Directory of Open Access Journals (Sweden)

    Luís Ronan Marquez Ferreira de Souza

    2007-03-01

    Full Text Available CONTEXT AND OBJECTIVE: Recent studies have shown noncontrast computed tomography (NCT to be more effective than ultrasound (US for imaging acute ureterolithiasis. However, to our knowledge, there are few studies directly comparing these techniques in an emergency teaching hospital setting. The objectives of this study were to compare the diagnostic accuracy of US and NCT performed by senior radiology residents for diagnosing acute ureterolithiasis; and to assess interobserver agreement on tomography interpretations by residents and experienced abdominal radiologists. DESIGN AND SETTING: Prospective study of 52 consecutive patients, who underwent both US and NCT within an interval of eight hours, at Hospital São Paulo. METHODS: US scans were performed by senior residents and read by experienced radiologists. NCT scan images were read by senior residents, and subsequently by three abdominal radiologists. The interobserver variability was assessed using the kappa statistic. RESULTS: Ureteral calculi were found in 40 out of 52 patients (77%. US presented sensitivity of 22% and specificity of 100%. When collecting system dilatation was associated, US demonstrated 73% sensitivity, 82% specificity. The interobserver agreement in NCT analysis was very high with regard to identification of calculi, collecting system dilatation and stranding of perinephric fat. CONCLUSIONS: US has limited value for identifying ureteral calculi in comparison with NCT, even when collecting system dilatation is present. Residents and abdominal radiologists demonstrated excellent agreement rates for ureteral calculi, identification of collecting system dilatation and stranding of perinephric fat on NCT.

  19. Image Guided Virtual Autopsy: An Adjunct with Radiographic and Computed Tomography Modalities - An Important Tool in Forensic Identification

    Directory of Open Access Journals (Sweden)

    Shalu Rai

    2017-01-01

    Full Text Available The forensic examination of dead bodies is very helpful in order to identify the person, cause of death, gender, and solving the mysterious cases. It includes a number of techniques, out of which autopsy is the primary investigation that is performed in every medicolegal case. Because of mutilation technologies, traditional autopsy technique is most disturbing in terms of emotions and rituals of relatives. The use of radiology in forensic science comprises performance, interpretation, and reporting of radiographs that is helpful in detecting those changes that are not clinically visible. Forensic radiology plays an important role for identification of humans in mass disasters, criminal investigations, and evaluation of cause of death. The introduction of radiological modalities in autopsy techniques is a complementary tool for forensic identification and is known as virtual autopsy. The advance imaging techniques such as computed tomography (CT and magnetic resonance imaging (MRI is used in virtual autopsy in order to visualize and reconstruct the internal organs to know the site, type, and depth of injury. This review elaborates the role of maxillofacial imaging in image-guided virtual autopsy.

  20. An eye movement study for identification of suitable font characters for presentation on a computer screen.

    Science.gov (United States)

    Banerjee, Jayeeta; Majumdar, Dhurjati; Majumdar, Deepti; Pal, Madhu Sudan

    2010-06-01

    We are experiencing a shifting of media: from the printed paper to the computer screen. This transition is modifying the process of how we read and understand a text. It is very difficult to conclude on suitability of font characters based upon subjective evaluation method only. Present study evaluates the effect of font type on human cognitive workload during perception of individual alphabets on a computer screen. Twenty six young subjects volunteered for this study. Here, subjects have been shown individual characters of different font types and their eye movements have been recorded. A binocular eye movement recorder was used for eye movement recording. The results showed that different eye movement parameters such as pupil diameter, number of fixations, fixation duration were less for font type Verdana. The present study recommends the use of font type Verdana for presentation of individual alphabets on various electronic displays in order to reduce cognitive workload.

  1. Identification of a unique cause of ring artifact seen in computed tomography trans-axial images

    International Nuclear Information System (INIS)

    Jha, Ashish Kumar; Purandare, Nilendu C; Shah, Sneha; Agrawal, Archi; Puranik, Ameya D; Rangarajan, Venkatesh

    2013-01-01

    Artifacts present in computed tomography (CT) image often degrade the image quality and ultimately, the diagnostic outcome. Ring artifact in trans-axial image is caused by either miscalibrated or defective detector element of detector row, which is often categorized as scanner based artifact. A ring artifact detected on trans-axial CT image of positron emission tomography/computed tomography (PET/CT), was caused by contamination of CT tube aperture by droplet of injectable contrast medium. This artifact was corrected by removal of contrast droplet from CT tube aperture. The ring artifact is a very common artifact, commonly cited in the literature. Our case puts forward an uncommon cause of this artifact and its method of correction, which also, has no mention in the existing literature

  2. Identification and analysis of unsatisfactory psychosocial work situations: a participatory approach employing video-computer interaction.

    Science.gov (United States)

    Hanse, J J; Forsman, M

    2001-02-01

    A method for psychosocial evaluation of potentially stressful or unsatisfactory situations in manual work was developed. It focuses on subjective responses regarding specific situations and is based on interactive worker assessment when viewing video recordings of oneself. The worker is first video-recorded during work. The video is then displayed on the computer terminal, and the filmed worker clicks on virtual controls on the screen whenever an unsatisfactory psychosocial situation appears; a window of questions regarding psychological demands, mental strain and job control is then opened. A library with pictorial information and comments on the selected situations is formed in the computer. The evaluation system, called PSIDAR, was applied in two case studies, one of manual materials handling in an automotive workshop and one of a group of workers producing and testing instrument panels. The findings indicate that PSIDAR can provide data that are useful in a participatory ergonomic process of change.

  3. Identification of an Adaptable Computer Program Design for Analyzing a Modular Organizational Assessment Instrument.

    Science.gov (United States)

    1981-09-01

    ber) Survey-guided development Organizational effectiveness Computer program Organizational diagnosis Management 20. ABSTRACT (Continue an reverse...Army. Doctoral dissertation, Purdue University, December 1977. (DTIC AD-A059-542) Bowers, D. G. Organizational diagnosis : A review and a proposed method...G. E. Compara- tive issues and methods in organizational diagnosis . Ann Arbor MI: Institute for Social Research, University of Michigan, November 1977

  4. Identification of Fetal Inflammatory Cells in Eosinophilic/T-cell Chorionic Vasculitis Using Fluorescent In Situ Hybridization.

    Science.gov (United States)

    Katzman, Philip J; Li, LiQiong; Wang, Nancy

    2015-01-01

    Eosinophilic/T-cell chorionic vasculitis (ETCV) is an inflammatory lesion of placental fetal vessels. In contrast to acute chorionic vasculitis, inflammation in ETCV is seen in chorionic vessel walls opposite the amnionic surface. It is not known whether inflammation in ETCV consists of maternal cells from the intervillous space or fetal cells migrating from the vessel. We used fluorescent in situ hybridization (FISH) to differentiate fetal versus maternal cells in ETCV. Placentas with ETCV, previously identified for a published study, were used. Infant sex in each case was identified using the electronic medical record. For male infants, 3-μm sections were cut from archived tissue blocks from placentas involving ETCV and stained with fluorescent X- and Y-chromosome centromeric probes. A consecutive hematoxylin/eosin-stained section was used for correlation. FISH analysis was performed on 400 interphase nuclei at the site of ETCV to determine the proportion of XX, XY, X, and Y cells. Of 31 ETCV cases, 20 were female and 10 were male (1 sex not recorded). Six of 10 cases with male infants had recuts with visible ETCV. In these 6 cases the average percentages (ranges) of XY cells, X-only cells, and Y-only cells in the region of inflammation were 81 (70-90), 11 (6-17), and 8 (2-14), respectively. There was a 2:1 female:male infant ratio in ETCV. Similar to acute chorionic vasculitis, the inflammation in ETCV is of fetal origin. It is still unknown, however, whether the stimulus for ETCV is of fetal or maternal origin.

  5. Identification of differentially expressed genes in SHSY5Y cells exposed to okadaic acid by suppression subtractive hybridization

    Directory of Open Access Journals (Sweden)

    Valdiglesias Vanessa

    2012-01-01

    Full Text Available Abstract Background Okadaic acid (OA, a toxin produced by several dinoflagellate species is responsible for frequent food poisonings associated to shellfish consumption. Although several studies have documented the OA effects on different processes such as cell transformation, apoptosis, DNA repair or embryogenesis, the molecular mechanistic basis for these and other effects is not completely understood and the number of controversial data on OA is increasing in the literature. Results In this study, we used suppression subtractive hybridization in SHSY5Y cells to identify genes that are differentially expressed after OA exposure for different times (3, 24 and 48 h. A total of 247 subtracted clones which shared high homology with known genes were isolated. Among these, 5 specific genes associated with cytoskeleton and neurotransmission processes (NEFM, TUBB, SEPT7, SYT4 and NPY were selected to confirm their expression levels by real-time PCR. Significant down-regulation of these genes was obtained at the short term (3 and 24 h OA exposure, excepting for NEFM, but their expression was similar to the controls at 48 h. Conclusions From all the obtained genes, 114 genes were up-regulated and 133 were down-regulated. Based on the NCBI GenBank and Gene Ontology databases, most of these genes are involved in relevant cell functions such as metabolism, transport, translation, signal transduction and cell cycle. After quantitative PCR analysis, the observed underexpression of the selected genes could underlie the previously reported OA-induced cytoskeleton disruption, neurotransmission alterations and in vivo neurotoxic effects. The basal expression levels obtained at 48 h suggested that surviving cells were able to recover from OA-caused gene expression alterations.

  6. Technology for Large-Scale Translation of Clinical Practice Guidelines: A Pilot Study of the Performance of a Hybrid Human and Computer-Assisted Approach.

    Science.gov (United States)

    Van de Velde, Stijn; Macken, Lieve; Vanneste, Koen; Goossens, Martine; Vanschoenbeek, Jan; Aertgeerts, Bert; Vanopstal, Klaar; Vander Stichele, Robert; Buysschaert, Joost

    2015-10-09

    The construction of EBMPracticeNet, a national electronic point-of-care information platform in Belgium, began in 2011 to optimize quality of care by promoting evidence-based decision making. The project involved, among other tasks, the translation of 940 EBM Guidelines of Duodecim Medical Publications from English into Dutch and French. Considering the scale of the translation process, it was decided to make use of computer-aided translation performed by certificated translators with limited expertise in medical translation. Our consortium used a hybrid approach, involving a human translator supported by a translation memory (using SDL Trados Studio), terminology recognition (using SDL MultiTerm terminology databases) from medical terminology databases, and support from online machine translation. This resulted in a validated translation memory, which is now in use for the translation of new and updated guidelines. The objective of this experiment was to evaluate the performance of the hybrid human and computer-assisted approach in comparison with translation unsupported by translation memory and terminology recognition. A comparison was also made with the translation efficiency of an expert medical translator. We conducted a pilot study in which two sets of 30 new and 30 updated guidelines were randomized to one of three groups. Comparable guidelines were translated (1) by certificated junior translators without medical specialization using the hybrid method, (2) by an experienced medical translator without this support, and (3) by the same junior translators without the support of the validated translation memory. A medical proofreader who was blinded for the translation procedure, evaluated the translated guidelines for acceptability and adequacy. Translation speed was measured by recording translation and post-editing time. The human translation edit rate was calculated as a metric to evaluate the quality of the translation. A further evaluation was made of

  7. In silico fragmentation for computer assisted identification of metabolite mass spectra

    Directory of Open Access Journals (Sweden)

    Müller-Hannemann Matthias

    2010-03-01

    Full Text Available Abstract Background Mass spectrometry has become the analytical method of choice in metabolomics research. The identification of unknown compounds is the main bottleneck. In addition to the precursor mass, tandem MS spectra carry informative fragment peaks, but the coverage of spectral libraries of measured reference compounds are far from covering the complete chemical space. Compound libraries such as PubChem or KEGG describe a larger number of compounds, which can be used to compare their in silico fragmentation with spectra of unknown metabolites. Results We created the MetFrag suite to obtain a candidate list from compound libraries based on the precursor mass, subsequently ranked by the agreement between measured and in silico fragments. In the evaluation MetFrag was able to rank most of the correct compounds within the top 3 candidates returned by an exact mass query in KEGG. Compared to a previously published study, MetFrag obtained better results than the commercial MassFrontier software. Especially for large compound libraries, the candidates with a good score show a high structural similarity or just different stereochemistry, a subsequent clustering based on chemical distances reduces this redundancy. The in silico fragmentation requires less than a second to process a molecule, and MetFrag performs a search in KEGG or PubChem on average within 30 to 300 seconds, respectively, on an average desktop PC. Conclusions We presented a method that is able to identify small molecules from tandem MS measurements, even without spectral reference data or a large set of fragmentation rules. With today's massive general purpose compound libraries we obtain dozens of very similar candidates, which still allows a confident estimate of the correct compound class. Our tool MetFrag improves the identification of unknown substances from tandem MS spectra and delivers better results than comparable commercial software. MetFrag is available through a web

  8. Pulmonary Nodule Volumetry at Different Low Computed Tomography Radiation Dose Levels With Hybrid and Model-Based Iterative Reconstruction: A Within Patient Analysis.

