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Sample records for time-efficient sequence protocol

  1. Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

    Science.gov (United States)

    Aigrain, Louise; Gu, Yong; Quail, Michael A

    2016-06-13

    The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification.

  2. Quantum broadcast communication and authentication protocol with a quantum one-time pad

    International Nuclear Information System (INIS)

    Chang Yan; Xu Chun-Xiang; Zhang Shi-Bin; Yan Li-Li

    2014-01-01

    A quantum broadcast communication and authentication protocol with a quantum one-time pad based on the Greenberger—Horne—Zeilinger state is proposed. A binary string is used to express the identity of the receiver, which is encoded as a single sequence of photons. The encoded photon sequence acts as a detection sequence and implements authentication. An XOR operation serves as a one-time pad and is used to ensure the security of the protocol. The binary string is reused even in a noisy channel and proves to be unconditionally secure. In contrast with the protocols proposed by Wang et al. [Chin. Phys. 16 1868 (2007)] and Yang et al. [Chin. Phys. B 19 070304 (2010)], the protocol in this study implements the identity authentication with a reusable binary string; no hash function or local unitary operation is used. The protocol in this study is also easier to implement and highly efficient without losing security. (general)

  3. An energy efficient and dynamic time synchronization protocol for wireless sensor networks

    Science.gov (United States)

    Zhang, Anran; Bai, Fengshan

    2017-01-01

    Time synchronization is an important support technology of WSN(Wireless Sensor Network), and plays an irreplaceable role in the development of WSN. In view of the disadvantage of the traditional timing sync protocol for sensor networks (TPSN), we present a Physical Timing-sync Protocol (PTPSN) that aims at reducing the energy consumption of the synchronization process and realizes a dynamic Network. The algorithm broadcasts reference message to select some nodes in specific area. The receiver calculate offset of every selected node, and then calculate the average of offset to compensate for clock skew . At the same time ,we add time-filter process to ensure the security of the algorithm for time synchronization. The experiment results show that our algorithm is efficient in both saving energy consumption and dynamic network, and it can effectively resist attacks.

  4. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  5. Rapid and Easy Protocol for Quantification of Next-Generation Sequencing Libraries.

    Science.gov (United States)

    Hawkins, Steve F C; Guest, Paul C

    2018-01-01

    The emergence of next-generation sequencing (NGS) over the last 10 years has increased the efficiency of DNA sequencing in terms of speed, ease, and price. However, the exact quantification of a NGS library is crucial in order to obtain good data on sequencing platforms developed by the current market leader Illumina. Different approaches for DNA quantification are available currently and the most commonly used are based on analysis of the physical properties of the DNA through spectrophotometric or fluorometric methods. Although these methods are technically simple, they do not allow exact quantification as can be achieved using a real-time quantitative PCR (qPCR) approach. A qPCR protocol for DNA quantification with applications in NGS library preparation studies is presented here. This can be applied in various fields of study such as medical disorders resulting from nutritional programming disturbances.

  6. Efficient secure two-party protocols

    CERN Document Server

    Hazay, Carmit

    2010-01-01

    The authors present a comprehensive study of efficient protocols and techniques for secure two-party computation -- both general constructions that can be used to securely compute any functionality, and protocols for specific problems of interest. The book focuses on techniques for constructing efficient protocols and proving them secure. In addition, the authors study different definitional paradigms and compare the efficiency of protocols achieved under these different definitions.The book opens with a general introduction to secure computation and then presents definitions of security for a

  7. An improved protocol for efficient transformation and regeneration of diverse indica rice cultivars

    Directory of Open Access Journals (Sweden)

    Sahoo Khirod K

    2011-12-01

    Full Text Available Abstract Background Rice genome sequencing projects have generated remarkable amount of information about genes and genome architecture having tremendous potential to be utilized in both basic and applied research. Success in transgenics is paving the way for preparing a road map of functional genomics which is expected to correlate action of a gene to a trait in cellular and organismal context. However, the lack of a simple and efficient method for transformation and regeneration is a major constraint for such studies in this important cereal crop. Results In the present study, we have developed an easy, rapid and highly efficient transformation and regeneration protocol using mature seeds as explants and found its successful applicability to a choice of elite indica rice genotypes. We have optimized various steps of transformation and standardized different components of the regeneration medium including growth hormones and the gelling agent. The modified regeneration medium triggers production of large number of shoots from smaller number of calli and promotes their faster growth, hence significantly advantageous over the existing protocols where the regeneration step requires maximum time. Using this protocol, significantly higher transformation efficiency (up to 46% and regeneration frequency (up to 92% for the untransformed calli and 59% for the transformed calli were achieved for the four tested cultivars. We have used this protocol to produce hundreds of independent transgenic lines of different indica rice genotypes. Upon maturity, these transgenic lines were fertile thereby indicating that faster regeneration during tissue culture did not affect their reproductive potential. Conclusions This speedy, yet less labor-intensive, protocol overcomes major limitations associated with genetic manipulation in rice. Moreover, our protocol uses mature seeds as the explant, which can easily be obtained in quantity throughout the year and kept

  8. Abbreviated protocol for breast MRI: Are multiple sequences needed for cancer detection?

    International Nuclear Information System (INIS)

    Mango, Victoria L.; Morris, Elizabeth A.; David Dershaw, D.; Abramson, Andrea; Fry, Charles; Moskowitz, Chaya S.; Hughes, Mary; Kaplan, Jennifer; Jochelson, Maxine S.

    2015-01-01

    Highlights: • Abbreviated breast MR demonstrates high sensitivity for breast carcinoma detection. • Time to perform/interpret the abbreviated exam is shorter than a standard MRI exam. • An abbreviated breast MRI could reduce costs and make MRI screening more available. - Abstract: Objective: To evaluate the ability of an abbreviated breast magnetic resonance imaging (MRI) protocol, consisting of a precontrast T1 weighted (T1W) image and single early post-contrast T1W image, to detect breast carcinoma. Materials and methods: A HIPAA compliant Institutional Review Board approved review of 100 consecutive breast MRI examinations in patients with biopsy proven unicentric breast carcinoma. 79% were invasive carcinomas and 21% were ductal carcinoma in situ. Four experienced breast radiologists, blinded to carcinoma location, history and prior examinations, assessed the abbreviated protocol evaluating only the first post-contrast T1W image, post-processed subtracted first post-contrast and subtraction maximum intensity projection images. Detection and localization of tumor were compared to the standard full diagnostic examination consisting of 13 pre-contrast, post-contrast and post-processed sequences. Results: All 100 cancers were visualized on initial reading of the abbreviated protocol by at least one reader. The mean sensitivity for each sequence was 96% for the first post-contrast sequence, 96% for the first post-contrast subtraction sequence and 93% for the subtraction MIP sequence. Within each sequence, there was no significant difference between the sensitivities among the 4 readers (p = 0.471, p = 0.656, p = 0.139). Mean interpretation time was 44 s (range 11–167 s). The abbreviated imaging protocol could be performed in approximately 10–15 min, compared to 30–40 min for the standard protocol. Conclusion: An abbreviated breast MRI protocol allows detection of breast carcinoma. One pre and post-contrast T1W sequence may be adequate for detecting

  9. Abbreviated protocol for breast MRI: Are multiple sequences needed for cancer detection?

    Energy Technology Data Exchange (ETDEWEB)

    Mango, Victoria L., E-mail: vlm2125@columbia.edu [Columbia University Medical Center, Herbert Irving Pavilion, 161 Fort Washington Avenue, 10th Floor, New York, NY 10032 (United States); Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Morris, Elizabeth A., E-mail: morrise@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); David Dershaw, D., E-mail: dershawd@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Abramson, Andrea, E-mail: abramsoa@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Fry, Charles, E-mail: charles_fry@nymc.edu [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); New York Medical College, 40 Sunshine Cottage Rd, Valhalla, NY 10595 (United States); Moskowitz, Chaya S. [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Hughes, Mary, E-mail: hughesm@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Kaplan, Jennifer, E-mail: kaplanj@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States); Jochelson, Maxine S., E-mail: jochelsm@mskcc.org [Memorial Sloan-Kettering Cancer Center, Breast and Imaging Center, 300 East 66th Street, New York, NY 10065 (United States)

    2015-01-15

    Highlights: • Abbreviated breast MR demonstrates high sensitivity for breast carcinoma detection. • Time to perform/interpret the abbreviated exam is shorter than a standard MRI exam. • An abbreviated breast MRI could reduce costs and make MRI screening more available. - Abstract: Objective: To evaluate the ability of an abbreviated breast magnetic resonance imaging (MRI) protocol, consisting of a precontrast T1 weighted (T1W) image and single early post-contrast T1W image, to detect breast carcinoma. Materials and methods: A HIPAA compliant Institutional Review Board approved review of 100 consecutive breast MRI examinations in patients with biopsy proven unicentric breast carcinoma. 79% were invasive carcinomas and 21% were ductal carcinoma in situ. Four experienced breast radiologists, blinded to carcinoma location, history and prior examinations, assessed the abbreviated protocol evaluating only the first post-contrast T1W image, post-processed subtracted first post-contrast and subtraction maximum intensity projection images. Detection and localization of tumor were compared to the standard full diagnostic examination consisting of 13 pre-contrast, post-contrast and post-processed sequences. Results: All 100 cancers were visualized on initial reading of the abbreviated protocol by at least one reader. The mean sensitivity for each sequence was 96% for the first post-contrast sequence, 96% for the first post-contrast subtraction sequence and 93% for the subtraction MIP sequence. Within each sequence, there was no significant difference between the sensitivities among the 4 readers (p = 0.471, p = 0.656, p = 0.139). Mean interpretation time was 44 s (range 11–167 s). The abbreviated imaging protocol could be performed in approximately 10–15 min, compared to 30–40 min for the standard protocol. Conclusion: An abbreviated breast MRI protocol allows detection of breast carcinoma. One pre and post-contrast T1W sequence may be adequate for detecting

  10. A More Efficient Contextuality Distillation Protocol

    Science.gov (United States)

    Meng, Hui-xian; Cao, Huai-xin; Wang, Wen-hua; Fan, Ya-jing; Chen, Liang

    2018-03-01

    Based on the fact that both nonlocality and contextuality are resource theories, it is natural to ask how to amplify them more efficiently. In this paper, we present a contextuality distillation protocol which produces an n-cycle box B ∗ B ' from two given n-cycle boxes B and B '. It works efficiently for a class of contextual n-cycle ( n ≥ 4) boxes which we termed as "the generalized correlated contextual n-cycle boxes". For any two generalized correlated contextual n-cycle boxes B and B ', B ∗ B ' is more contextual than both B and B '. Moreover, they can be distilled toward to the maximally contextual box C H n as the times of iteration goes to infinity. Among the known protocols, our protocol has the strongest approximate ability and is optimal in terms of its distillation rate. What is worth noting is that our protocol can witness a larger set of nonlocal boxes that make communication complexity trivial than the protocol in Brunner and Skrzypczyk (Phys. Rev. Lett. 102, 160403 2009), this might be helpful for exploring the problem that why quantum nonlocality is limited.

  11. Maximally efficient protocols for direct secure quantum communication

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Anindita [Department of Physics and Materials Science Engineering, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP-201307 (India); Department of Physics and Center for Astroparticle Physics and Space Science, Bose Institute, Block EN, Sector V, Kolkata 700091 (India); Pathak, Anirban, E-mail: anirban.pathak@jiit.ac.in [Department of Physics and Materials Science Engineering, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, UP-201307 (India); RCPTM, Joint Laboratory of Optics of Palacky University and Institute of Physics of Academy of Science of the Czech Republic, Faculty of Science, Palacky University, 17. Listopadu 12, 77146 Olomouc (Czech Republic)

    2012-10-01

    Two protocols for deterministic secure quantum communication (DSQC) using GHZ-like states have been proposed. It is shown that one of these protocols is maximally efficient and that can be modified to an equivalent protocol of quantum secure direct communication (QSDC). Security and efficiency of the proposed protocols are analyzed and compared. It is shown that dense coding is sufficient but not essential for DSQC and QSDC protocols. Maximally efficient QSDC protocols are shown to be more efficient than their DSQC counterparts. This additional efficiency arises at the cost of message transmission rate. -- Highlights: ► Two protocols for deterministic secure quantum communication (DSQC) are proposed. ► One of the above protocols is maximally efficient. ► It is modified to an equivalent protocol of quantum secure direct communication (QSDC). ► It is shown that dense coding is sufficient but not essential for DSQC and QSDC protocols. ► Efficient QSDC protocols are always more efficient than their DSQC counterparts.

  12. Time Error Analysis of SOE System Using Network Time Protocol

    International Nuclear Information System (INIS)

    Keum, Jong Yong; Park, Geun Ok; Park, Heui Youn

    2005-01-01

    To find the accuracy of time in the fully digitalized SOE (Sequence of Events) system, we used a formal specification of the Network Time Protocol (NTP) Version 3, which is used to synchronize time keeping among a set of distributed computers. Through constructing a simple experimental environments and experimenting internet time synchronization, we analyzed the time errors of local clocks of SOE system synchronized with a time server via computer networks

  13. An one-time-pad key communication protocol with entanglement

    OpenAIRE

    Cai, Qing-yu

    2003-01-01

    We present an one-time-pad key communication protocol that allows secure direct communication with entanglement. Alice can send message to Bob in a deterministic manner by using local measurements and public communication. The theoretical efficiency of this protocol is double compared with BB84 protocol. We show this protocol is unconditional secure under arbitrary quantum attack. And we discuss that this protocol can be perfectly implemented with current technologies.

  14. Improvement The Transmission Efficiency For Wireless Packet Communication Systems Using Automatic Control for power And Time Slot Width Of Slotted Non persistent ISMA Protocol

    Directory of Open Access Journals (Sweden)

    Saad M. Hardan

    2013-05-01

    Full Text Available In packed communication systems which use a protocol, the protocol should perform the allocation of channels such that the transmission channel is used efficiently. Efficiency is usually measured in terms of channel throughput and the average transmission  delay. The Slotted Nonpersistent ISMA protocol is one of random access protocols used in packed communication systems. In this research a Slotted Nonpersistent ISMA protocol Model with automatic control for power and time slot is proposed. the suggested algorithm enable the base station(access point to control  the protocol time slot length and  transmission power in a dynamic way to control the normalized propagation delay d and to maintain all the uplink signals in the limit of captured power threshold (capture ratio in order to control the  throughput and the average transmission delay of the communication system by an automatic method. the computer simulation results  confirm the activity of the  proposed algorithm for increasing the  throughput and decreasing the average transmission delay by an accepted ratios.

  15. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    OpenAIRE

    Farkhondeh Saba; Moslem Papizadeh; Javad Khansha; Mahshid Sedghi; Mehrnoosh Rasooli; Mohammad Ali Amoozegar; Mohammad Reza Soudi; Seyed Abolhassan Shahzadeh Fazeli

    2016-01-01

    Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR). Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Me...

  16. Real-Time QoS Routing Protocols in Wireless Multimedia Sensor Networks: Study and Analysis.

    Science.gov (United States)

    Alanazi, Adwan; Elleithy, Khaled

    2015-09-02

    Many routing protocols have been proposed for wireless sensor networks. These routing protocols are almost always based on energy efficiency. However, recent advances in complementary metal-oxide semiconductor (CMOS) cameras and small microphones have led to the development of Wireless Multimedia Sensor Networks (WMSN) as a class of wireless sensor networks which pose additional challenges. The transmission of imaging and video data needs routing protocols with both energy efficiency and Quality of Service (QoS) characteristics in order to guarantee the efficient use of the sensor nodes and effective access to the collected data. Also, with integration of real time applications in Wireless Senor Networks (WSNs), the use of QoS routing protocols is not only becoming a significant topic, but is also gaining the attention of researchers. In designing an efficient QoS routing protocol, the reliability and guarantee of end-to-end delay are critical events while conserving energy. Thus, considerable research has been focused on designing energy efficient and robust QoS routing protocols. In this paper, we present a state of the art research work based on real-time QoS routing protocols for WMSNs that have already been proposed. This paper categorizes the real-time QoS routing protocols into probabilistic and deterministic protocols. In addition, both categories are classified into soft and hard real time protocols by highlighting the QoS issues including the limitations and features of each protocol. Furthermore, we have compared the performance of mobility-aware query based real-time QoS routing protocols from each category using Network Simulator-2 (NS2). This paper also focuses on the design challenges and future research directions as well as highlights the characteristics of each QoS routing protocol.

  17. Energy-Efficient Cluster Based Routing Protocol in Mobile Ad Hoc Networks Using Network Coding

    Directory of Open Access Journals (Sweden)

    Srinivas Kanakala

    2014-01-01

    Full Text Available In mobile ad hoc networks, all nodes are energy constrained. In such situations, it is important to reduce energy consumption. In this paper, we consider the issues of energy efficient communication in MANETs using network coding. Network coding is an effective method to improve the performance of wireless networks. COPE protocol implements network coding concept to reduce number of transmissions by mixing the packets at intermediate nodes. We incorporate COPE into cluster based routing protocol to further reduce the energy consumption. The proposed energy-efficient coding-aware cluster based routing protocol (ECCRP scheme applies network coding at cluster heads to reduce number of transmissions. We also modify the queue management procedure of COPE protocol to further improve coding opportunities. We also use an energy efficient scheme while selecting the cluster head. It helps to increase the life time of the network. We evaluate the performance of proposed energy efficient cluster based protocol using simulation. Simulation results show that the proposed ECCRP algorithm reduces energy consumption and increases life time of the network.

  18. A two-hop based adaptive routing protocol for real-time wireless sensor networks.

    Science.gov (United States)

    Rachamalla, Sandhya; Kancherla, Anitha Sheela

    2016-01-01

    One of the most important and challenging issues in wireless sensor networks (WSNs) is to optimally manage the limited energy of nodes without degrading the routing efficiency. In this paper, we propose an energy-efficient adaptive routing mechanism for WSNs, which saves energy of nodes by removing the much delayed packets without degrading the real-time performance of the used routing protocol. It uses the adaptive transmission power algorithm which is based on the attenuation of the wireless link to improve the energy efficiency. The proposed routing mechanism can be associated with any geographic routing protocol and its performance is evaluated by integrating with the well known two-hop based real-time routing protocol, PATH and the resulting protocol is energy-efficient adaptive routing protocol (EE-ARP). The EE-ARP performs well in terms of energy consumption, deadline miss ratio, packet drop and end-to-end delay.

  19. Efficient protocols for Stirling heat engines at the micro-scale

    Science.gov (United States)

    Muratore-Ginanneschi, Paolo; Schwieger, Kay

    2015-10-01

    We investigate the thermodynamic efficiency of sub-micro-scale Stirling heat engines operating under the conditions described by overdamped stochastic thermodynamics. We show how to construct optimal protocols such that at maximum power the efficiency attains for constant isotropic mobility the universal law η=2 ηC/(4-ηC) , where ηC is the efficiency of an ideal Carnot cycle. We show that these protocols are specified by the solution of an optimal mass transport problem. Such solution can be determined explicitly using well-known Monge-Ampère-Kantorovich reconstruction algorithms. Furthermore, we show that the same law describes the efficiency of heat engines operating at maximum work over short time periods. Finally, we illustrate the straightforward extension of these results to cases when the mobility is anisotropic and temperature dependent.

  20. Seismic Parameters of Mining-Induced Aftershock Sequences for Re-entry Protocol Development

    Science.gov (United States)

    Vallejos, Javier A.; Estay, Rodrigo A.

    2018-03-01

    A common characteristic of deep mines in hard rock is induced seismicity. This results from stress changes and rock failure around mining excavations. Following large seismic events, there is an increase in the levels of seismicity, which gradually decay with time. Restricting access to areas of a mine for enough time to allow this decay of seismic events is the main approach in re-entry strategies. The statistical properties of aftershock sequences can be studied with three scaling relations: (1) Gutenberg-Richter frequency magnitude, (2) the modified Omori's law (MOL) for the temporal decay, and (3) Båth's law for the magnitude of the largest aftershock. In this paper, these three scaling relations, in addition to the stochastic Reasenberg-Jones model are applied to study the characteristic parameters of 11 large magnitude mining-induced aftershock sequences in four mines in Ontario, Canada. To provide guidelines for re-entry protocol development, the dependence of the scaling relation parameters on the magnitude of the main event are studied. Some relations between the parameters and the magnitude of the main event are found. Using these relationships and the scaling relations, a space-time-magnitude re-entry protocol is developed. These findings provide a first approximation to concise and well-justified guidelines for re-entry protocol development applicable to the range of mining conditions found in Ontario, Canada.

  1. A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel.

    Science.gov (United States)

    Huang, Ling; Deng, Xiaohui; Li, Ronghua; Xia, Yanshi; Bai, Guihua; Siddique, Kadambot H M; Guo, Peiguo

    2018-04-20

    Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.

  2. Efficient medium access control protocol for geostationary satellite systems

    Institute of Scientific and Technical Information of China (English)

    王丽娜; 顾学迈

    2004-01-01

    This paper proposes an efficient medium access control (MAC) protocol based on multifrequency-time division multiple access (MF-TDMA) for geostationary satellite systems deploying multiple spot-beams and onboard processing,which uses a method of random reservation access with movable boundaries to dynamically request the transmission slots and can transmit different types of traffic. The simulation results have shown that our designed MAC protocol can achieve a high bandwidth utilization, while providing the required quality of service (QoS) for each class of service.

  3. Energy-efficient TDMA medium access control protocol scheduling

    NARCIS (Netherlands)

    Havinga, Paul J.M.; Smit, Gerard J.M.

    2000-01-01

    In this paper we study the energy efficiency and channel efficiency of TDMA MAC protocol scheduling mechanisms. Most MAC protocols are based on phase grouping that basically has three phases in a frame: uplink, downlink and reservation. We propose a new mechanism in which we have multiple uplink and

  4. Dynamical decoupling sequences for multi-qubit dephasing suppression and long-time quantum memory

    International Nuclear Information System (INIS)

    Paz-Silva, Gerardo A; Lee, Seung-Woo; Green, Todd J; Viola, Lorenza

    2016-01-01

    We consider a class of multi-qubit dephasing models that combine classical noise sources and linear coupling to a bosonic environment, and are controlled by arbitrary sequences of dynamical decoupling pulses. Building on a general transfer filter-function framework for open-loop control, we provide an exact representation of the controlled dynamics for arbitrary stationary non-Gaussian classical and quantum noise statistics, with analytical expressions emerging when all dephasing sources are Gaussian. This exact characterization is used to establish two main results. First, we construct multi-qubit sequences that ensure maximum high-order error suppression in both the time and frequency domain and that can be exponentially more efficient than existing ones in terms of total pulse number. Next, we show how long-time multi-qubit storage may be achieved by meeting appropriate conditions for the emergence of a fidelity plateau under sequence repetition, thereby generalizing recent results for single-qubit memory under Gaussian dephasing. In both scenarios, the key step is to endow multi-qubit sequences with a suitable displacement anti-symmetry property, which is of independent interest for applications ranging from environment-assisted entanglement generation to multi-qubit noise spectroscopy protocols. (paper)

  5. A time-efficient acquisition protocol for multipurpose diffusion-weighted microstructural imaging at 7 Tesla.

    Science.gov (United States)

    Sepehrband, Farshid; O'Brien, Kieran; Barth, Markus

    2017-12-01

    Several diffusion-weighted MRI techniques have been developed and validated during the past 2 decades. While offering various neuroanatomical inferences, these techniques differ in their proposed optimal acquisition design, preventing clinicians and researchers benefiting from all potential inference methods, particularly when limited time is available. This study reports an optimal design that enables for a time-efficient diffusion-weighted MRI acquisition scheme at 7 Tesla. The primary audience of this article is the typical end user, interested in diffusion-weighted microstructural imaging at 7 Tesla. We tested b-values in the range of 700 to 3000 s/mm 2 with different number of angular diffusion-encoding samples, against a data-driven "gold standard." The suggested design is a protocol with b-values of 1000 and 2500 s/mm 2 , with 25 and 50 samples, uniformly distributed over two shells. We also report a range of protocols in which the results of fitting microstructural models to the diffusion-weighted data had high correlation with the gold standard. We estimated minimum acquisition requirements that enable diffusion tensor imaging, higher angular resolution diffusion-weighted imaging, neurite orientation dispersion, and density imaging and white matter tract integrity across whole brain with isotropic resolution of 1.8 mm in less than 11 min. Magn Reson Med 78:2170-2184, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  6. Protocol compliance and time management in blunt trauma resuscitation.

    Science.gov (United States)

    Spanjersberg, W R; Bergs, E A; Mushkudiani, N; Klimek, M; Schipper, I B

    2009-01-01

    To study advanced trauma life support (ATLS) protocol adherence prospectively in trauma resuscitation and to analyse time management of daily multidisciplinary trauma resuscitation at a level 1 trauma centre, for both moderately and severely injured patients. All victims of severe blunt trauma were consecutively included. Patients with a revised trauma score (RTS) of 12 were resuscitated by a "minor trauma" team and patients with an RTS of less than 12 were resuscitated by a "severe trauma" team. Digital video recordings were used to analyse protocol compliance and time management during initial assessment. From 1 May to 1 September 2003, 193 resuscitations were included. The "minor trauma" team assessed 119 patients, with a mean injury severity score (ISS) of 7 (range 1-45). Overall protocol compliance was 42%, ranging from 0% for thoracic percussion to 93% for thoracic auscultation. The median resuscitation time was 45.9 minutes (range 39.7-55.9). The "severe team" assessed 74 patients, with a mean ISS of 22 (range 1-59). Overall protocol compliance was 53%, ranging from 4% for thoracic percussion to 95% for thoracic auscultation. Resuscitation took 34.8 minutes median (range 21.6-44.1). Results showed the current trauma resuscitation to be ATLS-like, with sometimes very low protocol compliance rates. Timing of secondary survey and radiology and thus time efficiency remains a challenge in all trauma patients. To assess the effect of trauma resuscitation protocols on outcome, protocol adherence needs to be improved.

  7. MR efficiency using automated MRI-desktop eProtocol

    Science.gov (United States)

    Gao, Fei; Xu, Yanzhe; Panda, Anshuman; Zhang, Min; Hanson, James; Su, Congzhe; Wu, Teresa; Pavlicek, William; James, Judy R.

    2017-03-01

    MRI protocols are instruction sheets that radiology technologists use in routine clinical practice for guidance (e.g., slice position, acquisition parameters etc.). In Mayo Clinic Arizona (MCA), there are over 900 MR protocols (ranging across neuro, body, cardiac, breast etc.) which makes maintaining and updating the protocol instructions a labor intensive effort. The task is even more challenging given different vendors (Siemens, GE etc.). This is a universal problem faced by all the hospitals and/or medical research institutions. To increase the efficiency of the MR practice, we designed and implemented a web-based platform (eProtocol) to automate the management of MRI protocols. It is built upon a database that automatically extracts protocol information from DICOM compliant images and provides a user-friendly interface to the technologists to create, edit and update the protocols. Advanced operations such as protocol migrations from scanner to scanner and capability to upload Multimedia content were also implemented. To the best of our knowledge, eProtocol is the first MR protocol automated management tool used clinically. It is expected that this platform will significantly improve the radiology operations efficiency including better image quality and exam consistency, fewer repeat examinations and less acquisition errors. These protocols instructions will be readily available to the technologists during scans. In addition, this web-based platform can be extended to other imaging modalities such as CT, Mammography, and Interventional Radiology and different vendors for imaging protocol management.

  8. Energy Efficient Network Protocols for Wireless and Mobile Networks

    National Research Council Canada - National Science Library

    Sivalingam, Krishna

    2001-01-01

    ... (also called power aware) network protocols for wireless and mobile networks. Battery power limitations are a very serious concern, and it is essential to study energy efficient protocol design at different layers of the network protocol stack...

  9. Energy-efficient cooperative protocols for full-duplex relay channels

    KAUST Repository

    Khafagy, Mohammad Galal

    2013-12-01

    In this work, energy-efficient cooperative protocols are studied for full-duplex relaying (FDR) with loopback interference. In these protocols, relay assistance is only sought under certain conditions on the different link outages to ensure effective cooperation. Recently, an energy-efficient selective decode-And-forward protocol was proposed for FDR, and was shown to outperform existing schemes in terms of outage. Here, we propose an incremental selective decode-And-forward protocol that offers additional power savings, while keeping the same outage performance. We compare the performance of the two protocols in terms of the end-to-end signal-to-noise ratio cumulative distribution function via closed-form expressions. Finally, we corroborate our theoretical results with simulation, and show the relative relay power savings in comparison to non-selective cooperation in which the relay cooperates regardless of channel conditions. © 2013 IEEE.

  10. Energy-efficient cooperative protocols for full-duplex relay channels

    KAUST Repository

    Khafagy, Mohammad Galal; Ismail, Amr; Alouini, Mohamed-Slim; Aï ssa, Sonia

    2013-01-01

    In this work, energy-efficient cooperative protocols are studied for full-duplex relaying (FDR) with loopback interference. In these protocols, relay assistance is only sought under certain conditions on the different link outages to ensure effective cooperation. Recently, an energy-efficient selective decode-And-forward protocol was proposed for FDR, and was shown to outperform existing schemes in terms of outage. Here, we propose an incremental selective decode-And-forward protocol that offers additional power savings, while keeping the same outage performance. We compare the performance of the two protocols in terms of the end-to-end signal-to-noise ratio cumulative distribution function via closed-form expressions. Finally, we corroborate our theoretical results with simulation, and show the relative relay power savings in comparison to non-selective cooperation in which the relay cooperates regardless of channel conditions. © 2013 IEEE.

  11. Energy Efficient Clustering Protocol to Enhance Performance of Heterogeneous Wireless Sensor Network: EECPEP-HWSN

    Directory of Open Access Journals (Sweden)

    Santosh V. Purkar

    2018-01-01

    Full Text Available Heterogeneous wireless sensor network (HWSN fulfills the requirements of researchers in the design of real life application to resolve the issues of unattended problem. But, the main constraint faced by researchers is the energy source available with sensor nodes. To prolong the life of sensor nodes and thus HWSN, it is necessary to design energy efficient operational schemes. One of the most suitable approaches to enhance energy efficiency is the clustering scheme, which enhances the performance parameters of WSN. A novel solution proposed in this article is to design an energy efficient clustering protocol for HWSN, to enhance performance parameters by EECPEP-HWSN. The proposed protocol is designed with three level nodes namely normal, advanced, and super, respectively. In the clustering process, for selection of cluster head we consider different parameters available with sensor nodes at run time that is, initial energy, hop count, and residual energy. This protocol enhances the energy efficiency of HWSN and hence improves energy remaining in the network, stability, lifetime, and hence throughput. It has been found that the proposed protocol outperforms than existing well-known LEACH, DEEC, and SEP with about 188, 150, and 141 percent respectively.

  12. Location of core diagnostic information across various sequences in brain MRI and implications for efficiency of MRI scanner utilization.

    Science.gov (United States)

    Sharma, Aseem; Chatterjee, Arindam; Goyal, Manu; Parsons, Matthew S; Bartel, Seth

    2015-04-01

    Targeting redundancy within MRI can improve its cost-effective utilization. We sought to quantify potential redundancy in our brain MRI protocols. In this retrospective review, we aggregated 207 consecutive adults who underwent brain MRI and reviewed their medical records to document clinical indication, core diagnostic information provided by MRI, and its clinical impact. Contributory imaging abnormalities constituted positive core diagnostic information whereas absence of imaging abnormalities constituted negative core diagnostic information. The senior author selected core sequences deemed sufficient for extraction of core diagnostic information. For validating core sequences selection, four readers assessed the relative ease of extracting core diagnostic information from the core sequences. Potential redundancy was calculated by comparing the average number of core sequences to the average number of sequences obtained. Scanning had been performed using 9.4±2.8 sequences over 37.3±12.3 minutes. Core diagnostic information was deemed extractable from 2.1±1.1 core sequences, with an assumed scanning time of 8.6±4.8 minutes, reflecting a potential redundancy of 74.5%±19.1%. Potential redundancy was least in scans obtained for treatment planning (14.9%±25.7%) and highest in scans obtained for follow-up of benign diseases (81.4%±12.6%). In 97.4% of cases, all four readers considered core diagnostic information to be either easily extractable from core sequences or the ease to be equivalent to that from the entire study. With only one MRI lacking clinical impact (0.48%), overutilization did not seem to contribute to potential redundancy. High potential redundancy that can be targeted for more efficient scanner utilization exists in brain MRI protocols.

  13. Chapter 10: Peak Demand and Time-Differentiated Energy Savings Cross-Cutting Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

    Energy Technology Data Exchange (ETDEWEB)

    Kurnik, Charles W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Stern, Frank [Navigant, Boulder, CO (United States); Spencer, Justin [Navigant, Boulder, CO (United States)

    2017-10-03

    Savings from electric energy efficiency measures and programs are often expressed in terms of annual energy and presented as kilowatt-hours per year (kWh/year). However, for a full assessment of the value of these savings, it is usually necessary to consider the measure or program's impact on peak demand as well as time-differentiated energy savings. This cross-cutting protocol describes methods for estimating the peak demand and time-differentiated energy impacts of measures implemented through energy efficiency programs.

  14. Time-Efficient Cloning Attacks Identification in Large-Scale RFID Systems

    Directory of Open Access Journals (Sweden)

    Ju-min Zhao

    2017-01-01

    Full Text Available Radio Frequency Identification (RFID is an emerging technology for electronic labeling of objects for the purpose of automatically identifying, categorizing, locating, and tracking the objects. But in their current form RFID systems are susceptible to cloning attacks that seriously threaten RFID applications but are hard to prevent. Existing protocols aimed at detecting whether there are cloning attacks in single-reader RFID systems. In this paper, we investigate the cloning attacks identification in the multireader scenario and first propose a time-efficient protocol, called the time-efficient Cloning Attacks Identification Protocol (CAIP to identify all cloned tags in multireaders RFID systems. We evaluate the performance of CAIP through extensive simulations. The results show that CAIP can identify all the cloned tags in large-scale RFID systems fairly fast with required accuracy.

  15. Data-Based Energy Efficient Clustered Routing Protocol for Wireless Sensors Networks – Tabuk Flood Monitoring System Case Study

    Directory of Open Access Journals (Sweden)

    Ammar Babiker

    2017-10-01

    Full Text Available Energy efficiency has been considered as the most important issue in wireless sensor networks. As in many applications, wireless sensors are scattered in a wide harsh area, where the battery replacement or charging will be quite difficult and it is the most important challenge. Therefore, the design of energy saving mechanism becomes mandatory in most recent research. In this paper, a new energy efficient clustered routing protocol is proposed: the proposed protocol is based on analyzing the data collected from the sensors in a base-station. Based on this analysis the cluster head will be selected as the one with the most useful data. Then, a variable time slot is specified to each sensor to minimize the transmission of repetitive and un-useful data. The proposed protocol Data-Based Energy Efficient Clustered Routing Protocol for Wireless Sensors Networks (DCRP was compared with the famous energy efficient LEACH protocol and also with one of the recent energy efficient routing protocols named Position Responsive Routing Protocol (PRRP. DCRP has been used in monitoring the floods in Tabuk area –Saudi Arabia. It shows comparatively better results.

  16. A Hierarchical Energy Efficient Reliable Transport Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Prabhudutta Mohanty

    2014-12-01

    Full Text Available The two important requirements for many Wireless Senor Networks (WSNs are prolonged network lifetime and end-to-end reliability. The sensor nodes consume more energy during data transmission than the data sensing. In WSN, the redundant data increase the energy consumption, latency and reduce reliability during data transmission. Therefore, it is important to support energy efficient reliable data transport in WSNs. In this paper, we present a Hierarchical Energy Efficient Reliable Transport Protocol (HEERTP for the data transmission within the WSN. This protocol maximises the network lifetime by controlling the redundant data transmission with the co-ordination of Base Station (BS. The proposed protocol also achieves end-to-end reliability using a hop-by-hop acknowledgement scheme. We evaluate the performance of the proposed protocol through simulation. The simulation results reveal that our proposed protocol achieves better performance in terms of energy efficiency, latency and reliability than the existing protocols.

  17. Recurrence time statistics: versatile tools for genomic DNA sequence analysis.

    Science.gov (United States)

    Cao, Yinhe; Tung, Wen-Wen; Gao, J B

    2004-01-01

    With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

  18. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

    Science.gov (United States)

    Marine, Rachel; Polson, Shawn W; Ravel, Jacques; Hatfull, Graham; Russell, Daniel; Sullivan, Matthew; Syed, Fraz; Dumas, Michael; Wommack, K Eric

    2011-11-01

    Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.

  19. Energy-Efficient Boarder Node Medium Access Control Protocol for Wireless Sensor Networks

    Science.gov (United States)

    Razaque, Abdul; Elleithy, Khaled M.

    2014-01-01

    This paper introduces the design, implementation, and performance analysis of the scalable and mobility-aware hybrid protocol named boarder node medium access control (BN-MAC) for wireless sensor networks (WSNs), which leverages the characteristics of scheduled and contention-based MAC protocols. Like contention-based MAC protocols, BN-MAC achieves high channel utilization, network adaptability under heavy traffic and mobility, and low latency and overhead. Like schedule-based MAC protocols, BN-MAC reduces idle listening time, emissions, and collision handling at low cost at one-hop neighbor nodes and achieves high channel utilization under heavy network loads. BN-MAC is particularly designed for region-wise WSNs. Each region is controlled by a boarder node (BN), which is of paramount importance. The BN coordinates with the remaining nodes within and beyond the region. Unlike other hybrid MAC protocols, BN-MAC incorporates three promising models that further reduce the energy consumption, idle listening time, overhearing, and congestion to improve the throughput and reduce the latency. One of the models used with BN-MAC is automatic active and sleep (AAS), which reduces the ideal listening time. When nodes finish their monitoring process, AAS lets them automatically go into the sleep state to avoid the idle listening state. Another model used in BN-MAC is the intelligent decision-making (IDM) model, which helps the nodes sense the nature of the environment. Based on the nature of the environment, the nodes decide whether to use the active or passive mode. This decision power of the nodes further reduces energy consumption because the nodes turn off the radio of the transceiver in the passive mode. The third model is the least-distance smart neighboring search (LDSNS), which determines the shortest efficient path to the one-hop neighbor and also provides cross-layering support to handle the mobility of the nodes. The BN-MAC also incorporates a semi

  20. Energy-efficient boarder node medium access control protocol for wireless sensor networks.

    Science.gov (United States)

    Razaque, Abdul; Elleithy, Khaled M

    2014-03-12

    This paper introduces the design, implementation, and performance analysis of the scalable and mobility-aware hybrid protocol named boarder node medium access control (BN-MAC) for wireless sensor networks (WSNs), which leverages the characteristics of scheduled and contention-based MAC protocols. Like contention-based MAC protocols, BN-MAC achieves high channel utilization, network adaptability under heavy traffic and mobility, and low latency and overhead. Like schedule-based MAC protocols, BN-MAC reduces idle listening time, emissions, and collision handling at low cost at one-hop neighbor nodes and achieves high channel utilization under heavy network loads. BN-MAC is particularly designed for region-wise WSNs. Each region is controlled by a boarder node (BN), which is of paramount importance. The BN coordinates with the remaining nodes within and beyond the region. Unlike other hybrid MAC protocols, BN-MAC incorporates three promising models that further reduce the energy consumption, idle listening time, overhearing, and congestion to improve the throughput and reduce the latency. One of the models used with BN-MAC is automatic active and sleep (AAS), which reduces the ideal listening time. When nodes finish their monitoring process, AAS lets them automatically go into the sleep state to avoid the idle listening state. Another model used in BN-MAC is the intelligent decision-making (IDM) model, which helps the nodes sense the nature of the environment. Based on the nature of the environment, the nodes decide whether to use the active or passive mode. This decision power of the nodes further reduces energy consumption because the nodes turn off the radio of the transceiver in the passive mode. The third model is the least-distance smart neighboring search (LDSNS), which determines the shortest efficient path to the one-hop neighbor and also provides cross-layering support to handle the mobility of the nodes. The BN-MAC also incorporates a semi

  1. Energy-Efficient Boarder Node Medium Access Control Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Abdul Razaque

    2014-03-01

    Full Text Available This paper introduces the design, implementation, and performance analysis of the scalable and mobility-aware hybrid protocol named boarder node medium access control (BN-MAC for wireless sensor networks (WSNs, which leverages the characteristics of scheduled and contention-based MAC protocols. Like contention-based MAC protocols, BN-MAC achieves high channel utilization, network adaptability under heavy traffic and mobility, and low latency and overhead. Like schedule-based MAC protocols, BN-MAC reduces idle listening time, emissions, and collision handling at low cost at one-hop neighbor nodes and achieves high channel utilization under heavy network loads. BN-MAC is particularly designed for region-wise WSNs. Each region is controlled by a boarder node (BN, which is of paramount importance. The BN coordinates with the remaining nodes within and beyond the region. Unlike other hybrid MAC protocols, BN-MAC incorporates three promising models that further reduce the energy consumption, idle listening time, overhearing, and congestion to improve the throughput and reduce the latency. One of the models used with BN-MAC is automatic active and sleep (AAS, which reduces the ideal listening time. When nodes finish their monitoring process, AAS lets them automatically go into the sleep state to avoid the idle listening state. Another model used in BN-MAC is the intelligent decision-making (IDM model, which helps the nodes sense the nature of the environment. Based on the nature of the environment, the nodes decide whether to use the active or passive mode. This decision power of the nodes further reduces energy consumption because the nodes turn off the radio of the transceiver in the passive mode. The third model is the least-distance smart neighboring search (LDSNS, which determines the shortest efficient path to the one-hop neighbor and also provides cross-layering support to handle the mobility of the nodes. The BN-MAC also incorporates a semi

  2. Secure and Efficient Protocol for Vehicular Ad Hoc Network with Privacy Preservation

    Directory of Open Access Journals (Sweden)

    Choi Hyoung-Kee

    2011-01-01

    Full Text Available Security is a fundamental issue for promising applications in a VANET. Designing a secure protocol for a VANET that accommodates efficiency, privacy, and traceability is difficult because of the contradictions between these qualities. In this paper, we present a secure yet efficient protocol for a VANET that satisfies these security requirements. Although much research has attempted to address similar issues, we contend that our proposed protocol outperforms other proposals that have been advanced. This claim is based on observations that show that the proposed protocol has such strengths as light computational load, efficient storage management, and dependability.

  3. Evaluating Protocol Lifecycle Time Intervals in HIV/AIDS Clinical Trials

    Science.gov (United States)

    Schouten, Jeffrey T.; Dixon, Dennis; Varghese, Suresh; Cope, Marie T.; Marci, Joe; Kagan, Jonathan M.

    2014-01-01

    Background Identifying efficacious interventions for the prevention and treatment of human diseases depends on the efficient development and implementation of controlled clinical trials. Essential to reducing the time and burden of completing the clinical trial lifecycle is determining which aspects take the longest, delay other stages, and may lead to better resource utilization without diminishing scientific quality, safety, or the protection of human subjects. Purpose In this study we modeled time-to-event data to explore relationships between clinical trial protocol development and implementation times, as well as identify potential correlates of prolonged development and implementation. Methods We obtained time interval and participant accrual data from 111 interventional clinical trials initiated between 2006 and 2011 by NIH’s HIV/AIDS Clinical Trials Networks. We determined the time (in days) required to complete defined phases of clinical trial protocol development and implementation. Kaplan-Meier estimates were used to assess the rates at which protocols reached specified terminal events, stratified by study purpose (therapeutic, prevention) and phase group (pilot/phase I, phase II, and phase III/ IV). We also examined several potential correlates to prolonged development and implementation intervals. Results Even though phase grouping did not determine development or implementation times of either therapeutic or prevention studies, overall we observed wide variation in protocol development times. Moreover, we detected a trend toward phase III/IV therapeutic protocols exhibiting longer developmental (median 2 ½ years) and implementation times (>3years). We also found that protocols exceeding the median number of days for completing the development interval had significantly longer implementation. Limitations The use of a relatively small set of protocols may have limited our ability to detect differences across phase groupings. Some timing effects

  4. An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases

    Directory of Open Access Journals (Sweden)

    Md. Rezaul Karim

    2012-03-01

    Full Text Available Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

  5. Efficient MAC Protocol for Hybrid Wireless Network with Heterogeneous Sensor Nodes

    Directory of Open Access Journals (Sweden)

    Md. Nasre Alam

    2016-01-01

    Full Text Available Although several Directional Medium Access Control (DMAC protocols have been designed for use with homogeneous networks, it can take a substantial amount of time to change sensor nodes that are equipped with an omnidirectional antenna for sensor nodes with a directional antenna. Thus, we require a novel MAC protocol for use with an intermediate wireless network that consists of heterogeneous sensor nodes equipped with either an omnidirectional antenna or a directional antenna. The MAC protocols that have been designed for use in homogeneous networks are not suitable for use in a hybrid network due to deaf, hidden, and exposed nodes. Therefore, we propose a MAC protocol that exploits the characteristics of a directional antenna and can also work efficiently with omnidirectional nodes in a hybrid network. In order to address the deaf, hidden, and exposed node problems, we define RTS/CTS for the neighbor (RTSN/CTSN and Neighbor Information (NIP packets. The performance of the proposed MAC protocol is evaluated through a numerical analysis using a Markov model. In addition, the analytical results of the MAC protocol are verified through an OPNET simulation.

  6. Implementation and Analysis of Real-Time Streaming Protocols.

    Science.gov (United States)

    Santos-González, Iván; Rivero-García, Alexandra; Molina-Gil, Jezabel; Caballero-Gil, Pino

    2017-04-12

    Communication media have become the primary way of interaction thanks to the discovery and innovation of many new technologies. One of the most widely used communication systems today is video streaming, which is constantly evolving. Such communications are a good alternative to face-to-face meetings, and are therefore very useful for coping with many problems caused by distance. However, they suffer from different issues such as bandwidth limitation, network congestion, energy efficiency, cost, reliability and connectivity. Hence, the quality of service and the quality of experience are considered the two most important issues for this type of communication. This work presents a complete comparative study of two of the most used protocols of video streaming, Real Time Streaming Protocol (RTSP) and the Web Real-Time Communication (WebRTC). In addition, this paper proposes two new mobile applications that implement those protocols in Android whose objective is to know how they are influenced by the aspects that most affect the streaming quality of service, which are the connection establishment time and the stream reception time. The new video streaming applications are also compared with the most popular video streaming applications for Android, and the experimental results of the analysis show that the developed WebRTC implementation improves the performance of the most popular video streaming applications with respect to the stream packet delay.

  7. ASAP: A MAC Protocol for Dense and Time-Constrained RFID Systems

    Directory of Open Access Journals (Sweden)

    Kyounghwan Lee

    2007-08-01

    Full Text Available We introduce a novel medium access control (MAC protocol for radio frequency identification (RFID systems which exploits the statistical information collected at the reader. The protocol, termed adaptive slotted ALOHA protocol (ASAP, is motivated by the need to significantly improve the total read time performance of the currently suggested MAC protocols for RFID systems. In order to accomplish this task, ASAP estimates the dynamic tag population and adapts the frame size in the subsequent round via a simple policy that maximizes an appropriately defined efficiency function. We demonstrate that ASAP provides significant improvement in total read time performance over the current RFID MAC protocols. We next extend the design to accomplish reliable performance of ASAP in realistic scenarios such as the existence of constraints on frame size, and mobile RFID systems where tags move at constant velocity in the reader's field. We also consider the case where tags may fail to respond because of a physical breakdown or a temporary malfunction, and show the robustness in those scenarios as well.

  8. An Efficient Data-Gathering Routing Protocol for Underwater Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Nadeem Javaid

    2015-11-01

    Full Text Available Most applications of underwater wireless sensor networks (UWSNs demand reliable data delivery over a longer period in an efficient and timely manner. However, the harsh and unpredictable underwater environment makes routing more challenging as compared to terrestrial WSNs. Most of the existing schemes deploy mobile sensors or a mobile sink (MS to maximize data gathering. However, the relatively high deployment cost prevents their usage in most applications. Thus, this paper presents an autonomous underwater vehicle (AUV-aided efficient data-gathering (AEDG routing protocol for reliable data delivery in UWSNs. To prolong the network lifetime, AEDG employs an AUV for data collection from gateways and uses a shortest path tree (SPT algorithm while associating sensor nodes with the gateways. The AEDG protocol also limits the number of associated nodes with the gateway nodes to minimize the network energy consumption and to prevent the gateways from overloading. Moreover, gateways are rotated with the passage of time to balance the energy consumption of the network. To prevent data loss, AEDG allows dynamic data collection at the AUV depending on the limited number of member nodes that are associated with each gateway. We also develop a sub-optimal elliptical trajectory of AUV by using a connected dominating set (CDS to further facilitate network throughput maximization. The performance of the AEDG is validated via simulations, which demonstrate the effectiveness of AEDG in comparison to two existing UWSN routing protocols in terms of the selected performance metrics.

  9. An Efficient Data-Gathering Routing Protocol for Underwater Wireless Sensor Networks.

    Science.gov (United States)

    Javaid, Nadeem; Ilyas, Naveed; Ahmad, Ashfaq; Alrajeh, Nabil; Qasim, Umar; Khan, Zahoor Ali; Liaqat, Tayyaba; Khan, Majid Iqbal

    2015-11-17

    Most applications of underwater wireless sensor networks (UWSNs) demand reliable data delivery over a longer period in an efficient and timely manner. However, the harsh and unpredictable underwater environment makes routing more challenging as compared to terrestrial WSNs. Most of the existing schemes deploy mobile sensors or a mobile sink (MS) to maximize data gathering. However, the relatively high deployment cost prevents their usage in most applications. Thus, this paper presents an autonomous underwater vehicle (AUV)-aided efficient data-gathering (AEDG) routing protocol for reliable data delivery in UWSNs. To prolong the network lifetime, AEDG employs an AUV for data collection from gateways and uses a shortest path tree (SPT) algorithm while associating sensor nodes with the gateways. The AEDG protocol also limits the number of associated nodes with the gateway nodes to minimize the network energy consumption and to prevent the gateways from overloading. Moreover, gateways are rotated with the passage of time to balance the energy consumption of the network. To prevent data loss, AEDG allows dynamic data collection at the AUV depending on the limited number of member nodes that are associated with each gateway. We also develop a sub-optimal elliptical trajectory of AUV by using a connected dominating set (CDS) to further facilitate network throughput maximization. The performance of the AEDG is validated via simulations, which demonstrate the effectiveness of AEDG in comparison to two existing UWSN routing protocols in terms of the selected performance metrics.

  10. Deployment Strategies and Clustering Protocols Efficiency

    Directory of Open Access Journals (Sweden)

    Chérif Diallo

    2017-06-01

    Full Text Available Wireless sensor networks face significant design challenges due to limited computing and storage capacities and, most importantly, dependence on limited battery power. Energy is a critical resource and is often an important issue to the deployment of sensor applications that claim to be omnipresent in the world of future. Thus optimizing the deployment of sensors becomes a major constraint in the design and implementation of a WSN in order to ensure better network operations. In wireless networking, clustering techniques add scalability, reduce the computation complexity of routing protocols, allow data aggregation and then enhance the network performance. The well-known MaxMin clustering algorithm was previously generalized, corrected and validated. Then, in a previous work we have improved MaxMin by proposing a Single- node Cluster Reduction (SNCR mechanism which eliminates single-node clusters and then improve energy efficiency. In this paper, we show that MaxMin, because of its original pathological case, does not support the grid deployment topology, which is frequently used in WSN architectures. The unreliability feature of the wireless links could have negative impacts on Link Quality Indicator (LQI based clustering protocols. So, in the second part of this paper we show how our distributed Link Quality based d- Clustering Protocol (LQI-DCP has good performance in both stable and high unreliable link environments. Finally, performance evaluation results also show that LQI-DCP fully supports the grid deployment topology and is more energy efficient than MaxMin.

  11. Computer network time synchronization the network time protocol

    CERN Document Server

    Mills, David L

    2006-01-01

    What started with the sundial has, thus far, been refined to a level of precision based on atomic resonance: Time. Our obsession with time is evident in this continued scaling down to nanosecond resolution and beyond. But this obsession is not without warrant. Precision and time synchronization are critical in many applications, such as air traffic control and stock trading, and pose complex and important challenges in modern information networks.Penned by David L. Mills, the original developer of the Network Time Protocol (NTP), Computer Network Time Synchronization: The Network Time Protocol

  12. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

    Science.gov (United States)

    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

  13. An efficient and reliable multi-hop geographical broadcast protocol in vehicular ad-hoc networks

    NARCIS (Netherlands)

    Rajendran, R.; Jongh, J. de

    2013-01-01

    In Intelligent Transportation Systems (ITS), disseminating warning messages in a timely and efficient way through wireless short-range communications can save many lives and reduce traffic congestion. A geographical broadcast protocol provides data delivery to specified geographical areas, using

  14. A Power-Efficient Access Point Operation for Infrastructure Basic Service Set in IEEE 802.11 MAC Protocol

    Directory of Open Access Journals (Sweden)

    Hua Ye Ming

    2006-01-01

    Full Text Available Infrastructure-based wireless LAN technology has been widely used in today's personal communication environment. Power efficiency and battery management have been the center of attention in the design of handheld devices with wireless LAN capability. In this paper, a hybrid protocol named improved PCF operation is proposed, which intelligently chooses the access point- (AP- assisted DCF (distributed coordinator function and enhanced PCF (point coordinator function transmission mechanism of IEEE 802.11 protocol in an infrastructure-based wireless LAN environment. Received signal strength indicator (RSSI is used to determine the tradeoff between direct mobile-to-mobile transmission and transmission routed by AP. Based on the estimation, mobile stations can efficiently communicate directly instead of being routed through AP if they are in the vicinity of each other. Furthermore, a smart AP protocol is proposed as extension to the improved PCF operation by utilizing the historical end-to-end delay information to decide the waking up time of mobile stations. Simulation results show that using the proposed protocol, energy consumption of mobile devices can be reduced at the cost of slightly longer end-to-end packet delay compared to traditional IEEE 802.11 PCF protocol. However, in a non-time-critical environment, this option can significantly prolong the operation time of mobile devices.

  15. Efficient alignment of pyrosequencing reads for re-sequencing applications

    Directory of Open Access Journals (Sweden)

    Russo Luis MS

    2011-05-01

    Full Text Available Abstract Background Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects. Results We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454 system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time. Conclusions The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.

  16. An Energy-Efficient Link Layer Protocol for Reliable Transmission over Wireless Networks

    Directory of Open Access Journals (Sweden)

    Iqbal Adnan

    2009-01-01

    Full Text Available In multihop wireless networks, hop-by-hop reliability is generally achieved through positive acknowledgments at the MAC layer. However, positive acknowledgments introduce significant energy inefficiencies on battery-constrained devices. This inefficiency becomes particularly significant on high error rate channels. We propose to reduce the energy consumption during retransmissions using a novel protocol that localizes bit-errors at the MAC layer. The proposed protocol, referred to as Selective Retransmission using Virtual Fragmentation (SRVF, requires simple modifications to the positive-ACK-based reliability mechanism but provides substantial improvements in energy efficiency. The main premise of the protocol is to localize bit-errors by performing partial checksums on disjoint parts or virtual fragments of a packet. In case of error, only the corrupted virtual fragments are retransmitted. We develop stochastic models of the Simple Positive-ACK-based reliability, the previously-proposed Packet Length Optimization (PLO protocol, and the SRVF protocol operating over an arbitrary-order Markov wireless channel. Our analytical models show that SRVF provides significant theoretical improvements in energy efficiency over existing protocols. We then use bit-error traces collected over different real networks to empirically compare the proposed and existing protocols. These experimental results further substantiate that SRVF provides considerably better energy efficiency than Simple Positive-ACK and Packet Length Optimization protocols.

  17. Advertisement-Based Energy Efficient Medium Access Protocols for Wireless Sensor Networks

    Science.gov (United States)

    Ray, Surjya Sarathi

    One of the main challenges that prevents the large-scale deployment of Wireless Sensor Networks (WSNs) is providing the applications with the required quality of service (QoS) given the sensor nodes' limited energy supplies. WSNs are an important tool in supporting applications ranging from environmental and industrial monitoring, to battlefield surveillance and traffic control, among others. Most of these applications require sensors to function for long periods of time without human intervention and without battery replacement. Therefore, energy conservation is one of the main goals for protocols for WSNs. Energy conservation can be performed in different layers of the protocol stack. In particular, as the medium access control (MAC) layer can access and control the radio directly, large energy savings is possible through intelligent MAC protocol design. To maximize the network lifetime, MAC protocols for WSNs aim to minimize idle listening of the sensor nodes, packet collisions, and overhearing. Several approaches such as duty cycling and low power listening have been proposed at the MAC layer to achieve energy efficiency. In this thesis, I explore the possibility of further energy savings through the advertisement of data packets in the MAC layer. In the first part of my research, I propose Advertisement-MAC or ADV-MAC, a new MAC protocol for WSNs that utilizes the concept of advertising for data contention. This technique lets nodes listen dynamically to any desired transmission and sleep during transmissions not of interest. This minimizes the energy lost in idle listening and overhearing while maintaining an adaptive duty cycle to handle variable loads. Additionally, ADV-MAC enables energy efficient MAC-level multicasting. An analytical model for the packet delivery ratio and the energy consumption of the protocol is also proposed. The analytical model is verified with simulations and is used to choose an optimal value of the advertisement period

  18. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    Directory of Open Access Journals (Sweden)

    Farkhondeh Saba

    2017-01-01

    Full Text Available Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR. Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods:  According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results:   This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion:   Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.

  19. A Rapid and Reproducible Genomic DNA Extraction Protocol for Sequence-Based Identification of Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and Green Algae

    Directory of Open Access Journals (Sweden)

    Farkhondeh Saba

    2016-09-01

    Full Text Available Background:  Sequence-based identification of various microorganisms including Archaea, Bacteria, Cyanobacteria, Diatoms, Fungi, and green algae necessitates an efficient and reproducible genome extraction procedure though which a pure template DNA is yielded and it can be used in polymerase chain reactions (PCR. Considering the fact that DNA extraction from these microorganisms is time consuming and laborious, we developed and standardized a safe, rapid and inexpensive miniprep protocol. Methods:  According to our results, amplification of various genomic regions including SSU, LSU, ITS, β-tubulin, actin, RPB2, and EF-1 resulted in a reproducible and efficient DNA extraction from a wide range of microorganisms yielding adequate pure genomic material for reproducible PCR-amplifications. Results:   This method relies on a temporary shock of increased concentrations of detergent which can be applied concomitant with multiple freeze-thaws to yield sufficient amount of DNA for PCR amplification of multiple or single fragments(s of the genome. As an advantage, the recipe seems very flexible, thus, various optional steps can be included depending on the samples used.Conclusion:   Having the needed flexibility in each step, this protocol is applicable on a very wide range of samples. Hence, various steps can be included depending on the desired quantity and quality.

  20. HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

    Science.gov (United States)

    Wan, Shixiang; Zou, Quan

    2017-01-01

    Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

  1. Energy efficient routing protocols for wireless sensor networks: comparison and future directions

    Directory of Open Access Journals (Sweden)

    Loganathan Murukesan

    2017-01-01

    Full Text Available Wireless sensor network consists of nodes with limited resources. Hence, it is important to design protocols or algorithms which increases energy efficiency in order to improve the network lifetime. In this paper, techniques used in the network layer (routing of the internet protocol stack to achieve energy efficiency are reviewed. Usually, the routing protocols are classified into four main schemes: (1 Network Structure, (2 Communication Model, (3 Topology Based, and (4 Reliable Routing. In this work, only network structure based routing protocols are reviewed due to the page constraint. Besides, this type of protocols are much popular among the researchers since they are fairly simple to implement and produce good results as presented in this paper. Also, the pros and cons of each protocols are presented. Finally, the paper concludes with possible further research directions.

  2. Optimal conditions to use Pfu exo(-) DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols.

    Science.gov (United States)

    Angers, M; Cloutier, J F; Castonguay, A; Drouin, R

    2001-08-15

    Ligation-Mediated Polymerase Chain Reaction (LMPCR) is the most sensitive sequencing technique available to map single-stranded DNA breaks at the nucleotide level of resolution using genomic DNA. LMPCR has been adapted to map DNA damage and reveal DNA-protein interactions inside living cells. However, the sequence context (GC content), the global break frequency and the current combination of DNA polymerases used in LMPCR affect the quality of the results. In this study, we developed and optimized an LMPCR protocol adapted for Pyrococcus furiosus exo(-) DNA polymerase (Pfu exo(-)). The relative efficiency of Pfu exo(-) was compared to T7-modified DNA polymerase (Sequenase 2.0) at the primer extension step and to Thermus aquaticus DNA polymerase (Taq) at the PCR amplification step of LMPCR. At all break frequencies tested, Pfu exo(-) proved to be more efficient than Sequenase 2.0. During both primer extension and PCR amplification steps, the ratio of DNA molecules per unit of DNA polymerase was the main determinant of the efficiency of Pfu exo(-), while the efficiency of Taq was less affected by this ratio. Substitution of NaCl for KCl in the PCR reaction buffer of Taq strikingly improved the efficiency of the DNA polymerase. Pfu exo(-) was clearly more efficient than Taq to specifically amplify extremely GC-rich genomic DNA sequences. Our results show that a combination of Pfu exo(-) at the primer extension step and Taq at the PCR amplification step is ideal for in vivo DNA analysis and DNA damage mapping using LMPCR.

