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Sample records for hemagglutinin matching patterns

  1. Neuraminidase and hemagglutinin matching patterns of a highly pathogenic avian and two pandemic H1N1 influenza A viruses.

    Yonghui Zhang

    Full Text Available BACKGROUND: Influenza A virus displays strong reassortment characteristics, which enable it to achieve adaptation in human infection. Surveying the reassortment and virulence of novel viruses is important in the prevention and control of an influenza pandemic. Meanwhile, studying the mechanism of reassortment may accelerate the development of anti-influenza strategies. METHODOLOGY/PRINCIPAL FINDINGS: The hemagglutinin (HA and neuraminidase (NA matching patterns of two pandemic H1N1 viruses (the 1918 and current 2009 strains and a highly pathogenic avian influenza A virus (H5N1 were studied using a pseudotyped particle (pp system. Our data showed that four of the six chimeric HA/NA combinations could produce infectious pps, and that some of the chimeric pps had greater infectivity than did their ancestors, raising the possibility of reassortment among these viruses. The NA of H5N1 (A/Anhui/1/2005 could hardly reassort with the HAs of the two H1N1 viruses. Many biological characteristics of HA and NA, including infectivity, hemagglutinating ability, and NA activity, are dependent on their matching pattern. CONCLUSIONS/SIGNIFICANCE: Our data suggest the existence of an interaction between HA and NA, and the HA NA matching pattern is critical for valid viral reassortment.

  2. Polytypic pattern matching

    Jeuring, J.T.

    1995-01-01

    The pattern matching problem can be informally specified as follows: given a pattern and a text, find all occurrences of the pattern in the text. The pattern and the text may both be lists, or they may both be trees, or they may both be multi-dimensional arrays, etc. This paper describes a general

  3. Pattern recognition and string matching

    Cheng, Xiuzhen

    2002-01-01

    The research and development of pattern recognition have proven to be of importance in science, technology, and human activity. Many useful concepts and tools from different disciplines have been employed in pattern recognition. Among them is string matching, which receives much theoretical and practical attention. String matching is also an important topic in combinatorial optimization. This book is devoted to recent advances in pattern recognition and string matching. It consists of twenty eight chapters written by different authors, addressing a broad range of topics such as those from classifica­ tion, matching, mining, feature selection, and applications. Each chapter is self-contained, and presents either novel methodological approaches or applications of existing theories and techniques. The aim, intent, and motivation for publishing this book is to pro­ vide a reference tool for the increasing number of readers who depend upon pattern recognition or string matching in some way. This includes student...

  4. Fuzzy automata and pattern matching

    Setzer, C. B.; Warsi, N. A.

    1986-01-01

    A wide-ranging search for articles and books concerned with fuzzy automata and syntactic pattern recognition is presented. A number of survey articles on image processing and feature detection were included. Hough's algorithm is presented to illustrate the way in which knowledge about an image can be used to interpret the details of the image. It was found that in hand generated pictures, the algorithm worked well on following the straight lines, but had great difficulty turning corners. An algorithm was developed which produces a minimal finite automaton recognizing a given finite set of strings. One difficulty of the construction is that, in some cases, this minimal automaton is not unique for a given set of strings and a given maximum length. This algorithm compares favorably with other inference algorithms. More importantly, the algorithm produces an automaton with a rigorously described relationship to the original set of strings that does not depend on the algorithm itself.

  5. A review on compressed pattern matching

    Surya Prakash Mishra

    2016-09-01

    Full Text Available Compressed pattern matching (CPM refers to the task of locating all the occurrences of a pattern (or set of patterns inside the body of compressed text. In this type of matching, pattern may or may not be compressed. CPM is very useful in handling large volume of data especially over the network. It has many applications in computational biology, where it is useful in finding similar trends in DNA sequences; intrusion detection over the networks, big data analytics etc. Various solutions have been provided by researchers where pattern is matched directly over the uncompressed text. Such solution requires lot of space and consumes lot of time when handling the big data. Various researchers have proposed the efficient solutions for compression but very few exist for pattern matching over the compressed text. Considering the future trend where data size is increasing exponentially day-by-day, CPM has become a desirable task. This paper presents a critical review on the recent techniques on the compressed pattern matching. The covered techniques includes: Word based Huffman codes, Word Based Tagged Codes; Wavelet Tree Based Indexing. We have presented a comparative analysis of all the techniques mentioned above and highlighted their advantages and disadvantages.

  6. On Tree Pattern Matching by Pushdown Automata

    T. Flouri

    2009-01-01

    Full Text Available Tree pattern matching is an important operation in Computer Science on which a number of tasks such as mechanical theorem proving, term-rewriting, symbolic computation and non-procedural programming languages are based on. Work has begun on a systematic approach to the construction of tree pattern matchers by deterministic pushdown automata which read subject trees in prefix notation. The method is analogous to the construction of string pattern matchers: for given patterns, a non-deterministic pushdown automaton is created and then it is determinised. In this first paper, we present the proposed non-deterministic pushdown automaton which will serve as a basis for the determinisation process, and prove its correctness. 

  7. Rewrite Systems, Pattern Matching, and Code Generation

    1988-06-09

    fmd a local set L’ which includes L and define the transformation on L’ instead of on L. 11 The straightforward way to define tree transformations...Proposition 2.19 Both B-ftt and T-ftt include: REL relabelings FTA (t ,t) such that t e RECOG HOM homomorphisms LHOM linear homomorphisms The capabilities...fsa for the set of the structures of the original pattern set. The LB-fsa IS used to fmd the structural subpatterns matching a: each node of the

  8. Patterns of predicted T-cell epitopes associated with antigenic drift in influenza H3N2 hemagglutinin.

    E Jane Homan

    Full Text Available Antigenic drift allowing escape from neutralizing antibodies is an important feature of transmission and survival of influenza viruses in host populations. Antigenic drift has been studied in particular detail for influenza A H3N2 and well defined antigenic clusters of this virus documented. We examine how host immunogenetics contributes to determination of the antibody spectrum, and hence the immune pressure bringing about antigenic drift. Using uTOPE™ bioinformatics analysis of predicted MHC binding, based on amino acid physical property principal components, we examined the binding affinity of all 9-mer and 15-mer peptides within the hemagglutinin 1 (HA1 of 447 H3N2 virus isolates to 35 MHC-I and 14 MHC-II alleles. We provide a comprehensive map of predicted MHC-I and MHC-II binding affinity for a broad array of HLA alleles for the H3N2 influenza HA1 protein. Each HLA allele exhibited a characteristic predicted binding pattern. Cluster analysis for each HLA allele shows that patterns based on predicted MHC binding mirror those described based on antibody binding. A single amino acid mutation or position displacement can result in a marked difference in MHC binding and hence potential T-helper function. We assessed the impact of individual amino acid changes in HA1 sequences between 10 virus isolates from 1968-2002, representative of antigenic clusters, to understand the changes in MHC binding over time. Gain and loss of predicted high affinity MHC-II binding sites with cluster transitions were documented. Predicted high affinity MHC-II binding sites were adjacent to antibody binding sites. We conclude that host MHC diversity may have a major determinant role in the antigenic drift of influenza A H3N2.

  9. Computationally Secure Pattern Matching in the Presence of Malicious Adversaries

    Hazay, Carmit; Toft, Tomas

    2014-01-01

    for important variations of the secure pattern matching problem that are significantly more efficient than the current state of art solutions: First, we deal with secure pattern matching with wildcards. In this variant the pattern may contain wildcards that match both 0 and 1. Our protocol requires O......We propose a protocol for the problem of secure two-party pattern matching, where Alice holds a text t∈{0,1}∗ of length n, while Bob has a pattern p∈{0,1}∗ of length m. The goal is for Bob to (only) learn where his pattern occurs in Alice’s text, while Alice learns nothing. Private pattern matching...... is an important problem that has many applications in the area of DNA search, computational biology and more. Our construction guarantees full simulation in the presence of malicious, polynomial-time adversaries (assuming the hardness of DDH assumption) and exhibits computation and communication costs of O...

  10. High Performance Embedded System for Real-Time Pattern Matching

    Sotiropoulou, Calliope Louisa; The ATLAS collaboration; Gkaitatzis, Stamatios; Citraro, Saverio; Giannetti, Paola; Dell'Orso, Mauro

    2016-01-01

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics (HEP) and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturised version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory (AM) chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering...

  11. Structural pattern matching of nonribosomal peptides

    Leclère Valérie

    2009-03-01

    Full Text Available Abstract Background Nonribosomal peptides (NRPs, bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents. NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database. Results We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph. Conclusion The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database.

  12. Statistical density modification using local pattern matching

    Terwilliger, Thomas C.

    2003-01-01

    Statistical density modification can make use of local patterns of density found in protein structures to improve crystallographic phases. A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using

  13. High performance embedded system for real-time pattern matching

    Sotiropoulou, C.-L.; Luciano, P.; Gkaitatzis, S.; Citraro, S.; Giannetti, P.; Dell'Orso, M.

    2017-01-01

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton–proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device. - Highlights: • A high performance embedded system for real-time pattern matching is proposed. • It is based on a system developed for High Energy Physics experiment triggers. • It mimics the operation of the human brain (cognitive image processing). • The process can be executed on 2D and 3D, black and white or grayscale images. • The implementation uses FPGAs and custom designed associative memory (AM) chips.

  14. High performance embedded system for real-time pattern matching

    Sotiropoulou, C.-L., E-mail: c.sotiropoulou@cern.ch [University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Luciano, P. [University of Cassino and Southern Lazio, Gaetano di Biasio 43, Cassino 03043 (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Gkaitatzis, S. [Aristotle University of Thessaloniki, 54124 Thessaloniki (Greece); Citraro, S. [University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Giannetti, P. [INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy); Dell' Orso, M. [University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa (Italy); INFN-Pisa Section, Largo B. Pontecorvo 3, 56127 Pisa (Italy)

    2017-02-11

    In this paper we present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton–proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain. The pattern matching can be executed by a custom designed Associative Memory chip. The reference patterns are chosen by a complex training algorithm implemented on an FPGA device. Post processing algorithms (e.g. pixel clustering) are also implemented on the FPGA. The pattern matching can be executed on a 2D or 3D space, on black and white or grayscale images, depending on the application and thus increasing exponentially the processing requirements of the system. We present the firmware implementation of the training and pattern matching algorithm, performance and results on a latest generation Xilinx Kintex Ultrascale FPGA device. - Highlights: • A high performance embedded system for real-time pattern matching is proposed. • It is based on a system developed for High Energy Physics experiment triggers. • It mimics the operation of the human brain (cognitive image processing). • The process can be executed on 2D and 3D, black and white or grayscale images. • The implementation uses FPGAs and custom designed associative memory (AM) chips.

  15. High Performance Embedded System for Real-Time Pattern Matching

    Sotiropoulou, Calliope Louisa; The ATLAS collaboration; Gkaitatzis, Stamatios; Citraro, Saverio; Giannetti, Paola; Dell'Orso, Mauro

    2016-01-01

    We present an innovative and high performance embedded system for real-time pattern matching. This system is based on the evolution of hardware and algorithms developed for the field of High Energy Physics (HEP) and more specifically for the execution of extremely fast pattern matching for tracking of particles produced by proton-proton collisions in hadron collider experiments. A miniaturized version of this complex system is being developed for pattern matching in generic image processing applications. The design uses the flexibility of Field Programmable Gate Arrays (FPGAs) and the powerful Associative Memory Chip (ASIC) to achieve real-time performance. The system works as a contour identifier able to extract the salient features of an image. It is based on the principles of cognitive image processing, which means that it executes fast pattern matching and data reduction mimicking the operation of the human brain.

  16. Sleep patterns and match performance in elite Australian basketball athletes.

    Staunton, Craig; Gordon, Brett; Custovic, Edhem; Stanger, Jonathan; Kingsley, Michael

    2017-08-01

    To assess sleep patterns and associations between sleep and match performance in elite Australian female basketball players. Prospective cohort study. Seventeen elite female basketball players were monitored across two consecutive in-season competitions (30 weeks). Total sleep time and sleep efficiency were determined using triaxial accelerometers for Baseline, Pre-match, Match-day and Post-match timings. Match performance was determined using the basketball efficiency statistic (EFF). The effects of match schedule (Regular versus Double-Header; Home versus Away) and sleep on EFF were assessed. The Double-Header condition changed the pattern of sleep when compared with the Regular condition (F (3,48) =3.763, P=0.017), where total sleep time Post-match was 11% less for Double-Header (mean±SD; 7.2±1.4h) compared with Regular (8.0±1.3h; P=0.007). Total sleep time for Double-Header was greater Pre-match (8.2±1.7h) compared with Baseline (7.1±1.6h; P=0.022) and Match-day (7.3±1.5h; P=0.007). Small correlations existed between sleep metrics at Pre-match and EFF for pooled data (r=-0.39 to -0.22; P≥0.238). Relationships between total sleep time and EFF ranged from moderate negative to large positive correlations for individual players (r=-0.37 to 0.62) and reached significance for one player (r=0.60; P=0.025). Match schedule can affect the sleep patterns of elite female basketball players. A large degree of inter-individual variability existed in the relationship between sleep and match performance; nevertheless, sleep monitoring might assist in the optimisation of performance for some athletes. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  17. Betting on Illusory Patterns: Probability Matching in Habitual Gamblers.

    Gaissmaier, Wolfgang; Wilke, Andreas; Scheibehenne, Benjamin; McCanney, Paige; Barrett, H Clark

    2016-03-01

    Why do people gamble? A large body of research suggests that cognitive distortions play an important role in pathological gambling. Many of these distortions are specific cases of a more general misperception of randomness, specifically of an illusory perception of patterns in random sequences. In this article, we provide further evidence for the assumption that gamblers are particularly prone to perceiving illusory patterns. In particular, we compared habitual gamblers to a matched sample of community members with regard to how much they exhibit the choice anomaly 'probability matching'. Probability matching describes the tendency to match response proportions to outcome probabilities when predicting binary outcomes. It leads to a lower expected accuracy than the maximizing strategy of predicting the most likely event on each trial. Previous research has shown that an illusory perception of patterns in random sequences fuels probability matching. So does impulsivity, which is also reported to be higher in gamblers. We therefore hypothesized that gamblers will exhibit more probability matching than non-gamblers, which was confirmed in a controlled laboratory experiment. Additionally, gamblers scored much lower than community members on the cognitive reflection task, which indicates higher impulsivity. This difference could account for the difference in probability matching between the samples. These results suggest that gamblers are more willing to bet impulsively on perceived illusory patterns.

  18. Kangaroo – A pattern-matching program for biological sequences

    Betel Doron

    2002-07-01

    Full Text Available Abstract Background Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/. Conclusion A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats.

  19. PATTERN CLASSIFICATION APPROACHES TO MATCHING BUILDING POLYGONS AT MULTIPLE SCALES

    X. Zhang

    2012-07-01

    Full Text Available Matching of building polygons with different levels of detail is crucial in the maintenance and quality assessment of multi-representation databases. Two general problems need to be addressed in the matching process: (1 Which criteria are suitable? (2 How to effectively combine different criteria to make decisions? This paper mainly focuses on the second issue and views data matching as a supervised pattern classification. Several classifiers (i.e. decision trees, Naive Bayes and support vector machines are evaluated for the matching task. Four criteria (i.e. position, size, shape and orientation are used to extract information for these classifiers. Evidence shows that these classifiers outperformed the weighted average approach.

  20. A new taxonomy of sublinear keyword pattern matching algorithms

    Cleophas, L.G.W.A.; Watson, B.W.; Zwaan, G.

    2004-01-01

    Abstract This paper presents a new taxonomy of sublinear (multiple) keyword pattern matching algorithms. Based on an earlier taxonomy by Watson and Zwaan [WZ96, WZ95], this new taxonomy includes not only suffix-based algorithms related to the Boyer-Moore, Commentz-Walter and Fan-Su algorithms, but

  1. Attention Modulates Visual-Tactile Interaction in Spatial Pattern Matching

    Göschl, Florian; Engel, Andreas K.; Friese, Uwe

    2014-01-01

    Factors influencing crossmodal interactions are manifold and operate in a stimulus-driven, bottom-up fashion, as well as via top-down control. Here, we evaluate the interplay of stimulus congruence and attention in a visual-tactile task. To this end, we used a matching paradigm requiring the identification of spatial patterns that were concurrently presented visually on a computer screen and haptically to the fingertips by means of a Braille stimulator. Stimulation in our paradigm was always bimodal with only the allocation of attention being manipulated between conditions. In separate blocks of the experiment, participants were instructed to (a) focus on a single modality to detect a specific target pattern, (b) pay attention to both modalities to detect a specific target pattern, or (c) to explicitly evaluate if the patterns in both modalities were congruent or not. For visual as well as tactile targets, congruent stimulus pairs led to quicker and more accurate detection compared to incongruent stimulation. This congruence facilitation effect was more prominent under divided attention. Incongruent stimulation led to behavioral decrements under divided attention as compared to selectively attending a single sensory channel. Additionally, when participants were asked to evaluate congruence explicitly, congruent stimulation was associated with better performance than incongruent stimulation. Our results extend previous findings from audiovisual studies, showing that stimulus congruence also resulted in behavioral improvements in visuotactile pattern matching. The interplay of stimulus processing and attentional control seems to be organized in a highly flexible fashion, with the integration of signals depending on both bottom-up and top-down factors, rather than occurring in an ‘all-or-nothing’ manner. PMID:25203102

  2. Attention modulates visual-tactile interaction in spatial pattern matching.

    Florian Göschl

    Full Text Available Factors influencing crossmodal interactions are manifold and operate in a stimulus-driven, bottom-up fashion, as well as via top-down control. Here, we evaluate the interplay of stimulus congruence and attention in a visual-tactile task. To this end, we used a matching paradigm requiring the identification of spatial patterns that were concurrently presented visually on a computer screen and haptically to the fingertips by means of a Braille stimulator. Stimulation in our paradigm was always bimodal with only the allocation of attention being manipulated between conditions. In separate blocks of the experiment, participants were instructed to (a focus on a single modality to detect a specific target pattern, (b pay attention to both modalities to detect a specific target pattern, or (c to explicitly evaluate if the patterns in both modalities were congruent or not. For visual as well as tactile targets, congruent stimulus pairs led to quicker and more accurate detection compared to incongruent stimulation. This congruence facilitation effect was more prominent under divided attention. Incongruent stimulation led to behavioral decrements under divided attention as compared to selectively attending a single sensory channel. Additionally, when participants were asked to evaluate congruence explicitly, congruent stimulation was associated with better performance than incongruent stimulation. Our results extend previous findings from audiovisual studies, showing that stimulus congruence also resulted in behavioral improvements in visuotactile pattern matching. The interplay of stimulus processing and attentional control seems to be organized in a highly flexible fashion, with the integration of signals depending on both bottom-up and top-down factors, rather than occurring in an 'all-or-nothing' manner.

  3. Highly Parallelized Pattern Matching Execution for the ATLAS Experiment

    Citraro, Saverio; The ATLAS collaboration

    2015-01-01

    The trigger system of the ATLAS experiment at LHC will extend its rejection capabilities during operations in 2015-2018 by introducing the Fast TracKer system (FTK). FTK is a hardware based system capable of finding charged particle tracks by analyzing hits in silicon detectors at the rate of 105 events per second. The core of track reconstruction is performed into two pipelined steps. At first step the candidate tracks are found by matching combination of low resolution hits to predefined patterns; then they are used in the second step to seed a more precise track fitting algorithm. The key FTK component is an Associative Memory (AM) system that is used to perform pattern matching with high degree of parallelism. The AM system implementation, the AM Serial Link Processor, is based on an extremely powerful network of 2 Gb/s serial links to sustain a huge traffic of data. We report on the design of the Serial Link Processor consisting of two types of boards, the Little Associative Memory Board (LAMB), a mezzan...

  4. Highly Parallelized Pattern Matching Execution for the ATLAS Experiment

    Citraro, Saverio; The ATLAS collaboration

    2015-01-01

    Abstract– The Associative Memory (AM) system of the Fast Tracker (FTK) processor has been designed to perform pattern matching using as input the data from the silicon tracker in the ATLAS experiment. The AM is the primary component of the FTK system and is designed using ASIC technology (the AM chip) to execute pattern matching with a high degree of parallelism. The FTK system finds track candidates at low resolution that are seeds for a full resolution track fitting. The AM system implementation is named “Serial Link Processor” and is based on an extremely powerful network of 2 Gb/s serial links to sustain a huge traffic of data. This paper reports on the design of the Serial Link Processor consisting of two types of boards, the Little Associative Memory Board (LAMB), a mezzanine where the AM chips are mounted, and the Associative Memory Board (AMB), a 9U VME motherboard which hosts four LAMB daughterboards. We also report on the performance of the prototypes (both hardware and firmware) produced and ...

  5. Optimizing Fukushima Emissions Through Pattern Matching and Genetic Algorithms

    Lucas, D. D.; Simpson, M. D.; Philip, C. S.; Baskett, R.

    2017-12-01

    Hazardous conditions during the Fukushima Daiichi nuclear power plant (NPP) accident hindered direct observations of the emissions of radioactive materials into the atmosphere. A wide range of emissions are estimated from bottom-up studies using reactor inventories and top-down approaches based on inverse modeling. We present a new inverse modeling estimate of cesium-137 emitted from the Fukushima NPP. Our estimate considers weather uncertainty through a large ensemble of Weather Research and Forecasting model simulations and uses the FLEXPART atmospheric dispersion model to transport and deposit cesium. The simulations are constrained by observations of the spatial distribution of cumulative cesium deposited on the surface of Japan through April 2, 2012. Multiple spatial metrics are used to quantify differences between observed and simulated deposition patterns. In order to match the observed pattern, we use a multi-objective genetic algorithm to optimize the time-varying emissions. We find that large differences with published bottom-up estimates are required to explain the observations. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  6. The effect of football matches on crime patterns in Barcelona

    Struse, Simon Planells; Montolio, Daniel

    2014-01-01

    Given the actual debate, in many European countries, about the need for public administrations to raise their revenues through taxing the crime externalities generated by some private leisure activities, this article analyzes the effect of football matches on crime focusing both on property crimes and interpersonal violent crimes. Our aim is to determine up to what extent a private leisure activity, such as football matches, induces negative crime externalities to the whole society. Using dat...

  7. RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

    Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

    2015-01-01

    Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

  8. Rotation and scale change invariant point pattern relaxation matching by the Hopfield neural network

    Sang, Nong; Zhang, Tianxu

    1997-12-01

    Relaxation matching is one of the most relevant methods for image matching. The original relaxation matching technique using point patterns is sensitive to rotations and scale changes. We improve the original point pattern relaxation matching technique to be invariant to rotations and scale changes. A method that makes the Hopfield neural network perform this matching process is discussed. An advantage of this is that the relaxation matching process can be performed in real time with the neural network's massively parallel capability to process information. Experimental results with large simulated images demonstrate the effectiveness and feasibility of the method to perform point patten relaxation matching invariant to rotations and scale changes and the method to perform this matching by the Hopfield neural network. In addition, we show that the method presented can be tolerant to small random error.

  9. What makes a pattern? Matching decoding methods to data in multivariate pattern analysis

    Philip A Kragel

    2012-11-01

    Full Text Available Research in neuroscience faces the challenge of integrating information across different spatial scales of brain function. A promising technique for harnessing information at a range of spatial scales is multivariate pattern analysis (MVPA of functional magnetic resonance imaging (fMRI data. While the prevalence of MVPA has increased dramatically in recent years, its typical implementations for classification of mental states utilize only a subset of the information encoded in local fMRI signals. We review published studies employing multivariate pattern classification since the technique’s introduction, which reveal an extensive focus on the improved detection power that linear classifiers provide over traditional analysis techniques. We demonstrate using simulations and a searchlight approach, however, that nonlinear classifiers are capable of extracting distinct information about interactions within a local region. We conclude that for spatially localized analyses, such as searchlight and region of interest, multiple classification approaches should be compared in order to match fMRI analyses to the properties of local circuits.

  10. Rating Algorithm for Pronunciation of English Based on Audio Feature Pattern Matching

    Li Kun

    2015-01-01

    Full Text Available With the increasing internationalization of China, language communication has become an important channel for us to adapt to the political and economic environment. How to improve English learners’ language learning efficiency in limited conditions has turned into a problem demanding prompt solution at present. This paper applies two pronunciation patterns according to the actual needs of English pronunciation rating: to-be-evaluated pronunciation pattern and standard pronunciation pattern. It will translate the patterns into English pronunciation rating results through European distance. Besides, this paper will introduce the design philosophy of the whole algorithm in combination with CHMM matching pattern. Each link of the CHMM pattern will be given selective analysis while a contrast experiment between the CHMM matching pattern and the other two patterns will be conducted. From the experiment results, it can be concluded that CHMM pattern is the best option.