    Science.gov (United States)

    den Harder, Annemarie M; Willemink, Martin J; van Hamersvelt, Robbert W; Vonken, Evertjan P A; Schilham, Arnold M R; Lammers, Jan-Willem J; Luijk, Bart; Budde, Ricardo P J; Leiner, Tim; de Jong, Pim A

    2016-01-01

    The aim of the study was to determine the effects of dose reduction and iterative reconstruction (IR) on pulmonary nodule volumetry. In this prospective study, 25 patients scheduled for follow-up of pulmonary nodules were included. Computed tomography acquisitions were acquired at 4 dose levels with a median of 2.1, 1.2, 0.8, and 0.6 mSv. Data were reconstructed with filtered back projection (FBP), hybrid IR, and model-based IR. Volumetry was performed using semiautomatic software. At the highest dose level, more than 91% (34/37) of the nodules could be segmented, and at the lowest dose level, this was more than 83%. Thirty-three nodules were included for further analysis. Filtered back projection and hybrid IR did not lead to significant differences, whereas model-based IR resulted in lower volume measurements with a maximum difference of -11% compared with FBP at routine dose. Pulmonary nodule volumetry can be accurately performed at a submillisievert dose with both FBP and hybrid IR.

  9. Hybrid MPI/OpenMP parallelization of the explicit Volterra integral equation solver for multi-core computer architectures

    KAUST Repository

    Al Jarro, Ahmed; Bagci, Hakan

    2011-01-01

    A hybrid MPI/OpenMP scheme for efficiently parallelizing the explicit marching-on-in-time (MOT)-based solution of the time-domain volume (Volterra) integral equation (TD-VIE) is presented. The proposed scheme equally distributes tested field values

  10. Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation.

    Science.gov (United States)

    Mourad, Raphaël; Cuvier, Olivier

    2016-05-01

    Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1.

  11. Cutting edge: identification of novel T cell epitopes in Lol p5a by computational prediction.

    Science.gov (United States)

    de Lalla, C; Sturniolo, T; Abbruzzese, L; Hammer, J; Sidoli, A; Sinigaglia, F; Panina-Bordignon, P

    1999-08-15

    Although atopic allergy affects Lol p5a allergen from rye grass. In vitro binding studies confirmed the promiscuous binding characteristics of these peptides. Moreover, most of the predicted ligands were novel T cell epitopes that were able to stimulate T cells from atopic patients. We generated a panel of Lol p5a-specific T cell clones, the majority of which recognized the peptides in a cross-reactive fashion. The computational prediction of DR ligands might thus allow the design of T cell epitopes with potential useful application in novel immunotherapy strategies.

  12. Identification of potential regional sources of atmospheric total gaseous mercury in Windsor, Ontario, Canada using hybrid receptor modeling

    Directory of Open Access Journals (Sweden)

    X. Xu

    2010-08-01

    Full Text Available Windsor (Ontario, Canada experiences trans-boundary air pollution as it is located on the border immediately downwind of industrialized regions of the United States of America. A study was conducted in 2007 to identify the potential regional sources of total gaseous mercury (TGM and investigate the effects of regional sources and other factors on seasonal variability of TGM concentrations in Windsor.

    TGM concentration was measured at the University of Windsor campus using a Tekran® 2537A Hg vapour analyzer. An annual mean of 2.02±1.63 ng/m3 was observed in 2007. The average TGM concentration was high in the summer (2.48±2.68 ng/m3 and winter (2.17±2.01 ng/m3, compared to spring (1.88±0.78 ng/m3 and fall (1.76±0.58 ng/m3. Hybrid receptor modeling potential source contribution function (PSCF was used by incorporating 72-h backward trajectories and measurements of TGM in Windsor. The results of PSCF were analyzed in conjunction with the Hg emissions inventory of North America (by state/province to identify regions affecting Windsor. In addition to annual modeling, seasonal PSCF modeling was also conducted. The potential source region was identified between 24–61° N and 51–143° W. Annual PSCF modeling identified major sources southwest of Windsor, stretching from Ohio to Texas. The emissions inventory also supported the findings, as Hg emissions were high in those regions. Results of seasonal PSCF modeling were analyzed to find the combined effects of regional sources, meteorological conditions, and surface re-emissions, on seasonal variability of Hg concentrations. It was found that the summer and winter highs of atmospheric Hg can be attributed to areas where large numbers of coal fired power plants are located in the USA. Weak atmospheric dispersion due to low winds and high re-emission from surfaces due to higher temperatures also contributed to high concentrations in

  13. Human mixed infections of Leishmania spp. and Leishmania-Trypanosoma cruzi in a sub Andean Bolivian area: identification by polymerase chain reaction/hybridization and isoenzyme

    Directory of Open Access Journals (Sweden)

    B Bastrenta

    2003-03-01

    Full Text Available Parasites belonging to Leishmania braziliensis, Leishmania donovani, Leishmania mexicana complexes and Trypanosoma cruzi (clones 20 and 39 were searched in blood, lesions and strains collected from 28 patients with active cutaneous leishmaniasis and one patient with visceral leishmaniasis. PCR-hybridization with specific probes of Leishmania complexes (L. braziliensis, L. donovani and L. mexicana and T. cruzi clones was applied to the different DNA samples. Over 29 patients, 8 (27.6% presented a mixed infection Leishmania complex species, 17 (58.6% a mixed infection Leishmania-T. cruzi, and 4 (13.8% a multi Leishmania-T. cruzi infection. Several patients were infected by the two Bolivian major clones 20 and 39 of T. cruzi (44.8%. The L. braziliensis complex was more frequently detected in lesions than in blood and a reverse result was observed for L. mexicana complex. The polymerase chain reaction-hybridization design offers new arguments supporting the idea of an underestimated rate of visceral leishmanisis in Bolivia. Parasites were isolated by culture from the blood of two patients and lesions of 10 patients. The UPGMA (unweighted pair-group method with arithmetic averages dendrogram computed from Jaccard's distances obtained from 11 isoenzyme loci data confirmed the presence of the three Leishmania complexes and undoubtedly identified human infections by L. (V. braziliensis, L. (L. chagasi and L. (L. mexicana species. Additional evidence of parasite mixtures was visualized through mixed isoenzyme profiles, L. (V. braziliensis-L. (L. mexicana and Leishmania spp.-T. cruzi.The epidemiological profile in the studied area appeared more complex than currently known. This is the first report of parasitological evidence of Bolivian patients with trypanosomatidae multi infections and consequences on the diseases' control and patient treatments are discussed.

  14. The identification of spinal pathology in chronic low back pain using single photon emission computed tomography

    International Nuclear Information System (INIS)

    Ryan, R.J.; Gibson, T.; Fogelman, I.

    1992-01-01

    Single photon emission computed tomography (SPECT) findings were investigated in 80 consecutive patients (aged 18-70 years, median 44) referred to a rheumatology outpatient clinic with low back pain persisting for more than 3 months. Lesions of the lumbar spine were demonstrated in 60% of patients using SPECT but in only 35% with planar imaging. Fifty-one per cent of all lesions were only detected by SPECT, and lesions visualized on SPECT could be precisely localized to the vertebral body, or different parts of the posterior elements. Fifty per cent of lesions involved the facetal joints of which almost 60% were identified on SPECT alone. X-rays of the lumbar spine, with posterior oblique views, failed to demonstrate abnormalities corresponding to almost all SPECT posterior element lesions although it identified abnormalities corresponding to over 60% of anterior SPECT lesions. Computed tomography (CT) was performed in 30 patients with a SPECT lesion and sites of facetal joint activity corresponded to facetal osteoarthritis in 82%. (author)

  15. Jimena: efficient computing and system state identification for genetic regulatory networks.

    Science.gov (United States)

    Karl, Stefan; Dandekar, Thomas

    2013-10-11

    Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial interpolation of Boolean genetic regulatory networks (GRNs) in cellular processes such as apoptosis or proliferation allows for the modeling of a wider range of node interactions than continuous activator-inhibitor models, but suffers from scaling problems for networks which contain nodes with more than ~10 inputs. Many GRNs from literature or new gene expression experiments exceed those limitations and a new approach was developed. (i) As a part of our new GRN simulation framework Jimena we introduce and setup Boolean-tree-based data structures; (ii) corresponding algorithms greatly expedite the calculation of the polynomial interpolation in almost all cases, thereby expanding the range of networks which can be simulated by this model in reasonable time. (iii) Stable states for discrete models are efficiently counted and identified using binary decision diagrams. As application example, we show how system states can now be sampled efficiently in small up to large scale hormone disease networks (Arabidopsis thaliana development and immunity, pathogen Pseudomonas syringae and modulation by cytokinins and plant hormones). Jimena simulates currently available GRNs about 10-100 times faster than the previous implementation of the polynomial interpolation model and even greater gains are achieved for large scale-free networks. This speed-up also facilitates a much more thorough sampling of continuous state spaces which may lead to the identification of new stable states. Mutants of large networks can be constructed and analyzed very quickly enabling new insights into network robustness and behavior.

  16. An incidentally found inflamed uterine myoma Causing low abdominal pain, using TC-99m-tektrotyd single photon emission computed tomography-CT hybrid imaging

    Energy Technology Data Exchange (ETDEWEB)

    Zandieh, Shahin; Schuetz, Matthias; Bernt, Reinhard; Zwerina, Jochen; Haller, Joerg [Hanusch-Hospital, Teaching Hospital of Medical University of Vienna, Vienna (Australia)

    2013-10-15

    We report the case of a 50-year-old woman presented with a history of right hemicolectomy due to an ileocecal neuroendocrine tumor and left breast metastasis. Owing to a slightly elevated chromogranin A-level and lower abdominal pain, single photon emission computed tomography-computer tomography (SPECT-CT) was performed. There were no signs of recurrence on the SPECT-CT scan, but the patient was incidentally found to have an inflamed intramural myoma. We believe that the slightly elevated chromogranin A-level was caused by the hypertension that the patient presented. In the clinical context, this is a report of an inflamed uterine myoma seen as a false positive result detected by TC-99m-Tc-EDDA/HYNIC-Tyr3-Octreotide (Tektrotyd) SPECT-CT hybrid imaging.

  17. Mobile, hybrid Compton/coded aperture imaging for detection, identification and localization of gamma-ray sources at stand-off distances

    Science.gov (United States)

    Tornga, Shawn R.

    The Stand-off Radiation Detection System (SORDS) program is an Advanced Technology Demonstration (ATD) project through the Department of Homeland Security's Domestic Nuclear Detection Office (DNDO) with the goal of detection, identification and localization of weak radiological sources in the presence of large dynamic backgrounds. The Raytheon-SORDS Tri-Modal Imager (TMI) is a mobile truck-based, hybrid gamma-ray imaging system able to quickly detect, identify and localize, radiation sources at standoff distances through improved sensitivity while minimizing the false alarm rate. Reconstruction of gamma-ray sources is performed using a combination of two imaging modalities; coded aperture and Compton scatter imaging. The TMI consists of 35 sodium iodide (NaI) crystals 5x5x2 in3 each, arranged in a random coded aperture mask array (CA), followed by 30 position sensitive NaI bars each 24x2.5x3 in3 called the detection array (DA). The CA array acts as both a coded aperture mask and scattering detector for Compton events. The large-area DA array acts as a collection detector for both Compton scattered events and coded aperture events. In this thesis, developed coded aperture, Compton and hybrid imaging algorithms will be described along with their performance. It will be shown that multiple imaging modalities can be fused to improve detection sensitivity over a broader energy range than either alone. Since the TMI is a moving system, peripheral data, such as a Global Positioning System (GPS) and Inertial Navigation System (INS) must also be incorporated. A method of adapting static imaging algorithms to a moving platform has been developed. Also, algorithms were developed in parallel with detector hardware, through the use of extensive simulations performed with the Geometry and Tracking Toolkit v4 (GEANT4). Simulations have been well validated against measured data. Results of image reconstruction algorithms at various speeds and distances will be presented as well as

  18. Computer-aided structure analysis. Structure identification by infrared and /sup 13/C NMR measurements

    Energy Technology Data Exchange (ETDEWEB)

    Szalontai, G; Simon, Z; Csapo, Z; Farkas, M; Pfeifer, Gy [Nehezvegyipari Kutato Intezet, Veszprem (Hungary)

    1980-01-01

    The results obtained from the computer-aided interpretation of /sup 13/C NMR and IR spectra using the artificial intelligence approach are presented. In its present state the output of the system is a list of functional groups which are resonable candidates for the final structural isomers. The input requires empirical formula, /sup 13/C NMR data (off resonance data also) and IR spectral data. The confirmation of the presence of a functional group is based on comparison of the experimental data with the spectral properties of functional groups stored in a property matrix. If the molecular weight of the compounds studied is less or equal 500, the output contains usually 1.5-2.5 times more groups than really present, in most cases without the loss of the real ones.

  19. Identification and red blood cell automated counting from blood smear images using computer-aided system.

    Science.gov (United States)

    Acharya, Vasundhara; Kumar, Preetham

    2018-03-01

    Red blood cell count plays a vital role in identifying the overall health of the patient. Hospitals use the hemocytometer to count the blood cells. Conventional method of placing the smear under microscope and counting the cells manually lead to erroneous results, and medical laboratory technicians are put under stress. A computer-aided system will help to attain precise results in less amount of time. This research work proposes an image-processing technique for counting the number of red blood cells. It aims to examine and process the blood smear image, in order to support the counting of red blood cells and identify the number of normal and abnormal cells in the image automatically. K-medoids algorithm which is robust to external noise is used to extract the WBCs from the image. Granulometric analysis is used to separate the red blood cells from the white blood cells. The red blood cells obtained are counted using the labeling algorithm and circular Hough transform. The radius range for the circle-drawing algorithm is estimated by computing the distance of the pixels from the boundary which automates the entire algorithm. A comparison is done between the counts obtained using the labeling algorithm and circular Hough transform. Results of the work showed that circular Hough transform was more accurate in counting the red blood cells than the labeling algorithm as it was successful in identifying even the overlapping cells. The work also intends to compare the results of cell count done using the proposed methodology and manual approach. The work is designed to address all the drawbacks of the previous research work. The research work can be extended to extract various texture and shape features of abnormal cells identified so that diseases like anemia of inflammation and chronic disease can be detected at the earliest.