  3. Efficient Cooperative Protocols for Full-Duplex Relaying over Nakagami-m Fading Channels

    KAUST Repository

    Khafagy, Mohammad Galal

    2015-02-24

    In this work, efficient protocols are studied for full-duplex relaying (FDR) with loopback interference over Nakagami-m block fading channels. Recently, a selective decodeand- forward (DF) protocol was proposed for FDR, and was shown to outperform existing protocols in terms of outage over Rayleigh-fading channels. In this work, we propose an incremental selective DF protocol that offers additional power savings, yet yields the same outage performance. We evaluate their outage performance over independent non-identically distributed Nakagami-m fading links, and study their relative performance in terms of the signal-to-noise ratio cumulative distribution function via closed-form expressions. The offered diversity gain is also derived. In addition, we study their performance relative to their half-duplex counterparts, as well as known non-selective FDR protocols. We corroborate our theoretical results with simulation, and confirm that selective cooperation protocols outperform the known non-selective protocols in terms of outage. Finally, we show that depending on the loopback interference level, the proposed protocols can outperform their half-duplex counterparts when high spectral efficiencies are targeted.

  4. Efficient Cooperative Protocols for Full-Duplex Relaying over Nakagami-m Fading Channels

    KAUST Repository

    Khafagy, Mohammad Galal; Tammam, Amr; Alouini, Mohamed-Slim; Aissa, Sonia

    2015-01-01

    In this work, efficient protocols are studied for full-duplex relaying (FDR) with loopback interference over Nakagami-m block fading channels. Recently, a selective decodeand- forward (DF) protocol was proposed for FDR, and was shown to outperform existing protocols in terms of outage over Rayleigh-fading channels. In this work, we propose an incremental selective DF protocol that offers additional power savings, yet yields the same outage performance. We evaluate their outage performance over independent non-identically distributed Nakagami-m fading links, and study their relative performance in terms of the signal-to-noise ratio cumulative distribution function via closed-form expressions. The offered diversity gain is also derived. In addition, we study their performance relative to their half-duplex counterparts, as well as known non-selective FDR protocols. We corroborate our theoretical results with simulation, and confirm that selective cooperation protocols outperform the known non-selective protocols in terms of outage. Finally, we show that depending on the loopback interference level, the proposed protocols can outperform their half-duplex counterparts when high spectral efficiencies are targeted.

  5. User-oriented end-to-end transport protocols for the real-time distribution of telemetry data from NASA spacecraft

    Science.gov (United States)

    Hooke, A. J.

    1979-01-01

    A set of standard telemetry protocols for downlink data flow facilitating the end-to-end transport of instrument data from the spacecraft to the user in real time is proposed. The direct switching of data by autonomous message 'packets' that are assembled by the source instrument on the spacecraft is discussed. The data system consists thus of a format on a message rather than word basis, and such packet telemetry would include standardized protocol headers. Standards are being developed within the NASA End-to-End Data System (NEEDS) program for the source packet and transport frame protocols. The source packet protocol contains identification of both the sequence number of the packet as it is generated by the source and the total length of the packet, while the transport frame protocol includes a sequence count defining the serial number of the frame as it is generated by the spacecraft data system, and a field specifying any 'options' selected in the format of the frame itself.

  6. Cost-Effective Encryption-Based Autonomous Routing Protocol for Efficient and Secure Wireless Sensor Networks.

    Science.gov (United States)

    Saleem, Kashif; Derhab, Abdelouahid; Orgun, Mehmet A; Al-Muhtadi, Jalal; Rodrigues, Joel J P C; Khalil, Mohammed Sayim; Ali Ahmed, Adel

    2016-03-31

    The deployment of intelligent remote surveillance systems depends on wireless sensor networks (WSNs) composed of various miniature resource-constrained wireless sensor nodes. The development of routing protocols for WSNs is a major challenge because of their severe resource constraints, ad hoc topology and dynamic nature. Among those proposed routing protocols, the biology-inspired self-organized secure autonomous routing protocol (BIOSARP) involves an artificial immune system (AIS) that requires a certain amount of time to build up knowledge of neighboring nodes. The AIS algorithm uses this knowledge to distinguish between self and non-self neighboring nodes. The knowledge-building phase is a critical period in the WSN lifespan and requires active security measures. This paper proposes an enhanced BIOSARP (E-BIOSARP) that incorporates a random key encryption mechanism in a cost-effective manner to provide active security measures in WSNs. A detailed description of E-BIOSARP is presented, followed by an extensive security and performance analysis to demonstrate its efficiency. A scenario with E-BIOSARP is implemented in network simulator 2 (ns-2) and is populated with malicious nodes for analysis. Furthermore, E-BIOSARP is compared with state-of-the-art secure routing protocols in terms of processing time, delivery ratio, energy consumption, and packet overhead. The findings show that the proposed mechanism can efficiently protect WSNs from selective forwarding, brute-force or exhaustive key search, spoofing, eavesdropping, replaying or altering of routing information, cloning, acknowledgment spoofing, HELLO flood attacks, and Sybil attacks.

  7. Cost-Effective Encryption-Based Autonomous Routing Protocol for Efficient and Secure Wireless Sensor Networks

    Science.gov (United States)

    Saleem, Kashif; Derhab, Abdelouahid; Orgun, Mehmet A.; Al-Muhtadi, Jalal; Rodrigues, Joel J. P. C.; Khalil, Mohammed Sayim; Ali Ahmed, Adel

    2016-01-01

    The deployment of intelligent remote surveillance systems depends on wireless sensor networks (WSNs) composed of various miniature resource-constrained wireless sensor nodes. The development of routing protocols for WSNs is a major challenge because of their severe resource constraints, ad hoc topology and dynamic nature. Among those proposed routing protocols, the biology-inspired self-organized secure autonomous routing protocol (BIOSARP) involves an artificial immune system (AIS) that requires a certain amount of time to build up knowledge of neighboring nodes. The AIS algorithm uses this knowledge to distinguish between self and non-self neighboring nodes. The knowledge-building phase is a critical period in the WSN lifespan and requires active security measures. This paper proposes an enhanced BIOSARP (E-BIOSARP) that incorporates a random key encryption mechanism in a cost-effective manner to provide active security measures in WSNs. A detailed description of E-BIOSARP is presented, followed by an extensive security and performance analysis to demonstrate its efficiency. A scenario with E-BIOSARP is implemented in network simulator 2 (ns-2) and is populated with malicious nodes for analysis. Furthermore, E-BIOSARP is compared with state-of-the-art secure routing protocols in terms of processing time, delivery ratio, energy consumption, and packet overhead. The findings show that the proposed mechanism can efficiently protect WSNs from selective forwarding, brute-force or exhaustive key search, spoofing, eavesdropping, replaying or altering of routing information, cloning, acknowledgment spoofing, HELLO flood attacks, and Sybil attacks. PMID:27043572

  8. Cost-Effective Encryption-Based Autonomous Routing Protocol for Efficient and Secure Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Kashif Saleem

    2016-03-01

    Full Text Available The deployment of intelligent remote surveillance systems depends on wireless sensor networks (WSNs composed of various miniature resource-constrained wireless sensor nodes. The development of routing protocols for WSNs is a major challenge because of their severe resource constraints, ad hoc topology and dynamic nature. Among those proposed routing protocols, the biology-inspired self-organized secure autonomous routing protocol (BIOSARP involves an artificial immune system (AIS that requires a certain amount of time to build up knowledge of neighboring nodes. The AIS algorithm uses this knowledge to distinguish between self and non-self neighboring nodes. The knowledge-building phase is a critical period in the WSN lifespan and requires active security measures. This paper proposes an enhanced BIOSARP (E-BIOSARP that incorporates a random key encryption mechanism in a cost-effective manner to provide active security measures in WSNs. A detailed description of E-BIOSARP is presented, followed by an extensive security and performance analysis to demonstrate its efficiency. A scenario with E-BIOSARP is implemented in network simulator 2 (ns-2 and is populated with malicious nodes for analysis. Furthermore, E-BIOSARP is compared with state-of-the-art secure routing protocols in terms of processing time, delivery ratio, energy consumption, and packet overhead. The findings show that the proposed mechanism can efficiently protect WSNs from selective forwarding, brute-force or exhaustive key search, spoofing, eavesdropping, replaying or altering of routing information, cloning, acknowledgment spoofing, HELLO flood attacks, and Sybil attacks.

  9. A Microfluidic Device for Preparing Next Generation DNA Sequencing Libraries and for Automating Other Laboratory Protocols That Require One or More Column Chromatography Steps

    Science.gov (United States)

    Tan, Swee Jin; Phan, Huan; Gerry, Benjamin Michael; Kuhn, Alexandre; Hong, Lewis Zuocheng; Min Ong, Yao; Poon, Polly Suk Yean; Unger, Marc Alexander; Jones, Robert C.; Quake, Stephen R.; Burkholder, William F.

    2013-01-01

    Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation. PMID:23894273

  10. A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.

    Directory of Open Access Journals (Sweden)

    Swee Jin Tan

    Full Text Available Library preparation for next-generation DNA sequencing (NGS remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.

  11. A hybrid MAC protocol design for energy-efficient very-high-throughput millimeter wave, wireless sensor communication networks

    Science.gov (United States)

    Jian, Wei; Estevez, Claudio; Chowdhury, Arshad; Jia, Zhensheng; Wang, Jianxin; Yu, Jianguo; Chang, Gee-Kung

    2010-12-01

    This paper presents an energy-efficient Medium Access Control (MAC) protocol for very-high-throughput millimeter-wave (mm-wave) wireless sensor communication networks (VHT-MSCNs) based on hybrid multiple access techniques of frequency division multiplexing access (FDMA) and time division multiplexing access (TDMA). An energy-efficient Superframe for wireless sensor communication network employing directional mm-wave wireless access technologies is proposed for systems that require very high throughput, such as high definition video signals, for sensing, processing, transmitting, and actuating functions. Energy consumption modeling for each network element and comparisons among various multi-access technologies in term of power and MAC layer operations are investigated for evaluating the energy-efficient improvement of proposed MAC protocol.

  12. An energy-efficient MAC protocol using dynamic queue management for delay-tolerant mobile sensor networks.

    Science.gov (United States)

    Li, Jie; Li, Qiyue; Qu, Yugui; Zhao, Baohua

    2011-01-01

    Conventional MAC protocols for wireless sensor network perform poorly when faced with a delay-tolerant mobile network environment. Characterized by a highly dynamic and sparse topology, poor network connectivity as well as data delay-tolerance, delay-tolerant mobile sensor networks exacerbate the severe power constraints and memory limitations of nodes. This paper proposes an energy-efficient MAC protocol using dynamic queue management (EQ-MAC) for power saving and data queue management. Via data transfers initiated by the target sink and the use of a dynamic queue management strategy based on priority, EQ-MAC effectively avoids untargeted transfers, increases the chance of successful data transmission, and makes useful data reach the target terminal in a timely manner. Experimental results show that EQ-MAC has high energy efficiency in comparison with a conventional MAC protocol. It also achieves a 46% decrease in packet drop probability, 79% increase in system throughput, and 25% decrease in mean packet delay.

  13. An Energy-Efficient MAC Protocol Using Dynamic Queue Management for Delay-Tolerant Mobile Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yugui Qu

    2011-02-01

    Full Text Available Conventional MAC protocols for wireless sensor network perform poorly when faced with a delay-tolerant mobile network environment. Characterized by a highly dynamic and sparse topology, poor network connectivity as well as data delay-tolerance, delay-tolerant mobile sensor networks exacerbate the severe power constraints and memory limitations of nodes. This paper proposes an energy-efficient MAC protocol using dynamic queue management (EQ-MAC for power saving and data queue management. Via data transfers initiated by the target sink and the use of a dynamic queue management strategy based on priority, EQ-MAC effectively avoids untargeted transfers, increases the chance of successful data transmission, and makes useful data reach the target terminal in a timely manner. Experimental results show that EQ-MAC has high energy efficiency in comparison with a conventional MAC protocol. It also achieves a 46% decrease in packet drop probability, 79% increase in system throughput, and 25% decrease in mean packet delay.

  14. Efficiency of different protocols for enamel clean-up after bracket debonding: an in vitro study

    Directory of Open Access Journals (Sweden)

    Lara Carvalho Freitas Sigilião

    2015-10-01

    Full Text Available Objective: This study aimed to assess the efficiency of six protocols for cleaning-up tooth enamel after bracket debonding.Methods:A total of 60 premolars were divided into six groups, according to the tools used for clean-up: 12-blade bur at low speed (G12L, 12-blade bur at high speed (G12H, 30-blade bur at low speed (G30L, DU10CO ORTHO polisher (GDU, Renew System (GR and Diagloss polisher (GD. Mean roughness (Ra and mean roughness depth (Rz of enamel surface were analyzed with a profilometer. Paired t-test was used to assess Ra and Rz before and after enamel clean-up. ANOVA/Tukey tests were used for intergroup comparison. The duration of removal procedures was recorded. The association between time and variation in enamel roughness (∆Ra, ∆Rz were evaluated by Pearson's correlation test. Enamel topography was assessed by scanning electron microscopy (SEM.Results:In Groups G12L and G12H, original enamel roughness did not change significantly. In Groups G30L, GDU, GR and GD, a smoother surface (p < 0.05 was found after clean-up. In Groups G30L and GD, the protocols used were more time-consuming than those used in the other groups. Negative and moderate correlation was observed between time and (∆Ra, ∆Rz; Ra and (∆Ra, ∆Rz; Rz (r = - 0.445, r = - 0.475, p < 0.01.Conclusion:All enamel clean-up protocols were efficient because they did not result in increased surface roughness. The longer the time spent performing the protocol, the lower the surface roughness.

  15. An efficient three-party password-based key agreement protocol using extended chaotic maps

    International Nuclear Information System (INIS)

    Shu Jian

    2015-01-01

    Three-party password-based key agreement protocols allow two users to authenticate each other via a public channel and establish a session key with the aid of a trusted server. Recently, Farash et al. [Farash M S, Attari M A 2014 “An efficient and provably secure three-party password-based authenticated key exchange protocol based on Chebyshev chaotic maps”, Nonlinear Dynamics 77(7): 399–411] proposed a three-party key agreement protocol by using the extended chaotic maps. They claimed that their protocol could achieve strong security. In the present paper, we analyze Farash et al.’s protocol and point out that this protocol is vulnerable to off-line password guessing attack and suffers communication burden. To handle the issue, we propose an efficient three-party password-based key agreement protocol using extended chaotic maps, which uses neither symmetric cryptosystems nor the server’s public key. Compared with the relevant schemes, our protocol provides better performance in terms of computation and communication. Therefore, it is suitable for practical applications. (paper)

  16. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  17. An efficient two-party quantum private comparison protocol with decoy photons and two-photon entanglement

    International Nuclear Information System (INIS)

    Yang Yuguang; Wen Qiaoyan

    2009-01-01

    Following some ideas of the quantum secret sharing (QSS) protocol (2008, Phys. Lett. A 372, 1957), we propose an efficient quantum private comparison (QPC) protocol for comparing information of equality with the help of a third party (TP). The protocol can ensure fairness, efficiency and security. The protocol is fair, which means that one party knows the sound result of the comparison if and only if the other one knows the result. The protocol is efficient with the help of the TP for calculating. However, the TP cannot learn any information about the players' respective private inputs and even about the comparison result and cannot collude with any player. The protocol is secure for the two players, that is, any information about their respective secret inputs will not leak except the final computation result. A precise proof of security of the protocol is presented. Applications of this protocol may include private bidding and auctions, secret ballot elections, commercial business, identification in a number of scenarios and so on

  18. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq.

    Science.gov (United States)

    Marchal, Claire; Sasaki, Takayo; Vera, Daniel; Wilson, Korey; Sima, Jiao; Rivera-Mulia, Juan Carlos; Trevilla-García, Claudia; Nogues, Coralin; Nafie, Ebtesam; Gilbert, David M

    2018-05-01

    This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and subnuclear position. Moreover, RT is regulated during development and is altered in diseases. Here, we describe E/L Repli-seq, an extension of our Repli-chip protocol. E/L Repli-seq is a rapid, robust and relatively inexpensive protocol for analyzing RT by next-generation sequencing (NGS), allowing genome-wide assessment of how cellular processes are linked to RT. Briefly, cells are pulse-labeled with BrdU, and early and late S-phase fractions are sorted by flow cytometry. Labeled nascent DNA is immunoprecipitated from both fractions and sequenced. Data processing leads to a single bedGraph file containing the ratio of nascent DNA from early versus late S-phase fractions. The results are comparable to those of Repli-chip, with the additional benefits of genome-wide sequence information and an increased dynamic range. We also provide computational pipelines for downstream analyses, for parsing phased genomes using single-nucleotide polymorphisms (SNPs) to analyze RT allelic asynchrony, and for direct comparison to Repli-chip data. This protocol can be performed in up to 3 d before sequencing, and requires basic cellular and molecular biology skills, as well as a basic understanding of Unix and R.

  19. Efficient production of isotopically labeled proteins by cell-free synthesis: A practical protocol

    Energy Technology Data Exchange (ETDEWEB)

    Torizawa, Takuya; Shimizu, Masato [Crest, Jst (Japan); Taoka, Masato [Tokyo Metropolitan University, Graduate School of Science (Japan); Miyano, Hiroshi [Ajinomoto Co., Inc. Institute of Life Sciences (Japan); Kainosho, Masatsune [Crest, Jst (Japan)], E-mail: kainosho@nmr.chem.metro-u.ac.jp

    2004-11-15

    We provide detailed descriptions of our refined protocols for the cell-free production of labeled protein samples for NMR spectroscopy. These methods are efficient and overcome two critical problems associated with the use of conventional Escherichia coli extract systems. Endogenous amino acids normally present in E. coli S30 extracts dilute the added labeled amino acids and degrade the quality of NMR spectra of the target protein. This problem was solved by altering the protocol used in preparing the S30 extract so as to minimize the content of endogenous amino acids. The second problem encountered in conventional E. coli cell-free protein production is non-uniformity in the N-terminus of the target protein, which can complicate the NMR spectra. This problem was solved by adding a DNA sequence to the construct that codes for a cleavable N-terminal peptide tag. Addition of the tag serves to increase the yield of the protein as well as to ensure a homogeneous protein product following tag cleavage. We illustrate the method by describing its stepwise application to the production of calmodulin samples with different stable isotope labeling patterns for NMR analysis.

  20. Efficient production of isotopically labeled proteins by cell-free synthesis: A practical protocol

    International Nuclear Information System (INIS)

    Torizawa, Takuya; Shimizu, Masato; Taoka, Masato; Miyano, Hiroshi; Kainosho, Masatsune

    2004-01-01

    We provide detailed descriptions of our refined protocols for the cell-free production of labeled protein samples for NMR spectroscopy. These methods are efficient and overcome two critical problems associated with the use of conventional Escherichia coli extract systems. Endogenous amino acids normally present in E. coli S30 extracts dilute the added labeled amino acids and degrade the quality of NMR spectra of the target protein. This problem was solved by altering the protocol used in preparing the S30 extract so as to minimize the content of endogenous amino acids. The second problem encountered in conventional E. coli cell-free protein production is non-uniformity in the N-terminus of the target protein, which can complicate the NMR spectra. This problem was solved by adding a DNA sequence to the construct that codes for a cleavable N-terminal peptide tag. Addition of the tag serves to increase the yield of the protein as well as to ensure a homogeneous protein product following tag cleavage. We illustrate the method by describing its stepwise application to the production of calmodulin samples with different stable isotope labeling patterns for NMR analysis

  1. QTL analysis by sequencing of Water Use Efficiency (WUE) in potato

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Sønderkær, Mads; Sørensen, Kirsten Kørup

    2013-01-01

    The traditional approach to potato breeding, the classical “mate and phenotype” approach is relatively costly and because phenotyping and growth capacity is limited, this are being slowly replaced by Marker Assisted Selection (MAS) breeding schemes. MAS is based on the presence of DNA polymorphic.......sparsipilum), phenotyped for water use efficiency. This population has also previously been phenotyped for the total glycoalkaloid (TGA) content....... and time consuming process. Here, a novel method for Quantitative Trait Locus (QTL) analysis has been developed, that allows for development of specific markers by use of genomic sequence reads and the recently published reference genome sequence for potato. Prior to sequencing the mapping population...

  2. Alignment efficiency and discomfort of three orthodontic archwire sequences: a randomized clinical trial.

    Science.gov (United States)

    Ong, Emily; Ho, Christopher; Miles, Peter

    2011-03-01

    To compare the efficiency of orthodontic archwire sequences produced by three manufacturers. Prospective, randomized clinical trial with three parallel groups. Private orthodontic practice in Caloundra, QLD, Australia. One hundred and thirty-two consecutive patients were randomized to one of three archwire sequence groups: (i) 3M Unitek, 0·014 inch Nitinol, 0·017 inch × 0·017 inch heat activated Ni-Ti; (ii) GAC international, 0·014 inch Sentalloy, 0·016 × 0·022 inch Bioforce; and (iii) Ormco corporation, 0·014 inch Damon Copper Ni-Ti, 0·014 × 0·025 inch Damon Copper Ni-Ti. All patients received 0·018 × 0·025 inch slot Victory Series™ brackets. Mandibular impressions were taken before the insertion of each archwire. Patients completed discomfort surveys according to a seven-point Likert Scale at 4 h, 24 h, 3 days and 7 days after the insertion of each archwire. Efficiency was measured by time required to reach the working archwire, mandibular anterior alignment and level of discomfort. No significant differences were found in the reduction of irregularity between the archwire sequences at any time-point (T1: P = 0·12; T2: P = 0·06; T3: P = 0·21) or in the time to reach the working archwire (P = 0·28). No significant differences were found in the overall discomfort scores between the archwire sequences (4 h: P = 0·30; 24 h: P = 0·18; 3 days: P = 0·53; 7 days: P = 0·47). When the time-points were analysed individually, the 3M Unitek archwire sequence induced significantly less discomfort than GAC and Ormco archwires 24 h after the insertion of the third archwire (P = 0·02). This could possibly be attributed to the progression in archwire material and archform. The archwire sequences were similar in alignment efficiency and overall discomfort. Progression in archwire dimension and archform may contribute to discomfort levels. This study provides clinical justification for three common archwire sequences in 0·018 × 0·025 inch slot brackets.

  3. Computationally Efficient Chaotic Spreading Sequence Selection for Asynchronous DS-CDMA

    Directory of Open Access Journals (Sweden)

    Litviņenko Anna

    2017-12-01

    Full Text Available The choice of the spreading sequence for asynchronous direct-sequence code-division multiple-access (DS-CDMA systems plays a crucial role for the mitigation of multiple-access interference. Considering the rich dynamics of chaotic sequences, their use for spreading allows overcoming the limitations of the classical spreading sequences. However, to ensure low cross-correlation between the sequences, careful selection must be performed. This paper presents a novel exhaustive search algorithm, which allows finding sets of chaotic spreading sequences of required length with a particularly low mutual cross-correlation. The efficiency of the search is verified by simulations, which show a significant advantage compared to non-selected chaotic sequences. Moreover, the impact of sequence length on the efficiency of the selection is studied.

  4. A Gossip-based Energy Efficient Protocol for Robust In-network Aggregation in Wireless Sensor Networks

    Science.gov (United States)

    Fauji, Shantanu

    We consider the problem of energy efficient and fault tolerant in--network aggregation for wireless sensor networks (WSNs). In-network aggregation is the process of aggregation while collecting data from sensors to the base station. This process should be energy efficient due to the limited energy at the sensors and tolerant to the high failure rates common in sensor networks. Tree based in--network aggregation protocols, although energy efficient, are not robust to network failures. Multipath routing protocols are robust to failures to a certain degree but are not energy efficient due to the overhead in the maintenance of multiple paths. We propose a new protocol for in-network aggregation in WSNs, which is energy efficient, achieves high lifetime, and is robust to the changes in the network topology. Our protocol, gossip--based protocol for in-network aggregation (GPIA) is based on the spreading of information via gossip. GPIA is not only adaptive to failures and changes in the network topology, but is also energy efficient. Energy efficiency of GPIA comes from all the nodes being capable of selective message reception and detecting convergence of the aggregation early. We experimentally show that GPIA provides significant improvement over some other competitors like the Ridesharing, Synopsis Diffusion and the pure version of gossip. GPIA shows ten fold, five fold and two fold improvement over the pure gossip, the synopsis diffusion and Ridesharing protocols in terms of network lifetime, respectively. Further, GPIA retains gossip's robustness to failures and improves upon the accuracy of synopsis diffusion and Ridesharing.

  5. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis

    DEFF Research Database (Denmark)

    Leon, Ileana R; Schwämmle, Veit; Jensen, Ole N

    2013-01-01

    a combination of qualitative and quantitative LC-MS/MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein...... conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents prior to analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative LC-MS/MS workflow quantified over 3700 distinct peptides with 96% completeness between all...... protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows...

  6. Securing statically-verified communications protocols against timing attacks

    DEFF Research Database (Denmark)

    Buchholtz, Mikael; Gilmore, Stephen; Hillston, Jane

    2004-01-01

    We present a federated analysis of communication protocols which considers both security properties and timing. These are not entirely independent observations of a protocol; by using timing observations of an executing protocol it is possible to deduce derived information about the nature...... of the communication even in the presence of unbreakable encryption. Our analysis is based on expressing the protocol as a process algebra model and deriving from this process models analysable by the Imperial PEPA Compiler and the LySatool....

  7. Accessibility in Public Buildings: Efficiency of Checklist Protocols.

    Science.gov (United States)

    Andersson, Jonas E; Skehan, Terry

    2016-01-01

    In Sweden, governmental agencies and bodies are required to implement a higher level of accessibility in their buildings than that stipulated by the National Building and Planning Act (PBL). The Swedish Agency for Participation (MFD, Myndigheten för delaktighet) develops holistic guidelines in order to conceptualize this higher level of accessibility. In conjunction to these guidelines, various checklist protocols have been produced. The present study focuses on the efficiency of such checklist protocols. The study revolved around the use of a checklist protocol in assessments of two buildings in Stockholm: the new head office for the National Authority for Social Insurances (ASI) and the School of Architecture at the Royal Institute of Technology (KTH). The study included three groups: Group 1 and Group 2 consisted of 50 real estate managers employed by the ASI, while Group 3 consisted of three participants in a course at the KTH. The results were similar in all of the groups. The use of the checklist protocol generated queries, which related mainly to two factors: (1) the accompanying factsheet consisted of textual explanations with no drawings, photographs or illustrations and (2) the order of the questions in the checklist protocol was difficult to correlate with the two buildings' spatial logic of accessing, egressing and making use of the built space.

  8. A Comparison Between Inter-Asterisk eXchange Protocol and Jingle Protocol: Session Time

    Directory of Open Access Journals (Sweden)

    H. S. Haj Aliwi

    2016-08-01

    Full Text Available Over the last few years, many multimedia conferencing and Voice over Internet Protocol (VoIP applications have been developed due to the use of signaling protocols in providing video, audio and text chatting services between at least two participants. This paper compares between two widely common signaling protocols: InterAsterisk eXchange Protocol (IAX and the extension of the eXtensible Messaging and Presence Protocol (Jingle in terms of delay time during call setup, call teardown, and media sessions.

  9. Efficient Communication Protocols for Deciding Edit Distance

    DEFF Research Database (Denmark)

    Jowhari, Hossein

    2012-01-01

    In this paper we present two communication protocols on computing edit distance. In our first result, we give a one-way protocol for the following Document Exchange problem. Namely given x ∈ Σn to Alice and y ∈ Σn to Bob and integer k to both, Alice sends a message to Bob so that he learns x...... or truthfully reports that the edit distance between x and y is greater than k. For this problem, we give a randomized protocol in which Alice transmits at most O ˜ (klog 2 n) bits and each party’s time complexity is O ˜ (nlogn+k 2 log 2 n) . Our second result is a simultaneous protocol for edit distance over...... permutations. Here Alice and Bob both send a message to a third party (the referee) who does not have access to the input strings. Given the messages, the referee decides if the edit distance between x and y is at most k or not. For this problem we give a protocol in which Alice and Bob run a O...

  10. A Distributed Snapshot Protocol for Efficient Artificial Intelligence Computation in Cloud Computing Environments

    Directory of Open Access Journals (Sweden)

    JongBeom Lim

    2018-01-01

    Full Text Available Many artificial intelligence applications often require a huge amount of computing resources. As a result, cloud computing adoption rates are increasing in the artificial intelligence field. To support the demand for artificial intelligence applications and guarantee the service level agreement, cloud computing should provide not only computing resources but also fundamental mechanisms for efficient computing. In this regard, a snapshot protocol has been used to create a consistent snapshot of the global state in cloud computing environments. However, the existing snapshot protocols are not optimized in the context of artificial intelligence applications, where large-scale iterative computation is the norm. In this paper, we present a distributed snapshot protocol for efficient artificial intelligence computation in cloud computing environments. The proposed snapshot protocol is based on a distributed algorithm to run interconnected multiple nodes in a scalable fashion. Our snapshot protocol is able to deal with artificial intelligence applications, in which a large number of computing nodes are running. We reveal that our distributed snapshot protocol guarantees the correctness, safety, and liveness conditions.

  11. Chapter 2: Commercial and Industrial Lighting Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

    Energy Technology Data Exchange (ETDEWEB)

    Kurnik, Charles W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Gowans, Dakers [Left Fork Energy, Harrison, NY (United States); Telarico, Chad [DNV GL, Mahwah, NJ (United States)

    2017-11-02

    The Commercial and Industrial Lighting Evaluation Protocol (the protocol) describes methods to account for gross energy savings resulting from the programmatic installation of efficient lighting equipment in large populations of commercial, industrial, and other nonresidential facilities. This protocol does not address savings resulting from changes in codes and standards, or from education and training activities. A separate Uniform Methods Project (UMP) protocol, Chapter 3: Commercial and Industrial Lighting Controls Evaluation Protocol, addresses methods for evaluating savings resulting from lighting control measures such as adding time clocks, tuning energy management system commands, and adding occupancy sensors.

  12. An energy-efficient data gathering protocol in large wireless sensor network

    Science.gov (United States)

    Wang, Yamin; Zhang, Ruihua; Tao, Shizhong

    2006-11-01

    Wireless sensor network consisting of a large number of small sensors with low-power transceiver can be an effective tool for gathering data in a variety of environment. The collected data must be transmitted to the base station for further processing. Since a network consists of sensors with limited battery energy, the method for data gathering and routing must be energy efficient in order to prolong the lifetime of the network. In this paper, we presented an energy-efficient data gathering protocol in wireless sensor network. The new protocol used data fusion technology clusters nodes into groups and builds a chain among the cluster heads according to a hybrid of the residual energy and distance to the base station. Results in stochastic geometry are used to derive the optimum parameter of our algorithm that minimizes the total energy spent in the network. Simulation results show performance superiority of the new protocol.

  13. Efficient forward propagation of time-sequences in convolutional neural networks using Deep Shifting

    NARCIS (Netherlands)

    K.L. Groenland (Koen); S.M. Bohte (Sander)

    2016-01-01

    textabstractWhen a Convolutional Neural Network is used for on-the-fly evaluation of continuously updating time-sequences, many redundant convolution operations are performed. We propose the method of Deep Shifting, which remembers previously calculated results of convolution operations in order

  14. Energy efficient medium access protocol for wireless medical body area sensor networks.

    Science.gov (United States)

    Omeni, O; Wong, A; Burdett, A J; Toumazou, C

    2008-12-01

    This paper presents a novel energy-efficient MAC Protocol designed specifically for wireless body area sensor networks (WBASN) focused towards pervasive healthcare applications. Wireless body area networks consist of wireless sensor nodes attached to the human body to monitor vital signs such as body temperature, activity or heart-rate. The network adopts a master-slave architecture, where the body-worn slave node periodically sends sensor readings to a central master node. Unlike traditional peer-to-peer wireless sensor networks, the nodes in this biomedical WBASN are not deployed in an ad hoc fashion. Joining a network is centrally managed and all communications are single-hop. To reduce energy consumption, all the sensor nodes are in standby or sleep mode until the centrally assigned time slot. Once a node has joined a network, there is no possibility of collision within a cluster as all communication is initiated by the central node and is addressed uniquely to a slave node. To avoid collisions with nearby transmitters, a clear channel assessment algorithm based on standard listen-before-transmit (LBT) is used. To handle time slot overlaps, the novel concept of a wakeup fallback time is introduced. Using single-hop communication and centrally controlled sleep/wakeup times leads to significant energy reductions for this application compared to more ldquoflexiblerdquo network MAC protocols such as 802.11 or Zigbee. As duty cycle is reduced, the overall power consumption approaches the standby power. The protocol is implemented in hardware as part of the Sensiumtrade system-on-chip WBASN ASIC, in a 0.13- mum CMOS process.

  15. An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

    Science.gov (United States)

    Yuan, Yongxian; Xu, Huaiqian; Leung, Ross Ka-Kit

    2016-05-26

    Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown. By using universal human reference RNA as the initial material, RNaseIII and chemical fragmentation methods in library construction showed similar result in gene and junction discovery number and expression level estimated accuracy. In contrast, sequencing quality, read length and the choice of software affected mapping rate to a much larger extent. Unspliced aligner TMAP attained the highest mapping rate (97.27 % to genome, 86.46 % to transcriptome), though 47.83 % of mapped reads were clipped. Long reads could paradoxically reduce mapping in junctions. With reference annotation guide, the mapping rate of TopHat2 significantly increased from 75.79 to 92.09 %, especially for long (>150 bp) reads. Sailfish, a k-mer based gene expression quantifier attained highly consistent results with that of TaqMan array and highest sensitivity. We provided for the first time, the reference statistics of library preparation methods, gene detection and quantification and junction discovery for RNA-Seq by the Ion Proton platform. Chemical fragmentation performed equally well with the enzyme-based one. The optimal Ion Proton sequencing options and analysis software have been evaluated.

  16. TreeMAC: Localized TDMA MAC protocol for real-time high-data-rate sensor networks

    Science.gov (United States)

    Song, W.-Z.; Huang, R.; Shirazi, B.; Husent, R.L.

    2009-01-01

    Earlier sensor network MAC protocols focus on energy conservation in low-duty cycle applications, while some recent applications involve real-time high-data-rate signals. This motivates us to design an innovative localized TDMA MAC protocol to achieve high throughput and low congestion in data collection sensor networks, besides energy conservation. TreeMAC divides a time cycle into frames and frame into slots. Parent determines children's frame assigmnent based on their relative bandwidth demand, and each node calculates its own slot assignment based on its hop-count to the sink. This innovative 2-dimensional frame-slot assignment algorithm has the following nice theory properties. Firstly, given any node, at any time slot, there is at most one active sender in its neighborhood (includ ing itself). Secondly, the packet scheduling with TreelMAC is bufferless, which therefore minimizes the probability of network congestion. Thirdly, the data throughput to gateway is at least 1/3 of the optimum assuming reliable links. Our experiments on a 24 node test bed demonstrate that TreeMAC protocol significantly improves network throughput and energy efficiency, by comparing to the TinyOS's default CSMA MAC protocol and a recent TDMA MAC protocol Funneling-MAC[8]. ?? 2009 IEEE.

  17. An Efficient and Secure Certificateless Authentication Protocol for Healthcare System on Wireless Medical Sensor Networks

    Science.gov (United States)

    Guo, Rui; Wen, Qiaoyan; Jin, Zhengping; Zhang, Hua

    2013-01-01

    Sensor networks have opened up new opportunities in healthcare systems, which can transmit patient's condition to health professional's hand-held devices in time. The patient's physiological signals are very sensitive and the networks are extremely vulnerable to many attacks. It must be ensured that patient's privacy is not exposed to unauthorized entities. Therefore, the control of access to healthcare systems has become a crucial challenge. An efficient and secure authentication protocol will thus be needed in wireless medical sensor networks. In this paper, we propose a certificateless authentication scheme without bilinear pairing while providing patient anonymity. Compared with other related protocols, the proposed scheme needs less computation and communication cost and preserves stronger security. Our performance evaluations show that this protocol is more practical for healthcare system in wireless medical sensor networks. PMID:23710147

  18. 1-RAAP: An Efficient 1-Round Anonymous Authentication Protocol for Wireless Body Area Networks.

    Science.gov (United States)

    Liu, Jingwei; Zhang, Lihuan; Sun, Rong

    2016-05-19

    Thanks to the rapid technological convergence of wireless communications, medical sensors and cloud computing, Wireless Body Area Networks (WBANs) have emerged as a novel networking paradigm enabling ubiquitous Internet services, allowing people to receive medical care, monitor health status in real-time, analyze sports data and even enjoy online entertainment remotely. However, because of the mobility and openness of wireless communications, WBANs are inevitably exposed to a large set of potential attacks, significantly undermining their utility and impeding their widespread deployment. To prevent attackers from threatening legitimate WBAN users or abusing WBAN services, an efficient and secure authentication protocol termed 1-Round Anonymous Authentication Protocol (1-RAAP) is proposed in this paper. In particular, 1-RAAP preserves anonymity, mutual authentication, non-repudiation and some other desirable security properties, while only requiring users to perform several low cost computational operations. More importantly, 1-RAAP is provably secure thanks to its design basis, which is resistant to the anonymous in the random oracle model. To validate the computational efficiency of 1-RAAP, a set of comprehensive comparative studies between 1-RAAP and other authentication protocols is conducted, and the results clearly show that 1-RAAP achieves the best performance in terms of computational overhead.

  19. 1-RAAP: An Efficient 1-Round Anonymous Authentication Protocol for Wireless Body Area Networks

    Directory of Open Access Journals (Sweden)

    Jingwei Liu

    2016-05-01

    Full Text Available Thanks to the rapid technological convergence of wireless communications, medical sensors and cloud computing, Wireless Body Area Networks (WBANs have emerged as a novel networking paradigm enabling ubiquitous Internet services, allowing people to receive medical care, monitor health status in real-time, analyze sports data and even enjoy online entertainment remotely. However, because of the mobility and openness of wireless communications, WBANs are inevitably exposed to a large set of potential attacks, significantly undermining their utility and impeding their widespread deployment. To prevent attackers from threatening legitimate WBAN users or abusing WBAN services, an efficient and secure authentication protocol termed 1-Round Anonymous Authentication Protocol (1-RAAP is proposed in this paper. In particular, 1-RAAP preserves anonymity, mutual authentication, non-repudiation and some other desirable security properties, while only requiring users to perform several low cost computational operations. More importantly, 1-RAAP is provably secure thanks to its design basis, which is resistant to the anonymous in the random oracle model. To validate the computational efficiency of 1-RAAP, a set of comprehensive comparative studies between 1-RAAP and other authentication protocols is conducted, and the results clearly show that 1-RAAP achieves the best performance in terms of computational overhead.

  20. Optimization of an Efficient and Sustainable Sonogashira Cross-Coupling Protocol

    KAUST Repository

    Walter, Philipp E.

    2012-12-01

    Cross coupling reactions are a well-established tool in modern organic synthesis and play a crucial role in the synthesis of a high number of organic compounds. Their importance is highlighted by the Nobel Prize in chemistry to Suzuki, Heck and Negishi in 2010. The increasing importance of sustainability requirements in chemical production has furthermore promoted the development of cross-coupling protocols that comply with the principles of “Green Chemistry”1. The Sonogashira reaction is today the most versatile and powerful way to generate aryl alkynes, a moiety recurring in many pharmaceutical and natural products. Despite many improvements to the original reaction, reports on generally applicable protocols that work under sustainable conditions are scarce. Our group recently reported an efficient protocol for a copperfree Sonogashira cross-coupling at low temperature, in aqueous medium and with no addition of organic solvents or additives2. The goal of this work was to further investigate the effects of different reaction parameters on the catalytic activity in order to optimize the protocol. Limitations of the protocol were tested in respect to reaction temperature, heating method, atmosphere, base type and amount, catalyst loading, reaction time and work up procedure. The reaction worked successfully under air and results were not affected by the presence of oxygen in the water phase. Among a variety of bases tested, triethylamine was confirmed to give the best results and its required excess could be reduced from nine to four equivalents. Catalyst loading could also be reduced by up to 90%: Good to near quantitative yields for a broad range of substrates were achieved using a catalyst concentration of 0.25mol% and 5 eq of Et3N at 50°C while more reactive substrates could be coupled with a catalyst concentration as low as 0.025mol%. Filtration experiments showed the possibility of a simplified work up procedure and a protocol completely free of organic

  1. Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Jared

    2011-10-13

    Wellcome Trust Sanger Institute's Jared Simpson on Memory efficient sequence analysis using compressed data structures at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  2. Time-zero efficiency of European power derivatives markets

    International Nuclear Information System (INIS)

    Peña, Juan Ignacio; Rodriguez, Rosa

    2016-01-01

    We study time-zero efficiency of electricity derivatives markets. By time-zero efficiency is meant a sequence of prices of derivatives contracts having the same underlying asset but different times to maturity which implies that prices comply with a set of efficiency conditions that prevent profitable time-zero arbitrage opportunities. We investigate whether statistical tests, based on the law of one price, and trading rules, based on price differentials and no-arbitrage violations, are useful for assessing time-zero efficiency. We apply tests and trading rules to daily data of three European power markets: Germany, France and Spain. In the case of the German market, after considering liquidity availability and transaction costs, results are not inconsistent with time-zero efficiency. However, in the case of the French and Spanish markets, limitations in liquidity and representativeness are challenges that prevent definite conclusions. Liquidity in French and Spanish markets should improve by using pricing and marketing incentives. These incentives should attract more participants into the electricity derivatives exchanges and should encourage them to settle OTC trades in clearinghouses. Publication of statistics on prices, volumes and open interest per type of participant should be promoted. - Highlights: •We test time-zero efficiency of derivatives power markets in Germany, France and Spain. •Prices in Germany, considering liquidity and transaction costs, are time-zero efficient. •In France and Spain, limitations in liquidity and representativeness prevent conclusions. •Liquidity in France and Spain should improve by using pricing and marketing incentives. •Incentives attract participants to exchanges and encourage them to settle OTC trades in clearinghouses.

  3. US stock market efficiency over weekly, monthly, quarterly and yearly time scales

    Science.gov (United States)

    Rodriguez, E.; Aguilar-Cornejo, M.; Femat, R.; Alvarez-Ramirez, J.

    2014-11-01

    In financial markets, the weak form of the efficient market hypothesis implies that price returns are serially uncorrelated sequences. In other words, prices should follow a random walk behavior. Recent developments in evolutionary economic theory (Lo, 2004) have tailored the concept of adaptive market hypothesis (AMH) by proposing that market efficiency is not an all-or-none concept, but rather market efficiency is a characteristic that varies continuously over time and across markets. Within the AMH framework, this work considers the Dow Jones Index Average (DJIA) for studying the deviations from the random walk behavior over time. It is found that the market efficiency also varies over different time scales, from weeks to years. The well-known detrended fluctuation analysis was used for the characterization of the serial correlations of the return sequences. The results from the empirical showed that interday and intraday returns are more serially correlated than overnight returns. Also, some insights in the presence of business cycles (e.g., Juglar and Kuznets) are provided in terms of time variations of the scaling exponent.

  4. Rapid whole-brain resting-state fMRI at 3 T: Efficiency-optimized three-dimensional EPI versus repetition time-matched simultaneous-multi-slice EPI.

    Science.gov (United States)

    Stirnberg, Rüdiger; Huijbers, Willem; Brenner, Daniel; Poser, Benedikt A; Breteler, Monique; Stöcker, Tony

    2017-12-01

    State-of-the-art simultaneous-multi-slice (SMS-)EPI and 3D-EPI share several properties that benefit functional MRI acquisition. Both sequences employ equivalent parallel imaging undersampling with controlled aliasing to achieve high temporal sampling rates. As a volumetric imaging sequence, 3D-EPI offers additional means of acceleration complementary to 2D-CAIPIRINHA sampling, such as fast water excitation and elliptical sampling. We performed an application-oriented comparison between a tailored, six-fold CAIPIRINHA-accelerated 3D-EPI protocol at 530 ms temporal and 2.4 mm isotropic spatial resolution and an SMS-EPI protocol with identical spatial and temporal resolution for whole-brain resting-state fMRI at 3 T. The latter required eight-fold slice acceleration to compensate for the lack of elliptical sampling and fast water excitation. Both sequences used vendor-supplied on-line image reconstruction. We acquired test/retest resting-state fMRI scans in ten volunteers, with simultaneous acquisition of cardiac and respiration data, subsequently used for optional physiological noise removal (nuisance regression). We found that the 3D-EPI protocol has significantly increased temporal signal-to-noise ratio throughout the brain as compared to the SMS-EPI protocol, especially when employing motion and nuisance regression. Both sequence types reliably identified known functional networks with stronger functional connectivity values for the 3D-EPI protocol. We conclude that the more time-efficient 3D-EPI primarily benefits from reduced parallel imaging noise due to a higher, actual k-space sampling density compared to SMS-EPI. The resultant BOLD sensitivity increase makes 3D-EPI a valuable alternative to SMS-EPI for whole-brain fMRI at 3 T, with voxel sizes well below 3 mm isotropic and sampling rates high enough to separate dominant cardiac signals from BOLD signals in the frequency domain. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Time-stretch microscopy based on time-wavelength sequence reconstruction from wideband incoherent source

    International Nuclear Information System (INIS)

    Zhang, Chi; Xu, Yiqing; Wei, Xiaoming; Tsia, Kevin K.; Wong, Kenneth K. Y.

    2014-01-01

    Time-stretch microscopy has emerged as an ultrafast optical imaging concept offering the unprecedented combination of the imaging speed and sensitivity. However, dedicated wideband and coherence optical pulse source with high shot-to-shot stability has been mandated for time-wavelength mapping—the enabling process for ultrahigh speed wavelength-encoded image retrieval. From the practical point of view, exploiting methods to relax the stringent requirements (e.g., temporal stability and coherence) for the source of time-stretch microscopy is thus of great value. In this paper, we demonstrated time-stretch microscopy by reconstructing the time-wavelength mapping sequence from a wideband incoherent source. Utilizing the time-lens focusing mechanism mediated by a narrow-band pulse source, this approach allows generation of a wideband incoherent source, with the spectral efficiency enhanced by a factor of 18. As a proof-of-principle demonstration, time-stretch imaging with the scan rate as high as MHz and diffraction-limited resolution is achieved based on the wideband incoherent source. We note that the concept of time-wavelength sequence reconstruction from wideband incoherent source can also be generalized to any high-speed optical real-time measurements, where wavelength is acted as the information carrier

  6. Formal Specification and Description Language and Message Sequence Chart to Model and Validate Session Initiation Protocol Services

    OpenAIRE

    Sa'ed Abed; Mohammad H. Al Shayeji; Ovais Ahmed; Sahel Alouneh

    2016-01-01

    Session Initiation Protocol (SIP) is a signaling layer protocol for building, adjusting and ending sessions among participants including Internet conferences, telephone calls and multimedia distribution. SIP facilitates user movement by proxying and forwarding requests to the present location of the user. In this paper, we provide a formal Specification and Description Language (SDL) and Message Sequence Chart (MSC) to model and define the Internet Engineering Task Force (IETF) SIP protocol a...

  7. Improving the efficiency of single and multiple teleportation protocols based on the direct use of partially entangled states

    Energy Technology Data Exchange (ETDEWEB)

    Fortes, Raphael; Rigolin, Gustavo, E-mail: rigolin@ifi.unicamp.br

    2013-09-15

    We push the limits of the direct use of partially pure entangled states to perform quantum teleportation by presenting several protocols in many different scenarios that achieve the optimal efficiency possible. We review and put in a single formalism the three major strategies known to date that allow one to use partially entangled states for direct quantum teleportation (no distillation strategies permitted) and compare their efficiencies in real world implementations. We show how one can improve the efficiency of many direct teleportation protocols by combining these techniques. We then develop new teleportation protocols employing multipartite partially entangled states. The three techniques are also used here in order to achieve the highest efficiency possible. Finally, we prove the upper bound for the optimal success rate for protocols based on partially entangled Bell states and show that some of the protocols here developed achieve such a bound. -- Highlights: •Optimal direct teleportation protocols using directly partially entangled states. •We put in a single formalism all strategies of direct teleportation. •We extend these techniques for multipartite partially entangle states. •We give upper bounds for the optimal efficiency of these protocols.

  8. A two-step recognition of signal sequences determines the translocation efficiency of proteins.

    Science.gov (United States)

    Belin, D; Bost, S; Vassalli, J D; Strub, K

    1996-02-01

    The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery.

  9. Improvement of methods for large scale sequencing; application to human Xq28

    Energy Technology Data Exchange (ETDEWEB)

    Gibbs, R.A.; Andersson, B.; Wentland, M.A. [Baylor College of Medicine, Houston, TX (United States)] [and others

    1994-09-01

    Sequencing of a one-metabase region of Xq28, spanning the FRAXA and IDS loci has been undertaken in order to investigate the practicality of the shotgun approach for large scale sequencing and as a platform to develop improved methods. The efficiency of several steps in the shotgun sequencing strategy has been increased using PCR-based approaches. An improved method for preparation of M13 libraries has been developed. This protocol combines a previously described adaptor-based protocol with the uracil DNA glycosylase (UDG)-cloning procedure. The efficiency of this procedure has been found to be up to 100-fold higher than that of previously used protocols. In addition the novel protocol is more reliable and thus easy to establish in a laboratory. The method has also been adapted for the simultaneous shotgun sequencing of multiple short fragments by concentrating them before library construction is presented. This protocol is suitable for rapid characterization of cDNA clones. A library was constructed from 15 PCR-amplified and concentrated human cDNA inserts, and the insert sequences could easily be identified as separate contigs during the assembly process and the sequence coverage was even along each fragment. Using this strategy, the fine structures of the FraxA and IDS loci have been revealed and several EST homologies indicating novel expressed sequences have been identified. Use of PCR to close repetitive regions that are difficult to clone was tested by determination of the sequence of a cosmid mapping DXS455 in Xq28, containing a polymorphic VNTR. The region containing the VNTR was not represented in the shotgun library, but by designing PCR primers in the sequences flanking the gap and by cloning and sequencing the PCR product, the fine structure of the VNTR has been determined. It was found to be an AT-rich VNTR with a repeated 25-mer at the center.

  10. Analysis of energy efficient routing protocols for implementation of a ubiquitous health system

    Science.gov (United States)

    Kwon, Jongwon; Park, Yongman; Koo, Sangjun; Ayurzana, Odgeral; Kim, Hiesik

    2007-12-01

    The innovative Ubiquitous-Health was born through convergence of medical service, with development of up to date information technologies and ubiquitous IT. The U-Health can be applied to a variety of special situations for managing functions of each medical center efficiently. This paper focuses on estimation of various routing protocols for implementation of U-health monitoring system. In order to facilitate wireless communication over the network, a routing protocol on the network layer is used to establish precise and efficient route between sensor nodes so that information acquired from sensors may be delivered in a timely manner. A route establishment should be considered to minimize overhead, data loss and power consumption because wireless networks for U-health are organized by a large number of sensor nodes which are small in size and have limited processing power, memory and battery life. In this paper a overview of wireless sensor network technologies commonly known is described as well as evaluation of three multi hop routing protocols which are flooding, gossiping and modified low energy adaptive clustering hierarchy(LEACH) for use with these networks using TOSSIM simulator. As a result of evaluation the integrated wireless sensor board was developed in particular. The board is embedded device based on AVR128 porting TinyOS. Also it employs bio sensor measures blood pressure, pulse frequency and ZigBee module for wireless communication. This paper accelerates the digital convergence age through continual research and development of technologies related the U-Health.

  11. An Efficient and QoS Supported Multichannel MAC Protocol for Vehicular Ad Hoc Networks.

    Science.gov (United States)

    Song, Caixia; Tan, Guozhen; Yu, Chao

    2017-10-09

    Vehicular Ad Hoc Networks (VANETs) employ multichannel to provide a variety of safety and non-safety (transport efficiency and infotainment) applications, based on the IEEE 802.11p and IEEE 1609.4 protocols. Different types of applications require different levels Quality-of-Service (QoS) support. Recently, transport efficiency and infotainment applications (e.g., electronic map download and Internet access) have received more and more attention, and this kind of applications is expected to become a big market driver in a near future. In this paper, we propose an Efficient and QoS supported Multichannel Medium Access Control (EQM-MAC) protocol for VANETs in a highway environment. The EQM-MAC protocol utilizes the service channel resources for non-safety message transmissions during the whole synchronization interval, and it dynamically adjusts minimum contention window size for different non-safety services according to the traffic conditions. Theoretical model analysis and extensive simulation results show that the EQM-MAC protocol can support QoS services, while ensuring the high saturation throughput and low transmission delay for non-safety applications.

  12. An Efficient and QoS Supported Multichannel MAC Protocol for Vehicular Ad Hoc Networks

    Directory of Open Access Journals (Sweden)

    Caixia Song

    2017-10-01

    Full Text Available Vehicular Ad Hoc Networks (VANETs employ multichannel to provide a variety of safety and non-safety (transport efficiency and infotainment applications, based on the IEEE 802.11p and IEEE 1609.4 protocols. Different types of applications require different levels Quality-of-Service (QoS support. Recently, transport efficiency and infotainment applications (e.g., electronic map download and Internet access have received more and more attention, and this kind of applications is expected to become a big market driver in a near future. In this paper, we propose an Efficient and QoS supported Multichannel Medium Access Control (EQM-MAC protocol for VANETs in a highway environment. The EQM-MAC protocol utilizes the service channel resources for non-safety message transmissions during the whole synchronization interval, and it dynamically adjusts minimum contention window size for different non-safety services according to the traffic conditions. Theoretical model analysis and extensive simulation results show that the EQM-MAC protocol can support QoS services, while ensuring the high saturation throughput and low transmission delay for non-safety applications.

  13. Robust and Efficient Authentication Scheme for Session Initiation Protocol

    Directory of Open Access Journals (Sweden)

    Yanrong Lu

    2015-01-01

    Full Text Available The session initiation protocol (SIP is a powerful application-layer protocol which is used as a signaling one for establishing, modifying, and terminating sessions among participants. Authentication is becoming an increasingly crucial issue when a user asks to access SIP services. Hitherto, many authentication schemes have been proposed to enhance the security of SIP. In 2014, Arshad and Nikooghadam proposed an enhanced authentication and key agreement scheme for SIP and claimed that their scheme could withstand various attacks. However, in this paper, we show that Arshad and Nikooghadam’s authentication scheme is still susceptible to key-compromise impersonation and trace attacks and does not provide proper mutual authentication. To conquer the flaws, we propose a secure and efficient ECC-based authentication scheme for SIP. Through the informal and formal security analyses, we demonstrate that our scheme is resilient to possible known attacks including the attacks found in Arshad et al.’s scheme. In addition, the performance analysis shows that our scheme has similar or better efficiency in comparison with other existing ECC-based authentication schemes for SIP.

  14. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

    Science.gov (United States)

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

    2013-01-01

    For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

  15. Combinatorial pooling enables selective sequencing of the barley gene space.

    Directory of Open Access Journals (Sweden)

    Stefano Lonardi

    2013-04-01

    Full Text Available For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  16. Combinatorial pooling enables selective sequencing of the barley gene space.

    Science.gov (United States)

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J

    2013-04-01

    For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  17. Comparison of a new whole-body continuous-table-movement protocol versus a standard whole-body MR protocol for the assessment of multiple myeloma

    International Nuclear Information System (INIS)

    Weckbach, S.; Michaely, H.J.; Schoenberg, S.O.; Dinter, D.J.; Stemmer, A.

    2010-01-01

    To evaluate a whole body (WB) continuous-table-movement (CTM) MR protocol for the assessment of multiple myeloma (MM) in comparison to a step-by-step WB protocol. Eighteen patients with MM were examined at 1.5T using a WB CTM protocol (axial T2-w fs BLADE, T1-w GRE sequence) and a step-by-step WB protocol including coronal/sagittal T1-w SE and STIR sequences as reference. Protocol time was assessed. Image quality, artefacts, liver/spleen assessability, and the ability to depict bone marrow lesions less than or greater than 1 cm as well as diffuse infiltration and soft tissue lesions were rated. Potential changes in the Durie and Salmon Plus stage and the detectability of complications were assessed. Mean protocol time was 6:38 min (CTM) compared to 24:32 min (standard). Image quality was comparable. Artefacts were more prominent using the CTM protocol (P = 0.0039). Organ assessability was better using the CTM protocol (P < 0.001). Depiction of bone marrow and soft tissue lesions was identical without a staging shift. Vertebral fractures were not detected using the CTM protocol. The new protocol allows a higher patient throughput and facilitates the depiction of extramedullary lesions. However, as long as vertebral fractures are not detectable, the protocol cannot be safely used for clinical routine without the acquisition of an additional sagittal sequence. (orig.)

  18. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    Full Text Available Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads. Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I. Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II. Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR

  19. Efficient in vitro regeneration protocol of Centella asiatica (L.) Urban ...

    African Journals Online (AJOL)

    The present communication reports an efficient in vitro plantlet regeneration protocol for endemic umbellifer Centella asiatica (L.) urban via callus mediated organogenesis from leaf and stem explants. The plant is pharmacologically very important and its consumption as underutilized green leafy vegetable affluent in ...

  20. Accessibility in Public Buildings: : Efficiency of Checklist Protocols

    OpenAIRE

    Andersson, Jonas E; Skehan, Terry

    2016-01-01

    In Sweden, governmental agencies and bodies are required to implement a higher level of accessibility in their buildings than that stipulated by the National Building and Planning Act (PBL). The Swedish Agency for Participation (MFD, Myndigheten för delaktighet) develops holistic guidelines in order to conceptualize this higher level of accessibility. In conjunction to these guidelines, various checklist protocols have been produced. The present study focuses on the efficiency of such checkli...

  1. In vivo evaluation of the effect of stimulus distribution on FIR statistical efficiency in event-related fMRI.

    Science.gov (United States)

    Jansma, J Martijn; de Zwart, Jacco A; van Gelderen, Peter; Duyn, Jeff H; Drevets, Wayne C; Furey, Maura L

    2013-05-15

    Technical developments in MRI have improved signal to noise, allowing use of analysis methods such as Finite impulse response (FIR) of rapid event related functional MRI (er-fMRI). FIR is one of the most informative analysis methods as it determines onset and full shape of the hemodynamic response function (HRF) without any a priori assumptions. FIR is however vulnerable to multicollinearity, which is directly related to the distribution of stimuli over time. Efficiency can be optimized by simplifying a design, and restricting stimuli distribution to specific sequences, while more design flexibility necessarily reduces efficiency. However, the actual effect of efficiency on fMRI results has never been tested in vivo. Thus, it is currently difficult to make an informed choice between protocol flexibility and statistical efficiency. The main goal of this study was to assign concrete fMRI signal to noise values to the abstract scale of FIR statistical efficiency. Ten subjects repeated a perception task with five random and m-sequence based protocol, with varying but, according to literature, acceptable levels of multicollinearity. Results indicated substantial differences in signal standard deviation, while the level was a function of multicollinearity. Experiment protocols varied up to 55.4% in standard deviation. Results confirm that quality of fMRI in an FIR analysis can significantly and substantially vary with statistical efficiency. Our in vivo measurements can be used to aid in making an informed decision between freedom in protocol design and statistical efficiency. Published by Elsevier B.V.

  2. OPTSDNA: Performance evaluation of an efficient distributed bioinformatics system for DNA sequence analysis.

    Science.gov (United States)

    Khan, Mohammad Ibrahim; Sheel, Chotan

    2013-01-01

    Storage of sequence data is a big concern as the amount of data generated is exponential in nature at several locations. Therefore, there is a need to develop techniques to store data using compression algorithm. Here we describe optimal storage algorithm (OPTSDNA) for storing large amount of DNA sequences of varying length. This paper provides performance analysis of optimal storage algorithm (OPTSDNA) of a distributed bioinformatics computing system for analysis of DNA sequences. OPTSDNA algorithm is used for storing various sizes of DNA sequences into database. DNA sequences of different lengths were stored by using this algorithm. These input DNA sequences are varied in size from very small to very large. Storage size is calculated by this algorithm. Response time is also calculated in this work. The efficiency and performance of the algorithm is high (in size calculation with percentage) when compared with other known with sequential approach.

  3. Real-time communication protocols: an overview

    NARCIS (Netherlands)

    Hanssen, F.T.Y.; Jansen, P.G.