  11. A Vision Chip for Color Segmentation and Pattern Matching

    Ralph Etienne-Cummings

    2003-06-01

    Full Text Available A 128(H × 64(V × RGB CMOS imager is integrated with region-of-interest selection, RGB-to-HSI transformation, HSI-based pixel segmentation, (36bins × 12bits-HSI histogramming, and sum-of-absolute-difference (SAD template matching. Thirty-two learned color templates are stored and compared to each image. The chip captures the R, G, and B images using in-pixel storage before passing the pixel content to a multiplying digital-to-analog converter (DAC for white balancing. The DAC can also be used to pipe in images for a PC. The color processing uses a biologically inspired color opponent representation and an analog lookup table to determine the Hue (H of each pixel. Saturation (S is computed using a loser-take-all circuit. Intensity (I is given by the sum of the color components. A histogram of the segments of the image, constructed by counting the number of pixels falling into 36 Hue intervals of 10 degrees, is stored on a chip and compared against the histograms of new segments using SAD comparisons. We demonstrate color-based image segmentation and object recognition with this chip. Running at 30 fps, it uses 1 mW. To our knowledge, this is the first chip that integrates imaging, color segmentation, and color-based object recognition at the focal plane.

  12. Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

    Chang-Ku Kang

    Full Text Available Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i whether a choice of resting orientation by moths depends on the properties of natural background, and ii what sensory cues moths use. We studied moths' behavior on natural (a tree log and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature. We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel to achieve crypticity in another sensory modality (visual. This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

  13. Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

    Kang, Chang-Ku; Moon, Jong-Yeol; Lee, Sang-Im; Jablonski, Piotr G

    2013-01-01

    Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i) whether a choice of resting orientation by moths depends on the properties of natural background, and ii) what sensory cues moths use. We studied moths' behavior on natural (a tree log) and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature). We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel) to achieve crypticity in another sensory modality (visual). This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

  14. Fast Partial Evaluation of Pattern Matching in Strings

    Ager, Mads Sig; Danvy, Olivier; Rohde, Henning Korsholm

    2006-01-01

    We show how to obtain all of Knuth, Morris, and Pratt's linear-time string matcher by specializing a quadratic-time string matcher with respect to a pattern string. Although it has been known for 15 years how to obtain this linear matcher by partial evaluation of a quadratic one, how to obtain...... it in linear time has remained an open problem. Obtaining a linear matcher by partial evaluation of a quadratic one is achieved by performing its backtracking at specialization time and memoizing its results. We show (1) how to rewrite the source matcher such that its static intermediate computations can...... be shared at specialization time and (2) how to extend the memoization capabilities of a partial evaluator to static functions. Such an extended partial evaluator, if its memoization is implemented efficiently, specializes the rewritten source matcher in linear time. Finally, we show that the method also...

  15. Fast Partial Evaluation of Pattern Matching in Strings

    Ager, Mads Sig; Danvy, Olivier; Rohde, Henning Korsholm

    2003-01-01

    We show how to obtain all of Knuth, Morris, and Pratt's linear-time string matcher by specializing a quadratic-time string matcher with respect to a pattern string. Although it has been known for 15 years how to obtain this linear matcher by partial evaluation of a quadratic one, how to obtain...... it in linear time has remained an open problem. Obtaining a linear matcher by partial evaluation of a quadratic one is achieved by performing its backtracking at specialization time and memoizing its results. We show (1) how to rewrite the source matcher such that its static intermediate computations can...... be shared at specialization time and (2) how to extend the memoization capabilities of a partial evaluator to static functions. Such an extended partial evaluator, if its memoization is implemented efficiently, specializes the rewritten source matcher in linear time. Finally, we show that the method also...

  16. Fast Partial Evaluation of Pattern Matching in Strings

    Ager, Mads Sig; Danvy, Olivier; Rohde, Henning Korsholm

    2003-01-01

    We show how to obtain all of Knuth, Morris, and Pratt's linear-time string matcher by partial evaluation of a quadratic-time string matcher with respect to a pattern string. Although it has been known for 15 years how to obtain this linear matcher by partial evaluation of a quadratic one, how...... to obtain it in linear time has remained an open problem.Obtaining a linear matcher by partial evaluation of a quadratic one is achieved by performing its backtracking at specialization time and memoizing its results. We show (1) how to rewrite the source matcher such that its static intermediate...... computations can be shared at specialization time and (2) how to extend the memoization capabilities of a partial evaluator to static functions. Such an extended partial evaluator, if its memoization is implemented efficiently, specializes the rewritten source matcher in linear time....

  17. Fan fault diagnosis based on symmetrized dot pattern analysis and image matching

    Xu, Xiaogang; Liu, Haixiao; Zhu, Hao; Wang, Songling

    2016-07-01

    To detect the mechanical failure of fans, a new diagnostic method based on the symmetrized dot pattern (SDP) analysis and image matching is proposed. Vibration signals of 13 kinds of running states are acquired on a centrifugal fan test bed and reconstructed by the SDP technique. The SDP pattern templates of each running state are established. An image matching method is performed to diagnose the fault. In order to improve the diagnostic accuracy, the single template, multiple templates and clustering fault templates are used to perform the image matching.

  18. A multi-pattern hash-binary hybrid algorithm for URL matching in the HTTP protocol.

    Ping Zeng

    Full Text Available In this paper, based on our previous multi-pattern uniform resource locator (URL binary-matching algorithm called HEM, we propose an improved multi-pattern matching algorithm called MH that is based on hash tables and binary tables. The MH algorithm can be applied to the fields of network security, data analysis, load balancing, cloud robotic communications, and so on-all of which require string matching from a fixed starting position. Our approach effectively solves the performance problems of the classical multi-pattern matching algorithms. This paper explores ways to improve string matching performance under the HTTP protocol by using a hash method combined with a binary method that transforms the symbol-space matching problem into a digital-space numerical-size comparison and hashing problem. The MH approach has a fast matching speed, requires little memory, performs better than both the classical algorithms and HEM for matching fields in an HTTP stream, and it has great promise for use in real-world applications.

  19. A Boyer-Moore (or Watson-Watson) type algorithm for regular tree pattern matching

    Watson, B.W.; Aarts, E.H.L.; Eikelder, ten H.M.M.; Hemerik, C.; Rem, M.

    1995-01-01

    In this chapter, I outline a new algorithm for regular tree pattern matching. The existence of this algorithm was first mentioned in the statements accompanying my dissertation, [2]. In order to avoid repeating the material in my dissertation, it is assumed that the reader is familiar with Chapters

  20. Length-Bounded Hybrid CPU/GPU Pattern Matching Algorithm for Deep Packet Inspection

    Yi-Shan Lin

    2017-01-01

    Full Text Available Since frequent communication between applications takes place in high speed networks, deep packet inspection (DPI plays an important role in the network application awareness. The signature-based network intrusion detection system (NIDS contains a DPI technique that examines the incoming packet payloads by employing a pattern matching algorithm that dominates the overall inspection performance. Existing studies focused on implementing efficient pattern matching algorithms by parallel programming on software platforms because of the advantages of lower cost and higher scalability. Either the central processing unit (CPU or the graphic processing unit (GPU were involved. Our studies focused on designing a pattern matching algorithm based on the cooperation between both CPU and GPU. In this paper, we present an enhanced design for our previous work, a length-bounded hybrid CPU/GPU pattern matching algorithm (LHPMA. In the preliminary experiment, the performance and comparison with the previous work are displayed, and the experimental results show that the LHPMA can achieve not only effective CPU/GPU cooperation but also higher throughput than the previous method.

  1. Two related algorithms for root-to-frontier tree pattern matching

    Cleophas, L.G.W.A.; Hemerik, C.; Zwaan, G.

    2006-01-01

    Tree pattern matching (TPM) algorithms on ordered, ranked trees play an important role in applications such as compilers and term rewriting systems. Many TPM algorithms appearing in the literature are based on tree automata. For efficiency, these automata should be deterministic, yet deterministic

  2. Post-decomposition optimizations using pattern matching and rule-based clustering for multi-patterning technology

    Wang, Lynn T.-N.; Madhavan, Sriram

    2018-03-01

    A pattern matching and rule-based polygon clustering methodology with DFM scoring is proposed to detect decomposition-induced manufacturability detractors and fix the layout designs prior to manufacturing. A pattern matcher scans the layout for pre-characterized patterns from a library. If a pattern were detected, rule-based clustering identifies the neighboring polygons that interact with those captured by the pattern. Then, DFM scores are computed for the possible layout fixes: the fix with the best score is applied. The proposed methodology was applied to two 20nm products with a chip area of 11 mm2 on the metal 2 layer. All the hotspots were resolved. The number of DFM spacing violations decreased by 7-15%.

  3. Effects of Pattern Matching, Pattern Discrimination, and Experience in the Development of Diagnostic Expertise.

    Papa, Frank; And Others

    1990-01-01

    In this study an artificial intelligence assessment tool used disease-by-feature frequency estimates to create disease prototypes for nine common causes of acute chest pain. The tool then used each subject's prototypes and a pattern-recognition-based decision-making mechanism to diagnose 18 myocardial infarction cases. (MLW)

  4. Receptive fields of locust brain neurons are matched to polarization patterns of the sky.

    Bech, Miklós; Homberg, Uwe; Pfeiffer, Keram

    2014-09-22

    Many animals, including insects, are able to use celestial cues as a reference for spatial orientation and long-distance navigation [1]. In addition to direct sunlight, the chromatic gradient of the sky and its polarization pattern are suited to serve as orientation cues [2-5]. Atmospheric scattering of sunlight causes a regular pattern of E vectors in the sky, which are arranged along concentric circles around the sun [5, 6]. Although certain insects rely predominantly on sky polarization for spatial orientation [7], it has been argued that detection of celestial E vector orientation may not suffice to differentiate between solar and antisolar directions [8, 9]. We show here that polarization-sensitive (POL) neurons in the brain of the desert locust Schistocerca gregaria can overcome this ambiguity. Extracellular recordings from POL units in the central complex and lateral accessory lobes revealed E vector tunings arranged in concentric circles within large receptive fields, matching the sky polarization pattern at certain solar positions. Modeling of neuronal responses under an idealized sky polarization pattern (Rayleigh sky) suggests that these "matched filter" properties allow locusts to unambiguously determine the solar azimuth by relying solely on the sky polarization pattern for compass navigation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization.

    Peng, Huan-Kai; Lee, Hao-Chih; Pan, Jia-Yu; Marculescu, Radu

    2016-01-01

    In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications.

  6. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Inoue, Kentaro; Shimozono, Shinichi; Yoshida, Hideaki; Kurata, Hiroyuki

    2012-01-01

    For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  7. Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

    Kentaro Inoue

    Full Text Available BACKGROUND: For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process. RESULTS: We propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts. CONCLUSIONS: Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

  8. Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization.

    Huan-Kai Peng

    Full Text Available In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications.

  9. Data-Driven Engineering of Social Dynamics: Pattern Matching and Profit Maximization

    Peng, Huan-Kai; Lee, Hao-Chih; Pan, Jia-Yu; Marculescu, Radu

    2016-01-01

    In this paper, we define a new problem related to social media, namely, the data-driven engineering of social dynamics. More precisely, given a set of observations from the past, we aim at finding the best short-term intervention that can lead to predefined long-term outcomes. Toward this end, we propose a general formulation that covers two useful engineering tasks as special cases, namely, pattern matching and profit maximization. By incorporating a deep learning model, we derive a solution using convex relaxation and quadratic-programming transformation. Moreover, we propose a data-driven evaluation method in place of the expensive field experiments. Using a Twitter dataset, we demonstrate the effectiveness of our dynamics engineering approach for both pattern matching and profit maximization, and study the multifaceted interplay among several important factors of dynamics engineering, such as solution validity, pattern-matching accuracy, and intervention cost. Finally, the method we propose is general enough to work with multi-dimensional time series, so it can potentially be used in many other applications. PMID:26771830

  10. Characterization of Hemagglutinin Negative Botulinum Progenitor Toxins

    Suzanne R. Kalb

    2017-06-01

    Full Text Available Botulism is a disease involving intoxication with botulinum neurotoxins (BoNTs, toxic proteins produced by Clostridium botulinum and other clostridia. The 150 kDa neurotoxin is produced in conjunction with other proteins to form the botulinum progenitor toxin complex (PTC, alternating in size from 300 kDa to 500 kDa. These progenitor complexes can be classified into hemagglutinin positive or hemagglutinin negative, depending on the ability of some of the neurotoxin-associated proteins (NAPs to cause hemagglutination. The hemagglutinin positive progenitor toxin complex consists of BoNT, nontoxic non-hemagglutinin (NTNH, and three hemagglutinin proteins; HA-70, HA-33, and HA-17. Hemagglutinin negative progenitor toxin complexes contain BoNT and NTNH as the minimally functional PTC (M-PTC, but not the three hemagglutinin proteins. Interestingly, the genome of hemagglutinin negative progenitor toxin complexes comprises open reading frames (orfs which encode for three proteins, but the existence of these proteins has not yet been extensively demonstrated. In this work, we demonstrate that these three proteins exist and form part of the PTC for hemagglutinin negative complexes. Several hemagglutinin negative strains producing BoNT/A, /E, and /F were found to contain the three open reading frame proteins. Additionally, several BoNT/A-containing bivalent strains were examined, and NAPs from both genes, including the open reading frame proteins, were associated with BoNT/A. The open reading frame encoded proteins are more easily removed from the botulinum complex than the hemagglutinin proteins, but are present in several BoNT/A and /F toxin preparations. These are not easily removed from the BoNT/E complex, however, and are present even in commercially-available purified BoNT/E complex.

  11. Robust real-time pattern matching using bayesian sequential hypothesis testing.

    Pele, Ofir; Werman, Michael

    2008-08-01

    This paper describes a method for robust real time pattern matching. We first introduce a family of image distance measures, the "Image Hamming Distance Family". Members of this family are robust to occlusion, small geometrical transforms, light changes and non-rigid deformations. We then present a novel Bayesian framework for sequential hypothesis testing on finite populations. Based on this framework, we design an optimal rejection/acceptance sampling algorithm. This algorithm quickly determines whether two images are similar with respect to a member of the Image Hamming Distance Family. We also present a fast framework that designs a near-optimal sampling algorithm. Extensive experimental results show that the sequential sampling algorithm performance is excellent. Implemented on a Pentium 4 3 GHz processor, detection of a pattern with 2197 pixels, in 640 x 480 pixel frames, where in each frame the pattern rotated and was highly occluded, proceeds at only 0.022 seconds per frame.

  12. A novel iris patterns matching algorithm of weighted polar frequency correlation

    Zhao, Weijie; Jiang, Linhua

    2014-11-01

    Iris recognition is recognized as one of the most accurate techniques for biometric authentication. In this paper, we present a novel correlation method - Weighted Polar Frequency Correlation(WPFC) - to match and evaluate two iris images, actually it can also be used for evaluating the similarity of any two images. The WPFC method is a novel matching and evaluating method for iris image matching, which is complete different from the conventional methods. For instance, the classical John Daugman's method of iris recognition uses 2D Gabor wavelets to extract features of iris image into a compact bit stream, and then matching two bit streams with hamming distance. Our new method is based on the correlation in the polar coordinate system in frequency domain with regulated weights. The new method is motivated by the observation that the pattern of iris that contains far more information for recognition is fine structure at high frequency other than the gross shapes of iris images. Therefore, we transform iris images into frequency domain and set different weights to frequencies. Then calculate the correlation of two iris images in frequency domain. We evaluate the iris images by summing the discrete correlation values with regulated weights, comparing the value with preset threshold to tell whether these two iris images are captured from the same person or not. Experiments are carried out on both CASIA database and self-obtained images. The results show that our method is functional and reliable. Our method provides a new prospect for iris recognition system.

  13. Dietary pattern analysis: a comparison between matched vegetarian and omnivorous subjects.

    Clarys, Peter; Deriemaeker, Peter; Huybrechts, Inge; Hebbelinck, Marcel; Mullie, Patrick

    2013-06-13

    Dietary pattern analysis, based on the concept that foods eaten together are as important as a reductive methodology characterized by a single food or nutrient analysis, has emerged as an alternative approach to study the relation between nutrition and disease. The aim of the present study was to compare nutritional intake and the results of dietary pattern analysis in properly matched vegetarian and omnivorous subjects. Vegetarians (n = 69) were recruited via purposeful sampling and matched non-vegetarians (n = 69) with same age, gender, health and lifestyle characteristics were searched for via convenience sampling. Two dietary pattern analysis methods, the Healthy Eating Index-2010 (HEI-2010) and the Mediterranean Diet Score (MDS) were calculated and analysed in function of the nutrient intake. Mean total energy intake was comparable between vegetarians and omnivorous subjects (p > 0.05). Macronutrient analysis revealed significant differences between the mean values for vegetarians and omnivorous subjects (absolute and relative protein and total fat intake were significantly lower in vegetarians, while carbohydrate and fibre intakes were significantly higher in vegetarians than in omnivorous subjects). The HEI and MDS were significantly higher for the vegetarians (HEI = 53.8.1 ± 11.2; MDS = 4.3 ± 1.3) compared to the omnivorous subjects (HEI = 46.4 ± 15.3; MDS = 3.8 ± 1.4). Our results indicate a more nutrient dense pattern, closer to the current dietary recommendations for the vegetarians compared to the omnivorous subjects. Both indexing systems were able to discriminate between the vegetarians and the non-vegetarians with higher scores for the vegetarian subjects.

  14. Crack displacement sensing and measurement in concrete using circular grating moire fringes and pattern matching

    Chan, H. M.; Yen, K. S.; Ratnam, M. M.

    2008-09-01

    The moire method has been extensively studied in the past and applied in various engineering applications. Several techniques are available for generating the moire fringes in these applications, which include moire interferometry, projection moire, shadow moire, moire deflectometry etc. Most of these methods use the superposition of linear gratings to generate the moire patterns. The use of non-linear gratings, such as circular, radial and elongated gratings has received less attention from the research community. The potential of non-linear gratings in engineering measurement has been realized in a limited number of applications, such as rotation measurement, measurement of linear displacement, measurement of expansion coefficients of materials and measurement of strain distribution. In this work, circular gratings of different pitch were applied to the sensing and measurement of crack displacement in concrete structures. Gratings of pitch 0.50 mm and 0.55 mm were generated using computer software and attached to two overlapping acrylic plates that were bonded to either side of the crack. The resulting moire patterns were captured using a standard digital camera and compared with a set of reference patterns generated using a precision positioning stage. Using several image pre-processing stages, such as filtering and morphological operations, and pattern matching the magnitude displacements along two orthogonal axes can be detected with a resolution of 0.05 mm.

  15. Nutritional Status and Daytime Pattern of Protein Intake on Match, Post-Match, Rest and Training Days in Senior Professional and Youth Elite Soccer Players.

    Bettonviel A, E O; Brinkmans N, Y J; Russcher, Kris; Wardenaar, Floris C; Witard, Oliver C

    2016-06-01

    The nutritional status of elite soccer players across match, postmatch, training and rest days has not been defined. Recent evidence suggests the pattern of dietary protein intake impacts the daytime turnover of muscle proteins and, as such, influences muscle recovery. We assessed the nutritional status and daytime pattern of protein intake in senior professional and elite youth soccer players and compared findings against published recommendations. Fourteen senior professional (SP) and 15 youth elite (YP) soccer players from the Dutch premier division completed nutritional assessments using a 24-hr web-based recall method. Recall days consisted of a match, postmatch, rest, and training day. Daily energy intake over the 4-day period was similar between SP (2988 ± 583 kcal/day) and YP (2938 ± 465 kcal/day; p = .800). Carbohydrate intake over the combined 4-day period was lower in SP (4.7 ± 0.7 g·kg-1 BM·day-1) vs. YP (6.0 ± 1.5 g·kg-1 BM·day-1, p = .006) and SP failed to meet recommended carbohydrate intakes on match and training days. Conversely, recommended protein intakes were met for SP (1.9 ± 0.3 g·kg-1 BM·day-1) and YP (1.7 ± 0.4 g·kg-1 BM·day-1), with no differences between groups (p = .286). Accordingly, both groups met or exceeded recommended daily protein intakes on individual match, postmatch, rest and training days. A similar "balanced" daytime pattern of protein intake was observed in SP and YP. To conclude, SP increased protein intake on match and training days to a greater extent than YP, however at the expense of carbohydrate intake. The daytime distribution of protein intake for YP and SP aligned with current recommendations of a balanced protein meal pattern.

  16. Pattern Matching Framework to Estimate the Urgency of Off-Normal Situations in NPPs

    Shin, Jin Soo; Park, Sang Jun; Heo, Gyun Young [Kyung Hee University, Yongin (Korea, Republic of); Park, Jin Kyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Kim, Hyo Jin; Park, Soon Yeol [Korea Hydro and Nuclear Power, Yeonggwang (Korea, Republic of)

    2010-10-15

    According to power plant operators, it was said that they could quite well recognize off-normal situations from an incipient stage and also anticipate the possibility of upcoming trips in case of skilled operators, even though it is difficult to clarify the cause of the off-normal situation. From the interview, we could assure the feasibility of two assumptions for the diagnosis of off-normal conditions: One is that we can predict whether an accidental shutdown happens or not if we observe the early stage when an off-normal starts to grow. The other is the observation at the early stage can provide the remaining time to a trip as well as the cause of such an off-normal situation. For this purpose, the development of on-line monitoring systems using various data processing techniques in nuclear power plants (NPPs) has been the subject of increasing attention and becomes important contributor to improve performance and economics. Many of studies have suggested the diagnostic methodologies. One of representative methods was to use the distance discrimination as a similarity measure, for example, such as the Euclidean distance. A variety of artificial intelligence techniques such as a neural network have been developed as well. In addition, some of these methodologies were to reduce the data dimensions for more effectively work. While sharing the same motivation with the previous achievements, this study proposed non-parametric pattern matching techniques to reduce the uncertainty in pursuance of selection of models and modeling processes. This could be characterized by the following two aspects: First, for overcoming considering only a few typical scenarios in the most of the studies, this study is getting the entire sets of off-normal situations which are anticipated in NPPs, which are created by a full-scope simulator. Second, many of the existing researches adopted the process of forming a diagnosis model which is so-called a training technique or a parametric

  17. Pattern Matching Framework to Estimate the Urgency of Off-Normal Situations in NPPs

    Shin, Jin Soo; Park, Sang Jun; Heo, Gyun Young; Park, Jin Kyun; Kim, Hyo Jin; Park, Soon Yeol

    2010-01-01

    According to power plant operators, it was said that they could quite well recognize off-normal situations from an incipient stage and also anticipate the possibility of upcoming trips in case of skilled operators, even though it is difficult to clarify the cause of the off-normal situation. From the interview, we could assure the feasibility of two assumptions for the diagnosis of off-normal conditions: One is that we can predict whether an accidental shutdown happens or not if we observe the early stage when an off-normal starts to grow. The other is the observation at the early stage can provide the remaining time to a trip as well as the cause of such an off-normal situation. For this purpose, the development of on-line monitoring systems using various data processing techniques in nuclear power plants (NPPs) has been the subject of increasing attention and becomes important contributor to improve performance and economics. Many of studies have suggested the diagnostic methodologies. One of representative methods was to use the distance discrimination as a similarity measure, for example, such as the Euclidean distance. A variety of artificial intelligence techniques such as a neural network have been developed as well. In addition, some of these methodologies were to reduce the data dimensions for more effectively work. While sharing the same motivation with the previous achievements, this study proposed non-parametric pattern matching techniques to reduce the uncertainty in pursuance of selection of models and modeling processes. This could be characterized by the following two aspects: First, for overcoming considering only a few typical scenarios in the most of the studies, this study is getting the entire sets of off-normal situations which are anticipated in NPPs, which are created by a full-scope simulator. Second, many of the existing researches adopted the process of forming a diagnosis model which is so-called a training technique or a parametric

  18. GPUs for fast triggering and pattern matching at the CERN experiment NA62

    Lamanna, Gianluca; Collazuol, Gianmaria; Sozzi, Marco

    2011-01-01

    In rare decays experiments an effective trigger is crucial to reduce both the quantity of data written on tape and the bandwidth requirements for the DAQ (Data Acquisition) system. A multilevel architecture is commonly used to achieve a higher reduction factor, exploiting dedicated custom hardware and flexible software in standard computers. In this paper we discuss the possibility to use commercial video card processors (GPU) to build a fast and effective trigger system, both at hardware and software level. The case of fast pattern matching in the RICH detector of the NA62 experiment at CERN aiming at measuring the Branching Ratio of the ultra rare decay K + →π + νν-bar is considered as use case although the versatility and the customizability of this approach easily allow exporting the concept to different contexts.

  19. ISOLATED SPEECH RECOGNITION SYSTEM FOR TAMIL LANGUAGE USING STATISTICAL PATTERN MATCHING AND MACHINE LEARNING TECHNIQUES

    VIMALA C.

    2015-05-01

    Full Text Available In recent years, speech technology has become a vital part of our daily lives. Various techniques have been proposed for developing Automatic Speech Recognition (ASR system and have achieved great success in many applications. Among them, Template Matching techniques like Dynamic Time Warping (DTW, Statistical Pattern Matching techniques such as Hidden Markov Model (HMM and Gaussian Mixture Models (GMM, Machine Learning techniques such as Neural Networks (NN, Support Vector Machine (SVM, and Decision Trees (DT are most popular. The main objective of this paper is to design and develop a speaker-independent isolated speech recognition system for Tamil language using the above speech recognition techniques. The background of ASR system, the steps involved in ASR, merits and demerits of the conventional and machine learning algorithms and the observations made based on the experiments are presented in this paper. For the above developed system, highest word recognition accuracy is achieved with HMM technique. It offered 100% accuracy during training process and 97.92% for testing process.