  20. Computational Identification of Potential Multi-drug Combinations for Reduction of Microglial Inflammation in Alzheimer Disease

    Directory of Open Access Journals (Sweden)

    Thomas J. Anastasio

    2015-06-01

    Full Text Available Like other neurodegenerative diseases, Alzheimer Disease (AD has a prominent inflammatory component mediated by brain microglia. Reducing microglial inflammation could potentially halt or at least slow the neurodegenerative process. A major challenge in the development of treatments targeting brain inflammation is the sheer complexity of the molecular mechanisms that determine whether microglia become inflammatory or take on a more neuroprotective phenotype. The process is highly multifactorial, raising the possibility that a multi-target/multi-drug strategy could be more effective than conventional monotherapy. This study takes a computational approach in finding combinations of approved drugs that are potentially more effective than single drugs in reducing microglial inflammation in AD. This novel approach exploits the distinct advantages of two different computer programming languages, one imperative and the other declarative. Existing programs written in both languages implement the same model of microglial behavior, and the input/output relationships of both programs agree with each other and with data on microglia over an extensive test battery. Here the imperative program is used efficiently to screen the model for the most efficacious combinations of 10 drugs, while the declarative program is used to analyze in detail the mechanisms of action of the most efficacious combinations. Of the 1024 possible drug combinations, the simulated screen identifies only 7 that are able to move simulated microglia at least 50% of the way from a neurotoxic to a neuroprotective phenotype. Subsequent analysis shows that of the 7 most efficacious combinations, 2 stand out as superior both in strength and reliability. The model offers many experimentally testable and therapeutically relevant predictions concerning effective drug combinations and their mechanisms of action.

  1. Computational identification of potential multi-drug combinations for reduction of microglial inflammation in Alzheimer disease.

    Science.gov (United States)

    Anastasio, Thomas J

    2015-01-01

    Like other neurodegenerative diseases, Alzheimer Disease (AD) has a prominent inflammatory component mediated by brain microglia. Reducing microglial inflammation could potentially halt or at least slow the neurodegenerative process. A major challenge in the development of treatments targeting brain inflammation is the sheer complexity of the molecular mechanisms that determine whether microglia become inflammatory or take on a more neuroprotective phenotype. The process is highly multifactorial, raising the possibility that a multi-target/multi-drug strategy could be more effective than conventional monotherapy. This study takes a computational approach in finding combinations of approved drugs that are potentially more effective than single drugs in reducing microglial inflammation in AD. This novel approach exploits the distinct advantages of two different computer programming languages, one imperative and the other declarative. Existing programs written in both languages implement the same model of microglial behavior, and the input/output relationships of both programs agree with each other and with data on microglia over an extensive test battery. Here the imperative program is used efficiently to screen the model for the most efficacious combinations of 10 drugs, while the declarative program is used to analyze in detail the mechanisms of action of the most efficacious combinations. Of the 1024 possible drug combinations, the simulated screen identifies only 7 that are able to move simulated microglia at least 50% of the way from a neurotoxic to a neuroprotective phenotype. Subsequent analysis shows that of the 7 most efficacious combinations, 2 stand out as superior both in strength and reliability. The model offers many experimentally testable and therapeutically relevant predictions concerning effective drug combinations and their mechanisms of action.

  2. Rapid identification of pearl powder from Hyriopsis cumingii by Tri-step infrared spectroscopy combined with computer vision technology

    Science.gov (United States)

    Liu, Siqi; Wei, Wei; Bai, Zhiyi; Wang, Xichang; Li, Xiaohong; Wang, Chuanxian; Liu, Xia; Liu, Yuan; Xu, Changhua

    2018-01-01

    Pearl powder, an important raw material in cosmetics and Chinese patent medicines, is commonly uneven in quality and frequently adulterated with low-cost shell powder in the market. The aim of this study is to establish an adequate approach based on Tri-step infrared spectroscopy with enhancing resolution combined with chemometrics for qualitative identification of pearl powder originated from three different quality grades of pearls and quantitative prediction of the proportions of shell powder adulterated in pearl powder. Additionally, computer vision technology (E-eyes) can investigate the color difference among different pearl powders and make it traceable to the pearl quality trait-visual color categories. Though the different grades of pearl powder or adulterated pearl powder have almost identical IR spectra, SD-IR peak intensity at about 861 cm- 1 (v2 band) exhibited regular enhancement with the increasing quality grade of pearls, while the 1082 cm- 1 (v1 band), 712 cm- 1 and 699 cm- 1 (v4 band) were just the reverse. Contrastly, only the peak intensity at 862 cm- 1 was enhanced regularly with the increasing concentration of shell powder. Thus, the bands in the ranges of (1550-1350 cm- 1, 730-680 cm- 1) and (830-880 cm- 1, 690-725 cm- 1) could be exclusive ranges to discriminate three distinct pearl powders and identify adulteration, respectively. For massive sample analysis, a qualitative classification model and a quantitative prediction model based on IR spectra was established successfully by principal component analysis (PCA) and partial least squares (PLS), respectively. The developed method demonstrated great potential for pearl powder quality control and authenticity identification in a direct, holistic manner.

  3. Synthesis of hydrazide-functionalized hydrophilic polymer hybrid graphene oxide for highly efficient N-glycopeptide enrichment and identification by mass spectrometry.

    Science.gov (United States)

    Bai, Haihong; Pan, Yiting; Guo, Cong; Zhao, Xinyuan; Shen, Bingquan; Wang, Xinghe; Liu, Zeyuan; Cheng, Yuanguo; Qin, Weijie; Qian, Xiaohong

    2017-08-15

    Protein N-glycosylation is one of the most important post-translational modifications, participating in many key biological and pathological processes. Large-scale and precise identification of N-glycosylated proteins and peptides is especially beneficial for understanding their biological functions and for discovery of new clinical biomarkers and therapeutic drug targets. However, protein N-glycosylation is microheterogeneous and low abundant in living organisms, therefore specific enrichment of N-glycosylated proteins/peptides before mass spectrometry analysis is a prerequisite. In this work, we developed a new type of polymer hybrid graphene oxide (GO) by in situ growth of hydrazide-functionalized hydrophilic polymer chains on the GO surface (GO-PAAH) for selective N-glycopeptide enrichment and identification by mass spectrometry. The densely attached and low steric hindrance hydrazide groups as well as the highly hydrophilic nature of GO-PAAH facilitate N-glycopeptide enrichment by the combination of hydrazide capturing and HILIC interaction. Taking advantage of the unique features of GO-PAAH, all of the three N-glycopeptides of bovine fetuin were successfully enriched and identified with significantly enhanced signal intensities from a digest mixture of bovine fetuin and bovine serum albumin at a mass ratio of 1:100, demonstrating the excellent enrichment selectivity of GO-PAAH. Furthermore, a total of 507 N-glycosylation sites and 480 N-glycopeptides in 232 N-glycoproteins were enriched and identified from 10μL of human serum by three replicates using this novel enrichment material, which is nearly two times higher than the commercial hydrazide resin based method (280 N-glycosylation sites, 261 N-glycopeptides and 144 N-glycoproteins in three experiments). Among the identified, 95 N-glycosylation sites were not reported in the Uniprot database, and 106 N-glycoproteins were disease related in the Nextprot database, indicating the potential of this new

  4. Steady state characteristics of an adjustable hybrid gas bearing – Computational fluid dynamics, modified Reynolds equation and experimental validation

    DEFF Research Database (Denmark)

    Pierart Vásquez, Fabián Gonzalo; Santos, Ilmar

    2015-01-01

    To include the effect of external pressurization in hybrid gas bearings an extra term is added to Reynolds Equation to accommodate the gas jet. Two cases are considered: cylindrical and annular flow profiles. Validation of theoretical results obtained using the modified version of Reynolds equation....... By introducing such coefficients into the modified Reynolds equation, good agreement with experiments is achieved in terms of journal equilibrium position and resulting aerodynamic forces....

  5. MULTIDETECTOR COMPUTED TOMOGRAPHY FOR IDENTIFICATION OF INSTABILITY OF AORTIC ANEURYSM WALL

    Directory of Open Access Journals (Sweden)

    M. V. Vishnyakova Jr.

    2015-01-01

    Full Text Available Background: Aortic aneurysm is characterized by high incidence, polymorphic clinical features and sudden onset of severe complications.Aim: To develop a standard multidetector computed tomography (MDCT protocol for aortic aneurysm examination and image analysis for detection the signs of aortic wall instability.Materials and methods: The data of 279 patients with aortic aneurysm who underwent MDCT examination during 2009–2014 was analyzed to identify aortic wall instability signs.Results: Complicated course of aortic aneurysm was observed in 100 cases (36%. The most common sign of aortic wall instability was aortic dissection. According to our results, a new definition of aortic aneurysm complications was elaborated. It included signs of aortic wall instability with incomplete and/or complete disruption of aortic wall layers. A scheme of the most common patterns of aortic wall abnormalities was proposed, allowing a radiologist to reach high accuracy in characterizing this pathology.Conclusion: A dedicated MDCT protocol for aortic aneurysm detection and image analysis can increase quality of radiologic assessment of aneurysm wall allowing to approach to the level of histological accuracy.

  6. Seismocardiography-Based Cardiac Computed Tomography Gating Using Patient-Specific Template Identification and Detection.

    Science.gov (United States)

    Yao, Jingting; Tridandapani, Srini; Wick, Carson A; Bhatti, Pamela T

    2017-01-01

    To more accurately trigger cardiac computed tomography angiography (CTA) than electrocardiography (ECG) alone, a sub-system is proposed as an intermediate step toward fusing ECG with seismocardiography (SCG). Accurate prediction of quiescent phases is crucial to prospectively gating CTA, which is susceptible to cardiac motion and, thus, can affect the diagnostic quality of images. The key innovation of this sub-system is that it identifies the SCG waveform corresponding to heart sounds and determines their phases within the cardiac cycles. Furthermore, this relationship is modeled as a linear function with respect to heart rate. For this paper, B-mode echocardiography is used as the gold standard for identifying the quiescent phases. We analyzed synchronous ECG, SCG, and echocardiography data acquired from seven healthy subjects (mean age: 31; age range: 22-48; males: 4) and 11 cardiac patients (mean age: 56; age range: 31-78; males: 6). On average, the proposed algorithm was able to successfully identify 79% of the SCG waveforms in systole and 68% in diastole. The simulated results show that SCG-based prediction produced less average phase error than that of ECG. It was found that the accuracy of ECG-based gating is more susceptible to increases in heart rate variability, while SCG-based gating is susceptible to high cycle to cycle variability in morphology. This pilot work of prediction using SCG waveforms enriches the framework of a comprehensive system with multiple modalities that could potentially, in real time, improve the image quality of CTA.

  7. Computational Prediction of Human Salivary Proteins from Blood Circulation and Application to Diagnostic Biomarker Identification

    Science.gov (United States)

    Wang, Jiaxin; Liang, Yanchun; Wang, Yan; Cui, Juan; Liu, Ming; Du, Wei; Xu, Ying

    2013-01-01

    Proteins can move from blood circulation into salivary glands through active transportation, passive diffusion or ultrafiltration, some of which are then released into saliva and hence can potentially serve as biomarkers for diseases if accurately identified. We present a novel computational method for predicting salivary proteins that come from circulation. The basis for the prediction is a set of physiochemical and sequence features we found to be discerning between human proteins known to be movable from circulation to saliva and proteins deemed to be not in saliva. A classifier was trained based on these features using a support-vector machine to predict protein secretion into saliva. The classifier achieved 88.56% average recall and 90.76% average precision in 10-fold cross-validation on the training data, indicating that the selected features are informative. Considering the possibility that our negative training data may not be highly reliable (i.e., proteins predicted to be not in saliva), we have also trained a ranking method, aiming to rank the known salivary proteins from circulation as the highest among the proteins in the general background, based on the same features. This prediction capability can be used to predict potential biomarker proteins for specific human diseases when coupled with the information of differentially expressed proteins in diseased versus healthy control tissues and a prediction capability for blood-secretory proteins. Using such integrated information, we predicted 31 candidate biomarker proteins in saliva for breast cancer. PMID:24324552

  8. Computational identification of potent inhibitors for Streptomycin 3″-adenylyltransferase of Serratia marcescens.

    Science.gov (United States)

    Prabhu, Dhamodharan; Vidhyavathi, Ramasamy; Jeyakanthan, Jeyaraman

    2017-02-01

    Serratia marcescens is an opportunistic pathogen responsible for the respiratory and urinary tract infections in humans. The antibiotic resistance mechanism of S. marcescens is mediated through aminoglycoside modification enzyme that transfer adenyl group from substrate to antibiotic through regiospecific transfers for the inactivation of antibiotics. Streptomycin 3 ″ -adenylyltransferase acts on the 3' position of the antibiotic and considered as a novel drug target to overcome bacterial antibiotic resistance. Till now, there is no experimentally solved crystal structure of Streptomycin 3″-adenylyltransferase in S. marcescens. Hence, the present study was initiated to construct the three dimensional structure of Streptomycin 3″-adenylyltransferase in order to understand the binding mechanism. The modeled structure was subjected to structure-based virtual screening to identify potent compounds from the five chemical structure databases. Furthermore, different computational methods such as molecular docking, molecular dynamics simulations, ADME toxicity assessment, free energy and density functional theory calculations predicted the structural, binding and pharmacokinetic properties of the best five compounds. Overall, the results suggested that stable binding confirmation of the five potent compounds were mediated through hydrophobic, π-π stacking, salt bridges and hydrogen bond interactions. The identified compounds could pave way for the development of anti-pathogenic agents as potential drug entities. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Identification and simulation of the power quality problems using computer models

    International Nuclear Information System (INIS)

    Abro, M.R.; Memon, A.P.; Memon, Z.A.