    2003-01-01

    This paper describes several existing data link layer protocols that provide real-time capabilities on wired networks, focusing on token-ring and Carrier Sense Multiple Access based networks. Existing modifications to provide better real-time capabilities and performance are also described. Finally

  4. A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis

    Directory of Open Access Journals (Sweden)

    Polyana Kelly Martins

    2015-06-01

    Full Text Available The production and use of sugarcane in Brazil is very important for bioenergy production and is recognized as one of the most efficient in the world. In our laboratory, Setaria viridis is being tested as a model plant for sugarcane. S. viridis has biological attributes (rapid life cycle, small genome, diploid, short stature and simple growth requirements that make it suitable for use as a model system. We report a highly efficient protocol for Agrobacterium-mediated genetic transformation of S. viridis. The optimization of several steps in tissue culture allowed the rapid regeneration of plants and increased the rate of transformation up to 29%. This protocol could become a powerful tool for functional genomics in sugarcane.

  5. DELIMINATE--a fast and efficient method for loss-less compression of genomic sequences: sequence analysis.

    Science.gov (United States)

    Mohammed, Monzoorul Haque; Dutta, Anirban; Bose, Tungadri; Chadaram, Sudha; Mande, Sharmila S

    2012-10-01

    An unprecedented quantity of genome sequence data is currently being generated using next-generation sequencing platforms. This has necessitated the development of novel bioinformatics approaches and algorithms that not only facilitate a meaningful analysis of these data but also aid in efficient compression, storage, retrieval and transmission of huge volumes of the generated data. We present a novel compression algorithm (DELIMINATE) that can rapidly compress genomic sequence data in a loss-less fashion. Validation results indicate relatively higher compression efficiency of DELIMINATE when compared with popular general purpose compression algorithms, namely, gzip, bzip2 and lzma. Linux, Windows and Mac implementations (both 32 and 64-bit) of DELIMINATE are freely available for download at: http://metagenomics.atc.tcs.com/compression/DELIMINATE. sharmila@atc.tcs.com Supplementary data are available at Bioinformatics online.

  6. Efficient RNA extraction protocol for the wood mangrove species Laguncularia racemosa suited for next-generation RNA sequencing

    International Nuclear Information System (INIS)

    Wilwerth, M. W.; Rossetto, P.

    2016-01-01

    Mangrove flora and habitat have immeasurable importance in marine and coastal ecology as well as in the economy. Despite their importance, they are constantly threatened by oil spill accidents and environmental contamination; therefore, it is crucial to understand the changes in gene expression to better predict toxicity in these plants. Among the species of Atlantic coast mangrove (Americas and Africa), Laguncularia racemosa, or white mangrove, is a conspicuous species. The wide distribution of L. racemosa in areas where marine oil exploration is rapidly increasing make it a candidate mangrove species model to uncover the impact of oil spills at the molecular level with the use of massive transcriptome sequencing. However, for this purpose, the RNA extraction protocol should ensure low levels of contaminants and structure integrity. In this study, eight RNA extraction methods were tested and analysed using downstream applications. The InviTrap Spin Plant RNA Mini Kit performed best with regard to purity and integrity. Moreover, the obtained RNA was submitted to cDNA synthesis and RT-PCR, successfully generating amplification products of the expected size. These Results show the applicability of the RNA obtained here for downstream methodologies, such as the construction of cDNA libraries for the Illumina Hi-seq platform. (author)

  7. Real-Time Fault Tolerant Networking Protocols

    National Research Council Canada - National Science Library

    Henzinger, Thomas A

    2004-01-01

    We made significant progress in the areas of video streaming, wireless protocols, mobile ad-hoc and sensor networks, peer-to-peer systems, fault tolerant algorithms, dependability and timing analysis...

  8. Efficient and exact sampling of simple graphs with given arbitrary degree sequence.

    Directory of Open Access Journals (Sweden)

    Charo I Del Genio

    Full Text Available Uniform sampling from graphical realizations of a given degree sequence is a fundamental component in simulation-based measurements of network observables, with applications ranging from epidemics, through social networks to Internet modeling. Existing graph sampling methods are either link-swap based (Markov-Chain Monte Carlo algorithms or stub-matching based (the Configuration Model. Both types are ill-controlled, with typically unknown mixing times for link-swap methods and uncontrolled rejections for the Configuration Model. Here we propose an efficient, polynomial time algorithm that generates statistically independent graph samples with a given, arbitrary, degree sequence. The algorithm provides a weight associated with each sample, allowing the observable to be measured either uniformly over the graph ensemble, or, alternatively, with a desired distribution. Unlike other algorithms, this method always produces a sample, without back-tracking or rejections. Using a central limit theorem-based reasoning, we argue, that for large , and for degree sequences admitting many realizations, the sample weights are expected to have a lognormal distribution. As examples, we apply our algorithm to generate networks with degree sequences drawn from power-law distributions and from binomial distributions.

  9. An Efficient and Secure Arbitrary N-Party Quantum Key Agreement Protocol Using Bell States

    Science.gov (United States)

    Liu, Wen-Jie; Xu, Yong; Yang, Ching-Nung; Gao, Pei-Pei; Yu, Wen-Bin

    2018-01-01

    Two quantum key agreement protocols using Bell states and Bell measurement were recently proposed by Shukla et al. (Quantum Inf. Process. 13(11), 2391-2405, 2014). However, Zhu et al. pointed out that there are some security flaws and proposed an improved version (Quantum Inf. Process. 14(11), 4245-4254, 2015). In this study, we will show Zhu et al.'s improvement still exists some security problems, and its efficiency is not high enough. For solving these problems, we utilize four Pauli operations { I, Z, X, Y} to encode two bits instead of the original two operations { I, X} to encode one bit, and then propose an efficient and secure arbitrary N-party quantum key agreement protocol. In the protocol, the channel checking with decoy single photons is introduced to avoid the eavesdropper's flip attack, and a post-measurement mechanism is used to prevent against the collusion attack. The security analysis shows the present protocol can guarantee the correctness, security, privacy and fairness of quantum key agreement.

  10. An Efficient Causal Group Communication Protocol for Free Scale Peer-to-Peer Networks

    Directory of Open Access Journals (Sweden)

    Grigory Evropeytsev

    2016-08-01

    Full Text Available In peer-to-peer (P2P overlay networks, a group of n (≥2 peer processes have to cooperate with each other. Each peer sends messages to every peer and receives messages from every peer in a group. In group communications, each message sent by a peer is required to be causally delivered to every peer. Most of the protocols designed to ensure causal message order are designed for networks with a plain architecture. These protocols can be adapted to use in free scale and hierarchical topologies; however, the amount of control information is O(n, where n is the number of peers in the system. Some protocols are designed for a free scale or hierarchical networks, but in general they force the whole system to accomplish the same order viewed by a super peer. In this paper, we present a protocol that is specifically designed to work with a free scale peer-to-peer network. By using the information about the network’s architecture and by representing message dependencies on a bit level, the proposed protocol ensures causal message ordering without enforcing super peers order. The designed protocol is simulated and compared with the Immediate Dependency Relation and the Dependency Sequences protocols to show its lower overhead.

  11. Emission Trading and the Kyoto protocol: Are they efficient economic instruments?

    International Nuclear Information System (INIS)

    Ibanez Londono, Ana Maria

    1998-02-01

    The Kyoto Protocol establishes a tradeable permits market for green house gases -GHG- emissions to reduce the costs of meeting the Protocol obligations. Economic theory provides the arguments to support the creation of GHG tradeable permits. Several economic researches have shown that vis-a-vis command and control regulations, tradeable permits induce economic agents to achieve environmental goals at a minimum cost. However, the conditions to minimize costs through tradeable permits are stringent. Tradeable permits require well functioning markets, e.g. perfect competition and perfect information. The tradeable permits market created by the Kyoto Protocol hardly meet these necessary conditions. Some countries like Japan, Great Britain and the United Stated are large emitters and thus may exert market power. Price manipulation may have implications over the static and dynamic efficiency of the permits. This paper takes a first look to the consequences of imperfect markets on the tradeable permit system of the Kyoto Protocol

  12. Computer network time synchronization the network time protocol on earth and in space

    CERN Document Server

    Mills, David L

    2010-01-01

    Carefully coordinated, reliable, and accurate time synchronization is vital to a wide spectrum of fields-from air and ground traffic control, to buying and selling goods and services, to TV network programming. Ill-gotten time could even lead to the unimaginable and cause DNS caches to expire, leaving the entire Internet to implode on the root servers.Written by the original developer of the Network Time Protocol (NTP), Computer Network Time Synchronization: The Network Time Protocol on Earth and in Space, Second Edition addresses the technological infrastructure of time dissemination, distrib

  13. An efficient protocol for the Agrobacterium-mediated genetic transformation of microalga Chlamydomonas reinhardtii.

    Science.gov (United States)

    Pratheesh, P T; Vineetha, M; Kurup, G Muraleedhara

    2014-06-01

    Algal-based recombinant protein production has gained immense interest in recent years. The development of algal expression system was earlier hindered due to the lack of efficient and cost-effective transformation techniques capable of heterologous gene integration and expression. The recent development of Agrobacterium-mediated genetic transformation method is expected to be the ideal solution for these problems. We have developed an efficient protocol for the Agrobacterium-mediated genetic transformation of microalga Chlamydomonas reinhardtii. Pre-treatment of Agrobacterium in TAP induction medium (pH 5.2) containing 100 μM acetosyringone and 1 mM glycine betaine and infection of Chlamydomonas with the induced Agrobacterium greatly improved transformation frequency. This protocol was found to double the number of transgenic events on selection media compared to that of previous reports. PCR was used successfully to amplify fragments of the hpt and GUS genes from transformed cells, while Southern blot confirmed the integration of GUS gene into the genome of C. reinhardtii. RT-PCR, Northern blot and GUS histochemical analyses confirm GUS gene expression in the transgenic cell lines of Chlamydomonas. This protocol provides a quick, efficient, economical and high-frequency transformation method for microalgae.

  14. An Energy Efficient Protocol For The Internet Of Things

    Science.gov (United States)

    Venčkauskas, Algimantas; Jusas, Nerijus; Kazanavičius, Egidijus; Štuikys, Vytautas

    2015-01-01

    The Internet of Things (IoT) is a technological revolution that represents the future of computing and communications. One of the most important challenges of IoT is security: protection of data and privacy. The SSL protocol is the de-facto standard for secure Internet communications. The extra energy cost of encrypting and authenticating of the application data with SSL is around 15%. For IoT devices, where energy resources are limited, the increase in the cost of energy is a very significant factor. In this paper we present the energy efficient SSL protocol which ensures the maximum bandwidth and the required level of security with minimum energy consumption. The proper selection of the security level and CPU multiplier, can save up to 85% of the energy required for data encryption.

  15. Highly multiplexed targeted DNA sequencing from single nuclei.

    Science.gov (United States)

    Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

    2016-02-01

    Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

  16. Dynamic-Threshold-Limited Timed-Token (DTLTT) Protocol | Kalu ...

    African Journals Online (AJOL)

    An improved version of the Static-Threshold-Limited On-Demand Guaranteed Service Timed-Token (STOGSTT) Media Access Control (MAC) protocol for channel capacity allocation to the asynchronous trac in Multiservice Local Area Network (MLANs) was developed and analyzed. TLODGSTT protocol uses static value of ...

  17. Efficient error correction for next-generation sequencing of viral amplicons.

    Science.gov (United States)

    Skums, Pavel; Dimitrova, Zoya; Campo, David S; Vaughan, Gilberto; Rossi, Livia; Forbi, Joseph C; Yokosawa, Jonny; Zelikovsky, Alex; Khudyakov, Yury

    2012-06-25

    Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error identification and correction. Most error-correction methods to date are not optimized for amplicon analysis and assume that the error rate is randomly distributed. Recent quality assessment of amplicon sequences obtained using 454-sequencing showed that the error rate is strongly linked to the presence and size of homopolymers, position in the sequence and length of the amplicon. All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing. In this paper, we present two new efficient error correction algorithms optimized for viral amplicons: (i) k-mer-based error correction (KEC) and (ii) empirical frequency threshold (ET). Both were compared to a previously published clustering algorithm (SHORAH), in order to evaluate their relative performance on 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. All three algorithms show similar accuracy in finding true haplotypes. However, KEC and ET were significantly more efficient than SHORAH in removing false haplotypes and estimating the frequency of true ones. Both algorithms, KEC and ET, are highly suitable for rapid recovery of error-free haplotypes obtained by 454-sequencing of amplicons from heterogeneous viruses.The implementations of the algorithms and data sets used for their testing are available at: http://alan.cs.gsu.edu/NGS/?q=content/pyrosequencing-error-correction-algorithm.

  18. Space Network Time Distribution and Synchronization Protocol Development for Mars Proximity Link

    Science.gov (United States)

    Woo, Simon S.; Gao, Jay L.; Mills, David

    2010-01-01

    Time distribution and synchronization in deep space network are challenging due to long propagation delays, spacecraft movements, and relativistic effects. Further, the Network Time Protocol (NTP) designed for terrestrial networks may not work properly in space. In this work, we consider the time distribution protocol based on time message exchanges similar to Network Time Protocol (NTP). We present the Proximity-1 Space Link Interleaved Time Synchronization (PITS) algorithm that can work with the CCSDS Proximity-1 Space Data Link Protocol. The PITS algorithm provides faster time synchronization via two-way time transfer over proximity links, improves scalability as the number of spacecraft increase, lowers storage space requirement for collecting time samples, and is robust against packet loss and duplication which underlying protocol mechanisms provide.

  19. The analysis of energy-time sequences in the nuclear power plants construction

    International Nuclear Information System (INIS)

    Milivojevic, S.; Jovanovic, V.; Riznic, J.

    1983-01-01

    The current nuclear energy development pose many problems; one of them is nuclear power plant construction. They are evaluated energy and time features of the construction and their relative ratios by the analysis of available data. The results point at the reached efficiency of the construction and, in the same time, they are the basis for real estimation of energy-time sequences of the construction in the future. (author)

  20. Multiprocessor Real-Time Locking Protocols for Replicated Resources

    Science.gov (United States)

    2016-07-01

    assignment problem, the ac- tual identities of the allocated replicas must be known. When locking protocols are used, tasks may experience delays due to both...Multiprocessor Real-Time Locking Protocols for Replicated Resources ∗ Catherine E. Jarrett1, Kecheng Yang1, Ming Yang1, Pontus Ekberg2, and James H...replicas to execute. In prior work on replicated resources, k-exclusion locks have been used, but this restricts tasks to lock only one replica at a time. To

  1. Energy Efficiency in Ethernet Passive Optical Networks (EPONs): Protocol Design and Performance Evaluation

    DEFF Research Database (Denmark)

    Yan, Ying; Dittmann, Lars

    2011-01-01

    a suitable wakeup time scheduler at the Optical Line Terminal (OLT). A generic EPON system is considered, which is composed of an OLT and several ONUs that are EMM enabled. An energy consumption optimization problem aimed at saving energy is proposed and two heuristic sleep mode scheduling policies......As concerns about energy consumption grow, the power consumption of the EPON becomes a matter of increasing importance. In respect of energy efficiency, the current standard has no management protocols aiming to reduce power consumption in EPONs. In this paper, we propose an Energy Management...... and guaranteeing the network performance at the same time. Simulation results show that an EMM-based EPON with well designed scheduling disciplines is essential to achieving significant energy saving while meeting the delay constraint....

  2. Scrutinizing virus genome termini by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Shasha Li

    Full Text Available Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.

  3. Network-topology-adaptive quantum conference protocols

    International Nuclear Information System (INIS)

    Zhang Sheng; Wang Jian; Tang Chao-Jing; Zhang Quan

    2011-01-01

    As an important application of the quantum network communication, quantum multiparty conference has made multiparty secret communication possible. Previous quantum multiparty conference schemes based on quantum data encryption are insensitive to network topology. However, the topology of the quantum network significantly affects the communication efficiency, e.g., parallel transmission in a channel with limited bandwidth. We have proposed two distinctive protocols, which work in two basic network topologies with efficiency higher than the existing ones. We first present a protocol which works in the reticulate network using Greeberger—Horne—Zeilinger states and entanglement swapping. Another protocol, based on quantum multicasting with quantum data compression, which can improve the efficiency of the network, works in the star-like network. The security of our protocols is guaranteed by quantum key distribution and one-time-pad encryption. In general, the two protocols can be applied to any quantum network where the topology can be equivalently transformed to one of the two structures we propose in our protocols. (general)

  4. Whole genome sequence analysis of the arctic-lineage strain responsible for distemper in Italian wolves and dogs through a fast and robust next generation sequencing protocol.

    Science.gov (United States)

    Marcacci, Maurilia; Ancora, Massimo; Mangone, Iolanda; Teodori, Liana; Di Sabatino, Daria; De Massis, Fabrizio; Camma', Cesare; Savini, Giovanni; Lorusso, Alessio

    2014-06-01

    Dynamic surveillance and characterization of canine distemper virus (CDV) circulating strains are essential against possible vaccine breakthroughs events. This study describes the setup of a fast and robust next-generation sequencing (NGS) Ion PGM™ protocol that was used to obtain the complete genome sequence of a CDV isolate (CDV2784/2013). CDV2784/2013 is the prototype of CDV strains responsible for severe clinical distemper in dogs and wolves in Italy during 2013. CDV2784/2013 was isolated on cell culture and total RNA was used for NGS sample preparation. A total of 112.3 Mb of reads were assembled de novo using MIRA version 4.0rc4, which yielded a total number of 403 contigs with 12.1% coverage. The whole genome (15,690 bp) was recovered successfully and compared to those of existing CDV whole genomes. CDV2784/2013 was shown to have 92% nt identity with the Onderstepoort vaccine strain. This study describes for the first time a fast and robust Ion PGM™ platform-based whole genome amplification protocol for non-segmented negative stranded RNA viruses starting from total cell-purified RNA. Additionally, this is the first study reporting the whole genome analysis of an Arctic lineage strain that is known to circulate widely in Europe, Asia and USA. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. IoT real time data acquisition using MQTT protocol

    Science.gov (United States)

    Atmoko, R. A.; Riantini, R.; Hasin, M. K.

    2017-05-01

    The Internet of Things (IoT) provides ease to monitor and to gain sensor data through the Internet [1]. The need of high quality data is increasing to the extent that data monitoring and acquisition system in real time is required, such as smart city or telediagnostic in medical areas [2]. Therefore, an appropriate communication protocol is required to resolve these problems. Lately, researchers have developed a lot of communication protocols for IoT, of which each has advantages and disadvantages. This study proposes the utilization of MQTT as a communication protocol, which is one of data communication protocols for IoT. This study used temperature and humidity sensors because the physical parameters are often needed as parameters of environment condition [3]. Data acquisition was done in real-time and stored in MySQL database. This study is also completed by interface web-based and mobile for online monitoring. This result of this study is the enhancement of data quality and reliability using MQTT protocol.

  6. An efficient multi-carrier position-based packet forwarding protocol for wireless sensor networks

    KAUST Repository

    Bader, Ahmed

    2012-01-01

    Beaconless position-based forwarding protocols have recently evolved as a promising solution for packet forwarding in wireless sensor networks. However, as the node density grows, the overhead incurred in the process of relay selection grows significantly. As such, end-to-end performance in terms of energy and latency is adversely impacted. With the motivation of developing a packet forwarding mechanism that is tolerant to variation in node density, an alternative position-based protocol is proposed in this paper. In contrast to existing beaconless protocols, the proposed protocol is designed such that it eliminates the need for potential relays to undergo a relay selection process. Rather, any eligible relay may decide to forward the packet ahead, thus significantly reducing the underlying overhead. The operation of the proposed protocol is empowered by exploiting favorable features of orthogonal frequency division multiplexing (OFDM) at the physical layer. The end-to-end performance of the proposed protocol is evaluated against existing beaconless position-based protocols analytically and as well by means of simulations. The proposed protocol is demonstrated in this paper to be more efficient. In particular, it is shown that for the same amount of energy the proposed protocol transports one bit from source to destination much quicker. © 2012 IEEE.

  7. dynamic-threshold-limited timed-token (dtltt) protocol

    African Journals Online (AJOL)

    2013-03-01

    Mar 1, 2013 ... Token (STOGSTT) Media Access Control (MAC) protocol for channel capacity allocation to the asynchronous traffic in ... Keywords: multi-access, multiservice, network, synchronous, asynchronous, traffic, timed-token. 1. Introduction .... Messages generated in the system at run time may be classified as ...

  8. Protocol Processing for 100 Gbit/s and Beyond - A Soft Real-Time Approach in Hardware and Software

    Science.gov (United States)

    Büchner, Steffen; Lopacinski, Lukasz; Kraemer, Rolf; Nolte, Jörg

    2017-09-01

    100 Gbit/s wireless communication protocol processing stresses all parts of a communication system until the outermost. The efficient use of upcoming 100 Gbit/s and beyond transmission technology requires the rethinking of the way protocols are processed by the communication endpoints. This paper summarizes the achievements of the project End2End100. We will present a comprehensive soft real-time stream processing approach that allows the protocol designer to develop, analyze, and plan scalable protocols for ultra high data rates of 100 Gbit/s and beyond. Furthermore, we will present an ultra-low power, adaptable, and massively parallelized FEC (Forward Error Correction) scheme that detects and corrects bit errors at line rate with an energy consumption between 1 pJ/bit and 13 pJ/bit. The evaluation results discussed in this publication show that our comprehensive approach allows end-to-end communication with a very low protocol processing overhead.

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

    Science.gov (United States)

    Petursdottir, Anna Ingeborg; Carr, James E

    2011-01-01

    We review recommendations for sequencing instruction in receptive and expressive language objectives in early and intensive behavioral intervention (EIBI) programs. Several books recommend completing receptive protocols before introducing corresponding expressive protocols. However, this recommendation has little empirical support, and some evidence exists that the reverse sequence may be more efficient. Alternative recommendations include teaching receptive and expressive skills simultaneously (M. L. Sundberg & Partington, 1998) and building learning histories that lead to acquisition of receptive and expressive skills without direct instruction (Greer & Ross, 2008). Empirical support for these recommendations also is limited. Future research should assess the relative efficiency of receptive-before-expressive, expressive-before-receptive, and simultaneous training with children who have diagnoses of autism spectrum disorders. In addition, further evaluation is needed of the potential benefits of multiple-exemplar training and other variables that may influence the efficiency of receptive and expressive instruction.

  10. Energy Efficient Medium Access Control Protocol for Clustered Wireless Sensor Networks with Adaptive Cross-Layer Scheduling.

    Science.gov (United States)

    Sefuba, Maria; Walingo, Tom; Takawira, Fambirai

    2015-09-18

    This paper presents an Energy Efficient Medium Access Control (MAC) protocol for clustered wireless sensor networks that aims to improve energy efficiency and delay performance. The proposed protocol employs an adaptive cross-layer intra-cluster scheduling and an inter-cluster relay selection diversity. The scheduling is based on available data packets and remaining energy level of the source node (SN). This helps to minimize idle listening on nodes without data to transmit as well as reducing control packet overhead. The relay selection diversity is carried out between clusters, by the cluster head (CH), and the base station (BS). The diversity helps to improve network reliability and prolong the network lifetime. Relay selection is determined based on the communication distance, the remaining energy and the channel quality indicator (CQI) for the relay cluster head (RCH). An analytical framework for energy consumption and transmission delay for the proposed MAC protocol is presented in this work. The performance of the proposed MAC protocol is evaluated based on transmission delay, energy consumption, and network lifetime. The results obtained indicate that the proposed MAC protocol provides improved performance than traditional cluster based MAC protocols.

  11. A parallel reconfigurable platform for efficient sequence alignment ...

    African Journals Online (AJOL)

    Bioinformatics is one of the emerging trends in today's world. The major part of bioinformatics is dealing with DNA. Analysis of DNA requires more memory and high efficient computations to produce accurate outputs. Researchers use various bioinformatics algorithms for sequencing and pattern detection techniques, but still ...

  12. BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

    Directory of Open Access Journals (Sweden)

    Schomburg D

    2010-12-01

    Full Text Available Abstract Background Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. Other methods can support these techniques: We have developed an automatic method "BrEPS" that creates highly specific sequence patterns for the functional annotation of enzymes. Results The enzymes in the UniprotKB are identified and their sequences compared against each other with BLAST. The enzymes are then clustered into a number of trees, where each tree node is associated with a set of EC-numbers. The enzyme sequences in the tree nodes are aligned with ClustalW. The conserved columns of the resulting multiple alignments are used to construct sequence patterns. In the last step, we verify the quality of the patterns by computing their specificity. Patterns with low specificity are omitted and recomputed further down in the tree. The final high-quality patterns can be used for functional annotation. We ran our protocol on a recent Swiss-Prot release and show statistics, as well as a comparison to PRIAM, a probabilistic method that is also specialized on the functional annotation of enzymes. We determine the amount of true positive annotations for five common microorganisms with data from BRENDA and AMENDA serving as standard of truth. BrEPS is almost on par with PRIAM, a fact which we discuss in the context of five manually investigated cases. Conclusions Our protocol computes highly specific sequence patterns that can be used to support the functional annotation of enzymes. The main advantages of our method are that it is automatic and unsupervised, and quite fast once the patterns are evaluated. The results show that BrEPS can be a valuable addition to the reconstruction of metabolic networks.

  13. Cryptanalysis and improvement of quantum broadcast communication and authentication protocol with a quantum one-time pad

    International Nuclear Information System (INIS)

    Liu Zhi-Hao; Chen Han-Wu

    2016-01-01

    The security of quantum broadcast communication (QBC) and authentication protocol based on Greenberger–Horne–Zeilinger (GHZ) state and quantum one-time pad is analyzed. It is shown that there are some security issues in this protocol. Firstly, an external eavesdropper can take the intercept–measure–resend attack strategy to eavesdrop on 0.369 bit of every bit of the identity string of each receiver without being detected. Meanwhile, 0.524 bit of every bit of the secret message can be eavesdropped on without being detected. Secondly, an inner receiver can take the intercept–measure–resend attack strategy to eavesdrop on half of the identity string of the other’s definitely without being checked. In addition, an alternative attack called the CNOT-operation attack is discussed. As for the multi-party QBC protocol, the attack efficiency increases with the increase of the number of users. Finally, the QBC protocol is improved to a secure one. (paper)

  14. Musculoskeletal MRI at 3.0 T and 7.0 T: a comparison of relaxation times and image contrast.

    Science.gov (United States)

    Jordan, Caroline D; Saranathan, Manojkumar; Bangerter, Neal K; Hargreaves, Brian A; Gold, Garry E

    2013-05-01

    The purpose of this study was to measure and compare the relaxation times of musculoskeletal tissues at 3.0 T and 7.0 T, and to use these measurements to select appropriate parameters for musculoskeletal protocols at 7.0 T. We measured the T₁ and T₂ relaxation times of cartilage, muscle, synovial fluid, bone marrow and subcutaneous fat at both 3.0 T and 7.0 T in the knees of five healthy volunteers. The T₁ relaxation times were measured using a spin-echo inversion recovery sequence with six inversion times. The T₂ relaxation times were measured using a spin-echo sequence with seven echo times. The accuracy of both the T₁ and T₂ measurement techniques was verified in phantoms at both magnetic field strengths. We used the measured relaxation times to help design 7.0 T musculoskeletal protocols that preserve the favorable contrast characteristics of our 3.0 T protocols, while achieving significantly higher resolution at higher SNR efficiency. The T₁ relaxation times in all tissues at 7.0 T were consistently higher than those measured at 3.0 T, while the T₂ relaxation times at 7.0 T were consistently lower than those measured at 3.0 T. The measured relaxation times were used to help develop high resolution 7.0 T protocols that had similar fluid-to-cartilage contrast to that of the standard clinical 3.0 T protocols for the following sequences: proton-density-weighted fast spin-echo (FSE), T₂-weighted FSE, and 3D-FSE-Cube. The T₁ and T₂ changes were within the expected ranges. Parameters for musculoskeletal protocols at 7.0 T can be optimized based on these values, yielding improved resolution in musculoskeletal imaging with similar contrast to that of standard 3.0 T clinical protocols. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  15. Musculoskeletal MRI at 3.0 T and 7.0 T: A comparison of relaxation times and image contrast

    International Nuclear Information System (INIS)

    Jordan, Caroline D.; Saranathan, Manojkumar; Bangerter, Neal K.; Hargreaves, Brian A.; Gold, Garry E.

    2013-01-01

    Objective: The purpose of this study was to measure and compare the relaxation times of musculoskeletal tissues at 3.0 T and 7.0 T, and to use these measurements to select appropriate parameters for musculoskeletal protocols at 7.0 T. Materials and methods: We measured the T 1 and T 2 relaxation times of cartilage, muscle, synovial fluid, bone marrow and subcutaneous fat at both 3.0 T and 7.0 T in the knees of five healthy volunteers. The T 1 relaxation times were measured using a spin-echo inversion recovery sequence with six inversion times. The T 2 relaxation times were measured using a spin-echo sequence with seven echo times. The accuracy of both the T 1 and T 2 measurement techniques was verified in phantoms at both magnetic field strengths. We used the measured relaxation times to help design 7.0 T musculoskeletal protocols that preserve the favorable contrast characteristics of our 3.0 T protocols, while achieving significantly higher resolution at higher SNR efficiency. Results: The T 1 relaxation times in all tissues at 7.0 T were consistently higher than those measured at 3.0 T, while the T 2 relaxation times at 7.0 T were consistently lower than those measured at 3.0 T. The measured relaxation times were used to help develop high resolution 7.0 T protocols that had similar fluid-to-cartilage contrast to that of the standard clinical 3.0 T protocols for the following sequences: proton-density-weighted fast spin-echo (FSE), T 2 -weighted FSE, and 3D-FSE-Cube. Conclusion: The T 1 and T 2 changes were within the expected ranges. Parameters for musculoskeletal protocols at 7.0 T can be optimized based on these values, yielding improved resolution in musculoskeletal imaging with similar contrast to that of standard 3.0 T clinical protocols

  16. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  17. Evaluation of the Efficiency of Two Different Freezing Media and Two Different Protocols to Preserve Human Spermatozoa from Cryoinjury

    Directory of Open Access Journals (Sweden)

    Gemma Fabozzi

    2016-01-01

    Full Text Available It is universally recognized that cryopreservation impairs sperm quality. In order to improve postthawing sperm survival and motility, media of different composition and different protocols have been proposed. However, no clear evidence is available to understand which are the most efficient protocol and medium for sperm cryopreservation. The present study evaluates the efficiency of two different cryopreservation protocols and two common freezing media (FM containing different cryoprotectants (CPs, TEST Yolk Buffer (TYB and Sperm Freeze (SF, to preserve human sperm quality. Our data suggest that TYB is better than SF both in terms of postthaw viability and in terms of progressive motility, while the direct addition of FM to the sperm sample resulted in the most efficient protocol in terms of postthaw viability but not in terms of progressive motility.

  18. Blocking Optimality in Distributed Real-Time Locking Protocols

    Directory of Open Access Journals (Sweden)

    Björn Bernhard Brandenburg

    2014-09-01

    Full Text Available Lower and upper bounds on the maximum priority inversion blocking (pi-blocking that is generally unavoidable in distributed multiprocessor real-time locking protocols (where resources may be accessed only from specific synchronization processors are established. Prior work on suspension-based shared-memory multiprocessor locking protocols (which require resources to be accessible from all processors has established asymptotically tight bounds of Ω(m and Ω(n maximum pi-blocking under suspension-oblivious and suspension-aware analysis, respectively, where m denotes the total number of processors and n denotes the number of tasks. In this paper, it is shown that, in the case of distributed semaphore protocols, there exist two different task allocation scenarios that give rise to distinct lower bounds. In the case of co-hosted task allocation, where application tasks may also be assigned to synchronization processors (i.e., processors hosting critical sections, Ω(Φ · n maximum pi-blocking is unavoidable for some tasks under any locking protocol under both suspension-aware and suspension-oblivious schedulability analysis, where Φ denotes the ratio of the maximum response time to the shortest period. In contrast, in the case of disjoint task allocation (i.e., if application tasks may not be assigned to synchronization processors, only Ω(m and Ω(n maximum pi-blocking is fundamentally unavoidable under suspension-oblivious and suspension-aware analysis, respectively, as in the shared-memory case. These bounds are shown to be asymptotically tight with the construction of two new distributed real-time locking protocols that ensure O(m and O(n maximum pi-blocking under suspension-oblivious and suspension-aware analysis, respectively.

  19. Efficient one-out-of-two quantum oblivious transfer based on four-coherent-state postselection protocol

    International Nuclear Information System (INIS)

    Chen, I-C; Hwang Tzonelih; Li C-M

    2008-01-01

    On the basis of the modified four-coherent-state post-selection quantum key distribution protocol (Namiki and Hirano 2006 Preprint quant-ph/0608144v1), two 1-out-of-2 quantum oblivious transfer (QOT 2 1 ) protocols are proposed. The first proposed protocol (called the receiver-based QOT 2 1 protocol) requires the coherent states to be prepared by the receiver, whereas the second protocol (called the sender-based QOT 2 1 protocol) allows the coherent states to be generated by the sender. The main advantages of the proposed protocols are that (i) no quantum bit commitment schemes and the assumption of quantum memory are needed; (ii) less communication cost between participants is required, i.e. the receiver-based QOT 2 1 protocol requires only one quantum communication and one classical communication and the sender-based QOT 2 1 protocol requires only one quantum communication between participants during protocol execution; and (iii) the utilization of quantum states is very efficient, wherein the receiver-based and the sender-based QOT 2 1 protocols use only two coherent pulses and one coherent pulse respectively for sending the sender's two messages

  20. Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol

    Science.gov (United States)

    Huang, Xiaowan; Singh, Anu; Smolka, Scott A.

    2010-01-01

    We use the UPPAAL model checker for Timed Automata to verify the Timing-Sync time-synchronization protocol for sensor networks (TPSN). The TPSN protocol seeks to provide network-wide synchronization of the distributed clocks in a sensor network. Clock-synchronization algorithms for sensor networks such as TPSN must be able to perform arithmetic on clock values to calculate clock drift and network propagation delays. They must be able to read the value of a local clock and assign it to another local clock. Such operations are not directly supported by the theory of Timed Automata. To overcome this formal-modeling obstacle, we augment the UPPAAL specification language with the integer clock derived type. Integer clocks, which are essentially integer variables that are periodically incremented by a global pulse generator, greatly facilitate the encoding of the operations required to synchronize clocks as in the TPSN protocol. With this integer-clock-based model of TPSN in hand, we use UPPAAL to verify that the protocol achieves network-wide time synchronization and is devoid of deadlock. We also use the UPPAAL Tracer tool to illustrate how integer clocks can be used to capture clock drift and resynchronization during protocol execution

  1. Fuzzy Extractor and Elliptic Curve Based Efficient User Authentication Protocol for Wireless Sensor Networks and Internet of Things

    Directory of Open Access Journals (Sweden)

    Anup Kumar Maurya

    2017-10-01

    Full Text Available To improve the quality of service and reduce the possibility of security attacks, a secure and efficient user authentication mechanism is required for Wireless Sensor Networks (WSNs and the Internet of Things (IoT. Session key establishment between the sensor node and the user is also required for secure communication. In this paper, we perform the security analysis of A.K.Das’s user authentication scheme (given in 2015, Choi et al.’s scheme (given in 2016, and Park et al.’s scheme (given in 2016. The security analysis shows that their schemes are vulnerable to various attacks like user impersonation attack, sensor node impersonation attack and attacks based on legitimate users. Based on the cryptanalysis of these existing protocols, we propose a secure and efficient authenticated session key establishment protocol which ensures various security features and overcomes the drawbacks of existing protocols. The formal and informal security analysis indicates that the proposed protocol withstands the various security vulnerabilities involved in WSNs. The automated validation using AVISPA and Scyther tool ensures the absence of security attacks in our scheme. The logical verification using the Burrows-Abadi-Needham (BAN logic confirms the correctness of the proposed protocol. Finally, the comparative analysis based on computational overhead and security features of other existing protocol indicate that the proposed user authentication system is secure and efficient. In future, we intend to implement the proposed protocol in real-world applications of WSNs and IoT.

  2. Time and Space Efficient Algorithms for Two-Party Authenticated Data Structures

    Science.gov (United States)

    Papamanthou, Charalampos; Tamassia, Roberto

    Authentication is increasingly relevant to data management. Data is being outsourced to untrusted servers and clients want to securely update and query their data. For example, in database outsourcing, a client's database is stored and maintained by an untrusted server. Also, in simple storage systems, clients can store very large amounts of data but at the same time, they want to assure their integrity when they retrieve them. In this paper, we present a model and protocol for two-party authentication of data structures. Namely, a client outsources its data structure and verifies that the answers to the queries have not been tampered with. We provide efficient algorithms to securely outsource a skip list with logarithmic time overhead at the server and client and logarithmic communication cost, thus providing an efficient authentication primitive for outsourced data, both structured (e.g., relational databases) and semi-structured (e.g., XML documents). In our technique, the client stores only a constant amount of space, which is optimal. Our two-party authentication framework can be deployed on top of existing storage applications, thus providing an efficient authentication service. Finally, we present experimental results that demonstrate the practical efficiency and scalability of our scheme.

  3. A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq.

    Science.gov (United States)

    Logan, Grace; Freimanis, Graham L; King, David J; Valdazo-González, Begoña; Bachanek-Bankowska, Katarzyna; Sanderson, Nicholas D; Knowles, Nick J; King, Donald P; Cottam, Eleanor M

    2014-09-30

    Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.

  4. Implementing voice over Internet protocol in mobile ad hoc network – analysing its features regarding efficiency, reliability and security

    Directory of Open Access Journals (Sweden)

    Naveed Ahmed Sheikh

    2014-05-01

    Full Text Available Providing secure and efficient real-time voice communication in mobile ad hoc network (MANET environment is a challenging problem. Voice over Internet protocol (VoIP has originally been developed over the past two decades for infrastructure-based networks. There are strict timing constraints for acceptable quality VoIP services, in addition to registration and discovery issues in VoIP end-points. In MANETs, ad hoc nature of networks and multi-hop wireless environment with significant packet loss and delays present formidable challenges to the implementation. Providing a secure real-time VoIP service on MANET is the main design objective of this paper. The authors have successfully developed a prototype system that establishes reliable and efficient VoIP communication and provides an extremely flexible method for voice communication in MANETs. The authors’ cooperative mesh-based MANET implementation can be used for rapidly deployable VoIP communication with survivable and efficient dynamic networking using open source software.

  5. Optimized workflow and imaging protocols for whole-body oncologic PET/MRI.

    Science.gov (United States)

    Ishii, Shirou; Hara, Takamitsu; Nanbu, Takeyuki; Suenaga, Hiroki; Sugawara, Shigeyasu; Kuroiwa, Daichi; Sekino, Hirofumi; Miyajima, Masayuki; Kubo, Hitoshi; Oriuchi, Noboru; Ito, Hiroshi

    2016-11-01

    Although PET/MRI has the advantages of a simultaneous acquisition of PET and MRI, high soft-tissue contrast of the MRI images, and reduction of radiation exposure, its low profitability and long acquisition time are significant problems in clinical settings. Thus, MRI protocols that meet oncological purposes need to be used in order to reduce examination time while securing detectability. Currently, half-Fourier acquisition single-shot turbo spin echo and 3D-T1 volumetric interpolated breath-hold examination may be the most commonly used sequences for whole-body imaging due to their shorter acquisition time and higher diagnostic accuracy. Although there have been several reports that adding diffusion weighted image (DWI) to PET/MRI protocol has had no effect on tumor detection to date, in cases of liver, kidney, bladder, and prostate cancer, the use of DWI may be beneficial in detecting lesions. Another possible option is to scan each region with different MRI sequences instead of scanning the whole body using one sequence continuously. We herein report a workflow and imaging protocols for whole-body oncologic PET/MRI using an integrated system in the clinical routine, designed for the detection, for example by cancer screening, of metastatic lesions, in order to help future users optimize their workflow and imaging protocols.

  6. Efficient Implementation of a Symbol Timing Estimator for Broadband PLC.

    Science.gov (United States)

    Nombela, Francisco; García, Enrique; Mateos, Raúl; Hernández, Álvaro

    2015-08-21

    Broadband Power Line Communications (PLC) have taken advantage of the research advances in multi-carrier modulations to mitigate frequency selective fading, and their adoption opens up a myriad of applications in the field of sensory and automation systems, multimedia connectivity or smart spaces. Nonetheless, the use of these multi-carrier modulations, such as Wavelet-OFDM, requires a highly accurate symbol timing estimation for reliably recovering of transmitted data. Furthermore, the PLC channel presents some particularities that prevent the direct use of previous synchronization algorithms proposed in wireless communication systems. Therefore more research effort should be involved in the design and implementation of novel and robust synchronization algorithms for PLC, thus enabling real-time synchronization. This paper proposes a symbol timing estimator for broadband PLC based on cross-correlation with multilevel complementary sequences or Zadoff-Chu sequences and its efficient implementation in a FPGA; the obtained results show a 90% of success rate in symbol timing estimation for a certain PLC channel model and a reduced resource consumption for its implementation in a Xilinx Kyntex FPGA.

  7. Efficient Implementation of a Symbol Timing Estimator for Broadband PLC

    Directory of Open Access Journals (Sweden)

    Francisco Nombela

    2015-08-01

    Full Text Available Broadband Power Line Communications (PLC have taken advantage of the research advances in multi-carrier modulations to mitigate frequency selective fading, and their adoption opens up a myriad of applications in the field of sensory and automation systems, multimedia connectivity or smart spaces. Nonetheless, the use of these multi-carrier modulations, such as Wavelet-OFDM, requires a highly accurate symbol timing estimation for reliably recovering of transmitted data. Furthermore, the PLC channel presents some particularities that prevent the direct use of previous synchronization algorithms proposed in wireless communication systems. Therefore more research effort should be involved in the design and implementation of novel and robust synchronization algorithms for PLC, thus enabling real-time synchronization. This paper proposes a symbol timing estimator for broadband PLC based on cross-correlation with multilevel complementary sequences or Zadoff-Chu sequences and its efficient implementation in a FPGA; the obtained results show a 90% of success rate in symbol timing estimation for a certain PLC channel model and a reduced resource consumption for its implementation in a Xilinx Kyntex FPGA.

  8. Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

    Science.gov (United States)

    Chatterjee, Aniruddha; Rodger, Euan J.; Stockwell, Peter A.; Weeks, Robert J.; Morison, Ian M.

    2012-01-01

    Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background. PMID:23193365

  9. Cluster chain based energy efficient routing protocol for moblie WSN

    Directory of Open Access Journals (Sweden)

    WU Ziyu

    2016-04-01

    Full Text Available With the ubiquitous smart devices acting as mobile sensor nodes in the wireless sensor networks(WSNs to sense and transmit physical information,routing protocols should be designed to accommodate the mobility issues,in addition to conventional considerations on energy efficiency.However,due to frequent topology change,traditional routing schemes cannot perform well.Moreover,existence of mobile nodes poses new challenges on energy dissipation and packet loss.In this paper,a novel routing scheme called cluster chain based routing protocol(CCBRP is proposed,which employs a combination of cluster and chain structure to accomplish data collection and transmission and thereafter selects qualified cluster heads as chain leaders to transmit data to the sink.Furthermore,node mobility is handled based on periodical membership update of mobile nodes.Simulation results demonstrate that CCBRP has a good performance in terms of network lifetime and packet delivery,also strikes a better balance between successful packet reception and energy consumption.

  10. Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol.

    Science.gov (United States)

    Russell, Joseph A; Campos, Brittany; Stone, Jennifer; Blosser, Erik M; Burkett-Cadena, Nathan; Jacobs, Jonathan L

    2018-04-03

    The future of infectious disease surveillance and outbreak response is trending towards smaller hand-held solutions for point-of-need pathogen detection. Here, samples of Culex cedecei mosquitoes collected in Southern Florida, USA were tested for Venezuelan Equine Encephalitis Virus (VEEV), a previously-weaponized arthropod-borne RNA-virus capable of causing acute and fatal encephalitis in animal and human hosts. A single 20-mosquito pool tested positive for VEEV by quantitative reverse transcription polymerase chain reaction (RT-qPCR) on the Biomeme two3. The virus-positive sample was subjected to unbiased metatranscriptome sequencing on the Oxford Nanopore MinION and shown to contain Everglades Virus (EVEV), an alphavirus in the VEEV serocomplex. Our results demonstrate, for the first time, the use of unbiased sequence-based detection and subtyping of a high-consequence biothreat pathogen directly from an environmental sample using field-forward protocols. The development and validation of methods designed for field-based diagnostic metagenomics and pathogen discovery, such as those suitable for use in mobile "pocket laboratories", will address a growing demand for public health teams to carry out their mission where it is most urgent: at the point-of-need.

  11. Using Ovsynch protocol versus Cosynch protocol in dairy cows

    Directory of Open Access Journals (Sweden)

    Ion Valeriu Caraba

    2013-10-01

    Full Text Available As a research on the reproductive physiology and endocrinology surrounding the estrous cycle in dairy cattle has been compiled, several estrous synchronization programs have been developed for use with dairy cows. These include several programs that facilitate the mass breeding of all animals at a predetermined time (timed-AI rather than the detection of estrus. We studied on 15 dary cows which were synchronized by Ovsynch and Cosynch programs. The estrus response for cows in Ovsynch protocol was of 63%. Pregnancy per insemination at 60 days was of 25%. Estrus response for cow in Cosynch protocol was of 57%. Pregnancy per insemination at 60 days was of 57%. Synchronization of ovulation using Ovsynch protocols can provide an effective way to manage reproduction in lactating dairy cows by eliminating the need for estrus detection. These are really efficient management programs for TAI of dairy cows that are able to reduce both the labour costs and the extra handling to daily estrus detection and AI.

  12. Abbreviated Combined MR Protocol: A New Faster Strategy for Characterizing Breast Lesions.

    Science.gov (United States)

    Moschetta, Marco; Telegrafo, Michele; Rella, Leonarda; Stabile Ianora, Amato Antonio; Angelelli, Giuseppe

    2016-06-01

    The use of an abbreviated magnetic resonance (MR) protocol has been recently proposed for cancer screening. The aim of our study is to evaluate the diagnostic accuracy of an abbreviated MR protocol combining short TI inversion recovery (STIR), turbo-spin-echo (TSE)-T2 sequences, a pre-contrast T1, and a single intermediate (3 minutes after contrast injection) post-contrast T1 sequence for characterizing breast lesions. A total of 470 patients underwent breast MR examination for screening, problem solving, or preoperative staging. Two experienced radiologists evaluated both standard and abbreviated protocols in consensus. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy for both protocols were calculated (with the histological findings and 6-month ultrasound follow-up as the reference standard) and compared with the McNemar test. The post-processing and interpretation times for the MR images were compared with the paired t test. In 177 of 470 (38%) patients, the MR sequences detected 185 breast lesions. Standard and abbreviated protocols obtained sensitivity, specificity, diagnostic accuracy, PPV, and NPV values respectively of 92%, 92%, 92%, 68%, and 98% and of 89%, 91%, 91%, 64%, and 98% with no statistically significant difference (P < .0001). The mean post-processing and interpretation time were, respectively, 7 ± 1 minutes and 6 ± 3.2 minutes for the standard protocol and 1 ± 1.2 minutes and 2 ± 1.2 minutes for the abbreviated protocol, with a statistically significant difference (P < .01). An abbreviated combined MR protocol represents a time-saving tool for radiologists and patients with the same diagnostic potential as the standard protocol in patients undergoing breast MRI for screening, problem solving, or preoperative staging. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Evaluation of the articular cartilage of the knee joint: value of adding a T2 mapping sequence to a routine MR imaging protocol.

    Science.gov (United States)

    Kijowski, Richard; Blankenbaker, Donna G; Munoz Del Rio, Alejandro; Baer, Geoffrey S; Graf, Ben K

    2013-05-01

    To determine whether the addition of a T2 mapping sequence to a routine magnetic resonance (MR) imaging protocol could improve diagnostic performance in the detection of surgically confirmed cartilage lesions within the knee joint at 3.0 T. This prospective study was approved by the institutional review board, and the requirement to obtain informed consent was waived. The study group consisted of 150 patients (76 male and 74 female patients with an average age of 41.2 and 41.5 years, respectively) who underwent MR imaging and arthroscopy of the knee joint. MR imaging was performed at 3.0 T by using a routine protocol with the addition of a sagittal T2 mapping sequence. Images from all MR examinations were reviewed in consensus by two radiologists before surgery to determine the presence or absence of cartilage lesions on each articular surface, first by using the routine MR protocol alone and then by using the routine MR protocol with T2 maps. Each articular surface was then evaluated at arthroscopy. Generalized estimating equation models were used to compare the sensitivity and specificity of the routine MR imaging protocol with and without T2 maps in the detection of surgically confirmed cartilage lesions. The sensitivity and specificity in the detection of 351 cartilage lesions were 74.6% and 97.8%, respectively, for the routine MR protocol alone and 88.9% and 93.1% for the routine MR protocol with T2 maps. Differences in sensitivity and specificity were statistically significant (P T2 maps to the routine MR imaging protocol significantly improved the sensitivity in the detection of 24 areas of cartilage softening (from 4.2% to 62%, P T2 mapping sequence to a routine MR protocol at 3.0 T improved sensitivity in the detection of cartilage lesions within the knee joint from 74.6% to 88.9%, with only a small reduction in specificity. The greatest improvement in sensitivity with use of the T2 maps was in the identification of early cartilage degeneration. © RSNA

  14. Low Latency MAC Protocol in Wireless Sensor Networks Using Timing Offset

    Science.gov (United States)

    Choi, Seung Sik

    This paper proposes a low latency MAC protocol that can be used in sensor networks. To extend the lifetime of sensor nodes, the conventional solution is to synchronize active/sleep periods of all sensor nodes. However, due to these synchronized sensor nodes, packets in the intermediate nodes must wait until the next node wakes up before it can forward a packet. This induces a large delay in sensor nodes. To solve this latency problem, a clustered sensor network which uses two types of sensor nodes and layered architecture is considered. Clustered heads in each cluster are synchronized with different timing offsets to reduce the sleep delay. Using this concept, the latency problem can be solved and more efficient power usage can be obtained.

  15. Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

    Science.gov (United States)

    Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

    2015-12-29

    Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

  16. Effects of a Short Drilling Implant Protocol on Osteotomy Site Temperature and Drill Torque.

    Science.gov (United States)

    Mihali, Sorin G; Canjau, Silvana; Cernescu, Anghel; Bortun, Cristina M; Wang, Hom-Lay; Bratu, Emanuel

    2018-02-01

    To establish a protocol for reducing the drilling sequence during implant site preparation based on temperature and insertion torque. The traditional conventional drilling sequence (used several drills with 0.6-mm increment each time) was compared with the proposed short drilling protocol (only used 2 drills: initial and final drill). One hundred drilling osteotomies were performed in bovine and porcine bones. Sets of 2 osteotomy sites were created in 5 bone densities using 2 types of drilling protocols. Thermographic pictures were captured throughout all drilling procedures and analyzed using ThermaCAM Researcher Professional 2.10. Torque values were determined during drilling by measuring electrical input and drill speed. There were statistically significant differences in bone temperature between the conventional and short drilling protocols during implant site preparation (analysis of variance P = 0.0008). However, there were no significant differences between the 2 types of drilling protocols for both implant diameters. Implant site preparation time was significantly reduced when using the short drilling protocol compared with the conventional drilling protocol (P drilling protocol proposed herein may represent a safe approach for implant site preparation.

  17. Effectiveness of a Rapid Lumbar Spine MRI Protocol Using 3D T2-Weighted SPACE Imaging Versus a Standard Protocol for Evaluation of Degenerative Changes of the Lumbar Spine.

    Science.gov (United States)

    Sayah, Anousheh; Jay, Ann K; Toaff, Jacob S; Makariou, Erini V; Berkowitz, Frank

    2016-09-01

    Reducing lumbar spine MRI scanning time while retaining diagnostic accuracy can benefit patients and reduce health care costs. This study compares the effectiveness of a rapid lumbar MRI protocol using 3D T2-weighted sampling perfection with application-optimized contrast with different flip-angle evolutions (SPACE) sequences with a standard MRI protocol for evaluation of lumbar spondylosis. Two hundred fifty consecutive unenhanced lumbar MRI examinations performed at 1.5 T were retrospectively reviewed. Full, rapid, and complete versions of each examination were interpreted for spondylotic changes at each lumbar level, including herniations and neural compromise. The full examination consisted of sagittal T1-weighted, T2-weighted turbo spin-echo (TSE), and STIR sequences; and axial T1- and T2-weighted TSE sequences (time, 18 minutes 40 seconds). The rapid examination consisted of sagittal T1- and T2-weighted SPACE sequences, with axial SPACE reformations (time, 8 minutes 46 seconds). The complete examination consisted of the full examination plus the T2-weighted SPACE sequence. Sensitivities and specificities of the full and rapid examinations were calculated using the complete study as the reference standard. The rapid and full studies had sensitivities of 76.0% and 69.3%, with specificities of 97.2% and 97.9%, respectively, for all degenerative processes. Rapid and full sensitivities were 68.7% and 66.3% for disk herniation, 85.2% and 81.5% for canal compromise, 82.9% and 69.1% for lateral recess compromise, and 76.9% and 69.7% for foraminal compromise, respectively. Isotropic SPACE T2-weighted imaging provides high-quality imaging of lumbar spondylosis, with multiplanar reformatting capability. Our SPACE-based rapid protocol had sensitivities and specificities for herniations and neural compromise comparable to those of the protocol without SPACE. This protocol fits within a 15-minute slot, potentially reducing costs and discomfort for a large subgroup of

  18. A Proof-checked Verification of a Real-Time Communication Protocol

    NARCIS (Netherlands)

    Polak, I.

    We present an analysis of a protocol developed by Philips to connect several components of an audio-system. The verification of the protocol is carried out using the timed I/O-automata model of Lynch and Vaandrager. The verification has been partially proof-checked with the interactive proof

  19. Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes

    Directory of Open Access Journals (Sweden)

    Knut Rudi

    2003-01-01

    Full Text Available Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

  20. Time Synchronization and Distribution Mechanisms for Space Networks

    Science.gov (United States)

    Woo, Simon S.; Gao, Jay L.; Clare, Loren P.; Mills, David L.

    2011-01-01

    This work discusses research on the problems of synchronizing and distributing time information between spacecraft based on the Network Time Protocol (NTP), where NTP is a standard time synchronization protocol widely used in the terrestrial network. The Proximity-1 Space Link Interleaved Time Synchronization (PITS) Protocol was designed and developed for synchronizing spacecraft that are in proximity where proximity is less than 100,000 km distant. A particular application is synchronization between a Mars orbiter and rover. Lunar scenarios as well as outer-planet deep space mother-ship-probe missions may also apply. Spacecraft with more accurate time information functions as a time-server, and the other spacecraft functions as a time-client. PITS can be easily integrated and adaptable to the CCSDS Proximity-1 Space Link Protocol with minor modifications. In particular, PITS can take advantage of the timestamping strategy that underlying link layer functionality provides for accurate time offset calculation. The PITS algorithm achieves time synchronization with eight consecutive space network time packet exchanges between two spacecraft. PITS can detect and avoid possible errors from receiving duplicate and out-of-order packets by comparing with the current state variables and timestamps. Further, PITS is able to detect error events and autonomously recover from unexpected events that can possibly occur during the time synchronization and distribution process. This capability achieves an additional level of protocol protection on top of CRC or Error Correction Codes. PITS is a lightweight and efficient protocol, eliminating the needs for explicit frame sequence number and long buffer storage. The PITS protocol is capable of providing time synchronization and distribution services for a more general domain where multiple entities need to achieve time synchronization using a single point-to-point link.

  1. Cross-layer cluster-based energy-efficient protocol for wireless sensor networks.

    Science.gov (United States)

    Mammu, Aboobeker Sidhik Koyamparambil; Hernandez-Jayo, Unai; Sainz, Nekane; de la Iglesia, Idoia

    2015-04-09

    Recent developments in electronics and wireless communications have enabled the improvement of low-power and low-cost wireless sensors networks (WSNs). One of the most important challenges in WSNs is to increase the network lifetime due to the limited energy capacity of the network nodes. Another major challenge in WSNs is the hot spots that emerge as locations under heavy traffic load. Nodes in such areas quickly drain energy resources, leading to disconnection in network services. In such an environment, cross-layer cluster-based energy-efficient algorithms (CCBE) can prolong the network lifetime and energy efficiency. CCBE is based on clustering the nodes to different hexagonal structures. A hexagonal cluster consists of cluster members (CMs) and a cluster head (CH). The CHs are selected from the CMs based on nodes near the optimal CH distance and the residual energy of the nodes. Additionally, the optimal CH distance that links to optimal energy consumption is derived. To balance the energy consumption and the traffic load in the network, the CHs are rotated among all CMs. In WSNs, energy is mostly consumed during transmission and reception. Transmission collisions can further decrease the energy efficiency. These collisions can be avoided by using a contention-free protocol during the transmission period. Additionally, the CH allocates slots to the CMs based on their residual energy to increase sleep time. Furthermore, the energy consumption of CH can be further reduced by data aggregation. In this paper, we propose a data aggregation level based on the residual energy of CH and a cost-aware decision scheme for the fusion of data. Performance results show that the CCBE scheme performs better in terms of network lifetime, energy consumption and throughput compared to low-energy adaptive clustering hierarchy (LEACH) and hybrid energy-efficient distributed clustering (HEED).

  2. Cross-Layer Cluster-Based Energy-Efficient Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Aboobeker Sidhik Koyamparambil Mammu

    2015-04-01

    Full Text Available Recent developments in electronics and wireless communications have enabled the improvement of low-power and low-cost wireless sensors networks (WSNs. One of the most important challenges in WSNs is to increase the network lifetime due to the limited energy capacity of the network nodes. Another major challenge in WSNs is the hot spots that emerge as locations under heavy traffic load. Nodes in such areas quickly drain energy resources, leading to disconnection in network services. In such an environment, cross-layer cluster-based energy-efficient algorithms (CCBE can prolong the network lifetime and energy efficiency. CCBE is based on clustering the nodes to different hexagonal structures. A hexagonal cluster consists of cluster members (CMs and a cluster head (CH. The CHs are selected from the CMs based on nodes near the optimal CH distance and the residual energy of the nodes. Additionally, the optimal CH distance that links to optimal energy consumption is derived. To balance the energy consumption and the traffic load in the network, the CHs are rotated among all CMs. In WSNs, energy is mostly consumed during transmission and reception. Transmission collisions can further decrease the energy efficiency. These collisions can be avoided by using a contention-free protocol during the transmission period. Additionally, the CH allocates slots to the CMs based on their residual energy to increase sleep time. Furthermore, the energy consumption of CH can be further reduced by data aggregation. In this paper, we propose a data aggregation level based on the residual energy of CH and a cost-aware decision scheme for the fusion of data. Performance results show that the CCBE scheme performs better in terms of network lifetime, energy consumption and throughput compared to low-energy adaptive clustering hierarchy (LEACH and hybrid energy-efficient distributed clustering (HEED.

  3. A Decentralized Fuzzy C-Means-Based Energy-Efficient Routing Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Osama Moh’d Alia

    2014-01-01

    Full Text Available Energy conservation in wireless sensor networks (WSNs is a vital consideration when designing wireless networking protocols. In this paper, we propose a Decentralized Fuzzy Clustering Protocol, named DCFP, which minimizes total network energy dissipation to promote maximum network lifetime. The process of constructing the infrastructure for a given WSN is performed only once at the beginning of the protocol at a base station, which remains unchanged throughout the network’s lifetime. In this initial construction step, a fuzzy C-means algorithm is adopted to allocate sensor nodes into their most appropriate clusters. Subsequently, the protocol runs its rounds where each round is divided into a CH-Election phase and a Data Transmission phase. In the CH-Election phase, the election of new cluster heads is done locally in each cluster where a new multicriteria objective function is proposed to enhance the quality of elected cluster heads. In the Data Transmission phase, the sensing and data transmission from each sensor node to their respective cluster head is performed and cluster heads in turn aggregate and send the sensed data to the base station. Simulation results demonstrate that the proposed protocol improves network lifetime, data delivery, and energy consumption compared to other well-known energy-efficient protocols.

  4. A decentralized fuzzy C-means-based energy-efficient routing protocol for wireless sensor networks.

    Science.gov (United States)

    Alia, Osama Moh'd

    2014-01-01

    Energy conservation in wireless sensor networks (WSNs) is a vital consideration when designing wireless networking protocols. In this paper, we propose a Decentralized Fuzzy Clustering Protocol, named DCFP, which minimizes total network energy dissipation to promote maximum network lifetime. The process of constructing the infrastructure for a given WSN is performed only once at the beginning of the protocol at a base station, which remains unchanged throughout the network's lifetime. In this initial construction step, a fuzzy C-means algorithm is adopted to allocate sensor nodes into their most appropriate clusters. Subsequently, the protocol runs its rounds where each round is divided into a CH-Election phase and a Data Transmission phase. In the CH-Election phase, the election of new cluster heads is done locally in each cluster where a new multicriteria objective function is proposed to enhance the quality of elected cluster heads. In the Data Transmission phase, the sensing and data transmission from each sensor node to their respective cluster head is performed and cluster heads in turn aggregate and send the sensed data to the base station. Simulation results demonstrate that the proposed protocol improves network lifetime, data delivery, and energy consumption compared to other well-known energy-efficient protocols.