  20. A Hybrid CPU/GPU Pattern-Matching Algorithm for Deep Packet Inspection.

    Chun-Liang Lee

    Full Text Available The large quantities of data now being transferred via high-speed networks have made deep packet inspection indispensable for security purposes. Scalable and low-cost signature-based network intrusion detection systems have been developed for deep packet inspection for various software platforms. Traditional approaches that only involve central processing units (CPUs are now considered inadequate in terms of inspection speed. Graphic processing units (GPUs have superior parallel processing power, but transmission bottlenecks can reduce optimal GPU efficiency. In this paper we describe our proposal for a hybrid CPU/GPU pattern-matching algorithm (HPMA that divides and distributes the packet-inspecting workload between a CPU and GPU. All packets are initially inspected by the CPU and filtered using a simple pre-filtering algorithm, and packets that might contain malicious content are sent to the GPU for further inspection. Test results indicate that in terms of random payload traffic, the matching speed of our proposed algorithm was 3.4 times and 2.7 times faster than those of the AC-CPU and AC-GPU algorithms, respectively. Further, HPMA achieved higher energy efficiency than the other tested algorithms.

  1. Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

    Du, Pan; Kibbe, Warren A; Lin, Simon M

    2006-09-01

    A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods. Most peak detection algorithms simply identify peaks based on amplitude, ignoring the additional information present in the shape of the peaks in a spectrum. In our experience, 'true' peaks have characteristic shapes, and providing a shape-matching function that provides a 'goodness of fit' coefficient should provide a more robust peak identification method. Based on these observations, a continuous wavelet transform (CWT)-based peak detection algorithm has been devised that identifies peaks with different scales and amplitudes. By transforming the spectrum into wavelet space, the pattern-matching problem is simplified and in addition provides a powerful technique for identifying and separating the signal from the spike noise and colored noise. This transformation, with the additional information provided by the 2D CWT coefficients can greatly enhance the effective signal-to-noise ratio. Furthermore, with this technique no baseline removal or peak smoothing preprocessing steps are required before peak detection, and this improves the robustness of peak detection under a variety of conditions. The algorithm was evaluated with SELDI-TOF spectra with known polypeptide positions. Comparisons with two other popular algorithms were performed. The results show the CWT-based algorithm can identify both strong and weak peaks while keeping false positive rate low. The algorithm is implemented in R and will be

  2. A Data-Driven Modeling Strategy for Smart Grid Power Quality Coupling Assessment Based on Time Series Pattern Matching

    Hao Yu

    2018-01-01

    Full Text Available This study introduces a data-driven modeling strategy for smart grid power quality (PQ coupling assessment based on time series pattern matching to quantify the influence of single and integrated disturbance among nodes in different pollution patterns. Periodic and random PQ patterns are constructed by using multidimensional frequency-domain decomposition for all disturbances. A multidimensional piecewise linear representation based on local extreme points is proposed to extract the patterns features of single and integrated disturbance in consideration of disturbance variation trend and severity. A feature distance of pattern (FDP is developed to implement pattern matching on univariate PQ time series (UPQTS and multivariate PQ time series (MPQTS to quantify the influence of single and integrated disturbance among nodes in the pollution patterns. Case studies on a 14-bus distribution system are performed and analyzed; the accuracy and applicability of the FDP in the smart grid PQ coupling assessment are verified by comparing with other time series pattern matching methods.

  3. Oscillatory signatures of crossmodal congruence effects: An EEG investigation employing a visuotactile pattern matching paradigm.

    Göschl, Florian; Friese, Uwe; Daume, Jonathan; König, Peter; Engel, Andreas K

    2015-08-01

    Coherent percepts emerge from the accurate combination of inputs from the different sensory systems. There is an ongoing debate about the neurophysiological mechanisms of crossmodal interactions in the brain, and it has been proposed that transient synchronization of neurons might be of central importance. Oscillatory activity in lower frequency ranges (congruence. Analysis of the behavioral data showed benefits for congruent visuotactile stimulus combinations. Differences in oscillatory dynamics related to crossmodal congruence within the two tasks were observed in the beta-band for crossmodal target detection, as well as in the theta-band for congruence evaluation. Contrasting ongoing activity preceding visuotactile stimulation between the two tasks revealed differences in the alpha- and beta-bands. Source reconstruction of between-task differences showed prominent involvement of premotor cortex, supplementary motor area, somatosensory association cortex and the supramarginal gyrus. These areas not only exhibited more involvement in the pre-stimulus interval for target detection compared to congruence evaluation, but were also crucially involved in post-stimulus differences related to crossmodal stimulus congruence within the detection task. These results add to the increasing evidence that low frequency oscillations are functionally relevant for integration in distributed brain networks, as demonstrated for crossmodal interactions in visuotactile pattern matching in the current study. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Infiltration patterns in monoclonal plasma cell disorders: correlation of magnetic resonance imaging with matched bone marrow histology

    Andrulis, Mindaugas [Institute of Pathology, University of Heidelberg, Heidelberg (Germany); Bäuerle, Tobias [Department of Diagnostic and Interventional Radiology, University of Hamburg, Hamburg (Germany); Goldschmidt, Hartmut [Department of Hematology and Oncology, University of Heidelberg, Heidelberg (Germany); Delorme, Stefan [Department of Radiology, German Cancer Research Center (DKFZ), Heidelberg (Germany); Landgren, Ola [Multiple Myeloma Section, Metabolism Branch, National Cancer Institute, Bethesda (United States); Schirmacher, Peter [Institute of Pathology, University of Heidelberg, Heidelberg (Germany); Hillengass, Jens, E-mail: jens.hillengass@med.uni-heidelberg.de [Department of Hematology and Oncology, University of Heidelberg, Heidelberg (Germany); Department of Radiology, German Cancer Research Center (DKFZ), Heidelberg (Germany)

    2014-06-15

    Objectives: To investigate how plasma cell infiltration patterns detected by MRI match the plasma cell distribution in bone marrow biopsy. Methods: We assessed 50 patients with monoclonal plasma cell disorders of all clinical stages. MRI infiltration pattern was compared with matched BM histology from the same anatomic region. Results: MRI revealed a minimal (n = 11, 22%), focal (n = 5, 10%), diffuse (n = 14, 28%) and mixed (n = 20, 40%) infiltration pattern. Diffuse MRI pattern was predominant in smoldering myeloma patients whereas the MRI patterns with “focal component” (i.e. focal and mixed) were most common in symptomatic myeloma (p < 0.01). In histology an interstitial (n = 13, 26%), nodular (n = 23, 46%) and packed marrow (n = 14, 28%) was found respectively. All three histological types of infiltration were observed in patients with diffuse and mixed MRI patterns. Minimal MRI pattern was found in all MGUS patients and was associated with an interstitial BM infiltration. In two patients with minimal MRI pattern an extensive micro-nodular BM infiltration was found in histology. Conclusions: Infiltration patterns in MRI represent different histological growth patterns of plasma cells, but the MRI resolution is not sufficient to visualize micro-nodular aggregates of plasma cells.

  5. Infiltration patterns in monoclonal plasma cell disorders: correlation of magnetic resonance imaging with matched bone marrow histology

    Andrulis, Mindaugas; Bäuerle, Tobias; Goldschmidt, Hartmut; Delorme, Stefan; Landgren, Ola; Schirmacher, Peter; Hillengass, Jens

    2014-01-01

    Objectives: To investigate how plasma cell infiltration patterns detected by MRI match the plasma cell distribution in bone marrow biopsy. Methods: We assessed 50 patients with monoclonal plasma cell disorders of all clinical stages. MRI infiltration pattern was compared with matched BM histology from the same anatomic region. Results: MRI revealed a minimal (n = 11, 22%), focal (n = 5, 10%), diffuse (n = 14, 28%) and mixed (n = 20, 40%) infiltration pattern. Diffuse MRI pattern was predominant in smoldering myeloma patients whereas the MRI patterns with “focal component” (i.e. focal and mixed) were most common in symptomatic myeloma (p < 0.01). In histology an interstitial (n = 13, 26%), nodular (n = 23, 46%) and packed marrow (n = 14, 28%) was found respectively. All three histological types of infiltration were observed in patients with diffuse and mixed MRI patterns. Minimal MRI pattern was found in all MGUS patients and was associated with an interstitial BM infiltration. In two patients with minimal MRI pattern an extensive micro-nodular BM infiltration was found in histology. Conclusions: Infiltration patterns in MRI represent different histological growth patterns of plasma cells, but the MRI resolution is not sufficient to visualize micro-nodular aggregates of plasma cells

  6. CERN Computing Colloquia Spring Series: IT Security - A High-Performance Pattern Matching Engine for Intrusion Detection

    CERN. Geneva

    2006-01-01

    The flexible and modular design of the engine allows a broad spectrum of applications, ranging from high-end enterprise level network devices that need to match hundreds of thousands of patterns at speeds of tens of gigabits per second, to low-end dev...

  7. Two tree-formation methods for fast pattern search using nearest-neighbour and nearest-centroid matching

    Schomaker, Lambertus; Mangalagiu, D.; Vuurpijl, Louis; Weinfeld, M.; Schomaker, Lambert; Vuurpijl, Louis

    2000-01-01

    This paper describes tree­based classification of character images, comparing two methods of tree formation and two methods of matching: nearest neighbor and nearest centroid. The first method, Preprocess Using Relative Distances (PURD) is a tree­based reorganization of a flat list of patterns,

  8. GPUs for fast pattern matching in the RICH of the NA62 experiment

    Lamanna, Gianluca; Collazuol, Gianmaria; Sozzi, Marco

    2011-01-01

    In rare decays experiments an effective online selection is a fundamental part of the data acquisition system (DAQ) in order to reduce both the quantity of data written on tape and the bandwidth requirements for the DAQ system. A multilevel architecture is commonly used to achieve a higher reduction factor, exploiting dedicated custom hardware and flexible software in standard computers. In this paper we discuss the possibility to use commercial video card processors (GPU) to build a fast and effective trigger system, both at hardware and software level. The computing power of the GPUs allows to design a real-time system in which trigger decisions are taken directly in the video processor with a defined maximum latency. This allows building lowest trigger levels based on standard off-the-shelf PCs with CPU and GPU (instead of the commonly adopted solutions based on custom electronics with FPGA or ASICs) with enhanced and high performance computation capabilities, resulting in high rejection power, high efficiency and simpler low level triggers. The ongoing work presented here shows the results achieved in the case of fast pattern matching in the RICH detector of the NA62 at CERN, aiming at measuring the Branching Ratio of the ultra rare decay K + →π + νν-bar, is considered as use case, although the versatility and the customizability of this approach easily allow exporting the concept to different contexts. In particular the application is related to particle identification in the RICH detector of the NA62 experiment, where the rate of events to be analyzed will be around 10 MHz. The results obtained in lab tests are very encouraging to go towards a working prototype. Due to the use of off-the-shelf technology, in continuous development for other purposes (Video Games, image editing,...), the architecture described would be easily exported into other experiments, for building powerful, flexible and fully customizable trigger systems.

  9. GPUs for fast pattern matching in the RICH of the NA62 experiment

    Lamanna, Gianluca, E-mail: gianluca.lamanna@cern.c [CERN, 1211 Geneve 23 (Switzerland); Collazuol, Gianmaria, E-mail: gianmaria.collazuol@cern.c [INFN Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy); Sozzi, Marco, E-mail: marco.sozzi@cern.c [University and INFN Pisa, Largo Pontecorvo 3, 56127 Pisa (Italy)

    2011-05-21

    In rare decays experiments an effective online selection is a fundamental part of the data acquisition system (DAQ) in order to reduce both the quantity of data written on tape and the bandwidth requirements for the DAQ system. A multilevel architecture is commonly used to achieve a higher reduction factor, exploiting dedicated custom hardware and flexible software in standard computers. In this paper we discuss the possibility to use commercial video card processors (GPU) to build a fast and effective trigger system, both at hardware and software level. The computing power of the GPUs allows to design a real-time system in which trigger decisions are taken directly in the video processor with a defined maximum latency. This allows building lowest trigger levels based on standard off-the-shelf PCs with CPU and GPU (instead of the commonly adopted solutions based on custom electronics with FPGA or ASICs) with enhanced and high performance computation capabilities, resulting in high rejection power, high efficiency and simpler low level triggers. The ongoing work presented here shows the results achieved in the case of fast pattern matching in the RICH detector of the NA62 at CERN, aiming at measuring the Branching Ratio of the ultra rare decay K{sup +}{yields}{pi}{sup +}{nu}{nu}-bar, is considered as use case, although the versatility and the customizability of this approach easily allow exporting the concept to different contexts. In particular the application is related to particle identification in the RICH detector of the NA62 experiment, where the rate of events to be analyzed will be around 10 MHz. The results obtained in lab tests are very encouraging to go towards a working prototype. Due to the use of off-the-shelf technology, in continuous development for other purposes (Video Games, image editing,...), the architecture described would be easily exported into other experiments, for building powerful, flexible and fully customizable trigger systems.

  10. Advanced optical correlation and digital methods for pattern matching—50th anniversary of Vander Lugt matched filter

    Millán, María S.

    2012-10-01

    On the verge of the 50th anniversary of Vander Lugt’s formulation for pattern matching based on matched filtering and optical correlation, we acknowledge the very intense research activity developed in the field of correlation-based pattern recognition during this period of time. The paper reviews some domains that appeared as emerging fields in the last years of the 20th century and have been developed later on in the 21st century. Such is the case of three-dimensional (3D) object recognition, biometric pattern matching, optical security and hybrid optical-digital processors. 3D object recognition is a challenging case of multidimensional image recognition because of its implications in the recognition of real-world objects independent of their perspective. Biometric recognition is essentially pattern recognition for which the personal identification is based on the authentication of a specific physiological characteristic possessed by the subject (e.g. fingerprint, face, iris, retina, and multifactor combinations). Biometric recognition often appears combined with encryption-decryption processes to secure information. The optical implementations of correlation-based pattern recognition processes still rely on the 4f-correlator, the joint transform correlator, or some of their variants. But the many applications developed in the field have been pushing the systems for a continuous improvement of their architectures and algorithms, thus leading towards merged optical-digital solutions.

  11. Advanced optical correlation and digital methods for pattern matching—50th anniversary of Vander Lugt matched filter

    Millán, María S

    2012-01-01

    On the verge of the 50th anniversary of Vander Lugt’s formulation for pattern matching based on matched filtering and optical correlation, we acknowledge the very intense research activity developed in the field of correlation-based pattern recognition during this period of time. The paper reviews some domains that appeared as emerging fields in the last years of the 20th century and have been developed later on in the 21st century. Such is the case of three-dimensional (3D) object recognition, biometric pattern matching, optical security and hybrid optical–digital processors. 3D object recognition is a challenging case of multidimensional image recognition because of its implications in the recognition of real-world objects independent of their perspective. Biometric recognition is essentially pattern recognition for which the personal identification is based on the authentication of a specific physiological characteristic possessed by the subject (e.g. fingerprint, face, iris, retina, and multifactor combinations). Biometric recognition often appears combined with encryption–decryption processes to secure information. The optical implementations of correlation-based pattern recognition processes still rely on the 4f-correlator, the joint transform correlator, or some of their variants. But the many applications developed in the field have been pushing the systems for a continuous improvement of their architectures and algorithms, thus leading towards merged optical–digital solutions. (review article)

  12. Rapid Diagnostic Assay for Intact Influenza Virus Using a High Affinity Hemagglutinin Binding Protein.

    Anderson, Caitlin E; Holstein, Carly A; Strauch, Eva-Maria; Bennett, Steven; Chevalier, Aaron; Nelson, Jorgen; Fu, Elain; Baker, David; Yager, Paul

    2017-06-20

    Influenza is a ubiquitous and recurring infection that results in approximately 500 000 deaths globally each year. Commercially available rapid diagnostic tests are based upon detection of the influenza nucleoprotein, which are limited in that they are unable to differentiate by species and require an additional viral lysis step. Sample preprocessing can be minimized or eliminated by targeting the intact influenza virus, thereby reducing assay complexity and leveraging the large number of hemagglutinin proteins on the surface of each virus. Here, we report the development of a paper-based influenza assay that targets the hemagglutinin protein; the assay employs a combination of antibodies and novel computationally designed, recombinant affinity proteins as the capture and detection agents. This system leverages the customizability of recombinant protein design to target the conserved receptor-binding pocket of the hemagglutinin protein and to match the trimeric nature of hemagglutinin for improved avidity. Using this assay, we demonstrate the first instance of intact influenza virus detection using a combination of antibody and affinity proteins within a porous network. The recombinant head region binder based assays yield superior analytical sensitivity as compared to the antibody based assay, with lower limits of detection of 3.54 × 10 7 and 1.34 × 10 7 CEID 50 /mL for the mixed and all binder stacks, respectively. Not only does this work describe the development of a novel influenza assay, it also demonstrates the power of recombinant affinity proteins for use in rapid diagnostic assays.

  13. Network-level accident-mapping: Distance based pattern matching using artificial neural network.

    Deka, Lipika; Quddus, Mohammed

    2014-04-01

    The objective of an accident-mapping algorithm is to snap traffic accidents onto the correct road segments. Assigning accidents onto the correct segments facilitate to robustly carry out some key analyses in accident research including the identification of accident hot-spots, network-level risk mapping and segment-level accident risk modelling. Existing risk mapping algorithms have some severe limitations: (i) they are not easily 'transferable' as the algorithms are specific to given accident datasets; (ii) they do not perform well in all road-network environments such as in areas of dense road network; and (iii) the methods used do not perform well in addressing inaccuracies inherent in and type of road environment. The purpose of this paper is to develop a new accident mapping algorithm based on the common variables observed in most accident databases (e.g. road name and type, direction of vehicle movement before the accident and recorded accident location). The challenges here are to: (i) develop a method that takes into account uncertainties inherent to the recorded traffic accident data and the underlying digital road network data, (ii) accurately determine the type and proportion of inaccuracies, and (iii) develop a robust algorithm that can be adapted for any accident set and road network of varying complexity. In order to overcome these challenges, a distance based pattern-matching approach is used to identify the correct road segment. This is based on vectors containing feature values that are common in the accident data and the network data. Since each feature does not contribute equally towards the identification of the correct road segments, an ANN approach using the single-layer perceptron is used to assist in "learning" the relative importance of each feature in the distance calculation and hence the correct link identification. The performance of the developed algorithm was evaluated based on a reference accident dataset from the UK confirming that

  14. A pattern-matched Twitter analysis of US cancer-patient sentiments.

    Crannell, W Christian; Clark, Eric; Jones, Chris; James, Ted A; Moore, Jesse

    2016-12-01

    Twitter has been recognized as an important source of organic sentiment and opinion. This study aimed to (1) characterize the content of tweets authored by the United States cancer patients; and (2) use patient tweets to compute the average happiness of cancer patients for each cancer diagnosis. A large sample of English tweets from March 2014 through December 2014 was obtained from Twitter. Using regular expression software pattern matching, the tweets were filtered by cancer diagnosis. For each cancer-specific tweetset, individual patients were extracted, and the content of the tweet was categorized. The patients' Twitter identification numbers were used to gather all tweets for each patient, and happiness values for patient tweets were calculated using a quantitative hedonometric analysis. The most frequently tweeted cancers were breast (n = 15,421, 11% of total cancer tweets), lung (n = 2928, 2.0%), prostate (n = 1036, 0.7%), and colorectal (n = 773, 0.5%). Patient tweets pertained to the treatment course (n = 73, 26%), diagnosis (n = 65, 23%), and then surgery and/or biopsy (n = 42, 15%). Computed happiness values for each cancer diagnosis revealed higher average happiness values for thyroid (h_avg = 6.1625), breast (h_avg = 6.1485), and lymphoma (h_avg = 6.0977) cancers and lower average happiness values for pancreatic (h_avg = 5.8766), lung (h_avg = 5.8733), and kidney (h_avg = 5.8464) cancers. The study confirms that patients are expressing themselves openly on social media about their illness and that unique cancer diagnoses are correlated with varying degrees of happiness. Twitter can be employed as a tool to identify patient needs and as a means to gauge the cancer patient experience. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Movement patterns and muscle damage during simulated rugby sevens matches in National team players.

    Pereira, Lucas A; Nakamura, Fábio Y; Moraes, José E; Kitamura, Katia; Ramos, Solange P; Loturco, Irineu

    2017-02-23

    The aim of this study was to analyze the match performance (i.e., distance covered in different intensities), signs of muscle damage (assessed by means of creatine kinase [CK] activity and rate of force development [RFD]), and neuromuscular fatigue (using linear sprint and vertical jump performances) following three single-day simulated matches performed by rugby sevens players from the Brazilian National Team. Ten male rugby sevens players (25.2 ± 3.6 years; 88.7 ± 7.1 kg; 182.2 ± 6.3 cm) participated in this study. On the day prior to the matches, the athletes performed a 40-m sprint, a vertical jump assessment and a maximal isometric force test. In the morning of the match day, blood samples were collected to analyze the CK activity. Afterwards, three simulated rugby sevens' matches were performed with 2-h intermission periods. The match performance (encompassing total distance and distance covered in different velocity ranges and body loads [BL]) were obtained from global positioning system units. The statistical analysis was performed by using a mixed model approach and the effect sizes (ES) of the differences. The statistical significance level was set at P0.8) and significant (P< 0.05) reductions were demonstrated in the total distance and BL when comparing the 2 with the 1 halves. Decrements in the explosive force capacity (assessed by means of RFD) and the squat jump were noticed (ES varying from 0.55 to 1.14; P< 0.05). The CK activity increased after the matches (ES = 1.29; P< 0.05). The rugby sevens players were able to maintain the physical performance across three successive matches simulating the first day of a tournament. The augmented CK activity and the decreases in the squat jump and RFD suggest that increased levels of muscle damage were experienced on the day after the matches. Therefore, the technical staff are encouraged to implement recovery strategies and planned substitutions during multi-day tournaments in order to reduce the impact of

  16. How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

    Barbara Diana

    2017-08-01

    Full Text Available The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance. This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg. The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

  17. How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

    Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

    2017-01-01

    The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

  18. Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses

    Yuki Furuse

    2016-11-01

    Full Text Available Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1 multiple lineages have been circulating globally; (2 there have been weak and infrequent selective bottlenecks; (3 the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4 there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

  19. Generalized Phase contrast and matched filtering for speckle‐free patterned illumination

    Palima, Darwin; Bañas, Andrew Rafael; Villangca, Mark Jayson

    2013-01-01

    Generalized Phase Contrast (GPC) and matched‐filtering GPC use tandem diffractive phase elements on Fourier‐conjugate planes of a 4f optical processor to efficiently reshape incident light into a pattern that resembles the input phase modulation pattern. The synthesized patterns are inherently...... to optically trap and mechanically manipulate microparticles, GPC has also been applied for laser beamshaping, optical phase cryptography, and greyscale image projection. Recent reports from our collaborators highlight that GPC‐based spatial lightshaping, when combined with temporal focusing and multiphoton...... excitation, exhibits some robustness against light scattering and, hence, makes a promising tool for spatially precise targeting of deeper subsurface neurons using minimally speckled patterned illumination for multiphoton excitation....

  20. Pattern formation without diffraction matching in optical parametric oscillators with a metamaterial.

    Tassin, Philippe; Van der Sande, Guy; Veretennicoff, Irina; Kockaert, Pascal; Tlidi, Mustapha

    2009-05-25

    We consider a degenerate optical parametric oscillator containing a left-handed material. We show that the inclusion of a left-handed material layer allows for controlling the strength and sign of the diffraction coefficient at either the pump or the signal frequency. Subsequently, we demonstrate the existence of stable dissipative structures without diffraction matching, i.e., without the usual relationship between the diffraction coefficients of the signal and pump fields. Finally, we investigate the size scaling of these light structures with decreasing diffraction strength.

  1. Spatio-temporal dynamics of global H5N1 outbreaks match bird migration patterns

    Yali Si

    2009-11-01

    Full Text Available The global spread of highly pathogenic avian influenza H5N1 in poultry, wild birds and humans, poses a significant pandemic threat and a serious public health risk. An efficient surveillance and disease control system relies on the understanding of the dispersion patterns and spreading mechanisms of the virus. A space-time cluster analysis of H5N1 outbreaks was used to identify spatio-temporal patterns at a global scale and over an extended period of time. Potential mechanisms explaining the spread of the H5N1 virus, and the role of wild birds, were analyzed. Between December 2003 and December 2006, three global epidemic phases of H5N1 influenza were identified. These H5N1 outbreaks showed a clear seasonal pattern, with a high density of outbreaks in winter and early spring (i.e., October to March. In phase I and II only the East Asia Australian flyway was affected. During phase III, the H5N1 viruses started to appear in four other flyways: the Central Asian flyway, the Black Sea Mediterranean flyway, the East Atlantic flyway and the East Africa West Asian flyway. Six disease cluster patterns along these flyways were found to be associated with the seasonal migration of wild birds. The spread of the H5N1 virus, as demonstrated by the space-time clusters, was associated with the patterns of migration of wild birds. Wild birds may therefore play an important role in the spread of H5N1 over long distances. Disease clusters were also detected at sites where wild birds are known to overwinter and at times when migratory birds were present. This leads to the suggestion that wild birds may also be involved in spreading the H5N1 virus over short distances.