    2005-01-01

    The Power Quality has become the main factor in our life. If this quality of power is being polluted over the Electrical Power Network, serious problems could arise within the modem social structure and its conveniences. The Nonlinear Characteristics of various office and Industrial equipment connected to the power grid could cause electrical disturbances to poor power quality. In many cases the electric power consumed is first converted to different form and such conversion process introduces harmonic pollution in the grid. These electrical disturbances could destroy certain sensitive equipment connected to the grid or in some cases could cause them to malfunction. In the huge power network identifying the source of such disturbance without causing interruption to the supply is a big problem. This paper attempts to study the power quality problem caused by typical loads using computer models paving the way to identify the source of the problem. PSB (Power System Blockset) Toolbox of MATLAB is used for this paper, which is designed to provide modem tool that rapidly and easily builds models and simulates the power system. The blockset uses the Simulink environment, allowing a model to be built using simple click and drag procedures. (author)

  10. Three-dimensional maximum principal strain using cardiac computed tomography for identification of myocardial infarction

    Energy Technology Data Exchange (ETDEWEB)

    Tanabe, Yuki; Kido, Teruhito; Kurata, Akira; Sawada, Shun; Suekuni, Hiroshi; Kido, Tomoyuki; Yokoi, Takahiro; Miyagawa, Masao; Mochizuki, Teruhito [Ehime University Graduate School of Medicine, Department of Radiology, Toon City, Ehime (Japan); Uetani, Teruyoshi; Inoue, Katsuji [Ehime University Graduate School of Medicine, Department of Cardiology, Pulmonology, Hypertension and Nephrology, Toon City, Ehime (Japan)

    2017-04-15

    To evaluate the feasibility of three-dimensional (3D) maximum principal strain (MP-strain) derived from cardiac computed tomography (CT) for detecting myocardial infarction (MI). Forty-three patients who underwent cardiac CT and magnetic resonance imaging (MRI) were retrospectively selected. Using the voxel tracking of motion coherence algorithm, the peak CT MP-strain was measured using the 16-segment model. With the trans-mural extent of late gadolinium enhancement (LGE) and the distance from MI, all segments were classified into four groups (infarcted, border, adjacent, and remote segments); infarcted and border segments were defined as MI with LGE positive. Diagnostic performance of MP-strain for detecting MI was compared with per cent systolic wall thickening (%SWT) assessed by MRI using receiver-operating characteristic curve analysis at a segment level. Of 672 segments excluding16 segments influenced by artefacts, 193 were diagnosed as MI. Sensitivity and specificity of peak MP-strain to identify MI were 81 % [95 % confidence interval (95 % CI): 74-88 %] and 86 % (81-92 %) compared with %SWT: 76 % (60-95 %) and 68 % (48-84 %), respectively. The area under the curve of peak MP-strain was superior to %SWT [0.90 (0.87-0.93) vs. 0.80 (0.76-0.83), p < 0.05]. CT MP-strain has a potential to provide incremental value to coronary CT angiography for detecting MI. (orig.)

  11. Whole-genome in-silico subtractive hybridization (WISH - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Parrinello Hugues

    2010-06-01

    Full Text Available Abstract Background Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison. We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni. Results Genomic DNA was extracted from male and female (heterogametic S. mansoni adults and sequenced with a Genome Analyzer (Illumina. Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome. The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome. Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite. Conclusion Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex. It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars or even closely related species.

  12. Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis.

    Science.gov (United States)

    Chowdhury, Md Rabiul Hossain; Bhuiyan, Md IqbalKaiser; Saha, Ayan; Mosleh, Ivan Mhai; Mondol, Sobuj; Ahmed, C M Sabbir

    2014-01-01

    Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim-sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein-protein interaction. In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic pathways were revealed by this research. Active sites and druggable pockets of these selected proteins were investigated with bioinformatic techniques. In addition, this study also mentions the activity of those proteins, as well as their interactions with the other proteins. Our findings helped to identify the type of protein to be considered as an efficient drug target. This study will pave the way for researchers to develop and discover more effective and specific

  13. Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis

    Science.gov (United States)

    Chowdhury, Md Rabiul Hossain; Bhuiyan, Md IqbalKaiser; Saha, Ayan; Mosleh, Ivan MHAI; Mondol, Sobuj; Ahmed, C M Sabbir

    2014-01-01

    Purpose Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim–sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. Materials and methods In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein–protein interaction. Results In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic pathways were revealed by this research. Active sites and druggable pockets of these selected proteins were investigated with bioinformatic techniques. In addition, this study also mentions the activity of those proteins, as well as their interactions with the other proteins. Conclusion Our findings helped to identify the type of protein to be considered as an efficient drug target. This study will pave the way for researchers to

  14. Hybrid computational phantoms of the 15-year male and female adolescent: Applications to CT organ dosimetry for patients of variable morphometry

    International Nuclear Information System (INIS)

    Lee, Choonsik; Lodwick, Daniel; Williams, Jonathan L.; Bolch, Wesley E.

    2008-01-01

    Currently, two classes of the computational phantoms have been developed for dosimetry calculation: (1) stylized (or mathematical) and (2) voxel (or tomographic) phantoms describing human anatomy through mathematical surface equations and three-dimensional labeled voxel matrices, respectively. Mathematical surface equations in stylized phantoms provide flexibility in phantom design and alteration, but the resulting anatomical description is, in many cases, not very realistic. Voxel phantoms display far better anatomical realism, but they are limited in terms of their ability to alter organ shape, position, and depth, as well as body posture. A new class of computational phantoms - called hybrid phantoms - takes advantage of the best features of stylized and voxel phantoms - flexibility and anatomical realism, respectively. In the current study, hybrid computational phantoms representing reference 15-year male and female body anatomy and anthropometry are presented. For the male phantom, organ contours were extracted from the University of Florida (UF) 14-year series B male voxel phantom, while for the female phantom, original computed tomography (CT) data from two 14-year female patients were used. Polygon mesh models for the major organs and tissues were reconstructed for nonuniform rational B-spline (NURBS) surface modeling. The resulting NURBS/polygon mesh models representing body contour and internal anatomy were matched to anthropometric data and reference organ mass data provided by the Centers for Disease Control and Prevention (CDC) and the International Commission on Radiation Protection (ICRP), respectively. Finally, two hybrid 15-year male and female phantoms were completed where a total of eight anthropometric data categories were matched to standard values within 4% and organ masses matched to ICRP data within 1% with the exception of total skin. To highlight the flexibility of the hybrid phantoms, 10th and 90th weight percentile 15-year male and

  15. Identification and analysis of potential targets in Streptococcus sanguinis using computer aided protein data analysis

    Directory of Open Access Journals (Sweden)

    Chowdhury MRH

    2014-11-01

    Full Text Available Md Rabiul Hossain Chowdhury,1 Md IqbalKaiser Bhuiyan,2 Ayan Saha,2 Ivan MHAI Mosleh,2 Sobuj Mondol,2 C M Sabbir Ahmed3 1Department of Pharmacy, University of Science and Technology Chittagong, Chittagong, Bangladesh; 2Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh; 3Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh Purpose: Streptococcus sanguinis is a Gram-positive, facultative aerobic bacterium that is a member of the viridans streptococcus group. It is found in human mouths in dental plaque, which accounts for both dental cavities and bacterial endocarditis, and which entails a mortality rate of 25%. Although a range of remedial mediators have been found to control this organism, the effectiveness of agents such as penicillin, amoxicillin, trimethoprim–sulfamethoxazole, and erythromycin, was observed. The emphasis of this investigation was on finding substitute and efficient remedial approaches for the total destruction of this bacterium. Materials and methods: In this computational study, various databases and online software were used to ascertain some specific targets of S. sanguinis. Particularly, the Kyoto Encyclopedia of Genes and Genomes databases were applied to determine human nonhomologous proteins, as well as the metabolic pathways involved with those proteins. Different software such as Phyre2, CastP, DoGSiteScorer, the Protein Function Predictor server, and STRING were utilized to evaluate the probable active drug binding site with its known function and protein–protein interaction. Results: In this study, among 218 essential proteins of this pathogenic bacterium, 81 nonhomologous proteins were accrued, and 15 proteins that are unique in several metabolic pathways of S. sanguinis were isolated through metabolic pathway analysis. Furthermore, four essentially membrane-bound unique proteins that are involved in distinct metabolic

  16. Identification of Requirements for Computer-Supported Matching of Food Consumption Data with Food Composition Data

    Directory of Open Access Journals (Sweden)

    Barbara Koroušić Seljak

    2018-03-01

    Full Text Available This paper identifies the requirements for computer-supported food matching, in order to address not only national and European but also international current related needs and represents an integrated research contribution of the FP7 EuroDISH project. The available classification and coding systems and the specific problems of food matching are summarized and a new concept for food matching based on optimization methods and machine-based learning is proposed. To illustrate and test this concept, a study has been conducted in four European countries (i.e., Germany, The Netherlands, Italy and the UK using different classification and coding systems. This real case study enabled us to evaluate the new food matching concept and provide further recommendations for future work. In the first stage of the study, we prepared subsets of food consumption data described and classified using different systems, that had already been manually matched with national food composition data. Once the food matching algorithm was trained using this data, testing was performed on another subset of food consumption data. Experts from different countries validated food matching between consumption and composition data by selecting best matches from the options given by the matching algorithm without seeing the result of the previously made manual match. The evaluation of study results stressed the importance of the role and quality of the food composition database as compared to the selected classification and/or coding systems and the need to continue compiling national food composition data as eating habits and national dishes still vary between countries. Although some countries managed to collect extensive sets of food consumption data, these cannot be easily matched with food composition data if either food consumption or food composition data are not properly classified and described using any classification and coding systems. The study also showed that the

  17. Identification of Requirements for Computer-Supported Matching of Food Consumption Data with Food Composition Data

    Science.gov (United States)

    Korošec, Peter; Eftimov, Tome; Ocke, Marga; van der Laan, Jan; Roe, Mark; Berry, Rachel; Turrini, Aida; Krems, Carolin; Slimani, Nadia; Finglas, Paul

    2018-01-01

    This paper identifies the requirements for computer-supported food matching, in order to address not only national and European but also international current related needs and represents an integrated research contribution of the FP7 EuroDISH project. The available classification and coding systems and the specific problems of food matching are summarized and a new concept for food matching based on optimization methods and machine-based learning is proposed. To illustrate and test this concept, a study has been conducted in four European countries (i.e., Germany, The Netherlands, Italy and the UK) using different classification and coding systems. This real case study enabled us to evaluate the new food matching concept and provide further recommendations for future work. In the first stage of the study, we prepared subsets of food consumption data described and classified using different systems, that had already been manually matched with national food composition data. Once the food matching algorithm was trained using this data, testing was performed on another subset of food consumption data. Experts from different countries validated food matching between consumption and composition data by selecting best matches from the options given by the matching algorithm without seeing the result of the previously made manual match. The evaluation of study results stressed the importance of the role and quality of the food composition database as compared to the selected classification and/or coding systems and the need to continue compiling national food composition data as eating habits and national dishes still vary between countries. Although some countries managed to collect extensive sets of food consumption data, these cannot be easily matched with food composition data if either food consumption or food composition data are not properly classified and described using any classification and coding systems. The study also showed that the level of human

  18. A Soft Computing Approach to Crack Detection and Impact Source Identification with Field-Programmable Gate Array Implementation

    Directory of Open Access Journals (Sweden)

    Arati M. Dixit

    2013-01-01

    Full Text Available The real-time nondestructive testing (NDT for crack detection and impact source identification (CDISI has attracted the researchers from diverse areas. This is apparent from the current work in the literature. CDISI has usually been performed by visual assessment of waveforms generated by a standard data acquisition system. In this paper we suggest an automation of CDISI for metal armor plates using a soft computing approach by developing a fuzzy inference system to effectively deal with this problem. It is also advantageous to develop a chip that can contribute towards real time CDISI. The objective of this paper is to report on efforts to develop an automated CDISI procedure and to formulate a technique such that the proposed method can be easily implemented on a chip. The CDISI fuzzy inference system is developed using MATLAB’s fuzzy logic toolbox. A VLSI circuit for CDISI is developed on basis of fuzzy logic model using Verilog, a hardware description language (HDL. The Xilinx ISE WebPACK9.1i is used for design, synthesis, implementation, and verification. The CDISI field-programmable gate array (FPGA implementation is done using Xilinx’s Spartan 3 FPGA. SynaptiCAD’s Verilog Simulators—VeriLogger PRO and ModelSim—are used as the software simulation and debug environment.

  19. Computed Tomography Image Origin Identification Based on Original Sensor Pattern Noise and 3-D Image Reconstruction Algorithm Footprints.