  5. A Decentralized Fuzzy C-Means-Based Energy-Efficient Routing Protocol for Wireless Sensor Networks

    Science.gov (United States)

    2014-01-01

    Energy conservation in wireless sensor networks (WSNs) is a vital consideration when designing wireless networking protocols. In this paper, we propose a Decentralized Fuzzy Clustering Protocol, named DCFP, which minimizes total network energy dissipation to promote maximum network lifetime. The process of constructing the infrastructure for a given WSN is performed only once at the beginning of the protocol at a base station, which remains unchanged throughout the network's lifetime. In this initial construction step, a fuzzy C-means algorithm is adopted to allocate sensor nodes into their most appropriate clusters. Subsequently, the protocol runs its rounds where each round is divided into a CH-Election phase and a Data Transmission phase. In the CH-Election phase, the election of new cluster heads is done locally in each cluster where a new multicriteria objective function is proposed to enhance the quality of elected cluster heads. In the Data Transmission phase, the sensing and data transmission from each sensor node to their respective cluster head is performed and cluster heads in turn aggregate and send the sensed data to the base station. Simulation results demonstrate that the proposed protocol improves network lifetime, data delivery, and energy consumption compared to other well-known energy-efficient protocols. PMID:25162060

  6. MR colonography with fecal tagging: comparison between 2D turbo FLASH and 3D FLASH sequences

    International Nuclear Information System (INIS)

    Papanikolaou, Nickolas; Grammatikakis, John; Maris, Thomas; Prassopoulos, Panos; Gourtsoyiannis, Nicholas; Lauenstein, Thomas

    2003-01-01

    The objective of this study was to compare inversion recovery turbo 2D fast low-angle shot (FLASH) and 3D FLASH sequences for fecal-tagged MR colonography studies. Fifteen consecutive patients with indications for colonoscopy underwent MR colonography with fecal tagging. An inversion recovery turbo-FLASH sequence was applied and compared in terms of artifacts presence, efficiency for masking residual stool, and colonic wall conspicuity with a fat-saturated 3D FLASH sequence. Both sequences were acquired following administration of paramagnetic contrast agent. Contrast-to-noise ratio and relative contrast between colonic wall and lumen were calculated and compared for both sequences. Turbo 2D FLASH provided fewer artifacts, higher efficiency for masking the residual stool, and colonic wall conspicuity equivalent to 3D FLASH. An inversion time of 10 ms provided homogeneously low signal intensity of the colonic lumen. Contrast to noise between colonic wall and lumen was significantly higher in the 3D FLASH images, whereas differences in relative contrast were not statistically significant. An optimized inversion-recovery 2D turbo-FLASH sequence provides better fecal tagging results and should be added to the 3D FLASH sequence when designing dark-lumen MR colonography examination protocols. (orig.)

  7. Inaudible functional MRI using a truly mute gradient echo sequence

    International Nuclear Information System (INIS)

    Marcar, V.L.; Girard, F.; Rinkel, Y.; Schneider, J.F.; Martin, E.

    2002-01-01

    We performed functional MRI experiments using a mute version of a gradient echo sequence on adult volunteers using either a simple visual stimulus (flicker goggles: 4 subjects) or an auditory stimulus (music: 4 subjects). Because the mute sequence delivers fewer images per unit time than a fast echo planar imaging (EPI) sequence, we explored our data using a parametric ANOVA test and a non-parametric Wilcoxon-Mann-Whitney test in addition to performing a cross-correlation analysis. All three methods were in close agreement regarding the location of the BOLD contrast signal change. We demonstrated that, using appropriate statistical analysis, functional MRI using an MR sequence that is acoustically inaudible to the subject is feasible. Furthermore compared with the ''silent'' event-related procedures involving an EPI protocol, our mGE protocol compares favourably with respect to experiment time and the BOLD signal. (orig.)

  8. Magnetic resonance imaging protocols for paediatric neuroradiology

    International Nuclear Information System (INIS)

    Saunders, Dawn E.; Thompson, Clare; Gunny, Roxanne; Jones, Rod; Cox, Tim; Chong, Wui Khean

    2007-01-01

    Increasingly, radiologists are encouraged to have protocols for all imaging studies and to include imaging guidelines in care pathways set up by the referring clinicians. This is particularly advantageous in MRI where magnet time is limited and a radiologist's review of each patient's images often results in additional sequences and longer scanning times without the advantage of improvement in diagnostic ability. The difficulties of imaging small children and the challenges presented to the radiologist as the brain develops are discussed. We present our protocols for imaging the brain and spine of children based on 20 years experience of paediatric neurological MRI. The protocols are adapted to suit children under the age of 2 years, small body parts and paediatric clinical scenarios. (orig.)

  9. An efficient genetic algorithm for a hybrid flow shop scheduling problem with time lags and sequence-dependent setup time

    Directory of Open Access Journals (Sweden)

    Farahmand-Mehr Mohammad

    2014-01-01

    Full Text Available In this paper, a hybrid flow shop scheduling problem with a new approach considering time lags and sequence-dependent setup time in realistic situations is presented. Since few works have been implemented in this field, the necessity of finding better solutions is a motivation to extend heuristic or meta-heuristic algorithms. This type of production system is found in industries such as food processing, chemical, textile, metallurgical, printed circuit board, and automobile manufacturing. A mixed integer linear programming (MILP model is proposed to minimize the makespan. Since this problem is known as NP-Hard class, a meta-heuristic algorithm, named Genetic Algorithm (GA, and three heuristic algorithms (Johnson, SPTCH and Palmer are proposed. Numerical experiments of different sizes are implemented to evaluate the performance of presented mathematical programming model and the designed GA in compare to heuristic algorithms and a benchmark algorithm. Computational results indicate that the designed GA can produce near optimal solutions in a short computational time for different size problems.

  10. An efficient protocol for the palladium-catalysed Suzuki-Miyaura cross-coupling

    KAUST Repository

    Marziale, Alexander N.; Jantke, Dominik; Faul, Stefan Holger; Reiner, Thomas; Herdtweck, Eberhardt; Eppinger, Jö rg

    2011-01-01

    The palladacyclic catalyst precursor received by ortho-palladation of ([1,1′-biphenyl]-2-yloxy)diisopropyl-phosphine represents a highly active system for Suzuki-Miyaura cross-coupling reactions when used in neat water. An efficient, broadly applicable and sustainable aqueous protocol was developed using 2.5 eq. of Na2CO3 as base, allowing the reaction to be performed under air and at ambient temperature with Pd loadings of 0.04 mol%. Coupling products are obtained in high yields and excellent purity by simple filtration with no organic solvents needed throughout the whole reaction. A broad variety of functional groups are tolerated and a large number of substrates can be applied with this protocol. The crystal structure of the palladacyclic catalyst precursor is presented as well as investigations targeting the nature of catalyst activation and the active catalytic species. © 2011 The Royal Society of Chemistry.

  11. A Rapid and Efficient Sonogashira Protocol and Improved Synthesis of Free Fatty Acid 1 (FFA1) Receptor Agonists

    DEFF Research Database (Denmark)

    Christiansen, Elisabeth; Due-Hansen, Maria E; Ulven, Trond

    2010-01-01

    A protocol for rapid and efficient Pd/Cu-catalyzed coupling of aryl bromides and iodides to terminal alkynes has been developed with use of 2-(di-tert-butylphosphino)-N-phenylindole (cataCXium PIntB) as ligand in TMEDA and water. The new protocol successfully couples substrates which failed...

  12. Analysis of the LTE Access Reservation Protocol for Real-Time Traffic

    DEFF Research Database (Denmark)

    Thomsen, Henning; Kiilerich Pratas, Nuno; Stefanovic, Cedomir

    2013-01-01

    LTE is increasingly seen as a system for serving real-time Machine-to-Machine (M2M) communication needs. The asynchronous M2M user access in LTE is obtained through a two-phase access reservation protocol (contention and data phase). Existing analysis related to these protocols is based...... of the two-phase LTE reservation protocol and asses its performance, when assumptions (1) and (2) do not hold....

  13. Design of an autonomous decentralized MAC protocol for wireless sensor networks

    NARCIS (Netherlands)

    van Hoesel, L.F.W.; Dal Pont, L.; Havinga, Paul J.M.

    In this document the design of a MAC protocol for wireless sensor networks is discussed. The autonomous decentralized TDMA based MAC protocol minimizes power consumtion by efficiency implementing unicast/omnicast, scheduled rendezvous times and wakeup calls. The MAC protocol is an ongoing research

  14. Evaluation of MRI sequences for quantitative T1 brain mapping

    Science.gov (United States)

    Tsialios, P.; Thrippleton, M.; Glatz, A.; Pernet, C.

    2017-11-01

    T1 mapping constitutes a quantitative MRI technique finding significant application in brain imaging. It allows evaluation of contrast uptake, blood perfusion, volume, providing a more specific biomarker of disease progression compared to conventional T1-weighted images. While there are many techniques for T1-mapping there is a wide range of reported T1-values in tissues, raising the issue of protocols reproducibility and standardization. The gold standard for obtaining T1-maps is based on acquiring IR-SE sequence. Widely used alternative sequences are IR-SE-EPI, VFA (DESPOT), DESPOT-HIFI and MP2RAGE that speed up scanning and fitting procedures. A custom MRI phantom was used to assess the reproducibility and accuracy of the different methods. All scans were performed using a 3T Siemens Prisma scanner. The acquired data processed using two different codes. The main difference was observed for VFA (DESPOT) which grossly overestimated T1 relaxation time by 214 ms [126 270] compared to the IR-SE sequence. MP2RAGE and DESPOT-HIFI sequences gave slightly shorter time than IR-SE (~20 to 30ms) and can be considered as alternative and time-efficient methods for acquiring accurate T1 maps of the human brain, while IR-SE-EPI gave identical result, at a cost of a lower image quality.

  15. Software Modules for the Proximity-1 Space Link Interleaved Time Synchronization (PITS) Protocol

    Science.gov (United States)

    Woo, Simon S.; Veregge, John R.; Gao, Jay L.; Clare, Loren P.; Mills, David

    2012-01-01

    The Proximity-1 Space Link Interleaved Time Synchronization (PITS) protocol provides time distribution and synchronization services for space systems. A software prototype implementation of the PITS algorithm has been developed that also provides the test harness to evaluate the key functionalities of PITS with simulated data source and sink. PITS integrates time synchronization functionality into the link layer of the CCSDS Proximity-1 Space Link Protocol. The software prototype implements the network packet format, data structures, and transmit- and receive-timestamp function for a time server and a client. The software also simulates the transmit and receive-time stamp exchanges via UDP (User Datagram Protocol) socket between a time server and a time client, and produces relative time offsets and delay estimates.

  16. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

  17. Mathematical modeling of efficient protocols to control glioma growth.

    Science.gov (United States)

    Branco, J R; Ferreira, J A; de Oliveira, Paula

    2014-09-01

    In this paper we propose a mathematical model to describe the evolution of glioma cells taking into account the viscoelastic properties of brain tissue. The mathematical model is established considering that the glioma cells are of two phenotypes: migratory and proliferative. The evolution of the migratory cells is described by a diffusion-reaction equation of non Fickian type deduced considering a mass conservation law with a non Fickian migratory mass flux. The evolution of the proliferative cells is described by a reaction equation. A stability analysis that leads to the design of efficient protocols is presented. Numerical simulations that illustrate the behavior of the mathematical model are included. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Efficient Threshold Zero-Knowledge with Applications to User-Centric Protocols

    DEFF Research Database (Denmark)

    Mikkelsen, Gert Læssøe; Keller, Marcel; Rupp, Andy

    2012-01-01

    , such as identification schemes, electronic cash (e-cash), and anonymous credentials. We present a security model for threshold proofs of knowledge and develop threshold versions of well-known primitives such as range proofs, zero-knowledge proofs for preimages of homomorphisms (which generalizes PoKs of discrete...... efficient (when compared to a general MPC approach). In comparison to the original protocols only the prover’s (or user’s) side is modified while the other side stays untouched. In particular, it is oblivious to the other party whether it interacts with a distributed prover (or user) or one as defined...

  19. Inaudible functional MRI using a truly mute gradient echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Marcar, V.L. [University of Zurich, Department of Psychology, Neuropsychology, Treichlerstrasse 10, 8032 Zurich (Switzerland); Girard, F. [GE Medical Systems SA, 283, rue de la Miniere B.P. 34, 78533 Buc Cedex (France); Rinkel, Y.; Schneider, J.F.; Martin, E. [University Children' s Hospital, Neuroradiology and Magnetic Resonance, Department of Diagnostic Imaging, Steinwiesstrasse 75, 8032 Zurich (Switzerland)

    2002-11-01

    We performed functional MRI experiments using a mute version of a gradient echo sequence on adult volunteers using either a simple visual stimulus (flicker goggles: 4 subjects) or an auditory stimulus (music: 4 subjects). Because the mute sequence delivers fewer images per unit time than a fast echo planar imaging (EPI) sequence, we explored our data using a parametric ANOVA test and a non-parametric Wilcoxon-Mann-Whitney test in addition to performing a cross-correlation analysis. All three methods were in close agreement regarding the location of the BOLD contrast signal change. We demonstrated that, using appropriate statistical analysis, functional MRI using an MR sequence that is acoustically inaudible to the subject is feasible. Furthermore compared with the ''silent'' event-related procedures involving an EPI protocol, our mGE protocol compares favourably with respect to experiment time and the BOLD signal. (orig.)

  20. Kajian Literatur Sinkronisasi Waktu Dengan Network Time Protocol Untuk Pemantauan Aktivitas Jaringan Telekomunikasi

    Directory of Open Access Journals (Sweden)

    Ahmad Budi Setiawan

    2015-12-01

    Abstract Network providers are providing services or networks that enable the implementation of electronic transactions. Each network operator is required to align the time in electronic transactions. The purpose is to provide time alignment of the time standard and provide a time frame for all forms of electronic transactions with the principles of accuracy and traceability. Indonesian Time Alignment System uses the principle of traceability and accuracy principles. The protocols used in the alignment of the time server in Indonesia-based Network Time Protocol. This study discusses the implementation of time synchronization with a network time protocol as a form of telecommunications network security monitoring. The method used in this study is a descriptive narrative on the implementation of time synchronization. Results of this study are input to the policy in the security of electronic transactions through time synchronization

  1. Use of plan quality degradation to evaluate tradeoffs in delivery efficiency and clinical plan metrics arising from IMRT optimizer and sequencer compromises

    Science.gov (United States)

    Wilkie, Joel R.; Matuszak, Martha M.; Feng, Mary; Moran, Jean M.; Fraass, Benedick A.

    2013-01-01

    Purpose: Plan degradation resulting from compromises made to enhance delivery efficiency is an important consideration for intensity modulated radiation therapy (IMRT) treatment plans. IMRT optimization and/or multileaf collimator (MLC) sequencing schemes can be modified to generate more efficient treatment delivery, but the effect those modifications have on plan quality is often difficult to quantify. In this work, the authors present a method for quantitative assessment of overall plan quality degradation due to tradeoffs between delivery efficiency and treatment plan quality, illustrated using comparisons between plans developed allowing different numbers of intensity levels in IMRT optimization and/or MLC sequencing for static segmental MLC IMRT plans. Methods: A plan quality degradation method to evaluate delivery efficiency and plan quality tradeoffs was developed and used to assess planning for 14 prostate and 12 head and neck patients treated with static IMRT. Plan quality was evaluated using a physician's predetermined “quality degradation” factors for relevant clinical plan metrics associated with the plan optimization strategy. Delivery efficiency and plan quality were assessed for a range of optimization and sequencing limitations. The “optimal” (baseline) plan for each case was derived using a clinical cost function with an unlimited number of intensity levels. These plans were sequenced with a clinical MLC leaf sequencer which uses >100 segments, assuring delivered intensities to be within 1% of the optimized intensity pattern. Each patient's optimal plan was also sequenced limiting the number of intensity levels (20, 10, and 5), and then separately optimized with these same numbers of intensity levels. Delivery time was measured for all plans, and direct evaluation of the tradeoffs between delivery time and plan degradation was performed. Results: When considering tradeoffs, the optimal number of intensity levels depends on the treatment

  2. Global profiling of DNA replication timing and efficiency reveals that efficient replication/firing occurs late during S-phase in S. pombe.

    Directory of Open Access Journals (Sweden)

    Majid Eshaghi

    Full Text Available BACKGROUND: During S. pombe S-phase, initiation of DNA replication occurs at multiple sites (origins that are enriched with AT-rich sequences, at various times. Current studies of genome-wide DNA replication profiles have focused on the DNA replication timing and origin location. However, the replication and/or firing efficiency of the individual origins on the genomic scale remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: Using the genome-wide ORF-specific DNA microarray analysis, we show that in S. pombe, individual origins fire with varying efficiencies and at different times during S-phase. The increase in DNA copy number plotted as a function of time is approximated to the near-sigmoidal model, when considering the replication start and end timings at individual loci in cells released from HU-arrest. Replication efficiencies differ from origin to origin, depending on the origin's firing efficiency. We have found that DNA replication is inefficient early in S-phase, due to inefficient firing at origins. Efficient replication occurs later, attributed to efficient but late-firing origins. Furthermore, profiles of replication timing in cds1Delta cells are abnormal, due to the failure in resuming replication at the collapsed forks. The majority of the inefficient origins, but not the efficient ones, are found to fire in cds1Delta cells after HU removal, owing to the firing at the remaining unused (inefficient origins during HU treatment. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that efficient DNA replication/firing occurs late in S-phase progression in cells after HU removal, due to efficient late-firing origins. Additionally, checkpoint kinase Cds1p is required for maintaining the efficient replication/firing late in S-phase. We further propose that efficient late-firing origins are essential for ensuring completion of DNA duplication by the end of S-phase.

  3. High-Throughput Next-Generation Sequencing of Polioviruses

    Science.gov (United States)

    Montmayeur, Anna M.; Schmidt, Alexander; Zhao, Kun; Magaña, Laura; Iber, Jane; Castro, Christina J.; Chen, Qi; Henderson, Elizabeth; Ramos, Edward; Shaw, Jing; Tatusov, Roman L.; Dybdahl-Sissoko, Naomi; Endegue-Zanga, Marie Claire; Adeniji, Johnson A.; Oberste, M. Steven; Burns, Cara C.

    2016-01-01

    ABSTRACT The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance. PMID:27927929

  4. Backup key generation model for one-time password security protocol

    Science.gov (United States)

    Jeyanthi, N.; Kundu, Sourav

    2017-11-01

    The use of one-time password (OTP) has ushered new life into the existing authentication protocols used by the software industry. It introduced a second layer of security to the traditional username-password authentication, thus coining the term, two-factor authentication. One of the drawbacks of this protocol is the unreliability of the hardware token at the time of authentication. This paper proposes a simple backup key model that can be associated with the real world applications’user database, which would allow a user to circumvent the second authentication stage, in the event of unavailability of the hardware token.

  5. A Review on State of Art Variants of LEACH Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yuvaraj P.

    2015-03-01

    Full Text Available Recent advances in wireless communication lead to many improvements in application specific wireless sensor network (WSN deployment. Sensing different data from different environments is essential to monitor and control the situations. For instance, it is very important to sense the forest fire as early as possible to control the upshot. So efficient and timely gathering of the data from a network of small sensor nodes is necessary. In WSN, the small sized sensor nodes are working with very small batteries with limited energy. Since those are randomly deployed over a wide area, replacement of battery or recharging is not feasible. So, for getting prolonged life time of WSN, energy efficient operation is the key factor. Among many protocols proposed for enhancing the life time of WSN, the clustering based hierarchical protocols are popular and gaining the attention of researchers because of their high energy efficiency. Low Energy Adaptive Clustering Hierarchy (LEACH is energy efficient hierarchical, clustering based protocol. It is considered as the base of many hierarchical clustering protocols. In this paper, some of the recent tailored protocols proposed to strengthen LEACH are examined.

  6. A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

    Science.gov (United States)

    Groussin, M; Boussau, B; Gouy, M

    2013-07-01

    Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

  7. Implementasi Sinkronisasi Waktu dengan Network Time Protocol untuk Pemantauan Keamanan Aktivitas Jaringan Telekomunikasi

    Directory of Open Access Journals (Sweden)

    Ahmad Budi Setiawan

    2017-03-01

    Full Text Available Abstrak           Penyelenggara Jaringan adalah menyediakan dan atau memberikan pelayanan jaringan yang memungkinkan terselenggaranya transaksi elektronik. Setiap penyelenggara jaringan diwajibkan untuk menyelaraskan waktu dalam transaksi elektronik. Tujuan dilakukannya penyelarasan waktu adalah untuk menyediakan waktu yang standar dan menyediakan acuan waktu untuk segala bentuk transaksi elektronik dengan prinsip keakuratan dan ketertelusuran. Sistem Penyelarasan Waktu Indonesia menggunakan prinsip ketertelusuran dan prinsip keakuratan. Protokol yang digunakan dalam penyelarasan waktu server di Indonesia berbasis Network Time Protocol. Kajian ini membahas mengenai implementasi sinkronisasi waktu dengan network time protocol sebagai salah satu bentuk pemantauan keamanan jaringan telekomunikasi. Metode yang digunakan dalam kajian ini adalah naratif deskriptif mengenai implementasi sinkronisasi waktu.Hasil kajian ini adalah masukan untuk kebijakan dalam keamanan transaksi elektronik melalui sinkronisasi waktu.    Abstract Network providers are providing services or networks that enable the implementation of electronic transactions. Each network operator is required to align the time in electronic transactions. The purpose is to provide time alignment of the time standard and provide a time frame for all forms of electronic transactions with the principles of accuracy and traceability. Indonesian Time Alignment System uses the principle of traceability and accuracy principles. The protocols used in the alignment of the time server in Indonesia-based Network Time Protocol. This study discusses the implementation of time synchronization with a network time protocol as a form of telecommunications network security monitoring. The method used in this study is a descriptive narrative on the implementation of time synchronization. Results of this study are input to the policy in the security of electronic transactions through time

  8. Quantification protocol for energy efficiency in commercial and institutional buildings

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-10-15

    Alberta Environment has developed an approved methodology that can be used to quantify the reduction of direct and indirect greenhouse gas emission observed after the implementation of energy efficiency measures in commercial and institutional buildings. This methodology concerns energy conservation measures that target the heating system, the ventilation, the air conditioning and lightning systems, but also includes building envelope, tap water heating, elevators, occupant small electrical equipment, outdoor lighting, swimming pool pumping or heating. Calculation methodologies for energy conservation proposed by the Efficiency Valuation Organization were adapted by Alberta Environment. The protocol detailed in this document is based on the fact that emissions reductions are represented by the difference between the energy use in the project condition and a baseline. This approach proposes simple and advanced calculation methodologies that allow project developers to use one or the other, depending on the availability of data and on the limitations of the project, to maximize the greenhouse gas emissions reductions quantified. 14 refs., 11 tabs., 5 figs.

  9. Efficient SCT Protocol for Post Disaster Communication

    Science.gov (United States)

    Ramesh, T. K.; Giriraja, C. V.

    2017-08-01

    Natural and catastrophic disasters can cause damage to the communication system, the damage may be complete or it may be partial. In such areas communication and exchange of information plays a very important role and become difficult to happen in such situations. So, the rescue systems should be installed in those areas for the rescue operations and to take important decisions about how to make a connection from there to the outside world. Wireless communication network architecture should be setup in disaster areas for the communication to happen and to gather information. Wireless ad-hoc network architecture is proposed in this paper with access nodes. These access nodes acts as hotspot for certain area in which they are set up such that the Wi-Fi capable devices get connected to them for communication to happen. If the mobile battery is drained in such situations wireless charging using microwave is shown in this paper. Performance analysis of the communication transport layer protocols is shown and Efficient SCTP (ESTP) algorithm is developed which shows better results in terms of cumulative packet loss.

  10. MR imaging of the knee: Improvement of signal and contrast efficiency of T1-weighted turbo spin echo sequences by applying a driven equilibrium (DRIVE) pulse

    Energy Technology Data Exchange (ETDEWEB)

    Radlbauer, Rudolf, E-mail: rudolf.radlbauer@stpoelten.lknoe.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Lomoschitz, Friedrich, E-mail: friedrich.lomoschitz@stpoelten.lknoe.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Salomonowitz, Erich, E-mail: erich.salomonowitz@stpoelten.lknoe.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Eberhardt, Knut E., E-mail: info@mrt-kompetenzzentrum.d [MRT Competence Center Schloss Werneck, Balthasar-Neumann-Platz 2, 97440 Werneck (Germany); Stadlbauer, Andreas, E-mail: andi@nmr.a [MR Physics Group, Department of Radiology, Landesklinikum St. Poelten, Propst Fuehrer Strasse 4, 3100 St. Poelten (Austria); Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, 91054 Erlangen (Germany)

    2010-08-15

    The purpose of this study was to assess the effect of a driven equilibrium (DRIVE) pulse incorporated in a standard T1-weighted turbo spin echo (TSE) sequence as used in our routine MRI protocol for examination of pathologies of the knee. Sixteen consecutive patients with knee disorders were examined using the routine MRI protocol, including T1-weighted TSE-sequences with and without a DRIVE pulse. Signal-to-noise ratios (SNRs) and contrast-to-noise ratio (CNR) of anatomical structures and pathologies were calculated and compared for both sequences. The differences in diagnostic value of the T1-weighted images with and without DRIVE pulse were assessed. SNR was significantly higher on images acquired with DRIVE pulse for fluid, effusion, cartilage and bone. Differences in the SNR of meniscus and muscle between the two sequences were not statistically significant. CNR was significantly increased between muscle and effusion, fluid and cartilage, fluid and meniscus, cartilage and meniscus, bone and cartilage on images acquired using the DRIVE pulse. Diagnostic value of the T1-weighted images was found to be improved for delineation of anatomic structures and for diagnosing a variety of pathologies when a DRIVE pulse is incorporated in the sequence. Incorporation of a DRIVE pulse into a standard T1-weighted TSE-sequence leads to significant increase of SNR and CNR of both, anatomical structures and pathologies, and consequently to an increase in diagnostic value within the same acquisition time.

  11. MR imaging of the knee: Improvement of signal and contrast efficiency of T1-weighted turbo spin echo sequences by applying a driven equilibrium (DRIVE) pulse

    International Nuclear Information System (INIS)

    Radlbauer, Rudolf; Lomoschitz, Friedrich; Salomonowitz, Erich; Eberhardt, Knut E.; Stadlbauer, Andreas

    2010-01-01

    The purpose of this study was to assess the effect of a driven equilibrium (DRIVE) pulse incorporated in a standard T1-weighted turbo spin echo (TSE) sequence as used in our routine MRI protocol for examination of pathologies of the knee. Sixteen consecutive patients with knee disorders were examined using the routine MRI protocol, including T1-weighted TSE-sequences with and without a DRIVE pulse. Signal-to-noise ratios (SNRs) and contrast-to-noise ratio (CNR) of anatomical structures and pathologies were calculated and compared for both sequences. The differences in diagnostic value of the T1-weighted images with and without DRIVE pulse were assessed. SNR was significantly higher on images acquired with DRIVE pulse for fluid, effusion, cartilage and bone. Differences in the SNR of meniscus and muscle between the two sequences were not statistically significant. CNR was significantly increased between muscle and effusion, fluid and cartilage, fluid and meniscus, cartilage and meniscus, bone and cartilage on images acquired using the DRIVE pulse. Diagnostic value of the T1-weighted images was found to be improved for delineation of anatomic structures and for diagnosing a variety of pathologies when a DRIVE pulse is incorporated in the sequence. Incorporation of a DRIVE pulse into a standard T1-weighted TSE-sequence leads to significant increase of SNR and CNR of both, anatomical structures and pathologies, and consequently to an increase in diagnostic value within the same acquisition time.

  12. Factors affecting the efficient transformation of Colletotrichum species

    Science.gov (United States)

    Redman, Regina S.; Rodriguez, Rusty J.

    1994-01-01

    Factors affecting the efficient transformation of Colletotrichum species. Experimental Mycology, 18, 230-246. Twelve isolates representing four species of Colletotrichum were transformed either by enhanced protoplast, restriction enzyme-mediated integration (REMI), or electroporation-mediated protocols. The enhanced protoplast transformation protocol resulted in 100- and 50-fold increases in the transformation efficiencies of Colletotrichum lindemuthianum and C. magna , respectively. REMI transformation involved the use of Hin dIII and vector DNA linearized with HindIII to increase the number of integration events and potential gene disruptions in the fungal genome. Combining the enhanced protoplast and the REMI protocols resulted in a 22-fold increase in the number of hygromycin/nystatin-resistant mutants in C. lindemuthianum . Electroporation-mediated transformation was performed on mycelial fragments and spores of four Colletotrichum species, resulting in efficiencies of up to 1000 transformants/μg DNA. The pHA1.3 vector which confers hygromycin resistance contains telomeric sequences from Fusarium oxysporum , transforms by autonomous replication and genomic integration, and was essential for elevated transformation efficiencies of 100 to 10,000 transformants/μg DNA. Modifications of pHA1.3 occurred during bacterial amplification and post fungal transformation resulting in plasmids capable of significantly elevated transformation efficiencies in C. lindemuthianum.

  13. Development of high-reliable real-time communication network protocol for SMART

    Energy Technology Data Exchange (ETDEWEB)

    Song, Ki Sang; Kim, Young Sik [Korea National University of Education, Chongwon (Korea); No, Hee Chon [Korea Advanced Institute of Science and Technology, Taejon (Korea)

    1999-04-01

    In this research, we first define protocol subsets for SMART(System-integrated Modular Advanced Reactor) communication network based on the requirement of SMART MMIS transmission delay and traffic requirements and OSI(Open System Interconnection) 7 layers' network protocol functions. Also, current industrial purpose LAN protocols are analyzed and the applicability of commercialized protocols are checked. For the suitability test, we have applied approximated SMART data traffic and maximum allowable transmission delay requirement. With the simulation results, we conclude that IEEE 802.5 and FDDI which is an ANSI standard, is the most suitable for SMART. We further analyzed the FDDI and token ring protocols for SMART and nuclear plant network environment including IEEE 802.4, IEEE 802.5, and ARCnet. The most suitable protocol for SMART is FDDI and FDDI MAC and RMT protocol specifications have been verified with LOTOS and the verification results show that FDDI MAC and RMT satisfy the reachability and liveness, but does not show deadlock and livelock. Therefore, we conclude that FDDI MAC and RMT is highly reliable protocol for SMART MMIS network. After that, we consider the stacking fault of IEEE 802.5 token ring protocol and propose a fault tolerant MAM(Modified Active Monitor) protocol. The simulation results show that the MAM protocol improves lower priority traffic service rate when stacking fault occurs. Therefore, proposed MAM protocol can be applied to SMART communication network for high reliability and hard real-time communication purpose in data acquisition and inter channel network. (author). 37 refs., 79 figs., 39 tabs.

  14. A novel bioinformatics method for efficient knowledge discovery by BLSOM from big genomic sequence data.

    Science.gov (United States)

    Bai, Yu; Iwasaki, Yuki; Kanaya, Shigehiko; Zhao, Yue; Ikemura, Toshimichi

    2014-01-01

    With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a "genome signature," and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).

  15. Using high-throughput barcode sequencing to efficiently map connectomes.

    Science.gov (United States)

    Peikon, Ian D; Kebschull, Justus M; Vagin, Vasily V; Ravens, Diana I; Sun, Yu-Chi; Brouzes, Eric; Corrêa, Ivan R; Bressan, Dario; Zador, Anthony M

    2017-07-07

    The function of a neural circuit is determined by the details of its synaptic connections. At present, the only available method for determining a neural wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, a method for converting the connectome into a form that can exploit the speed and low cost of modern high-throughput DNA sequencing. In SYNseq, each neuron is labeled with a unique random nucleotide sequence-an RNA 'barcode'-which is targeted to the synapse using engineered proteins. Barcodes in pre- and postsynaptic neurons are then associated through protein-protein crosslinking across the synapse, extracted from the tissue, and joined into a form suitable for sequencing. Although our failure to develop an efficient barcode joining scheme precludes the widespread application of this approach, we expect that with further development SYNseq will enable tracing of complex circuits at high speed and low cost. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Comparable efficiency of different extraction protocols for wheat and rye prolamins

    Directory of Open Access Journals (Sweden)

    Peter Socha

    2016-01-01

    Full Text Available The identification and quantification of cereal storage proteins is of interest of many researchers. Their structural or functional properties are usually affected by the way how they are extracted. The efficiency of extraction process depends on the cereal source and working conditions. Here, we described various commonly used extraction protocols differing in the extraction conditions (pre-extraction of albumins/globulins, sequential extraction of individual protein fractions or co-extraction of gluten proteins, heating or non-heating, reducing or non-reducing conditions. The total protein content of all fractions extracted from commercially available wheat and rye flours was measured by the Bradford method. Tris-Tricine SDS-PAGE was used to determine the molecular weights of wheat gliadins, rye secalins and high-molecular weight glutelins which are the main triggering factors causing celiac disease. Moreover, we were able to distinguish individual subunits (α/β-, γ-, ω-gliadins and 40k-γ-, 75k-γ-, ω-secalins of wheat/rye prolamins. Generally, modified extraction protocols against classical Osborne procedure were more effective and yields higher protein content in all protein fractions. Bradford measurement led into underestimation of results in three extraction procedures, while all protein fractions were clearly identified on SDS-PAGE gels. Co-extraction of gluten proteins resulted in appearance of both, low-molecular weight fractions (wheat gliadins and rye secalins as well as high-molecular weight glutelins which means that is not necessary to extract gluten proteins separately. The two of three extraction protocols showed high technical reproducibility with coefficient of variation less than 20%. Carefully optimized extraction protocol can be advantageous for further analyses of cereal prolamins.  Normal 0 21 false false false SK X-NONE X-NONE

  17. Energy Efficient Clustering Based Network Protocol Stack for 3D Airborne Monitoring System

    Directory of Open Access Journals (Sweden)

    Abhishek Joshi

    2017-01-01

    Full Text Available Wireless Sensor Network consists of large number of nodes densely deployed in ad hoc manner. Usually, most of the application areas of WSNs require two-dimensional (2D topology. Various emerging application areas such as airborne networks and underwater wireless sensor networks are usually deployed using three-dimensional (3D network topology. In this paper, a static 3D cluster-based network topology has been proposed for airborne networks. A network protocol stack consisting of various protocols such as TDMA MAC and dynamic routing along with services such as time synchronization, Cluster Head rotation, and power level management has been proposed for this airborne network. The proposed protocol stack has been implemented on the hardware platform consisting of number of TelosB nodes. This 3D airborne network architecture can be used to measure Air Quality Index (AQI in an area. Various parameters of network such as energy consumption, Cluster Head rotation, time synchronization, and Packet Delivery Ratio (PDR have been analyzed. Detailed description of the implementation of the protocol stack along with results of implementation has been provided in this paper.

  18. Efficient Algorithms for Segmentation of Item-Set Time Series

    Science.gov (United States)

    Chundi, Parvathi; Rosenkrantz, Daniel J.

    We propose a special type of time series, which we call an item-set time series, to facilitate the temporal analysis of software version histories, email logs, stock market data, etc. In an item-set time series, each observed data value is a set of discrete items. We formalize the concept of an item-set time series and present efficient algorithms for segmenting a given item-set time series. Segmentation of a time series partitions the time series into a sequence of segments where each segment is constructed by combining consecutive time points of the time series. Each segment is associated with an item set that is computed from the item sets of the time points in that segment, using a function which we call a measure function. We then define a concept called the segment difference, which measures the difference between the item set of a segment and the item sets of the time points in that segment. The segment difference values are required to construct an optimal segmentation of the time series. We describe novel and efficient algorithms to compute segment difference values for each of the measure functions described in the paper. We outline a dynamic programming based scheme to construct an optimal segmentation of the given item-set time series. We use the item-set time series segmentation techniques to analyze the temporal content of three different data sets—Enron email, stock market data, and a synthetic data set. The experimental results show that an optimal segmentation of item-set time series data captures much more temporal content than a segmentation constructed based on the number of time points in each segment, without examining the item set data at the time points, and can be used to analyze different types of temporal data.

  19. Chapter 22: Compressed Air Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

    Energy Technology Data Exchange (ETDEWEB)

    Kurnik, Charles W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Benton, Nathanael [Nexant, Inc., San Francisco, CA (United States); Burns, Patrick [Nexant, Inc., San Francisco, CA (United States)

    2017-10-18

    Compressed-air systems are used widely throughout industry for many operations, including pneumatic tools, packaging and automation equipment, conveyors, and other industrial process operations. Compressed-air systems are defined as a group of subsystems composed of air compressors, air treatment equipment, controls, piping, pneumatic tools, pneumatically powered machinery, and process applications using compressed air. A compressed-air system has three primary functional subsystems: supply, distribution, and demand. Air compressors are the primary energy consumers in a compressed-air system and are the primary focus of this protocol. The two compressed-air energy efficiency measures specifically addressed in this protocol are: High-efficiency/variable speed drive (VSD) compressor replacing modulating, load/unload, or constant-speed compressor; and Compressed-air leak survey and repairs. This protocol provides direction on how to reliably verify savings from these two measures using a consistent approach for each.

  20. An Adaptive Information Quantity-Based Broadcast Protocol for Safety Services in VANET

    Directory of Open Access Journals (Sweden)

    Wenjie Wang

    2016-01-01

    Full Text Available Vehicle-to-vehicle communication plays a significantly important role in implementing safe and efficient road traffic. When disseminating safety messages in the network, the information quantity on safety packets changes over time and space. However, most of existing protocols view each packet the same to disseminate, preventing vehicles from collecting more recent and precise safety information. Hence, an information quantity-based broadcast protocol is proposed in this paper to ensure the efficiency of safety messages dissemination. In particular, we propose the concept of emergency-degree to evaluate packets’ information quantity. Then we present EDCast, an emergency-degree-based broadcast protocol. EDCast differentiates each packet’s priority for accessing the channel based on its emergency-degree so as to provide vehicles with more safety information timely and accurately. In addition, an adaptive scheme is presented to ensure fast dissemination of messages in different network condition. We compare the performance of EDCast with those of three other representative protocols in a typical highway scenario. Simulation results indicate that EDCast achieves higher broadcast efficiency and less redundancy with less delivery delay. What we found demonstrates that it is feasible and necessary for incorporating information quantity of messages in designing an efficient safety message broadcast protocol.

  1. Real-time probabilistic covariance tracking with efficient model update.

    Science.gov (United States)

    Wu, Yi; Cheng, Jian; Wang, Jinqiao; Lu, Hanqing; Wang, Jun; Ling, Haibin; Blasch, Erik; Bai, Li

    2012-05-01

    The recently proposed covariance region descriptor has been proven robust and versatile for a modest computational cost. The covariance matrix enables efficient fusion of different types of features, where the spatial and statistical properties, as well as their correlation, are characterized. The similarity between two covariance descriptors is measured on Riemannian manifolds. Based on the same metric but with a probabilistic framework, we propose a novel tracking approach on Riemannian manifolds with a novel incremental covariance tensor learning (ICTL). To address the appearance variations, ICTL incrementally learns a low-dimensional covariance tensor representation and efficiently adapts online to appearance changes of the target with only O(1) computational complexity, resulting in a real-time performance. The covariance-based representation and the ICTL are then combined with the particle filter framework to allow better handling of background clutter, as well as the temporary occlusions. We test the proposed probabilistic ICTL tracker on numerous benchmark sequences involving different types of challenges including occlusions and variations in illumination, scale, and pose. The proposed approach demonstrates excellent real-time performance, both qualitatively and quantitatively, in comparison with several previously proposed trackers.

  2. DRUG: An Energy-Efficient Data-Centric Routing Protocol for Wireless Sensor Networks

    OpenAIRE

    Sahoo, B. P. S.; Puthal, Deepak

    2014-01-01

    In general, sensor nodes are deployed in left unattended area. In such situation feeding energy to the batteries or replacing the batteries is difficult or even sometimes impossible too. Therefore, prolonging the network lifetime is an important optimization goal in this aspect. In this paper, we propose a new Energy-efficient Datacentric RoUtinG protocol called DRUG. In this paper, we propose an adaptive Data centric approach to find an optimal routing path from source to sink when the senso...

  3. Intelligent routing protocol for ad hoc wireless network

    Science.gov (United States)

    Peng, Chaorong; Chen, Chang Wen

    2006-05-01

    A novel routing scheme for mobile ad hoc networks (MANETs), which combines hybrid and multi-inter-routing path properties with a distributed topology discovery route mechanism using control agents is proposed in this paper. In recent years, a variety of hybrid routing protocols for Mobile Ad hoc wireless networks (MANETs) have been developed. Which is proactively maintains routing information for a local neighborhood, while reactively acquiring routes to destinations beyond the global. The hybrid protocol reduces routing discovery latency and the end-to-end delay by providing high connectivity without requiring much of the scarce network capacity. On the other side the hybrid routing protocols in MANETs likes Zone Routing Protocol still need route "re-discover" time when a route between zones link break. Sine the topology update information needs to be broadcast routing request on local zone. Due to this delay, the routing protocol may not be applicable for real-time data and multimedia communication. We utilize the advantages of a clustering organization and multi-routing path in routing protocol to achieve several goals at the same time. Firstly, IRP efficiently saves network bandwidth and reduces route reconstruction time when a routing path fails. The IRP protocol does not require global periodic routing advertisements, local control agents will automatically monitor and repair broke links. Secondly, it efficiently reduces congestion and traffic "bottlenecks" for ClusterHeads in clustering network. Thirdly, it reduces significant overheads associated with maintaining clusters. Fourthly, it improves clusters stability due to dynamic topology changing frequently. In this paper, we present the Intelligent Routing Protocol. First, we discuss the problem of routing in ad hoc networks and the motivation of IRP. We describe the hierarchical architecture of IRP. We describe the routing process and illustrate it with an example. Further, we describe the control manage

  4. Improving treatment times for patients with in-hospital stroke using a standardized protocol.

    Science.gov (United States)

    Koge, Junpei; Matsumoto, Shoji; Nakahara, Ichiro; Ishii, Akira; Hatano, Taketo; Sadamasa, Nobutake; Kai, Yasutoshi; Ando, Mitsushige; Saka, Makoto; Chihara, Hideo; Takita, Wataru; Tokunaga, Keisuke; Kamata, Takahiko; Nishi, Hidehisa; Hashimoto, Tetsuya; Tsujimoto, Atsushi; Kira, Jun-Ichi; Nagata, Izumi

    2017-10-15

    Previous reports have shown significant delays in treatment of in-hospital stroke (IHS). We developed and implemented our IHS alert protocol in April 2014. We aimed to determine the influence of implementation of our IHS alert protocol. Our implementation processes comprise the following four main steps: IHS protocol development, workshops for hospital staff to learn about the protocol, preparation of standardized IHS treatment kits, and obtaining feedback in a monthly hospital staff conference. We retrospectively compared protocol metrics and clinical outcomes of patients with IHS treated with intravenous thrombolysis and/or endovascular therapy between before (January 2008-March 2014) and after implementation (April 2014-December 2016). Fifty-five patients were included (pre, 25; post, 30). After the implementation, significant reductions occurred in the median time from stroke recognition to evaluation by a neurologist (30 vs. 13.5min, pvs. 26.5min, pvs. 16min, p=0.02). The median time from first neuroimaging to endovascular therapy had a tendency to decrease (75 vs. 53min, p=0.08). There were no differences in the favorable outcomes (modified Rankin scale score of 0-2) at discharge or the incidence of symptomatic intracranial hemorrhage between the two periods. Our IHS alert protocol implementation saved time in treating patients with IHS without compromising safety. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Protocol compliance and time management in blunt trauma resuscitation.

    NARCIS (Netherlands)

    Spanjersberg, W.R.; Bergs, E.A.; Mushkudiani, N.; Klimek, M.; Schipper, I.B.

    2009-01-01

    OBJECTIVES: To study advanced trauma life support (ATLS) protocol adherence prospectively in trauma resuscitation and to analyse time management of daily multidisciplinary trauma resuscitation at a level 1 trauma centre, for both moderately and severely injured patients. PATIENTS AND METHODS: All

  6. Enhanced just-in-time plus protocol for optical burst switching networks

    Science.gov (United States)

    Rodrigues, Joel J. P. C.; Gregório, José M. B.; Vasilakos, Athanasios V.

    2010-07-01

    We propose a new one-way resource reservation protocol for optical burst switching (OBS) networks, called Enhanced Just-in-Time Plus (E-JIT+). The protocol is described in detail, and its formal specification is presented, following an extended finite state machine approach. The performance evaluation of E-JIT+ is analyzed in comparison with other proposed OBS protocols (JIT+ and E-JIT) for the following network topologies: rings; degree-two, degree-three, and degree-four chordal rings; mesh-torus; NSFNET; ARPANET; FCCN-NET; and the European Optical Network. We evaluate and compare the performance of the different protocols in terms of burst loss probability, taking into account the most important OBS network parameters. It was shown that E-JIT+ performs better than available one-way resource reservation protocols for all the evaluated network topologies. Moreover, the scalability of E-JIT+ was observed, and when the network traffic increases, the burst loss probability also increases, leading to a worse network performance.

  7. A System Architecture for Efficient Transmission of Massive DNA Sequencing Data.

    Science.gov (United States)

    Sağiroğlu, Mahmut Şamİl; Külekcİ, M Oğuzhan

    2017-11-01

    The DNA sequencing data analysis pipelines require significant computational resources. In that sense, cloud computing infrastructures appear as a natural choice for this processing. However, the first practical difficulty in reaching the cloud computing services is the transmission of the massive DNA sequencing data from where they are produced to where they will be processed. The daily practice here begins with compressing the data in FASTQ file format, and then sending these data via fast data transmission protocols. In this study, we address the weaknesses in that daily practice and present a new system architecture that incorporates the computational resources available on the client side while dynamically adapting itself to the available bandwidth. Our proposal considers the real-life scenarios, where the bandwidth of the connection between the parties may fluctuate, and also the computing power on the client side may be of any size ranging from moderate personal computers to powerful workstations. The proposed architecture aims at utilizing both the communication bandwidth and the computing resources for satisfying the ultimate goal of reaching the results as early as possible. We present a prototype implementation of the proposed architecture, and analyze several real-life cases, which provide useful insights for the sequencing centers, especially on deciding when to use a cloud service and in what conditions.

  8. FTR: Performance-Aware and Energy-Efficient Communication Protocol for Integrating Sensor Networks into the Internet

    Directory of Open Access Journals (Sweden)

    Sinung Suakanto

    2014-11-01

    Full Text Available Integrating sensor networks into the Internet brings many advantages. For example, users can monitor or control the state of the sensors remotely without visiting the field. Some researchers have proposed methods using a REST-based web service or HTTP to establish communication between sensors and server via the Internet. Unfortunately, as we know, HTTP is a best-effort service. In some cases this means that if the number of sensors increases the end-to-end Quality of Service will decrease. The end-to-end network delay increases, as well as the failure rate of data sending caused by HTTP timeouts. In this paper, we propose Finite Time Response (FTR HTTP as a communication protocol suitable for integrating sensor networks into the Internet. We have defined a cross-layer approach that coordinates between the application layer and the physical layer to control not only performance but also energy efficiency. The HTTP request-response delay measured at the application layer is used as the decision factor at the physical layer to control the active and sleep periods. We also propose a forced-sleep period as a control mechanism to guarantee average performance for all nodes. The experimental results have shown that FTR has the ability to maintain better performance, indicated by a lower average response time and a lower average timeout experience. Optimization is still needed to gain better performance and better energy efficiency while also considering the average value of the update time.

  9. An Optimized Protocol to Increase Virus-Induced Gene Silencing Efficiency and Minimize Viral Symptoms in Petunia

    OpenAIRE

    Broderick, Shaun R.; Jones, Michelle L.

    2013-01-01

    Virus-induced gene silencing (VIGS) is used to down-regulate endogenous plant genes. VIGS efficiency depends on viral proliferation and systemic movement throughout the plant. Although tobacco rattle virus (TRV)-based VIGS has been successfully used in petunia (Petunia × hybrida), the protocol has not been thoroughly optimized for efficient and uniform gene down-regulation in this species. Therefore, we evaluated six parameters that improved VIGS in petunia. Inoculation of mechanically wounde...

  10. Design Aspects of An Energy-Efficient, Lightweight Medium Access Control Protocol for Wireless Sensor Networks

    NARCIS (Netherlands)

    van Hoesel, L.F.W.; Havinga, Paul J.M.

    2006-01-01

    This document gives an overview of the most relevant design aspects of the lightweight medium access control (LMAC) protocol [16] for wireless sensor networks (WSNs). These aspects include selfconfiguring and localized operation of the protocol, time synchronization in multi-hop networks, network

  11. Power Saving MAC Protocols for WSNs and Optimization of S-MAC Protocol

    Directory of Open Access Journals (Sweden)

    Simarpreet Kaur

    2012-11-01

    Full Text Available Low power MAC protocols have received a lot of consideration in the last few years because of their influence on the lifetime of wireless sensor networks. Since, sensors typically operate on batteries, replacement of which is often difficult. A lot of work has been done to minimize the energy expenditure and prolong the sensor lifetime through energy efficient designs, across layers. Meanwhile, the sensor network should be able to maintain a certain throughput in order to fulfill the QoS requirements of the end user, and to ensure the constancy of the network. This paper introduces different types of MAC protocols used for WSNs and proposes S‐MAC, a Medium‐Access Control protocol designed for Wireless Sensor Networks. S‐MAC uses a few innovative techniques to reduce energy consumption and support selfconfiguration. A new protocol is suggested to improve the energy efficiency, latency and throughput of existing MAC protocol for WSNs. A modification of the protocol is then proposed to eliminate the need for some nodes to stay awake longer than the other nodes which improves the energy efficiency, latency and throughput and hence increases the life span of a wireless sensor network.

  12. The Simplest Protocol for Oblivious Transfer

    DEFF Research Database (Denmark)

    Chou, Tung; Orlandi, Claudio

    2015-01-01

    Oblivious Transfer (OT) is the fundamental building block of cryptographic protocols. In this paper we describe the simplest and most efficient protocol for 1-out-of-n OT to date, which is obtained by tweaking the Diffie-Hellman key-exchange protocol. The protocol achieves UC-security against...... active and adaptive corruptions in the random oracle model. Due to its simplicity, the protocol is extremely efficient and it allows to perform m 1-out-of-n OTs using only: - Computation: (n+1)m+2 exponentiations (mn for the receiver, mn+2 for the sender) and - Communication: 32(m+1) bytes (for the group...... optimizations) is at least one order of magnitude faster than previous work. Category / Keywords: cryptographic protocols / Oblivious Transfer, UC Security, Elliptic Curves, Efficient Implementation...

  13. Comprehensive small animal imaging strategies on a clinical 3 T dedicated head MR-scanner; adapted methods and sequence protocols in CNS pathologies.

    Directory of Open Access Journals (Sweden)

    Deepu R Pillai

    Full Text Available BACKGROUND: Small animal models of human diseases are an indispensable aspect of pre-clinical research. Being dynamic, most pathologies demand extensive longitudinal monitoring to understand disease mechanisms, drug efficacy and side effects. These considerations often demand the concomitant development of monitoring systems with sufficient temporal and spatial resolution. METHODOLOGY AND RESULTS: This study attempts to configure and optimize a clinical 3 Tesla magnetic resonance scanner to facilitate imaging of small animal central nervous system pathologies. The hardware of the scanner was complemented by a custom-built, 4-channel phased array coil system. Extensive modification of standard sequence protocols was carried out based on tissue relaxometric calculations. Proton density differences between the gray and white matter of the rodent spinal cord along with transverse relaxation due to magnetic susceptibility differences at the cortex and striatum of both rats and mice demonstrated statistically significant differences. The employed parallel imaging reconstruction algorithms had distinct properties dependent on the sequence type and in the presence of the contrast agent. The attempt to morphologically phenotype a normal healthy rat brain in multiple planes delineated a number of anatomical regions, and all the clinically relevant sequels following acute cerebral ischemia could be adequately characterized. Changes in blood-brain-barrier permeability following ischemia-reperfusion were also apparent at a later time. Typical characteristics of intra-cerebral haemorrhage at acute and chronic stages were also visualized up to one month. Two models of rodent spinal cord injury were adequately characterized and closely mimicked the results of histological studies. In the employed rodent animal handling system a mouse model of glioblastoma was also studied with unequivocal results. CONCLUSIONS: The implemented customizations including extensive

  14. Comprehensive Small Animal Imaging Strategies on a Clinical 3 T Dedicated Head MR-Scanner; Adapted Methods and Sequence Protocols in CNS Pathologies

    Science.gov (United States)

    Pillai, Deepu R.; Heidemann, Robin M.; Lanz, Titus; Dittmar, Michael S.; Sandner, Beatrice; Beier, Christoph P.; Weidner, Norbert; Greenlee, Mark W.; Schuierer, Gerhard; Bogdahn, Ulrich; Schlachetzki, Felix

    2011-01-01

    Background Small animal models of human diseases are an indispensable aspect of pre-clinical research. Being dynamic, most pathologies demand extensive longitudinal monitoring to understand disease mechanisms, drug efficacy and side effects. These considerations often demand the concomitant development of monitoring systems with sufficient temporal and spatial resolution. Methodology and Results This study attempts to configure and optimize a clinical 3 Tesla magnetic resonance scanner to facilitate imaging of small animal central nervous system pathologies. The hardware of the scanner was complemented by a custom-built, 4-channel phased array coil system. Extensive modification of standard sequence protocols was carried out based on tissue relaxometric calculations. Proton density differences between the gray and white matter of the rodent spinal cord along with transverse relaxation due to magnetic susceptibility differences at the cortex and striatum of both rats and mice demonstrated statistically significant differences. The employed parallel imaging reconstruction algorithms had distinct properties dependent on the sequence type and in the presence of the contrast agent. The attempt to morphologically phenotype a normal healthy rat brain in multiple planes delineated a number of anatomical regions, and all the clinically relevant sequels following acute cerebral ischemia could be adequately characterized. Changes in blood-brain-barrier permeability following ischemia-reperfusion were also apparent at a later time. Typical characteristics of intra-cerebral haemorrhage at acute and chronic stages were also visualized up to one month. Two models of rodent spinal cord injury were adequately characterized and closely mimicked the results of histological studies. In the employed rodent animal handling system a mouse model of glioblastoma was also studied with unequivocal results. Conclusions The implemented customizations including extensive sequence protocol

  15. SeqAn An efficient, generic C++ library for sequence analysis

    Directory of Open Access Journals (Sweden)

    Rausch Tobias

    2008-01-01

    Full Text Available Abstract Background The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome 1 would not have been possible without advanced assembly algorithms. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there is a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use. Results To remedy this trend we propose the use of SeqAn, a library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development. In this paper we describe the design and content of SeqAn and demonstrate its use by giving two examples. In the first example we show an application of SeqAn as an experimental platform by comparing different exact string matching algorithms. The second example is a simple version of the well-known MUMmer tool rewritten in SeqAn. Results indicate that our implementation is very efficient and versatile to use. Conclusion We anticipate that SeqAn greatly simplifies the rapid development of new bioinformatics tools by providing a collection of readily usable, well-designed algorithmic components which are fundamental for the field of sequence analysis. This leverages not only the implementation of new algorithms, but also enables a sound analysis and comparison of existing algorithms.

  16. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  17. ECS: Efficient Communication Scheduling for Underwater Sensor Networks

    Directory of Open Access Journals (Sweden)

    Lu Hong

    2011-03-01

    Full Text Available TDMA protocols have attracted a lot of attention for underwater acoustic sensor networks (UWSNs, because of the unique characteristics of acoustic signal propagation such as great energy consumption in transmission, long propagation delay and long communication range. Previous TDMA protocols all allocated transmission time to nodes based on discrete time slots. This paper proposes an efficient continuous time scheduling TDMA protocol (ECS for UWSNs, including the continuous time based and sender oriented conflict analysis model, the transmission moment allocation algorithm and the distributed topology maintenance algorithm. Simulation results confirm that ECS improves network throughput by 20% on average, compared to existing MAC protocols.

  18. Seqüência de Robin: protocolo único de tratamento Robin sequence: a single treatment protocol

    Directory of Open Access Journals (Sweden)

    Ilza L. Marques

    2005-02-01

    Full Text Available OBJETIVO: Apresentar protocolo único que possa atender tanto às dificuldades respiratórias como às dificuldades alimentares dos neonatos e lactentes com seqüência de Robin. FONTE DE DADOS: O artigo foi desenvolvido tomando como base as publicações mais recentes disponíveis em bancos de dados bibliográficos e livros que discutem o tratamento da seqüência de Robin, em especial os estudos realizados no Hospital de Reabilitação de Anomalias Craniofaciais da Universidade de São Paulo (HRAC/USP. SÍNTESE DE DADOS: O artigo apresenta os aspectos morfológicos e genéticos da seqüência de Robin e conceitos sobre nasofaringoscopia e suas implicações clínicas, discute o tratamento das dificuldades respiratórias e alimentares e apresenta um protocolo único para atender a todos os casos de seqüência de Robin, independentemente de sua gravidade e complexidade. CONCLUSÕES: A seqüência de Robin não é somente uma patologia obstrutiva anatômica para ser resolvida com procedimentos cirúrgicos, mas os conhecimentos sobre crescimento e desenvolvimento devem ser aplicados por uma equipe multidisciplinar, porque possibilitam a rápida recuperação da permeabilidade das vias aéreas e da capacidade de alimentação oral, evitando-se, muitas vezes, os procedimentos cirúrgicos e seus riscos, principalmente quando realizados em neonatos e lactentes pequenos.OBJECTIVE: To present a single protocol that might cover both the respiratory and feeding difficulties of neonates and infants with Robin sequence. SOURCES OF DATA: The article was prepared on the basis of the most recent publications available in bibliographic databases and in books that discuss the treatment of Robin sequence, especially the studies conducted at the Hospital for Rehabilitation of Craniofacial Anomalies of Universidade de São Paulo (HRAC/USP. SUMMARY OF THE FINDINGS: We present the morphological and genetic aspects of Robin sequence and concepts about

  19. Combined microfluidization and ultrasonication: a synergistic protocol for high-efficient processing of SWCNT dispersions with high quality

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Sida, E-mail: s.luo@buaa.edu.cn [Beihang University, School of Mechanical Engineering and Automation (China); Liu, Tao, E-mail: tliu@fsu.edu [Florida State University, High-Performance Materials Institute (United States); Wang, Yong; Li, Liuhe [Beihang University, School of Mechanical Engineering and Automation (China); Wang, Guantao; Luo, Yun [China University of Geosciences, Center of Safety Research, School of Engineering and Technology (China)

    2016-08-15

    High-efficient and large-scale production of high-quality CNT dispersions is necessary for meeting the future needs to develop various CNT-based electronic devices. Herein, we have designed novel processing protocols by combining conventional ultrasonication process with a new microfluidization technique to produce high-quality SWCNT dispersions with improved processing efficiency. To judge the quality of SWCNT dispersions, one critical factor is the degree of exfoliation, which could be quantified by both geometrical dimension of the exfoliated nanotubes and percentage of individual tubes in a given dispersion. In this paper, the synergistic effect of the combined protocols was systematically investigated through evaluating SWCNT dispersions with newly developed characterization techniques, namely preparative ultracentrifuge method (PUM) and simultaneous Raman scattering and photoluminescence spectroscopy (SRSPL). The results of both techniques draw similar conclusions that as compared with either of the processes operated separately, a low-pass microfluidization followed by a reasonable duration of ultrasonication could substantially improve the processing efficiency to produce high-quality SWCNT dispersions with averaged particle length and diameter as small as ~600 and ~2 nm, respectively.Graphical abstract.

  20. Diagnostic performance of the three-dimensional fast spin echo-Cube sequence in comparison with a conventional imaging protocol in evaluation of the lachrymal drainage system

    International Nuclear Information System (INIS)

    Zhang, Jing; Chen, Lang; Wang, Qiu-Xia; Zhu, Wen-Zhen; Luo, Xin; Peng, Li; Liu, Rong; Xiong, Wei

    2015-01-01

    To compare the three-dimensional (3D)-fast spin-echo (FSE)-Cube with a conventional imaging protocol in evaluation of dacryostenosis. Thirty-three patients with epiphora underwent examinations using Cube magnetic resonance dacryocystography (MRD) and a conventional protocol, which included 3D fast-recovery fast spin-echo (FRFSE) MRD and two-dimensional (2D)-FSE sequences at 3.0 T. Using lachrymal endoscopic findings as the reference standard, we calculated the sensitivity and specificity of both protocols for detecting lachrymal drainage system (LDS) obstruction and their accuracies in depicting the level of obstruction. Comparable coronal and axial images were selected for bot sequences. Two neuroradiologists graded paired images for blurring, artefacts, anatomic details, and overall image quality. The two methods showed no significant difference in sensitivity (89.5 % vs. 94.7 %; p =0.674), specificity (64.3 %; p =1) or accuracy (86.8 %; p =1) in detecting or depicting LDS obstruction. Blurring and artefacts were significantly better on 2D-FSE images (p 0.05). In comparison with the conventional protocol, Cube MRD demonstrates satisfactory image quality and similar diagnostic capability for cases of possible LDS disease. (orig.)