  2. Neural network based pattern matching and spike detection tools and services--in the CARMEN neuroinformatics project.

    Fletcher, Martyn; Liang, Bojian; Smith, Leslie; Knowles, Alastair; Jackson, Tom; Jessop, Mark; Austin, Jim

    2008-10-01

    In the study of information flow in the nervous system, component processes can be investigated using a range of electrophysiological and imaging techniques. Although data is difficult and expensive to produce, it is rarely shared and collaboratively exploited. The Code Analysis, Repository and Modelling for e-Neuroscience (CARMEN) project addresses this challenge through the provision of a virtual neuroscience laboratory: an infrastructure for sharing data, tools and services. Central to the CARMEN concept are federated CARMEN nodes, which provide: data and metadata storage, new, thirdparty and legacy services, and tools. In this paper, we describe the CARMEN project as well as the node infrastructure and an associated thick client tool for pattern visualisation and searching, the Signal Data Explorer (SDE). We also discuss new spike detection methods, which are central to the services provided by CARMEN. The SDE is a client application which can be used to explore data in the CARMEN repository, providing data visualization, signal processing and a pattern matching capability. It performs extremely fast pattern matching and can be used to search for complex conditions composed of many different patterns across the large datasets that are typical in neuroinformatics. Searches can also be constrained by specifying text based metadata filters. Spike detection services which use wavelet and morphology techniques are discussed, and have been shown to outperform traditional thresholding and template based systems. A number of different spike detection and sorting techniques will be deployed as services within the CARMEN infrastructure, to allow users to benchmark their performance against a wide range of reference datasets.

  3. Patterns of somatic alterations between matched primary and metastatic colorectal tumors characterized by whole-genome sequencing.

    Xie, Tao; Cho, Yong Beom; Wang, Kai; Huang, Donghui; Hong, Hye Kyung; Choi, Yoon-La; Ko, Young Hyeh; Nam, Do-Hyun; Jin, Juyoun; Yang, Heekyoung; Fernandez, Julio; Deng, Shibing; Rejto, Paul A; Lee, Woo Yong; Mao, Mao

    2014-10-01

    Colorectal cancer (CRC) patients have poor prognosis after formation of distant metastasis. Understanding the molecular mechanisms by which genetic changes facilitate metastasis is critical for the development of targeted therapeutic strategies aimed at controlling disease progression while minimizing toxic side effects. A comprehensive portrait of somatic alterations in CRC and the changes between primary and metastatic tumors has yet to be developed. We performed whole genome sequencing of two primary CRC tumors and their matched liver metastases. By comparing to matched germline DNA, we catalogued somatic alterations at multiple scales, including single nucleotide variations, small insertions and deletions, copy number aberrations and structural variations in both the primary and matched metastasis. We found that the majority of these somatic alterations are present in both sites. Despite the overall similarity, several de novo alterations in the metastases were predicted to be deleterious, in genes including FBXW7, DCLK1 and FAT2, which might contribute to the initiation and progression of distant metastasis. Through careful examination of the mutation prevalence among tumor cells at each site, we also proposed distinct clonal evolution patterns between primary and metastatic tumors in the two cases. These results suggest that somatic alterations may play an important role in driving the development of colorectal cancer metastasis and present challenges and opportunities when considering the choice of treatment. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Pattern Matching for Volcano Status Assessment: what monitoring data alone can say about Mt. Etna activity

    Cannavo, F.; Cannata, A.; Cassisi, C.

    2017-12-01

    The importance of assessing the ongoing status of active volcanoes is crucial not only for exposures to the local population but due to possible presence of tephra also for airline traffic. Adequately monitoring of active volcanoes, hence, plays a key role for civil protection purposes. In last decades, in order to properly monitor possible threats, continuous measuring networks have been designed and deployed on most of potentially hazardous volcanos. Nevertheless, at the present, volcano real-time surveillance is basically delegated to one or more human experts in volcanology, who interpret data coming from different kind of monitoring networks using their experience and non-measurable information (e.g. information from the field) to infer the volcano status. In some cases, raw data are used in some models to obtain more clues on the ongoing activity. In the last decades, with the development of volcano monitoring networks, huge amount of data of different geophysical, geochemical and volcanological types have been collected and stored in large databases. Having such big data sets with many examples of volcanic activity allows us to study volcano monitoring from a machine learning perspective. Thus, exploiting opportunities offered by the abundance of volcano monitoring time-series data we can try to address the following questions: Are the monitored parameters sufficient to discriminate the volcano status? Is it possible to infer/distinguish the volcano status only from the multivariate patterns of measurements? Are all the kind of measurements in the pattern equally useful for status assessment? How accurate would be an automatic system of status inference based only on pattern recognition of data? Here we present preliminary results of the data analysis we performed on a set of data and activity covering the period 2011-2017 at Mount Etna (Italy). In the considered period, we had 52 events of lava fountaining and long periods of Strombolian activity. We

  5. Estimation of subcriticality and fuel concentration by using 'pattern matching' of neutron flux distribution under non uniformed system

    Ishitani, Kazuki; Yamane, Yoshihiro

    1999-01-01

    In nuclear fuel reprocessing plants, monitoring the spatial profile of neutron flux to infer subcriticality and distribution of fuel concentration using detectors such as PSPC, is very beneficial in sight of criticality safety. In this paper a method of subcriticality and fuel concentration estimation which is supposed to use under non-uniformed system is proposed. Its basic concept is the pattern matching between measured neutron flux distribution and beforehand calculated one. In any kind of subcriticality estimation, we can regard that measured neutron counts put any kind of black box, and then this black box outputs subcriticality. We proposed the use of artificial neural network or 'pattern matching' as black box which have no theoretical clear base. These method are wholly based on the calculated value as recently advancement of computer code accuracy for criticality safety. The most difference between indirect bias estimation method and our method is that our new approach target are the unknown non-uniform system. (J.P.N.)

  6. Investigation of cortical thickness abnormalities in lithium-free adults with bipolar type I disorder using cortical pattern matching

    Foland-Ross, Lara C.; Thompson, Paul M.; Sugar, Catherine A.; Madsen, Sarah K.; Shen, Jim K.; Penfold, Conor; Ahlf, Kyle; Rasser, Paul E.; Fischer, Jeffrey; Yang, Yilan; Townsend, Jennifer; Bookheimer, Susan Y.; Altshuler, Lori L.

    2013-01-01

    Objective Several lines of evidence implicate gray matter abnormalities in the prefrontal cortex and anterior cingulate cortex in patients with bipolar disorder. Findings however, have been largely inconsistent across studies. Differences in patients’ medication status or mood state, or the application of traditional volumetric methods that are insensitive to subtle neuroanatomic differences may have contributed to these inconsistent findings. Given this, we used magnetic resonance imaging (MRI) in conjunction with cortical pattern matching methods to assess cortical thickness abnormalities in euthymic bipolar subjects who were not treated with lithium. Method Sixty-five subjects, including 34 lithium-free euthymic subjects with bipolar (type I) disorder and 31 healthy subjects were scanned using magnetic resonance imaging (MRI). Data were processed to measure cortical gray matter thickness. Cortical pattern matching methods associated homologous brain regions across subjects. Spatially normalized thickness maps were analyzed to assess illness effects and associations with clinical variables. Results Relative to healthy subjects, euthymic bipolar I subjects had significantly thinner gray matter in bilateral prefrontal cortex (Brodmann Areas 11, 10, 8 and 44) and left anterior cingulate cortex (Brodmann Areas 24/32). Additionally, thinning in these regions was more pronounced in patients with a history of psychosis. No areas of thicker cortex were detected in bipolar subjects versus healthy subjects. Conclusions Using a technique that is highly sensitive to subtle neuroanatomic differences, significant regional cortical thinning was found in euthymic subjects with bipolar disorder. Clinical implications are discussed. PMID:21285139

  7. Improving the Pattern Reproducibility of Multiple-Point-Based Prior Models Using Frequency Matching

    Cordua, Knud Skou; Hansen, Thomas Mejer; Mosegaard, Klaus

    2014-01-01

    Some multiple-point-based sampling algorithms, such as the snesim algorithm, rely on sequential simulation. The conditional probability distributions that are used for the simulation are based on statistics of multiple-point data events obtained from a training image. During the simulation, data...... events with zero probability in the training image statistics may occur. This is handled by pruning the set of conditioning data until an event with non-zero probability is found. The resulting probability distribution sampled by such algorithms is a pruned mixture model. The pruning strategy leads...... to a probability distribution that lacks some of the information provided by the multiple-point statistics from the training image, which reduces the reproducibility of the training image patterns in the outcome realizations. When pruned mixture models are used as prior models for inverse problems, local re...

  8. Radioimmunoassay of measles virus hemagglutinin protein G

    Lund, G.A.; Salmi, A.A.

    1982-01-01

    Guinea pig and rabbit antisera from animals immunized with purified measles virus hemagglutinin (G) protein were used to establish a solid-phase four-layer radioimmunoassay for quantitative measurement of the G protein. The sensitivity of the assay was 2 ng of purified G protein, and 200 μg of protein from uninfected Vero cells neither decreased the sensitivity nor reacted non-specifically in the assay. Radioimmunoassay standard dose-response curves were established and unknown values interpolated from these using the logit program of a desktop computer. Using this procedure, a measles virus growth curve in infected Vero cells was determined by measurement of G protein production. Under these same conditions, hemagglutination was not sensitive enough to detect early hemagglutinin production. Viral antigens in canine distemper virus, Newcastle disease virus, parainfluenza viruses 1-4, simian virus 5, and respiratory syncytial virus-infected cell lysates did not cross-react in the radioimmunoassay. A small degree of cross-reactivity was detected with mumps viral antigens, both with Vero cell-derived (wild-type strain) and egg-derived (Enders strain) purified virus preparations and with a cell lysate antigen prepared from wild-type mumps virus-infected Vero cells. (Auth.)

  9. Radioimmunoassay of measles virus hemagglutinin protein G

    Lund, G A; Salmi, A A [Turku Univ. (Finland)

    1982-08-01

    Guinea pig and rabbit antisera from animals immunized with purified measles virus hemagglutinin (G) protein were used to establish a solid-phase four-layer radioimmunoassay for quantitative measurement of the G protein. The sensitivity of the assay was 2 ng of purified G protein, and 200 ..mu..g of protein from uninfected Vero cells neither decreased the sensitivity nor reacted non-specifically in the assay. Radioimmunoassay standard dose-response curves were established and unknown values interpolated from these using the logit program of a desktop computer. Using this procedure, a measles virus growth curve in infected Vero cells was determined by measurement of G protein production. Under these same conditions, hemagglutination was not sensitive enough to detect early hemagglutinin production. Viral antigens in canine distemper virus, Newcastle disease virus, parainfluenza viruses 1-4, simian virus 5, and respiratory syncytial virus-infected cell lysates did not cross-react in the radioimmunoassay. A small degree of cross-reactivity was detected with mumps viral antigens, both with Vero cell-derived (wild-type strain) and egg-derived (Enders strain) purified virus preparations and with a cell lysate antigen prepared from wild-type mumps virus-infected Vero cells.

  10. A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin

    Andrew R. Dalby

    2014-10-01

    Full Text Available A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species.The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment.The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.

  11. Continuous Acetylsalicylic Acid Treatment Does Not Influence Bleeding Pattern or Outcome of Aneurysmal Subarachnoid Hemorrhage: A Matched-Pair Analysis.

    Bruder, Markus; Won, Sae-Yeon; Wagner, Marlies; Brawanski, Nina; Dinc, Nazife; Kashefiolasl, Sepide; Seifert, Volker; Konczalla, Juergen

    2018-05-01

    Demographic changes are leading to an aging society with a growing number of patients with cardiovascular diseases, relying on antiplatelet drugs like acetylsalicylic acid (ASA). Although antiplatelet agents are suspected to be protective not only in the cardiologic but in the neurovascular field, the alteration of the coagulating process could have a major impact on the course and outcome after rupture of intracranial aneurysms. Between June 1999 and December 2014, 1422 patients were treated for aneurysmal SAH in our institution, 144 (10.1%) with continuous ASA at the time of aneurysm rupture. A matched-pair analysis was performed. The rate of patients with continuous ASA treatment while rupture of the aneurysm is rising significantly (P bleeding pattern. Outcome was not different in the matched-pair analysis. There was no statistical difference in treatment related-complication rates of microsurgical and endovascular procedures. Therefore, ASA use should not influence treatment decision of the ruptured aneurysm. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. Fixed-pattern noise correction method based on improved moment matching for a TDI CMOS image sensor.

    Xu, Jiangtao; Nie, Huafeng; Nie, Kaiming; Jin, Weimin

    2017-09-01

    In this paper, an improved moment matching method based on a spatial correlation filter (SCF) and bilateral filter (BF) is proposed to correct the fixed-pattern noise (FPN) of a time-delay-integration CMOS image sensor (TDI-CIS). First, the values of row FPN (RFPN) and column FPN (CFPN) are estimated and added to the original image through SCF and BF, respectively. Then the filtered image will be processed by an improved moment matching method with a moving window. Experimental results based on a 128-stage TDI-CIS show that, after correcting the FPN in the image captured under uniform illumination, the standard deviation of row mean vector (SDRMV) decreases from 5.6761 LSB to 0.1948 LSB, while the standard deviation of the column mean vector (SDCMV) decreases from 15.2005 LSB to 13.1949LSB. In addition, for different images captured by different TDI-CISs, the average decrease of SDRMV and SDCMV is 5.4922/2.0357 LSB, respectively. Comparative experimental results indicate that the proposed method can effectively correct the FPNs of different TDI-CISs while maintaining image details without any auxiliary equipment.

  13. Human Identification by Cross-Correlation and Pattern Matching of Personalized Heartbeat: Influence of ECG Leads and Reference Database Size.

    Jekova, Irena; Krasteva, Vessela; Schmid, Ramun

    2018-01-27

    Human identification (ID) is a biometric task, comparing single input sample to many stored templates to identify an individual in a reference database. This paper aims to present the perspectives of personalized heartbeat pattern for reliable ECG-based identification. The investigations are using a database with 460 pairs of 12-lead resting electrocardiograms (ECG) with 10-s durations recorded at time-instants T1 and T2 > T1 + 1 year. Intra-subject long-term ECG stability and inter-subject variability of personalized PQRST (500 ms) and QRS (100 ms) patterns is quantified via cross-correlation, amplitude ratio and pattern matching between T1 and T2 using 7 features × 12-leads. Single and multi-lead ID models are trained on the first 230 ECG pairs. Their validation on 10, 20, ... 230 reference subjects (RS) from the remaining 230 ECG pairs shows: (i) two best single-lead ID models using lead II for a small population RS = (10-140) with identification accuracy AccID = (89.4-67.2)% and aVF for a large population RS = (140-230) with AccID = (67.2-63.9)%; (ii) better performance of the 6-lead limb vs. the 6-lead chest ID model-(91.4-76.1)% vs. (90.9-70)% for RS = (10-230); (iii) best performance of the 12-lead ID model-(98.4-87.4)% for RS = (10-230). The tolerable reference database size, keeping AccID > 80%, is RS = 30 in the single-lead ID scenario (II); RS = 50 (6 chest leads); RS = 100 (6 limb leads), RS > 230-maximal population in this study (12-lead ECG).

  14. Outsourced pattern matching

    Faust, Sebastian; Hazay, Carmit; Venturi, Daniele

    2013-01-01

    In secure delegatable computation, computationally weak devices (or clients) wish to outsource their computation and data to an untrusted server in the cloud. While most earlier work considers the general question of how to securely outsource any computation to the cloud server, we focus...... that contain confidential data (e.g., health related data about patient history). Our constructions offer simulation-based security in the presence of semi-honest and malicious adversaries (in the random oracle model) and limit the communication in the query phase to O(m) bits plus the number of occurrences...

  15. Boxed Permutation Pattern Matching

    Amit, Mika; Bille, Philip; Cording, Patrick Hagge

    2016-01-01

    the goal is to only find the boxed subsequences of T that are order-isomorphic to P. This problem was introduced by Bruner and Lackner who showed that it can be solved in O(n3) time. Cho et al. [CPM 2015] gave an O(n2m) time algorithm and improved it to O(n2 logm). In this paper we present a solution...

  16. Specific Patterns of Emotion Recognition from Faces in Children with ASD: Results of a Cross-Modal Matching Paradigm

    Golan, Ofer; Gordon, Ilanit; Fichman, Keren; Keinan, Giora

    2018-01-01

    Children with ASD show emotion recognition difficulties, as part of their social communication deficits. We examined facial emotion recognition (FER) in intellectually disabled children with ASD and in younger typically developing (TD) controls, matched on mental age. Our emotion-matching paradigm employed three different modalities: facial, vocal…

  17. Matching theory

    Plummer, MD

    1986-01-01

    This study of matching theory deals with bipartite matching, network flows, and presents fundamental results for the non-bipartite case. It goes on to study elementary bipartite graphs and elementary graphs in general. Further discussed are 2-matchings, general matching problems as linear programs, the Edmonds Matching Algorithm (and other algorithmic approaches), f-factors and vertex packing.

  18. Foods Served in Child Care Facilities Participating in the Child and Adult Care Food Program: Menu Match and Agreement with the New Meal Patterns and Best Practices.

    Dave, Jayna M; Cullen, Karen W

    2018-02-20

    To assess the agreement of posted menus with foods served to 3- to 5-year-old children attending federal Child and Adult Care Food Program (CACFP)-enrolled facilities, and the degree to which the facilities met the new meal patterns and best practices. On-site observations and menu coding. Nine early care and education centers. Agreement of posted menus with foods served, and comparison of foods served and consumed with the new CACFP meal guidelines and best practices. Data were compiled for each meal (breakfast, lunch, and snacks). Frequencies and percentages of agreement with the posted menu (coded matches, substitutions, additions, and omissions) were calculated for each food component in the CACFP menu guidelines. Menu total match was created by summing the menu match plus acceptable substitutions. Menus were compared with the new CACFP meal guidelines and best practices. The match between the posted menus and foods actually served to children at breakfast, lunch, and snack was high when the acceptable menu substitutions were considered (approximately 94% to 100% total match). Comparing the menus with the new meal guidelines and best practices, the 1 guideline that was fully implemented was serving only unflavored, low-fat, or 1% milk; fruit and vegetable guidelines were partially met; fruit juice was not served often, nor were legumes; the guideline for 1 whole grain-rich serving/d was not met; and regular beef and full-fat cheese products were commonly served. Early care and education centers enrolled in CACFP provided meals that met the current CACFP guidelines. Some menu improvements are needed for the centers to meet the new guidelines and best practices. Copyright © 2018 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  19. Matched filtering Generalized Phase Contrast using binary phase for dynamic spot- and line patterns in biophotonics and structured lighting

    Bañas, Andrew Rafael; Aabo, Thomas; Palima, Darwin

    2013-01-01

    as a combination of Generalized Phase Contrast and phase-only correlation. Such an analysis makes it convenient to optimize an mGPC system for different setup conditions. Results showing binary-only phase generation of dynamic spot arrays and line patterns are presented. © 201 Optical Society of America...

  20. Local gradient Gabor pattern (LGGP) with applications in face recognition, cross-spectral matching, and soft biometrics

    Chen, Cunjian; Ross, Arun

    2013-05-01

    Researchers in face recognition have been using Gabor filters for image representation due to their robustness to complex variations in expression and illumination. Numerous methods have been proposed to model the output of filter responses by employing either local or global descriptors. In this work, we propose a novel but simple approach for encoding Gradient information on Gabor-transformed images to represent the face, which can be used for identity, gender and ethnicity assessment. Extensive experiments on the standard face benchmark FERET (Visible versus Visible), as well as the heterogeneous face dataset HFB (Near-infrared versus Visible), suggest that the matching performance due to the proposed descriptor is comparable against state-of-the-art descriptor-based approaches in face recognition applications. Furthermore, the same feature set is used in the framework of a Collaborative Representation Classification (CRC) scheme for deducing soft biometric traits such as gender and ethnicity from face images in the AR, Morph and CAS-PEAL databases.

  1. Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

    Grötzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jörg

    2014-01-01

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  2. Mining a database of single amplified genomes from Red Sea brine pool extremophiles – Improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA

    Stefan Wolfgang Grötzinger

    2014-04-01

    Full Text Available Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs and poor homology of novel extremophile’s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the INDIGO data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes may translate into false positives when searching for specific functions. The Profile & Pattern Matching (PPM strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO-terms (which represent enzyme function profiles and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern. The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2,577 E.C. numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from 6 different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter and PROSITE IDs (pattern filter. Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.

  3. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    Grötzinger, Stefan W.

    2014-04-07

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile\\'s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  4. Ring-enhancement pattern on contrast-enhanced CT predicts adenosquamous carcinoma of the pancreas: a matched case-control study.

    Imaoka, Hiroshi; Shimizu, Yasuhiro; Mizuno, Nobumasa; Hara, Kazuo; Hijioka, Susumu; Tajika, Masahiro; Tanaka, Tsutomu; Ishihara, Makoto; Ogura, Takeshi; Obayashi, Tomohiko; Shinagawa, Akihide; Sakaguchi, Masafumi; Yamaura, Hidekazu; Kato, Mina; Niwa, Yasumasa; Yamao, Kenji

    2014-01-01

    Adenosquamous carcinoma of the pancreas (ASC) is a rare malignant neoplasm of the pancreas, exhibiting both glandular and squamous differentiation. However, little is known about its imaging features. This study examined the imaging features of pancreatic ASC. We evaluated images of contrast-enhanced computed tomography (CT) and endoscopic ultrasonography (EUS). As controls, solid pancreatic neoplasms matched in a 2:1 ratio to ASC cases for age, sex and tumor location were also evaluated. Twenty-three ASC cases were examined, and 46 solid pancreatic neoplasms (43 pancreatic ductal adenocarcinomas, two pancreatic neuroendocrine tumors and one acinar cell carcinoma) were matched as controls. Univariate analysis demonstrated significant differences in the outline and vascularity of tumors on contrast-enhanced CT in the ASC and control groups (P outline, cystic changes, and the ring-enhancement pattern on contrast-enhanced CT were seen to have significant predictive powers by stepwise forward logistic regression analysis (P = 0.044, P = 0.010, and P = 0.001, respectively). Of the three, the ring-enhancement pattern was the most useful, and its predictive diagnostic sensitivity, specificity, positive predictive value and negative predictive value for diagnosis of ASC were 65.2%, 89.6%, 75.0% and 84.3%, respectively. These results demonstrate that presence of the ring-enhancement pattern on contrast-enhanced CT is the most useful predictive factor for ASC. Copyright © 2014 IAP and EPC. Published by Elsevier B.V. All rights reserved.

  5. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

    Strauch, Eva-Maria; Bernard, Steffen M.; La, David; Bohn, Alan J.; Lee, Peter S.; Anderson, Caitlin E.; Nieusma, Travis; Holstein, Carly A.; Garcia, Natalie K.; Hooper, Kathryn A.; Ravichandran, Rashmi; Nelson, Jorgen W.; Sheffler, William; Bloom, Jesse D.; Lee, Kelly K.; Ward, Andrew B.; Yager, Paul; Fuller, Deborah H.; Wilson, Ian A.; Baker , David (UWASH); (Scripps); (FHCRC)

    2017-06-12

    Many viral surface glycoproteins and cell surface receptors are homo-oligomers1, 2, 3, 4, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites5, 6, 7, 8. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.

  6. Possible impact of global warming on the evolution of hemagglutinins from influenza a viruses.

    Yan, Shaomin; Wu, Guang

    2011-02-01

    To determine if global warming has an impact on the evolution of hemagglutinins from influenza A viruses, because both global warming and influenza pandemics/epidemics threaten the world. 4 706 hemagglutinins from influenza A viruses sampled from 1956 to 2009 were converted to a time-series to show their evolutionary process and compared with the global, northern hemisphere and southern hemisphere temperatures, to determine if their trends run in similar or opposite directions. Point-to-point comparisons between temperature and quantified hemagglutinins were performed for all species and for the major prevailing species. The comparisons show that the trends for both hemagglutinin evolution and temperature change run in a similar direction. Global warming has a consistent and progressive impact on the hemagglutinin evolution of influenza A viruses.

  7. Topics in combinatorial pattern matching

    Vildhøj, Hjalte Wedel

    Problem. Given m documents of total length n, we consider the problem of finding a longest string common to at least d ≥ 2 of the documents. This problem is known as the longest common substring (LCS) problem and has a classic O(n) space and O(n) time solution (Weiner [FOCS’73], Hui [CPM’92]). However...

  8. Unique Structural Features of Influenza Virus H15 Hemagglutinin

    Tzarum, Netanel; McBride, Ryan; Nycholat, Corwin M.; Peng, Wenjie; Paulson, James C.; Wilson, Ian A. (Scripps)

    2017-04-12

    Influenza A H15 viruses are members of a subgroup (H7-H10-H15) of group 2 hemagglutinin (HA) subtypes that include H7N9 and H10N8 viruses that were isolated from humans during 2013. The isolation of avian H15 viruses is, however, quite rare and, until recently, geographically restricted to wild shorebirds and waterfowl in Australia. The HAs of H15 viruses contain an insertion in the 150-loop (loop beginning at position 150) of the receptor-binding site common to this subgroup and a unique insertion in the 260-loop compared to any other subtype. Here, we show that the H15 HA has a high preference for avian receptor analogs by glycan array analyses. The H15 HA crystal structure reveals that it is structurally closest to H7N9 HA, but the head domain of the H15 trimer is wider than all other HAs due to a tilt and opening of the HA1 subunits of the head domain. The extended 150-loop of the H15 HA retains the conserved conformation as in H7 and H10 HAs. Furthermore, the elongated 260-loop increases the exposed HA surface and can contribute to antigenic variation in H15 HAs. Since avian-origin H15 HA viruses have been shown to cause enhanced disease in mammalian models, further characterization and immune surveillance of H15 viruses are warranted.