    Science.gov (United States)

    Duan, Yuping; Bouslimi, Dalel; Yang, Guanyu; Shu, Huazhong; Coatrieux, Gouenou

    2017-07-01

    In this paper, we focus on the "blind" identification of the computed tomography (CT) scanner that has produced a CT image. To do so, we propose a set of noise features derived from the image chain acquisition and which can be used as CT-scanner footprint. Basically, we propose two approaches. The first one aims at identifying a CT scanner based on an original sensor pattern noise (OSPN) that is intrinsic to the X-ray detectors. The second one identifies an acquisition system based on the way this noise is modified by its three-dimensional (3-D) image reconstruction algorithm. As these reconstruction algorithms are manufacturer dependent and kept secret, our features are used as input to train a support vector machine (SVM) based classifier to discriminate acquisition systems. Experiments conducted on images issued from 15 different CT-scanner models of 4 distinct manufacturers demonstrate that our system identifies the origin of one CT image with a detection rate of at least 94% and that it achieves better performance than sensor pattern noise (SPN) based strategy proposed for general public camera devices.

  20. Logistic regression model for identification of right ventricular dysfunction in patients with acute pulmonary embolism by means of computed tomography

    International Nuclear Information System (INIS)

    Staskiewicz, Grzegorz; Czekajska-Chehab, Elżbieta; Uhlig, Sebastian; Przegalinski, Jerzy; Maciejewski, Ryszard; Drop, Andrzej

    2013-01-01

    Purpose: Diagnosis of right ventricular dysfunction in patients with acute pulmonary embolism (PE) is known to be associated with increased risk of mortality. The aim of the study was to calculate a logistic regression model for reliable identification of right ventricular dysfunction (RVD) in patients diagnosed with computed tomography pulmonary angiography. Material and methods: Ninety-seven consecutive patients with acute pulmonary embolism were divided into groups with and without RVD basing upon echocardiographic measurement of pulmonary artery systolic pressure (PASP). PE severity was graded with the pulmonary obstruction score. CT measurements of heart chambers and mediastinal vessels were performed; position of interventricular septum and presence of contrast reflux into the inferior vena cava were also recorded. The logistic regression model was prepared by means of stepwise logistic regression. Results: Among the used parameters, the final model consisted of pulmonary obstruction score, short axis diameter of right ventricle and diameter of inferior vena cava. The calculated model is characterized by 79% sensitivity and 81% specificity, and its performance was significantly better than single CT-based measurements. Conclusion: Logistic regression model identifies RVD significantly better, than single CT-based measurements

  1. Identification of the Procedural Accidents During Root Canal Preparation Using Digital Intraoral Radiography and Cone Beam Computed Tomography

    Directory of Open Access Journals (Sweden)

    Csinszka K.-Ivácson A.-

    2016-09-01

    Full Text Available Crown or root perforation, ledge formation, fractured instruments and perforation of the roots are the most important accidents which appear during endodontic therapy. Our objective was to evaluate the value of digital intraoral periapical radiographs compared to cone beam computed tomography images (CBCT used to diagnose some procedural accidents. Material and methods: Eleven extracted molars were used in this study. A total of 18 perforations and 13 ledges were created artifically and 10 instruments were fractured in the root canals. Digital intraoral periapical radiographs from two angles and CBCT scans were made with the teeth fixed in position. The images were evaluated and the number of detected accidents were stated in percentages. Statistical analysis was performed using the chi square-test. Results: On digital periapical radiographs the evaluators identified 12 (66.66% perforations, 10 (100 % separated instruments and 10 (76.9% created ledges. The CBCT scans made possible the recognition of 17 (94.66 % perforations, 9 (90 % separated instruments and 13 (100% ledges. The totally recognized accidental procedures showed significant differences between the two groups. (p<0.05 Conclusion: Digital periapical radiographs are the most common imaging modalities used during endodontic treatments. Though, the CBCT allows a better identification of the procedural accidents.

  2. A computer program for automatic gamma-ray spectra analysis with isotope identification for the purpose of activation analysis

    International Nuclear Information System (INIS)

    Weigel, H.; Dauk, J.

    1974-01-01

    A FORTRAN IV program for a PDP-9 computer, with 16K storage capacity, is developed performing automatic analysis of complex gamma-spectra, taken with Ge/Li/ detectors. It searches for full energy peaks and evaluates the peak areas. The program features and automatically performed isotope identifiaction. It is written in such a flexible manner that after reactor irradiation, spectra from samples of any composition can be evaluated for activation analysis. The peak search rutin is based on the following criteria: the counting rate has to increase for two succesive channels; and the amplitude of the corresponding maximum has to be greater than/or equal to F 1 times the statistical error of the counting rate in the valley just before the maximum. In order to detect superimposed peaks, it is assumed that the dependence of FWHM on channel number is roughly approximated by a linear function, and the actual and''theoretical''FWHM values are compared. To determine the net peak area a Gaussian based function is fitted to each peak. The isotope identification is based on the procedure developed by ADAMS and DAMS. (T.G.)

  3. Automatic identification of watercourses in flat and engineered landscapes by computing the skeleton of a LiDAR point cloud

    Science.gov (United States)

    Broersen, Tom; Peters, Ravi; Ledoux, Hugo

    2017-09-01

    Drainage networks play a crucial role in protecting land against floods. It is therefore important to have an accurate map of the watercourses that form the drainage network. Previous work on the automatic identification of watercourses was typically based on grids, focused on natural landscapes, and used mostly the slope and curvature of the terrain. We focus in this paper on areas that are characterised by low-lying, flat, and engineered landscapes; these are characteristic to the Netherlands for instance. We propose a new methodology to identify watercourses automatically from elevation data, it uses solely a raw classified LiDAR point cloud as input. We show that by computing twice a skeleton of the point cloud-once in 2D and once in 3D-and that by using the properties of the skeletons we can identify most of the watercourses. We have implemented our methodology and tested it for three different soil types around Utrecht, the Netherlands. We were able to detect 98% of the watercourses for one soil type, and around 75% for the worst case, when we compared to a reference dataset that was obtained semi-automatically.

  4. [Possibilities of a software-based hybrid single photon emission computed tomography/magnetic resonance imaging in the diagnosis of complicated diabetic foot syndrome].

    Science.gov (United States)

    Zavadovskaya, V D; Zorkal'tsev, M A; Udodov, V D; Zamyshevskaya, M A; Kilina, O Yu; Kurazhov, A P; Popov, K M

    2015-01-01

    To give the results of a software-based hybrid single photon emission computed tomography/magnetic resonance imaging (SPECT/MRI) in detecting osteomyelitis (OM) in patients with diabetic foot syndrome (DFS). Seventy-six patients (35 men and 41 women) (mean age, 59.4 +/- 7.1 years) with type 1 and 2 diabetes mellitus and suspected OM were examined. The investigation enrolled patients with neuropathic (n = 25), ischemic (n = 13), and mixed (n = 38) DFS. All the patients underwent (99m)Tc-HMPAO/ (99m)Tc-technefit labeled leukocyte scintigraphy; magnetic resonance imaging was performed in 30 patients. The results were combined using RView 9.06 software (Colin Studholme). Labeled leukocyte SPECT to Diagnose OM yielded 255 true positive (TP), 38 true negative (TN), 12 false negative (FP), and 1 false negative (FN) results. The accuracy of the technique was 82.9%. The FP results were due to the low resolution of the technique and to the small sizes of the object under study. One FN result was detected in a patient with ischemic DFS because of reduced blood flow. MRI to identify OM in patients with DFS provided 20 TP, 16 TN, 4 FP, and 2 FN results. Its diagnostic accuracy was 85.7%. The relative low specificity of MRI was associated with the presence of FP results due to the complexity of differential diagnosis of bone marrow edema and inflammatory infiltration. Assessing 42 hybrid SPECT/MR-images revealed 21 TP, 17 TN, 3 FP, and I FN results. The diagnostic accuracy was equal to 95.9%. Thus, comparing MRI (90.9% sensitivity and 80.0% specificity), labeled leukocyte scintigraphy (96.2% sensitivity and 76.0% specificity), and hybrid SPECT/MRI (95.5% sensitivity and 85.0% specificity) showed the high diagnostic efficiency of the latter.

  5. Interactions among biotic and abiotic factors affect the reliability of tungsten microneedles puncturing in vitro and in vivo peripheral nerves: A hybrid computational approach

    Energy Technology Data Exchange (ETDEWEB)

    Sergi, Pier Nicola, E-mail: p.sergi@sssup.it [Translational Neural Engineering Laboratory, The Biorobotics Institute, Scuola Superiore Sant' Anna, Viale Rinaldo Piaggio 34, Pontedera, 56025 (Italy); Jensen, Winnie [Department of Health Science and Technology, Fredrik Bajers Vej 7, 9220 Aalborg (Denmark); Yoshida, Ken [Department of Biomedical Engineering, Indiana University - Purdue University Indianapolis, 723 W. Michigan St., SL220, Indianapolis, IN 46202 (United States)

    2016-02-01

    Tungsten is an elective material to produce slender and stiff microneedles able to enter soft tissues and minimize puncture wounds. In particular, tungsten microneedles are used to puncture peripheral nerves and insert neural interfaces, bridging the gap between the nervous system and robotic devices (e.g., hand prostheses). Unfortunately, microneedles fail during the puncture process and this failure is not dependent on stiffness or fracture toughness of the constituent material. In addition, the microneedles' performances decrease during in vivo trials with respect to the in vitro ones. This further effect is independent on internal biotic effects, while it seems to be related to external biotic causes. Since the exact synergy of phenomena decreasing the in vivo reliability is still not known, this work explored the connection between in vitro and in vivo behavior of tungsten microneedles through the study of interactions between biotic and abiotic factors. A hybrid computational approach, simultaneously using theoretical relationships and in silico models of nerves, was implemented to model the change of reliability varying the microneedle diameter, and to predict in vivo performances by using in vitro reliability and local differences between in vivo and in vitro mechanical response of nerves. - Highlights: • We provide phenomenological Finite Element (FE) models of peripheral nerves to study the interactions with W microneedles • We provide a general interaction-based approach to model the reliability of slender microneedles • We evaluate the reliability of W microneedels to puncture in vivo nerves • We provide a novel synergistic hybrid approach (theory + simulations) involving interactions among biotic and abiotic factors • We validate the hybrid approach by using experimental data from literature.

  6. Interactions among biotic and abiotic factors affect the reliability of tungsten microneedles puncturing in vitro and in vivo peripheral nerves: A hybrid computational approach

    International Nuclear Information System (INIS)

    Sergi, Pier Nicola; Jensen, Winnie; Yoshida, Ken

    2016-01-01

    Tungsten is an elective material to produce slender and stiff microneedles able to enter soft tissues and minimize puncture wounds. In particular, tungsten microneedles are used to puncture peripheral nerves and insert neural interfaces, bridging the gap between the nervous system and robotic devices (e.g., hand prostheses). Unfortunately, microneedles fail during the puncture process and this failure is not dependent on stiffness or fracture toughness of the constituent material. In addition, the microneedles' performances decrease during in vivo trials with respect to the in vitro ones. This further effect is independent on internal biotic effects, while it seems to be related to external biotic causes. Since the exact synergy of phenomena decreasing the in vivo reliability is still not known, this work explored the connection between in vitro and in vivo behavior of tungsten microneedles through the study of interactions between biotic and abiotic factors. A hybrid computational approach, simultaneously using theoretical relationships and in silico models of nerves, was implemented to model the change of reliability varying the microneedle diameter, and to predict in vivo performances by using in vitro reliability and local differences between in vivo and in vitro mechanical response of nerves. - Highlights: • We provide phenomenological Finite Element (FE) models of peripheral nerves to study the interactions with W microneedles • We provide a general interaction-based approach to model the reliability of slender microneedles • We evaluate the reliability of W microneedels to puncture in vivo nerves • We provide a novel synergistic hybrid approach (theory + simulations) involving interactions among biotic and abiotic factors • We validate the hybrid approach by using experimental data from literature

  7. An EEG/EOG-based hybrid brain-neural computer interaction (BNCI) system to control an exoskeleton for the paralyzed hand.

    Science.gov (United States)

    Soekadar, Surjo R; Witkowski, Matthias; Vitiello, Nicola; Birbaumer, Niels

    2015-06-01

    The loss of hand function can result in severe physical and psychosocial impairment. Thus, compensation of a lost hand function using assistive robotics that can be operated in daily life is very desirable. However, versatile, intuitive, and reliable control of assistive robotics is still an unsolved challenge. Here, we introduce a novel brain/neural-computer interaction (BNCI) system that integrates electroencephalography (EEG) and electrooculography (EOG) to improve control of assistive robotics in daily life environments. To evaluate the applicability and performance of this hybrid approach, five healthy volunteers (HV) (four men, average age 26.5 ± 3.8 years) and a 34-year-old patient with complete finger paralysis due to a brachial plexus injury (BPI) used EEG (condition 1) and EEG/EOG (condition 2) to control grasping motions of a hand exoskeleton. All participants were able to control the BNCI system (BNCI control performance HV: 70.24 ± 16.71%, BPI: 65.93 ± 24.27%), but inclusion of EOG significantly improved performance across all participants (HV: 80.65 ± 11.28, BPI: 76.03 ± 18.32%). This suggests that hybrid BNCI systems can achieve substantially better control over assistive devices, e.g., a hand exoskeleton, than systems using brain signals alone and thus may increase applicability of brain-controlled assistive devices in daily life environments.

  8. Fluorescence background subtraction technique for hybrid fluorescence molecular tomography/x-ray computed tomography imaging of a mouse model of early stage lung cancer.