  1. Selection of mRNA 5'-untranslated region sequence with high translation efficiency through ribosome display

    International Nuclear Information System (INIS)

    Mie, Masayasu; Shimizu, Shun; Takahashi, Fumio; Kobatake, Eiry

    2008-01-01

    The 5'-untranslated region (5'-UTR) of mRNAs functions as a translation enhancer, promoting translation efficiency. Many in vitro translation systems exhibit a reduced efficiency in protein translation due to decreased translation initiation. The use of a 5'-UTR sequence with high translation efficiency greatly enhances protein production in these systems. In this study, we have developed an in vitro selection system that favors 5'-UTRs with high translation efficiency using a ribosome display technique. A 5'-UTR random library, comprised of 5'-UTRs tagged with a His-tag and Renilla luciferase (R-luc) fusion, were in vitro translated in rabbit reticulocytes. By limiting the translation period, only mRNAs with high translation efficiency were translated. During translation, mRNA, ribosome and translated R-luc with His-tag formed ternary complexes. They were collected with translated His-tag using Ni-particles. Extracted mRNA from ternary complex was amplified using RT-PCR and sequenced. Finally, 5'-UTR with high translation efficiency was obtained from random 5'-UTR library

  2. Timing Analysis of Rate Constrained Traffic for the TTEthernet Communication Protocol

    DEFF Research Database (Denmark)

    Tamas-Selicean, Domitian; Pop, Paul; Steiner, Wilfried

    2015-01-01

    Ethernet is a low-cost communication solution offering high transmission speeds. Although its applications extend beyond computer networking, Ethernet is not suitable for real-time and safety-critical systems. To alleviate this, several real-time Ethernet-based communication protocols have been...

  3. PVT: an efficient computational procedure to speed up next-generation sequence analysis.

    Science.gov (United States)

    Maji, Ranjan Kumar; Sarkar, Arijita; Khatua, Sunirmal; Dasgupta, Subhasis; Ghosh, Zhumur

    2014-06-04

    High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the different types of NGS data, there are certain common challenging steps involved in analysing those data. Spliced alignment is one such fundamental step in NGS data analysis which is extremely computational intensive as well as time consuming. There exists serious problem even with the most widely used spliced alignment tools. TopHat is one such widely used spliced alignment tools which although supports multithreading, does not efficiently utilize computational resources in terms of CPU utilization and memory. Here we have introduced PVT (Pipelined Version of TopHat) where we take up a modular approach by breaking TopHat's serial execution into a pipeline of multiple stages, thereby increasing the degree of parallelization and computational resource utilization. Thus we address the discrepancies in TopHat so as to analyze large NGS data efficiently. We analysed the SRA dataset (SRX026839 and SRX026838) consisting of single end reads and SRA data SRR1027730 consisting of paired-end reads. We used TopHat v2.0.8 to analyse these datasets and noted the CPU usage, memory footprint and execution time during spliced alignment. With this basic information, we designed PVT, a pipelined version of TopHat that removes the redundant computational steps during 'spliced alignment' and breaks the job into a pipeline of multiple stages (each comprising of different step(s)) to improve its resource utilization, thus reducing the execution time. PVT provides an improvement over TopHat for spliced alignment of NGS data analysis. PVT thus resulted in the reduction of the execution time to ~23% for the single end read dataset. Further, PVT designed for paired end reads showed an

  4. Time sequence photography of Roosters Comb

    Science.gov (United States)

    The importance of understanding natural landscape changes is key in properly determining rangeland ecology. Time sequence photography allows a landscape snapshot to be documented and enables the ability to compare natural changes overtime. Photographs of Roosters Comb were taken from the same vantag...

  5. Energy efficient structure-free data aggregation and delivery in WSN

    Directory of Open Access Journals (Sweden)

    Prabhudutta Mohanty

    2016-11-01

    Full Text Available In Wireless Sensor Networks (WSNs, the energy consumption due to the sensed data transmission is more than processing data locally within the sensor node. The data aggregation is one of the techniques to conserve energy by eliminating the redundant data transmission in dense WSNs. In this paper, we propose an energy efficient structure-free data aggregation and delivery (ESDAD protocol, which aggregates the redundant data in the intermediate nodes. In the proposed protocol, waiting time for packets at each intermediate node is calculated very sensibly so that data can be aggregated efficiently in the routing path. The sensed data packets are transmitted judicially to the aggregation point for data aggregation. The ESDAD protocol computes a cost function for structure-free, next-hop node selection and performs near source data aggregation. The buffer of each node is partitioned to maintain different types of flows for fair and efficient data delivery. The transmission rates of the sources and intermediate nodes are adjusted during congestion. The performance of the proposed protocol is evaluated through extensive simulations. The simulation results reveal that it outperforms the existing structure-free protocols in terms of energy efficiency, reliability and on-time delivery ratio.

  6. An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

    KAUST Repository

    Han, Renmin

    2017-12-24

    Long-reads, point-of-care, and PCR-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the global mapping between the raw electrical current signal sequence and the expected signal sequence from the pore model serves as the key building block to base calling, reads mapping, variant identification, and methylation detection. However, the ultra-long reads of nanopore sequencing and an order of magnitude difference in the sampling speeds of the two sequences make the classical dynamic time warping (DTW) and its variants infeasible to solve the problem. Here, we propose a novel multi-level DTW algorithm, cwDTW, based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa, as well as two benchmark datasets from previous studies, demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can almost always generate warping paths that are very close to the original DTW, which are remarkably more accurate than the state-of-the-art methods including FastDTW and PrunedDTW. Meanwhile, on the real nanopore datasets, cwDTW is about 440 times faster than FastDTW and 3000 times faster than the original DTW. Our program is available at https://github.com/realbigws/cwDTW.

  7. The Development of a Course Sequence in Real-Time Systems Design

    Science.gov (United States)

    1993-08-01

    This project deals with the development of a senior level course sequence in software intensive real - time systems . The sequence consists of a course...for an engineering industrial career in real - time systems development. The course sequence emphasizes practical standards, techniques, and tools for...system development. Few universities include real - time systems development in their undergraduate Computer Engineering or Computer Science curriculum

  8. Distributed synchronization of networked drive-response systems: A nonlinear fixed-time protocol.

    Science.gov (United States)

    Zhao, Wen; Liu, Gang; Ma, Xi; He, Bing; Dong, Yunfeng

    2017-11-01

    The distributed synchronization of networked drive-response systems is investigated in this paper. A novel nonlinear protocol is proposed to ensure that the tracking errors converge to zeros in a fixed-time. By comparison with previous synchronization methods, the present method considers more practical conditions and the synchronization time is not dependent of arbitrary initial conditions but can be offline pre-assign according to the task assignment. Finally, the feasibility and validity of the presented protocol have been illustrated by a numerical simulation. Copyright © 2017. Published by Elsevier Ltd.

  9. Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features

    KAUST Repository

    Wang, Bing; Zhang, Jun; Chen, Peng; Ji, Zhiwei; Deng, Shuping; Li, Chi

    2013-01-01

    Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.

  10. Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features

    KAUST Repository

    Wang, Bing

    2013-05-09

    Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.

  11. Differential phase-time shifting protocol for QKD (DPTS)

    DEFF Research Database (Denmark)

    Usuga Castaneda, Mario A.; Bacco, Davide; Christensen, Jesper Bjerge

    2016-01-01

    We explore the implementation of a novel protocol for fiber-based high-dimensional quantum key distribution (QKD) which improves over the traditional DPS-QKD and COW protocols.......We explore the implementation of a novel protocol for fiber-based high-dimensional quantum key distribution (QKD) which improves over the traditional DPS-QKD and COW protocols....

  12. Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses

    Directory of Open Access Journals (Sweden)

    Hironobu Yanagisawa

    2016-03-01

    Full Text Available The presence of high molecular weight double-stranded RNA (dsRNA within plant cells is an indicator of infection with RNA viruses as these possess genomic or replicative dsRNA. DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing analysis has been shown to be capable of detecting unknown viruses. We postulated that a combination of DECS analysis and next-generation sequencing (NGS would improve detection efficiency and usability of the technique. Here, we describe a model case in which we efficiently detected the presumed genome sequence of Blueberry shoestring virus (BSSV, a member of the genus Sobemovirus, which has not so far been reported. dsRNAs were isolated from BSSV-infected blueberry plants using the dsRNA-binding protein, reverse-transcribed, amplified, and sequenced using NGS. A contig of 4,020 nucleotides (nt that shared similarities with sequences from other Sobemovirus species was obtained as a candidate of the BSSV genomic sequence. Reverse transcription (RT-PCR primer sets based on sequences from this contig enabled the detection of BSSV in all BSSV-infected plants tested but not in healthy controls. A recombinant protein encoded by the putative coat protein gene was bound by the BSSV-antibody, indicating that the candidate sequence was that of BSSV itself. Our results suggest that a combination of DECS analysis and NGS, designated here as “DECS-C,” is a powerful method for detecting novel plant viruses.

  13. Connectivity-Based Reliable Multicast MAC Protocol for IEEE 802.11 Wireless LANs

    Directory of Open Access Journals (Sweden)

    Woo-Yong Choi

    2009-01-01

    Full Text Available We propose the efficient reliable multicast MAC protocol based on the connectivity information among the recipients. Enhancing the BMMM (Batch Mode Multicast MAC protocol, the reliable multicast MAC protocol significantly reduces the RAK (Request for ACK frame transmissions in a reasonable computational time and enhances the MAC performance. By the analytical performance analysis, the throughputs of the BMMM protocol and our proposed MAC protocol are derived. Numerical examples show that our proposed MAC protocol increases the reliable multicast MAC performance for IEEE 802.11 wireless LANs.

  14. Detection of Tropical Fungi in Formalin-Fixed, Paraffin-Embedded Tissue: Still an Indication for Microscopy in Times of Sequence-Based Diagnosis?

    Directory of Open Access Journals (Sweden)

    Hagen Frickmann

    2015-01-01

    Full Text Available Introduction. The aim of the study was the evaluation of panfungal PCR protocols with subsequent sequence analysis for the diagnostic identification of invasive mycoses in formalin-fixed, paraffin-embedded tissue samples with rare tropical mycoses. Materials and Methods. Five different previously described panfungal PCR/sequencing protocols targeting 18S and 28S ribosomal RNA gene fragments as well as internal transcribed spacer 1 and 2 fragments were evaluated with a collection of 17 formalin-fixed, paraffin-embedded tissue samples of patients with rare and/or tropical invasive mycoses, comprising chromoblastomycosis, coccidioidomycosis, cryptococcosis, histoplasmosis, mucormycosis, mycetoma/maduromycosis, and rhinosporidiosis, in a proof-of-principle analysis. Results. The primers of the panfungal PCRs readily and predominantly reacted with contaminating environmental fungi that had deposited on the paraffin blocks. Altogether three sequence results of histoplasmosis and mycetoma samples that matched the histological assessment were associated with sample age <10 years and virtually without PCR inhibition. Conclusions. The high risk of amplifying environmental contaminants severely reduces the usefulness of the assessed panfungal PCR/sequencing protocols for the identification of rare and/or tropical mycoses in stored formalin-fixed, paraffin-embedded tissues. Histological assessment remains valuable for such indications if cultural differentiation is impossible from inactivated sample material.

  15. Energy Consumption Research of Mobile Data Collection Protocol for Underwater Nodes Using an USV

    Directory of Open Access Journals (Sweden)

    Zhichao Lv

    2018-04-01

    Full Text Available The Unmanned Surface Vehicle (USV integrated with an acoustic modem is a novel mobile vehicle for data collection, which has an advantage in terms of mobility, efficiency, and collection cost. In the scenario of data collection, the USV is controlled autonomously along the planning trajectory and the data of underwater nodes are dynamically collected. In order to improve the efficiency of data collection and extend the life of the underwater nodes, a mobile data collection protocol for underwater nodes using the USV was proposed. In the protocol, the stop-and-wait ARQ transmission mechanism is adopted, where the duty cycle is designed considering the ratio between the sleep mode and the detection mode, and the transmission ratio is defined by the duty cycle, wake-up signal cycles, and USV’s speed. According to protocol, the evaluation index for energy consumption is constructed based on the duty cycle and the transmission ratio. The energy consumption of the protocol is simulated and analyzed using the mobile communication experiment data of USV, taking into consideration USV’s speed, data sequence length, and duty cycle. Optimized protocol parameters are identified, which in turn denotes the proposed protocol’s feasibility and effectiveness.

  16. Detection of short repeated genomic sequences on metaphase chromosomes using padlock probes and target primed rolling circle DNA synthesis

    Directory of Open Access Journals (Sweden)

    Stougaard Magnus

    2007-11-01

    Full Text Available Abstract Background In situ detection of short sequence elements in genomic DNA requires short probes with high molecular resolution and powerful specific signal amplification. Padlock probes can differentiate single base variations. Ligated padlock probes can be amplified in situ by rolling circle DNA synthesis and detected by fluorescence microscopy, thus enhancing PRINS type reactions, where localized DNA synthesis reports on the position of hybridization targets, to potentially reveal the binding of single oligonucleotide-size probe molecules. Such a system has been presented for the detection of mitochondrial DNA in fixed cells, whereas attempts to apply rolling circle detection to metaphase chromosomes have previously failed, according to the literature. Methods Synchronized cultured cells were fixed with methanol/acetic acid to prepare chromosome spreads in teflon-coated diagnostic well-slides. Apart from the slide format and the chromosome spreading everything was done essentially according to standard protocols. Hybridization targets were detected in situ with padlock probes, which were ligated and amplified using target primed rolling circle DNA synthesis, and detected by fluorescence labeling. Results An optimized protocol for the spreading of condensed metaphase chromosomes in teflon-coated diagnostic well-slides was developed. Applying this protocol we generated specimens for target primed rolling circle DNA synthesis of padlock probes recognizing a 40 nucleotide sequence in the male specific repetitive satellite I sequence (DYZ1 on the Y-chromosome and a 32 nucleotide sequence in the repetitive kringle IV domain in the apolipoprotein(a gene positioned on the long arm of chromosome 6. These targets were detected with good efficiency, but the efficiency on other target sites was unsatisfactory. Conclusion Our aim was to test the applicability of the method used on mitochondrial DNA to the analysis of nuclear genomes, in particular as

  17. A Power-Optimized Cooperative MAC Protocol for Lifetime Extension in Wireless Sensor Networks.

    Science.gov (United States)

    Liu, Kai; Wu, Shan; Huang, Bo; Liu, Feng; Xu, Zhen

    2016-10-01

    In wireless sensor networks, in order to satisfy the requirement of long working time of energy-limited nodes, we need to design an energy-efficient and lifetime-extended medium access control (MAC) protocol. In this paper, a node cooperation mechanism that one or multiple nodes with higher channel gain and sufficient residual energy help a sender relay its data packets to its recipient is employed to achieve this objective. We first propose a transmission power optimization algorithm to prolong network lifetime by optimizing the transmission powers of the sender and its cooperative nodes to maximize their minimum residual energy after their data packet transmissions. Based on it, we propose a corresponding power-optimized cooperative MAC protocol. A cooperative node contention mechanism is designed to ensure that the sender can effectively select a group of cooperative nodes with the lowest energy consumption and the best channel quality for cooperative transmissions, thus further improving the energy efficiency. Simulation results show that compared to typical MAC protocol with direct transmissions and energy-efficient cooperative MAC protocol, the proposed cooperative MAC protocol can efficiently improve the energy efficiency and extend the network lifetime.

  18. Optimizing the magnetization-prepared rapid gradient-echo (MP-RAGE sequence.

    Directory of Open Access Journals (Sweden)

    Jinghua Wang

    Full Text Available The three-dimension (3D magnetization-prepared rapid gradient-echo (MP-RAGE sequence is one of the most popular sequences for structural brain imaging in clinical and research settings. The sequence captures high tissue contrast and provides high spatial resolution with whole brain coverage in a short scan time. In this paper, we first computed the optimal k-space sampling by optimizing the contrast of simulated images acquired with the MP-RAGE sequence at 3.0 Tesla using computer simulations. Because the software of our scanner has only limited settings for k-space sampling, we then determined the optimal k-space sampling for settings that can be realized on our scanner. Subsequently we optimized several major imaging parameters to maximize normal brain tissue contrasts under the optimal k-space sampling. The optimal parameters are flip angle of 12°, effective inversion time within 900 to 1100 ms, and delay time of 0 ms. In vivo experiments showed that the quality of images acquired with our optimal protocol was significantly higher than that of images obtained using recommended protocols in prior publications. The optimization of k-spacing sampling and imaging parameters significantly improved the quality and detection sensitivity of brain images acquired with MP-RAGE.

  19. The Generation of Human Induced Pluripotent Stem Cells from Blood Cells: An Efficient Protocol Using Serial Plating of Reprogrammed Cells by Centrifugation

    Directory of Open Access Journals (Sweden)

    Youngkyun Kim

    2016-01-01

    Full Text Available Human induced pluripotent stem cells (hiPSCs have demonstrated great potential for differentiation into diverse tissues. We report a straightforward and highly efficient method for the generation of iPSCs from PBMCs. By plating the cells serially to a newly coated plate by centrifugation, this protocol provides multiple healthy iPSC colonies even from a small number of PBMCs. The generated iPSCs expressed pluripotent markers and differentiated into all three germ layer lineages. The protocol can also be used with umbilical cord blood mononuclear cells (CBMCs. In this study, we present a simple and efficient protocol that improved the yield of iPSCs from floating cells such as PBMCs and CBMCs by serial plating and centrifugation.

  20. E-SAP: efficient-strong authentication protocol for healthcare applications using wireless medical sensor networks.

    Science.gov (United States)

    Kumar, Pardeep; Lee, Sang-Gon; Lee, Hoon-Jae

    2012-01-01

    A wireless medical sensor network (WMSN) can sense humans' physiological signs without sacrificing patient comfort and transmit patient vital signs to health professionals' hand-held devices. The patient physiological data are highly sensitive and WMSNs are extremely vulnerable to many attacks. Therefore, it must be ensured that patients' medical signs are not exposed to unauthorized users. Consequently, strong user authentication is the main concern for the success and large scale deployment of WMSNs. In this regard, this paper presents an efficient, strong authentication protocol, named E-SAP, for healthcare application using WMSNs. The proposed E-SAP includes: (1) a two-factor (i.e., password and smartcard) professional authentication; (2) mutual authentication between the professional and the medical sensor; (3) symmetric encryption/decryption for providing message confidentiality; (4) establishment of a secure session key at the end of authentication; and (5) professionals can change their password. Further, the proposed protocol requires three message exchanges between the professional, medical sensor node and gateway node, and achieves efficiency (i.e., low computation and communication cost). Through the formal analysis, security analysis and performance analysis, we demonstrate that E-SAP is more secure against many practical attacks, and allows a tradeoff between the security and the performance cost for healthcare application using WMSNs.

  1. E-SAP: Efficient-Strong Authentication Protocol for Healthcare Applications Using Wireless Medical Sensor Networks

    Directory of Open Access Journals (Sweden)

    Hoon-Jae Lee

    2012-02-01

    Full Text Available A wireless medical sensor network (WMSN can sense humans’ physiological signs without sacrificing patient comfort and transmit patient vital signs to health professionals’ hand-held devices. The patient physiological data are highly sensitive and WMSNs are extremely vulnerable to many attacks. Therefore, it must be ensured that patients’ medical signs are not exposed to unauthorized users. Consequently, strong user authentication is the main concern for the success and large scale deployment of WMSNs. In this regard, this paper presents an efficient, strong authentication protocol, named E-SAP, for healthcare application using WMSNs. The proposed E-SAP includes: (1 a two-factor (i.e., password and smartcard professional authentication; (2 mutual authentication between the professional and the medical sensor; (3 symmetric encryption/decryption for providing message confidentiality; (4 establishment of a secure session key at the end of authentication; and (5 professionals can change their password. Further, the proposed protocol requires three message exchanges between the professional, medical sensor node and gateway node, and achieves efficiency (i.e., low computation and communication cost. Through the formal analysis, security analysis and performance analysis, we demonstrate that E-SAP is more secure against many practical attacks, and allows a tradeoff between the security and the performance cost for healthcare application using WMSNs.

  2. Effects of Sequences of Cognitions on Group Performance Over Time.

    Science.gov (United States)

    Molenaar, Inge; Chiu, Ming Ming

    2017-04-01

    Extending past research showing that sequences of low cognitions (low-level processing of information) and high cognitions (high-level processing of information through questions and elaborations) influence the likelihoods of subsequent high and low cognitions, this study examines whether sequences of cognitions are related to group performance over time; 54 primary school students (18 triads) discussed and wrote an essay about living in another country (32,375 turns of talk). Content analysis and statistical discourse analysis showed that within each lesson, groups with more low cognitions or more sequences of low cognition followed by high cognition added more essay words. Groups with more high cognitions, sequences of low cognition followed by low cognition, or sequences of high cognition followed by an action followed by low cognition, showed different words and sequences, suggestive of new ideas. The links between cognition sequences and group performance over time can inform facilitation and assessment of student discussions.

  3. An efficient binomial model-based measure for sequence comparison and its application.

    Science.gov (United States)

    Liu, Xiaoqing; Dai, Qi; Li, Lihua; He, Zerong

    2011-04-01

    Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.

  4. Protocol-transparent resource sharing in hierarchically scheduled real-time systems

    NARCIS (Netherlands)

    Heuvel, van den M.M.H.P.; Bril, R.J.; Lukkien, J.J.

    2010-01-01

    Hierarchical scheduling frameworks (HSFs) provide means for composing complex real-time systems from well-defined, independently analyzed subsystems. To support resource sharing within two-level HSFs, three synchronization protocols based on the stack resource policy (SRP) have recently been

  5. Efficiency of SBR Process with a Six Sequence Aerobic-Anaerobic Cycle for Phosphorus and Organic Material Removal from Municipal Wastewater

    Directory of Open Access Journals (Sweden)

    Nadiya Shahandeh

    2018-02-01

    Full Text Available Background: Various chemical, physical and biologic treatment methods are being used to remove nitrogen and phosphorus from wastewater. Sequencing batch reactor (SBR is a modified activated sludge process that removes phosphorus and organic material from sanitary wastewater, biologically. Methods: This study was conducted in 2016.The performance of an aerobic-anaerobic SBR pilot device, located at Ahwaz West Wastewater Treatment Plant, Ahwaz, southern Iran in phosphorus and organic material removal was evaluated to determine the effect of the aerobic-anaerobic step time on the efficiency of nitrogen and phosphorus removal, the effect of changing the sequence of steps and the effect of time ratio on phosphorus removal efficiency. A reactor of 8 L was used. Influent contained 397 and 10.7 mg/l COD and phosphorus, respectively. The pilot plant started with a 24 h cycle including four cycles of 6 h, as follows: 1- Loading (15 min, 2-Anaerobic (2 h-Aerobic (2 h, 3- Settling (1 h, Idleness (30 min and 5- decant (15 min. Results: After reaching steady conditions (6 months, Removal percentages of phosphorus, BOD5, COD, and TSS in The SBR over a period of 6 months was 79%, 86%, 89% and 83%, respectively. Conclusion: Result of this study can be used for designing and optimum operation of sequencing batch reactors.

  6. Energy-Efficient Cluster Based Routing Protocol in Mobile Ad Hoc Networks Using Network Coding

    OpenAIRE

    Srinivas Kanakala; Venugopal Reddy Ananthula; Prashanthi Vempaty

    2014-01-01

    In mobile ad hoc networks, all nodes are energy constrained. In such situations, it is important to reduce energy consumption. In this paper, we consider the issues of energy efficient communication in MANETs using network coding. Network coding is an effective method to improve the performance of wireless networks. COPE protocol implements network coding concept to reduce number of transmissions by mixing the packets at intermediate nodes. We incorporate COPE into cluster based routing proto...

  7. VANET Routing Protocols: Pros and Cons

    OpenAIRE

    Paul, Bijan; Ibrahim, Md.; Bikas, Md. Abu Naser

    2012-01-01

    VANET (Vehicular Ad-hoc Network) is a new technology which has taken enormous attention in the recent years. Due to rapid topology changing and frequent disconnection makes it difficult to design an efficient routing protocol for routing data among vehicles, called V2V or vehicle to vehicle communication and vehicle to road side infrastructure, called V2I. The existing routing protocols for VANET are not efficient to meet every traffic scenarios. Thus design of an efficient routing protocol h...

  8. An expert protocol for immunofluorescent detection of calcium channels in tsA-201 cells.

    Science.gov (United States)

    Koch, Peter; Herzig, Stefan; Matthes, Jan

    Pore-forming subunits of voltage gated calcium channels (VGCC) are large membrane proteins (260kDa) containing 24 transmembrane domains. Despite transfection with viral promoter driven vectors, biochemical analysis of VGCC is often hampered by rather low expression levels in heterologous systems rendering VGCC challenging targets. Especially in immunofluorescent detection, calcium channels are demanding proteins. We provide an expert step-by-step protocol with adapted conditions for handling procedures (tsA-201 cell culture, transient transfection, incubation time and temperature at 28°C or 37°C and immunostaining) to address the L-type calcium-channel pore Ca v 1.2 in an immunofluorescent approach. We performed immunocytochemical analysis of Ca v 1.2 expression at single-cell level in combination with detection of different markers for cellular organelles. We show confluency levels and shapes of tsA-201 cells at different time points during an experiment. Our experiments reveal sufficient levels of Ca v 1.2 protein and a correct Ca v 1.2 expression pattern in polygonal shaped cells already 12h after transfection. A sequence of elaborated protocol modifications allows subcellular localization analysis of Ca v 1.2 in an immunocytochemical approach. We provide a protocol that may be used to achieve insights into physiological and pathophysiological processes involving voltage gated calcium channels. Our protocol may be used for expression analysis of other challenging proteins and efficient overexpression may be exploited in related biochemical techniques requiring immunolabels. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Time fluctuation analysis of forest fire sequences

    Science.gov (United States)

    Vega Orozco, Carmen D.; Kanevski, Mikhaïl; Tonini, Marj; Golay, Jean; Pereira, Mário J. G.

    2013-04-01

    Forest fires are complex events involving both space and time fluctuations. Understanding of their dynamics and pattern distribution is of great importance in order to improve the resource allocation and support fire management actions at local and global levels. This study aims at characterizing the temporal fluctuations of forest fire sequences observed in Portugal, which is the country that holds the largest wildfire land dataset in Europe. This research applies several exploratory data analysis measures to 302,000 forest fires occurred from 1980 to 2007. The applied clustering measures are: Morisita clustering index, fractal and multifractal dimensions (box-counting), Ripley's K-function, Allan Factor, and variography. These algorithms enable a global time structural analysis describing the degree of clustering of a point pattern and defining whether the observed events occur randomly, in clusters or in a regular pattern. The considered methods are of general importance and can be used for other spatio-temporal events (i.e. crime, epidemiology, biodiversity, geomarketing, etc.). An important contribution of this research deals with the analysis and estimation of local measures of clustering that helps understanding their temporal structure. Each measure is described and executed for the raw data (forest fires geo-database) and results are compared to reference patterns generated under the null hypothesis of randomness (Poisson processes) embedded in the same time period of the raw data. This comparison enables estimating the degree of the deviation of the real data from a Poisson process. Generalizations to functional measures of these clustering methods, taking into account the phenomena, were also applied and adapted to detect time dependences in a measured variable (i.e. burned area). The time clustering of the raw data is compared several times with the Poisson processes at different thresholds of the measured function. Then, the clustering measure value

  10. Correct mutual information, quantum bit error rate and secure transmission efficiency in Wojcik's eavesdropping scheme on ping-pong protocol

    OpenAIRE

    Zhang, Zhanjun

    2004-01-01

    Comment: The wrong mutual information, quantum bit error rate and secure transmission efficiency in Wojcik's eavesdropping scheme [PRL90(03)157901]on ping-pong protocol have been pointed out and corrected

  11. A Lightweight Protocol for Secure Video Streaming.

    Science.gov (United States)

    Venčkauskas, Algimantas; Morkevicius, Nerijus; Bagdonas, Kazimieras; Damaševičius, Robertas; Maskeliūnas, Rytis

    2018-05-14

    The Internet of Things (IoT) introduces many new challenges which cannot be solved using traditional cloud and host computing models. A new architecture known as fog computing is emerging to address these technological and security gaps. Traditional security paradigms focused on providing perimeter-based protections and client/server point to point protocols (e.g., Transport Layer Security (TLS)) are no longer the best choices for addressing new security challenges in fog computing end devices, where energy and computational resources are limited. In this paper, we present a lightweight secure streaming protocol for the fog computing "Fog Node-End Device" layer. This protocol is lightweight, connectionless, supports broadcast and multicast operations, and is able to provide data source authentication, data integrity, and confidentiality. The protocol is based on simple and energy efficient cryptographic methods, such as Hash Message Authentication Codes (HMAC) and symmetrical ciphers, and uses modified User Datagram Protocol (UDP) packets to embed authentication data into streaming data. Data redundancy could be added to improve reliability in lossy networks. The experimental results summarized in this paper confirm that the proposed method efficiently uses energy and computational resources and at the same time provides security properties on par with the Datagram TLS (DTLS) standard.

  12. Improving the time efficiency of the Fourier synthesis method for slice selection in magnetic resonance imaging.

    Science.gov (United States)

    Tahayori, B; Khaneja, N; Johnston, L A; Farrell, P M; Mareels, I M Y

    2016-01-01

    The design of slice selective pulses for magnetic resonance imaging can be cast as an optimal control problem. The Fourier synthesis method is an existing approach to solve these optimal control problems. In this method the gradient field as well as the excitation field are switched rapidly and their amplitudes are calculated based on a Fourier series expansion. Here, we provide a novel insight into the Fourier synthesis method via representing the Bloch equation in spherical coordinates. Based on the spherical Bloch equation, we propose an alternative sequence of pulses that can be used for slice selection which is more time efficient compared to the original method. Simulation results demonstrate that while the performance of both methods is approximately the same, the required time for the proposed sequence of pulses is half of the original sequence of pulses. Furthermore, the slice selectivity of both sequences of pulses changes with radio frequency field inhomogeneities in a similar way. We also introduce a measure, referred to as gradient complexity, to compare the performance of both sequences of pulses. This measure indicates that for a desired level of uniformity in the excited slice, the gradient complexity for the proposed sequence of pulses is less than the original sequence. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  13. Leader-Following Consensus Stability of Discrete-Time Linear Multiagent Systems with Observer-Based Protocols

    Directory of Open Access Journals (Sweden)

    Bingbing Xu

    2013-01-01

    Full Text Available We consider the leader-following consensus problem of discrete-time multiagent systems on a directed communication topology. Two types of distributed observer-based consensus protocols are considered to solve such a problem. The observers involved in the proposed protocols include full-order observer and reduced-order observer, which are used to reconstruct the state variables. Two algorithms are provided to construct the consensus protocols, which are based on the modified discrete-time algebraic Riccati equation and Sylvester equation. In light of graph and matrix theory, some consensus conditions are established. Finally, a numerical example is provided to illustrate the obtained result.

  14. Optimizing the MRI protocol of the sacroiliac joints in Spondyloarthritis: which para-axial sequence should be used?

    Energy Technology Data Exchange (ETDEWEB)

    Giraudo, Chiara; Weber, Michael; Platzgummer, Hannes; Kainberger, Franz; Schueller-Weidekamm, Claudia [Medical University of Vienna, Vienna General Hospital, Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging und Image-guided Therapy, Vienna (Austria); Magnaldi, Silvia [Fondazione Poliambulanza Istituto Ospedaliero, Dipartimento di Radiologia e Diagnostica per Immagini, Brescia (Italy); Puchner, Antonia [Medical University of Vienna, Vienna General Hospital, Division of Rheumatology, Department of Internal Medicine III, Vienna (Austria)

    2016-01-15

    To assess the diagnostic value of para-axial T2w-TSE (paT2) and fat-suppressed proton density (paPD-FS) MRI sequences for the evaluation of the sacroiliac joint (SIJ) of patients with axial Spondylarthritis (SpA). One hundred and six patients with clinical findings suggestive of SpA underwent an MR protocol of the SIJ with additional paPD-FS (41 patients) and paT2 (105 patients). Acute (bone marrow oedema [BME], enthesitis, capsulitis, synovitis) and chronic findings (erosions, ankylosis) were assessed by paPD-FS and compared with the gold standard post-contrast sequences, whereas chronic features (because of the lack of fat suppression) were evaluated on paT2 and compared with pcT1. paPD-FS demonstrated high sensitivity (98.9 %) and specificity (99.1 %) for BME; sensitivity and specificity for synovitis and enthesitis were 100 %; 85.7 % and 100 %, respectively, for capsulitis. paPD-FS and paT2 showed 100 % sensitivity and specificity for ankylosis; for erosions, paT2 demonstrated 85.3 % sensitivity and 100 % specificity, whereas paPD-FS, respectively, 98 % and 100 %. PaT2 and paPD-FS provided precious information enabling an accurate interpretation of the heterogeneous findings of SpA. paPD-FS showed good results in detecting acute and chronic lesions and its inclusion in a routine MR examination of the SIJ could increase the diagnostic performance of a pre-contrast protocol. (orig.)

  15. Can a 15-sec FLAIR replace conventional FLAIR sequence in stroke MR protocols?

    Science.gov (United States)

    Benzakoun, J; Maïer, B; Calvet, D; Edjlali, M; Turc, G; Lion, S; Legrand, L; Ben Hassen, W; Naggara, O; Meder, J F; Mas, J L; Oppenheim, C

    2017-06-01

    Triage imaging facilitates the timely recognition of acute stroke with prognostic implications. Improvement in MR acquisition speed is needed given the extreme time constraints before treatment. We compared an ultrafast Echo-Planar FLAIR sequence (EPI-FLAIR) and a conventional FLAIR sequence (cFLAIR) for their diagnostic performances and ability to estimate the age of infarction. Between June and August 2014, 125 consecutive patients (age 69±18 years, 48% men) admitted for a suspicion of acute (≤48-hrs) stroke were explored by both FLAIR sequences at 1.5-Tesla. EPI-FLAIR (15-sec) and cFLAIR (2-min and 15-sec) were compared by two readers, blinded to clinical data. EPI-FLAIR was less prone to kinetic artefacts than cFLAIR (2-3% vs. 23-49% depending on the reader, P0.9). Amongst 8 hemorrhages, one subarachnoid hemorrhage presenting as a sudden deficit was missed on EPI-FLAIR sequence. Amongst 60 infarctions, cFLAIR and EPI-FLAIR were concordant in 50 (83%), while signal changes were visible on cFLAIR only in the remaining 10 (17%) cases. Amongst the 43 patients with known onset time (n=17 within 4.5hrs), FLAIR-DWI mismatch identified<4.5-hrs infarction with the same sensitivity (65%) using cFLAIR and EPI-FLAIR, but the positive predictive value (PPV) was higher for cFLAIR than for EPI-FLAIR (73% vs. 50%, P=0.008). EPI-FLAIR allows a drastic reduction of acquisition time devoted to FLAIR sequence and minimizes motion artifacts. Compared with cFLAIR, it is however associated with increased risk of undiagnosed stroke mimics and lower PPV for identifying<4.5-hrs infarctions. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  16. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  17. Sequencing games with Just-in-Time arrival, and related games

    NARCIS (Netherlands)

    Lohmann, E.R.M.A.; Borm, P.E.M.; Slikker, M.

    2014-01-01

    In this paper sequencing situations with Just-in-Time (JiT) arrival are introduced. This new type of one-machine sequencing situations assumes that a job is available to be handled by the machine as soon as its predecessor is finished. A basic predecessor dependent set-up time is incorporated in the

  18. The Time Division Multi-Channel Communication Model and the Correlative Protocol Based on Quantum Time Division Multi-Channel Communication

    International Nuclear Information System (INIS)

    Liu Xiao-Hui; Pei Chang-Xing; Nie Min

    2010-01-01

    Based on the classical time division multi-channel communication theory, we present a scheme of quantum time-division multi-channel communication (QTDMC). Moreover, the model of quantum time division switch (QTDS) and correlative protocol of QTDMC are proposed. The quantum bit error rate (QBER) is analyzed and the QBER simulation test is performed. The scheme shows that the QTDS can carry out multi-user communication through quantum channel, the QBER can also reach the reliability requirement of communication, and the protocol of QTDMC has high practicability and transplantable. The scheme of QTDS may play an important role in the establishment of quantum communication in a large scale in the future. (general)

  19. An Eco-Friendly Improved Protocol for the Synthesis of Bis(3-indolyl)methanes Using Poly(4-vinylpyridinium)hydrogen Sulfate as Efficient, Heterogeneous, and Recyclable Solid Acid Catalyst

    Science.gov (United States)

    Banothu, Janardhan; Gali, Rajitha; Velpula, Ravibabu; Bavantula, Rajitha; Crooks, Peter A.

    2013-01-01

    Highly efficient and eco-friendly protocol for the synthesis of bis(3-indolyl)methanes by the electrophilic substitution reaction of indole with aldehydes catalyzed by poly(4-vinylpyridinium)hydrogen sulfate was described. Excellent yields, shorter reaction times, simple work-up procedure, avoiding hazardous organic solvents, and reusability of the catalyst are the most obvious advantages of this method. PMID:24052864

  20. Suppressing traffic-driven epidemic spreading by use of the efficient routing protocol

    International Nuclear Information System (INIS)

    Yang, Han-Xin; Wu, Zhi-Xi

    2014-01-01

    Despite extensive work on the interplay between traffic dynamics and epidemic spreading, the control of epidemic spreading by routing strategies has not received adequate attention. In this paper, we study the impact of an efficient routing protocol on epidemic spreading. In the case of infinite node-delivery capacity, where the traffic is free of congestion, we find that that there exist optimal values of routing parameter, leading to the maximal epidemic threshold. This means that epidemic spreading can be effectively controlled by fine tuning the routing scheme. Moreover, we find that an increase in the average network connectivity and the emergence of traffic congestion can suppress the epidemic outbreak. (paper)

  1. Quantum Communication Attacks on Classical Cryptographic Protocols

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre

    , one can show that the protocol remains secure even under such an attack. However, there are also cases where the honest players are quantum as well, even if the protocol uses classical communication. For instance, this is the case when classical multiparty computation is used as a “subroutine......In the literature on cryptographic protocols, it has been studied several times what happens if a classical protocol is attacked by a quantum adversary. Usually, this is taken to mean that the adversary runs a quantum algorithm, but communicates classically with the honest players. In several cases......” in quantum multiparty computation. Furthermore, in the future, players in a protocol may employ quantum computing simply to improve efficiency of their local computation, even if the communication is supposed to be classical. In such cases, it no longer seems clear that a quantum adversary must be limited...

  2. Quantum Communication Attacks on Classical Cryptographic Protocols

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre

    , one can show that the protocol remains secure even under such an attack. However, there are also cases where the honest players are quantum as well, even if the protocol uses classical communication. For instance, this is the case when classical multiparty computation is used as a “subroutine......” in quantum multiparty computation. Furthermore, in the future, players in a protocol may employ quantum computing simply to improve efficiency of their local computation, even if the communication is supposed to be classical. In such cases, it no longer seems clear that a quantum adversary must be limited......In the literature on cryptographic protocols, it has been studied several times what happens if a classical protocol is attacked by a quantum adversary. Usually, this is taken to mean that the adversary runs a quantum algorithm, but communicates classically with the honest players. In several cases...

  3. White Rabbit Precision Time Protocol on Long-Distance Fiber Links

    NARCIS (Netherlands)

    Dierikx, E.F.; Dierikx, A.E.; Fordell, T.; Myyry, J.; Koponen, P.; Merimaa, M.; Pinkert, T.J.; Koelemeij, J.C.J.; Peek, H.Z.; Smets, R.

    2016-01-01

    The application of White Rabbit precision time protocol (WR-PTP) in long-distance optical fiber links has been investigated. WR-PTP is an implementation of PTP in synchronous Ethernet optical fiber networks, originally intended for synchronization of equipment within a range of 10 km. This paper

  4. Reactive GTS Allocation Protocol for Sporadic Events Using the IEEE 802.15.4

    Directory of Open Access Journals (Sweden)

    Mukhtar Azeem

    2014-01-01

    by the IEEE 802.15.4 standard. The proposed control protocol ensures that a given offline sporadic schedule can be adapted online in a timely manner such that the static periodic schedule has not been disturbed and the IEEE 802.15.4 standard compliance remains intact. The proposed protocol is simulated in OPNET. The simulation results are analyzed and presented in this paper to prove the correctness of the proposed protocol regarding the efficient real-time sporadic event delivery along with the periodic event propagation.

  5. Formal description of the jumpstart just-in-time signaling protocol using EFSM

    Science.gov (United States)

    Zaim, A. H.; Baldine, Ilia; Cassada, Mark; Rouskas, George N.; Perros, Harry G.; Stevenson, Daniel S.

    2002-07-01

    We present a formal protocol description for a Just-In-Time (JIT) signaling scheme running over a core dWDM network which utilizes Optical Burst Switches (OBS). We apply an eight-tuple extended finite state machine (EFSM) model to formally specify the protocol. Using the EFSM model, we define the communication between a source client node and a destination client node through an ingress and one or multiple intermediate switches. We worked on single burst connections that means setting up the connection just before sending a single burst and then closing the connection as soon as the burst is sent. The communication between the EFSMs is handled through message transfer between protocol entities.

  6. A Secure and Efficient Handover Authentication Protocol for Wireless Networks

    Directory of Open Access Journals (Sweden)

    Weijia Wang

    2014-06-01

    Full Text Available Handover authentication protocol is a promising access control technology in the fields of WLANs and mobile wireless sensor networks. In this paper, we firstly review an effcient handover authentication protocol, named PairHand, and its existing security attacks and improvements. Then, we present an improved key recovery attack by using the linearly combining method and reanalyze its feasibility on the improved PairHand protocol. Finally, we present a new handover authentication protocol, which not only achieves the same desirable effciency features of PairHand, but enjoys the provable security in the random oracle model.

  7. A Concurrent Multiple Negotiation Protocol Based on Colored Petri Nets.

    Science.gov (United States)

    Niu, Lei; Ren, Fenghui; Zhang, Minjie; Bai, Quan

    2017-11-01

    Concurrent multiple negotiation (CMN) provides a mechanism for an agent to simultaneously conduct more than one negotiation. There may exist different interdependency relationships among these negotiations and these interdependency relationships can impact the outcomes of these negotiations. The outcomes of these concurrent negotiations contribute together for the agent to achieve an overall negotiation goal. Handling a CMN while considering interdependency relationships among multiple negotiations is a challenging research problem. This paper: 1) comprehensively highlights research problems of negotiations at concurrent negotiation level; 2) provides a graph-based CMN model with consideration of the interdependency relationships; and 3) proposes a colored Petri net-based negotiation protocol for conducting CMNs. With the proposed protocol, a CMN can be efficiently and concurrently processed and negotiation agreements can be efficiently achieved. Experimental results indicate the effectiveness and efficiency of the proposed protocol in terms of the negotiation success rate, the negotiation time and the negotiation outcome.

  8. Multimode Communication Protocols Enabling Reconfigurable Radios

    Directory of Open Access Journals (Sweden)

    Berlemann Lars

    2005-01-01

    Full Text Available This paper focuses on the realization and application of a generic protocol stack for reconfigurable wireless communication systems. This focus extends the field of software-defined radios which usually concentrates on the physical layer. The generic protocol stack comprises common protocol functionality and behavior which are extended through specific parts of the targeted radio access technology. This paper considers parameterizable modules of basic protocol functions residing in the data link layer of the ISO/OSI model. System-specific functionality of the protocol software is realized through adequate parameterization and composition of the generic modules. The generic protocol stack allows an efficient realization of reconfigurable protocol software and enables a completely reconfigurable wireless communication system. It is a first step from side-by-side realized, preinstalled modes in a terminal towards a dynamic reconfigurable anymode terminal. The presented modules of the generic protocol stack can also be regarded as a toolbox for the accelerated and cost-efficient development of future communication protocols.

  9. Time-varying value of electric energy efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Mims, Natalie A.; Eckman, Tom; Goldman, Charles

    2017-06-30

    Electric energy efficiency resources save energy and may reduce peak demand. Historically, quantification of energy efficiency benefits has largely focused on the economic value of energy savings during the first year and lifetime of the installed measures. Due in part to the lack of publicly available research on end-use load shapes (i.e., the hourly or seasonal timing of electricity savings) and energy savings shapes, consideration of the impact of energy efficiency on peak demand reduction (i.e., capacity savings) has been more limited. End-use load research and the hourly valuation of efficiency savings are used for a variety of electricity planning functions, including load forecasting, demand-side management and evaluation, capacity and demand response planning, long-term resource planning, renewable energy integration, assessing potential grid modernization investments, establishing rates and pricing, and customer service. This study reviews existing literature on the time-varying value of energy efficiency savings, provides examples in four geographically diverse locations of how consideration of the time-varying value of efficiency savings impacts the calculation of power system benefits, and identifies future research needs to enhance the consideration of the time-varying value of energy efficiency in cost-effectiveness screening analysis. Findings from this study include: -The time-varying value of individual energy efficiency measures varies across the locations studied because of the physical and operational characteristics of the individual utility system (e.g., summer or winter peaking, load factor, reserve margin) as well as the time periods during which savings from measures occur. -Across the four locations studied, some of the largest capacity benefits from energy efficiency are derived from the deferral of transmission and distribution system infrastructure upgrades. However, the deferred cost of such upgrades also exhibited the greatest range

  10. Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing.

    Science.gov (United States)

    Wu, Wells W; Phue, Je-Nie; Lee, Chun-Ting; Lin, Changyi; Xu, Lai; Wang, Rong; Zhang, Yaqin; Shen, Rong-Fong

    2018-05-04

    Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage). A well-tested sub-nanomolar library preparation protocol for Illumina sequencers has however not been reported. The aim of this study is to provide a much needed working protocol for sub-nanomolar libraries to achieve outcomes as informative as those obtained with the higher library input (≥ 2 nM) recommended by Illumina's protocols. Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples. The utility of our protocol was further explored for PhiX library concentrations as low as 25 pM, which generated only slightly fewer than 50% of the reads achieved under the standard Illumina protocol starting with > 2 nM. A sub-nanomolar library preparation protocol (100 pM) could generate next generation sequencing (NGS) results as robust as the standard Illumina protocol. Following the sub-nanomolar protocol, libraries with initial concentrations as low as 25 pM could also be sequenced to yield satisfactory and reproducible sequencing results.

  11. The Singapore protocol [for quantum cryptography

    International Nuclear Information System (INIS)

    Englert, B.

    2005-01-01

    The qubit protocol for quantum key distribution presented in this talk is fully tomographic and more efficient than other tomographic protocols. Under ideal circumstances the efficiency is log 2 (4/3) = 0.415 key bits per qubit sent, which is 25% more than the efficiency of 1/3 = 0.333 for the standard 6-state protocol. One can extract 0.4 key bits per qubit by a simple two-way communication scheme, and can so get close to the information-theoretical limit. The noise thresholds for secure key bit generation in the presence of unbiased noise will be reported and discussed. (author)

  12. Treatment Protocol for High Velocity/High Energy Gunshot Injuries to the Face

    Science.gov (United States)

    Peled, Micha; Leiser, Yoav; Emodi, Omri; Krausz, Amir

    2011-01-01

    Major causes of facial combat injuries include blasts, high-velocity/high-energy missiles, and low-velocity missiles. High-velocity bullets fired from assault rifles encompass special ballistic properties, creating a transient cavitation space with a small entrance wound and a much larger exit wound. There is no dispute regarding the fact that primary emergency treatment of ballistic injuries to the face commences in accordance with the current advanced trauma life support (ATLS) recommendations; the main areas in which disputes do exist concern the question of the timing, sequence, and modes of surgical treatment. The aim of the present study is to present the treatment outcome of high-velocity/high-energy gunshot injuries to the face, using a protocol based on the experience of a single level I trauma center. A group of 23 injured combat soldiers who sustained bullet and shrapnel injuries to the maxillofacial region during a 3-week regional military conflict were evaluated in this study. Nine patients met the inclusion criteria (high-velocity/high-energy injuries) and were included in the study. According to our protocol, upon arrival patients underwent endotracheal intubation and were hemodynamically stabilized in the shock-trauma unit and underwent total-body computed tomography with 3-D reconstruction of the head and neck and computed tomography angiography. All patients underwent maxillofacial surgery upon the day of arrival according to the protocol we present. In view of our treatment outcomes, results, and low complication rates, we conclude that strict adherence to a well-founded and structured treatment protocol based on clinical experience is mandatory in providing efficient, appropriate, and successful treatment to a relatively large group of patients who sustain various degrees of maxillofacial injuries during a short period of time. PMID:23449809

  13. RFID Cryptographic Protocol Based on Cyclic Redundancy Check for High Efficiency

    Directory of Open Access Journals (Sweden)

    Nian Liu

    2014-04-01

    Full Text Available In this paper, RFID encryption protocol is proposed based on the security problems in wireless signal channel. In order to solve the privacy issues of electronic tags, the most commonly way is to improve algorithms based on Hash function. However, there are some problems that can only play roles in some specific domains. Due to the limitations in various kinds of algorithms, in this paper we put forward a new kind of agreement. When it is required to locate target labels accurately and rapidly in a movement environment, using this agreement can achieve high efficiency through combining the Hash function, the two division search algorithm and CRC check. The results show that this algorithm can accurately identify the tags with merits of low cost, execution rate and anti-attack ability etc.

  14. A protocol for measuring spatial variables in soft-sediment tide pools

    Directory of Open Access Journals (Sweden)

    Marina R. Brenha-Nunes

    2016-01-01

    Full Text Available ABSTRACT We present a protocol for measuring spatial variables in large (>50 m2 soft-sediment tide pool. Secondarily, we present the fish capture efficiency of a sampling protocol that based on such spatial variables to calculate relative abundances. The area of the pool is estimated by summing areas of basic geometric forms; the depth, by taken representative measurements of the depth variability of each pool's sector, previously determined according to its perimeter; and the volume, by considering the pool as a prism. These procedures were a trade-off between the acquisition of reliable estimates and the minimization of both the cost of operating and the time spent in field. The fish sampling protocol is based on two con secutive stages: 1 two people search for fishes under structures (e.g., rocks and litters on the pool and capture them with hand seines; 2 these structures are removed and then a beach-seine is hauled over the whole pool. Our method is cheaper than others and fast to operate considering the time in low tides. The method to sample fish is quite efficient resulting in a capture efficiency of 89%.

  15. A distributed Synchronous reservation multiple access control protocol for mobile Ad hoc networks

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yanling; SUN Xianpu; LI Jiandong

    2007-01-01

    This study proposes a new multiple access control protocol named distributed synchronous reservation multiple access control protocol.in which the hidden and exposed terminal problems are solved,and the quality of service(QoS)requirements for real-time traffic are guaranteed.The protocol is founded on time division multiplex address and a different type of traffic is assigned to difierent priority,according to which a node should compete for and reserve the free slots in a different method.Moreover,there is a reservation acknowledgement process before data transmit in each reserved slot,so that the intruded terminal problem is solved.The throughput and average packets drop probability of this protocol are analyzed and simulated in a fully connected network.the results of which indicate that this protocol is efficient enough to support the real-time traffic.and it is more suitable to MANETs.

  16. A Selective-Awakening MAC Protocol for Energy-Efficient Data Forwarding in Linear Sensor Networks

    Directory of Open Access Journals (Sweden)

    Iclia Villordo-Jimenez

    2018-01-01

    Full Text Available We introduce the Selective-Awakening MAC (SA-MAC protocol which is a synchronized duty-cycled protocol with pipelined scheduling for Linear Sensor Networks (LSNs. In the proposed protocol, nodes selectively awake depending on node density and traffic load conditions and on the state of the buffers of the receiving nodes. In order to characterize the performance of the proposed protocol, we present a Discrete-Time Markov Chain-based analysis that is validated through extensive discrete-event simulations. Our results show that SA-MAC significantly outperforms previous proposals in terms of energy consumption, throughput, and packet loss probability. This is particularly true under high node density and high traffic load conditions, which are expected to be common scenarios in the context of IoT applications. We also present an analysis by grade (i.e., the number of hops to the sink, which is located at one end of the LSN that reveals that LSNs exhibit heterogeneous performance depending on the nodes’ grade. Such results can be used as a design guideline for future LSN implementations.

  17. Optimizing functional MR urography: prime time for a 30-minutes-or-less fMRU

    Energy Technology Data Exchange (ETDEWEB)

    Delgado, Jorge; Bedoya, Maria A.; Adeb, Melkamu; Carson, Robert H.; Khrichenko, Dmitry [The Children' s Hospital of Philadelphia, Department of Radiology, Philadelphia, PA (United States); Johnson, Ann M.; Darge, Kassa [The Children' s Hospital of Philadelphia, Department of Radiology, Philadelphia, PA (United States); University of Pennsylvania, Department of Radiology, The Perelman School of Medicine, Philadelphia, PA (United States); Canning, Douglas A. [University of Pennsylvania, Division of Urology, Department of Surgery, The Children' s Hospital of Philadelphia, The Perelman School of Medicine, Philadelphia, PA (United States)

    2015-08-15

    Current protocols for functional MR urography (fMRU) require long scan times, limiting its widespread use. Our goal was to use pre-defined criteria to reduce the number of sequences and thus the examination time without compromising the morphological and functional results. The standard fMRU protocol in our department consists of eight sequences, including a 17-min dynamic post-contrast scan. Ninety-nine children and young adults (43 male, 56 female, mean age 7 years) were evaluated with this protocol. Each sequence was retrospectively analyzed for its utility and factors that affect its duration. Mean scan time to perform the eight sequences, without including the variable time between sequences, was 40.5 min. Five sequences were categorized as essential: (1) sagittal T2 for planning the oblique coronal plane, (2) axial T2 with fat saturation for the assessment of corticomedullary differentiation and parenchymal thickness, (3) coronal 3-D T2 with fat saturation for multiplanar and 3-D reconstructions, (4) pre-contrast coronal T1 with fat saturation to ensure an appropriate scan prior to injecting the contrast material and (5) the coronal post-contrast dynamic series. Functional information was obtained after 8 min of dynamic imaging in the majority of children. The coronal fat-saturated T2, coronal T1, and post-contrast sagittal fat-saturated T1 sequences did not provide additional information. Because of the effects of pelvicalyceal dilation and ureteropelvic angle on the renal transit time, prone position is recommended, at least in children with high-grade pelvicalyceal dilation. Comprehensive fMRU requires approximately 19 min for sequence acquisition. Allowing for time between sequences and motion correction, the total study time can be reduced to about 30 min. Four pre-contrast sequences and a shortened post-contrast dynamic scan, optimally with the child in prone position, are sufficient. (orig.)

  18. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

    Science.gov (United States)

    Lea, Amanda J.

    2015-01-01

    Identifying sources of variation in DNA methylation levels is important for understanding gene regulation. Recently, bisulfite sequencing has become a popular tool for investigating DNA methylation levels. However, modeling bisulfite sequencing data is complicated by dramatic variation in coverage across sites and individual samples, and because of the computational challenges of controlling for genetic covariance in count data. To address these challenges, we present a binomial mixed model and an efficient, sampling-based algorithm (MACAU: Mixed model association for count data via data augmentation) for approximate parameter estimation and p-value computation. This framework allows us to simultaneously account for both the over-dispersed, count-based nature of bisulfite sequencing data, as well as genetic relatedness among individuals. Using simulations and two real data sets (whole genome bisulfite sequencing (WGBS) data from Arabidopsis thaliana and reduced representation bisulfite sequencing (RRBS) data from baboons), we show that our method provides well-calibrated test statistics in the presence of population structure. Further, it improves power to detect differentially methylated sites: in the RRBS data set, MACAU detected 1.6-fold more age-associated CpG sites than a beta-binomial model (the next best approach). Changes in these sites are consistent with known age-related shifts in DNA methylation levels, and are enriched near genes that are differentially expressed with age in the same population. Taken together, our results indicate that MACAU is an efficient, effective tool for analyzing bisulfite sequencing data, with particular salience to analyses of structured populations. MACAU is freely available at www.xzlab.org/software.html. PMID:26599596

  19. Hybrid Pareto artificial bee colony algorithm for multi-objective single machine group scheduling problem with sequence-dependent setup times and learning effects.

    Science.gov (United States)

    Yue, Lei; Guan, Zailin; Saif, Ullah; Zhang, Fei; Wang, Hao

    2016-01-01

    Group scheduling is significant for efficient and cost effective production system. However, there exist setup times between the groups, which require to decrease it by sequencing groups in an efficient way. Current research is focused on a sequence dependent group scheduling problem with an aim to minimize the makespan in addition to minimize the total weighted tardiness simultaneously. In most of the production scheduling problems, the processing time of jobs is assumed as fixed. However, the actual processing time of jobs may be reduced due to "learning effect". The integration of sequence dependent group scheduling problem with learning effects has been rarely considered in literature. Therefore, current research considers a single machine group scheduling problem with sequence dependent setup times and learning effects simultaneously. A novel hybrid Pareto artificial bee colony algorithm (HPABC) with some steps of genetic algorithm is proposed for current problem to get Pareto solutions. Furthermore, five different sizes of test problems (small, small medium, medium, large medium, large) are tested using proposed HPABC. Taguchi method is used to tune the effective parameters of the proposed HPABC for each problem category. The performance of HPABC is compared with three famous multi objective optimization algorithms, improved strength Pareto evolutionary algorithm (SPEA2), non-dominated sorting genetic algorithm II (NSGAII) and particle swarm optimization algorithm (PSO). Results indicate that HPABC outperforms SPEA2, NSGAII and PSO and gives better Pareto optimal solutions in terms of diversity and quality for almost all the instances of the different sizes of problems.

  20. Whole genome sequencing: an efficient approach to ensuring food safety

    Science.gov (United States)

    Lakicevic, B.; Nastasijevic, I.; Dimitrijevic, M.

    2017-09-01

    Whole genome sequencing is an effective, powerful tool that can be applied to a wide range of public health and food safety applications. A major difference between WGS and the traditional typing techniques is that WGS allows all genes to be included in the analysis, instead of a well-defined subset of genes or variable intergenic regions. Also, the use of WGS can facilitate the understanding of contamination/colonization routes of foodborne pathogens within the food production environment, and can also afford efficient tracking of pathogens’ entry routes and distribution from farm-to-consumer. Tracking foodborne pathogens in the food processing-distribution-retail-consumer continuum is of the utmost importance for facilitation of outbreak investigations and rapid action in controlling/preventing foodborne outbreaks. Therefore, WGS likely will replace most of the numerous workflows used in public health laboratories to characterize foodborne pathogens into one consolidated, efficient workflow.

  1. Cryptographic protocol security analysis based on bounded constructing algorithm

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    An efficient approach to analyzing cryptographic protocols is to develop automatic analysis tools based on formal methods. However, the approach has encountered the high computational complexity problem due to reasons that participants of protocols are arbitrary, their message structures are complex and their executions are concurrent. We propose an efficient automatic verifying algorithm for analyzing cryptographic protocols based on the Cryptographic Protocol Algebra (CPA) model proposed recently, in which algebraic techniques are used to simplify the description of cryptographic protocols and their executions. Redundant states generated in the analysis processes are much reduced by introducing a new algebraic technique called Universal Polynomial Equation and the algorithm can be used to verify the correctness of protocols in the infinite states space. We have implemented an efficient automatic analysis tool for cryptographic protocols, called ACT-SPA, based on this algorithm, and used the tool to check more than 20 cryptographic protocols. The analysis results show that this tool is more efficient, and an attack instance not offered previously is checked by using this tool.

  2. Demarcation of Security in Authentication Protocols

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2011-01-01

    Security analysis of communication protocols is a slippery business; many “secure” protocols later turn out to be insecure. Among many, two complains are more frequent: inadequate definition of security and unstated assumptions in the security model. In our experience, one principal cause...... for such state of affairs is an apparent overlap of security and correctness, which may lead to many sloppy security definitions and security models. Although there is no inherent need to separate security and correctness requirements, practically, such separation is significant. It makes security analysis...... easier, and enables us to define security goals with a fine granularity. We present one such separation, by introducing the notion of binding sequence as a security primitive. A binding sequence, roughly speaking, is the only required security property of an authentication protocol. All other...

  3. A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites

    DEFF Research Database (Denmark)

    Uren, Anthony G; Mikkers, Harald; Kool, Jaap

    2009-01-01

    sites has been a major limitation to performing screens on this scale. Here we present a method for the high-throughput isolation of insertion sites using a highly efficient splinkerette-PCR method coupled with capillary or 454 sequencing. This protocol includes a description of the procedure for DNA......Insertional mutagens such as viruses and transposons are a useful tool for performing forward genetic screens in mice to discover cancer genes. These screens are most effective when performed using hundreds of mice; however, until recently, the cost-effective isolation and sequencing of insertion...