    IMPORTANCEIn the last 2 decades, an apparent increase has been reported for cases of human infection by emerging avian influenza A virus subtypes, including H7N9 and H10N8 viruses isolated during 2013. H15 is the other member of the subgroup of influenza A virus group 2 hemagglutinins (HAs) that also include H7 and H10. H15 viruses have been restricted to Australia, but recent isolation of H15 viruses in western Siberia suggests that they could be spread more globally via the avian flyways that converge and emanate from this region. Here we report on characterization of the three-dimensional structure and receptor specificity of the H15 hemagglutinin, revealing distinct features and specificities that can

  9. Anti-Hemagglutinin Antibody Derived Lead Peptides for Inhibitors of Influenza Virus Binding.

    Henry Memczak

    Full Text Available Antibodies against spike proteins of influenza are used as a tool for characterization of viruses and therapeutic approaches. However, development, production and quality control of antibodies is expensive and time consuming. To circumvent these difficulties, three peptides were derived from complementarity determining regions of an antibody heavy chain against influenza A spike glycoprotein. Their binding properties were studied experimentally, and by molecular dynamics simulations. Two peptide candidates showed binding to influenza A/Aichi/2/68 H3N2. One of them, termed PeB, with the highest affinity prevented binding to and infection of target cells in the micromolar region without any cytotoxic effect. PeB matches best the conserved receptor binding site of hemagglutinin. PeB bound also to other medical relevant influenza strains, such as human-pathogenic A/California/7/2009 H1N1, and avian-pathogenic A/Mute Swan/Rostock/R901/2006 H7N1. Strategies to improve the affinity and to adapt specificity are discussed and exemplified by a double amino acid substituted peptide, obtained by substitutional analysis. The peptides and their derivatives are of great potential for drug development as well as biosensing.

  10. Matching Message Design and Depressed Cognition: An Exploration of Attention Patterns for Gain- and Loss-Framed Depression Help-Seeking Messages.

    Lueck, Jennifer A

    2017-07-01

    Although disproportionally affected by depression, most depressed college students do not seek the help they need. Research has recently uncovered the potential negative effects of depression help-seeking messages if depressed cognition is not considered in the health message design process. It is unclear if depression determines whether and how individuals pay attention to gain- and loss-framed depression help-seeking messages-a mechanism that has significant implications for the strategic planning of health communication interventions. In order to enable the effective matching of message design and audience features, this study investigated attention patterns for gain (n = 75)- and loss (n = 78)-framed depression help-seeking messages using eye-tracking technology and self-report measures. The results confirmed that depression is a characteristic of risk avoidance and negative cognition. Depressed participants tended to pay more attention to disease information that was placed in a loss-framed rather than a gain-framed depression help-seeking message. Using negative message framing strategies for health messages seeking to educate about depression symptoms might therefore be a useful persuasive strategy-particularly when disseminated to vulnerable populations affected by depression. Furthermore, the present study emphasizes the effective use of eye-tracking technology in communication research.

  11. Computation of Hemagglutinin Free Energy Difference by the Confinement Method

    2017-01-01

    Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs. PMID:29151344

  12. Biosynthesis of measles virus hemagglutinin in persistently infected cells

    Bellini, W.J.; Silver, G.D.; McFarlin, D.E.

    1983-01-01

    The synthesis of the hemagglutinin (HA) glycoprotein of measles virus was investigated in a persistently infected cell line using a monoclonal anti-HA. The synthesis of the HA protein was shown to be associated with the rough endoplasmic reticulum. The unglycosylated (HA 0 ) apoprotein is synthesized as a 65.000 dalton peptide and is inserted into the rough endoplasmic reticulum as a transmembrane protein with approximately 2 to 3000 daltons of the peptide exposed to the cytoplasmic membrane surface. Primary glycosylation of the HA protein was found to occur through the lipid-linked carrier, dolichol-phosphate, as determined by inhibition of glycosylation by tunicamycin. Glycosylation, however, was not a prerequisite for membrane insertion. Endo-β-N-acetyl-Glucosaminidase H digestion of the fully glycosylated HA protein indicated that both simple and complex oligosaccharides are present on the surface glycoprotein. (Author)

  13. Potent Inhibitors against Newcastle Disease Virus Hemagglutinin-Neuraminidase.

    Rota, Paola; La Rocca, Paolo; Piccoli, Marco; Montefiori, Marco; Cirillo, Federica; Olsen, Lars; Orioli, Marica; Allevi, Pietro; Anastasia, Luigi

    2018-02-06

    Neuraminidase activity is essential for the infection and propagation of paramyxoviruses, including human parainfluenza viruses (hPIVs) and the Newcastle disease virus (NDV). Thus, many inhibitors have been developed based on the 2-deoxy-2,3-didehydro-d-N-acetylneuraminic acid inhibitor (DANA) backbone. Along this line, herein we report a series of neuraminidase inhibitors, having C4 (p-toluenesulfonamido and azido substituents) and C5 (N-perfluorinated chains) modifications to the DANA backbone, resulting in compounds with 5- to 15-fold greater potency than the currently most active compound, the N-trifluoroacetyl derivative of DANA (FANA), toward the NDV hemagglutinin-neuraminidase (NDV-HN). Remarkably, these inhibitors were found to be essentially inactive against the human sialidase NEU3, which is present on the outer layer of the cell membrane and is highly affected by the current NDV inhibitor FANA. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Hemagglutinin Typing as an Aid in Identification of Biochemically Atypical Escherichia coli Strains

    Crichton, Pamela B.; Ip, S. M.; Old, D. C.

    1981-01-01

    Tests for the presence of mannose-sensitive and mannose-resistant, eluting hemagglutinins and fimbriae were helpful in indicating whether biochemically atypical strains of the tribe Escherichieae might be escherichiae or shigellae.

  15. Hemagglutinin Typing as an Aid in Identification of Biochemically Atypical Escherichia coli Strains

    Crichton, Pamela B.; Ip, S. M.; Old, D. C.

    1981-01-01

    Tests for the presence of mannose-sensitive and mannose-resistant, eluting hemagglutinins and fimbriae were helpful in indicating whether biochemically atypical strains of the tribe Escherichieae might be escherichiae or shigellae. PMID:7334072

  16. Matching Organs

    ... to know FAQ Living donation What is living donation? Organs Types Being a living donor First steps Being ... brochures What Every Patient Needs to Know Living Donation Multiple Listing Visit UNOS Store Learn more How organs are matched How to become a living donor ...

  17. Gnarled-trunk evolutionary model of influenza A virus hemagglutinin.

    Kimihito Ito

    Full Text Available Human influenza A viruses undergo antigenic changes with gradual accumulation of amino acid substitutions on the hemagglutinin (HA molecule. A strong antigenic mismatch between vaccine and epidemic strains often requires the replacement of influenza vaccines worldwide. To establish a practical model enabling us to predict the future direction of the influenza virus evolution, relative distances of amino acid sequences among past epidemic strains were analyzed by multidimensional scaling (MDS. We found that human influenza viruses have evolved along a gnarled evolutionary pathway with an approximately constant curvature in the MDS-constructed 3D space. The gnarled pathway indicated that evolution on the trunk favored multiple substitutions at the same amino acid positions on HA. The constant curvature was reasonably explained by assuming that the rate of amino acid substitutions varied from one position to another according to a gamma distribution. Furthermore, we utilized the estimated parameters of the gamma distribution to predict the amino acid substitutions on HA in subsequent years. Retrospective prediction tests for 12 years from 1997 to 2009 showed that 70% of actual amino acid substitutions were correctly predicted, and that 45% of predicted amino acid substitutions have been actually observed. Although it remains unsolved how to predict the exact timing of antigenic changes, the present results suggest that our model may have the potential to recognize emerging epidemic strains.

  18. Genetic Characterization of the Hemagglutinin Genes of Wild-Type Measles Virus Circulating in China, 1993–2009

    Zhu, Zhen; Liu, Chunyu; Mao, Naiying; Ji, Yixin; Wang, Huiling; Jiang, Xiaohong; Li, Chongshan; Tang, Wei; Feng, Daxing; Wang, Changyin; Zheng, Lei; Lei, Yue; Ling, Hua; Zhao, Chunfang; Ma, Yan; He, Jilan; Wang, Yan; Li, Ping; Guan, Ronghui; Zhou, Shujie; Zhou, Jianhui; Wang, Shuang; Zhang, Hong; Zheng, Huanying; Liu, Leng; Ma, Hemuti; Guan, Jing; Lu, Peishan; Feng, Yan; Zhang, Yanjun; Zhou, Shunde; Xiong, Ying; Ba, Zhuoma; Chen, Hui; Yang, Xiuhui; Bo, Fang; Ma, Yujie; Liang, Yong; Lei, Yake; Gu, Suyi; Liu, Wei; Chen, Meng; Featherstone, David; Jee, Youngmee; Bellini, William J.; Rota, Paul A.; Xu, Wenbo

    2013-01-01

    Background China experienced several large measles outbreaks in the past two decades, and a series of enhanced control measures were implemented to achieve the goal of measles elimination. Molecular epidemiologic surveillance of wild-type measles viruses (MeV) provides valuable information about the viral transmission patterns. Since 1993, virologic surveillnace has confirmed that a single endemic genotype H1 viruses have been predominantly circulating in China. A component of molecular surveillance is to monitor the genetic characteristics of the hemagglutinin (H) gene of MeV, the major target for virus neutralizing antibodies. Principal Findings Analysis of the sequences of the complete H gene from 56 representative wild-type MeV strains circulating in China during 1993–2009 showed that the H gene sequences were clustered into 2 groups, cluster 1 and cluster 2. Cluster1 strains were the most frequently detected cluster and had a widespread distribution in China after 2000. The predicted amino acid sequences of the H protein were relatively conserved at most of the functionally significant amino acid positions. However, most of the genotype H1 cluster1 viruses had an amino acid substitution (Ser240Asn), which removed a predicted N-linked glycosylation site. In addition, the substitution of Pro397Leu in the hemagglutinin noose epitope (HNE) was identified in 23 of 56 strains. The evolutionary rate of the H gene of the genotype H1 viruses was estimated to be approximately 0.76×10−3 substitutions per site per year, and the ratio of dN to dS (dN/dS) was measles in China. PMID:24073194

  19. 78 FR 9355 - Influenza Viruses Containing the Hemagglutinin From the Goose/Guangdong/1/96 Lineage

    2013-02-08

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES [Docket: CDC-2012-0010] 42 CFR Part 73 Influenza Viruses... influenza (HPAI) H5N1 viruses that contain a hemagglutinin (HA) from the Goose/Guangdong/1/96 lineage, and... concerning highly pathogenic avian influenza (HPAI) H5N1 viruses that contain a hemagglutinin (HA) from the...

  20. Hemagglutinin-specific neutralization of subacute sclerosing panencephalitis viruses.

    Miguel Ángel Muñoz-Alía

    Full Text Available Subacute sclerosing panencephalitis (SSPE is a progressive, lethal complication of measles caused by particular mutants of measles virus (MeV that persist in the brain despite high levels of neutralizing antibodies. We addressed the hypothesis that antigenic drift is involved in the pathogenetic mechanism of SSPE by analyzing antigenic alterations in the MeV envelope hemagglutinin protein (MeV-H found in patients with SSPE in relation to major circulating MeV genotypes. To this aim, we obtained cDNA for the MeV-H gene from tissue taken at brain autopsy from 3 deceased persons with SSPE who had short (3-4 months, SMa79, average (3.5 years, SMa84, and long (18 years, SMa94 disease courses. Recombinant MeVs with a substituted MeV-H gene were generated by a reverse genetic system. Virus neutralization assays with a panel of anti-MeV-H murine monoclonal antibodies (mAbs or vaccine-immunized mouse anti-MeV-H polyclonal sera were performed to determine the antigenic relatedness. Functional and receptor-binding analysis of the SSPE MeV-H showed activity in a SLAM/nectin-4-dependent manner. Similar to our panel of wild-type viruses, our SSPE viruses showed an altered antigenic profile. Genotypes A, G3, and F (SSPE case SMa79 were the exception, with an intact antigenic structure. Genotypes D7 and F (SSPE SMa79 showed enhanced neutralization by mAbs targeting antigenic site IIa. Genotypes H1 and the recently reported D4.2 were the most antigenically altered genotypes. Epitope mapping of neutralizing mAbs BH015 and BH130 reveal a new antigenic site on MeV-H, which we designated Φ for its intermediate position between previously defined antigenic sites Ia and Ib. We conclude that SSPE-causing viruses show similar antigenic properties to currently circulating MeV genotypes. The absence of a direct correlation between antigenic changes and predisposition of a certain genotype to cause SSPE does not lend support to the proposed antigenic drift as a

  1. Incidental Prophylactic Nodal Irradiation and Patterns of Nodal Relapse in Inoperable Early Stage NSCLC Patients Treated With SBRT: A Case-Matched Analysis

    Lao, Louis [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Department of Radiation Oncology, Auckland City Hospital, Auckland (New Zealand); Hope, Andrew J. [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Maganti, Manjula [Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Brade, Anthony; Bezjak, Andrea; Saibishkumar, Elantholi P.; Giuliani, Meredith; Sun, Alexander [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada); Cho, B. C. John, E-mail: john.cho@rmp.uhn.on.ca [Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario (Canada)

    2014-09-01

    Purpose: Reported rates of non-small cell lung cancer (NSCLC) nodal failure following stereotactic body radiation therapy (SBRT) are lower than those reported in the surgical series when matched for stage. We hypothesized that this effect was due to incidental prophylactic nodal irradiation. Methods and Materials: A prospectively collected group of medically inoperable early stage NSCLC patients from 2004 to 2010 was used to identify cases with nodal relapses. Controls were matched to cases, 2:1, controlling for tumor volume (ie, same or greater) and tumor location (ie, same lobe). Reference (normalized to equivalent dose for 2-Gy fractions [EQD2]) point doses at the ipsilateral hilum and carina, demographic data, and clinical outcomes were extracted from the medical records. Univariate conditional logistical regression analyses were performed with variables of interest. Results: Cases and controls were well matched except for size. The controls, as expected, had larger gross tumor volumes (P=.02). The mean ipsilateral hilar doses were 9.6 Gy and 22.4 Gy for cases and controls, respectively (P=.014). The mean carinal doses were 7.0 Gy and 9.2 Gy, respectively (P=.13). Mediastinal nodal relapses, with and without ipsilateral hilar relapse, were associated with mean ipsilateral hilar doses of 3.6 Gy and 19.8 Gy, respectively (P=.01). The conditional density plot appears to demonstrate an inverse dose-effect relationship between ipsilateral hilar normalized total dose and risk of ipsilateral hilar relapse. Conclusions: Incidental hilar dose greater than 20 Gy is significantly associated with fewer ipsilateral hilar relapses in inoperable early stage NSCLC patients treated with SBRT.

  2. Incidental Prophylactic Nodal Irradiation and Patterns of Nodal Relapse in Inoperable Early Stage NSCLC Patients Treated With SBRT: A Case-Matched Analysis

    Lao, Louis; Hope, Andrew J.; Maganti, Manjula; Brade, Anthony; Bezjak, Andrea; Saibishkumar, Elantholi P.; Giuliani, Meredith; Sun, Alexander; Cho, B. C. John

    2014-01-01

    Purpose: Reported rates of non-small cell lung cancer (NSCLC) nodal failure following stereotactic body radiation therapy (SBRT) are lower than those reported in the surgical series when matched for stage. We hypothesized that this effect was due to incidental prophylactic nodal irradiation. Methods and Materials: A prospectively collected group of medically inoperable early stage NSCLC patients from 2004 to 2010 was used to identify cases with nodal relapses. Controls were matched to cases, 2:1, controlling for tumor volume (ie, same or greater) and tumor location (ie, same lobe). Reference (normalized to equivalent dose for 2-Gy fractions [EQD2]) point doses at the ipsilateral hilum and carina, demographic data, and clinical outcomes were extracted from the medical records. Univariate conditional logistical regression analyses were performed with variables of interest. Results: Cases and controls were well matched except for size. The controls, as expected, had larger gross tumor volumes (P=.02). The mean ipsilateral hilar doses were 9.6 Gy and 22.4 Gy for cases and controls, respectively (P=.014). The mean carinal doses were 7.0 Gy and 9.2 Gy, respectively (P=.13). Mediastinal nodal relapses, with and without ipsilateral hilar relapse, were associated with mean ipsilateral hilar doses of 3.6 Gy and 19.8 Gy, respectively (P=.01). The conditional density plot appears to demonstrate an inverse dose-effect relationship between ipsilateral hilar normalized total dose and risk of ipsilateral hilar relapse. Conclusions: Incidental hilar dose greater than 20 Gy is significantly associated with fewer ipsilateral hilar relapses in inoperable early stage NSCLC patients treated with SBRT

  3. Dual function of the hemagglutinin H5 fused to chicken CD154 in a ...

    Dual function of the hemagglutinin H5 fused to chicken CD154 in a potential strategy of DIVA against avian influenza disease: preliminary study. AG Pose, ES Rodriguez, AC Mendez, JN Gomez, AV Redondo, ER Rodriguez, EMG Ramos, AA Gutierrez, MPR Molto, DG Roche, YS Ugalde, AM Lopez ...

  4. A Novel Hemagglutinin with Antiproliferative Activity against Tumor Cells from the Hallucinogenic Mushroom Boletus speciosus

    Jian Sun

    2014-01-01

    Full Text Available Little was known about bioactive compounds from the hallucinogenic mushroom Boletus speciosus. In the present study, a hemagglutinin (BSH, B. speciosus hemagglutinin was isolated from its fruiting bodies and enzymatic properties were also tested. The chromatographic procedure utilized comprised anion exchange chromatography on Q-Sepharose, cation exchange chromatography on CM-Cellulose, cation exchange chromatography on SP-Sepharose, and gel filtration by FPLC on Superdex 75. The hemagglutinin was a homodimer which was estimated to be approximately 31 kDa in size. The activity of BSH was stable up to 60°C, while there was a precipitous drop in activity when the temperature was elevated to 70°C. BSH retained 25% hemagglutinating activity when exposed to 100 mM NaOH and 25 mM HCl. The activity was potently inhibited by 1.25 mM Hg2+ and slightly inhibited by Fe2+, Ca2+, and Pb2+. None of the sugars tested showed inhibition towards BSH. Its hemagglutinating activity towards human erythrocytes type A, type B, and type AB was higher than type O. The hemagglutinin showed antiproliferative activity towards hepatoma Hep G2 cells and mouse lymphocytic leukemia cells (L1210 in vitro, with IC50 of 4.7 μM and 7.0 μM, respectively. It also exhibited HIV-1 reverse transcriptase inhibitory activity with an IC50 of 7.1 μM.

  5. A novel hemagglutinin with antiproliferative activity against tumor cells from the hallucinogenic mushroom Boletus speciosus.

    Sun, Jian; Ng, Tzi-Bun; Wang, Hexiang; Zhang, Guoqing

    2014-01-01

    Little was known about bioactive compounds from the hallucinogenic mushroom Boletus speciosus. In the present study, a hemagglutinin (BSH, B. speciosus hemagglutinin) was isolated from its fruiting bodies and enzymatic properties were also tested. The chromatographic procedure utilized comprised anion exchange chromatography on Q-Sepharose, cation exchange chromatography on CM-Cellulose, cation exchange chromatography on SP-Sepharose, and gel filtration by FPLC on Superdex 75. The hemagglutinin was a homodimer which was estimated to be approximately 31 kDa in size. The activity of BSH was stable up to 60°C, while there was a precipitous drop in activity when the temperature was elevated to 70°C. BSH retained 25% hemagglutinating activity when exposed to 100 mM NaOH and 25 mM HCl. The activity was potently inhibited by 1.25 mM Hg(2+) and slightly inhibited by Fe(2+), Ca(2+), and Pb(2+). None of the sugars tested showed inhibition towards BSH. Its hemagglutinating activity towards human erythrocytes type A, type B, and type AB was higher than type O. The hemagglutinin showed antiproliferative activity towards hepatoma Hep G2 cells and mouse lymphocytic leukemia cells (L1210) in vitro, with IC50 of 4.7 μ M and 7.0 μ M, respectively. It also exhibited HIV-1 reverse transcriptase inhibitory activity with an IC50 of 7.1 μ M.

  6. Dual function of the hemagglutinin H5 fused to chicken CD154 in a ...

    Dual function of the hemagglutinin H5 fused to chicken CD154 in a potential strategy of DIVA against avian influenza disease: preliminary study. ... The PDF file you selected should load here if your Web browser has a PDF reader plug-in installed (for example, a recent version of Adobe Acrobat Reader). If you would like ...

  7. Filamentous hemagglutinin of Bordetella pertussis: a key adhesin with immunomodulatory properties?

    Romero, Rodrigo, Villarino; Osička, Radim; Šebo, Peter

    2014-01-01

    Roč. 9, č. 12 (2014), s. 1339-1360 ISSN 1746-0913 R&D Projects: GA ČR(CZ) P302/11/0580; GA ČR(CZ) GA13-14547S Institutional support: RVO:61388971 Keywords : Bordetella * adhesion * integrins * filamentous hemagglutinin Subject RIV: EE - Microbiology, Virology Impact factor: 4.275, year: 2014

  8. [Serum immunoglobulin IgG subclass distribution of antibody responses to pertussis toxin and filamentous hemagglutinin of Bordetella pertussis in patients with whooping cough].

    Rastawicki, Waldemar; Smietańska, Karolina; Rokosz-Chudziak, Natalia; Jagielski, Marek

    2013-01-01

    The present study was aimed at determining the IgG subclass distribution against pertussis toxin (PT) and filamentous hemagglutinin (FHA) of Bordetella pertussis in patients with whooping cough. The total number of 222 serum samples obtained from patients suspected in clinical investigation for pertussis were tested separately by in-house ELISA for the presence of IgG antibodies to pertussis toxin and filamentous hemagglutinin. The percentage distribution of specific anti-PT and anti-FHA IgG subclass response was calculated only on the basis of group of sera confirmed in the present study as positive for total IgG antibodies (183 sera to PT antigen and 129 to FHA antigen). Paired serum specimens were obtained from 36 patients. Based on the results of determining the level of antibodies in the sera of 40 blood donors, the cut-off limit of serum antibodies for each subclass was set at arithmetic mean plus two standard deviations. Antibodies of IgG1 to pertussis toxin and filamentous hemagglutinin were diagnosed in 151 (82.5%) and 99 (76.7%), IgG2 in 72 (39.0%) and 50 (38.8%), IgG3 in 17 (9.3%) and 43 (33.3%), IgG4 in 55 (30.1%) and 53 (41.1%) serum samples, respectively. There were no significant differences in percentage of sera with IgG1, IgG2 and IgG3 in relation to age of the patients. However, the frequency of occurrence of IgG4 antibodies was highest in the group of the youngest children to the age of 6 years old (61.8% for PT and 68.0% for FHA), and decrease with age, reaching the minimum in the group of patients above 40 years old (13.2% and 4.2% for PT and FHA, respectively). We also found significantly higher frequency of IgG4 to PT and FHA antigens in men than in women. Statistically significant, essential changes in the pattern of IgG subclass during the course of infection were not found. In conclusion, this study showed that all four subclasses of IgG antibodies to pertussis toxin and filamentous hemagglutinin are produced during whooping cough.

  9. Foods served in child care facilities participating in the Child and Adult Care Food Program: Menu match and agreement with the new meal patterns and best practices

    Our objective was to assess the agreement of posted menus with foods served to 3- to 5-year-old children attending federal Child and Adult Care Food Program (CACFP)-enrolled facilities, and the degree to which the facilities met the new meal patterns and best practices. On-site observations and menu...

  10. Playing Hide and Seek: How Glycosylation of the Influenza Virus Hemagglutinin Can Modulate the Immune Response to Infection

    Michelle D. Tate

    2014-03-01

    Full Text Available Seasonal influenza A viruses (IAV originate from pandemic IAV and have undergone changes in antigenic structure, including addition of glycans to the hemagglutinin (HA glycoprotein. The viral HA is the major target recognized by neutralizing antibodies and glycans have been proposed to shield antigenic sites on HA, thereby promoting virus survival in the face of widespread vaccination and/or infection. However, addition of glycans can also interfere with the receptor binding properties of HA and this must be compensated for by additional mutations, creating a fitness barrier to accumulation of glycosylation sites. In addition, glycans on HA are also recognized by phylogenetically ancient lectins of the innate immune system and the benefit provided by evasion of humoral immunity is balanced by attenuation of infection. Therefore, a fine balance must exist regarding the optimal pattern of HA glycosylation to offset competing pressures associated with recognition by innate defenses, evasion of humoral immunity and maintenance of virus fitness. In this review, we examine HA glycosylation patterns of IAV associated with pandemic and seasonal influenza and discuss recent advancements in our understanding of interactions between IAV glycans and components of innate and adaptive immunity.

  11. Playing Hide and Seek: How Glycosylation of the Influenza Virus Hemagglutinin Can Modulate the Immune Response to Infection

    Tate, Michelle D.; Job, Emma R.; Deng, Yi-Mo; Gunalan, Vithiagaran; Maurer-Stroh, Sebastian; Reading, Patrick C.