    Science.gov (United States)

    Ale, Angelique; Ermolayev, Vladimir; Deliolanis, Nikolaos C; Ntziachristos, Vasilis

    2013-05-01

    The ability to visualize early stage lung cancer is important in the study of biomarkers and targeting agents that could lead to earlier diagnosis. The recent development of hybrid free-space 360-deg fluorescence molecular tomography (FMT) and x-ray computed tomography (XCT) imaging yields a superior optical imaging modality for three-dimensional small animal fluorescence imaging over stand-alone optical systems. Imaging accuracy was improved by using XCT information in the fluorescence reconstruction method. Despite this progress, the detection sensitivity of targeted fluorescence agents remains limited by nonspecific background accumulation of the fluorochrome employed, which complicates early detection of murine cancers. Therefore we examine whether x-ray CT information and bulk fluorescence detection can be combined to increase detection sensitivity. Correspondingly, we research the performance of a data-driven fluorescence background estimator employed for subtraction of background fluorescence from acquisition data. Using mice containing known fluorochromes ex vivo, we demonstrate the reduction of background signals from reconstructed images and sensitivity improvements. Finally, by applying the method to in vivo data from K-ras transgenic mice developing lung cancer, we find small tumors at an early stage compared with reconstructions performed using raw data. We conclude with the benefits of employing fluorescence subtraction in hybrid FMT-XCT for early detection studies.

  9. Identification of Lycopersicon spp. hybrids on the basis of morphological and molecular (RAPD properties as well as evaluation of resistance to Tomato Spotted Wilt Virus (TSWV

    Directory of Open Access Journals (Sweden)

    Zbigniew Rusinowski

    2014-01-01

    Full Text Available The aim of the study was to evaluate the plants obtained as a result of cultivated tomato crosses with wild species meant to transfer resistance to TSWV. Six viable plants were obtained from L. esculentum x L. chilense and L. esculentum x L. peruvianum crosses after the application of in vitro embryo culture. In terms of such morphological traits as growth habit of plants, size and shape of leaves, the length and colour of internodes in branching stems, the plants displayed intermediate traits, resembling, nonetheless, the wild form. RAPD analysis with 8 primers revealed that all the hybrids had bands typical of the paternal forms. This confirms the paternal component in hybrid development. As far as the resistance to Polish TSWV isolates is concerned, two hybrids exhibited a high level of resistance, similar to negative control, three hybrids - enhanced resistance and one hybrid was susceptible to TSWV infection.

  10. Imaging of pharmacokinetic rates of indocyanine green in mouse liver with a hybrid fluorescence molecular tomography/x-ray computed tomography system.

    Science.gov (United States)

    Zhang, Guanglei; Liu, Fei; Zhang, Bin; He, Yun; Luo, Jianwen; Bai, Jing

    2013-04-01

    Pharmacokinetic rates have the potential to provide quantitative physiological and pathological information for biological studies and drug development. Fluorescence molecular tomography (FMT) is an attractive imaging tool for three-dimensionally resolving fluorophore distribution in small animals. In this letter, pharmacokinetic rates of indocyanine green (ICG) in mouse liver are imaged with a hybrid FMT and x-ray computed tomography (XCT) system. A recently developed FMT method using structural priors from an XCT system is adopted to improve the quality of FMT reconstruction. In the in vivo experiments, images of uptake and excretion rates of ICG in mouse liver are obtained, which can be used to quantitatively evaluate liver function. The accuracy of the results is validated by a fiber-based fluorescence measurement system.

  11. Hybrid Human-Computing Distributed Sense-Making: Extending the SOA Paradigm for Dynamic Adjudication and Optimization of Human and Computer Roles

    Science.gov (United States)

    Rimland, Jeffrey C.

    2013-01-01

    In many evolving systems, inputs can be derived from both human observations and physical sensors. Additionally, many computation and analysis tasks can be performed by either human beings or artificial intelligence (AI) applications. For example, weather prediction, emergency event response, assistive technology for various human sensory and…

  12. SU-E-CAMPUS-I-02: Estimation of the Dosimetric Error Caused by the Voxelization of Hybrid Computational Phantoms Using Triangle Mesh-Based Monte Carlo Transport

    Energy Technology Data Exchange (ETDEWEB)

    Lee, C [Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD (United States); Badal, A [U.S. Food ' Drug Administration (CDRH/OSEL), Silver Spring, MD (United States)

    2014-06-15

    Purpose: Computational voxel phantom provides realistic anatomy but the voxel structure may result in dosimetric error compared to real anatomy composed of perfect surface. We analyzed the dosimetric error caused from the voxel structure in hybrid computational phantoms by comparing the voxel-based doses at different resolutions with triangle mesh-based doses. Methods: We incorporated the existing adult male UF/NCI hybrid phantom in mesh format into a Monte Carlo transport code, penMesh that supports triangle meshes. We calculated energy deposition to selected organs of interest for parallel photon beams with three mono energies (0.1, 1, and 10 MeV) in antero-posterior geometry. We also calculated organ energy deposition using three voxel phantoms with different voxel resolutions (1, 5, and 10 mm) using MCNPX2.7. Results: Comparison of organ energy deposition between the two methods showed that agreement overall improved for higher voxel resolution, but for many organs the differences were small. Difference in the energy deposition for 1 MeV, for example, decreased from 11.5% to 1.7% in muscle but only from 0.6% to 0.3% in liver as voxel resolution increased from 10 mm to 1 mm. The differences were smaller at higher energies. The number of photon histories processed per second in voxels were 6.4×10{sup 4}, 3.3×10{sup 4}, and 1.3×10{sup 4}, for 10, 5, and 1 mm resolutions at 10 MeV, respectively, while meshes ran at 4.0×10{sup 4} histories/sec. Conclusion: The combination of hybrid mesh phantom and penMesh was proved to be accurate and of similar speed compared to the voxel phantom and MCNPX. The lowest voxel resolution caused a maximum dosimetric error of 12.6% at 0.1 MeV and 6.8% at 10 MeV but the error was insignificant in some organs. We will apply the tool to calculate dose to very thin layer tissues (e.g., radiosensitive layer in gastro intestines) which cannot be modeled by voxel phantoms.

  13. COMPUTING

    CERN Multimedia

    M. Kasemann

    Overview In autumn the main focus was to process and handle CRAFT data and to perform the Summer08 MC production. The operational aspects were well covered by regular Computing Shifts, experts on duty and Computing Run Coordination. At the Computing Resource Board (CRB) in October a model to account for service work at Tier 2s was approved. The computing resources for 2009 were reviewed for presentation at the C-RRB. The quarterly resource monitoring is continuing. Facilities/Infrastructure operations Operations during CRAFT data taking ran fine. This proved to be a very valuable experience for T0 workflows and operations. The transfers of custodial data to most T1s went smoothly. A first round of reprocessing started at the Tier-1 centers end of November; it will take about two weeks. The Computing Shifts procedure was tested full scale during this period and proved to be very efficient: 30 Computing Shifts Persons (CSP) and 10 Computing Resources Coordinators (CRC). The shift program for the shut down w...

  14. Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum).

    Science.gov (United States)

    Li, Xuyan; Hou, Yanming; Zhang, Li; Zhang, Wenhao; Quan, Chen; Cui, Yuhai; Bian, Shaomin

    2014-01-01

    MicroRNAs (miRNAs) are a class of endogenous, approximately 21nt in length, non-coding RNA, which mediate the expression of target genes primarily at post-transcriptional levels. miRNAs play critical roles in almost all plant cellular and metabolic processes. Although numerous miRNAs have been identified in the plant kingdom, the miRNAs in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNAs and their targets in blueberry. By conducting an EST-based comparative genomics approach, 9 potential vco-miRNAs were discovered from 22,402 blueberry ESTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNA and its target transcript, 34 target ESTs from blueberry and 70 targets from other species were identified for the vco-miRNAs. The targets were found to be involved in transcription, RNA splicing and binding, DNA duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNAs.

  15. A hybrid finite element analysis and evolutionary computation method for the design of lightweight lattice components with optimized strut diameter

    DEFF Research Database (Denmark)

    Salonitis, Konstantinos; Chantzis, Dimitrios; Kappatos, Vasileios

    2017-01-01

    approaches or with the use of topology optimization methodologies. An optimization approach utilizing multipurpose optimization algorithms has not been proposed yet. This paper presents a novel user-friendly method for the design optimization of lattice components towards weight minimization, which combines...... finite element analysis and evolutionary computation. The proposed method utilizes the cell homogenization technique in order to reduce the computational cost of the finite element analysis and a genetic algorithm in order to search for the most lightweight lattice configuration. A bracket consisting...

  16. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction CMS distributed computing system performed well during the 2011 start-up. The events in 2011 have more pile-up and are more complex than last year; this results in longer reconstruction times and harder events to simulate. Significant increases in computing capacity were delivered in April for all computing tiers, and the utilisation and load is close to the planning predictions. All computing centre tiers performed their expected functionalities. Heavy-Ion Programme The CMS Heavy-Ion Programme had a very strong showing at the Quark Matter conference. A large number of analyses were shown. The dedicated heavy-ion reconstruction facility at the Vanderbilt Tier-2 is still involved in some commissioning activities, but is available for processing and analysis. Facilities and Infrastructure Operations Facility and Infrastructure operations have been active with operations and several important deployment tasks. Facilities participated in the testing and deployment of WMAgent and WorkQueue+Request...

  17. COMPUTING

    CERN Multimedia

    P. McBride

    The Computing Project is preparing for a busy year where the primary emphasis of the project moves towards steady operations. Following the very successful completion of Computing Software and Analysis challenge, CSA06, last fall, we have reorganized and established four groups in computing area: Commissioning, User Support, Facility/Infrastructure Operations and Data Operations. These groups work closely together with groups from the Offline Project in planning for data processing and operations. Monte Carlo production has continued since CSA06, with about 30M events produced each month to be used for HLT studies and physics validation. Monte Carlo production will continue throughout the year in the preparation of large samples for physics and detector studies ramping to 50 M events/month for CSA07. Commissioning of the full CMS computing system is a major goal for 2007. Site monitoring is an important commissioning component and work is ongoing to devise CMS specific tests to be included in Service Availa...

  18. COMPUTING

    CERN Multimedia

    M. Kasemann

    Overview During the past three months activities were focused on data operations, testing and re-enforcing shift and operational procedures for data production and transfer, MC production and on user support. Planning of the computing resources in view of the new LHC calendar in ongoing. Two new task forces were created for supporting the integration work: Site Commissioning, which develops tools helping distributed sites to monitor job and data workflows, and Analysis Support, collecting the user experience and feedback during analysis activities and developing tools to increase efficiency. The development plan for DMWM for 2009/2011 was developed at the beginning of the year, based on the requirements from the Physics, Computing and Offline groups (see Offline section). The Computing management meeting at FermiLab on February 19th and 20th was an excellent opportunity discussing the impact and for addressing issues and solutions to the main challenges facing CMS computing. The lack of manpower is particul...

  19. Blending Synchronous Face-to-Face and Computer-Supported Cooperative Learning in a Hybrid Doctoral Seminar

    Science.gov (United States)

    Roseth, Cary; Akcaoglu, Mete; Zellner, Andrea

    2013-01-01

    Online education is often assumed to be synonymous with asynchronous instruction, existing apart from or supplementary to face-to-face instruction in traditional bricks-and-mortar classrooms. However, expanding access to computer-mediated communication technologies now make new models possible, including distance learners synchronous online…

  20. [Identification of a novel WART-like chromosome rearrangement in complex heterozygotes in an interracial hybrid zone of the common shrew Sorex araneus L].

    Science.gov (United States)

    Pavlova, S V; Bulatova, N Sh

    2010-09-01

    Karyotypes uncharacteristic of pure races or hybrids were identified in the interracial hybrid zones of the common shrew Sorex araneus L. that were recently discovered in the European part of Russia. This suggests the actual existence in natural populations of WART-like rearrangements (whole-arm reciprocal translocations) along with Robertsonian fusions of acrocentrics. Demonstration of new and still rare chromosome variants is the aim of this communication.

  1. Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples

    DEFF Research Database (Denmark)

    Jensen, Annette Nygaard; Andersen, M. T.; Dalsgaard, Anders

    2005-01-01

    species-specific detection of Campylobacter spp. in naturally infected pig faecal samples after an enrichment step, whereas the hybridization approach enhanced the specific isolation of C. jejuni (present in minority to C. coli) from pigs. Conclusions: The rt-PCR was specific for Campylobacter jejuni, C...... by phenotypic methods and the developed rt-PCR provides an easy and fast method for such differentiation. Detection of C. jejuni by colony hybridization may increase the isolation rate of this species from pig faeces....

  2. Numerical solution to generalized Burgers'-Fisher equation using Exp-function method hybridized with heuristic computation.

    Directory of Open Access Journals (Sweden)

    Suheel Abdullah Malik

    Full Text Available In this paper, a new heuristic scheme for the approximate solution of the generalized Burgers'-Fisher equation is proposed. The scheme is based on the hybridization of Exp-function method with nature inspired algorithm. The given nonlinear partial differential equation (NPDE through substitution is converted into a nonlinear ordinary differential equation (NODE. The travelling wave solution is approximated by the Exp-function method with unknown parameters. The unknown parameters are estimated by transforming the NODE into an equivalent global error minimization problem by using a fitness function. The popular genetic algorithm (GA is used to solve the minimization problem, and to achieve the unknown parameters. The proposed scheme is successfully implemented to solve the generalized Burgers'-Fisher equation. The comparison of numerical results with the exact solutions, and the solutions obtained using some traditional methods, including adomian decomposition method (ADM, homotopy perturbation method (HPM, and optimal homotopy asymptotic method (OHAM, show that the suggested scheme is fairly accurate and viable for solving such problems.

  3. Numerical solution to generalized Burgers'-Fisher equation using Exp-function method hybridized with heuristic computation.