  4. Time-Varying Value of Energy Efficiency in Michigan

    Energy Technology Data Exchange (ETDEWEB)

    Mims, Natalie; Eckman, Tom; Schwartz, Lisa C.

    2018-04-02

    Quantifying the time-varying value of energy efficiency is necessary to properly account for all of its benefits and costs and to identify and implement efficiency resources that contribute to a low-cost, reliable electric system. Historically, most quantification of the benefits of efficiency has focused largely on the economic value of annual energy reduction. Due to the lack of statistically representative metered end-use load shape data in Michigan (i.e., the hourly or seasonal timing of electricity savings), the ability to confidently characterize the time-varying value of energy efficiency savings in the state, especially for weather-sensitive measures such as central air conditioning, is limited. Still, electric utilities in Michigan can take advantage of opportunities to incorporate the time-varying value of efficiency into their planning. For example, end-use load research and hourly valuation of efficiency savings can be used for a variety of electricity planning functions, including load forecasting, demand-side management and evaluation, capacity planning, long-term resource planning, renewable energy integration, assessing potential grid modernization investments, establishing rates and pricing, and customer service (KEMA 2012). In addition, accurately calculating the time-varying value of efficiency may help energy efficiency program administrators prioritize existing offerings, set incentive or rebate levels that reflect the full value of efficiency, and design new programs.

  5. Improvement of Network Efficiency on the Grounds of Change Communication Protocol

    Directory of Open Access Journals (Sweden)

    Jiri Vychodil

    2012-01-01

    Full Text Available This article deals with both theoretical and practical application of Extensible Messaging and Presence Protocol instead of different solution described detailed in the article. It uses periodically HTTP method POST to gain information about a state, which a client stands in. During this process a new connection is created and closed, what enormously makes network traffic mote intensive. Instead of this we used XMPP, this technology eliminates disadvantages of synchronous HTTP connection by its adapting for real time connection. It uses stable connection, what does not need to create it any time any information needs to be sent. It decreased amount of transported data through a network and a time, in which is a client informed about an event due to a fact, that the new solution works in real time.

  6. Light water reactor sequence timing: its significance to probabilistic safety assessment modeling

    International Nuclear Information System (INIS)

    Bley, D.C.; Buttemer, D.R.; Stetkar, J.W.

    1988-01-01

    This paper examines event sequence timing in light water reactor plants from the viewpoint of probabilistic safety assessment (PSA). The analytical basis for the ideas presented here come primarily from the authors' work in support of more than 20 PSA studies over the past several years. Timing effects are important for establishing success criteria for support and safety system response and for identifying the time available for operator recovery actions. The principal results of this paper are as follows: 1. Analysis of event sequence timing is necessary for meaningful probabilistic safety assessment - both the success criteria for systems performance and the probability of recovery are tightly linked to sequence timing. 2. Simple engineering analyses based on first principles are often sufficient to provide adequate resolution of the time available for recovery of PSA scenarios. Only those parameters that influence sequence timing and its variability and uncertainty need be examined. 3. Time available for recovery is the basic criterion for evaluation of human performance, whether time is an explicit parameter of the operator actions analysis or not. (author)

  7. Software for rapid time dependent ChIP-sequencing analysis (TDCA).

    Science.gov (United States)

    Myschyshyn, Mike; Farren-Dai, Marco; Chuang, Tien-Jui; Vocadlo, David

    2017-11-25

    Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) and associated methods are widely used to define the genome wide distribution of chromatin associated proteins, post-translational epigenetic marks, and modifications found on DNA bases. An area of emerging interest is to study time dependent changes in the distribution of such proteins and marks by using serial ChIP-seq experiments performed in a time resolved manner. Despite such time resolved studies becoming increasingly common, software to facilitate analysis of such data in a robust automated manner is limited. We have designed software called Time-Dependent ChIP-Sequencing Analyser (TDCA), which is the first program to automate analysis of time-dependent ChIP-seq data by fitting to sigmoidal curves. We provide users with guidance for experimental design of TDCA for modeling of time course (TC) ChIP-seq data using two simulated data sets. Furthermore, we demonstrate that this fitting strategy is widely applicable by showing that automated analysis of three previously published TC data sets accurately recapitulates key findings reported in these studies. Using each of these data sets, we highlight how biologically relevant findings can be readily obtained by exploiting TDCA to yield intuitive parameters that describe behavior at either a single locus or sets of loci. TDCA enables customizable analysis of user input aligned DNA sequencing data, coupled with graphical outputs in the form of publication-ready figures that describe behavior at either individual loci or sets of loci sharing common traits defined by the user. TDCA accepts sequencing data as standard binary alignment map (BAM) files and loci of interest in browser extensible data (BED) file format. TDCA accurately models the number of sequencing reads, or coverage, at loci from TC ChIP-seq studies or conceptually related TC sequencing experiments. TC experiments are reduced to intuitive parametric values that facilitate biologically

  8. Highly efficient and eco-friendly gold-catalyzed synthesis of homoallylic ketones

    KAUST Repository

    Gó mez-Suá rez, Adriá n; Gasperini, Danila; Vummaleti, Sai V. C.; Poater, Albert; Cavallo, Luigi; Nolan, Steven P.

    2014-01-01

    We report a new catalytic protocol for the synthesis of γ,δ-unsaturated carbonyl units from simple starting materials, allylic alcohols and alkynes, via a hydroxalkoxylation/Claisen rearrangement sequence. This new process is more efficient (higher TON and TOF) and more eco-friendly (increased mass efficiency) than the previous state-of-the-art technique. In addition, this method tolerates both terminal and internal alkynes. Moreover, computational studies have been carried out in order to shed light on how the Claisen rearrangement is initiated. © 2014 American Chemical Society.

  9. Highly efficient and eco-friendly gold-catalyzed synthesis of homoallylic ketones

    KAUST Repository

    Gómez-Suárez, Adrián

    2014-08-01

    We report a new catalytic protocol for the synthesis of γ,δ-unsaturated carbonyl units from simple starting materials, allylic alcohols and alkynes, via a hydroxalkoxylation/Claisen rearrangement sequence. This new process is more efficient (higher TON and TOF) and more eco-friendly (increased mass efficiency) than the previous state-of-the-art technique. In addition, this method tolerates both terminal and internal alkynes. Moreover, computational studies have been carried out in order to shed light on how the Claisen rearrangement is initiated. © 2014 American Chemical Society.

  10. Novel protocol for highly efficient gas-phase chemical derivatization of surface amine groups using trifluoroacetic anhydride

    Science.gov (United States)

    Duchoslav, Jiri; Kehrer, Matthias; Hinterreiter, Andreas; Duchoslav, Vojtech; Unterweger, Christoph; Fürst, Christian; Steinberger, Roland; Stifter, David

    2018-06-01

    In the current work, chemical derivatization of amine (NH2) groups with trifluoroacetic anhydride (TFAA) as an analytical method to improve the information scope of X-ray photoelectron spectroscopy (XPS) is investigated. TFAA is known to successfully label hydroxyl (OH) groups. With the introduction of a newly developed gas-phase derivatization protocol conducted at ambient pressure and using a catalyst also NH2 groups can now efficiently be labelled with a high yield and without the formation of unwanted by-products. By establishing a comprehensive and self-consistent database of reference binding energies for XPS a promising approach for distinguishing hydroxyl from amine groups is presented. The protocol was verified on different polymers, including poly(allylamine), poly(ethyleneimine), poly(vinylalcohol) and chitosan, the latter one containing both types of addressed chemical groups.

  11. Revised Mechanism and Improved Efficiency of the QuikChange Site-Directed Mutagenesis Method.

    Science.gov (United States)

    Xia, Yongzhen; Xun, Luying

    2017-01-01

    Site-directed mutagenesis has been widely used for the substitution, addition or deletion of nucleotide residues in a defined DNA sequence. QuikChange™ site-directed mutagenesis and its related protocols have been widely used for this purpose because of convenience and efficiency. We have recently demonstrated that the mechanism of the QuikChange™ site-directed mutagenesis process is different from that being proposed. The new mechanism promotes the use of partially overlapping primers and commercial PCR enzymes for efficient PCR and mutagenesis.

  12. Waiting Time Distributions for Pattern Occurrence in a Constrained Sequence

    Directory of Open Access Journals (Sweden)

    Valeri Stefanov

    2007-01-01

    Full Text Available A binary sequence of zeros and ones is called a (d,k-sequence if it does not contain runs of zeros of length either less than d or greater than k, where d and k are arbitrary, but fixed, non-negative integers and d < k. Such sequences find an abundance of applications in communications, in particular for magnetic and optical recording. Occasionally, one requires that (d,k-sequences do not contain a specific pattern w. Therefore, distribution results concerning pattern occurrence in (d,k-sequences are of interest. In this paper we study the distribution of the waiting time until the r th occurrence of a pattern w in a random (d,k-sequence generated by a Markov source. Numerical examples are also provided.

  13. Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

    Science.gov (United States)

    Xu, Chang; Nezami Ranjbar, Mohammad R; Wu, Zhong; DiCarlo, John; Wang, Yexun

    2017-01-03

    Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models. We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions. We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.

  14. High Efficiency of Two Efficient QSDC with Authentication Is at the Cost of Their Security

    International Nuclear Information System (INIS)

    Su-Juan, Qin; Qiao-Yan, Wen; Luo-Ming, Meng; Fu-Chen, Zhu

    2009-01-01

    Two efficient protocols of quantum secure direct communication with authentication [Chin. Phys. Lett. 25 (2008) 2354] were recently proposed by Liu et al. to improve the efficiency of two protocols presented in [Phys. Rev. A 75 (2007) 026301] by four Pauli operations. We show that the high efficiency of the two protocols is at the expense of their security. The authenticator Trent can reach half the secret by a particular attack strategy in the first protocol. In the second protocol, not only Trent but also an eavesdropper outside can elicit half-information about the secret from the public declaration

  15. A Pareto-Based Adaptive Variable Neighborhood Search for Biobjective Hybrid Flow Shop Scheduling Problem with Sequence-Dependent Setup Time

    Directory of Open Access Journals (Sweden)

    Huixin Tian

    2016-01-01

    Full Text Available Different from most researches focused on the single objective hybrid flowshop scheduling (HFS problem, this paper investigates a biobjective HFS problem with sequence dependent setup time. The two objectives are the minimization of total weighted tardiness and the total setup time. To efficiently solve this problem, a Pareto-based adaptive biobjective variable neighborhood search (PABOVNS is developed. In the proposed PABOVNS, a solution is denoted as a sequence of all jobs and a decoding procedure is presented to obtain the corresponding complete schedule. In addition, the proposed PABOVNS has three major features that can guarantee a good balance of exploration and exploitation. First, an adaptive selection strategy of neighborhoods is proposed to automatically select the most promising neighborhood instead of the sequential selection strategy of canonical VNS. Second, a two phase multiobjective local search based on neighborhood search and path relinking is designed for each selected neighborhood. Third, an external archive with diversity maintenance is adopted to store the nondominated solutions and at the same time provide initial solutions for the local search. Computational results based on randomly generated instances show that the PABOVNS is efficient and even superior to some other powerful multiobjective algorithms in the literature.

  16. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

    Science.gov (United States)

    Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

    2015-08-01

    RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time). Breaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. © The Author 2015. Published by Oxford University Press.

  17. Latency-Optimized and Energy-Efficient MAC Protocol for Underwater Acoustic Sensor Networks: A Cross-Layer Approach

    Directory of Open Access Journals (Sweden)

    Cheng Xiuzhen

    2010-01-01

    Full Text Available Considering the energy constraint for fixed sensor nodes and the unacceptable long propagation delay, especially for latency sensitive applications of underwater acoustic sensor networks, we propose a MAC protocol that is latency-optimized and energy-efficient scheme and combines the physical layer and the MAC layer to shorten transmission delay. On physical layer, we apply convolution coding and interleaver for transmitted information. Moreover, dynamic code rate is exploited at the receiver side to accelerate data reception rate. On MAC layer, unfixed frame length scheme is applied to reduce transmission delay, and to ensure the data successful transmission rate at the same time. Furthermore, we propose a network topology: an underwater acoustic sensor network with mobile agent. Through fully utilizing the supper capabilities on computation and mobility of autonomous underwater vehicles, the energy consumption for fixed sensor nodes can be extremely reduced, so that the lifetime of networks is extended.

  18. Cluster Based Hierarchical Routing Protocol for Wireless Sensor Network

    OpenAIRE

    Rashed, Md. Golam; Kabir, M. Hasnat; Rahim, Muhammad Sajjadur; Ullah, Shaikh Enayet

    2012-01-01

    The efficient use of energy source in a sensor node is most desirable criteria for prolong the life time of wireless sensor network. In this paper, we propose a two layer hierarchical routing protocol called Cluster Based Hierarchical Routing Protocol (CBHRP). We introduce a new concept called head-set, consists of one active cluster head and some other associate cluster heads within a cluster. The head-set members are responsible for control and management of the network. Results show that t...

  19. Denoising time-resolved microscopy image sequences with singular value thresholding

    Energy Technology Data Exchange (ETDEWEB)

    Furnival, Tom, E-mail: tjof2@cam.ac.uk; Leary, Rowan K., E-mail: rkl26@cam.ac.uk; Midgley, Paul A., E-mail: pam33@cam.ac.uk

    2017-07-15

    Time-resolved imaging in microscopy is important for the direct observation of a range of dynamic processes in both the physical and life sciences. However, the image sequences are often corrupted by noise, either as a result of high frame rates or a need to limit the radiation dose received by the sample. Here we exploit both spatial and temporal correlations using low-rank matrix recovery methods to denoise microscopy image sequences. We also make use of an unbiased risk estimator to address the issue of how much thresholding to apply in a robust and automated manner. The performance of the technique is demonstrated using simulated image sequences, as well as experimental scanning transmission electron microscopy data, where surface adatom motion and nanoparticle structural dynamics are recovered at rates of up to 32 frames per second. - Highlights: • Correlations in space and time are harnessed to denoise microscopy image sequences. • A robust estimator provides automated selection of the denoising parameter. • Motion tracking and automated noise estimation provides a versatile algorithm. • Application to time-resolved STEM enables study of atomic and nanoparticle dynamics.

  20. ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time.

    Science.gov (United States)

    Cai, Yunpeng; Zheng, Wei; Yao, Jin; Yang, Yujie; Mai, Volker; Mao, Qi; Sun, Yijun

    2017-04-01

    The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analysis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences. The algorithm achieves subquadratic time and space complexity and maintains a high clustering accuracy comparable to the standard method. The basic idea is to organize sequences into a pseudo-metric based partitioning tree for sub-linear time searching of nearest neighbors, and then use a new multiple-pair merging criterion to construct clusters in parallel using multiple threads. The new algorithm was tested on the human microbiome project (HMP) dataset, currently one of the largest published microbial 16S rRNA sequence dataset. Our experiment demonstrated that with the power of parallel computing it is now compu- tationally feasible to perform hierarchical clustering analysis of tens of millions of sequences. The software is available at http://www.acsu.buffalo.edu/∼yijunsun/lab/ESPRIT-Forest.html.

  1. Simultaneous quantitative assessment of circulating cell-free mitochondrial and nuclear DNA by multiplex real-time PCR

    Directory of Open Access Journals (Sweden)

    Peng Xia

    2009-01-01

    Full Text Available Quantification of circulating nucleic acids in plasma and serum could be used as a non-invasive diagnostic tool for monitoring a wide variety of diseases and conditions. We describe here a rapid, simple and accurate multiplex real-time PCR method for direct synchronized analysis of circulating cell-free (ccf mitochondrial (mtDNA and nuclear (nDNA DNA in plasma and serum samples. The method is based on one-step multiplex real-time PCR using a FAM-labeled MGB probe and primers to amplify the mtDNA sequence of the ATP 8 gene, and a VIC-labeled MGB probe and primers to amplify the nDNA sequence of the glycerinaldehyde-3-phosphate-dehydrogenase (GAPDH gene, in plasma and serum samples simultaneously. The efficiencies of the multiplex assays were measured in serial dilutions. Based on the simulation of the PCR reaction kinetics, the relative quantities of ccf mtDNA were calculated using a very simple equation. Using our optimised real-time PCR conditions, close to 100% efficiency was obtained from the two assays. The two assays performed in the dilution series showed very good and reproducible correlation to each other. This optimised multiplex real-time PCR protocol can be widely used for synchronized quantification of mtDNA and nDNA in different samples, with a very high rate of efficiency.

  2. A Review of Protocol Implementations and Energy Efficient Cross-Layer Design for Wireless Body Area Networks

    Directory of Open Access Journals (Sweden)

    Tao Chen

    2012-11-01

    Full Text Available The issues inherent in caring for an ever-increasing aged population has been the subject of endless debate and continues to be a hot topic for political discussion. The use of hospital-based facilities for the monitoring of chronic physiological conditions is expensive and ties up key healthcare professionals. The introduction of wireless sensor devices as part of a Wireless Body Area Network (WBAN integrated within an overall eHealth solution could bring a step change in the remote management of patient healthcare. Sensor devices small enough to be placed either inside or on the human body can form a vital part of an overall health monitoring network. An effectively designed energy efficient WBAN should have a minimal impact on the mobility and lifestyle of the patient. WBAN technology can be deployed within a hospital, care home environment or in the patient’s own home. This study is a review of the existing research in the area of WBAN technology and in particular protocol adaptation and energy efficient cross-layer design. The research reviews the work carried out across various layers of the protocol stack and highlights how the latest research proposes to resolve the various challenges inherent in remote continual healthcare monitoring.

  3. Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

    Science.gov (United States)

    Mackey, Aaron J; Pearson, William R

    2004-10-01

    Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

  4. Towards designing energy-efficient routing protocol for wireless mesh networks

    CSIR Research Space (South Africa)

    Dludla, AG

    2009-08-01

    Full Text Available Different studies have proposed number of routing protocols to overcome data transmission challenges. Very few of these protocols consider node energy. In this study, the state of art work from various studies is reviewed and compared based...

  5. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

    Science.gov (United States)

    Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

    2015-01-01

    Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O(n6). Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity (≥ quartic time). Results: Breaking this barrier, we introduce the novel Sankoff-style algorithm ‘sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)’, which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff’s original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics. Availability and implementation: SPARSE is freely available at http://www.bioinf.uni-freiburg.de/Software/SPARSE. Contact: backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25838465

  6. Efficient theory of dipolar recoupling in solid-state nuclear magnetic resonance of rotating solids using Floquet-Magnus expansion: application on BABA and C7 radiofrequency pulse sequences.

    Science.gov (United States)

    Mananga, Eugene S; Reid, Alicia E; Charpentier, Thibault

    2012-02-01

    This article describes the use of an alternative expansion scheme called Floquet-Magnus expansion (FME) to study the dynamics of spin system in solid-state NMR. The main tool used to describe the effect of time-dependent interactions in NMR is the average Hamiltonian theory (AHT). However, some NMR experiments, such as sample rotation and pulse crafting, seem to be more conveniently described using the Floquet theory (FT). Here, we present the first report highlighting the basics of the Floquet-Magnus expansion (FME) scheme and hint at its application on recoupling sequences that excite more efficiently double-quantum coherences, namely BABA and C7 radiofrequency pulse sequences. The use of Λ(n)(t) functions available only in the FME scheme, allows the comparison of the efficiency of BABA and C7 sequences. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. An Authentication Protocol for Future Sensor Networks.

    Science.gov (United States)

    Bilal, Muhammad; Kang, Shin-Gak

    2017-04-28

    Authentication is one of the essential security services in Wireless Sensor Networks (WSNs) for ensuring secure data sessions. Sensor node authentication ensures the confidentiality and validity of data collected by the sensor node, whereas user authentication guarantees that only legitimate users can access the sensor data. In a mobile WSN, sensor and user nodes move across the network and exchange data with multiple nodes, thus experiencing the authentication process multiple times. The integration of WSNs with Internet of Things (IoT) brings forth a new kind of WSN architecture along with stricter security requirements; for instance, a sensor node or a user node may need to establish multiple concurrent secure data sessions. With concurrent data sessions, the frequency of the re-authentication process increases in proportion to the number of concurrent connections. Moreover, to establish multiple data sessions, it is essential that a protocol participant have the capability of running multiple instances of the protocol run, which makes the security issue even more challenging. The currently available authentication protocols were designed for the autonomous WSN and do not account for the above requirements. Hence, ensuring a lightweight and efficient authentication protocol has become more crucial. In this paper, we present a novel, lightweight and efficient key exchange and authentication protocol suite called the Secure Mobile Sensor Network (SMSN) Authentication Protocol. In the SMSN a mobile node goes through an initial authentication procedure and receives a re-authentication ticket from the base station. Later a mobile node can use this re-authentication ticket when establishing multiple data exchange sessions and/or when moving across the network. This scheme reduces the communication and computational complexity of the authentication process. We proved the strength of our protocol with rigorous security analysis (including formal analysis using the BAN

  8. Sequencing the real time of the elderly: Evidence from South Africa

    Directory of Open Access Journals (Sweden)

    Erofili Grapsa

    2016-09-01

    Full Text Available Background: Understanding how the elderly in developing countries spend their time has received little attention. Moreover, the potential of time use data to discern variation in activity patterns has not been fully realized by methods which use a mean added time approach. Objective: To uncover patterns of time use among the elderly (60 years and older in South Africa by applying an innovative methodology that incorporates the timing, duration, and frequency of activities in the analysis. Methods: We use sequence analysis, which treats the daily series of activities of each individual as a sequence, and cluster analysis, to group these sequences into common clusters of time use behaviour. We then estimate multinomial logit regressions to identify the characteristics of the elderly which predict cluster membership. Results: We find that the time use behaviour of the elderly in South Africa can be divided into five distinct clusters, according to the relative importance in their day of personal care, household maintenance, work, mass media, and social or cultural activities. In comparison to men, women are overrepresented in the cluster where household work dominates, while they are underrepresented in the cluster of the elderly who engage in production work. A range of other individual and household characteristics are also important in predicting cluster membership. Contribution: Sequence and cluster analysis permit a nuanced examination of the differences and commonalities in time use patterns among the elderly in South Africa. There is considerable potential to extend these methods to other studies of time use behaviour.

  9. The PiGeOn project: protocol of a longitudinal study examining psychosocial and ethical issues and outcomes in germline genomic sequencing for cancer.

    Science.gov (United States)

    Best, Megan; Newson, Ainsley J; Meiser, Bettina; Juraskova, Ilona; Goldstein, David; Tucker, Kathy; Ballinger, Mandy L; Hess, Dominique; Schlub, Timothy E; Biesecker, Barbara; Vines, Richard; Vines, Kate; Thomas, David; Young, Mary-Anne; Savard, Jacqueline; Jacobs, Chris; Butow, Phyllis

    2018-04-23

    Advances in genomics offer promise for earlier detection or prevention of cancer, by personalisation of medical care tailored to an individual's genomic risk status. However genome sequencing can generate an unprecedented volume of results for the patient to process with potential implications for their families and reproductive choices. This paper describes a protocol for a study (PiGeOn) that aims to explore how patients and their blood relatives experience germline genomic sequencing, to help guide the appropriate future implementation of genome sequencing into routine clinical practice. We have designed a mixed-methods, prospective, cohort sub-study of a germline genomic sequencing study that targets adults with cancer suggestive of a genetic aetiology. One thousand probands and 2000 of their blood relatives will undergo germline genomic sequencing as part of the parent study in Sydney, Australia between 2016 and 2020. Test results are expected within12-15 months of recruitment. For the PiGeOn sub-study, participants will be invited to complete surveys at baseline, three months and twelve months after baseline using self-administered questionnaires, to assess the experience of long waits for results (despite being informed that results may not be returned) and expectations of receiving them. Subsets of both probands and blood relatives will be purposively sampled and invited to participate in three semi-structured qualitative interviews (at baseline and each follow-up) to triangulate the data. Ethical themes identified in the data will be used to inform critical revisions of normative ethical concepts or frameworks. This will be one of the first studies internationally to follow the psychosocial impact on probands and their blood relatives who undergo germline genome sequencing, over time. Study results will inform ongoing ethical debates on issues such as informed consent for genomic sequencing, and informing participants and their relatives of specific

  10. Time Separation Between Events in a Sequence: a Regional Property?

    Science.gov (United States)

    Muirwood, R.; Fitzenz, D. D.

    2013-12-01

    Earthquake sequences are loosely defined as events occurring too closely in time and space to appear unrelated. Depending on the declustering method, several, all, or no event(s) after the first large event might be recognized as independent mainshocks. It can therefore be argued that a probabilistic seismic hazard assessment (PSHA, traditionally dealing with mainshocks only) might already include the ground shaking effects of such sequences. Alternatively all but the largest event could be classified as an ';aftershock' and removed from the earthquake catalog. While in PSHA the question is only whether to keep or remove the events from the catalog, for Risk Management purposes, the community response to the earthquakes, as well as insurance risk transfer mechanisms, can be profoundly affected by the actual timing of events in such a sequence. In particular the repetition of damaging earthquakes over a period of weeks to months can lead to businesses closing and families evacuating from the region (as happened in Christchurch, New Zealand in 2011). Buildings that are damaged in the first earthquake may go on to be damaged again, even while they are being repaired. Insurance also functions around a set of critical timeframes - including the definition of a single 'event loss' for reinsurance recoveries within the 192 hour ';hours clause', the 6-18 month pace at which insurance claims are settled, and the annual renewal of insurance and reinsurance contracts. We show how temporal aspects of earthquake sequences need to be taken into account within models for Risk Management, and what time separation between events are most sensitive, both in terms of the modeled disruptions to lifelines and business activity as well as in the losses to different parties (such as insureds, insurers and reinsurers). We also explore the time separation between all events and between loss causing events for a collection of sequences from across the world and we point to the need to

  11. Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol.

    Science.gov (United States)

    Sun, Bing; Shen, Feng; McCalla, Stephanie E; Kreutz, Jason E; Karymov, Mikhail A; Ismagilov, Rustem F

    2013-02-05

    Here we used a SlipChip microfluidic device to evaluate the performance of digital reverse transcription-loop-mediated isothermal amplification (dRT-LAMP) for quantification of HIV viral RNA. Tests are needed for monitoring HIV viral load to control the emergence of drug resistance and to diagnose acute HIV infections. In resource-limited settings, in vitro measurement of HIV viral load in a simple format is especially needed, and single-molecule counting using a digital format could provide a potential solution. We showed here that when one-step dRT-LAMP is used for quantification of HIV RNA, the digital count is lower than expected and is limited by the yield of desired cDNA. We were able to overcome the limitations by developing a microfluidic protocol to manipulate many single molecules in parallel through a two-step digital process. In the first step we compartmentalize the individual RNA molecules (based on Poisson statistics) and perform reverse transcription on each RNA molecule independently to produce DNA. In the second step, we perform the LAMP amplification on all individual DNA molecules in parallel. Using this new protocol, we increased the absolute efficiency (the ratio between the concentration calculated from the actual count and the expected concentration) of dRT-LAMP 10-fold, from ∼2% to ∼23%, by (i) using a more efficient reverse transcriptase, (ii) introducing RNase H to break up the DNA:RNA hybrid, and (iii) adding only the BIP primer during the RT step. We also used this two-step method to quantify HIV RNA purified from four patient samples and found that in some cases, the quantification results were highly sensitive to the sequence of the patient's HIV RNA. We learned the following three lessons from this work: (i) digital amplification technologies, including dLAMP and dPCR, may give adequate dilution curves and yet have low efficiency, thereby providing quantification values that underestimate the true concentration. Careful

  12. Sequencing of Isotope-Labeled Small RNA Using Femtosecond Laser Ablation Time-of-Flight Mass Spectrometry

    Science.gov (United States)

    Kurata-Nishimura, Mizuki; Ando, Yoshinari; Kobayashi, Tohru; Matsuo, Yukari; Suzuki, Harukazu; Hayashizaki, Yoshihide; Kawai, Jun

    2010-04-01

    A novel method for the analysis of sequences of small RNAs using nucleotide triphosphates labeled with stable isotopes has been developed using time-of-flight mass spectroscopy combined with femtosecond laser ablation (fsLA-TOF-MS). Small RNAs synthesized with nucleotides enriched in 13C and 15N were efficiently atomized and ionized by single-shot fsLA and the isotope ratios 13C/12C and 15N/14N were evaluated using the TOF-MS method. By comparing the isotope ratios among four different configurations, the number of nucleotide contents of the control RNA sample were successfully reproduced.

  13. Using SQL Databases for Sequence Similarity Searching and Analysis.

    Science.gov (United States)

    Pearson, William R; Mackey, Aaron J

    2017-09-13

    Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  14. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

  15. Alcohol handrubbing and chlorhexidine handwashing protocols for routine hospital practice: A randomized clinical trial of protocol efficacy and time effectiveness

    NARCIS (Netherlands)

    Chow, Angela; Arah, Onyebuchi A.; Chan, Siew-Pang; Poh, Bee-Fong; Krishnan, Prabha; Ng, Woei-Kian; Choudhury, Saugata; Chan, Joey; Ang, Brenda

    2012-01-01

    Background: The World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) recommend the use of alcohol handrubs to prevent health care-associated infections. However, the efficacy and time effectiveness of different alcohol handrubbing protocols have yet to be

  16. Disinfection Contact Time study plan (100-N Area tracer protocol). Revision 1

    International Nuclear Information System (INIS)

    Kretzschmar, S.P.; Bedi, G.S.; Martinez, P.; Ervin, K.

    1996-07-01

    Bechtel Hanford, Inc. will prepare an Engineering Tracer Study Protocol for the determination of contact time for the disinfection process at Group A Non-transient Non-community water treatment plant for the 100-N Water Plant at the Hanford Site in Richland, Washington. Included in this report are the results of a study that determine the actual detention time within the plant clearwell, and thus the disinfection contact time at several clearwell effluent flow rates

  17. A time warping approach to multiple sequence alignment.

    Science.gov (United States)

    Arribas-Gil, Ana; Matias, Catherine

    2017-04-25

    We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise alignments of all the sequences (viewed as paths in a certain space), we construct a median path that represents the MSA we are looking for. We establish a proof of concept that our method could be an interesting ingredient to include into refined MSA techniques. We present a simple synthetic experiment as well as the study of a benchmark dataset, together with comparisons with 2 widely used MSA softwares.

  18. A rapid and efficient DNA extraction protocol from fresh and frozen human blood samples.

    Science.gov (United States)

    Guha, Pokhraj; Das, Avishek; Dutta, Somit; Chaudhuri, Tapas Kumar

    2018-01-01

    Different methods available for extraction of human genomic DNA suffer from one or more drawbacks including low yield, compromised quality, cost, time consumption, use of toxic organic solvents, and many more. Herein, we aimed to develop a method to extract DNA from 500 μL of fresh or frozen human blood. Five hundred microliters of fresh and frozen human blood samples were used for standardization of the extraction procedure. Absorbance at 260 and 280 nm, respectively, (A 260 /A 280 ) were estimated to check the quality and quantity of the extracted DNA sample. Qualitative assessment of the extracted DNA was checked by Polymerase Chain reaction and double digestion of the DNA sample. Our protocol resulted in average yield of 22±2.97 μg and 20.5±3.97 μg from 500 μL of fresh and frozen blood, respectively, which were comparable to many reference protocols and kits. Besides yielding bulk amount of DNA, our protocol is rapid, economical, and avoids toxic organic solvents such as Phenol. Due to unaffected quality, the DNA is suitable for downstream applications. The protocol may also be useful for pursuing basic molecular researches in laboratories having limited funds. © 2017 Wiley Periodicals, Inc.

  19. Development of an efficient regeneration protocol for three genotypes of brassica juncea

    International Nuclear Information System (INIS)

    Bano, R.; Khan, M.H.; Rashid, H.

    2010-01-01

    Two phytohormones, auxins (Naphthalene acetic acid and Indole acetic acid) and cytokinins (Benzyl aminopurine and Kinetin) with concentrations were used to develop an efficient regeneration protocol for 3 genotypes of Brassica juncea (UCD-635, RL-18 and NIFA RAYE). The explants were cultured on MS-medium supplemented with BAP 1.0 mgL/sup -1//NAA 0.1 mgL-1, BAP 2.0 mg L/sup -1//NAA 0.2 mg L/sup -1/, BAP 3.0 mgL/sup -1/ NAA 0.3 mg L-1 and Kinetin 1.0 mg L/sup -1/ IAA 0.1 mg L/sup -1/, Kinetin 2.0 mg L/sup -1//IAA 0.2 mg L/sup -1/, Kinetin 3.0mg L-1/IAA 0.3 mg L/sup -1/. Maximum callus production (65.55) was observed on MS medium containing with BAP 2.0 mgL-1/NAA 0.2 mg L/sup -1/. Maximum shooting (22.31) was observed BAP 3.0 mg L/sup -1//NAA 0.3 mg L/sup -1/ and KIN 3.0 mg L-1/IAA 0.3 mg L/sup -1/. Regeneration efficiency was found maximum (7.13) with BAP 3.0 mg L/sup -1//NAA 0.3 mg L/sup -1/. The three genotypes were found significantly different at p greater or equal to 0.05 in shoots production and regeneration efficiency. (author)

  20. BTP: a Block Transfer Protocol for Delay Tolerant Wireless Sensor Networks

    DEFF Research Database (Denmark)

    Hansen, Morten Tranberg; Biagioni, Edoardo S.

    2010-01-01

    Wireless sensor networks that are energy-constrained must transmit and receive data as efficiently as possible.  If the transmission is delay tolerant, transferring blocks of accumulated data can be more efficient than transferring each sensed measurement as soon as it is available.  This paper...... proposes a Block Transfer Protocol (BTP) designed for efficient and reliable transmission in wireless sensor networks.  BTP reduces the time it takes to reliably transfer a block of packets compared to conventional link layer protocols, by piggybacking in data packets information about the transfer......, minimizing the number of acknowledgements needed for reliable transmission, and reducing the need for timeouts, which can substantially slow down communication when transmission is unreliable.  In addition, BTP improves reliability by handling false positive acknowledgements and by letting the receivers...

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

    Science.gov (United States)

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

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

  2. Real-time SPARSE-SENSE cardiac cine MR imaging: optimization of image reconstruction and sequence validation.

    Science.gov (United States)

    Goebel, Juliane; Nensa, Felix; Bomas, Bettina; Schemuth, Haemi P; Maderwald, Stefan; Gratz, Marcel; Quick, Harald H; Schlosser, Thomas; Nassenstein, Kai

    2016-12-01

    Improved real-time cardiac magnetic resonance (CMR) sequences have currently been introduced, but so far only limited practical experience exists. This study aimed at image reconstruction optimization and clinical validation of a new highly accelerated real-time cine SPARSE-SENSE sequence. Left ventricular (LV) short-axis stacks of a real-time free-breathing SPARSE-SENSE sequence with high spatiotemporal resolution and of a standard segmented cine SSFP sequence were acquired at 1.5 T in 11 volunteers and 15 patients. To determine the optimal iterations, all volunteers' SPARSE-SENSE images were reconstructed using 10-200 iterations, and contrast ratios, image entropies, and reconstruction times were assessed. Subsequently, the patients' SPARSE-SENSE images were reconstructed with the clinically optimal iterations. LV volumetric values were evaluated and compared between both sequences. Sufficient image quality and acceptable reconstruction times were achieved when using 80 iterations. Bland-Altman plots and Passing-Bablok regression showed good agreement for all volumetric parameters. 80 iterations are recommended for iterative SPARSE-SENSE image reconstruction in clinical routine. Real-time cine SPARSE-SENSE yielded comparable volumetric results as the current standard SSFP sequence. Due to its intrinsic low image acquisition times, real-time cine SPARSE-SENSE imaging with iterative image reconstruction seems to be an attractive alternative for LV function analysis. • A highly accelerated real-time CMR sequence using SPARSE-SENSE was evaluated. • SPARSE-SENSE allows free breathing in real-time cardiac cine imaging. • For clinically optimal SPARSE-SENSE image reconstruction, 80 iterations are recommended. • Real-time SPARSE-SENSE imaging yielded comparable volumetric results as the reference SSFP sequence. • The fast SPARSE-SENSE sequence is an attractive alternative to standard SSFP sequences.

  3. A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia.

    Science.gov (United States)

    Dan, Tong; Liu, Wenjun; Sun, Zhihong; Lv, Qiang; Xu, Haiyan; Song, Yuqin; Zhang, Heping

    2014-06-09

    Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China. Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates. Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.

  4. Mac protocols for wireless sensor network (wsn): a comparative study

    International Nuclear Information System (INIS)

    Arshad, J.; Akram, Q.; Saleem, Y.

    2014-01-01

    Data communication between nodes is carried out under Medium Access Control (MAC) protocol which is defined at data link layer. The MAC protocols are responsible to communicate and coordinate between nodes according to the defined standards in WSN (Wireless Sensor Networks). The design of a MAC protocol should also address the issues of energy efficiency and transmission efficiency. There are number of MAC protocols that exist in the literature proposed for WSN. In this paper, nine MAC protocols which includes S-MAC, T-MAC, Wise-MAC, Mu-MAC, Z-MAC, A-MAC, D-MAC, B-MAC and B-MAC+ for WSN have been explored, studied and analyzed. These nine protocols are classified in contention based and hybrid (combination of contention and schedule based) MAC protocols. The goal of this comparative study is to provide a basis for MAC protocols and to highlight different mechanisms used with respect to parameters for the evaluation of energy and transmission efficiency in WSN. This study also aims to give reader a better understanding of the concepts, processes and flow of information used in these MAC protocols for WSN. A comparison with respect to energy reservation scheme, idle listening avoidance, latency, fairness, data synchronization, and throughput maximization has been presented. It was analyzed that contention based MAC protocols are less energy efficient as compared to hybrid MAC protocols. From the analysis of contention based MAC protocols in term of energy consumption, it was being observed that protocols based on preamble sampling consume lesser energy than protocols based on static or dynamic sleep schedule. (author)

  5. Energy-Efficient Boarder Node Medium Access Control Protocol for Wireless Sensor Networks

    OpenAIRE

    Razaque, Abdul; Elleithy, Khaled M.

    2014-01-01

    This paper introduces the design, implementation, and performance analysis of the scalable and mobility-aware hybrid protocol named boarder node medium access control (BN-MAC) for wireless sensor networks (WSNs), which leverages the characteristics of scheduled and contention-based MAC protocols. Like contention-based MAC protocols, BN-MAC achieves high channel utilization, network adaptability under heavy traffic and mobility, and low latency and overhead. Like schedule-based MAC protocols,...

  6. A reliable, delay bounded and less complex communication protocol for multicluster FANETs

    Directory of Open Access Journals (Sweden)

    Wajiya Zafar

    2017-02-01

    Full Text Available Recently, Flying Ad-hoc Networks (FANETs, enabling ad-hoc networking between Unmanned Aerial Vehicles (UAVs is gaining importance in several military and civilian applications. The sensitivity of the applications requires adaptive; efficient; delay bounded and scalable communication network among UAVs for data transmission. Due to communication protocol complexity; rigidity; cost of commercial-off-the-shelf (COT components; limited radio bandwidth; high mobility and computational resources; maintaining the desired level of Quality of Service (QoS becomes a daunting task. For the first time in this research we propose multicluster FANETs for efficient network management; the proposed scheme considerably reduces communication cost and optimizes network performance as well as exploit low power; less complex and low cost IEEE 802.15.4 (MAC protocol for intercluster and intracluster communication. In this research both beacon enabled mode and beaconless modes have been investigated with Guaranteed Time Slots (GTS and virtual Time Division Multiple Access (TDMA respectively. The methodology plays a key role towards reserving bandwidth for latency critical applications; eliminate collisions and medium access delays. Moreover analysis ad-hoc routing protocols including two proactive (OLSR, DSDV and one reactive (AODV is also presented. The results shows that the proposed scheme guarantees high packet delivery ratios while maintaining acceptable levels of latency requirements comparable with more complex and dedicatedly designed protocols in literature.

  7. Power-Efficient Communication Protocol for Integrated WWAN and WLAN

    Directory of Open Access Journals (Sweden)

    Golmie Nada

    2008-01-01

    Full Text Available Abstract One of the most impending requirements to support a seamless communication environment in heterogeneous wireless networks comes from the limited power supply of small-size and low-cost mobile terminals as in stand-alone WLANs or cellular networks. Thus, it is a challenge to design new techniques so that mobile terminals are able to not only maintain their active connection as they move across different types of wireless networks, but also minimize their power consumption. There have been several efforts aimed at having mobile devices equipped with multiple interfaces connect optimally to the access network that minimizes their power consumption. However, a study of existing schemes for WLAN notes that in the idle state, a device with both a WLAN and a WWAN interface needs to keep both interfaces on in order to receive periodic beacon messages from the access point (AP: WLAN and downlink control information from the base station (WWAN, resulting in significant power consumption. Therefore, in this paper, we propose a power-efficient communication protocol (PCP that includes turning off the WLAN interface after it enters the idle state and using the paging channel of WWAN in order to wake up the WLAN interface when there is incoming long-lived multimedia data. This scheme is known to limit the power consumption, while at the same time, it makes use of the paging channel in cellular networks. Further, our proposed scheme is designed to avoid repeatedly turning on and off WLAN interfaces, that consumes a significant amount of power. We propose turning on the WLAN interface when the number of packets in the radio network controller (RNC's buffer reaches a certain threshold level. The tradeoffs between the power saving and the number of packets dropped at the buffer are investigated analytically through the study of an on/off traffic model. Simulation results for scenarios of interest are also provided.

  8. Power-Efficient Communication Protocol for Integrated WWAN and WLAN

    Directory of Open Access Journals (Sweden)

    SuKyoung Lee

    2008-01-01

    Full Text Available One of the most impending requirements to support a seamless communication environment in heterogeneous wireless networks comes from the limited power supply of small-size and low-cost mobile terminals as in stand-alone WLANs or cellular networks. Thus, it is a challenge to design new techniques so that mobile terminals are able to not only maintain their active connection as they move across different types of wireless networks, but also minimize their power consumption. There have been several efforts aimed at having mobile devices equipped with multiple interfaces connect optimally to the access network that minimizes their power consumption. However, a study of existing schemes for WLAN notes that in the idle state, a device with both a WLAN and a WWAN interface needs to keep both interfaces on in order to receive periodic beacon messages from the access point (AP: WLAN and downlink control information from the base station (WWAN, resulting in significant power consumption. Therefore, in this paper, we propose a power-efficient communication protocol (PCP that includes turning off the WLAN interface after it enters the idle state and using the paging channel of WWAN in order to wake up the WLAN interface when there is incoming long-lived multimedia data. This scheme is known to limit the power consumption, while at the same time, it makes use of the paging channel in cellular networks. Further, our proposed scheme is designed to avoid repeatedly turning on and off WLAN interfaces, that consumes a significant amount of power. We propose turning on the WLAN interface when the number of packets in the radio network controller (RNC's buffer reaches a certain threshold level. The tradeoffs between the power saving and the number of packets dropped at the buffer are investigated analytically through the study of an on/off traffic model. Simulation results for scenarios of interest are also provided.

  9. Efficient Server-Aided 2PC for Mobile Phones

    Directory of Open Access Journals (Sweden)

    Mohassel Payman

    2016-04-01

    Full Text Available Secure Two-Party Computation (2PC protocols allow two parties to compute a function of their private inputs without revealing any information besides the output of the computation. There exist low cost general-purpose protocols for semi-honest parties that can be efficiently executed even on smartphones. However, for the case of malicious parties, current 2PC protocols are significantly less efficient, limiting their use to more resourceful devices. In this work we present an efficient 2PC protocol that is secure against malicious parties and is light enough to be used on mobile phones. The protocol is an adaptation of the protocol of Nielsen et al. (Crypto, 2012 to the Server-Aided setting, a natural relaxation of the plain model for secure computation that allows the parties to interact with a server (e.g., a cloud who is assumed not to collude with any of the parties. Our protocol has two stages: In an offline stage - where no party knows which function is to be computed, nor who else is participating - each party interacts with the server and downloads a file. Later, in the online stage, when two parties decide to execute a 2PC together, they can use the files they have downloaded earlier to execute the computation with cost that is lower than the currently best semi-honest 2PC protocols. We show an implementation of our protocol for Android mobile phones, discuss several optimizations and report on its evaluation for various circuits. For example, the online stage for evaluating a single AES circuit requires only 2.5 seconds and can be further reduced to 1 second (amortized time with multiple executions.

  10. The Generation of Human Induced Pluripotent Stem Cells from Blood Cells: An Efficient Protocol Using Serial Plating of Reprogrammed Cells by Centrifugation

    OpenAIRE

    Youngkyun Kim; Yeri Alice Rim; Hyoju Yi; Narae Park; Sung-Hwan Park; Ji Hyeon Ju

    2016-01-01

    Human induced pluripotent stem cells (hiPSCs) have demonstrated great potential for differentiation into diverse tissues. We report a straightforward and highly efficient method for the generation of iPSCs from PBMCs. By plating the cells serially to a newly coated plate by centrifugation, this protocol provides multiple healthy iPSC colonies even from a small number of PBMCs. The generated iPSCs expressed pluripotent markers and differentiated into all three germ layer lineages. The protocol...

  11. CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones.

    Science.gov (United States)

    Veeranagouda, Yaligara; Debono-Lagneaux, Delphine; Fournet, Hamida; Thill, Gilbert; Didier, Michel

    2018-01-16

    The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

  12. Cryptanalysis of quantum broadcast communication and authentication protocol with a one-time pad

    International Nuclear Information System (INIS)

    Cao Ya; Gao Fei

    2016-01-01

    Chang et al . [ Chin. Phys. B 23 010305 (2014)] have proposed a quantum broadcast communication and authentication protocol. However, we find that an intercept-resend attack can be preformed successfully by a potential eavesdropper, who will be able to destroy the authentication function. Afterwards, he or she can acquire the secret transmitted message or even modify it while escaping detection, by implementing an efficient man-in-the-middle attack. Furthermore, we show a simple scheme to defend this attack, that is, applying non-reusable identity strings. (paper)

  13. Privacy-Preserving Meter Report Protocol of Isolated Smart Grid Devices

    Directory of Open Access Journals (Sweden)

    Zhiwei Wang

    2017-01-01

    Full Text Available Smart grid aims to improve the reliability, efficiency, and security of the traditional grid, which allows two-way transmission and efficiency-driven response. However, a main concern of this new technique is that the fine-grained metering data may leak the personal privacy information of the customers. Thus, the data aggregation mechanism for privacy protection is required for the meter report protocol in smart grid. In this paper, we propose an efficient privacy-preserving meter report protocol for the isolated smart grid devices. Our protocol consists of an encryption scheme with additively homomorphic property and a linearly homomorphic signature scheme, where the linearly homomorphic signature scheme is suitable for privacy-preserving data aggregation. We also provide security analysis of our protocol in the context of some typical attacks in smart grid. The implementation of our protocol on the Intel Edison platform shows that our protocol is efficient enough for the physical constrained devices, like smart meters.

  14. Symmetric cryptographic protocols

    CERN Document Server

    Ramkumar, Mahalingam

    2014-01-01

    This book focuses on protocols and constructions that make good use of symmetric pseudo random functions (PRF) like block ciphers and hash functions - the building blocks for symmetric cryptography. Readers will benefit from detailed discussion of several strategies for utilizing symmetric PRFs. Coverage includes various key distribution strategies for unicast, broadcast and multicast security, and strategies for constructing efficient digests of dynamic databases using binary hash trees.   •        Provides detailed coverage of symmetric key protocols •        Describes various applications of symmetric building blocks •        Includes strategies for constructing compact and efficient digests of dynamic databases

  15. An enhanced method for sequence walking and paralog mining: TOPO® Vector-Ligation PCR

    Directory of Open Access Journals (Sweden)

    Davis Thomas M

    2010-03-01

    Full Text Available Abstract Background Although technological advances allow for the economical acquisition of whole genome sequences, many organisms' genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO® Vector-Ligation PCR (or TVL-PCR that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining. Findings TVL-PCR exploits the ligation efficiency of the pCR®4-TOPO® (Invitrogen, Carlsbad, California vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3' adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes. Conclusions TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.

  16. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    Science.gov (United States)

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  17. Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability

    Directory of Open Access Journals (Sweden)

    Ranbir Singh Fougat

    2014-06-01

    Full Text Available Isabgol (Plantago ovata Forsk. is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™ to obtain simple sequence repeats (SSRs for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata.

  18. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  19. Field-based species identification in eukaryotes using real-time nanopore sequencing.

    OpenAIRE

    Papadopulos, Alexander; Devey, Dion; Helmstetter, Andrew; Parker, Joe

    2017-01-01

    Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored. Recently, portable, real-time, nanopore sequencing (RTnS) has become available. This offers opportunities to rapidly collect and analyse genomic data anywhere. However, the generation of datasets from large, complex genomes has been constrained to laboratories. The portability and long DNA sequences of RTnS offer great potenti...

  20. An Efficient Explicit-time Description Method for Timed Model Checking

    Directory of Open Access Journals (Sweden)

    Hao Wang

    2009-12-01

    Full Text Available Timed model checking, the method to formally verify real-time systems, is attracting increasing attention from both the model checking community and the real-time community. Explicit-time description methods verify real-time systems using general model constructs found in standard un-timed model checkers. Lamport proposed an explicit-time description method using a clock-ticking process (Tick to simulate the passage of time together with a group of global variables to model time requirements. Two methods, the Sync-based Explicit-time Description Method using rendezvous synchronization steps and the Semaphore-based Explicit-time Description Method using only one global variable were proposed; they both achieve better modularity than Lamport's method in modeling the real-time systems. In contrast to timed automata based model checkers like UPPAAL, explicit-time description methods can access and store the current time instant for future calculations necessary for many real-time systems, especially those with pre-emptive scheduling. However, the Tick process in the above three methods increments the time by one unit in each tick; the state spaces therefore grow relatively fast as the time parameters increase, a problem when the system's time period is relatively long. In this paper, we propose a more efficient method which enables the Tick process to leap multiple time units in one tick. Preliminary experimental results in a high performance computing environment show that this new method significantly reduces the state space and improves both the time and memory efficiency.

  1. Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens.

    Directory of Open Access Journals (Sweden)

    Linxiang Chen

    Full Text Available Conventional Sanger sequencing remains time-consuming and laborious. In this study, we developed a rapid improved sequencing protocol of 16S rRNA for pathogens identification by using a new combination of SYBR Green I real-time PCR and Sanger sequencing with FTA® cards. To compare the sequencing quality of this method with conventional Sanger sequencing, 12 strains, including three kinds of strains (1 reference strain and 3 clinical strains, which were previously identified by biochemical tests, which have 4 Pseudomonas aeruginosa, 4 Staphyloccocus aureus and 4 Escherichia coli, were targeted. Additionally, to validate the sequencing results and bacteria identification, expanded specimens with 90 clinical strains, also comprised of the three kinds of strains which included 30 samples respectively, were performed as just described. The results showed that although statistical differences (P<0.05 were found in sequencing quality between the two methods, their identification results were all correct and consistent. The workload, the time consumption and the cost per batch were respectively light versus heavy, 8 h versus 11 h and $420 versus $400. In the 90 clinical strains, all of the Pseudomonas aeruginosa and Staphyloccocus aureus strains were correctly identified, but only 26.7% of the Escherichia coli strains were recognized as Escherichia coli, while 33.3% as Shigella sonnei and 40% as Shigella dysenteriae. The protocol described here is a rapid, reliable, stable and convenient method for 16S rRNA sequencing, and can be used for Pseudomonas aeruginosa and Staphyloccocus aureus identification, yet it is not completely suitable for discriminating Escherichia coli and Shigella strains.

  2. A Lightweight Medium Access Protocol (LMAC) for Wireless Sensor Networks: Reducing Preamble Transmissions and Transceiver State Switches

    NARCIS (Netherlands)

    van Hoesel, L.F.W.; Havinga, Paul J.M.

    2004-01-01

    In this paper, we present an energy-efficient medium access protocol designed for wireless sensor networks. Although the protocol uses TDMA to give nodes in the WSN the opportunity to communicate collision-free, the network is self-organizing in terms of time slot assignment and synchronization. The

  3. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens.

    Science.gov (United States)

    Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J; Rohan, Thomas; Ben-Dov, Iddo Z

    2017-03-14

    Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.

  4. Ant System-Corner Insertion Sequence: An Efficient VLSI Hard Module Placer

    Directory of Open Access Journals (Sweden)

    HOO, C.-S.

    2013-02-01

    Full Text Available Placement is important in VLSI physical design as it determines the time-to-market and chip's reliability. In this paper, a new floorplan representation which couples with Ant System, namely Corner Insertion Sequence (CIS is proposed. Though CIS's search complexity is smaller than the state-of-the-art representation Corner Sequence (CS, CIS adopts a preset boundary on the placement and hence, leading to search bound similar to CS. This enables the previous unutilized corner edges to become viable. Also, the redundancy of CS representation is eliminated in CIS leads to a lower search complexity of CIS. Experimental results on Microelectronics Center of North Carolina (MCNC hard block benchmark circuits show that the proposed algorithm performs comparably in terms of area yet at least two times faster than CS.

  5. Microplastics in seafood: Benchmark protocol for their extraction and characterization.

    Science.gov (United States)

    Dehaut, Alexandre; Cassone, Anne-Laure; Frère, Laura; Hermabessiere, Ludovic; Himber, Charlotte; Rinnert, Emmanuel; Rivière, Gilles; Lambert, Christophe; Soudant, Philippe; Huvet, Arnaud; Duflos, Guillaume; Paul-Pont, Ika

    2016-08-01

    Pollution of the oceans by microplastics (studies have investigated the level of contamination of marine organisms collected in situ. For extraction and characterization of microplastics in biological samples, the crucial step is the identification of solvent(s) or chemical(s) that efficiently dissolve organic matter without degrading plastic polymers for their identification in a time and cost effective way. Most published papers, as well as OSPAR recommendations for the development of a common monitoring protocol for plastic particles in fish and shellfish at the European level, use protocols containing nitric acid to digest the biological tissues, despite reports of polyamide degradation with this chemical. In the present study, six existing approaches were tested and their effects were compared on up to 15 different plastic polymers, as well as their efficiency in digesting biological matrices. Plastic integrity was evaluated through microscopic inspection, weighing, pyrolysis coupled with gas chromatography and mass spectrometry, and Raman spectrometry before and after digestion. Tissues from mussels, crabs and fish were digested before being filtered on glass fibre filters. Digestion efficiency was evaluated through microscopical inspection of the filters and determination of the relative removal of organic matter content after digestion. Five out of the six tested protocols led to significant degradation of plastic particles and/or insufficient tissue digestion. The protocol using a KOH 10% solution and incubation at 60 °C during a 24 h period led to an efficient digestion of biological tissues with no significant degradation on all tested polymers, except for cellulose acetate. This protocol appeared to be the best compromise for extraction and later identification of microplastics in biological samples and should be implemented in further monitoring studies to ensure relevance and comparison of environmental and seafood product quality studies

  6. On using multiple routing metrics with destination sequenced distance vector protocol for MultiHop wireless ad hoc networks

    Science.gov (United States)

    Mehic, M.; Fazio, P.; Voznak, M.; Partila, P.; Komosny, D.; Tovarek, J.; Chmelikova, Z.

    2016-05-01

    A mobile ad hoc network is a collection of mobile nodes which communicate without a fixed backbone or centralized infrastructure. Due to the frequent mobility of nodes, routes connecting two distant nodes may change. Therefore, it is not possible to establish a priori fixed paths for message delivery through the network. Because of its importance, routing is the most studied problem in mobile ad hoc networks. In addition, if the Quality of Service (QoS) is demanded, one must guarantee the QoS not only over a single hop but over an entire wireless multi-hop path which may not be a trivial task. In turns, this requires the propagation of QoS information within the network. The key to the support of QoS reporting is QoS routing, which provides path QoS information at each source. To support QoS for real-time traffic one needs to know not only minimum delay on the path to the destination but also the bandwidth available on it. Therefore, throughput, end-to-end delay, and routing overhead are traditional performance metrics used to evaluate the performance of routing protocol. To obtain additional information about the link, most of quality-link metrics are based on calculation of the lost probabilities of links by broadcasting probe packets. In this paper, we address the problem of including multiple routing metrics in existing routing packets that are broadcasted through the network. We evaluate the efficiency of such approach with modified version of DSDV routing protocols in ns-3 simulator.

  7. MR pulse sequences for selective relaxation time measurements: a phantom study

    DEFF Research Database (Denmark)

    Thomsen, C; Jensen, K E; Jensen, M

    1990-01-01

    a Siemens Magnetom wholebody magnetic resonance scanner operating at 1.5 Tesla was used. For comparison six imaging pulse sequences for relaxation time measurements were tested on the same phantom. The spectroscopic pulse sequences all had an accuracy better than 10% of the reference values....

  8. Medium Access Control Protocols for Cognitive Radio Ad Hoc Networks: A Survey

    Directory of Open Access Journals (Sweden)

    Mahdi Zareei

    2017-09-01

    Full Text Available New wireless network paradigms will demand higher spectrum use and availability to cope with emerging data-hungry devices. Traditional static spectrum allocation policies cause spectrum scarcity, and new paradigms such as Cognitive Radio (CR and new protocols and techniques need to be developed in order to have efficient spectrum usage. Medium Access Control (MAC protocols are accountable for recognizing free spectrum, scheduling available resources and coordinating the coexistence of heterogeneous systems and users. This paper provides an ample review of the state-of-the-art MAC protocols, which mainly focuses on Cognitive Radio Ad Hoc Networks (CRAHN. First, a description of the cognitive radio fundamental functions is presented. Next, MAC protocols are divided into three groups, which are based on their channel access mechanism, namely time-slotted protocol, random access protocol and hybrid protocol. In each group, a detailed and comprehensive explanation of the latest MAC protocols is presented, as well as the pros and cons of each protocol. A discussion on future challenges for CRAHN MAC protocols is included with a comparison of the protocols from a functional perspective.

  9. Intelligent QoS routing algorithm based on improved AODV protocol for Ad Hoc networks

    Science.gov (United States)

    Huibin, Liu; Jun, Zhang

    2016-04-01

    Mobile Ad Hoc Networks were playing an increasingly important part in disaster reliefs, military battlefields and scientific explorations. However, networks routing difficulties are more and more outstanding due to inherent structures. This paper proposed an improved cuckoo searching-based Ad hoc On-Demand Distance Vector Routing protocol (CSAODV). It elaborately designs the calculation methods of optimal routing algorithm used by protocol and transmission mechanism of communication-package. In calculation of optimal routing algorithm by CS Algorithm, by increasing QoS constraint, the found optimal routing algorithm can conform to the requirements of specified bandwidth and time delay, and a certain balance can be obtained among computation spending, bandwidth and time delay. Take advantage of NS2 simulation software to take performance test on protocol in three circumstances and validate the feasibility and validity of CSAODV protocol. In results, CSAODV routing protocol is more adapt to the change of network topological structure than AODV protocol, which improves package delivery fraction of protocol effectively, reduce the transmission time delay of network, reduce the extra burden to network brought by controlling information, and improve the routing efficiency of network.

  10. Continuous- and Discrete-Time Stimulus Sequences for High Stimulus Rate Paradigm in Evoked Potential Studies

    Directory of Open Access Journals (Sweden)

    Tao Wang

    2013-01-01

    Full Text Available To obtain reliable transient auditory evoked potentials (AEPs from EEGs recorded using high stimulus rate (HSR paradigm, it is critical to design the stimulus sequences of appropriate frequency properties. Traditionally, the individual stimulus events in a stimulus sequence occur only at discrete time points dependent on the sampling frequency of the recording system and the duration of stimulus sequence. This dependency likely causes the implementation of suboptimal stimulus sequences, sacrificing the reliability of resulting AEPs. In this paper, we explicate the use of continuous-time stimulus sequence for HSR paradigm, which is independent of the discrete electroencephalogram (EEG recording system. We employ simulation studies to examine the applicability of the continuous-time stimulus sequences and the impacts of sampling frequency on AEPs in traditional studies using discrete-time design. Results from these studies show that the continuous-time sequences can offer better frequency properties and improve the reliability of recovered AEPs. Furthermore, we find that the errors in the recovered AEPs depend critically on the sampling frequencies of experimental systems, and their relationship can be fitted using a reciprocal function. As such, our study contributes to the literature by demonstrating the applicability and advantages of continuous-time stimulus sequences for HSR paradigm and by revealing the relationship between the reliability of AEPs and sampling frequencies of the experimental systems when discrete-time stimulus sequences are used in traditional manner for the HSR paradigm.

  11. Evaluation of automatic time gain compensated in-vivo ultrasound sequences

    DEFF Research Database (Denmark)

    Axelsen, Martin Christian; Røeboe, Kristian Frostholm; Hemmsen, Martin Christian

    2010-01-01

    algorithm for automatic time gain compensation (TGC) on in-vivo ultrasound sequences. Forty ultrasound sequences were recorded from the abdomen of two healthy volunteers. Each sequence of 5 sec was recorded with 40 frames/sec. Post processing each frame, a mask is created wherein anechoic and hyper echoic...... regions are mapped. Near field hyper intensity and deep areas with low signal strength are also included in the mask. The algorithm uses this mask to create a parallel image where anechoic and hyper echoic regions are eliminated. From this, the mean power is calculated as a function of depth. The power...