    2014-01-01

    Seasonal influenza A viruses (IAV) originate from pandemic IAV and have undergone changes in antigenic structure, including addition of glycans to the hemagglutinin (HA) glycoprotein. The viral HA is the major target recognized by neutralizing antibodies and glycans have been proposed to shield antigenic sites on HA, thereby promoting virus survival in the face of widespread vaccination and/or infection. However, addition of glycans can also interfere with the receptor binding properties of HA and this must be compensated for by additional mutations, creating a fitness barrier to accumulation of glycosylation sites. In addition, glycans on HA are also recognized by phylogenetically ancient lectins of the innate immune system and the benefit provided by evasion of humoral immunity is balanced by attenuation of infection. Therefore, a fine balance must exist regarding the optimal pattern of HA glycosylation to offset competing pressures associated with recognition by innate defenses, evasion of humoral immunity and maintenance of virus fitness. In this review, we examine HA glycosylation patterns of IAV associated with pandemic and seasonal influenza and discuss recent advancements in our understanding of interactions between IAV glycans and components of innate and adaptive immunity. PMID:24638204

  12. Contemporary Avian Influenza A Virus Subtype H1, H6, H7, H10, and H15 Hemagglutinin Genes Encode a Mammalian Virulence Factor Similar to the 1918 Pandemic Virus H1 Hemagglutinin

    Qi, Li; Pujanauski, Lindsey M.; Davis, A. Sally; Schwartzman, Louis M.; Chertow, Daniel S.; Baxter, David; Scherler, Kelsey; Hartshorn, Kevan L.; Slemons, Richard D.; Walters, Kathie-Anne; Kash, John C.; Taubenberger, Jeffery K.

    2014-01-01

    ABSTRACT Zoonotic avian influenza virus infections may lead to epidemics or pandemics. The 1918 pandemic influenza virus has an avian influenza virus-like genome, and its H1 hemagglutinin was identified as a key mammalian virulence factor. A chimeric 1918 virus expressing a contemporary avian H1 hemagglutinin, however, displayed murine pathogenicity indistinguishable from that of the 1918 virus. Here, isogenic chimeric avian influenza viruses were constructed on an avian influenza virus backb...

  13. Exploring the Role of the Food Environment on Food Shopping Patterns in Philadelphia, PA, USA: A Semiquantitative Comparison of Two Matched Neighborhood Groups

    Amy Hillier

    2013-01-01

    Full Text Available Increasing research has focused on the built food environment and nutrition-related outcomes, yet what constitutes a food environment and how this environment influences individual behavior still remain unclear. This study assesses whether travel mode and distance to food shopping venues differ among individuals in varying food environments and whether individual- and household-level factors are associated with food shopping patterns. Fifty neighbors who share a traditionally defined food environment (25 in an unfavorable environment and 25 in a favorable environment were surveyed using a mix of close- and open-ended survey questions. Food shopping patterns were mapped using Geographic Information Systems (GIS. Stores visited were beyond the 0.5-mile (805 meters radius traditionally used to represent the extent of an individual’s food environment in an urban area. We found no significant difference in shopping frequency or motivating factor behind store choice between the groups. No differences existed between the two groups for big food shopping trips. For small trips, individuals in the favorable food environment traveled shorter distances and were more likely to walk than drive. Socioeconomic status, including car ownership, education, and income influenced distance traveled. These findings highlight the complexities involved in the study and measurement of food environments.

  14. Exploring the role of the food environment on food shopping patterns in Philadelphia, PA, USA: a semiquantitative comparison of two matched neighborhood groups.

    Hirsch, Jana A; Hillier, Amy

    2013-01-14

    Increasing research has focused on the built food environment and nutrition-related outcomes, yet what constitutes a food environment and how this environment influences individual behavior still remain unclear. This study assesses whether travel mode and distance to food shopping venues differ among individuals in varying food environments and whether individual- and household-level factors are associated with food shopping patterns. Fifty neighbors who share a traditionally defined food environment (25 in an unfavorable environment and 25 in a favorable environment) were surveyed using a mix of close- and open-ended survey questions. Food shopping patterns were mapped using Geographic Information Systems (GIS). Stores visited were beyond the 0.5-mile (805 meters) radius traditionally used to represent the extent of an individual's food environment in an urban area. We found no significant difference in shopping frequency or motivating factor behind store choice between the groups. No differences existed between the two groups for big food shopping trips. For small trips, individuals in the favorable food environment traveled shorter distances and were more likely to walk than drive. Socioeconomic status, including car ownership, education, and income influenced distance traveled. These findings highlight the complexities involved in the study and measurement of food environments.

  15. Optimal background matching camouflage.

    Michalis, Constantine; Scott-Samuel, Nicholas E; Gibson, David P; Cuthill, Innes C

    2017-07-12

    Background matching is the most familiar and widespread camouflage strategy: avoiding detection by having a similar colour and pattern to the background. Optimizing background matching is straightforward in a homogeneous environment, or when the habitat has very distinct sub-types and there is divergent selection leading to polymorphism. However, most backgrounds have continuous variation in colour and texture, so what is the best solution? Not all samples of the background are likely to be equally inconspicuous, and laboratory experiments on birds and humans support this view. Theory suggests that the most probable background sample (in the statistical sense), at the size of the prey, would, on average, be the most cryptic. We present an analysis, based on realistic assumptions about low-level vision, that estimates the distribution of background colours and visual textures, and predicts the best camouflage. We present data from a field experiment that tests and supports our predictions, using artificial moth-like targets under bird predation. Additionally, we present analogous data for humans, under tightly controlled viewing conditions, searching for targets on a computer screen. These data show that, in the absence of predator learning, the best single camouflage pattern for heterogeneous backgrounds is the most probable sample. © 2017 The Authors.

  16. Techniques Used in String Matching for Network Security

    Jamuna Bhandari

    2014-01-01

    String matching also known as pattern matching is one of primary concept for network security. In this area the effectiveness and efficiency of string matching algorithms is important for applications in network security such as network intrusion detection, virus detection, signature matching and web content filtering system. This paper presents brief review on some of string matching techniques used for network security.

  17. Charge pattern matching as a ‘fuzzy’ mode of molecular recognition for the functional phase separations of intrinsically disordered proteins

    Lin, Yi-Hsuan; Brady, Jacob P.; Forman-Kay, Julie D.; Chan, Hue Sun

    2017-11-01

    Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for distributing different IDP sequences into various cellular membraneless compartments. Pertinent physics was addressed recently by applying random-phase-approximation (RPA) polymer theory to electrostatics, which is a major energetic component governing IDP phase properties. RPA accounts for charge patterns and thus has advantages over Flory-Huggins (FH) and Overbeek-Voorn mean-field theories. To make progress toward deciphering the phase behaviors of multiple IDP sequences, the RPA formulation for one IDP species plus solvent is hereby extended to treat polyampholyte solutions containing two IDP species plus solvent. The new formulation generally allows for binary coexistence of two phases, each containing a different set of volume fractions ({φ }1,{φ }2) for the two different IDP sequences. The asymmetry between the two predicted coexisting phases with regard to their {φ }1/{φ }2 ratios for the two sequences increases with increasing mismatch between their charge patterns. This finding points to a multivalent, stochastic, ‘fuzzy’ mode of molecular recognition that helps populate various IDP sequences differentially into separate phase compartments. An intuitive illustration of this trend is provided by FH models, whereby a hypothetical case of ternary coexistence is also explored. Augmentations of the present RPA theory with a relative permittivity {ɛ }{{r}}(φ ) that depends on IDP volume fraction φ ={φ }1+{φ }2 lead to higher propensities to phase separate, in line with the case with one IDP species we studied previously. Notably, the cooperative, phase-separation-enhancing effects predicted by the prescriptions for {ɛ }{{r}}(φ ) we deem physically plausible are much more prominent than that entailed by common

  18. Hemithoracic Intensity Modulated Radiation Therapy After Pleurectomy/Decortication for Malignant Pleural Mesothelioma: Toxicity, Patterns of Failure, and a Matched Survival Analysis

    Chance, William W. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Rice, David C. [Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Allen, Pamela K. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Tsao, Anne S. [Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Fontanilla, Hiral P. [Princeton Radiation Oncology, Monroe Township, New Jersey (United States); Liao, Zhongxing; Chang, Joe Y.; Tang, Chad; Pan, Hubert Y.; Welsh, James W. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Mehran, Reza J. [Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Gomez, Daniel R., E-mail: dgomez@mdanderson.org [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States)

    2015-01-01

    Purpose: To investigate safety, efficacy, and recurrence after hemithoracic intensity modulated radiation therapy after pleurectomy/decortication (PD-IMRT) and after extrapleural pneumonectomy (EPP-IMRT). Methods and Materials: In 2009-2013, 24 patients with mesothelioma underwent PD-IMRT to the involved hemithorax to a dose of 45 Gy, with an optional integrated boost; 22 also received chemotherapy. Toxicity was scored with the Common Terminology Criteria for Adverse Events v4.0. Pulmonary function was compared at baseline, after surgery, and after IMRT. Kaplan-Meier analysis was used to calculate overall survival (OS), progression-free survival (PFS), time to locoregional failure, and time to distant metastasis. Failures were in-field, marginal, or out of field. Outcomes were compared with those of 24 patients, matched for age, nodal status, performance status, and chemotherapy, who had received EPP-IMRT. Results: Median follow-up time was 12.2 months. Grade 3 toxicity rates were 8% skin and 8% pulmonary. Pulmonary function declined from baseline to after surgery (by 21% for forced vital capacity, 16% for forced expiratory volume in 1 second, and 19% for lung diffusion of carbon monoxide [P for all = .01]) and declined still further after IMRT (by 31% for forced vital capacity [P=.02], 25% for forced expiratory volume in 1 second [P=.01], and 30% for lung diffusion of carbon monoxide [P=.01]). The OS and PFS rates were 76% and 67%, respectively, at 1 year and 56% and 34% at 2 years. Median OS (28.4 vs 14.2 months, P=.04) and median PFS (16.4 vs 8.2 months, P=.01) favored PD-IMRT versus EPP-IMRT. No differences were found in grade 4-5 toxicity (0 of 24 vs 3 of 24, P=.23), median time to locoregional failure (18.7 months vs not reached, P not calculable), or median time to distant metastasis (18.8 vs 11.8 months, P=.12). Conclusions: Hemithoracic intensity modulated radiation therapy after pleurectomy/decortication produced little high-grade toxicity but

  19. The role of carbohydrate in determining the immunochemical properties of the hemagglutinin of influenza A virus

    Gitelman, A.K.; Berezin, V.A.; Kharitonenkov, I.G.

    1981-01-01

    Most of the carbohydrate was removed from influenza with MRC II (H3N2) and its purified hemagglutinin (HA) on treatment with glycosidases, including α-mannosidase, #betta#-N-acetylglucosaminidase, #betta#-galactosidase and α-fucosidase. The release of 50 per cent of the carbohydrate from intact virus particles significantly affected hemagglutinating activity. The ability of untreated and glycosidase-treated virus to inhibit the binding of antibodies directed against the hemagglutinin was almost indistinguishable by competitive radioimmunoassay (RIA). Up to 60 per cent of the carbohydrate from the purified HA of influenza virus could be removed. The antigenicity of glycosidase treated HA molecules decreased 8-fold compared to intact HAs as measured by competitive RIA. In addition, glycosidase digestion of 125 I-labeled HA resulted in a decrease in its reactivity in direct RIA. We conclude that the carbohydrate portion of the HA of influenza virus is not of major importance in defining the antigenicity of HA. (Author)

  20. Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival

    Sankaranarayanan, Preethi; Schomay, Theodore E.; Aiello, Katherine A.; Alter, Orly

    2015-01-01

    The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD), which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV) tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs). We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient’s prognosis, is independent of the tumor’s stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell’s immortality, and a patient’s shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival. In Xq

  1. Tensor GSVD of patient- and platform-matched tumor and normal DNA copy-number profiles uncovers chromosome arm-wide patterns of tumor-exclusive platform-consistent alterations encoding for cell transformation and predicting ovarian cancer survival.

    Preethi Sankaranarayanan

    Full Text Available The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD, which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs. We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient's prognosis, is independent of the tumor's stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell's immortality, and a patient's shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival

  2. Computational design of protein interactions: designing proteins that neutralize influenza by inhibiting its hemagglutinin surface protein

    Fleishman, Sarel

    2012-02-01

    Molecular recognition underlies all life processes. Design of interactions not seen in nature is a test of our understanding of molecular recognition and could unlock the vast potential of subtle control over molecular interaction networks, allowing the design of novel diagnostics and therapeutics for basic and applied research. We developed the first general method for designing protein interactions. The method starts by computing a region of high affinity interactions between dismembered amino acid residues and the target surface and then identifying proteins that can harbor these residues. Designs are tested experimentally for binding the target surface and successful ones are affinity matured using yeast cell surface display. Applied to the conserved stem region of influenza hemagglutinin we designed two unrelated proteins that, following affinity maturation, bound hemagglutinin at subnanomolar dissociation constants. Co-crystal structures of hemagglutinin bound to the two designed binders were within 1Angstrom RMSd of their models, validating the accuracy of the design strategy. One of the designed proteins inhibits the conformational changes that underlie hemagglutinin's cell-invasion functions and blocks virus infectivity in cell culture, suggesting that such proteins may in future serve as diagnostics and antivirals against a wide range of pathogenic influenza strains. We have used this method to obtain experimentally validated binders of several other target proteins, demonstrating the generality of the approach. We discuss the combination of modeling and high-throughput characterization of design variants which has been key to the success of this approach, as well as how we have used the data obtained in this project to enhance our understanding of molecular recognition. References: Science 332:816 JMB, in press Protein Sci 20:753

  3. Chimeric Hemagglutinin Constructs Induce Broad Protection against Influenza B Virus Challenge in the Mouse Model.

    Ermler, Megan E; Kirkpatrick, Ericka; Sun, Weina; Hai, Rong; Amanat, Fatima; Chromikova, Veronika; Palese, Peter; Krammer, Florian

    2017-06-15

    Seasonal influenza virus epidemics represent a significant public health burden. Approximately 25% of all influenza virus infections are caused by type B viruses, and these infections can be severe, especially in children. Current influenza virus vaccines are an effective prophylaxis against infection but are impacted by rapid antigenic drift, which can lead to mismatches between vaccine strains and circulating strains. Here, we describe a broadly protective vaccine candidate based on chimeric hemagglutinins, consisting of globular head domains from exotic influenza A viruses and stalk domains from influenza B viruses. Sequential vaccination with these constructs in mice leads to the induction of broadly reactive antibodies that bind to the conserved stalk domain of influenza B virus hemagglutinin. Vaccinated mice are protected from lethal challenge with diverse influenza B viruses. Results from serum transfer experiments and antibody-dependent cell-mediated cytotoxicity (ADCC) assays indicate that this protection is antibody mediated and based on Fc effector functions. The present data suggest that chimeric hemagglutinin-based vaccination is a viable strategy to broadly protect against influenza B virus infection. IMPORTANCE While current influenza virus vaccines are effective, they are affected by mismatches between vaccine strains and circulating strains. Furthermore, the antiviral drug oseltamivir is less effective for treating influenza B virus infections than for treating influenza A virus infections. A vaccine that induces broad and long-lasting protection against influenza B viruses is therefore urgently needed. Copyright © 2017 American Society for Microbiology.

  4. Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin.

    Doud, Michael B; Bloom, Jesse D

    2016-06-03

    Influenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We and others have combined high-throughput mutagenesis with deep sequencing to estimate the effects of large numbers of mutations to influenza genes. However, these measurements have suffered from substantial experimental noise due to a variety of technical problems, the most prominent of which is bottlenecking during the generation of mutant viruses from plasmids. Here we describe advances that ameliorate these problems, enabling us to measure with greatly improved accuracy and reproducibility the effects of all amino-acid mutations to an H1 influenza hemagglutinin on viral replication in cell culture. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm at much higher resolution the results of previous studies suggesting that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. We also show that other regions of hemagglutinin-including the stalk epitopes targeted by broadly neutralizing antibodies-have a much lower inherent capacity to tolerate point mutations. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.

  5. Towards optimal packed string matching

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2014-01-01

    -size string-matching instruction wssm is available in contemporary commodity processors. The other word-size maximum-suffix instruction wslm is only required during the pattern pre-processing. Benchmarks show that our solution can be efficiently implemented, unlike some prior theoretical packed string...

  6. Contemporary avian influenza A virus subtype H1, H6, H7, H10, and H15 hemagglutinin genes encode a mammalian virulence factor similar to the 1918 pandemic virus H1 hemagglutinin.

    Qi, Li; Pujanauski, Lindsey M; Davis, A Sally; Schwartzman, Louis M; Chertow, Daniel S; Baxter, David; Scherler, Kelsey; Hartshorn, Kevan L; Slemons, Richard D; Walters, Kathie-Anne; Kash, John C; Taubenberger, Jeffery K

    2014-11-18

    Zoonotic avian influenza virus infections may lead to epidemics or pandemics. The 1918 pandemic influenza virus has an avian influenza virus-like genome, and its H1 hemagglutinin was identified as a key mammalian virulence factor. A chimeric 1918 virus expressing a contemporary avian H1 hemagglutinin, however, displayed murine pathogenicity indistinguishable from that of the 1918 virus. Here, isogenic chimeric avian influenza viruses were constructed on an avian influenza virus backbone, differing only by hemagglutinin subtype expressed. Viruses expressing the avian H1, H6, H7, H10, and H15 subtypes were pathogenic in mice and cytopathic in normal human bronchial epithelial cells, in contrast to H2-, H3-, H5-, H9-, H11-, H13-, H14-, and H16-expressing viruses. Mouse pathogenicity was associated with pulmonary macrophage and neutrophil recruitment. These data suggest that avian influenza virus hemagglutinins H1, H6, H7, H10, and H15 contain inherent mammalian virulence factors and likely share a key virulence property of the 1918 virus. Consequently, zoonotic infections with avian influenza viruses bearing one of these hemagglutinins may cause enhanced disease in mammals. Influenza viruses from birds can cause outbreaks in humans and may contribute to the development of pandemics. The 1918 pandemic influenza virus has an avian influenza virus-like genome, and its main surface protein, an H1 subtype hemagglutinin, was identified as a key mammalian virulence factor. In a previous study, a 1918 virus expressing an avian H1 gene was as virulent in mice as the reconstructed 1918 virus. Here, a set of avian influenza viruses was constructed, differing only by hemagglutinin subtype. Viruses with the avian H1, H6, H7, H10, and H15 subtypes caused severe disease in mice and damaged human lung cells. Consequently, infections with avian influenza viruses bearing one of these hemagglutinins may cause enhanced disease in mammals, and therefore surveillance for human infections

  7. Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody

    Raymond, Donald D.; Bajic, Goran; Ferdman, Jack; Suphaphiphat, Pirada; Settembre, Ethan C.; Moody, M. Anthony; Schmidt, Aaron G.; Harrison, Stephen C. (Duke-MED); (CH-Boston); (Seqirus)

    2017-12-18

    Antigenic variation requires frequent revision of annual influenza vaccines. Next-generation vaccine design strategies aim to elicit a broader immunity by directing the human immune response toward conserved sites on the principal viral surface protein, the hemagglutinin (HA). We describe a group of antibodies that recognize a hitherto unappreciated, conserved site on the HA of H1 subtype influenza viruses. Mutations in that site, which required a change in the H1 component of the 2017 vaccine, had not previously “taken over” among circulating H1 viruses. Our results encourage vaccine design strategies that resurface a protein to focus the immune response on a specific region.

  8. The Use of Recombinant Hemagglutinine Protein of Rinderpest Virus in Enzyme Immunoassay

    BULUT, Hakan; BOLAT, Yusuf

    2003-01-01

    In this study, Rinderpest virus (RPV) recombinant hemagglutinine protein (rH) fused with protein A region of Staphylococcus aureus was expressed in Escherichia coli and purified by IgG affinity chromatography. rH protein was also used to establish enzyme immunoassay. Therefore, to prevent IgG binding to the protein A the wells coated with the rH proteins were blocked by human serum. Afterwards, RPV antigens were added to the wells to evaluate this assay. To this end, serum from mice immunized...

  9. Stinging Insect Matching Game

    ... for Kids ▸ Stinging Insect Matching Game Share | Stinging Insect Matching Game Stinging insects can ruin summer fun for those who are ... the difference between the different kinds of stinging insects in order to keep your summer safe and ...

  10. The recombinant EHV-1 vector producing CDV hemagglutinin as potential vaccine against canine distemper.

    Pan, Zihao; Liu, Jin; Ma, Jiale; Jin, Qiuli; Yao, Huochun; Osterrieder, Nikolaus

    2017-10-01

    Canine distemper virus (CDV), is a pantropic agent of morbillivirus that causes fetal disease in dogs. Base on a broad host rang of CDV, the continued vaccines inoculation is unavoidable to pose gene recombination risk in vaccine virus and wild virus. The current study presents the construction of novel vectors, using equine herpesvirus type 1 (EHV-1) expressing the canine distemper virus (CDV). The recent field strain hemagglutinin protein and nucleoprotein were used for the construction of the viral vector vaccines. Based on the Bacterial artificial chromosome (BAC) genomes of EHV-1 RacH strain, the recombinant EHV-1 vaccine virus encoding CDV hemagglutinin protein (EHV-H) or CDV nucleoprotein (EHV-N) was constructed separately. The constructed BACs were rescued after 72 h post infection, and the expression of H or N in the recombinant viruses was confirmed by western-blotting. Furthermore, high levels of neutralizing antibodies were induced persistently following vaccination in the groups EHV-H&EHV-N and EHV-H, but the EHV-N group. The groups of vaccinated EHV-H and EHV-H&EHV-N pups were monitored for clinical signs, whereas the vaccinated EHV-N group developed moderate symptoms. The present study demonstrated that EHV-1 based recombinant virus carrying CDV H could be a promising vaccine candidate against canine distemper. Copyright © 2017. Published by Elsevier Ltd.

  11. Fusion peptide of influenza hemagglutinin requires a fixed angle boomerang structure for activity.

    Lai, Alex L; Park, Heather; White, Judith M; Tamm, Lukas K

    2006-03-03

    The fusion peptide of influenza hemagglutinin is crucial for cell entry of this virus. Previous studies showed that this peptide adopts a boomerang-shaped structure in lipid model membranes at the pH of membrane fusion. To examine the role of the boomerang in fusion, we changed several residues proposed to stabilize the kink in this structure and measured fusion. Among these, mutants E11A and W14A expressed hemagglutinins with hemifusion and no fusion activities, and F9A and N12A had no effect on fusion, respectively. Binding enthalpies and free energies of mutant peptides to model membranes and their ability to perturb lipid bilayer structures correlated well with the fusion activities of the parent full-length molecules. The structure of W14A determined by NMR and site-directed spin labeling features a flexible kink that points out of the membrane, in sharp contrast to the more ordered boomerang of the wild-type, which points into the membrane. A specific fixed angle boomerang structure is thus required to support membrane fusion.

  12. Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

    Michael B. Doud

    2016-06-01

    Full Text Available Influenza genes evolve mostly via point mutations, and so knowing the effect of every amino-acid mutation provides information about evolutionary paths available to the virus. We and others have combined high-throughput mutagenesis with deep sequencing to estimate the effects of large numbers of mutations to influenza genes. However, these measurements have suffered from substantial experimental noise due to a variety of technical problems, the most prominent of which is bottlenecking during the generation of mutant viruses from plasmids. Here we describe advances that ameliorate these problems, enabling us to measure with greatly improved accuracy and reproducibility the effects of all amino-acid mutations to an H1 influenza hemagglutinin on viral replication in cell culture. The largest improvements come from using a helper virus to reduce bottlenecks when generating viruses from plasmids. Our measurements confirm at much higher resolution the results of previous studies suggesting that antigenic sites on the globular head of hemagglutinin are highly tolerant of mutations. We also show that other regions of hemagglutinin—including the stalk epitopes targeted by broadly neutralizing antibodies—have a much lower inherent capacity to tolerate point mutations. The ability to accurately measure the effects of all influenza mutations should enhance efforts to understand and predict viral evolution.

  13. Best matching theory & applications

    Moghaddam, Mohsen

    2017-01-01

    Mismatch or best match? This book demonstrates that best matching of individual entities to each other is essential to ensure smooth conduct and successful competitiveness in any distributed system, natural and artificial. Interactions must be optimized through best matching in planning and scheduling, enterprise network design, transportation and construction planning, recruitment, problem solving, selective assembly, team formation, sensor network design, and more. Fundamentals of best matching in distributed and collaborative systems are explained by providing: § Methodical analysis of various multidimensional best matching processes § Comprehensive taxonomy, comparing different best matching problems and processes § Systematic identification of systems’ hierarchy, nature of interactions, and distribution of decision-making and control functions § Practical formulation of solutions based on a library of best matching algorithms and protocols, ready for direct applications and apps development. Design...