    Science.gov (United States)

    Malik, Suheel Abdullah; Qureshi, Ijaz Mansoor; Amir, Muhammad; Malik, Aqdas Naveed; Haq, Ihsanul

    2015-01-01

    In this paper, a new heuristic scheme for the approximate solution of the generalized Burgers'-Fisher equation is proposed. The scheme is based on the hybridization of Exp-function method with nature inspired algorithm. The given nonlinear partial differential equation (NPDE) through substitution is converted into a nonlinear ordinary differential equation (NODE). The travelling wave solution is approximated by the Exp-function method with unknown parameters. The unknown parameters are estimated by transforming the NODE into an equivalent global error minimization problem by using a fitness function. The popular genetic algorithm (GA) is used to solve the minimization problem, and to achieve the unknown parameters. The proposed scheme is successfully implemented to solve the generalized Burgers'-Fisher equation. The comparison of numerical results with the exact solutions, and the solutions obtained using some traditional methods, including adomian decomposition method (ADM), homotopy perturbation method (HPM), and optimal homotopy asymptotic method (OHAM), show that the suggested scheme is fairly accurate and viable for solving such problems.

  4. Computer simulation of lower-hybrid heating and current drive in tokamaks. Progress report, September 1, 1982-July 1, 1983

    International Nuclear Information System (INIS)

    Ogden, J.M.

    1983-07-01

    A lower hybrid ray tracing package has been adapted for use in the PPPL 1-D tokamak transport code TRANSP. The code LHRAY has been written in OLYMPUS format and is suitable for use as a separate simulation program or in conjunction with TRANSP. The generality of the OLYMPUS conventions was chosen in order to make LHRAY easily transferable to other OLYMPUS style transport codes such as BALDUR. The details of LHRAY are described in this report. The physical model documented in our first progress report has been used with one major modification. Instead of solving the 1-D Fokker-Planck equations numerically to give the electron distribution function F/sub e/ in the presence of a background electric field, we have approximated F/sub e/ analytically using the theory of Liu et al for runaway electron distributions. The organization of LHRAY is given and the naming conventions are noted. Finally, preliminary results are presented. Program documentation and a listing of the code are included as appendices

  5. Magnetic resonance imaging and computational fluid dynamics (CFD) simulations of rabbit nasal airflows for the development of hybrid CFD/PBPK models.

    Science.gov (United States)

    Corley, R A; Minard, K R; Kabilan, S; Einstein, D R; Kuprat, A P; Harkema, J R; Kimbell, J S; Gargas, M L; Kinzell, John H

    2009-05-01

    The percentages of total airflows over the nasal respiratory and olfactory epithelium of female rabbits were calculated from computational fluid dynamics (CFD) simulations of steady-state inhalation. These airflow calculations, along with nasal airway geometry determinations, are critical parameters for hybrid CFD/physiologically based pharmacokinetic models that describe the nasal dosimetry of water-soluble or reactive gases and vapors in rabbits. CFD simulations were based upon three-dimensional computational meshes derived from magnetic resonance images of three adult female New Zealand White (NZW) rabbits. In the anterior portion of the nose, the maxillary turbinates of rabbits are considerably more complex than comparable regions in rats, mice, monkeys, or humans. This leads to a greater surface area to volume ratio in this region and thus the potential for increased extraction of water soluble or reactive gases and vapors in the anterior portion of the nose compared to many other species. Although there was considerable interanimal variability in the fine structures of the nasal turbinates and airflows in the anterior portions of the nose, there was remarkable consistency between rabbits in the percentage of total inspired airflows that reached the ethmoid turbinate region (approximately 50%) that is presumably lined with olfactory epithelium. These latter results (airflows reaching the ethmoid turbinate region) were higher than previous published estimates for the male F344 rat (19%) and human (7%). These differences in regional airflows can have significant implications in interspecies extrapolations of nasal dosimetry.

  6. COMPUTING

    CERN Multimedia

    I. Fisk

    2013-01-01

    Computing activity had ramped down after the completion of the reprocessing of the 2012 data and parked data, but is increasing with new simulation samples for analysis and upgrade studies. Much of the Computing effort is currently involved in activities to improve the computing system in preparation for 2015. Operations Office Since the beginning of 2013, the Computing Operations team successfully re-processed the 2012 data in record time, not only by using opportunistic resources like the San Diego Supercomputer Center which was accessible, to re-process the primary datasets HTMHT and MultiJet in Run2012D much earlier than planned. The Heavy-Ion data-taking period was successfully concluded in February collecting almost 500 T. Figure 3: Number of events per month (data) In LS1, our emphasis is to increase efficiency and flexibility of the infrastructure and operation. Computing Operations is working on separating disk and tape at the Tier-1 sites and the full implementation of the xrootd federation ...

  7. A computable phenotype for asthma case identification in adult and pediatric patients: External validation in the Chicago Area Patient-Outcomes Research Network (CAPriCORN).

    Science.gov (United States)

    Afshar, Majid; Press, Valerie G; Robison, Rachel G; Kho, Abel N; Bandi, Sindhura; Biswas, Ashvini; Avila, Pedro C; Kumar, Harsha Vardhan Madan; Yu, Byung; Naureckas, Edward T; Nyenhuis, Sharmilee M; Codispoti, Christopher D

    2017-10-13

    Comprehensive, rapid, and accurate identification of patients with asthma for clinical care and engagement in research efforts is needed. The original development and validation of a computable phenotype for asthma case identification occurred at a single institution in Chicago and demonstrated excellent test characteristics. However, its application in a diverse payer mix, across different health systems and multiple electronic health record vendors, and in both children and adults was not examined. The objective of this study is to externally validate the computable phenotype across diverse Chicago institutions to accurately identify pediatric and adult patients with asthma. A cohort of 900 asthma and control patients was identified from the electronic health record between January 1, 2012 and November 30, 2014. Two physicians at each site independently reviewed the patient chart to annotate cases. The inter-observer reliability between the physician reviewers had a κ-coefficient of 0.95 (95% CI 0.93-0.97). The accuracy, sensitivity, specificity, negative predictive value, and positive predictive value of the computable phenotype were all above 94% in the full cohort. The excellent positive and negative predictive values in this multi-center external validation study establish a useful tool to identify asthma cases in in the electronic health record for research and care. This computable phenotype could be used in large-scale comparative-effectiveness trials.

  8. OPTICAL correlation identification technology applied in underwater laser imaging target identification

    Science.gov (United States)

    Yao, Guang-tao; Zhang, Xiao-hui; Ge, Wei-long

    2012-01-01

    The underwater laser imaging detection is an effective method of detecting short distance target underwater as an important complement of sonar detection. With the development of underwater laser imaging technology and underwater vehicle technology, the underwater automatic target identification has gotten more and more attention, and is a research difficulty in the area of underwater optical imaging information processing. Today, underwater automatic target identification based on optical imaging is usually realized with the method of digital circuit software programming. The algorithm realization and control of this method is very flexible. However, the optical imaging information is 2D image even 3D image, the amount of imaging processing information is abundant, so the electronic hardware with pure digital algorithm will need long identification time and is hard to meet the demands of real-time identification. If adopt computer parallel processing, the identification speed can be improved, but it will increase complexity, size and power consumption. This paper attempts to apply optical correlation identification technology to realize underwater automatic target identification. The optics correlation identification technology utilizes the Fourier transform characteristic of Fourier lens which can accomplish Fourier transform of image information in the level of nanosecond, and optical space interconnection calculation has the features of parallel, high speed, large capacity and high resolution, combines the flexibility of calculation and control of digital circuit method to realize optoelectronic hybrid identification mode. We reduce theoretical formulation of correlation identification and analyze the principle of optical correlation identification, and write MATLAB simulation program. We adopt single frame image obtained in underwater range gating laser imaging to identify, and through identifying and locating the different positions of target, we can improve

  9. A Ternary Hybrid EEG-NIRS Brain-Computer Interface for the Classification of Brain Activation Patterns during Mental Arithmetic, Motor Imagery, and Idle State.

    Science.gov (United States)

    Shin, Jaeyoung; Kwon, Jinuk; Im, Chang-Hwan

    2018-01-01

    The performance of a brain-computer interface (BCI) can be enhanced by simultaneously using two or more modalities to record brain activity, which is generally referred to as a hybrid BCI. To date, many BCI researchers have tried to implement a hybrid BCI system by combining electroencephalography (EEG) and functional near-infrared spectroscopy (NIRS) to improve the overall accuracy of binary classification. However, since hybrid EEG-NIRS BCI, which will be denoted by hBCI in this paper, has not been applied to ternary classification problems, paradigms and classification strategies appropriate for ternary classification using hBCI are not well investigated. Here we propose the use of an hBCI for the classification of three brain activation patterns elicited by mental arithmetic, motor imagery, and idle state, with the aim to elevate the information transfer rate (ITR) of hBCI by increasing the number of classes while minimizing the loss of accuracy. EEG electrodes were placed over the prefrontal cortex and the central cortex, and NIRS optodes were placed only on the forehead. The ternary classification problem was decomposed into three binary classification problems using the "one-versus-one" (OVO) classification strategy to apply the filter-bank common spatial patterns filter to EEG data. A 10 × 10-fold cross validation was performed using shrinkage linear discriminant analysis (sLDA) to evaluate the average classification accuracies for EEG-BCI, NIRS-BCI, and hBCI when the meta-classification method was adopted to enhance classification accuracy. The ternary classification accuracies for EEG-BCI, NIRS-BCI, and hBCI were 76.1 ± 12.8, 64.1 ± 9.7, and 82.2 ± 10.2%, respectively. The classification accuracy of the proposed hBCI was thus significantly higher than those of the other BCIs ( p < 0.005). The average ITR for the proposed hBCI was calculated to be 4.70 ± 1.92 bits/minute, which was 34.3% higher than that reported for a previous binary hBCI study.

  10. Optimization of hybrid iterative reconstruction level and evaluation of image quality and radiation dose for pediatric cardiac computed tomography angiography

    International Nuclear Information System (INIS)

    Yang, Lin; Liang, Changhong; Zhuang, Jian; Huang, Meiping; Liu, Hui

    2017-01-01

    Hybrid iterative reconstruction can reduce image noise and produce better image quality compared with filtered back-projection (FBP), but few reports describe optimization of the iteration level. We optimized the iteration level of iDose"4 and evaluated image quality for pediatric cardiac CT angiography. Children (n = 160) with congenital heart disease were enrolled and divided into full-dose (n = 84) and half-dose (n = 76) groups. Four series were reconstructed using FBP, and iDose"4 levels 2, 4 and 6; we evaluated subjective quality of the series using a 5-grade scale and compared the series using a Kruskal-Wallis H test. For FBP and iDose"4-optimal images, we compared contrast-to-noise ratios (CNR) and size-specific dose estimates (SSDE) using a Student's t-test. We also compared diagnostic-accuracy of each group using a Kruskal-Wallis H test. Mean scores for iDose"4 level 4 were the best in both dose groups (all P < 0.05). CNR was improved in both groups with iDose"4 level 4 as compared with FBP. Mean decrease in SSDE was 53% in the half-dose group. Diagnostic accuracy for the four datasets were in the range 92.6-96.2% (no statistical difference). iDose"4 level 4 was optimal for both the full- and half-dose groups. Protocols with iDose"4 level 4 allowed 53% reduction in SSDE without significantly affecting image quality and diagnostic accuracy. (orig.)

  11. Optimization of hybrid iterative reconstruction level and evaluation of image quality and radiation dose for pediatric cardiac computed tomography angiography

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Lin; Liang, Changhong [Southern Medical University, Guangzhou (China); Guangdong Academy of Medical Sciences, Dept. of Radiology, Guangdong General Hospital, Guangzhou (China); Zhuang, Jian [Guangdong Academy of Medical Sciences, Dept. of Cardiac Surgery, Guangdong Cardiovascular Inst., Guangdong Provincial Key Lab. of South China Structural Heart Disease, Guangdong General Hospital, Guangzhou (China); Huang, Meiping [Guangdong Academy of Medical Sciences, Dept. of Radiology, Guangdong General Hospital, Guangzhou (China); Guangdong Academy of Medical Sciences, Dept. of Catheterization Lab, Guangdong Cardiovascular Inst., Guangdong Provincial Key Lab. of South China Structural Heart Disease, Guangdong General Hospital, Guangzhou (China); Liu, Hui [Guangdong Academy of Medical Sciences, Dept. of Radiology, Guangdong General Hospital, Guangzhou (China)

    2017-01-15

    Hybrid iterative reconstruction can reduce image noise and produce better image quality compared with filtered back-projection (FBP), but few reports describe optimization of the iteration level. We optimized the iteration level of iDose{sup 4} and evaluated image quality for pediatric cardiac CT angiography. Children (n = 160) with congenital heart disease were enrolled and divided into full-dose (n = 84) and half-dose (n = 76) groups. Four series were reconstructed using FBP, and iDose{sup 4} levels 2, 4 and 6; we evaluated subjective quality of the series using a 5-grade scale and compared the series using a Kruskal-Wallis H test. For FBP and iDose{sup 4}-optimal images, we compared contrast-to-noise ratios (CNR) and size-specific dose estimates (SSDE) using a Student's t-test. We also compared diagnostic-accuracy of each group using a Kruskal-Wallis H test. Mean scores for iDose{sup 4} level 4 were the best in both dose groups (all P < 0.05). CNR was improved in both groups with iDose{sup 4} level 4 as compared with FBP. Mean decrease in SSDE was 53% in the half-dose group. Diagnostic accuracy for the four datasets were in the range 92.6-96.2% (no statistical difference). iDose{sup 4} level 4 was optimal for both the full- and half-dose groups. Protocols with iDose{sup 4} level 4 allowed 53% reduction in SSDE without significantly affecting image quality and diagnostic accuracy. (orig.)