  12. Protocols development for security and privacy of radio frequency identification systems

    Science.gov (United States)

    Sabbagha, Fatin

    There are benefits to adopting radio frequency identification (RFID) technology, although there are methods of attack that can compromise the system. This research determined how that may happen and what possible solutions can keep that from happening. Protocols were developed to implement better security. In addition, new topologies were developed to handle the problems of the key management. Previously proposed protocols focused on providing mutual authentication and privacy between readers and tags. However, those protocols are still vulnerable to be attacked. These protocols were analyzed and the disadvantages shown for each one. Previous works assumed that the channels between readers and the servers were secure. In the proposed protocols, a compromised reader is considered along with how to prevent tags from being read by that reader. The new protocols provide mutual authentication between readers and tags and, at the same time, remove the compromised reader from the system. Three protocols are proposed. In the first protocol, a mutual authentication is achieved and a compromised reader is not allowed in the network. In the second protocol, the number of times a reader contacts the server is reduced. The third protocol provides authentication and privacy between tags and readers using a trusted third party. The developed topology is implemented using python language and simulates work to check the efficiency regarding the processing time. The three protocols are implemented by writing codes in C language and then compiling them in MSP430. IAR Embedded workbench is used, which is an integrated development environment with the C/C++ compiler to generate a faster code and to debug the microcontroller. In summary, the goal of this research is to find solutions for the problems on previously proposed protocols, handle a compromised reader, and solve key management problems.

  13. An Enhanced Biometric Based Authentication with Key-Agreement Protocol for Multi-Server Architecture Based on Elliptic Curve Cryptography.

    Science.gov (United States)

    Reddy, Alavalapati Goutham; Das, Ashok Kumar; Odelu, Vanga; Yoo, Kee-Young

    2016-01-01

    Biometric based authentication protocols for multi-server architectures have gained momentum in recent times due to advancements in wireless technologies and associated constraints. Lu et al. recently proposed a robust biometric based authentication with key agreement protocol for a multi-server environment using smart cards. They claimed that their protocol is efficient and resistant to prominent security attacks. The careful investigation of this paper proves that Lu et al.'s protocol does not provide user anonymity, perfect forward secrecy and is susceptible to server and user impersonation attacks, man-in-middle attacks and clock synchronization problems. In addition, this paper proposes an enhanced biometric based authentication with key-agreement protocol for multi-server architecture based on elliptic curve cryptography using smartcards. We proved that the proposed protocol achieves mutual authentication using Burrows-Abadi-Needham (BAN) logic. The formal security of the proposed protocol is verified using the AVISPA (Automated Validation of Internet Security Protocols and Applications) tool to show that our protocol can withstand active and passive attacks. The formal and informal security analyses and performance analysis demonstrates that the proposed protocol is robust and efficient compared to Lu et al.'s protocol and existing similar protocols.

  14. Energy Efficiency and Emissions Trading. A PEEREA perspective after the entry into force of the Kyoto Protocol and of the EU ETS

    International Nuclear Information System (INIS)

    2006-01-01

    The year 2005 was of particular importance for the climate change discussions. The Kyoto Protocol entered into force in February, following the Russian ratification. At the same time, the largest emission-trading scheme for CO2, the EU ETS came into operation. By the end of the year the first Meeting of the Parties to the UNFCCC took place in Montreal. The PEEREA Group discussed on several occasions the contribution of the Kyoto flexible mechanisms to boosting energy efficiency improvements. The role of energy efficiency projects in achieving climate change objectives was equally underlined. In 2004 a report was elaborated and subsequently printed on Carbon Trading and Energy Efficiency, with the understanding that the PEEREA Group will revisit the subject in order to reflect on new developments in this area. This paper, prepared by the Secretariat with the consultancy support of EcoSecurities, served the discussion and debate in the PEEREA Group on the latest developments and opportunities for energy efficiency in the climate change process. The paper provides only a brief introduction of the main concepts, as they were presented and discussed in the 2004 report. The focus is now on the operation of the EU ETS and on the implications for both EU and non EU PEEREA countries of the Linking Directive on the use of JI/CDM mechanisms in relation to improving energy efficiency

  15. Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection.

    Science.gov (United States)

    Bernsen, M R; Dijkman, H B; de Vries, E; Figdor, C G; Ruiter, D J; Adema, G J; van Muijen, G N

    1998-10-01

    Molecular analysis of small tissue samples has become increasingly important in biomedical studies. Using a laser dissection microscope and modified nucleic acid isolation protocols, we demonstrate that multiple mRNA as well as DNA sequences can be identified from a single-cell sample. In addition, we show that the specificity of procurement of tissue samples is not compromised by smear contamination resulting from scraping of the microtome knife during sectioning of lesions. The procedures described herein thus allow for efficient RT-PCR or PCR analysis of multiple nucleic acid sequences from small tissue samples obtained by laser-assisted microdissection.

  16. Arbitrary digital pulse sequence generator with delay-loop timing

    Science.gov (United States)

    Hošák, Radim; Ježek, Miroslav

    2018-04-01

    We propose an idea of an electronic multi-channel arbitrary digital sequence generator with temporal granularity equal to two clock cycles. We implement the generator with 32 channels using a low-cost ARM microcontroller and demonstrate its capability to produce temporal delays ranging from tens of nanoseconds to hundreds of seconds, with 24 ns timing granularity and linear scaling of delay with respect to the number of delay loop iterations. The generator is optionally synchronized with an external clock source to provide 100 ps jitter and overall sequence repeatability within the whole temporal range. The generator is fully programmable and able to produce digital sequences of high complexity. The concept of the generator can be implemented using different microcontrollers and applied for controlling of various optical, atomic, and nuclear physics measurement setups.

  17. Chapter 5: Residential Furnaces and Boilers Evaluation Protocol. The Uniform Methods Project: Methods for Determining Energy Efficiency Savings for Specific Measures

    Energy Technology Data Exchange (ETDEWEB)

    Kurnik, Charles W. [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Jacobson, David [Jacobson Energy Research, Providence, RI (United States)

    2017-09-01

    The high-efficiency boiler and furnace measure produces gas heating savings resulting from installation of more energy-efficient heating equipment in a residence. Such equipment, which ranges in size from 60 kBtu/hr to 300 kBtu/hr, is installed primarily in single-family homes and multifamily buildings with individual heating systems for each dwelling unit. This protocol does not cover integrated heating and water heating units which can be used in lieu of space heating only equipment.

  18. ADAPTIVE GOSSIP BASED PROTOCOL FOR ENERGY EFFICIENT MOBILE ADHOC NETWORK

    Directory of Open Access Journals (Sweden)

    S. Rajeswari

    2012-03-01

    Full Text Available In Gossip Sleep Protocol, network performance is enhanced based on energy resource. But energy conservation is achieved with the reduced throughput. In this paper, it has been proposed a new Protocol for Mobile Ad hoc Network to achieve reliability with energy conservation. Based on the probability (p values, the value of sleep nodes is fixed initially. The probability value can be adaptively adjusted by Remote Activated Switch during the transmission process. The adaptiveness of gossiping probability is determined by the Packet Delivery Ratio. For performance comparison, we have taken Routing overhead, Packet Delivery Ratio, Number of dropped packets and Energy consumption with the increasing number of forwarding nodes. We used UDP based traffic models to analyze the performance of this protocol. We analyzed TCP based traffic models for average end to end delay. We have used the NS-2 simulator.

  19. Optimal protocol for maximum work extraction in a feedback process with a time-varying potential

    Science.gov (United States)

    Kwon, Chulan

    2017-12-01

    The nonequilibrium nature of information thermodynamics is characterized by the inequality or non-negativity of the total entropy change of the system, memory, and reservoir. Mutual information change plays a crucial role in the inequality, in particular if work is extracted and the paradox of Maxwell's demon is raised. We consider the Brownian information engine where the protocol set of the harmonic potential is initially chosen by the measurement and varies in time. We confirm the inequality of the total entropy change by calculating, in detail, the entropic terms including the mutual information change. We rigorously find the optimal values of the time-dependent protocol for maximum extraction of work both for the finite-time and the quasi-static process.

  20. Two-party quantum key agreement protocols under collective noise channel

    Science.gov (United States)

    Gao, Hao; Chen, Xiao-Guang; Qian, Song-Rong

    2018-06-01

    Recently, quantum communication has become a very popular research field. The quantum key agreement (QKA) plays an important role in the field of quantum communication, based on its unconditional security in terms of theory. Among all kinds of QKA protocols, QKA protocols resisting collective noise are widely being studied. In this paper, we propose improved two-party QKA protocols resisting collective noise and present a feasible plan for information reconciliation. Our protocols' qubit efficiency has achieved 26.67%, which is the best among all the two-party QKA protocols against collective noise, thus showing that our protocol can improve the transmission efficiency of quantum key agreement.

  1. Real Time MODBUS Transmissions and Cryptography Security Designs and Enhancements of Protocol Sensitive Information

    Directory of Open Access Journals (Sweden)

    Aamir Shahzad

    2015-07-01

    Full Text Available Information technology (IT security has become a major concern due to the growing demand for information and massive development of client/server applications for various types of applications running on modern IT infrastructure. How has security been taken into account and which paradigms are necessary to minimize security issues while increasing efficiency, reducing the influence on transmissions, ensuring protocol independency and achieving substantial performance? We have found cryptography to be an absolute security mechanism for client/server architectures, and in this study, a new security design was developed with the MODBUS protocol, which is considered to offer phenomenal performance for future development and enhancement of real IT infrastructure. This study is also considered to be a complete development because security is tested in almost all ways of MODBUS communication. The computed measurements are evaluated to validate the overall development, and the results indicate a substantial improvement in security that is differentiated from conventional methods.

  2. Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease.

    Science.gov (United States)

    Dilliott, Allison A; Farhan, Sali M K; Ghani, Mahdi; Sato, Christine; Liang, Eric; Zhang, Ming; McIntyre, Adam D; Cao, Henian; Racacho, Lemuel; Robinson, John F; Strong, Michael J; Masellis, Mario; Bulman, Dennis E; Rogaeva, Ekaterina; Lang, Anthony; Tartaglia, Carmela; Finger, Elizabeth; Zinman, Lorne; Turnbull, John; Freedman, Morris; Swartz, Rick; Black, Sandra E; Hegele, Robert A

    2018-04-04

    Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The technique is highly efficient with millions of sequencing reads being produced in a short time span and at relatively low cost. Specifically, targeted NGS is able to focus investigations to genomic regions of particular interest based on the disease of study. Not only does this further reduce costs and increase the speed of the process, but it lessens the computational burden that often accompanies NGS. Although targeted NGS is restricted to certain regions of the genome, preventing identification of potential novel loci of interest, it can be an excellent technique when faced with a phenotypically and genetically heterogeneous disease, for which there are previously known genetic associations. Because of the complex nature of the sequencing technique, it is important to closely adhere to protocols and methodologies in order to achieve sequencing reads of high coverage and quality. Further, once sequencing reads are obtained, a sophisticated bioinformatics workflow is utilized to accurately map reads to a reference genome, to call variants, and to ensure the variants pass quality metrics. Variants must also be annotated and curated based on their clinical significance, which can be standardized by applying the American College of Medical Genetics and Genomics Pathogenicity Guidelines. The methods presented herein will display the steps involved in generating and analyzing NGS data from a targeted sequencing panel, using the ONDRISeq neurodegenerative disease panel as a model, to identify variants that may be of clinical significance.

  3. Nitrogen and phosphorus treatment of marine wastewater by a laboratory-scale sequencing batch reactor with eco-friendly marine high-efficiency sediment.

    Science.gov (United States)

    Cho, Seonghyeon; Kim, Jinsoo; Kim, Sungchul; Lee, Sang-Seob

    2017-06-22

    We screened and identified a NH 3 -N-removing bacterial strain, Bacillus sp. KGN1, and a [Formula: see text] removing strain, Vibrio sp. KGP1, from 960 indigenous marine isolates from seawater and marine sediment from Tongyeong, South Korea. We developed eco-friendly high-efficiency marine sludge (eco-HEMS), and inoculated these marine bacterial strains into the marine sediment. A laboratory-scale sequencing batch reactor (SBR) system using the eco-HEMS for marine wastewater from land-based fish farms improved the treatment performance as indicated by 88.2% removal efficiency (RE) of total nitrogen (initial: 5.6 mg/L) and 90.6% RE of total phosphorus (initial: 1.2 mg/L) under the optimal operation conditions (food and microorganism (F/M) ratio, 0.35 g SCOD Cr /g mixed liquor volatile suspended solids (MLVSS)·d; dissolved oxygen (DO) 1.0 ± 0.2 mg/L; hydraulic retention time (HRT), 6.6 h; solids retention time (SRT), 12 d). The following kinetic parameters were obtained: cell yield (Y), 0.29 g MLVSS/g SCOD Cr ; specific growth rate (µ), 0.06 d -1 ; specific nitrification rate (SNR), 0.49 mg NH 3 -N/g MLVSS·h; specific denitrification rate (SDNR), 0.005 mg [Formula: see text]/g MLVSS·h; specific phosphorus uptake rate (SPUR), 0.12 mg [Formula: see text]/g MLVSS·h. The nitrogen- and phosphorus-removing bacterial strains comprised 18.4% of distribution rate in the microbial community of eco-HEMS under the optimal operation conditions. Therefore, eco-HEMS effectively removed nitrogen and phosphorus from highly saline marine wastewater from land-based fish farms with improving SNR, SDNR, and SPUR values in more diverse microbial communities. DO: dissolved oxygen; Eco-HEMS: eco-friendly high efficiency marine sludge; F/M: food and microorganism ratio; HRT: hydraulic retention time; ML(V)SS: mixed liquor (volatile) suspended solids; NCBI: National Center for Biotechnology Information; ND: not determined; qPCR: quantitative real-time polymerase

  4. An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.

    Science.gov (United States)

    Ye, Kai; Kosters, Walter A; Ijzerman, Adriaan P

    2007-03-15

    Pattern discovery in protein sequences is often based on multiple sequence alignments (MSA). The procedure can be computationally intensive and often requires manual adjustment, which may be particularly difficult for a set of deviating sequences. In contrast, two algorithms, PRATT2 (http//www.ebi.ac.uk/pratt/) and TEIRESIAS (http://cbcsrv.watson.ibm.com/) are used to directly identify frequent patterns from unaligned biological sequences without an attempt to align them. Here we propose a new algorithm with more efficiency and more functionality than both PRATT2 and TEIRESIAS, and discuss some of its applications to G protein-coupled receptors, a protein family of important drug targets. In this study, we designed and implemented six algorithms to mine three different pattern types from either one or two datasets using a pattern growth approach. We compared our approach to PRATT2 and TEIRESIAS in efficiency, completeness and the diversity of pattern types. Compared to PRATT2, our approach is faster, capable of processing large datasets and able to identify the so-called type III patterns. Our approach is comparable to TEIRESIAS in the discovery of the so-called type I patterns but has additional functionality such as mining the so-called type II and type III patterns and finding discriminating patterns between two datasets. The source code for pattern growth algorithms and their pseudo-code are available at http://www.liacs.nl/home/kosters/pg/.

  5. Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing.

    Science.gov (United States)

    Leo, Stefano; Gaïa, Nadia; Ruppé, Etienne; Emonet, Stephane; Girard, Myriam; Lazarevic, Vladimir; Schrenzel, Jacques

    2017-09-20

    The applications of whole-metagenome shotgun sequencing (WMGS) in routine clinical analysis are still limited. A combination of a DNA extraction procedure, sequencing, and bioinformatics tools is essential for the removal of human DNA and for improving bacterial species identification in a timely manner. We tackled these issues with a broncho-alveolar lavage (BAL) sample from an immunocompromised patient who had developed severe chronic pneumonia. We extracted DNA from the BAL sample with protocols based either on sequential lysis of human and bacterial cells or on the mechanical disruption of all cells. Metagenomic libraries were sequenced on Illumina HiSeq platforms. Microbial community composition was determined by k-mer analysis or by mapping to taxonomic markers. Results were compared to those obtained by conventional clinical culture and molecular methods. Compared to mechanical cell disruption, a sequential lysis protocol resulted in a significantly increased proportion of bacterial DNA over human DNA and higher sequence coverage of Mycobacterium abscessus , Corynebacterium jeikeium and Rothia dentocariosa , the bacteria reported by clinical microbiology tests. In addition, we identified anaerobic bacteria not searched for by the clinical laboratory. Our results further support the implementation of WMGS in clinical routine diagnosis for bacterial identification.

  6. A DNA sequence element that advances replication origin activation time in Saccharomyces cerevisiae.

    Science.gov (United States)

    Pohl, Thomas J; Kolor, Katherine; Fangman, Walton L; Brewer, Bonita J; Raghuraman, M K

    2013-11-06

    Eukaryotic origins of DNA replication undergo activation at various times in S-phase, allowing the genome to be duplicated in a temporally staggered fashion. In the budding yeast Saccharomyces cerevisiae, the activation times of individual origins are not intrinsic to those origins but are instead governed by surrounding sequences. Currently, there are two examples of DNA sequences that are known to advance origin activation time, centromeres and forkhead transcription factor binding sites. By combining deletion and linker scanning mutational analysis with two-dimensional gel electrophoresis to measure fork direction in the context of a two-origin plasmid, we have identified and characterized a 19- to 23-bp and a larger 584-bp DNA sequence that are capable of advancing origin activation time.

  7. ASSESSMENT OF RIP-V1 AND OSPF-V2 PROTOCOL WITH CONSIDERATION OF CONVERGENCE CRITERIA AND SENDING PROTOCOLS TRAFFIC

    Directory of Open Access Journals (Sweden)

    Hamed Jelodar

    2014-03-01

    Full Text Available Routing Protocols are underlying principles in networks like internet, transport and mobile. Routing Protocols include a series of rules and algorithms that consider routing metric and select the best way for sending healthy data packets from origin to destination. Dynamic routing protocol compatible to topology has a changeable state. RIP and OSPF are dynamic routing protocol that we consider criteria like convergence and sending protocols traffic assessment RIP first version and OSPF second version. By the test we have done on OPNET stimulation we understood that the OSPF protocol was more efficient than RIP protocol.

  8. A CHANGE DETECTION AND RESOURCE-AWARE DATA SENSING APPROACHES FOR IMPROVING THE REPORTING PROTOCOL MECHANISM FOR MOBILE USER

    Directory of Open Access Journals (Sweden)

    annisaa sri indrawanti

    2015-08-01

    Full Text Available Update mechanism is an important process that relays information to the end-user by sending the data from the client to the server. There are several kinds of update mechanism that are used, one of them is reporting protocol. Reporting protocol sends the data from the client to the server continuously in a certain time interval. Reporting protocol occasionally sends the same information repeatedly to the end-user and sometimes the data aren’t needed by the end-user. This is an issue, because it can cause a large amount of bandwidth usage. In this research, we have developed an improvement of the reporting protocol mechanism for mobile user using change detection and resource-aware data sensing to minimize the bandwidth and resource usage. The improvement of reporting protocol that is implemented reduces frequency of data transfer with the prediction of the changes in user activity and position. The prediction is used as a trigger when the data is about to be sent. The results have shown that the adaptive reporting protocol could improve the performance of the overall reporting protocol. This is shown by the improvement of the bandwidth efficiency up to 36-97%, memory efficiency at 1.5-6% and battery efficiency at 7-13%.

  9. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

    Science.gov (United States)

    Nagar, Anurag; Hahsler, Michael

    2013-01-01

    Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to

  10. Outdoor Irrigation Measurement and Verification Protocol

    Energy Technology Data Exchange (ETDEWEB)

    Kurnik, Charles W. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Stoughton, Kate M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Figueroa, Jorge [Western Resource Advocates, Boulder, CO (United States)

    2017-12-05

    This measurement and verification (M&V) protocol provides procedures for energy service companies (ESCOs) and water efficiency service companies (WESCOs) to determine water savings resulting from water conservation measures (WCMs) in energy performance contracts associated with outdoor irrigation efficiency projects. The water savings are determined by comparing the baseline water use to the water use after the WCM has been implemented. This protocol outlines the basic structure of the M&V plan, and details the procedures to use to determine water savings.

  11. Design and realization of real-time processing system for seismic exploration

    International Nuclear Information System (INIS)

    Zhang Sifeng; Cao Ping; Song Kezhu; Yao Lin

    2010-01-01

    For solving real-time seismic data processing problems, a high-speed, large-capacity and real-time data processing system is designed based on FPGA and ARM. With the advantages of multi-processor, DRPS has the characteristics of high-speed data receiving, large-capacity data storage, protocol analysis, data splicing, data converting from time sequence into channel sequence, no dead time data ping-pong storage, etc. And with the embedded Linux operating system, DRPS has the characteristics of flexibility and reliability. (authors)

  12. Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides

    Directory of Open Access Journals (Sweden)

    Ho Antoine

    2011-12-01

    Full Text Available Abstract Background Sequencing-by-ligation (SBL is one of several next-generation sequencing methods that has been developed for massive sequencing of DNA immobilized on arrayed beads (or other clonal amplicons. SBL has the advantage of being easy to implement and accessible to all because it can be performed with off-the-shelf reagents. However, SBL has the limitation of very short read lengths. Results To overcome the read length limitation, research groups have developed complex library preparation processes, which can be time-consuming, difficult, and result in low complexity libraries. Herein we describe a variation on traditional SBL protocols that extends the number of sequential bases that can be sequenced by using Endonuclease V to nick a query primer, thus leaving a ligatable end extended into the unknown sequence for further SBL cycles. To demonstrate the protocol, we constructed a known DNA sequence and utilized our SBL variation, cyclic SBL (cSBL, to resequence this region. Using our method, we were able to read thirteen contiguous bases in the 3' - 5' direction. Conclusions Combining this read length with sequencing in the 5' - 3' direction would allow a read length of over twenty bases on a single tage. Implementing mate-paired tags and this SBL variation could enable > 95% coverage of the genome.

  13. Cluster protocols in Underwater Sensor Networks: a Research Review

    Directory of Open Access Journals (Sweden)

    K. Ovaliadis

    2014-07-01

    Full Text Available Underwater Wireless Sensor Networks (UWSN have different characteristics in relation to terrestrial wireless sensor networks; such as limited bandwidth capacity, high propagation delays and limited battery power. Although there has been much work completed in developing protocols and models for terrestrial networks, these are rarely applicable for underwater sensor networks. Up to today major efforts have been made for designing efficient protocols while considering the underwater communication characteristics. An important issue on this research area is the construction of an efficient clustering algorithm. Clustering in the context of UWSN is important as it contributes a great deal towards the efficient use of energy resources. This paper reviews the most significant cluster based protocols proposed for UWSN. Major performance issues of these protocols with respect to the network conditions such as packet delivery ratio, average packet delay, node mobility effect and energy consumption are examined. The advantages and disadvantages of each protocol are also pointed out.

  14. Time-clustering behavior of sharp fluctuation sequences in Chinese stock markets

    International Nuclear Information System (INIS)

    Yuan Ying; Zhuang Xintian; Liu Zhiying; Huang Weiqiang

    2012-01-01

    Sharp fluctuations (in particular, extreme fluctuations) of asset prices have a great impact on financial markets and risk management. Therefore, investigating the time dynamics of sharp fluctuation is a challenge in the financial fields. Using two different representations of the sharp fluctuations (inter-event times and series of counts), the time clustering behavior in the sharp fluctuation sequences of stock markets in China is studied with several statistical tools, including coefficient of variation, Allan Factor, Fano Factor as well as R/S (rescaled range) analysis. All of the empirical results indicate that the time dynamics of the sharp fluctuation sequences can be considered as a fractal process with a high degree of time-clusterization of the events. It can help us to get a better understanding of the nature and dynamics of sharp fluctuation of stock price in stock markets.

  15. Strategies for merging microbial fuel cell technologies in water desalination processes: Start-up protocol and desalination efficiency assessment

    Science.gov (United States)

    Borjas, Zulema; Esteve-Núñez, Abraham; Ortiz, Juan Manuel

    2017-07-01

    Microbial Desalination Cells constitute an innovative technology where microbial fuel cell and electrodialysis merge in the same device for obtaining fresh water from saline water with no energy-associated cost for the user. In this work, an anodic biofilm of the electroactive bacteria Geobacter sulfurreducens was able to efficiently convert the acetate present in synthetic waste water into electric current (j = 0.32 mA cm-2) able to desalinate water. .Moreover, we implemented an efficient start-up protocol where desalination up to 90% occurred in a desalination cycle (water production:0.308 L m-2 h-1, initial salinity: 9 mS cm-1, final salinity: osmosis (RO) or reverse electrodialysis.

  16. Field Measurements of Heating Efficiency of Electric Forced-Air Furnaces in Six Manufactured Homes.

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Bob; Palmiter, Larry S.; Siegel, Jeff

    1994-07-26

    This report presents the results of field measurements of heating efficiency for six manufactured homes in the Pacific Northwest heated with electric forced-air systems. This is the first in a series of regional and national efforts to measure in detail the heating efficiency of manufactured homes. Only six homes were included in this study because of budgetary constraints; therefore this is not a representative sample. These investigations do provide some useful information on the heating efficiency of these homes. Useful comparisons can be drawn between these study homes and site-built heating efficiencies measured with a similar protocol. The protocol used to test these homes is very similar to another Ecotope protocol used in the study conducted in 1992 and 1993 for the Bonneville Power Administration to test the heating efficiency of 24 homes. This protocol combined real-time power measurements of furnace energy usage with energy usage during co-heat periods. Accessory data such as house and duct tightness measurements and tracer gas measurements were used to describe these homes and their heating system efficiency. Ensuring that manufactured housing is constructed in an energy and resource efficient manner is of increasing concern to manufactured home builders and consumers. No comparable work has been done to measure the heating system efficiency of MCS manufactured homes, although some co-heat tests have been performed on manufactured homes heated with natural gas to validate HUD thermal standards. It is expected that later in 1994 more research of this kind will be conducted, and perhaps a less costly and less time-consuming method for testing efficiencies will be develops.

  17. An Enhanced Biometric Based Authentication with Key-Agreement Protocol for Multi-Server Architecture Based on Elliptic Curve Cryptography

    Science.gov (United States)

    Reddy, Alavalapati Goutham; Das, Ashok Kumar; Odelu, Vanga; Yoo, Kee-Young

    2016-01-01

    Biometric based authentication protocols for multi-server architectures have gained momentum in recent times due to advancements in wireless technologies and associated constraints. Lu et al. recently proposed a robust biometric based authentication with key agreement protocol for a multi-server environment using smart cards. They claimed that their protocol is efficient and resistant to prominent security attacks. The careful investigation of this paper proves that Lu et al.’s protocol does not provide user anonymity, perfect forward secrecy and is susceptible to server and user impersonation attacks, man-in-middle attacks and clock synchronization problems. In addition, this paper proposes an enhanced biometric based authentication with key-agreement protocol for multi-server architecture based on elliptic curve cryptography using smartcards. We proved that the proposed protocol achieves mutual authentication using Burrows-Abadi-Needham (BAN) logic. The formal security of the proposed protocol is verified using the AVISPA (Automated Validation of Internet Security Protocols and Applications) tool to show that our protocol can withstand active and passive attacks. The formal and informal security analyses and performance analysis demonstrates that the proposed protocol is robust and efficient compared to Lu et al.’s protocol and existing similar protocols. PMID:27163786

  18. An Enhanced Biometric Based Authentication with Key-Agreement Protocol for Multi-Server Architecture Based on Elliptic Curve Cryptography.

    Directory of Open Access Journals (Sweden)

    Alavalapati Goutham Reddy

    Full Text Available Biometric based authentication protocols for multi-server architectures have gained momentum in recent times due to advancements in wireless technologies and associated constraints. Lu et al. recently proposed a robust biometric based authentication with key agreement protocol for a multi-server environment using smart cards. They claimed that their protocol is efficient and resistant to prominent security attacks. The careful investigation of this paper proves that Lu et al.'s protocol does not provide user anonymity, perfect forward secrecy and is susceptible to server and user impersonation attacks, man-in-middle attacks and clock synchronization problems. In addition, this paper proposes an enhanced biometric based authentication with key-agreement protocol for multi-server architecture based on elliptic curve cryptography using smartcards. We proved that the proposed protocol achieves mutual authentication using Burrows-Abadi-Needham (BAN logic. The formal security of the proposed protocol is verified using the AVISPA (Automated Validation of Internet Security Protocols and Applications tool to show that our protocol can withstand active and passive attacks. The formal and informal security analyses and performance analysis demonstrates that the proposed protocol is robust and efficient compared to Lu et al.'s protocol and existing similar protocols.

  19. Adaptive MAC-layer protocol for multiservice digital access via tree and branch communication networks

    Science.gov (United States)

    Sriram, Kotikalapudi; Li, Chia-Chang; Magill, Peter; Whitaker, Norman A.; Dail, James E.; Dajer, Miguel A.; Siller, Curtis A.

    1995-11-01

    Described here is an adaptive MAC-layer protocol that supports multiservice (STM and ATM) applications in the context of subscriber access to tree and branch (e.g., fiber-coaxial cable) networks. The protocol adapts to changing demands for a mix of circuit and cell mode applications, and efficiently allocates upstream and downstream bandwidth to a variety of bursty and isochronous traffic sources. In the case of a hybrid fiber-coaxial (HFC) network the protocol resides in customer premises equipment and a common head-end controller. A medium-access control (MAC) processor provides for dividing the time domain for a given digital bitstream into successive frames, each with multiple STM and ATM time slots. Within the STM region of a frame, variable length time slots are allocated to calls (e.g., telephony, video telephony) requiring different amounts of bandwidth. A contention access signaling channel is also provided in this region for call control and set-up requests. Within the ATM region fixed-length time slots accommodate one individual ATM cell. These ATM time slots may be reserved for a user for the duration of a call or burst of successive ATM cells, or shared via a contention process. At least one contention time slot is available for signaling messages related to ATM call control and set-up requests. Further, the fixed-length ATM time slots may be reserved by a user for the duration of a call, or shared through a contention process. This paper describes the MAC-layer protocol, its relation to circuit- and ATM- amenable applications, and its performance with respect to signaling throughput and latency, and bandwidth efficiency for several service scenarios.

  20. Experimental implementation of a real-time token-based network protocol on a microcontroller

    NARCIS (Netherlands)

    Hanssen, F.T.Y.; Krikke, Robert; Baron, Bert; Jansen, P.G.; Scholten, Johan

    The real-time token-based RTnet network protocol has been implemented on a standard Ethernet network to investigate the possibility to use cheap components with strict resource limitations while preserving Quality of Service guarantees. It will be shown that the proposed implementation is feasible

  1. Experimental implementation of a real-time token-based network protocol on a microcontroller

    NARCIS (Netherlands)

    Hanssen, F.T.Y.; Krikke, Robert; Baron, Bert; Jansen, P.G.; Scholten, Johan

    2004-01-01

    The real-time token-based RTnet network protocol has been implemented on a standard Ethernet network to investigate the possibility to use cheap components with strict resource limitations while preserving Quality of Service guarantees. It will be shown that the proposed implementation is feasible

  2. A PROPOSED MAPPING ARCHITECTURE BETWEEN IAX AND JINGLE PROTOCOLS

    Directory of Open Access Journals (Sweden)

    Hadeel Saleh Haj Aliwi

    2016-03-01

    Full Text Available Nowadays, multimedia communication has improved rapidly to allow people to communicate via the Internet. However, Internet users cannot communicate with each other unless they use the same chatting applications since each chatting application uses a certain signaling protocol to make the media call. The mapping architecture is a very critical issue since it solves the communication problems between any two protocols, as well as it enables people around the world to make a voice/video call even if they use different chatting applications. Providing the interoperability between different signaling protocols and multimedia applications takes the advantages of more than one protocol. Many mapping architectures have been proposed to ease exchanging the media between at least two users without facing any difficulties such as SIP-Jingle, IAX-RSW, H.323-MGCP, etc. However, the design of any of the existing mapping architectures has some weaknesses related to larger delay, time consuming, and security matters. The only way to overcome these problems is to propose an efficient mapping architecture. This paper proposed a new mapping architecture between Inter-Asterisk eXchange Protocol and Jingle Protocol. The proposed mapping architecture consists of IAX domain (IAX client, IAX server, IAX-to-Jingle gateway, and Jingle domain (Jingle client, Jingle server, Jingle-to-IAX gateway. The tasks of the translation gateways are represented by the URI conversion, media capability exchange, translator of call setup and teardown signals, and real time media transmission.

  3. Simulation of a MR–PET protocol for staging of head-and-neck cancer including Dixon MR for attenuation correction

    Energy Technology Data Exchange (ETDEWEB)

    Eiber, Matthias, E-mail: matthias.eiber@tum.de [Department of Radiology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); Souvatzoglou, Michael, E-mail: msouvatz@yahoo.de [Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); Pickhard, Anja, E-mail: a.pickhard@lrz.tum.de [Department of Otorhinolaryngology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); Loeffelbein, Denys J., E-mail: denys.loeffelbein@gmx.de [Department of Maxillofacial Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); Knopf, Andreas, E-mail: andreas.knopf@tum.de [Department of Otorhinolaryngology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); Holzapfel, Konstantin, E-mail: holzapfel@roe.med.tum.de [Department of Radiology, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); Martinez-Möller, Axel, E-mail: a.martinez-moller@lrz.tu-muenchen.de [Department of Nuclear Medicine, Klinikum rechts der Isar, Technische Universität München, Ismaninger Str. 22, 81675 Munich (Germany); and others

    2012-10-15

    Purpose: To simulate and optimize a MR protocol for squamous cell cancer of the head and neck (HNSCC) patients for potential future use in an integrated whole-body MR–PET scanner. Materials and methods: On a clinical 3T scanner, which is the basis for a recently introduced fully integrated whole-body MR–PET, 20 patients with untreated HNSCC routinely staged with 18F-FDG PET/CT underwent a dedicated MR protocol for the neck. Moreover, a whole-body Dixon MR-sequence was applied, which is used for attenuation correction on a recently introduced hybrid MR–PET scanner. In a subset of patients volume-interpolated-breathhold (VIBE) T1w-sequences for lungs and liver were added. Total imaging time was analyzed for both groups. The quality of the delineation of the primary tumor (scale 0–3) and the presence or absence of lymph node metastases (scale 1–5) was evaluated for CT, MR, PET/CT and a combination of MR and PET to ensure that the MR–PET fusion does not cause a loss of diagnostic capability. PET was used to identify distant metastases. The PET dataset for simulated MR/PET was based on a segmentation of the CT data into 4 classes according to the approach of the Dixon MR-sequence for MR–PET. Standard of reference was histopathology in 19 cases. In one case no histopathological confirmation of a primary tumor could be achieved. Results: Mean imaging time was 35:17 min (range: 31:08–42:42 min) for the protocol including sequences for local staging and attenuation correction and 44:17 min (range: 35:44–54:58) for the extended protocol. Although not statistically significant a combination of MR and PET performed better in the delineation of the primary tumor (mean 2.20) compared to CT (mean 1.40), MR (1.95) and PET/CT (2.15) especially in patients with dental implants. PET/CT and combining MR and PET performed slightly better than CT and MR for the assessment of lymph node metastases. Two patients with distant metastases were only identified by PET

  4. Advanced flooding-based routing protocols for underwater sensor networks

    OpenAIRE

    Isufi, E.; Dol, H.; Leus, G.J.T.

    2016-01-01

    Flooding-based protocols are a reliable solution to deliver packets in underwater sensor networks. However, these protocols potentially involve all the nodes in the forwarding process. Thus, the performance and energy efficiency are not optimal. In this work, we propose some advances of a flooding-based protocol with the goal to improve the performance and the energy efficiency. The first idea considers the node position information in order to reduce the number of relays that may apply flood...

  5. IEEE 802.11 Wireless LANs: Performance Analysis and Protocol Refinement

    Directory of Open Access Journals (Sweden)

    Chatzimisios P.

    2005-01-01

    Full Text Available The IEEE 802.11 protocol is emerging as a widely used standard and has become the most mature technology for wireless local area networks (WLANs. In this paper, we focus on the tuning of the IEEE 802.11 protocol parameters taking into consideration, in addition to throughput efficiency, performance metrics such as the average packet delay, the probability of a packet being discarded when it reaches the maximum retransmission limit, the average time to drop a packet, and the packet interarrival time. We present an analysis, which has been validated by simulation that is based on a Markov chain model commonly used in the literature. We further study the improvement on these performance metrics by employing suitable protocol parameters according to the specific communication needs of the IEEE 802.11 protocol for both basic access and RTS/CTS access schemes. We show that the use of a higher initial contention window size does not considerably degrade performance in small networks and performs significantly better in any other scenario. Moreover, we conclude that the combination of a lower maximum contention window size and a higher retry limit considerably improves performance. Results indicate that the appropriate adjustment of the protocol parameters enhances performance and improves the services that the IEEE 802.11 protocol provides to various communication applications.

  6. Use of limited MR protocol (coronal STIR) in the evaluation of patients with hip pain

    International Nuclear Information System (INIS)

    Khoury, N.J.; Birjawi, G.A.; Hourani, M.H.; Chaaya, M.

    2003-01-01

    To assess the role of a limited MR protocol (coronal STIR) as the initial part of the MR examination in patients with hip pain. Eighty-five patients presenting with hip pain, and normal radiographs of the pelvis, and who underwent our full MR protocol for hips were included retrospectively in the study. The full protocol consists of coronal T1-weighted and short tau inversion-recovery (STIR), and axial T2-weighted sequences. Ninety-three MR examinations were performed. Two radiologists interpreted the STIR (limited) examinations and the full studies separately, masked to each other's findings and to the final diagnosis. Comparison between the two protocols was then undertaken. For both readers, all normal MR examinations on the coronal STIR limited protocol were normal on the full protocol, with an interobserver reliability of 0.96. The STIR protocol was able to detect the presence or absence of an abnormality in 100% of cases (sensitivity). The STIR-only protocol provided a specific diagnosis in only 65% of cases (specificity). A normal coronal STIR study of the hips in patients with hip pain and normal radiographs precludes the need for further pelvic MR sequences. Any abnormality detected on this limited protocol should be further assessed by additional MR sequences. (orig.)

  7. Property - preserving convergent sequences of invariant sets for linear discrete - time systems

    NARCIS (Netherlands)

    Athanasopoulos, N.; Lazar, M.; Bitsoris, G.

    2014-01-01

    Abstract: New sequences of monotonically increasing sets are introduced, for linear discrete-time systems subject to input and state constraints. The elements of the set sequences are controlled invariant and admissible regions of stabilizability. They are generated from the iterative application of

  8. Preoperative magnetic resonance imaging protocol for endoscopic cranial base image-guided surgery.

    Science.gov (United States)

    Grindle, Christopher R; Curry, Joseph M; Kang, Melissa D; Evans, James J; Rosen, Marc R

    2011-01-01

    Despite the increasing utilization of image-guided surgery, no radiology protocols for obtaining magnetic resonance (MR) imaging of adequate quality are available in the current literature. At our institution, more than 300 endonasal cranial base procedures including pituitary, extended pituitary, and other anterior skullbase procedures have been performed in the past 3 years. To facilitate and optimize preoperative evaluation and assessment, there was a need to develop a magnetic resonance protocol. Retrospective Technical Assessment was performed. Through a collaborative effort between the otolaryngology, neurosurgery, and neuroradiology departments at our institution, a skull base MR image-guided (IGS) protocol was developed with several ends in mind. First, it was necessary to generate diagnostic images useful for the more frequently seen pathologies to improve work flow and limit the expense and inefficiency of case specific MR studies. Second, it was necessary to generate sequences useful for IGS, preferably using sequences that best highlight that lesion. Currently, at our institution, all MR images used for IGS are obtained using this protocol as part of preoperative planning. The protocol that has been developed allows for thin cut precontrast and postcontrast axial cuts that can be used to plan intraoperative image guidance. It also obtains a thin cut T2 axial series that can be compiled separately for intraoperative imaging, or may be fused with computed tomographic images for combined modality. The outlined protocol obtains image sequences effective for diagnostic and operative purposes for image-guided surgery using both T1 and T2 sequences. Copyright © 2011 Elsevier Inc. All rights reserved.

  9. Time step length versus efficiency of Monte Carlo burnup calculations

    International Nuclear Information System (INIS)

    Dufek, Jan; Valtavirta, Ville

    2014-01-01

    Highlights: • Time step length largely affects efficiency of MC burnup calculations. • Efficiency of MC burnup calculations improves with decreasing time step length. • Results were obtained from SIE-based Monte Carlo burnup calculations. - Abstract: We demonstrate that efficiency of Monte Carlo burnup calculations can be largely affected by the selected time step length. This study employs the stochastic implicit Euler based coupling scheme for Monte Carlo burnup calculations that performs a number of inner iteration steps within each time step. In a series of calculations, we vary the time step length and the number of inner iteration steps; the results suggest that Monte Carlo burnup calculations get more efficient as the time step length is reduced. More time steps must be simulated as they get shorter; however, this is more than compensated by the decrease in computing cost per time step needed for achieving a certain accuracy

  10. Ligand efficiency based approach for efficient virtual screening of compound libraries.

    Science.gov (United States)

    Ke, Yi-Yu; Coumar, Mohane Selvaraj; Shiao, Hui-Yi; Wang, Wen-Chieh; Chen, Chieh-Wen; Song, Jen-Shin; Chen, Chun-Hwa; Lin, Wen-Hsing; Wu, Szu-Huei; Hsu, John T A; Chang, Chung-Ming; Hsieh, Hsing-Pang

    2014-08-18

    Here we report for the first time the use of fit quality (FQ), a ligand efficiency (LE) based measure for virtual screening (VS) of compound libraries. The LE based VS protocol was used to screen an in-house database of 125,000 compounds to identify aurora kinase A inhibitors. First, 20 known aurora kinase inhibitors were docked to aurora kinase A crystal structure (PDB ID: 2W1C); and the conformations of docked ligand were used to create a pharmacophore (PH) model. The PH model was used to screen the database compounds, and rank (PH rank) them based on the predicted IC50 values. Next, LE_Scale, a weight-dependant LE function, was derived from 294 known aurora kinase inhibitors. Using the fit quality (FQ = LE/LE_Scale) score derived from the LE_Scale function, the database compounds were reranked (PH_FQ rank) and the top 151 (0.12% of database) compounds were assessed for aurora kinase A inhibition biochemically. This VS protocol led to the identification of 7 novel hits, with compound 5 showing aurora kinase A IC50 = 1.29 μM. Furthermore, testing of 5 against a panel of 31 kinase reveals that it is selective toward aurora kinase A & B, with <50% inhibition for other kinases at 10 μM concentrations and is a suitable candidate for further development. Incorporation of FQ score in the VS protocol not only helped identify a novel aurora kinase inhibitor, 5, but also increased the hit rate of the VS protocol by improving the enrichment factor (EF) for FQ based screening (EF = 828), compared to PH based screening (EF = 237) alone. The LE based VS protocol disclosed here could be applied to other targets for hit identification in an efficient manner. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  11. Harmonic spectral components in time sequences of Markov correlated events

    Science.gov (United States)

    Mazzetti, Piero; Carbone, Anna

    2017-07-01

    The paper concerns the analysis of the conditions allowing time sequences of Markov correlated events give rise to a line power spectrum having a relevant physical interest. It is found that by specializing the Markov matrix in order to represent closed loop sequences of events with arbitrary distribution, generated in a steady physical condition, a large set of line spectra, covering all possible frequency values, is obtained. The amplitude of the spectral lines is given by a matrix equation based on a generalized Markov matrix involving the Fourier transform of the distribution functions representing the time intervals between successive events of the sequence. The paper is a complement of a previous work where a general expression for the continuous power spectrum was given. In that case the Markov matrix was left in a more general form, thus preventing the possibility of finding line spectra of physical interest. The present extension is also suggested by the interest of explaining the emergence of a broad set of waves found in the electro and magneto-encephalograms, whose frequency ranges from 0.5 to about 40Hz, in terms of the effects produced by chains of firing neurons within the complex neural network of the brain. An original model based on synchronized closed loop sequences of firing neurons is proposed, and a few numerical simulations are reported as an application of the above cited equation.

  12. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases.

    Science.gov (United States)

    Citorik, Robert J; Mimee, Mark; Lu, Timothy K

    2014-11-01

    Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

  13. Enhanced DSR Routing Protocol for the Short Time Disconnected MANET

    Directory of Open Access Journals (Sweden)

    PAPAJ Ján

    2013-05-01

    Full Text Available Data delivery in Mobile Ad-Hoc network (MANET is a very difficult task due to the fact the sporadic connections between mobile nodes. For this reason, we introduce the new modified routing protocol that enables the data delivery in the case that the connections are disconnected. A key aspect of the protocol is a process of finding connections between source and destination nodes that can provide low end-to-end delay and better delivery performance in a disconnected MANET. The protocol provides the concepts of opportunistic routing of the routing packets in disconnected MANETs. In this paper we present a modification of the DSR routing protocol and also some results of a simulation.

  14. From the Copenhagen Accord to efficient technology protocols

    International Nuclear Information System (INIS)

    Kypreos, Socrates

    2012-01-01

    As the Copenhagen Conference of Parties (COP) failed to negotiate a binding Post-Kyoto agreement, an alternative is proposed based on the Copenhagen Accord (CA). The CA, as endorsed by COP16 in Cancun, aims to combat global warming with differentiated reduction targets of greenhouse gas emissions and by mobilizing resources supporting adaptation and carbon-free technology in developing countries (DCs). Using a special version of MERGE, we study the global implications of the CA postulating extensions of the Accord in the direction of Technology Transfer Protocols (TTPs). We assess scenarios needed to reach sustainable climate targets under such Protocols. It is shown that without binding commitments for DCs, the warming target of 2 °C will be exceeded with a probability above 50%, even if Annex B countries eliminate their emissions. However, moderate commitments of DCs (when they reach sufficient economic development), make the 2 °C scenario feasible. TTPs combined with binding emission reduction targets thus provide a mechanism to reduce climate change damages, and may generate significant secondary benefits. For example, the reduced tax-subsidy scenario (RTS20) has 77% to 40% chances to remain below 2 °C of warming and an undiscounted cumulative gross domestic product (GDP) cost of 0.75% relative to baseline (not accounting for the benefits of avoided damages). - Highlights: ► Based on the Copenhagen Accord we propose an extension of the Kyoto Protocol. ► The carbon tax-revenue of industrialized countries subsidizes Technology Transfer to DCs and R and D. ► Emissions of Kyoto gases are reduced such that the probability of exceeding 2 °C is well below 50%. ► These scenarios assume moderate binding commitments for DCs after 2030. ► The undiscounted cumulative GDP costs are 0.75% above baseline.

  15. Relaying Strategies and Protocols for Efficient Wireless Networks

    KAUST Repository

    Zafar, Ammar

    2014-10-01

    Next generation wireless networks are expected to provide high data rate and satisfy the Quality-of-Service (QoS) constraints of the users. A significant component of achieving these goals is to increase the effi ciency of wireless networks by either optimizing current architectures or exploring new technologies which achieve that. The latter includes revisiting technologies which were previously proposed, but due to a multitude of reasons were ignored at that time. One such technology is relaying which was initially proposed in the latter half of the 1960s and then was revived in the early 2000s. In this dissertation, we study relaying in conjunction with resource allocation to increase the effi ciency of wireless networks. In this regard, we differentiate between conventional relaying and relaying with buffers. Conventional relaying is traditional relaying where the relay forwards the signal it received immediately. On the other hand, in relaying with buffers or buffer-aided relaying as it is called, the relay can store received data in its buffer and forward it later on. This gives the benefit of taking advantage of good channel conditions as the relay can only transmit when the channel conditions are good. The dissertation starts with conventional relaying and considers the problem of minimizing the total consumed power while maintaining system QoS. After upper bounding the system performance, more practical algorithms which require reduced feedback overhead are explored. Buffer-aided relaying is then considered and the joint user-and-hop scheduler is introduced which exploits multi-user diversity (MUD) and 5 multi-hop diversity (MHD) gains together in dual-hop broadcast channels. Next joint user-and-hop scheduling is extended to the shared relay channel where two source-destination pairs share a single relay. The benefits of buffer-aided relaying in the bidirectional relay channel utilizing network coding are then explored. Finally, a new transmission protocol

  16. Efficient use of unlabeled data for protein sequence classification: a comparative study.

    Science.gov (United States)

    Kuksa, Pavel; Huang, Pai-Hsi; Pavlovic, Vladimir

    2009-04-29

    Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to particular folds or superfamilies, the so-called labeled data set, can attain significantly improved accuracy if this data is supplemented with protein sequences that lack any class tags-the unlabeled data. In this study, we present a principled and biologically motivated computational framework that more effectively exploits the unlabeled data by only using the sequence regions that are more likely to be biologically relevant for better prediction accuracy. As overly-represented sequences in large uncurated databases may bias the estimation of computational models that rely on unlabeled data, we also propose a method to remove this bias and improve performance of the resulting classifiers. Combined with state-of-the-art string kernels, our proposed computational framework achieves very accurate semi-supervised protein remote fold and homology detection on three large unlabeled databases. It outperforms current state-of-the-art methods and exhibits significant reduction in running time. The unlabeled sequences used under the semi-supervised setting resemble the unpolished gemstones; when used as-is, they may carry unnecessary features and hence compromise the classification accuracy but once cut and polished, they improve the accuracy of the classifiers considerably.

  17. Evaluation of ovsynch protocols for timed artificial insemination in water buffaloes in Bangladesh

    International Nuclear Information System (INIS)

    Hoque, M.N.; Talukder, A.K.; Akter, M.; Shamsuddin, M.

    2016-01-01

    Full text: A total of 65 water buffaloes (groups A, B, and C) at =>60 days postpartum with a body condition score (BCS) of =>2.5 were selected to evaluate ovsynch protocols for timed artificial insemination (TAI). The group A buffaloes (n = 25) were treated with a simple ovsynch protocol (GnRH - Day 7 - PGF alpha - Day 2 - GnRH - 16 h - TAI). The group B buffaloes (n = 22) received PGF2 alpha treatment 12 days before the initiation of simple ovsynch (PGF2 alpha at Day -12 + simple ovsynch; modified ovsynch). The group C buffaloes (n = 18) were treated with a double ovsynch protocol (GnRH - Day 7 - PGF2 alpha - Day 3 - GnRH - Day 7 - GnRH - Day 7 - PGF2 alpha - 48 h - GnRH - 16 h - TAI). Milk P4 ELISA was used for tracking ovulation and conception rates. Ovulation rates were higher in buffaloes that received the double ovsynch treatment (group C; 83.3%) than those with simple ovsynch (group A; 72.0%; P < 0.05). The group C cows (44.4%) achieved a higher concentration rate than the cows of groups A (28.0%) and B (36.4%) (P < 0.05) and multiparous buffaloes having BCS of =>3.5 responded better to the ovsynch treatments than the primiparous ones (P < 0.05). The double ovsynch protocol increases both ovulation and conception rates in comparison to the simple and modified ovsynch protocols and is more effective in multiparous cows than in primiparous ones. (author)

  18. Feeling Is Believing: A Secure Template Exchange Protocol

    NARCIS (Netherlands)

    Buhan, I.R.; Doumen, J.M.; Hartel, Pieter H.; Veldhuis, Raymond N.J.; Lee, Seong-Whan; Li, Stan Z.

    We use grip pattern based biometrics as a secure side channel to achieve pre-authentication in a protocol that sets up a secure channel between two hand held devices. The protocol efficiently calculates a shared secret key from biometric data. The protocol is used in an application where grip

  19. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.

    Science.gov (United States)

    Althammer, Sonja; González-Vallinas, Juan; Ballaré, Cecilia; Beato, Miguel; Eyras, Eduardo

    2011-12-15

    High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy eduardo.eyras@upf.edu Supplementary data are available at Bioinformatics online.

  20. A New Ultra-lightweight Authentication Protocol for Low Cost RFID Tags

    Directory of Open Access Journals (Sweden)

    Xin Wang

    2013-05-01

    Full Text Available The Radio Frequency Identification (RFID system has been widely used in almost every aspects of the society. At present, the problem of security and privacy become a key factor of severely blocking the widespread of its usage. However, due to restraints on RFID tag’s manufacturing cost, the traditional methods of encryption are not good candidate to defend the security of wireless communication channel between reader and tag. Designing lightweight or ultra-lightweight RFID authentication protocol has become a hot research topic recently. This paper proposes a new ultra-lightweight RFID authentication protocol with high robustness and execution efficiency. The proposed protocol requires only simple bit-wise operations, it has the characteristics of low storage requirement and communication cost. At the same time, through elaborate mechanism design, avoid the vulnerability of the existing ultra-lightweight authentication protocols.

  1. Efficient quantum secure communication with a publicly known key

    International Nuclear Information System (INIS)

    Li Chunyan; Li Xihan; Deng Fuguo; Zhou Hongyu

    2008-01-01

    This paper presents a simple way for an eavesdropper to eavesdrop freely the secret message in the experimental realization of quantum communication protocol proposed by Beige et al (2002 Acta Phys. Pol. A 101 357). Moreover, it introduces an efficient quantum secure communication protocol based on a publicly known key with decoy photons and two biased bases by modifying the original protocol. The total efficiency of this new protocol is double that of the original one. With a low noise quantum channel, this protocol can be used for transmitting a secret message. At present, this protocol is good for generating a private key efficiently. (general)

  2. Application Framework with Abstractions for Protocol and Agent Role

    DEFF Research Database (Denmark)

    Kristensen, Bent Bruun

    2016-01-01

    In multi-agent systems, agents interact by sending and receiving messages and the actual sequences of message form interaction structures between agents. Protocols and agents organized internally by agent roles support these interaction structures. Description and use of protocols based on agent ...... roles are supported by a simple and expressive application framework....

  3. Deterministic and efficient quantum cryptography based on Bell's theorem

    International Nuclear Information System (INIS)

    Chen Zengbing; Pan Jianwei; Zhang Qiang; Bao Xiaohui; Schmiedmayer, Joerg

    2006-01-01

    We propose a double-entanglement-based quantum cryptography protocol that is both efficient and deterministic. The proposal uses photon pairs with entanglement both in polarization and in time degrees of freedom; each measurement in which both of the two communicating parties register a photon can establish one and only one perfect correlation, and thus deterministically create a key bit. Eavesdropping can be detected by violation of local realism. A variation of the protocol shows a higher security, similar to the six-state protocol, under individual attacks. Our scheme allows a robust implementation under the current technology

  4. A simple, flexible and efficient PCR-fusion/Gateway cloning procedure for gene fusion, site-directed mutagenesis, short sequence insertion and domain deletions and swaps

    Directory of Open Access Journals (Sweden)

    Etchells J Peter

    2009-10-01

    Full Text Available Abstract Background The progress and completion of various plant genome sequencing projects has paved the way for diverse functional genomic studies that involve cloning, modification and subsequent expression of target genes. This requires flexible and efficient procedures for generating binary vectors containing: gene fusions, variants from site-directed mutagenesis, addition of protein tags together with domain swaps and deletions. Furthermore, efficient cloning procedures, ideally high throughput, are essential for pyramiding of multiple gene constructs. Results Here, we present a simple, flexible and efficient PCR-fusion/Gateway cloning procedure for construction of binary vectors for a range of gene fusions or variants with single or multiple nucleotide substitutions, short sequence insertions, domain deletions and swaps. Results from selected applications of the procedure which include ORF fusion, introduction of Cys>Ser mutations, insertion of StrepII tag sequence and domain swaps for Arabidopsis secondary cell wall AtCesA genes are demonstrated. Conclusion The PCR-fusion/Gateway cloning procedure described provides an elegant, simple and efficient solution for a wide range of diverse and complicated cloning tasks. Through streamlined cloning of sets of gene fusions and modification variants into binary vectors for systematic functional studies of gene families, our method allows for efficient utilization of the growing sequence and expression data.

  5. Efficient and secure authentication protocol for roaming user in ...

    Indian Academy of Sciences (India)

    BALU L PARNE

    2018-05-29

    May 29, 2018 ... 1 Department of Computer Science and Engineering, Visvesvaraya National Institute of Technology (VNIT), ... proposed protocol is presented by BAN logic and the security ..... with session key Sk of the HLR to protect from.

  6. The HMMER Web Server for Protein Sequence Similarity Search.

    Science.gov (United States)

    Prakash, Ananth; Jeffryes, Matt; Bateman, Alex; Finn, Robert D

    2017-12-08

    Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis. The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the HMMER Web server using various input formats and user defined parameters. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  7. A new energy-efficient MAC protocol with noise-based transmitted-reference modulation for wireless sensor network

    NARCIS (Netherlands)

    Morshed, S.; Heijenk, Geert; Meijerink, Arjan; Ye, D.; van der Zee, Ronan A.R.; Bentum, Marinus Jan

    2013-01-01

    Energy-constrained behavior of sensor nodes is one of the most important criteria for successful deployment of wireless sensor networks. The medium access control (MAC) protocol determines to a large extent the time a sensor node transceiver spends listening or transmitting, and hence the energy

  8. An efficient RFID authentication protocol to enhance patient medication safety using elliptic curve cryptography.

    Science.gov (United States)

    Zhang, Zezhong; Qi, Qingqing

    2014-05-01

    Medication errors are very dangerous even fatal since it could cause serious even fatal harm to patients. In order to reduce medication errors, automated patient medication systems using the Radio Frequency Identification (RFID) technology have been used in many hospitals. The data transmitted in those medication systems is very important and sensitive. In the past decade, many security protocols have been proposed to ensure its secure transition attracted wide attention. Due to providing mutual authentication between the medication server and the tag, the RFID authentication protocol is considered as the most important security protocols in those systems. In this paper, we propose a RFID authentication protocol to enhance patient medication safety using elliptic curve cryptography (ECC). The analysis shows the proposed protocol could overcome security weaknesses in previous protocols and has better performance. Therefore, the proposed protocol is very suitable for automated patient medication systems.

  9. Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

    Directory of Open Access Journals (Sweden)

    Chengxi Ye

    2016-06-01

    Full Text Available Motivation. The third generation sequencing (3GS technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS technologies (less than 1%. Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc.

  10. Saving time in a space-efficient simulation algorithm

    NARCIS (Netherlands)

    Markovski, J.

    2011-01-01

    We present an efficient algorithm for computing the simulation preorder and equivalence for labeled transition systems. The algorithm improves an existing space-efficient algorithm and improves its time complexity by employing a variant of the stability condition and exploiting properties of the

  11. Optimistic protocol for partitioned distributed database systems

    International Nuclear Information System (INIS)

    Davidson, S.B.

    1982-01-01

    A protocol for transaction processing during partition failures is presented which guarantees mutual consistency between copies of data-items after repair is completed. The protocol is optimistic in that transactions are processed without restrictions during the failure; conflicts are detected at repair time using a precedence graph and are resolved by backing out transactions according to some backout strategy. The protocol is then evaluated using simulation and probabilistic modeling. In the simulation, several parameters are varied such as the number of transactions processed in a group, the type of transactions processed, the number of data-items present in the database, and the distribution of references to data-items. The simulation also uses different backout strategies. From these results we note conditions under which the protocol performs well, i.e., conditions under which the protocol backs out a small percentage of the transaction run. A probabilistic model is developed to estimate the expected number of transactions backed out using most of the above database and transaction parameters, and is shown to agree with simulation results. Suggestions are then made on how to improve the performance of the protocol. Insights gained from the simulation and probabilistic modeling are used to develop a backout strategy which takes into account individual transaction costs and attempts to minimize total backout cost. Although the problem of choosing transactions to minimize total backout cost is, in general, NP-complete, the backout strategy is efficient and produces very good results

  12. Privacy-Preserving Data Aggregation Protocol for Fog Computing-Assisted Vehicle-to-Infrastructure Scenario

    Directory of Open Access Journals (Sweden)

    Yanan Chen

    2018-01-01

    Full Text Available Vehicle-to-infrastructure (V2I communication enables moving vehicles to upload real-time data about road surface situation to the Internet via fixed roadside units (RSU. Thanks to the resource restriction of mobile vehicles, fog computation-enhanced V2I communication scenario has received increasing attention recently. However, how to aggregate the sensed data from vehicles securely and efficiently still remains open to the V2I communication scenario. In this paper, a light-weight and anonymous aggregation protocol is proposed for the fog computing-based V2I communication scenario. With the proposed protocol, the data collected by the vehicles can be efficiently obtained by the RSU in a privacy-preserving manner. Particularly, we first suggest a certificateless aggregate signcryption (CL-A-SC scheme and prove its security in the random oracle model. The suggested CL-A-SC scheme, which is of independent interest, can achieve the merits of certificateless cryptography and signcryption scheme simultaneously. Then we put forward the anonymous aggregation protocol for V2I communication scenario as one extension of the suggested CL-A-SC scheme. Security analysis demonstrates that the proposed aggregation protocol achieves desirable security properties. The performance comparison shows that the proposed protocol significantly reduces the computation and communication overhead compared with the up-to-date protocols in this field.

  13. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    Science.gov (United States)

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp.