  14. Matching Students to Schools

    Dejan Trifunovic

    2017-08-01

    Full Text Available In this paper, we present the problem of matching students to schools by using different matching mechanisms. This market is specific since public schools are free and the price mechanism cannot be used to determine the optimal allocation of children in schools. Therefore, it is necessary to use different matching algorithms that mimic the market mechanism and enable us to determine the core of the cooperative game. In this paper, we will determine that it is possible to apply cooperative game theory in matching problems. This review paper is based on illustrative examples aiming to compare matching algorithms in terms of the incentive compatibility, stability and efficiency of the matching. In this paper we will present some specific problems that may occur in matching, such as improving the quality of schools, favoring minority students, the limited length of the list of preferences and generating strict priorities from weak priorities.

  15. The molecular determinants of antibody recognition and antigenic drift in the H3 hemagglutinin of swine influenza A virus

    Influenza A virus (IAV) of the H3 subtype is an important pathogen that affects both humans and swine. The main intervention strategy for preventing infection is vaccination to induce neutralizing antibodies against the surface glycoprotein hemagglutinin (HA). However, due to antigenic drift, vaccin...

  16. 77 FR 63783 - Influenza Viruses Containing the Hemagglutinin from the Goose/Guangdong/1/96 Lineage

    2012-10-17

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES 42 CFR Part 73 [Docket: CDC-2012-0010] Influenza Viruses... questions concerning highly pathogenic avian influenza (HPAI) H5N1 viruses that contain a hemagglutinin (HA... avian influenza (HPAI) H5N1 viruses with a mortality rate that exceeds 50 percent in hospitalized...

  17. Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls.

    R.A.M. Fouchier (Ron); V.J. Munster (Vincent); A. Wallensten (Anders); T.M. Bestebroer (Theo); S. Herfst (Sander); D.J. Smith (Derek James); G.F. Rimmelzwaan (Guus); B. Olsen (Björn); A.D.M.E. Osterhaus (Albert)

    2005-01-01

    textabstractIn wild aquatic birds and poultry around the world, influenza A viruses carrying 15 antigenic subtypes of hemagglutinin (HA) and 9 antigenic subtypes of neuraminidase (NA) have been described. Here we describe a previously unidentified antigenic subtype of HA (H16), detected in viruses

  18. Optimal Packed String Matching

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany

    2011-01-01

    In the packed string matching problem, each machine word accommodates – characters, thus an n-character text occupies n/– memory words. We extend the Crochemore-Perrin constantspace O(n)-time string matching algorithm to run in optimal O(n/–) time and even in real-time, achieving a factor – speed...

  19. Ontology Matching Across Domains

    2010-05-01

    matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

  20. The Length of N-Glycans of Recombinant H5N1 Hemagglutinin Influences the Oligomerization and Immunogenicity of Vaccine Antigen

    Edyta Kopera

    2017-04-01

    Full Text Available Hemagglutinin glycoprotein (HA is a principle influenza vaccine antigen. Recombinant HA-based vaccines become a potential alternative for traditional approach. Complexity and variation of HA N-glycosylation are considered as the important factors for the vaccine design. The number and location of glycan moieties in the HA molecule are also crucial. Therefore, we decided to study the effect of N-glycosylation pattern on the H5 antigen structure and its ability to induce immunological response. We also decided to change neither the number nor the position of the HA glycosylation sites but only the glycan length. Two variants of the H5 antigen with high mannose glycosylation (H5hm and with low-mannose glycosylation (H5Man5 were prepared utilizing different Pichia strains. Our structural studies demonstrated that only the highly glycosylated H5 antigen formed high molecular weight oligomers similar to viral particles. Further, the H5hm was much more immunogenic for mice than H5Man5. In summary, our results suggest that high mannose glycosylation of vaccine antigen is superior to the low glycosylation pattern. Our findings have strong implications for the recombinant HA-based influenza vaccine design.

  1. A Role for the Mannose-Sensitive Hemagglutinin in Biofilm Formation by Vibrio cholerae El Tor

    Watnick, Paula I.; Fullner, Karla Jean; Kolter, Roberto

    1999-01-01

    While much has been learned regarding the genetic basis of host-pathogen interactions, less is known about the molecular basis of a pathogen’s survival in the environment. Biofilm formation on abiotic surfaces represents a survival strategy utilized by many microbes. Here it is shown that Vibrio cholerae El Tor does not use the virulence-associated toxin-coregulated pilus to form biofilms on borosilicate but rather uses the mannose-sensitive hemagglutinin (MSHA) pilus, which plays no role in pathogenicity. In contrast, attachment of V. cholerae to chitin is shown to be independent of the MSHA pilus, suggesting divergent pathways for biofilm formation on nutritive and nonnutritive abiotic surfaces. PMID:10348878

  2. Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness.

    Canale, Aneth S; Venev, Sergey V; Whitfield, Troy W; Caffrey, Daniel R; Marasco, Wayne A; Schiffer, Celia A; Kowalik, Timothy F; Jensen, Jeffrey D; Finberg, Robert W; Zeldovich, Konstantin B; Wang, Jennifer P; Bolon, Daniel N A

    2018-04-13

    The fitness effects of synonymous mutations can provide insights into biological and evolutionary mechanisms. We analyzed the experimental fitness effects of all single-nucleotide mutations, including synonymous substitutions, at the beginning of the influenza A virus hemagglutinin (HA) gene. Many synonymous substitutions were deleterious both in bulk competition and for individually isolated clones. Investigating protein and RNA levels of a subset of individually expressed HA variants revealed that multiple biochemical properties contribute to the observed experimental fitness effects. Our results indicate that a structural element in the HA segment viral RNA may influence fitness. Examination of naturally evolved sequences in human hosts indicates a preference for the unfolded state of this structural element compared to that found in swine hosts. Our overall results reveal that synonymous mutations may have greater fitness consequences than indicated by simple models of sequence conservation, and we discuss the implications of this finding for commonly used evolutionary tests and analyses. Copyright © 2018. Published by Elsevier Ltd.

  3. Domain architecture and oligomerization properties of the paramyxovirus PIV 5 hemagglutinin-neuraminidase (HN) protein.

    Yuan, Ping; Leser, George P; Demeler, Borries; Lamb, Robert A; Jardetzky, Theodore S

    2008-09-01

    The mechanism by which the paramyxovirus hemagglutinin-neuraminidase (HN) protein couples receptor binding to activation of virus entry remains to be fully understood, but the HN stalk is thought to play an important role in the process. We have characterized ectodomain constructs of the parainfluenza virus 5 HN to understand better the underlying architecture and oligomerization properties that may influence HN functions. The PIV 5 neuraminidase (NA) domain is monomeric whereas the ectodomain forms a well-defined tetramer. The HN stalk also forms tetramers and higher order oligomers with high alpha-helical content. Together, the data indicate that the globular NA domains form weak intersubunit interactions at the end of the HN stalk tetramer, while stabilizing the stalk and overall oligomeric state of the ectodomain. Electron microscopy of the HN ectodomain reveals flexible arrangements of the NA and stalk domains, which may be important for understanding how these two HN domains impact virus entry.

  4. Roll of hemagglutinin gene in the biology of avian inflenza virus

    Masoud Soltanialvar

    2016-06-01

    Full Text Available The hemagglutinin (HA, the major envelope glycoprotein of influenza, plays an important role during the early stage of infection, and changes in the HA gene prior to the emergence of pathogenic avian influenza viruses. The HA protein controls viral entry through membrane fusion of the viral envelope with the host cell membrane and allows the genetic information released to initiate new virus synthesis. Sharp antigenic variation of HA remains the critical challenge to the development of effective vaccines. Therefore, we highlight the role of HA in need of review: structure of HA, the fusion process and the HA receptor binding specificity in interspecies transmission and the impact of multiple mutations at antigenic sites and host antibodies to the parental virus, and the host susceptibility to productive infection by the drift strains.

  5. Enhancement of the safety of live influenza vaccine by attenuating mutations from cold-adapted hemagglutinin

    Lee, Yoon Jae; Jang, Yo Han; Kim, Paul; Lee, Yun Ha; Lee, Young Jae; Byun, Young Ho; Lee, Kwang-Hee; Kim, Kyusik; Seong, Baik Lin

    2016-01-01

    In our previous study, X-31ca-based H5N1 LAIVs, in particular, became more virulent in mice than the X-31ca MDV, possibly by the introduction of the surface antigens of highly pathogenic H5N1 influenza virus, implying that additional attenuation is needed in this cases to increase the safety level of the vaccine. In this report we suggest an approach to further increase the safety of LAIV through additional cold-adapted mutations in the hemagglutinin. The cold-adaptation of X-31 virus resulted in four amino acid mutations in the HA. We generated a panel of 7:1 reassortant viruses each carrying the hemagglutinins with individual single amino acid mutations. We examined their phenotypes and found a major attenuating mutation, N81K. This attenuation marker conferred additional temperature-sensitive and attenuation phenotype to the LAIV. Our data indicate that the cold-adapted mutation in the HA confers additional attenuation to the LAIV strain, without compromising its productivity and immune response. - Highlights: • Cold-adaptation process induced four amino acid mutations in the HA of X-31 virus. • The four mutations in the HA also contributed to attenuation of the X-31ca virus • N81K mutation was the most significant marker for the attenuation of X-31ca virus. • Introduction of N81K mutation into H3N2 LAIV further attenuated the vaccine. • This approach provides a useful guideline for enhancing the safety of the LAIVs.

  6. Enhancement of the safety of live influenza vaccine by attenuating mutations from cold-adapted hemagglutinin

    Lee, Yoon Jae [Graduate Program in Biomaterials Science and Engineering, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Laboratory of Molecular Medicine, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Vaccine Translational Research Center, Yonsei University, Seoul (Korea, Republic of); Jang, Yo Han [Laboratory of Molecular Medicine, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Kim, Paul; Lee, Yun Ha; Lee, Young Jae [Laboratory of Molecular Medicine, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Vaccine Translational Research Center, Yonsei University, Seoul (Korea, Republic of); Byun, Young Ho; Lee, Kwang-Hee; Kim, Kyusik [Laboratory of Molecular Medicine, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Seong, Baik Lin, E-mail: blseong@yonsei.ac.kr [Graduate Program in Biomaterials Science and Engineering, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Laboratory of Molecular Medicine, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul (Korea, Republic of); Vaccine Translational Research Center, Yonsei University, Seoul (Korea, Republic of)

    2016-04-15

    In our previous study, X-31ca-based H5N1 LAIVs, in particular, became more virulent in mice than the X-31ca MDV, possibly by the introduction of the surface antigens of highly pathogenic H5N1 influenza virus, implying that additional attenuation is needed in this cases to increase the safety level of the vaccine. In this report we suggest an approach to further increase the safety of LAIV through additional cold-adapted mutations in the hemagglutinin. The cold-adaptation of X-31 virus resulted in four amino acid mutations in the HA. We generated a panel of 7:1 reassortant viruses each carrying the hemagglutinins with individual single amino acid mutations. We examined their phenotypes and found a major attenuating mutation, N81K. This attenuation marker conferred additional temperature-sensitive and attenuation phenotype to the LAIV. Our data indicate that the cold-adapted mutation in the HA confers additional attenuation to the LAIV strain, without compromising its productivity and immune response. - Highlights: • Cold-adaptation process induced four amino acid mutations in the HA of X-31 virus. • The four mutations in the HA also contributed to attenuation of the X-31ca virus • N81K mutation was the most significant marker for the attenuation of X-31ca virus. • Introduction of N81K mutation into H3N2 LAIV further attenuated the vaccine. • This approach provides a useful guideline for enhancing the safety of the LAIVs.

  7. Quantum learning and universal quantum matching machine

    Sasaki, Masahide; Carlini, Alberto

    2002-01-01

    Suppose that three kinds of quantum systems are given in some unknown states vertical bar f> xN , vertical bar g 1 > xK , and vertical bar g 2 > xK , and we want to decide which template state vertical bar g 1 > or vertical bar g 2 >, each representing the feature of the pattern class C 1 or C 2 , respectively, is closest to the input feature state vertical bar f>. This is an extension of the pattern matching problem into the quantum domain. Assuming that these states are known a priori to belong to a certain parametric family of pure qubit systems, we derive two kinds of matching strategies. The first one is a semiclassical strategy that is obtained by the natural extension of conventional matching strategies and consists of a two-stage procedure: identification (estimation) of the unknown template states to design the classifier (learning process to train the classifier) and classification of the input system into the appropriate pattern class based on the estimated results. The other is a fully quantum strategy without any intermediate measurement, which we might call as the universal quantum matching machine. We present the Bayes optimal solutions for both strategies in the case of K=1, showing that there certainly exists a fully quantum matching procedure that is strictly superior to the straightforward semiclassical extension of the conventional matching strategy based on the learning process

  8. Pediatric MATCH Infographic

    Infographic explaining NCI-COG Pediatric MATCH, a cancer treatment clinical trial for children and adolescents, from 1 to 21 years of age, that is testing the use of precision medicine for pediatric cancers.

  9. Data Matching Imputation System

    National Oceanic and Atmospheric Administration, Department of Commerce — The DMIS dataset is a flat file record of the matching of several data set collections. Primarily it consists of VTRs, dealer records, Observer data in conjunction...

  10. Magnetic safety matches

    Lindén, J.; Lindberg, M.; Greggas, A.; Jylhävuori, N.; Norrgrann, H.; Lill, J. O.

    2017-07-01

    In addition to the main ingredients; sulfur, potassium chlorate and carbon, ordinary safety matches contain various dyes, glues etc, giving the head of the match an even texture and appealing color. Among the common reddish-brown matches there are several types, which after ignition can be attracted by a strong magnet. Before ignition the match head is generally not attracted by the magnet. An elemental analysis based on proton-induced x-ray emission was performed to single out iron as the element responsible for the observed magnetism. 57Fe Mössbauer spectroscopy was used for identifying the various types of iron-compounds, present before and after ignition, responsible for the macroscopic magnetism: Fe2O3 before and Fe3O4 after. The reaction was verified by mixing the main chemicals in the match-head with Fe2O3 in glue and mounting the mixture on a match stick. The ash residue after igniting the mixture was magnetic.

  11. Latent palmprint matching.

    Jain, Anil K; Feng, Jianjiang

    2009-06-01

    The evidential value of palmprints in forensic applications is clear as about 30 percent of the latents recovered from crime scenes are from palms. While biometric systems for palmprint-based personal authentication in access control type of applications have been developed, they mostly deal with low-resolution (about 100 ppi) palmprints and only perform full-to-full palmprint matching. We propose a latent-to-full palmprint matching system that is needed in forensic applications. Our system deals with palmprints captured at 500 ppi (the current standard in forensic applications) or higher resolution and uses minutiae as features to be compatible with the methodology used by latent experts. Latent palmprint matching is a challenging problem because latent prints lifted at crime scenes are of poor image quality, cover only a small area of the palm, and have a complex background. Other difficulties include a large number of minutiae in full prints (about 10 times as many as fingerprints), and the presence of many creases in latents and full prints. A robust algorithm to reliably estimate the local ridge direction and frequency in palmprints is developed. This facilitates the extraction of ridge and minutiae features even in poor quality palmprints. A fixed-length minutia descriptor, MinutiaCode, is utilized to capture distinctive information around each minutia and an alignment-based minutiae matching algorithm is used to match two palmprints. Two sets of partial palmprints (150 live-scan partial palmprints and 100 latent palmprints) are matched to a background database of 10,200 full palmprints to test the proposed system. Despite the inherent difficulty of latent-to-full palmprint matching, rank-1 recognition rates of 78.7 and 69 percent, respectively, were achieved in searching live-scan partial palmprints and latent palmprints against the background database.

  12. Crystallization and preliminary crystallographic analysis of the measles virus hemagglutinin in complex with the CD46 receptor

    Santiago, César; Gutiérrez-Rodríguez, Angel; Tucker, Paul A.; Stehle, Thilo; Casasnovas, José M.

    2009-01-01

    A complex of the measles virus hemagglutinin and the CD46 receptor representing the initial step of the cell infection has been crystallized. The measles virus (MV) hemagglutinin (MV-H) mediates the attachment of MV particles to cell-surface receptors for entry into host cells. MV uses two receptors for attachment to host cells: the complement-control protein CD46 and the signalling lymphocyte activation molecule (SLAM). The MV-H glycoprotein from an Edmonston MV variant and the MV-binding fragment of the CD46 receptor were overproduced in mammalian cells and used to crystallize an MV-H–CD46 complex. Well diffracting crystals containing two complexes in the asymmetric unit were obtained and the structure of the complex was solved by the molecular-replacement method

  13. Sensitization with vaccinia virus encoding H5N1 hemagglutinin restores immune potential against H5N1 influenza virus.

    Yasui, Fumihiko; Itoh, Yasushi; Ikejiri, Ai; Kitabatake, Masahiro; Sakaguchi, Nobuo; Munekata, Keisuke; Shichinohe, Shintaro; Hayashi, Yukiko; Ishigaki, Hirohito; Nakayama, Misako; Sakoda, Yoshihiro; Kida, Hiroshi; Ogasawara, Kazumasa; Kohara, Michinori

    2016-11-28

    H5N1 highly pathogenic avian influenza (H5N1 HPAI) virus causes elevated mortality compared with seasonal influenza viruses like H1N1 pandemic influenza (H1N1 pdm) virus. We identified a mechanism associated with the severe symptoms seen with H5N1 HPAI virus infection. H5N1 HPAI virus infection induced a decrease of dendritic cell number in the splenic extrafollicular T-cell zone and impaired formation of the outer layers of B-cell follicles, resulting in insufficient levels of antibody production after infection. However, in animals vaccinated with a live recombinant vaccinia virus expressing the H5 hemagglutinin, infection with H5N1 HPAI virus induced parafollicular dendritic cell accumulation and efficient antibody production. These results indicate that a recombinant vaccinia encoding H5 hemagglutinin gene does not impair dendritic cell recruitment and can be a useful vaccine candidate.

  14. Identification of Key Residues in Virulent Canine Distemper Virus Hemagglutinin That Control CD150/SLAM-Binding Activity▿

    Zipperle, Ljerka; Langedijk, Johannes P. M.; Örvell, Claes; Vandevelde, Marc; Zurbriggen, Andreas; Plattet, Philippe

    2010-01-01

    Morbillivirus cell entry is controlled by hemagglutinin (H), an envelope-anchored viral glycoprotein determining interaction with multiple host cell surface receptors. Subsequent to virus-receptor attachment, H is thought to transduce a signal triggering the viral fusion glycoprotein, which in turn drives virus-cell fusion activity. Cell entry through the universal morbillivirus receptor CD150/SLAM was reported to depend on two nearby microdomains located within the hemagglutinin. Here, we provide evidence that three key residues in the virulent canine distemper virus A75/17 H protein (Y525, D526, and R529), clustering at the rim of a large recessed groove created by β-propeller blades 4 and 5, control SLAM-binding activity without drastically modulating protein surface expression or SLAM-independent F triggering. PMID:20631152

  15. A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses

    Macken, Catherine A.; Lewis, Nicola S.; Van Reeth, Kristien; Brown, Ian H.; Swenson, Sabrina L.; Simon, Gaëlle; Saito, Takehiko; Berhane, Yohannes; Ciacci-Zanella, Janice; Pereda, Ariel; Davis, C. Todd; Donis, Ruben O.; Webby, Richard J.

    2016-01-01

    ABSTRACT The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily to track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data. IMPORTANCE A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids

  16. Approaches for Stereo Matching

    Takouhi Ozanian

    1995-04-01

    Full Text Available This review focuses on the last decade's development of the computational stereopsis for recovering three-dimensional information. The main components of the stereo analysis are exposed: image acquisition and camera modeling, feature selection, feature matching and disparity interpretation. A brief survey is given of the well known feature selection approaches and the estimation parameters for this selection are mentioned. The difficulties in identifying correspondent locations in the two images are explained. Methods as to how effectively to constrain the search for correct solution of the correspondence problem are discussed, as are strategies for the whole matching process. Reasons for the occurrence of matching errors are considered. Some recently proposed approaches, employing new ideas in the modeling of stereo matching in terms of energy minimization, are described. Acknowledging the importance of computation time for real-time applications, special attention is paid to parallelism as a way to achieve the required level of performance. The development of trinocular stereo analysis as an alternative to the conventional binocular one, is described. Finally a classification based on the test images for verification of the stereo matching algorithms, is supplied.

  17. Identification of Xylella fastidiosa antivirulence genes: hemagglutinin adhesins contribute a biofilm maturation to X. fastidios and colonization and attenuate virulence.

    Guilhabert, Magalie R; Kirkpatrick, Bruce C

    2005-08-01

    Xylella fastidosa, a gram-negative, xylem-limited bacterium, is the causal agent of several economically important plant diseases, including Pierce's disease (PD) and citrus variegated chlorosis (CVC). Until recently, the inability to transform or produce transposon mutants of X. fastidosa had been a major impediment to identifying X. fastidosa genes that mediate pathogen and plant interactions. A random transposon (Tn5) library of X. fastidosa was constructed and screened for mutants showing more severe symptoms and earlier grapevine death (hypervirulence) than did vines infected with the wild type. Seven hypervirulent mutants identified in this screen moved faster and reached higher populations than the wild type in grapevines. These results suggest that X. fastidosa attenuates its virulence in planta and that movement is important in X. fastidosa virulence. The mutated genes were sequenced and none had been described previously as antivirulence genes, although six of them showed similarity with genes of known functions in other organisms. One transposon insertion inactivated a hemagglutinin adhesin gene (PD2118), which we named HxfA. Another mutant in a second putative X. fastidosa hemagglutinin gene, PD1792 (HxfB), was constructed, and further characterization of these hxf mutants suggests that X. fastidosa hemagglutinins mediate contact between X. fastidosa cells, which results in colony formation and biofilm maturation within the xylem vessels.

  18. A simple Pichia pastoris fermentation and downstream processing strategy for making recombinant pandemic Swine Origin Influenza a virus Hemagglutinin protein.

    Athmaram, T N; Singh, Anil Kumar; Saraswat, Shweta; Srivastava, Saurabh; Misra, Princi; Kameswara Rao, M; Gopalan, N; Rao, P V L

    2013-02-01

    The present Influenza vaccine manufacturing process has posed a clear impediment to initiation of rapid mass vaccination against spreading pandemic influenza. New vaccine strategies are therefore needed that can accelerate the vaccine production. Pichia offers several advantages for rapid and economical bulk production of recombinant proteins and, hence, can be attractive alternative for producing an effective influenza HA based subunit vaccine. The recombinant Pichia harboring the transgene was subjected to fed-batch fermentation at 10 L scale. A simple fermentation and downstream processing strategy is developed for high-yield secretory expression of the recombinant Hemagglutinin protein of pandemic Swine Origin Influenza A virus using Pichia pastoris via fed-batch fermentation. Expression and purification were optimized and the expressed recombinant Hemagglutinin protein was verified by sodium dodecyl sulfate polyacrylamide gel electrophoresis, Western blot and MALDI-TOF analysis. In this paper, we describe a fed-batch fermentation protocol for the secreted production of Swine Influenza A Hemagglutinin protein in the P. pastoris GS115 strain. We have shown that there is a clear relationship between product yield and specific growth rate. The fed-batch fermentation and downstream processing methods optimized in the present study have immense practical application for high-level production of the recombinant H1N1 HA protein in a cost effective way using P. pastoris.

  19. Purification and production of monospecific antibody to the hemagglutinin from Subtype H5N1 influenza virus

    Simson Tarigan

    2010-12-01

    Full Text Available The purpose of this study was to purify the hemagglutinin from H5N1 virus and to generate monospecific antibody appropriate for production of sensitive and specific immunoassay for H5N1 avian influenza. For this purpose, a local isolate H5N1 virus (A/Ck/West Java/Hamd/2006 was propagated in chicken embryos. The viral pellet was dissolved in a Triton-X-100 solution, undissolved viral particles were pelleted by ultracentrifuge, and the supernatant containing viral surface glycoproteins (Hemagglutinin and neuraminidase was collected. The neuraminidase in the supernatant was absorbed by passing the supernatant through an Oxamic-acid-superose column. After dialyzing extensively, the filtrate was further fractionated with an anion exchange chromatography (Q-sepharose column. Proteins adsorbed by the column were eluted stepwisely with 0.10, 0.25, 0.25 and 0.75 M NaCl in 20 mM Tris, ph 8. Hemagglutinin (H5 was found to be eluted from the column with the 0.5 M NaCl elution buffer. The purified H5 was free from other viral proteins based on immunoassays using commercial antibodies to H5N1 nucleoprotein and neuraminidase. When used as ELISA’s coating antigen, the purified H5 proved to be sensitive and specific for hemagglutinin H5. Cross reactions with other type-A-influenza virus, H6, H7 dan H9, were negligibly low. For the production of monospecific antiserum, the purified H5 was separated with SDS-PAGE, the band containing the H5 monomer was cut out , homogenised and injected into rabbits. The antiserum was capable of detecting the presence of inactivated H5N1 virus in a very dilute suspension, with a detection limit of 0.04 heagglutination (HA unit. The purified hemagglutinin and the serum raised against it should be useful for developing specific, sensitive and affordable immunoassay for H5N1 avian influenza.