  12. A Hybrid Computer-aided-diagnosis System for Prediction of Breast Cancer Recurrence (HPBCR) Using Optimized Ensemble Learning.

    Science.gov (United States)

    Mohebian, Mohammad R; Marateb, Hamid R; Mansourian, Marjan; Mañanas, Miguel Angel; Mokarian, Fariborz

    2017-01-01

    Cancer is a collection of diseases that involves growing abnormal cells with the potential to invade or spread to the body. Breast cancer is the second leading cause of cancer death among women. A method for 5-year breast cancer recurrence prediction is presented in this manuscript. Clinicopathologic characteristics of 579 breast cancer patients (recurrence prevalence of 19.3%) were analyzed and discriminative features were selected using statistical feature selection methods. They were further refined by Particle Swarm Optimization (PSO) as the inputs of the classification system with ensemble learning (Bagged Decision Tree: BDT). The proper combination of selected categorical features and also the weight (importance) of the selected interval-measurement-scale features were identified by the PSO algorithm. The performance of HPBCR (hybrid predictor of breast cancer recurrence) was assessed using the holdout and 4-fold cross-validation. Three other classifiers namely as supported vector machines, DT, and multilayer perceptron neural network were used for comparison. The selected features were diagnosis age, tumor size, lymph node involvement ratio, number of involved axillary lymph nodes, progesterone receptor expression, having hormone therapy and type of surgery. The minimum sensitivity, specificity, precision and accuracy of HPBCR were 77%, 93%, 95% and 85%, respectively in the entire cross-validation folds and the hold-out test fold. HPBCR outperformed the other tested classifiers. It showed excellent agreement with the gold standard (i.e. the oncologist opinion after blood tumor marker and imaging tests, and tissue biopsy). This algorithm is thus a promising online tool for the prediction of breast cancer recurrence.

  13. The UF/NCI family of hybrid computational phantoms representing the current US population of male and female children, adolescents, and adults—application to CT dosimetry

    International Nuclear Information System (INIS)

    Geyer, Amy M; O'Reilly, Shannon; Long, Daniel J; Bolch, Wesley E; Lee, Choonsik

    2014-01-01

    Substantial increases in pediatric and adult obesity in the US have prompted a major revision to the current UF/NCI (University of Florida/National Cancer Institute) family of hybrid computational phantoms to more accurately reflect current trends in larger body morphometry. A decision was made to construct the new library in a gridded fashion by height/weight without further reference to age-dependent weight/height percentiles as these become quickly outdated. At each height/weight combination, circumferential parameters were defined and used for phantom construction. All morphometric data for the new library were taken from the CDC NHANES survey data over the time period 1999–2006, the most recent reported survey period. A subset of the phantom library was then used in a CT organ dose sensitivity study to examine the degree to which body morphometry influences the magnitude of organ doses for patients that are underweight to morbidly obese in body size. Using primary and secondary morphometric parameters, grids containing 100 adult male height/weight bins, 93 adult female height/weight bins, 85 pediatric male height/weight bins and 73 pediatric female height/weight bins were constructed. These grids served as the blueprints for construction of a comprehensive library of patient-dependent phantoms containing 351 computational phantoms. At a given phantom standing height, normalized CT organ doses were shown to linearly decrease with increasing phantom BMI for pediatric males, while curvilinear decreases in organ dose were shown with increasing phantom BMI for adult females. These results suggest that one very useful application of the phantom library would be the construction of a pre-computed dose library for CT imaging as needed for patient dose-tracking. (paper)

  14. COMPUTING

    CERN Multimedia

    I. Fisk

    2010-01-01

    Introduction It has been a very active quarter in Computing with interesting progress in all areas. The activity level at the computing facilities, driven by both organised processing from data operations and user analysis, has been steadily increasing. The large-scale production of simulated events that has been progressing throughout the fall is wrapping-up and reprocessing with pile-up will continue. A large reprocessing of all the proton-proton data has just been released and another will follow shortly. The number of analysis jobs by users each day, that was already hitting the computing model expectations at the time of ICHEP, is now 33% higher. We are expecting a busy holiday break to ensure samples are ready in time for the winter conferences. Heavy Ion An activity that is still in progress is computing for the heavy-ion program. The heavy-ion events are collected without zero suppression, so the event size is much large at roughly 11 MB per event of RAW. The central collisions are more complex and...

  15. COMPUTING

    CERN Multimedia

    M. Kasemann P. McBride Edited by M-C. Sawley with contributions from: P. Kreuzer D. Bonacorsi S. Belforte F. Wuerthwein L. Bauerdick K. Lassila-Perini M-C. Sawley

    Introduction More than seventy CMS collaborators attended the Computing and Offline Workshop in San Diego, California, April 20-24th to discuss the state of readiness of software and computing for collisions. Focus and priority were given to preparations for data taking and providing room for ample dialog between groups involved in Commissioning, Data Operations, Analysis and MC Production. Throughout the workshop, aspects of software, operating procedures and issues addressing all parts of the computing model were discussed. Plans for the CMS participation in STEP’09, the combined scale testing for all four experiments due in June 2009, were refined. The article in CMS Times by Frank Wuerthwein gave a good recap of the highly collaborative atmosphere of the workshop. Many thanks to UCSD and to the organizers for taking care of this workshop, which resulted in a long list of action items and was definitely a success. A considerable amount of effort and care is invested in the estimate of the comput...

  16. SU-E-T-13: A Feasibility Study of the Use of Hybrid Computational Phantoms for Improved Historical Dose Reconstruction in the Study of Late Radiation Effects for Hodgkin's Lymphoma

    Energy Technology Data Exchange (ETDEWEB)

    Petroccia, H; O' Reilly, S; Bolch, W [J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL (United States); Mendenhall, N; Li, Z; Slopsema, R [Radiation Oncology, University of Florida Proton Therapy Institute, Jacksonville, FL (United States)

    2014-06-01

    Purpose: Radiation-induced cancer effects are well-documented following radiotherapy. Further investigation is needed to more accurately determine a dose-response relationship for late radiation effects. Recent dosimetry studies tend to use representative patients (Taylor 2009) or anthropomorphic phantoms (Wirth 2008) for estimating organ mean doses. In this study, we compare hybrid computational phantoms to patient-specific voxel phantoms to test the accuracy of University of Florida Hybrid Phantom Library (UFHP Library) for historical dose reconstructions. Methods: A cohort of 10 patients with CT images was used to reproduce the data that was collected historically for Hodgkin's lymphoma patients (i.e. caliper measurements and photographs). Four types of phantoms were generated to show a range of refinement from reference hybrid-computational phantom to patient-specific phantoms. Each patient is matched to a reference phantom from the UFHP Library based on height and weight. The reference phantom is refined in the anterior/posterior direction to create a ‘caliper-scaled phantom’. A photograph is simulated using a surface rendering from segmented CT images. Further refinement in the lateral direction is performed using ratios from a simulated-photograph to create a ‘photograph and caliper-scaled phantom’; breast size and position is visually adjusted. Patient-specific hybrid phantoms, with matched organ volumes, are generated and show the capabilities of the UF Hybrid Phantom Library. Reference, caliper-scaled, photograph and caliper-scaled, and patient-specific hybrid phantoms are compared with patient-specific voxel phantoms to determine the accuracy of the study. Results: Progression from reference phantom to patient specific hybrid shows good agreement with the patient specific voxel phantoms. Each stage of refinement shows an overall trend of improvement in dose accuracy within the study, which suggests that computational phantoms can show

  17. Utility and impact of early t(15;17) identification by Fluorescence In Situ Hybridization (FISH) in clinical decision making for patients in Acute Promyelocytic Leukemia (APL).

    Science.gov (United States)

    Kolhe, R; Mangaonkar, A; Mansour, J; Clemmons, A; Shaw, J; Dupont, B; Walczak, L; Mondal, A; Rojiani, A; Jillella, A; Kota, V

    2015-08-01

    Acute Promyelocytic Leukemia (APL) is a curable malignancy with studies showing above 90% survival. However, population-based studies looking at survival suggest that approximately 30% of patients with APL die during induction. Early demonstration of t(15;17) will lead to accurate decision making regarding treatment. The aim of this project was to validate earlier time frames for the Abbott Molecular Vysis LSI promyelocytic leukemia (PML)/ retinoic acid receptor alpha (RARA) fluorescence in situ hybridization (FISH) probe (ASR 6-16 h). Twenty patients (15 APL cases and five non-APL cases) were selected for validating various hybridization times for the FISH probe. Expected normal signal pattern was two red and two green signals (2R2G), and the most common expected abnormal signal pattern was two fusion (yellow) signals, one red and one green (2F1R1G) and/or one fusion, one red and one green (1F1R1G). The specificity of the probe ranged from 84% at 2 h, 86% at 4 h, 84% at 6 h, and 87% for overnight hybridization. The sensitivity increased from 79% at 2 h, 80% at 4 h, 81% at 6 h to 87% for overnight hybridization. Based on the validation studies, we recommend reading of FISH results at the 4-h incubation mark for a preliminary diagnosis and confirmation with overnight hybridization. © 2015 John Wiley & Sons Ltd.

  18. McGISH identification and phenotypic description of leaf rust and yellow rust resistant partial amphiploids originating from a wheat × Thinopyrum synthetic hybrid cross.

    Science.gov (United States)

    Kruppa, Klaudia; Türkösi, Edina; Mayer, Marianna; Tóth, Viola; Vida, Gyula; Szakács, Éva; Molnár-Láng, Márta

    2016-11-01

    A Thinopyrum intermedium × Thinopyrum ponticum synthetic hybrid wheatgrass is an excellent source of leaf and stem rust resistance produced by N.V.Tsitsin. Wheat line Mv9kr1 was crossed with this hybrid (Agropyron glael) in Hungary in order to transfer its advantageous agronomic traits into wheat. As the wheat parent was susceptible to leaf rust, the transfer of resistance was easily recognizable in the progenies. Three different partial amphiploid lines with leaf rust resistance were selected from the wheat/Thinopyrum hybrid derivatives by multicolour genomic in situ hybridization. Chromosome counting on the partial amphiploids revealed 58 chromosomes (18 wheatgrass) in line 194, 56 (14 wheatgrass) in line 195 and 54 (12 wheatgrass) in line 196. The wheat chromosomes present in these lines were identified and the wheatgrass chromosomes were characterized by fluorescence in situ hybridization using the repetitive DNA probes Afa-family, pSc119.2 and pTa71. The 3D wheat chromosome was missing from the lines. Molecular marker analysis showed the presence of the Lr24 leaf rust resistance gene in lines 195 and 196. The morphological traits were evaluated in the field during two consecutive seasons in two different locations.

  19. Deep learning for hybrid EEG-fNIRS brain–computer interface: application to motor imagery classification

    Science.gov (United States)

    Chiarelli, Antonio Maria; Croce, Pierpaolo; Merla, Arcangelo; Zappasodi, Filippo

    2018-06-01

    Objective. Brain–computer interface (BCI) refers to procedures that link the central nervous system to a device. BCI was historically performed using electroencephalography (EEG). In the last years, encouraging results were obtained by combining EEG with other neuroimaging technologies, such as functional near infrared spectroscopy (fNIRS). A crucial step of BCI is brain state classification from recorded signal features. Deep artificial neural networks (DNNs) recently reached unprecedented complex classification outcomes. These performances were achieved through increased computational power, efficient learning algorithms, valuable activation functions, and restricted or back-fed neurons connections. By expecting significant overall BCI performances, we investigated the capabilities of combining EEG and fNIRS recordings with state-of-the-art deep learning procedures. Approach. We performed a guided left and right hand motor imagery task on 15 subjects with a fixed classification response time of 1 s and overall experiment length of 10 min. Left versus right classification accuracy of a DNN in the multi-modal recording modality was estimated and it was compared to standalone EEG and fNIRS and other classifiers. Main results. At a group level we obtained significant increase in performance when considering multi-modal recordings and DNN classifier with synergistic effect. Significance. BCI performances can be significantly improved by employing multi-modal recordings that provide electrical and hemodynamic brain activity information, in combination with advanced non-linear deep learning classification procedures.

  20. Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model.

    Science.gov (United States)

    Boulanger, Eliot; Thiel, Walter

    2012-11-13

    Accurate quantum mechanical/molecular mechanical (QM/MM) treatments should account for MM polarization and properly include long-range electrostatic interactions. We report on a development that covers both these aspects. Our approach combines the classical Drude oscillator (DO) model for the electronic polarizability of the MM atoms with the generalized solvent boundary Potential (GSBP) and the solvated macromolecule boundary potential (SMBP). These boundary potentials (BP) are designed to capture the long-range effects of the outer region of a large system on its interior. They employ a finite difference approximation to the Poisson-Boltzmann equation for computing electrostatic interactions and take into account outer-region bulk solvent through a polarizable dielectric continuum (PDC). This approach thus leads to fully polarizable three-layer QM/MM-DO/BP methods. As the mutual responses of each of the subsystems have to be taken into account, we propose efficient schemes to converge the polarization of each layer simultaneously. For molecular dynamics (MD) simulations using GSBP, this is achieved by considering the MM polarizable model as a dynamical degree of freedom, and hence contributions from the boundary potential can be evaluated for a frozen state of polarization at every time step. For geometry optimizations using SMBP, we propose a dual self-consistent field approach for relaxing the Drude oscillators to their ideal positions and converging the QM wave function with the pr