  14. Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing.

    Science.gov (United States)

    Euskirchen, Philipp; Bielle, Franck; Labreche, Karim; Kloosterman, Wigard P; Rosenberg, Shai; Daniau, Mailys; Schmitt, Charlotte; Masliah-Planchon, Julien; Bourdeaut, Franck; Dehais, Caroline; Marie, Yannick; Delattre, Jean-Yves; Idbaih, Ahmed

    2017-11-01

    Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making. Here, we explored the potential of a pocket-size nanopore sequencing device for multimodal and rapid molecular diagnostics of cancer. Low-pass whole genome sequencing was used to simultaneously generate copy number (CN) and methylation profiles from native tumor DNA in the same sequencing run. Single nucleotide variants in IDH1, IDH2, TP53, H3F3A, and the TERT promoter region were identified using deep amplicon sequencing. Nanopore sequencing yielded ~0.1X genome coverage within 6 h and resulting CN and epigenetic profiles correlated well with matched microarray data. Diagnostically relevant alterations, such as 1p/19q codeletion, and focal amplifications could be recapitulated. Using ad hoc random forests, we could perform supervised pan-cancer classification to distinguish gliomas, medulloblastomas, and brain metastases of different primary sites. Single nucleotide variants in IDH1, IDH2, and H3F3A were identified using deep amplicon sequencing within minutes of sequencing. Detection of TP53 and TERT promoter mutations shows that sequencing of entire genes and GC-rich regions is feasible. Nanopore sequencing allows same-day detection of structural variants, point mutations, and methylation profiling using a single device with negligible capital cost. It

  15. Wireless Power Transfer Protocols in Sensor Networks: Experiments and Simulations

    Directory of Open Access Journals (Sweden)

    Sotiris Nikoletseas

    2017-04-01

    Full Text Available Rapid technological advances in the domain of Wireless Power Transfer pave the way for novel methods for power management in systems of wireless devices, and recent research works have already started considering algorithmic solutions for tackling emerging problems. In this paper, we investigate the problem of efficient and balanced Wireless Power Transfer in Wireless Sensor Networks. We employ wireless chargers that replenish the energy of network nodes. We propose two protocols that configure the activity of the chargers. One protocol performs wireless charging focused on the charging efficiency, while the other aims at proper balance of the chargers’ residual energy. We conduct detailed experiments using real devices and we validate the experimental results via larger scale simulations. We observe that, in both the experimental evaluation and the evaluation through detailed simulations, both protocols achieve their main goals. The Charging Oriented protocol achieves good charging efficiency throughout the experiment, while the Energy Balancing protocol achieves a uniform distribution of energy within the chargers.

  16. Design and Analysis of Transport Protocols for Reliable High-Speed Communications

    NARCIS (Netherlands)

    Oláh, A.

    1997-01-01

    The design and analysis of transport protocols for reliable communications constitutes the topic of this dissertation. These transport protocols guarantee the sequenced and complete delivery of user data over networks which may lose, duplicate and reorder packets. Reliable transport services are

  17. A modified FASP protocol for high-throughput preparation of protein samples for mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Jeremy Potriquet

    Full Text Available To facilitate high-throughput proteomic analyses we have developed a modified FASP protocol which improves the rate at which protein samples can be processed prior to mass spectrometry. Adapting the original FASP protocol to a 96-well format necessitates extended spin times for buffer exchange due to the low centrifugation speeds tolerated by these devices. However, by using 96-well plates with a more robust polyethersulfone molecular weight cutoff membrane, instead of the cellulose membranes typically used in these devices, we could use isopropanol as a wetting agent, decreasing spin times required for buffer exchange from an hour to 30 minutes. In a typical work flow used in our laboratory this equates to a reduction of 3 hours per plate, providing processing times similar to FASP for the processing of up to 96 samples per plate. To test whether our modified protocol produced similar results to FASP and other FASP-like protocols we compared the performance of our modified protocol to the original FASP and the more recently described eFASP and MStern-blot. We show that all FASP-like methods, including our modified protocol, display similar performance in terms of proteins identified and reproducibility. Our results show that our modified FASP protocol is an efficient method for the high-throughput processing of protein samples for mass spectral analysis.

  18. Model-Checking Driven Design of QoS-Based Routing Protocol for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Zhi Chen

    2015-01-01

    Full Text Available Accurate and reliable routing protocols with Quality of Service (QoS support determine the mission-critical application efficiency in WSNs. This paper proposes a model-checking design driven framework for designing the QoS-based routing protocols of WSNs, which involves the light-weight design process, the timed automata model, and the alternative QoS verification properties. The accurate feedback of continually model checking in the iterative design process effectively stimulates the parameter tuning of the protocols. We demonstrate the straightforward and modular characteristics of the proposed framework in designing a prototype QoS-based routing protocol. The prototype study shows that the model-checking design framework may complement other design methods and ensure the QoS implementation of the QoS-based routing protocol design for WSNs.

  19. A robust ECC based mutual authentication protocol with anonymity for session initiation protocol.

    Science.gov (United States)

    Mehmood, Zahid; Chen, Gongliang; Li, Jianhua; Li, Linsen; Alzahrani, Bander

    2017-01-01

    Over the past few years, Session Initiation Protocol (SIP) is found as a substantial application-layer protocol for the multimedia services. It is extensively used for managing, altering, terminating and distributing the multimedia sessions. Authentication plays a pivotal role in SIP environment. Currently, Lu et al. presented an authentication protocol for SIP and profess that newly proposed protocol is protected against all the familiar attacks. However, the detailed analysis describes that the Lu et al.'s protocol is exposed against server masquerading attack and user's masquerading attack. Moreover, it also fails to protect the user's identity as well as it possesses incorrect login and authentication phase. In order to establish a suitable and efficient protocol, having ability to overcome all these discrepancies, a robust ECC-based novel mutual authentication mechanism with anonymity for SIP is presented in this manuscript. The improved protocol contains an explicit parameter for user to cope the issues of security and correctness and is found to be more secure and relatively effective to protect the user's privacy, user's masquerading and server masquerading as it is verified through the comprehensive formal and informal security analysis.

  20. A robust ECC based mutual authentication protocol with anonymity for session initiation protocol.

    Directory of Open Access Journals (Sweden)

    Zahid Mehmood

    Full Text Available Over the past few years, Session Initiation Protocol (SIP is found as a substantial application-layer protocol for the multimedia services. It is extensively used for managing, altering, terminating and distributing the multimedia sessions. Authentication plays a pivotal role in SIP environment. Currently, Lu et al. presented an authentication protocol for SIP and profess that newly proposed protocol is protected against all the familiar attacks. However, the detailed analysis describes that the Lu et al.'s protocol is exposed against server masquerading attack and user's masquerading attack. Moreover, it also fails to protect the user's identity as well as it possesses incorrect login and authentication phase. In order to establish a suitable and efficient protocol, having ability to overcome all these discrepancies, a robust ECC-based novel mutual authentication mechanism with anonymity for SIP is presented in this manuscript. The improved protocol contains an explicit parameter for user to cope the issues of security and correctness and is found to be more secure and relatively effective to protect the user's privacy, user's masquerading and server masquerading as it is verified through the comprehensive formal and informal security analysis.

  1. A Rule-Based Data Transfer Protocol for On-Demand Data Exchange in Vehicular Environment

    Directory of Open Access Journals (Sweden)

    Liao Hsien-Chou

    2009-01-01

    Full Text Available The purpose of Intelligent Transport System (ITS is mainly to increase the driving safety and efficiency. Data exchange is an important way to achieve the purpose. An on-demand data exchange is especially useful to assist a driver avoiding some emergent events. In order to handle the data exchange under dynamic situations, a rule-based data transfer protocol is proposed in this paper. A set of rules is designed according to the principle of request-forward-reply (RFR. That is, they are used to determine the timing of data broadcasting, forwarding, and replying automatically. Two typical situations are used to demonstrate the operation of rules. One is the front view of a driver occluded by other vehicles. The other is the traffic jam. The proposed protocol is flexible and extensible for unforeseen situations. Three simulation tools were also implemented to demonstrate the feasibility of the protocol and measure the network transmission under high density of vehicles. The simulation results show that the rule-based protocol is efficient on data exchange to increase the driving safety.

  2. An efficient regeneration and rapid micropropagation protocol for Almond using dormant axillary buds as explants.

    Science.gov (United States)

    Choudhary, Ravish; Chaudhury, Rekha; Malik, Surendra Kumar; Sharma, Kailash Chandra

    2015-07-01

    An efficient in vitro protocol was standardized for Almond (Prunus dulcis) propagation using dormant axillary buds as explants. Explants were cultured on Murashige and Skoog (MS) and woody plant medium (WPM) supplemented with different concentration/combination(s) of phytohormones. MS basal medium showed lowest shoot induction and took longest duration for shoot initiation. Multiple shoots were induced in MS medium supplemented with the combination of BAP (0.5 mgL(-1)). Cultures showed poor response for rooting in all combinations of plant growth regulators (PGRs) and took 90 days for initiation. Rooting was higher in half strength of MS than in full-strength. The highest root induction (33.33%) was recorded in half MS medium supplemented with 0.1 mgL(-1) IBA (indole-3-butyric acid) followed by full strength of MS medium (20%) supplemented with IBA (0.1 mgL(-1)). α-Naphthalene acetic acid (NAA) was less effective for rooting than IBA. The highest root induction (25%) was found in half strength of MS medium supplemented with 0.1 mgL(-1) NAA followed by full strength of MS medium (20%). The protocol developed would be of use in mass propagation of almond and also support in vitro conservation.

  3. A SURVEY ON MULTICAST ROUTING PROTOCOLS FOR PERFORMANCE EVALUATION IN WIRELESS SENSOR NETWORK

    Directory of Open Access Journals (Sweden)

    A. Suruliandi

    2015-03-01

    Full Text Available Multicast is a process used to transfer same message to multiple receivers at the same time. This paper presents the simulation and analysis of the performance of six different multicast routing protocols for Wireless Sensor Network (WSN. They are On Demand Multicast Routing Protocol (ODMRP, Protocol for Unified Multicasting through Announcement (PUMA, Multicast Adhoc On demand Distance Vector Protocol (MAODV, Overlay Boruvka-based Adhoc Multicast Protocol (OBAMP, Application Layer Multicast Algorithm (ALMA and enhanced version of ALMA (ALMA-H for WSN. Among them, ODMRP, MAODV and PUMA are reactive protocols while OBAMP, ALMA and ALMA-H are proactive protocols. This paper compares the performance of these protocols with common parameters such as Throughput, Reliability, End-to-End delay and Packet Delivery Ratio (PDR with increasing the numbers of nodes and increasing the speed of the nodes. The main objective of this work is to select the efficient multicast routing protocol for WSN among six multicast routing protocol based on relative strength and weakness of each protocol. The summary of above six multicast routing protocols is presented with a table of different performance characteristics. Experimental result shows that ODMRP attains higher throughput, reliability and higher packet delivery ratio than other multicast routing protocol, while incurring far less end-to-end delay.

  4. FODA: a novel efficient multiple access protocol for highly dynamic self-organizing networks

    Science.gov (United States)

    Li, Hantao; Liu, Kai; Zhang, Jun

    2005-11-01

    Based on the concept of contention reservation for polling transmission and collision prevention strategy for collision resolution, a fair on-demand access (FODA) protocol for supporting node mobility and multihop architecture in highly dynamic self-organizing networks is proposed. In the protocol, a distributed clustering network architecture formed by self-organizing algorithm and a main idea of reserving channel resources to get polling service are adopted, so that the hidden terminal (HT) and exposed terminal (ET) problems existed in traffic transmission due to multihop architecture and wireless transmission can be eliminated completely. In addition, an improved collision prevention scheme based on binary countdown algorithm (BCA), called fair collision prevention (FCP) algorithm, is proposed to greatly eliminate unfair phenomena existed in contention access of newly active ordinary nodes and completely resolve access collisions. Finally, the performance comparison of the FODA protocol with carrier sense multiple access with collision avoidance (CSMA/CA) and polling protocols by OPNET simulation are presented. Simulation results show that the FODA protocol can overcome the disadvantages of CSMA/CA and polling protocols, and achieve higher throughput, lower average message delay and less average message dropping rate.

  5. A rapid infusion protocol is safe for total dose iron polymaltose: time for change.

    Science.gov (United States)

    Garg, M; Morrison, G; Friedman, A; Lau, A; Lau, D; Gibson, P R

    2011-07-01

    Intravenous correction of iron deficiency by total dose iron polymaltose is inexpensive and safe, but current protocols entail prolonged administration over more than 4 h. This results in reduced patient acceptance, and hospital resource strain. We aimed to assess prospectively the safety of a rapid intravenous protocol and compare this with historical controls. Consecutive patients in whom intravenous iron replacement was indicated were invited to have up to 1.5 g iron polymaltose by a 58-min infusion protocol after an initial 15-min test dose without pre-medication. Infusion-related adverse events (AE) and delayed AE over the ensuing 5 days were also prospectively documented and graded as mild, moderate or severe. One hundred patients, 63 female, mean age 54 (range 18-85) years were studied. Thirty-four infusion-related AE to iron polymaltose occurred in a total of 24 patients--25 mild, 8 moderate and 1 severe; higher than previously reported for a slow protocol iron infusion. Thirty-one delayed AE occurred in 26 patients--26 mild, 3 moderate and 2 severe; similar to previously reported. All but five patients reported they would prefer iron replacement through the rapid protocol again. The presence of inflammatory bowel disease (IBD) predicted infusion-related reactions (54% vs 14% without IBD, P cost, resource utilization and time benefits for the patient and hospital system. © 2011 The Authors. Internal Medicine Journal © 2011 Royal Australasian College of Physicians.

  6. New scheduling rules for a dynamic flexible flow line problem with sequence-dependent setup times

    Science.gov (United States)

    Kia, Hamidreza; Ghodsypour, Seyed Hassan; Davoudpour, Hamid

    2017-09-01

    In the literature, the application of multi-objective dynamic scheduling problem and simple priority rules are widely studied. Although these rules are not efficient enough due to simplicity and lack of general insight, composite dispatching rules have a very suitable performance because they result from experiments. In this paper, a dynamic flexible flow line problem with sequence-dependent setup times is studied. The objective of the problem is minimization of mean flow time and mean tardiness. A 0-1 mixed integer model of the problem is formulated. Since the problem is NP-hard, four new composite dispatching rules are proposed to solve it by applying genetic programming framework and choosing proper operators. Furthermore, a discrete-event simulation model is made to examine the performances of scheduling rules considering four new heuristic rules and the six adapted heuristic rules from the literature. It is clear from the experimental results that composite dispatching rules that are formed from genetic programming have a better performance in minimization of mean flow time and mean tardiness than others.

  7. Design of SIP transformation server for efficient media negotiation

    Science.gov (United States)

    Pack, Sangheon; Paik, Eun Kyoung; Choi, Yanghee

    2001-07-01

    Voice over IP (VoIP) is one of the advanced services supported by the next generation mobile communication. VoIP should support various media formats and terminals existing together. This heterogeneous environment may prevent diverse users from establishing VoIP sessions among them. To solve the problem an efficient media negotiation mechanism is required. In this paper, we propose the efficient media negotiation architecture using the transformation server and the Intelligent Location Server (ILS). The transformation server is an extended Session Initiation Protocol (SIP) proxy server. It can modify an unacceptable session INVITE message into an acceptable one using the ILS. The ILS is a directory server based on the Lightweight Directory Access Protocol (LDAP) that keeps userí*s location information and available media information. The proposed architecture can eliminate an unnecessary response and re-INVITE messages of the standard SIP architecture. It takes only 1.5 round trip times to negotiate two different media types while the standard media negotiation mechanism takes 2.5 round trip times. The extra processing time in message handling is negligible in comparison to the reduced round trip time. The experimental results show that the session setup time in the proposed architecture is less than the setup time in the standard SIP. These results verify that the proposed media negotiation mechanism is more efficient in solving diversity problems.

  8. Yield and Efficiency of Mental Health Screening: A Comparison of Screening Protocols at Intake to Prison.

    Science.gov (United States)

    Martin, Michael S; Potter, Beth K; Crocker, Anne G; Wells, George A; Colman, Ian

    2016-01-01

    The value of screening for mental illness has increasingly been questioned in low prevalence settings due to high false positive rates. However, since false positive rates are related to prevalence, screening may be more effective in higher prevalence settings, including correctional institutions. We compared the yield (i.e. newly detected cases) and efficiency (i.e. false positives) of five screening protocols to detect mental illness in prisons against the use of mental health history taking (the prior approach to detecting mental illness). We estimated the accuracy of the six approaches to detect an Axis I disorder among a sample of 467 newly admitted male inmates (83.1% participation rate). Mental health history taking identified only 41.0% (95% CI 32.1, 50.6) of all inmates with mental illness. Screening protocols identified between 61.9 and 85.7% of all cases, but referred between 2 and 3 additional individuals who did not have a mental illness for every additional case detected compared to the mental health history taking approach. In low prevalence settings (i.e. 10% or less) the screening protocols would have had between 4.6 and 16.2 false positives per true positive. While screening may not be practical in low prevalence settings, it may be beneficial in jails and prisons where the prevalence of mental illness is higher. Further consideration of the context in which screening is being implemented, and of the impacts of policies and clinical practices on the benefits and harms of screening is needed to determine the effectiveness of screening in these settings.

  9. Yield and Efficiency of Mental Health Screening: A Comparison of Screening Protocols at Intake to Prison.

    Directory of Open Access Journals (Sweden)

    Michael S Martin

    Full Text Available The value of screening for mental illness has increasingly been questioned in low prevalence settings due to high false positive rates. However, since false positive rates are related to prevalence, screening may be more effective in higher prevalence settings, including correctional institutions. We compared the yield (i.e. newly detected cases and efficiency (i.e. false positives of five screening protocols to detect mental illness in prisons against the use of mental health history taking (the prior approach to detecting mental illness.We estimated the accuracy of the six approaches to detect an Axis I disorder among a sample of 467 newly admitted male inmates (83.1% participation rate. Mental health history taking identified only 41.0% (95% CI 32.1, 50.6 of all inmates with mental illness. Screening protocols identified between 61.9 and 85.7% of all cases, but referred between 2 and 3 additional individuals who did not have a mental illness for every additional case detected compared to the mental health history taking approach. In low prevalence settings (i.e. 10% or less the screening protocols would have had between 4.6 and 16.2 false positives per true positive.While screening may not be practical in low prevalence settings, it may be beneficial in jails and prisons where the prevalence of mental illness is higher. Further consideration of the context in which screening is being implemented, and of the impacts of policies and clinical practices on the benefits and harms of screening is needed to determine the effectiveness of screening in these settings.

  10. A security analysis of version 2 of the Network Time Protocol (NTP): A report to the privacy and security research group

    Science.gov (United States)

    Bishop, Matt

    1991-01-01

    The Network Time Protocol is being used throughout the Internet to provide an accurate time service. The security requirements are examined of such a service, version 2 of the NTP protocol is analyzed to determine how well it meets these requirements, and improvements are suggested where appropriate.

  11. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    Science.gov (United States)

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  12. A Secure Cluster-Based Multipath Routing Protocol for WMSNs

    Directory of Open Access Journals (Sweden)

    Jamal N. Al-Karaki

    2011-04-01

    Full Text Available The new characteristics of Wireless Multimedia Sensor Network (WMSN and its design issues brought by handling different traffic classes of multimedia content (video streams, audio, and still images as well as scalar data over the network, make the proposed routing protocols for typical WSNs not directly applicable for WMSNs. Handling real-time multimedia data requires both energy efficiency and QoS assurance in order to ensure efficient utility of different capabilities of sensor resources and correct delivery of collected information. In this paper, we propose a Secure Cluster-based Multipath Routing protocol for WMSNs, SCMR, to satisfy the requirements of delivering different data types and support high data rate multimedia traffic. SCMR exploits the hierarchical structure of powerful cluster heads and the optimized multiple paths to support timeliness and reliable high data rate multimedia communication with minimum energy dissipation. Also, we present a light-weight distributed security mechanism of key management in order to secure the communication between sensor nodes and protect the network against different types of attacks. Performance evaluation from simulation results demonstrates a significant performance improvement comparing with existing protocols (which do not even provide any kind of security feature in terms of average end-to-end delay, network throughput, packet delivery ratio, and energy consumption.

  13. Single Machine Scheduling and Due Date Assignment with Past-Sequence-Dependent Setup Time and Position-Dependent Processing Time

    Directory of Open Access Journals (Sweden)

    Chuan-Li Zhao

    2014-01-01

    Full Text Available This paper considers single machine scheduling and due date assignment with setup time. The setup time is proportional to the length of the already processed jobs; that is, the setup time is past-sequence-dependent (p-s-d. It is assumed that a job's processing time depends on its position in a sequence. The objective functions include total earliness, the weighted number of tardy jobs, and the cost of due date assignment. We analyze these problems with two different due date assignment methods. We first consider the model with job-dependent position effects. For each case, by converting the problem to a series of assignment problems, we proved that the problems can be solved in On4 time. For the model with job-independent position effects, we proved that the problems can be solved in On3 time by providing a dynamic programming algorithm.

  14. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    Energy Technology Data Exchange (ETDEWEB)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Department of Radiology, Zurich (Switzerland); Espinosa, Norman [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Orthopedic Surgery, Zurich (Switzerland)

    2017-08-15

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  15. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    International Nuclear Information System (INIS)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja; Espinosa, Norman

    2017-01-01

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  16. Efficient generation of single and entangled photons on a silicon photonic integrated chip

    International Nuclear Information System (INIS)

    Mower, Jacob; Englund, Dirk

    2011-01-01

    We present a protocol for generating on-demand, indistinguishable single photons on a silicon photonic integrated chip. The source is a time-multiplexed spontaneous parametric down-conversion element that allows optimization of single-photon versus multiphoton emission while realizing high output rate and indistinguishability. We minimize both the scaling of active elements and the scaling of active element loss with multiplexing. We then discuss detection strategies and data processing to further optimize the procedure. We simulate an improvement in single-photon-generation efficiency over previous time-multiplexing protocols, assuming existing fabrication capabilities. We then apply this system to generate heralded Bell states. The generation efficiency of both nonclassical states could be increased substantially with improved fabrication procedures.

  17. High-throughput sequencing of forensic genetic samples using punches of FTA cards with buccal swabs.

    Science.gov (United States)

    Kampmann, Marie-Louise; Buchard, Anders; Børsting, Claus; Morling, Niels

    2016-01-01

    Here, we demonstrate that punches from buccal swab samples preserved on FTA cards can be used for high-throughput DNA sequencing, also known as massively parallel sequencing (MPS). We typed 44 reference samples with the HID-Ion AmpliSeq Identity Panel using washed 1.2 mm punches from FTA cards with buccal swabs and compared the results with those obtained with DNA extracted using the EZ1 DNA Investigator Kit. Concordant profiles were obtained for all samples. Our protocol includes simple punch, wash, and PCR steps, reducing cost and hands-on time in the laboratory. Furthermore, it facilitates automation of DNA sequencing.

  18. Efficient Sequence Detection of Multicarrier Transmissions over Doubly Dispersive Channels

    Directory of Open Access Journals (Sweden)

    Hwang Sung-Jun

    2006-01-01

    Full Text Available We propose a high-spectral-efficiency multicarrier system for communication over the doubly dispersive (DD channel which yields very low frame error rate (FER, with quadratic (in the frame length receiver complexity. To accomplish this, we combine a non-(biorthogonal multicarrier modulation (MCM scheme recently proposed by the authors with novel sequence detection (SD and channel estimation (CE algorithms. In particular, our MCM scheme allows us to accurately represent the DD channels otherwise complicated intercarrier interference (ICI and intersymbol interference (ISI response with a relatively small number of coefficients. The SD and CE algorithms then leverage this sparse ICI/ISI structure for low-complexity operation. Our SD algorithm combines a novel adaptive breadth-first search procedure with a new fast MMSE-GDFE preprocessor, while our CE algorithm uses a rank-reduced pilot-aided Wiener technique to estimate only the significant ICI/ISI coefficients.

  19. An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples.

    Directory of Open Access Journals (Sweden)

    Jonathan A Scolnick

    Full Text Available Fusion genes are known to be key drivers of tumor growth in several types of cancer. Traditionally, detecting fusion genes has been a difficult task based on fluorescent in situ hybridization to detect chromosomal abnormalities. More recently, RNA sequencing has enabled an increased pace of fusion gene identification. However, RNA-Seq is inefficient for the identification of fusion genes due to the high number of sequencing reads needed to detect the small number of fusion transcripts present in cells of interest. Here we describe a method, Single Primer Enrichment Technology (SPET, for targeted RNA sequencing that is customizable to any target genes, is simple to use, and efficiently detects gene fusions. Using SPET to target 5701 exons of 401 known cancer fusion genes for sequencing, we were able to identify known and previously unreported gene fusions from both fresh-frozen and formalin-fixed paraffin-embedded (FFPE tissue RNA in both normal tissue and cancer cells.

  20. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  1. A Practical and Time-Efficient High-Intensity Interval Training Program Modifies Cardio-Metabolic Risk Factors in Adults with Risk Factors for Type II Diabetes

    Directory of Open Access Journals (Sweden)

    Bethan E. Phillips

    2017-09-01

    Full Text Available IntroductionRegular physical activity (PA can reduce the risk of developing type 2 diabetes, but adherence to time-orientated (150 min week−1 or more PA guidelines is very poor. A practical and time-efficient PA regime that was equally efficacious at controlling risk factors for cardio-metabolic disease is one solution to this problem. Herein, we evaluate a new time-efficient and genuinely practical high-intensity interval training (HIT protocol in men and women with pre-existing risk factors for type 2 diabetes.Materials and methodsOne hundred eighty-nine sedentary women (n = 101 and men (n = 88 with impaired glucose tolerance and/or a body mass index >27 kg m−2 [mean (range age: 36 (18–53 years] participated in this multi-center study. Each completed a fully supervised 6-week HIT protocol at work-loads equivalent to ~100 or ~125% V˙O2 max. Change in V˙O2 max was used to monitor protocol efficacy, while Actiheart™ monitors were used to determine PA during four, weeklong, periods. Mean arterial (blood pressure (MAP and fasting insulin resistance [homeostatic model assessment (HOMA-IR] represent key health biomarker outcomes.ResultsThe higher intensity bouts (~125% V˙O2 max used during a 5-by-1 min HIT protocol resulted in a robust increase in V˙O2 max (136 participants, +10.0%, p < 0.001; large size effect. 5-by-1 HIT reduced MAP (~3%; p < 0.001 and HOMA-IR (~16%; p < 0.01. Physiological responses were similar in men and women while a sizeable proportion of the training-induced changes in V˙O2 max, MAP, and HOMA-IR was retained 3 weeks after cessation of training. The supervised HIT sessions accounted for the entire quantifiable increase in PA, and this equated to 400 metabolic equivalent (MET min week−1. Meta-analysis indicated that 5-by-1 HIT matched the efficacy and variability of a time-consuming 30-week PA program on V˙O2 max, MAP, and HOMA-IR.ConclusionWith a total time-commitment of

  2. Protocols for second-generation business satellites systems

    Science.gov (United States)

    Evans, B. G.; Coakley, F. P.; El Amin, M. H. M.

    The paper discusses the nature and mix of traffic in business satellite systems and describes the limitations on the protocol imposed by the differing impairments of speech, video, and data. A simple TDMA system protocol is presented which meets the requirements of mixed-service operation. The efficiency of the protocol together with implications for allocation, scheduling and synchronisation are discussed. Future-generation satellites will probably use on-board processing. Some initial work on protocols that make use of on-board processing and the implications for satellite and earth-station equipment are presented.

  3. Protocol for the building construction process with regard to the implementation trajectory protocols EWN and EUN. Manual for commissioners, contractors, building management offices and energy efficiency standard advisors; Handleiding opnameprotocollen EWN en EUN. Voor opdrachtgevers, aannemers, bouwmanagementbureaus en EPN-adviseurs

    Energy Technology Data Exchange (ETDEWEB)

    Neeleman, J. [DWA installatie- en energieadvies, Duitslandweg 4, Postbus 274, 2410 AG Bodegraven (Netherlands)

    2013-04-15

    In the year 2012 it was foreseen to base the energy label for new buildings on the Energy Efficiency Coefficient (EPC in Dutch). This is a protocol for residential and utility buildings, with the aim to check whether and to what extent buildings were constructed according the EPC and to determine the realized EPC. In order to gain experience with the new protocols and the voluntary ventilation test the Protocol for the Energy Label for New Houses (EWN in Dutch) and the Protocol for the Energy Label for New Utility Buildings (EUN in Dutch) were conducted in 12 newly built housing projects and 5 projects in the utility building sector. With this manual you can realize energy efficient houses and/or utility buildings that meet the standards [Dutch] In het jaar 2012 was voorzien om het nieuwbouwlabel te baseren op de EPC (Energie Prestatie Coefficient). Hiervoor is een opnameprotocol opgesteld voor de woningbouw en de utiliteitsbouw, met als doel te controleren of en in hoeverre conform de EPC is gebouwd en om de gerealiseerde EPC te bepalen. Om ervaring op te doen met de nieuwe opnameprotocollen en de vrijwillige ventilatietoets werden het Opnameprotocol Energielabel Woningen Nieuwbouw (EWN) en Opnameprotocol Energielabel Utiliteitsgebouwen Nieuwbouw (EUN) uitgevoerd bij 12 nieuwbouwprojecten in de woningbouw en 5 projecten in de utiliteitsbouw. Met deze handleiding realiseert u energiezuinige woningen en/of utiliteitsgebouwen die aan de verwachtingen voldoen.

  4. The Control Packet Collision Avoidance Algorithm for the Underwater Multichannel MAC Protocols via Time-Frequency Masking

    Directory of Open Access Journals (Sweden)

    Yang Yu

    2016-01-01

    Full Text Available Establishing high-speed and reliable underwater acoustic networks among multiunmanned underwater vehicles (UUVs is basic to realize cooperative and intelligent control among different UUVs. Nevertheless, different from terrestrial network, the propagation speed of the underwater acoustic network is 1500 m/s, which makes the design of the underwater acoustic network MAC protocols a big challenge. In accordance with multichannel MAC protocols, data packets and control packets are transferred through different channels, which lowers the adverse effect of acoustic network and gradually becomes the popular issues of underwater acoustic networks MAC protocol research. In this paper, we proposed a control packet collision avoidance algorithm utilizing time-frequency masking to deal with the control packets collision in the control channel. This algorithm is based on the scarcity of the noncoherent underwater acoustic communication signals, which regards collision avoiding as separation of the mixtures of communication signals from different nodes. We first measure the W-Disjoint Orthogonality of the MFSK signals and the simulation result demonstrates that there exists time-frequency mask which can separate the source signals from the mixture of the communication signals. Then we present a pairwise hydrophones separation system based on deep networks and the location information of the nodes. Consequently, the time-frequency mask can be estimated.

  5. Managing the wastewater microbiome: Rapid microbial surveillance using Nanopore DNA sequencing

    DEFF Research Database (Denmark)

    Andersen, Martin Hjorth; Kirkegaard, Rasmus Hansen; Albertsen, Mads

    and lead to process breakdown, leading to increased operational costs and potential environmental hazards[1,2]. With current methods, it is often impossible to predict a system crash before it is too late. Monitoring the microbial community for critical changes is tedious, as the process from sample...... to results generally take several days and requires expert knowledge as well as expensive lab facilities. A faster workflow is therefore necessary to ensure a more efficient wastewater management in the future. Experimental design Protocols were developed with focus on portability, ease-of-use and equipment...... (Oxford Nanopore Technologies, UK). The amplicon libraries were sequenced on a MinION (Oxford Nanopore Technologies, UK) and data for the first 10 minutes of sequencing was base-called on a local laptop, mapped to the MiDAS database using minimap2 and analysed in the R environment using the R package...

  6. Cacades: A reliable dissemination protocol for data collection sensor network

    Science.gov (United States)

    Peng, Y.; Song, W.; Huang, R.; Xu, M.; Shirazi, B.; LaHusen, R.; Pei, G.

    2009-01-01

    In this paper, we propose a fast and reliable data dissemination protocol Cascades to disseminate data from the sink(base station) to all or a subset of nodes in a data collection sensor network. Cascades makes use of the parentmonitor-children analogy to ensure reliable dissemination. Each node monitors whether or not its children have received the broadcast messages through snooping children's rebroadcasts or waiting for explicit ACKs. If a node detects a gap in its message sequences, it can fetch the missing messages from its neighbours reactively. Cascades also considers many practical issues for field deployment, such as dynamic topology, link/node failure, etc.. It therefore guarantees that a disseminated message from the sink will reach all intended receivers and the dissemination is terminated in a short time period. Notice that, all existing dissemination protocols either do not guarantee reliability or do not terminate [1, 2], which does not meet the requirement of real-time command control. We conducted experiment evaluations in both TOSSIM simulator and a sensor network testbed to compare Cascades with those existing dissemination protocols in TinyOS sensor networks, which show that Cascades achieves a higher degree of reliability, lower communication cost, and less delivery delay. ??2009 IEEE.

  7. Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time?

    Science.gov (United States)

    McGann, Patrick; Bunin, Jessica L; Snesrud, Erik; Singh, Seema; Maybank, Rosslyn; Ong, Ana C; Kwak, Yoon I; Seronello, Scott; Clifford, Robert J; Hinkle, Mary; Yamada, Stephen; Barnhill, Jason; Lesho, Emil

    2016-07-01

    Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations. Published by Elsevier Inc.

  8. In-memory interconnect protocol configuration registers

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Kevin Y.; Roberts, David A.

    2017-09-19

    Systems, apparatuses, and methods for moving the interconnect protocol configuration registers into the main memory space of a node. The region of memory used for storing the interconnect protocol configuration registers may also be made cacheable to reduce the latency of accesses to the interconnect protocol configuration registers. Interconnect protocol configuration registers which are used during a startup routine may be prefetched into the host's cache to make the startup routine more efficient. The interconnect protocol configuration registers for various interconnect protocols may include one or more of device capability tables, memory-side statistics (e.g., to support two-level memory data mapping decisions), advanced memory and interconnect features such as repair resources and routing tables, prefetching hints, error correcting code (ECC) bits, lists of device capabilities, set and store base address, capability, device ID, status, configuration, capabilities, and other settings.

  9. In-memory interconnect protocol configuration registers

    Science.gov (United States)

    Cheng, Kevin Y.; Roberts, David A.

    2017-09-19

    Systems, apparatuses, and methods for moving the interconnect protocol configuration registers into the main memory space of a node. The region of memory used for storing the interconnect protocol configuration registers may also be made cacheable to reduce the latency of accesses to the interconnect protocol configuration registers. Interconnect protocol configuration registers which are used during a startup routine may be prefetched into the host's cache to make the startup routine more efficient. The interconnect protocol configuration registers for various interconnect protocols may include one or more of device capability tables, memory-side statistics (e.g., to support two-level memory data mapping decisions), advanced memory and interconnect features such as repair resources and routing tables, prefetching hints, error correcting code (ECC) bits, lists of device capabilities, set and store base address, capability, device ID, status, configuration, capabilities, and other settings.

  10. Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments

    Energy Technology Data Exchange (ETDEWEB)

    Motackova, Veronika; Novacek, Jiri [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Zawadzka-Kazimierczuk, Anna; Kazimierczuk, Krzysztof [University of Warsaw, Faculty of Chemistry (Poland); Zidek, Lukas, E-mail: lzidek@chemi.muni.c [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic); Sanderova, Hana; Krasny, Libor [Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria and Department of Bacteriology, Institute of Microbiology (Czech Republic); Kozminski, Wiktor [University of Warsaw, Faculty of Chemistry (Poland); Sklenar, Vladimir [Masaryk University, Faculty of Science, National Centre for Biomolecular Research (Czech Republic)

    2010-11-15

    A strategy for complete backbone and side-chain resonance assignment of disordered proteins with highly repetitive sequence is presented. The protocol is based on three resolution-enhanced NMR experiments: 5D HN(CA)CONH provides sequential connectivity, 5D HabCabCONH is utilized to identify amino acid types, and 5D HC(CC-TOCSY)CONH is used to assign the side-chain resonances. The improved resolution was achieved by a combination of high dimensionality and long evolution times, allowed by non-uniform sampling in the indirect dimensions. Random distribution of the data points and Sparse Multidimensional Fourier Transform processing were used. Successful application of the assignment procedure to a particularly difficult protein, {delta} subunit of RNA polymerase from Bacillus subtilis, is shown to prove the efficiency of the strategy. The studied protein contains a disordered C-terminal region of 81 amino acids with a highly repetitive sequence. While the conventional assignment methods completely failed due to a very small differences in chemical shifts, the presented strategy provided a complete backbone and side-chain assignment.

  11. Biometrics based authentication scheme for session initiation protocol.

    Science.gov (United States)

    Xie, Qi; Tang, Zhixiong

    2016-01-01

    Many two-factor challenge-response based session initiation protocol (SIP) has been proposed, but most of them are vulnerable to smart card stolen attacks and password guessing attacks. In this paper, we propose a novel three-factor SIP authentication scheme using biometrics, password and smart card, and utilize the pi calculus-based formal verification tool ProVerif to prove that the proposed protocol achieves security and authentication. Furthermore, our protocol is highly efficient when compared to other related protocols.

  12. Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection.

    Science.gov (United States)

    Yang, Guanhua; Billings, Gabriel; Hubbard, Troy P; Park, Joseph S; Yin Leung, Ka; Liu, Qin; Davis, Brigid M; Zhang, Yuanxing; Wang, Qiyao; Waldor, Matthew K

    2017-10-03

    Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE). From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant's fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen) collected over a 2-week infection period from a natural host (the flatfish turbot). PACE uncovered more genes that affect E. piscicida 's fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses. IMPORTANCE Transposon insertion sequencing (TIS) enables genome-wide mapping of the genetic determinants of fitness, typically based on observations at a single sampling point. Here, we move beyond analysis of endpoint TIS data to create a framework for analysis of time series TIS data, termed pattern analysis of conditional essentiality (PACE). We applied PACE to identify genes that contribute to colonization of a natural host by the fish pathogen

  13. Using semantics for representing experimental protocols.

    Science.gov (United States)

    Giraldo, Olga; García, Alexander; López, Federico; Corcho, Oscar

    2017-11-13

    An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols. In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample. Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .

  14. Near-optimality of special periodic protocols for fluid models of single server switched networks with switchover times

    Science.gov (United States)

    Matveev, A. S.; Ishchenko, R.

    2017-11-01

    We consider a generic deterministic time-invariant fluid model of a single server switched network, which consists of finitely many infinite size buffers (queues) and receives constant rate inflows of jobs from the outside. Any flow undergoes a multi-phase service, entering a specific buffer after every phase, and ultimately leaves the network; the route of the flow over the buffers is pre-specified, and flows may merge inside the network. They share a common source of service, which can serve at most one buffer at a time and has to switch among buffers from time to time; any switch consumes a nonzero switchover period. With respect to the long-run maximal scaled wip (work in progress) performance metric, near-optimality of periodic scheduling and service protocols is established: the deepest optimum (that is over all feasible processes in the network, irrespective of the initial state) is furnished by such a protocol up to as small error as desired. Moreover, this can be achieved with a special periodic protocol introduced in the paper. It is also shown that the exhaustive policy is optimal for any buffer whose service at the maximal rate does not cause growth of the scaled wip.

  15. Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

    Science.gov (United States)

    Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

    2018-03-08

    Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

  16. Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus.

    Science.gov (United States)

    Yang, Ying-Jie; Wang, Ye; Li, Zhi-Feng; Gong, Ya; Zhang, Peng; Hu, Wen-Chao; Sheng, Duo-Hong; Li, Yue-Zhong

    2017-08-16

    The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content.

  17. The Traffic Adaptive Data Dissemination (TrAD Protocol for both Urban and Highway Scenarios

    Directory of Open Access Journals (Sweden)

    Bin Tian

    2016-06-01

    Full Text Available The worldwide economic cost of road crashes and injuries is estimated to be US$518 billion per year and the annual congestion cost in France is estimated to be €5.9 billion. Vehicular Ad hoc Networks (VANETs are one solution to improve transport features such as traffic safety, traffic jam and infotainment on wheels, where a great number of event-driven messages need to be disseminated in a timely way in a region of interest. In comparison with traditional wireless networks, VANETs have to consider the highly dynamic network topology and lossy links due to node mobility. Inter-Vehicle Communication (IVC protocols are the keystone of VANETs. According to our survey, most of the proposed IVC protocols focus on either highway or urban scenarios, but not on both. Furthermore, too few protocols, considering both scenarios, can achieve high performance. In this paper, an infrastructure-less Traffic Adaptive data Dissemination (TrAD protocol which takes into account road traffic and network traffic status for both highway and urban scenarios will be presented. TrAD has double broadcast suppression techniques and is designed to adapt efficiently to the irregular road topology. The performance of the TrAD protocol was evaluated quantitatively by means of realistic simulations taking into account different real road maps, traffic routes and vehicular densities. The obtained simulation results show that TrAD is more efficient in terms of packet delivery ratio, number of transmissions and delay in comparison with the performance of three well-known reference protocols. Moreover, TrAD can also tolerate a reasonable degree of GPS drift and still achieve efficient data dissemination.

  18. The Traffic Adaptive Data Dissemination (TrAD) Protocol for both Urban and Highway Scenarios.

    Science.gov (United States)

    Tian, Bin; Hou, Kun Mean; Zhou, Haiying

    2016-06-21

    The worldwide economic cost of road crashes and injuries is estimated to be US$518 billion per year and the annual congestion cost in France is estimated to be €5.9 billion. Vehicular Ad hoc Networks (VANETs) are one solution to improve transport features such as traffic safety, traffic jam and infotainment on wheels, where a great number of event-driven messages need to be disseminated in a timely way in a region of interest. In comparison with traditional wireless networks, VANETs have to consider the highly dynamic network topology and lossy links due to node mobility. Inter-Vehicle Communication (IVC) protocols are the keystone of VANETs. According to our survey, most of the proposed IVC protocols focus on either highway or urban scenarios, but not on both. Furthermore, too few protocols, considering both scenarios, can achieve high performance. In this paper, an infrastructure-less Traffic Adaptive data Dissemination (TrAD) protocol which takes into account road traffic and network traffic status for both highway and urban scenarios will be presented. TrAD has double broadcast suppression techniques and is designed to adapt efficiently to the irregular road topology. The performance of the TrAD protocol was evaluated quantitatively by means of realistic simulations taking into account different real road maps, traffic routes and vehicular densities. The obtained simulation results show that TrAD is more efficient in terms of packet delivery ratio, number of transmissions and delay in comparison with the performance of three well-known reference protocols. Moreover, TrAD can also tolerate a reasonable degree of GPS drift and still achieve efficient data dissemination.

  19. A Secure RFID Tag Authentication Protocol with Privacy Preserving in Telecare Medicine Information System.

    Science.gov (United States)

    Li, Chun-Ta; Weng, Chi-Yao; Lee, Cheng-Chi

    2015-08-01

    Radio Frequency Identification (RFID) based solutions are widely used for providing many healthcare applications include patient monitoring, object traceability, drug administration system and telecare medicine information system (TMIS) etc. In order to reduce malpractices and ensure patient privacy, in 2015, Srivastava et al. proposed a hash based RFID tag authentication protocol in TMIS. Their protocol uses lightweight hash operation and synchronized secret value shared between back-end server and tag, which is more secure and efficient than other related RFID authentication protocols. Unfortunately, in this paper, we demonstrate that Srivastava et al.'s tag authentication protocol has a serious security problem in that an adversary may use the stolen/lost reader to connect to the medical back-end server that store information associated with tagged objects and this privacy damage causing the adversary could reveal medical data obtained from stolen/lost readers in a malicious way. Therefore, we propose a secure and efficient RFID tag authentication protocol to overcome security flaws and improve the system efficiency. Compared with Srivastava et al.'s protocol, the proposed protocol not only inherits the advantages of Srivastava et al.'s authentication protocol for TMIS but also provides better security with high system efficiency.

  20. Memetic algorithms for de novo motif-finding in biomedical sequences.

    Science.gov (United States)

    Bi, Chengpeng

    2012-09-01

    The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

  1. SPP: A data base processor data communications protocol

    Science.gov (United States)

    Fishwick, P. A.

    1983-01-01

    The design and implementation of a data communications protocol for the Intel Data Base Processor (DBP) is defined. The protocol is termed SPP (Service Port Protocol) since it enables data transfer between the host computer and the DBP service port. The protocol implementation is extensible in that it is explicitly layered and the protocol functionality is hierarchically organized. Extensive trace and performance capabilities have been supplied with the protocol software to permit optional efficient monitoring of the data transfer between the host and the Intel data base processor. Machine independence was considered to be an important attribute during the design and implementation of SPP. The protocol source is fully commented and is included in Appendix A of this report.

  2. CENTERA: A Centralized Trust-Based Efficient Routing Protocol with Authentication for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Ayman Tajeddine

    2015-02-01

    Full Text Available In this paper, we present CENTERA, a CENtralized Trust-based Efficient Routing protocol with an appropriate authentication scheme for wireless sensor networks (WSN. CENTERA utilizes the more powerful base station (BS to gather minimal neighbor trust information from nodes and calculate the best routes after isolating different types of “bad” nodes. By periodically accumulating these simple local observations and approximating the nodes’ battery lives, the BS draws a global view of the network, calculates three quality metrics—maliciousness, cooperation, and compatibility—and evaluates the Data Trust and Forwarding Trust values of each node. Based on these metrics, the BS isolates “bad”, “misbehaving” or malicious nodes for a certain period, and put some nodes on probation. CENTERA increases the node’s bad/probation level with repeated “bad” behavior, and decreases it otherwise. Then it uses a very efficient method to distribute the routing information to “good” nodes. Based on its target environment, and if required, CENTERA uses an authentication scheme suitable for severely constrained nodes, ranging from the symmetric RC5 for safe environments under close administration, to pairing-based cryptography (PBC for hostile environments with a strong attacker model. We simulate CENTERA using TOSSIM and verify its correctness and show some energy calculations.

  3. CENTERA: a centralized trust-based efficient routing protocol with authentication for wireless sensor networks.

    Science.gov (United States)

    Tajeddine, Ayman; Kayssi, Ayman; Chehab, Ali; Elhajj, Imad; Itani, Wassim

    2015-02-02

    In this paper, we present CENTERA, a CENtralized Trust-based Efficient Routing protocol with an appropriate authentication scheme for wireless sensor networks (WSN). CENTERA utilizes the more powerful base station (BS) to gather minimal neighbor trust information from nodes and calculate the best routes after isolating different types of "bad" nodes. By periodically accumulating these simple local observations and approximating the nodes' battery lives, the BS draws a global view of the network, calculates three quality metrics-maliciousness, cooperation, and compatibility-and evaluates the Data Trust and Forwarding Trust values of each node. Based on these metrics, the BS isolates "bad", "misbehaving" or malicious nodes for a certain period, and put some nodes on probation. CENTERA increases the node's bad/probation level with repeated "bad" behavior, and decreases it otherwise. Then it uses a very efficient method to distribute the routing information to "good" nodes. Based on its target environment, and if required, CENTERA uses an authentication scheme suitable for severely constrained nodes, ranging from the symmetric RC5 for safe environments under close administration, to pairing-based cryptography (PBC) for hostile environments with a strong attacker model. We simulate CENTERA using TOSSIM and verify its correctness and show some energy calculations.

  4. Fast, efficient error reconciliation for quantum cryptography

    International Nuclear Information System (INIS)

    Buttler, W.T.; Lamoreaux, S.K.; Torgerson, J.R.; Nickel, G.H.; Donahue, C.H.; Peterson, C.G.

    2003-01-01

    We describe an error-reconciliation protocol, which we call Winnow, based on the exchange of parity and Hamming's 'syndrome' for N-bit subunits of a large dataset. The Winnow protocol was developed in the context of quantum-key distribution and offers significant advantages and net higher efficiency compared to other widely used protocols within the quantum cryptography community. A detailed mathematical analysis of the Winnow protocol is presented in the context of practical implementations of quantum-key distribution; in particular, the information overhead required for secure implementation is one of the most important criteria in the evaluation of a particular error-reconciliation protocol. The increase in efficiency for the Winnow protocol is largely due to the reduction in authenticated public communication required for its implementation

  5. Effect of sequence of insemination after simultaneous thawing of multiple semen straws on conception rate to timed AI in suckled multiparous Nelore cows.

    Science.gov (United States)

    Oliveira, L Z; Arruda, R P; de Andrade, A F C; Santos, R M; Beletti, M E; Peres, R F G; Martins, J P N; de Lima, V F M Hossepian

    2012-11-01

    The objective was to determine the effect of sequence of insemination after simultaneous thawing of multiple 0.5 mL semen straws on conception rate in suckled multiparous Nelore cows. The effect of this thawing procedure on in vitro sperm characteristics was also evaluated. All cows (N = 944) received the same timed AI protocol. Ten straws (0.5 mL) of frozen semen from the same batch were simultaneously thawed at 36 °C, for a minimum of 30 sec. One straw per cow was used for timed AI. Frozen semen from three Angus bulls was used. Timed AI records included sequence of insemination (first to tenth) and time of semen removal from thawing bath. For laboratory analyses, the same semen batches used in the field experiment were evaluated. Ten frozen straws from the same batch were thawed simultaneously in a thawing unit identical to that used in the field experiment. The following sperm characteristics were analyzed: sperm motility parameters, sperm thermal resistance, plasma and acrosomal membrane integrity, lipid peroxidation, chromatin structure, and sperm morphometry. Based on logistic regression, there were no significant effects of breeding group, body condition score, AI technician, and sire on conception rate, but there was an interaction between sire and straw group (P = 0.002). Semen from only one bull had decreased (P conception rates at timed AI, depending on the sire used. Nevertheless, the effects of this thawing environment on in vitro sperm characteristics, remain to be further investigated. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Energy-Aware RFID Anti-Collision Protocol.

    Science.gov (United States)

    Arjona, Laura; Simon, Hugo Landaluce; Ruiz, Asier Perallos

    2018-06-11

    The growing interest in mobile devices is transforming wireless identification technologies. Mobile and battery-powered Radio Frequency Identification (RFID) readers, such as hand readers and smart phones, are are becoming increasingly attractive. These RFID readers require energy-efficient anti-collision protocols to minimize the tag collisions and to expand the reader's battery life. Furthermore, there is an increasing interest in RFID sensor networks with a growing number of RFID sensor tags. Thus, RFID application developers must be mindful of tag anti-collision protocols. Energy-efficient protocols involve a low reader energy consumption per tag. This work presents a thorough study of the reader energy consumption per tag and analyzes the main factor that affects this metric: the frame size update strategy. Using the conclusion of this analysis, the anti-collision protocol Energy-Aware Slotted Aloha (EASA) is presented to decrease the energy consumption per tag. The frame size update strategy of EASA is configured to minimize the energy consumption per tag. As a result, EASA presents an energy-aware frame. The performance of the proposed protocol is evaluated and compared with several state of the art Aloha-based anti-collision protocols based on the current RFID standard. Simulation results show that EASA, with an average of 15 mJ consumed per tag identified, achieves a 6% average improvement in the energy consumption per tag in relation to the strategies of the comparison.

  7. MiSeq: A Next Generation Sequencing Platform for Genomic Analysis.

    Science.gov (United States)

    Ravi, Rupesh Kanchi; Walton, Kendra; Khosroheidari, Mahdieh

    2018-01-01

    MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

  8. Simulating efficiently the evolution of DNA sequences.

    Science.gov (United States)

    Schöniger, M; von Haeseler, A

    1995-02-01

    Two menu-driven FORTRAN programs are described that simulate the evolution of DNA sequences in accordance with a user-specified model. This general stochastic model allows for an arbitrary stationary nucleotide composition and any transition-transversion bias during the process of base substitution. In addition, the user may define any hypothetical model tree according to which a family of sequences evolves. The programs suggest the computationally most inexpensive approach to generate nucleotide substitutions. Either reproducible or non-repeatable simulations, depending on the method of initializing the pseudo-random number generator, can be performed. The corresponding options are offered by the interface menu.

  9. Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA.

    Science.gov (United States)

    Sproul, John S; Maddison, David R

    2017-11-01

    Despite advances that allow DNA sequencing of old museum specimens, sequencing small-bodied, historical specimens can be challenging and unreliable as many contain only small amounts of fragmented DNA. Dependable methods to sequence such specimens are especially critical if the specimens are unique. We attempt to sequence small-bodied (3-6 mm) historical specimens (including nomenclatural types) of beetles that have been housed, dried, in museums for 58-159 years, and for which few or no suitable replacement specimens exist. To better understand ideal approaches of sample preparation and produce preparation guidelines, we compared different library preparation protocols using low amounts of input DNA (1-10 ng). We also explored low-cost optimizations designed to improve library preparation efficiency and sequencing success of historical specimens with minimal DNA, such as enzymatic repair of DNA. We report successful sample preparation and sequencing for all historical specimens despite our low-input DNA approach. We provide a list of guidelines related to DNA repair, bead handling, reducing adapter dimers and library amplification. We present these guidelines to facilitate more economical use of valuable DNA and enable more consistent results in projects that aim to sequence challenging, irreplaceable historical specimens. © 2017 John Wiley & Sons Ltd.

  10. Temporal logics and real time expert systems.

    Science.gov (United States)

    Blom, J A

    1996-10-01

    This paper introduces temporal logics. Due to the eternal compromise between expressive adequacy and reasoning efficiency that must decided upon in any application, full (first order logic or modal logic based) temporal logics are frequently not suitable. This is especially true in real time expert systems, where a fixed (and usually small) response time must be guaranteed. One such expert system, Fagan's VM, is reviewed, and a delineation is given of how to formally describe and reason with time in medical protocols. It is shown that Petri net theory is a useful tool to check the correctness of formalised protocols.

  11. Real-Time Performance of Hybrid Mobile Robot Control Utilizing USB Protocol

    Directory of Open Access Journals (Sweden)

    Jacek Augustyn

    2015-02-01

    Full Text Available This article discusses the problem of usability of the USB 2.0 protocol in the area of real-time control of a mobile robot. Optimization methods of data transfer handling were proposed. The impact of the optimization results on the entire system's performance was examined in practice. As a test-bed, a hybrid system composed of two devices communicating by direct USB connection was implemented. The first of the mentioned devices was a 32-bit SoC micro-system serving as a direct control unit, and the second one was an off-the-shelf PDA providing supervisory control and logging. Due to this design, the system meets regimes of the real-time constraints and maintains continuity of a data stream at a large bandwidth. The real-time performances of subsystems and the entire system were experimentally examined depending on various operating conditions. Thanks to the performed experiments, the dependency of real-time limits on operational parameters has been determined.

  12. Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection

    Directory of Open Access Journals (Sweden)

    Guanhua Yang

    2017-10-01

    Full Text Available Transposon insertion sequencing (TIS is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection. Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE. From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant’s fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen collected over a 2-week infection period from a natural host (the flatfish turbot. PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses.

  13. Time- and sequence-dependent responses to cisplatin and radiation in the rat kidney

    International Nuclear Information System (INIS)

    Rongen, Eric van; Kuijpers, W.C.; Baten-Wittwer, Andrea

    1991-01-01

    The influence of time interval and sequence between administration of cisplatin and a radiation dose was studied in the rat kidney. Changes in glomerular function were only detected after 30 weeks following the higher drug dose (6.0 mg/kg). X-rays alone caused measurable alterations in both glomerular and tubular function after 16 weeks. In the combined treatment the influence of time and sequence was significant. If cisplatin was given at 7 to 1 days before X-rays the effect of time was minimal. Administration of cisplatin 12 h to 15 min before irradiation resulted in an increase of radiation damage with decreasing time interval. Total damage sharply decreased when both modalities were given at the same time, and decreased further with increasing time between irradiation and drug administration. (author)

  14. Adaptive GDDA-BLAST: fast and efficient algorithm for protein sequence embedding.

    Directory of Open Access Journals (Sweden)

    Yoojin Hong

    2010-10-01

    Full Text Available A major computational challenge in the genomic era is annotating structure/function to the vast quantities of sequence information that is now available. This problem is illustrated by the fact that most proteins lack comprehensive annotations, even when experimental evidence exists. We previously theorized that embedded-alignment profiles (simply "alignment profiles" hereafter provide a quantitative method that is capable of relating the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of alignment profiles lies in the interoperability of data format (e.g., alignment information, physio-chemical information, genomic information, etc.. Indeed, we have demonstrated that the Position Specific Scoring Matrices (PSSMs are an informative M-dimension that is scored by quantitatively measuring the embedded or unmodified sequence alignments. Moreover, the information obtained from these alignments is informative, and remains so even in the "twilight zone" of sequence similarity (<25% identity. Although our previous embedding strategy was powerful, it suffered from contaminating alignments (embedded AND unmodified and high computational costs. Herein, we describe the logic and algorithmic process for a heuristic embedding strategy named "Adaptive GDDA-BLAST." Adaptive GDDA-BLAST is, on average, up to 19 times faster than, but has similar sensitivity to our previous method. Further, data are provided to demonstrate the benefits of embedded-alignment measurements in terms of detecting structural homology in highly divergent protein sequences and isolating secondary structural elements of transmembrane and ankyrin-repeat domains. Together, these advances allow further exploration of the embedded alignment data space within sufficiently large data sets to eventually induce relevant statistical inferences. We show that sequence embedding could serve as one of the vehicles for measurement of low

  15. Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements.

    Science.gov (United States)

    Kumazawa, Yoshinori; Endo, Hideki

    2004-04-30

    The mitochondrial genome of the Komodo dragon (Varanus komodoensis) was nearly completely sequenced, except for two highly repetitive noncoding regions. An efficient sequencing method for squamate mitochondrial genomes was established by combining the long polymerase chain reaction (PCR) technology and a set of reptile-oriented primers designed for nested PCR amplifications. It was found that the mitochondrial genome had novel gene arrangements in which genes from NADH dehydrogenase subunit 6 to proline tRNA were extensively shuffled with duplicate control regions. These control regions had 99% sequence similarity over 700 bp. Although snake mitochondrial genomes are also known to possess duplicate control regions with nearly identical sequences, the location of the second control region suggested independent occurrence of the duplication on lineages leading to snakes and the Komodo dragon. Another feature of the mitochondrial genome of the Komodo dragon was the considerable number of tandem repeats, including sequences with a strong secondary structure, as a possible site for the slipped-strand mispairing in replication. These observations are consistent with hypotheses that tandem duplications via the slipped-strand mispairing may induce mitochondrial gene rearrangements and may serve to maintain similar copies of the control region.

  16. TR-MAC: an energy-efficient MAC protocol for wireless sensor networks exploiting noise-based transmitted reference modulation

    NARCIS (Netherlands)

    Morshed, S.; Dimitrova, D.C.; Brogle, M.; Braun, T.; Heijenk, Gerhard J.

    Energy-constrained behavior of sensor nodes is one of the most important criteria for successful deployment of wireless sensor net- works. The medium access control (MAC) protocol determines the time a sensor node transceiver spends listening or transmitting, and hence the energy consumption of the

  17. Establishment of Lipofection Protocol for Efficient miR-21 Transfection into Cortical Neurons In Vitro.

    Science.gov (United States)

    Han, Zhaoli; Ge, Xintong; Tan, Jin; Chen, Fanglian; Gao, Huabin; Lei, Ping; Zhang, Jianning

    2015-12-01

    Dysregulated microRNAs in neurons could cause many nervous system diseases. The therapeutic manipulation of these pathogenic microRNAs necessitates novel, efficient delivery systems to facilitate microRNA modulators targeting neurons with minimal off-target effects. The study aimed to establish a lipofection protocol to upregulate expression levels of miR-21 in neurons under different conditions, including different serum-free medium, transfection conditions, and reagent concentration, by evaluating the expression levels of miR-21 and neuron injury. The expression levels of miR-21 were higher in neurons transfected by Neurobasal-A than by DMEM. Expression levels of miR-21 were already the highest at the ratio RNAiMAX:miR-21 = 3:5, but the increase of RNAiMAX's concentration had not caused the further upregulation of expression level of miR-21. Neuron injury was condition dependent and dose dependent after transfection. Compared to S-Neurobasal groups, neurons have a smaller injury in N-Neurobasal groups, and compared to ratios RNAiMAX:miR-21 = 4:5, 5:5, neuron injury was smaller at ratios of RNAiMAX:miR-21 = 1:5, 2:5, 3:5. Without the pretreatment of starvation in vitro, the lipofection protocol was that RNAiMAX/miR-21 agomir complexes were diluted in Neurobasal-A at the ratio of RNAiMAX:miR-21 = 3:5.

  18. SMITH: a LIMS for handling next-generation sequencing workflows.

    Science.gov (United States)

    Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

    2014-01-01

    Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available

  19. SMITH: a LIMS for handling next-generation sequencing workflows

    Science.gov (United States)

    2014-01-01

    Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The

  20. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    Directory of Open Access Journals (Sweden)

    Carr Steven M

    2007-09-01

    Full Text Available Abstract Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a re-sequencing microarray when their sequences differ by