  20. Dewey Concentration Match.

    School Library Media Activities Monthly, 1996

    1996-01-01

    Giving students a chance to associate numbers with subjects can be useful in speeding their location of desired print or nonprint materials and helping students feel independent when browsing. A matching game for helping students learn the Dewey numbers is presented. Instructions for the library media specialist or teacher, instructions for…

  1. Matched-Filter Thermography

    Nima Tabatabaei

    2018-04-01

    Full Text Available Conventional infrared thermography techniques, including pulsed and lock-in thermography, have shown great potential for non-destructive evaluation of broad spectrum of materials, spanning from metals to polymers to biological tissues. However, performance of these techniques is often limited due to the diffuse nature of thermal wave fields, resulting in an inherent compromise between inspection depth and depth resolution. Recently, matched-filter thermography has been introduced as a means for overcoming this classic limitation to enable depth-resolved subsurface thermal imaging and improving axial/depth resolution. This paper reviews the basic principles and experimental results of matched-filter thermography: first, mathematical and signal processing concepts related to matched-fileting and pulse compression are discussed. Next, theoretical modeling of thermal-wave responses to matched-filter thermography using two categories of pulse compression techniques (linear frequency modulation and binary phase coding are reviewed. Key experimental results from literature demonstrating the maintenance of axial resolution while inspecting deep into opaque and turbid media are also presented and discussed. Finally, the concept of thermal coherence tomography for deconvolution of thermal responses of axially superposed sources and creation of depth-selective images in a diffusion-wave field is reviewed.

  2. Bayesian grid matching

    Hartelius, Karsten; Carstensen, Jens Michael

    2003-01-01

    A method for locating distorted grid structures in images is presented. The method is based on the theories of template matching and Bayesian image restoration. The grid is modeled as a deformable template. Prior knowledge of the grid is described through a Markov random field (MRF) model which r...

  3. Is Matching Innate?

    Gallistel, C. R.; King, Adam Philip; Gottlieb, Daniel; Balci, Fuat; Papachristos, Efstathios B.; Szalecki, Matthew; Carbone, Kimberly S.

    2007-01-01

    Experimentally naive mice matched the proportions of their temporal investments (visit durations) in two feeding hoppers to the proportions of the food income (pellets per unit session time) derived from them in three experiments that varied the coupling between the behavioral investment and food income, from no coupling to strict coupling.…

  4. Matching Supernovae to Galaxies

    Kohler, Susanna

    2016-12-01

    developed a new automated algorithm for matching supernovae to their host galaxies. Their work builds on currently existing algorithms and makes use of information about the nearby galaxies, accounts for the uncertainty of the match, and even includes a machine learning component to improve the matching accuracy.Gupta and collaborators test their matching algorithm on catalogs of galaxies and simulated supernova events to quantify how well the algorithm is able to accurately recover the true hosts.Successful MatchingThe matching algorithms accuracy (purity) as a function of the true supernova-host separation, the supernova redshift, the true hosts brightness, and the true hosts size. [Gupta et al. 2016]The authors find that when the basic algorithm is run on catalog data, it matches supernovae to their hosts with 91% accuracy. Including the machine learning component, which is run after the initial matching algorithm, improves the accuracy of the matching to 97%.The encouraging results of this work which was intended as a proof of concept suggest that methods similar to this could prove very practical for tackling future survey data. And the method explored here has use beyond matching just supernovae to their host galaxies: it could also be applied to other extragalactic transients, such as gamma-ray bursts, tidal disruption events, or electromagnetic counterparts to gravitational-wave detections.CitationRavi R. Gupta et al 2016 AJ 152 154. doi:10.3847/0004-6256/152/6/154

  5. Isolation of recombinant phage antibodies targeting the hemagglutinin cleavage site of highly pathogenic avian influenza virus.

    Jinhua Dong

    Full Text Available Highly pathogenic avian influenza (HPAI H5N1 viruses, which have emerged in poultry and other wildlife worldwide, contain a characteristic multi-basic cleavage site (CS in the hemagglutinin protein (HA. Because this arginine-rich CS is unique among influenza virus subtypes, antibodies against this site have the potential to specifically diagnose pathogenic H5N1. By immunizing mice with the CS peptide and screening a phage display library, we isolated four antibody Fab fragment clones that specifically bind the antigen peptide and several HPAI H5N1 HA proteins in different clades. The soluble Fab fragments expressed in Escherichia coli bound the CS peptide and the H5N1 HA protein with nanomolar affinity. In an immunofluorescence assay, these Fab fragments stained cells infected with HPAI H5N1 but not those infected with a less virulent strain. Lastly, all the Fab clones could detect the CS peptide and H5N1 HA protein by open sandwich ELISA. Thus, these recombinant Fab fragments will be useful novel reagents for the rapid and specific detection of HPAI H5N1 virus.

  6. MVA recombinants expressing the fusion and hemagglutinin genes of PPRV protects goats against virulent challenge.

    Chandran, Dev; Reddy, Kolli Bhaktavatsala; Vijayan, Shahana Pallichera; Sugumar, Parthasarthy; Rani, Gudavalli Sudha; Kumar, Ponsekaran Santha; Rajendra, Lingala; Srinivasan, Villuppanoor Alwar

    2010-09-01

    Peste des Petits Ruminants (PPR) is a highly contagious animal disease caused by the Peste des Petits Ruminants virus (PPRV) belonging to the genus morbillivirus and family Paramyxoviridae. The disease results in high morbidity and mortality in goats, sheep and in some small wild ruminants. The presence of large number of small ruminants reared in endemic areas makes PPR a notorious disease threatening the livelihood of poor farmers. Conventional vaccination using a live, attenuated vaccine gives adequate protection but cannot be used in case of eradication of the disease due to difficulty in differentiation of infected animals from the vaccinated ones.In the present study, we constructed two recombinant viruses using attenuated Modified Vaccinia virus Ankara virus (MVA) namely MVA-F and MVA-H expressing the full length PPRV fusion (F) and hemagglutinin (H) glycoproteins, respectively. Goats were vaccinated intramuscularly with 105 plaque forming units (PFU) each of the recombinant viruses and a live attenuated vaccine (RAKSHA PPR) and challenged 4 months later with PPRV challenge virus (10(3) goat LD(50)). All goats were completely protected from the clinical disease. This study gave an indication that mass vaccination of small ruminants with either of the above or both recombinant inexpensive virus vaccines could help in possible eradication of PPRV from endemic countries like India and subsequent seromonitoring of the disease for differentiation of infected animals from vaccinated ones.

  7. Stochastic acidification, activation of hemagglutinin and escape of influenza viruses from an endosome

    Lagache, Thibault; Sieben, Christian; Meyer, Tim; Herrmann, Andreas; Holcman, David

    2017-06-01

    Influenza viruses enter the cell inside an endosome. During the endosomal journey, acidification triggers a conformational change of the virus spike protein hemagglutinin (HA) that results in escape of the viral genome from the endosome into the cytoplasm. It is still unclear how the interplay between acidification and HA conformation changes affects the kinetics of the viral endosomal escape. We develop here a stochastic model to estimate the change of conformation of HAs inside the endosome nanodomain. Using a Markov process, we model the arrival of protons to HA binding sites and compute the kinetics of their accumulation. We compute the Mean First Passage Time (MFPT) of the number of HA bound sites to a threshold, which is used to estimate the HA activation rate for a given pH concentration. The present analysis reveals that HA proton binding sites possess a high chemical barrier, ensuring a stability of the spike protein at sub-acidic pH. We predict that activating more than 3 adjacent HAs is necessary to trigger endosomal fusion and this configuration prevents premature release of viruses from early endosomes

  8. Development and characterization of neutralizing monoclonal antibodies against canine distemper virus hemagglutinin protein.

    Bi, Zhenwei; Xia, Xingxia; Wang, Yongshan; Mei, Yongjie

    2015-04-01

    Canine distemper virus (CDV) causes a serious multisystemic disease in dogs and other carnivora. Hemagglutinin (H) protein-specific antibodies are mainly responsible for protective immunity against CDV infection. In the present study, six neutralizing MAbs to the H protein of CDV were newly obtained and characterized by immunizing BALB/c mice with a recent Chinese field isolate. Competitive binding inhibition assay revealed that they recognized four distinct antigenic regions of the H protein. Immunofluorescence assay and western blotting showed that all MAbs recognize the conformational rather than the linear epitopes of the H protein. Furthermore, in immunofluorescence and virus neutralization assays, two of the MAbs were found to react only with the recent Chinese field isolate and not with older CDV strains, including vaccine strain Onderstepoort, indicating there are neutralization-related antigenic variations between the recent Chinese field isolate and the older CDV strains examined in this study. The newly established MAbs are useful for differentiating the expanding CDV strains and could be used in immunotherapy and immunodiagnosis against infection with CDV. © 2015 The Societies and Wiley Publishing Asia Pty Ltd.

  9. Immunization with influenza virus hemagglutinin globular region containing the receptor-binding pocket.

    Jeon, Sung Ho; Arnon, Ruth

    2002-01-01

    The globular region of hemagglutinin (residues 91-261) membrane glycoprotein of influenza virus that encompasses the binding zone to the oligosaccharide receptor of target cells has been cloned by reverse transcriptase-polymerase chain reaction (RT-PCR). This protein segment (denoted HA91-261 peptide) induced significant immune response in mice. The serum antibodies and lung homogenates from the immunized mice cross-reacted with native virus particles. The cellular immunity was manifested by proliferative splenocyte responses and cytokine release indicating T helper type 1 activity. The plasmid DNA containing this segment (denoted pHA91-261) provoked, in addition, a significant cytotoxic T lymphocyte (CTL) response, whereas the HA91-261 protein fragment led to no such response. Both the DNA and the protein fragment of HA91-261 induced significant protection against viral challenge, although the immune response they induce might be along different pathways. Interestingly, the combined DNA priming-protein boosting immunization regimen did not induce protection against viral challenges even though it led to significant humoral immune responses similar to that induced by the peptide vaccine.

  10. Modulation of the NF-kappaB pathway by Bordetella pertussis filamentous hemagglutinin.

    Tzvia Abramson

    Full Text Available Filamentous hemagglutinin (FHA is a cell-associated and secreted adhesin produced by Bordetella pertussis with pro-apoptotic and pro-inflammatory activity in host cells. Given the importance of the NF-kappaB transcription factor family in these host cell responses, we examined the effect of FHA on NF-kappaB activation in macrophages and bronchial epithelial cells, both of which are relevant cell types during natural infection.Exposure to FHA of primary human monocytes and transformed U-937 macrophages, but not BEAS-2B epithelial cells, resulted in early activation of the NF-kappaB pathway, as manifested by the degradation of cytosolic IkappaB alpha, by NF-kappaB DNA binding, and by the subsequent secretion of NF-kappaB-regulated inflammatory cytokines. However, exposure of macrophages and human monocytes to FHA for two hours or more resulted in the accumulation of cytosolic IkappaB alpha, and the failure of TNF-alpha to activate NF-kappaB. Proteasome activity was attenuated following exposure of cells to FHA for 2 hours, as was the nuclear translocation of RelA in BEAS-2B cells.These results reveal a complex temporal dynamic, and suggest that despite short term effects to the contrary, longer exposures of host cells to this secreted adhesin may block NF-kappaB activation, and perhaps lead to a compromised immune response to this bacterial pathogen.

  11. PAR-1 mediated apoptosis of breast cancer cells by V. cholerae hemagglutinin protease.

    Ray, Tanusree; Pal, Amit

    2016-05-01

    Bacterial toxins have emerged as promising agents in cancer treatment strategy. Hemagglutinin (HAP) protease secreted by Vibrio cholerae induced apoptosis in breast cancer cells and regresses tumor growth in mice model. The success of novel cancer therapies depends on their selectivity for cancer cells with limited toxicity for normal tissues. Increased expression of Protease Activated Receptor-1 (PAR-1) has been reported in different malignant cells. In this study we report that HAP induced activation and over expression of PAR-1 in breast cancer cells (EAC). Immunoprecipitation studies have shown that HAP specifically binds with PAR-1. HAP mediated activation of PAR-1 caused nuclear translocation of p50-p65 and the phosphorylation of p38 which triggered the activation of NFκB and MAP kinase signaling pathways. These signaling pathways enhanced the cellular ROS level in malignant cells that induced the intrinsic pathway of cell apoptosis. PAR-1 mediated apoptosis by HAP of malignant breast cells without effecting normal healthy cells in the same environment makes it a good therapeutic agent for treatment of cancer.

  12. Gold nanoparticles conjugating recombinant influenza hemagglutinin trimers and flagellin enhanced mucosal cellular immunity.

    Wang, Chao; Zhu, Wandi; Luo, Yuan; Wang, Bao-Zhong

    2018-04-09

    The immunogenicity of subunit vaccines can be augmented by formulating them into nanoparticles. We conjugated recombinant trimetric influenza A/Aichi/2/68(H3N2) hemagglutinin (HA) onto functionalized gold nanoparticles (AuNPs) surfaces in a repetitive, oriented configuration. To further improve the immunogenicity, we generated Toll-like receptor 5 (TLR5) agonist flagellin (FliC)-coupled AuNPs as particulate adjuvants. Intranasal immunizations with an AuNP-HA and AuNP-FliC particle mixture elicited strong mucosal and systemic immune responses that protected hosts against lethal influenza challenges. Compared with the AuNP-HA alone group, the addition of AuNP-FliC improved mucosal B cell responses as characterized by elevated influenza specific IgA and IgG levels in nasal, tracheal, and lung washes. AuNP-HA/AuNP-FliC also stimulated antigen-specific interferon-γ (IFN-γ)-secreting CD4 + cell proliferation and induced strong effector CD8 + T cell activation. Our results indicate that intranasal co-delivery of antigen and adjuvant-displaying AuNPs enhanced vaccine efficacy by inducing potent cellular immune responses. Copyright © 2018. Published by Elsevier Inc.

  13. Application of recombinant hemagglutinin proteins as alternative antigen standards for pandemic influenza vaccines.

    Choi, Yejin; Kwon, Seong Yi; Oh, Ho Jung; Shim, Sunbo; Chang, Seokkee; Chung, Hye Joo; Kim, Do Keun; Park, Younsang; Lee, Younghee

    2017-09-01

    The single radial immunodiffusion (SRID) assay, used to quantify hemagglutinin (HA) in influenza vaccines, requires reference reagents; however, because centralized production of reference reagents may slow the emergency deployment of vaccines, alternatives are needed. We investigated the production of HA proteins using recombinant DNA technology, rather than a traditional egg-based production process. The HA proteins were then used in an SRID assay as a reference antigen. We found that HA can be quantified in both egg-based and cell-based influenza vaccines when recombinant HAs (rHAs) are used as the reference antigen. Furthermore, we confirmed that rHAs obtained from strains with pandemic potential, such as H5N1, H7N3, H7N9, and H9N2 strains, can be utilized in the SRID assay. The rHA production process takes just one month, in contrast to the traditional process that takes three to four months. The use of rHAs may reduce the time required to produce reference reagents and facilitate timely introduction of vaccines during emergencies.

  14. Occurrence of mannose resistant hemagglutinins in Escherichia coli strains isolated from porcine colibacillosis.

    Truszczyński, M; Osek, J

    1987-01-01

    Three-hundred and fifty-eight E. coli strains isolated from piglets were tested for the presence of hemagglutinins by the use of the active hemagglutination test with or without mannose. Additionally 86 strains from the mentioned number of strains were investigated for the presence of common fimbriae using the same method but growing the strains in media especially suited for the development of this kind of fimbriae. These 358 strains and additionally 202 E. coli strains were tested using antisera for 987P and K88 antigens. It was found, using the active hemagglutination test, that 51.4% of the strains were hemagglutinating. The hemagglutinating strains carried the K88 antigen. All these strains were isolated from new-born and weaned piglets with enterotoxic form of colibacillosis, called also E. coli diarrhea. From cases of this form of colibacillosis originated also 26.7% of the strains in which common fimbriae (type 1) were detected. This result was obtained when the BHI medium was used for cultivation. In case of TSA medium only 2.3% of strains were positive. No specific or common fimbriae were found in strains recovered from septic form of colibacillosis and oedema disease (called also enterotoxaemic form of colibacillosis). No strain of 560 examined showed the presence of fimbrial 987P antigen.

  15. Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic

    Xu, Rui; McBride, Ryan; Nycholat, Corwin M.; Paulson, James C.; Wilson, Ian A. (Scripps)

    2012-02-13

    Influenza virus hemagglutinin (HA) is the viral envelope protein that mediates viral attachment to host cells and elicits membrane fusion. The HA receptor-binding specificity is a key determinant for the host range and transmissibility of influenza viruses. In human pandemics of the 20th century, the HA normally has acquired specificity for human-like receptors before widespread infection. Crystal structures of the H1 HA from the 2009 human pandemic (A/California/04/2009 [CA04]) in complex with human and avian receptor analogs reveal conserved recognition of the terminal sialic acid of the glycan ligands. However, favorable interactions beyond the sialic acid are found only for {alpha}2-6-linked glycans and are mediated by Asp190 and Asp225, which hydrogen bond with Gal-2 and GlcNAc-3. For {alpha}2-3-linked glycan receptors, no specific interactions beyond the terminal sialic acid are observed. Our structural and glycan microarray analyses, in the context of other high-resolution HA structures with {alpha}2-6- and {alpha}2-3-linked glycans, now elucidate the structural basis of receptor-binding specificity for H1 HAs in human and avian viruses and provide a structural explanation for the preference for {alpha}2-6 siaylated glycan receptors for the 2009 pandemic swine flu virus.

  16. The Roles of Hemagglutinin Phe-95 in Receptor Binding and Pathogenicity of Influenza B Virus

    Ni, Fengyun; Mbawuike, Innocent Nnadi; Kondrashkina, Elena; Wang, Qinghua

    2014-01-01

    Diverged ~4,000 years ago, influenza B virus has several important differences from influenza A virus, including lower receptor-binding affinity and highly restricted host range. Based on our prior structural studies, we hypothesized that a single-residue difference in the receptor-binding site of hemagglutinin (HA), Phe-95 in influenza B virus versus Tyr-98 in influenza A/H1~H15, is possibly a key determinant for the low receptor-binding affinity. Here we demonstrate that the mutation Phe95→Tyr in influenza B virus HA restores all three hydrogen bonds made by Tyr-98 in influenza A/H3 HA and has the potential to enhance receptor binding. However, the full realization of this potential is influenced by the local environment into which the mutation is introduced. The binding and replication of the recombinant viruses correlate well with the receptor-binding capabilities of HA. These results are discussed in relation to the roles of Phe-95 in receptor binding and pathogenicity of influenza B virus. PMID:24503069

  17. Evaluation of multiplex assay platforms for detection of influenza hemagglutinin subtype specific antibody responses.

    Li, Zhu-Nan; Weber, Kimberly M; Limmer, Rebecca A; Horne, Bobbi J; Stevens, James; Schwerzmann, Joy; Wrammert, Jens; McCausland, Megan; Phipps, Andrew J; Hancock, Kathy; Jernigan, Daniel B; Levine, Min; Katz, Jacqueline M; Miller, Joseph D

    2017-05-01

    Influenza hemagglutination inhibition (HI) and virus microneutralization assays (MN) are widely used for seroprevalence studies. However, these assays have limited field portability and are difficult to fully automate for high throughput laboratory testing. To address these issues, three multiplex influenza subtype-specific antibody detection assays were developed using recombinant hemagglutinin antigens in combination with Chembio, Luminex ® , and ForteBio ® platforms. Assay sensitivity, specificity, and subtype cross-reactivity were evaluated using a panel of well characterized human sera. Compared to the traditional HI, assay sensitivity ranged from 87% to 92% and assay specificity in sera collected from unexposed persons ranged from 65% to 100% across the platforms. High assay specificity (86-100%) for A(H5N1) rHA was achieved for sera from exposed or unexposed to hetorosubtype influenza HAs. In contrast, assay specificity for A(H1N1)pdm09 rHA using sera collected from A/Vietnam/1204/2004 (H5N1) vaccinees in 2008 was low (22-30%) in all platforms. Although cross-reactivity against rHA subtype proteins was observed in each assay platform, the correct subtype specific responses were identified 78%-94% of the time when paired samples were available for analysis. These results show that high throughput and portable multiplex assays that incorporate rHA can be used to identify influenza subtype specific infections. Published by Elsevier B.V.

  18. [Propensity score matching in SPSS].

    Huang, Fuqiang; DU, Chunlin; Sun, Menghui; Ning, Bing; Luo, Ying; An, Shengli

    2015-11-01

    To realize propensity score matching in PS Matching module of SPSS and interpret the analysis results. The R software and plug-in that could link with the corresponding versions of SPSS and propensity score matching package were installed. A PS matching module was added in the SPSS interface, and its use was demonstrated with test data. Score estimation and nearest neighbor matching was achieved with the PS matching module, and the results of qualitative and quantitative statistical description and evaluation were presented in the form of a graph matching. Propensity score matching can be accomplished conveniently using SPSS software.

  19. Robust matching for voice recognition

    Higgins, Alan; Bahler, L.; Porter, J.; Blais, P.

    1994-10-01

    This paper describes an automated method of comparing a voice sample of an unknown individual with samples from known speakers in order to establish or verify the individual's identity. The method is based on a statistical pattern matching approach that employs a simple training procedure, requires no human intervention (transcription, work or phonetic marketing, etc.), and makes no assumptions regarding the expected form of the statistical distributions of the observations. The content of the speech material (vocabulary, grammar, etc.) is not assumed to be constrained in any way. An algorithm is described which incorporates frame pruning and channel equalization processes designed to achieve robust performance with reasonable computational resources. An experimental implementation demonstrating the feasibility of the concept is described.

  20. Adaptive Discrete Hypergraph Matching.

    Yan, Junchi; Li, Changsheng; Li, Yin; Cao, Guitao

    2018-02-01

    This paper addresses the problem of hypergraph matching using higher-order affinity information. We propose a solver that iteratively updates the solution in the discrete domain by linear assignment approximation. The proposed method is guaranteed to converge to a stationary discrete solution and avoids the annealing procedure and ad-hoc post binarization step that are required in several previous methods. Specifically, we start with a simple iterative discrete gradient assignment solver. This solver can be trapped in an -circle sequence under moderate conditions, where is the order of the graph matching problem. We then devise an adaptive relaxation mechanism to jump out this degenerating case and show that the resulting new path will converge to a fixed solution in the discrete domain. The proposed method is tested on both synthetic and real-world benchmarks. The experimental results corroborate the efficacy of our method.

  1. Electromagnetic wave matching device

    Hirata, Yosuke; Mitsunaka, Yoshika; Hayashi, Ken-ichi; Ito, Yasuyuki.

    1997-01-01

    The present invention provides a matching device capable of increasing an efficiency of combining beams of electromagnetic waves outputted from an output window of a gyrotron which is expected for plasma heating of a thermonuclear reactor and an electromagnetic wave transmission system as high as possible. Namely, an electromagnetic wave matching device reflects beams of electromagnetic waves incident from an inlet by a plurality of phase correction mirrors and combines them to an external transmission system through an exit. In this case, the phase correction mirrors change the phase of the beams of electromagnetic waves incident to the phase correction mirrors by a predetermined amount corresponding to the position of the reflection mirrors. Then, the beams of electromagnetic waves outputted, for example, from a gyrotron can properly be shaped as desired for the intensity and the phase. As a result, combination efficiency with the transmission system can be increased. (I.S.)

  2. Structure and receptor binding preferences of recombinant hemagglutinins from avian and human H6 and H10 influenza A virus subtypes.

    Yang, Hua; Carney, Paul J; Chang, Jessie C; Villanueva, Julie M; Stevens, James

    2015-04-01

    During 2013, three new avian influenza A virus subtypes, A(H7N9), A(H6N1), and A(H10N8), resulted in human infections. While the A(H7N9) virus resulted in a significant epidemic in China across 19 provinces and municipalities, both A(H6N1) and A(H10N8) viruses resulted in only a few human infections. This study focuses on the major surface glycoprotein hemagglutinins from both of these novel human viruses. The detailed structural and glycan microarray analyses presented here highlight the idea that both A(H6N1) and A(H10N8) virus hemagglutinins retain a strong avian receptor binding preference and thus currently pose a low risk for sustained human infections. Human infections with zoonotic influenza virus subtypes continue to be a great public health concern. We report detailed structural analysis and glycan microarray data for recombinant hemagglutinins from A(H6N1) and A(H10N8) viruses, isolated from human infections in 2013, and compare them with hemagglutinins of avian origin. This is the first structural report of an H6 hemagglutinin, and our results should further the understanding of these viruses and provide useful information to aid in the continuous surveillance of these zoonotic influenza viruses. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  3. Molecular Characterizations of Surface Proteins Hemagglutinin and Neuraminidase from Recent H5Nx Avian Influenza Viruses

    Yang, Hua; Carney, Paul J.; Mishin, Vasiliy P.; Guo, Zhu; Chang, Jessie C.; Wentworth, David E.; Gubareva, Larisa V.; Stevens, James; Schultz-Cherry, S.

    2016-04-06

    ABSTRACT

    During 2014, a subclade 2.3.4.4 highly pathogenic avian influenza (HPAI) A(H5N8) virus caused poultry outbreaks around the world. In late 2014/early 2015, the virus was detected in wild birds in Canada and the United States, and these viruses also gave rise to reassortant progeny, composed of viral RNA segments (vRNAs) from both Eurasian and North American lineages. In particular, viruses were found with N1, N2, and N8 neuraminidase vRNAs, and these are collectively referred to as H5Nx viruses. In the United States, more than 48 million domestic birds have been affected. Here we present a detailed structural and biochemical analysis of the surface antigens of H5N1, H5N2, and H5N8 viruses in addition to those of a recent human H5N6 virus. Our results with recombinant hemagglutinin reveal that these viruses have a strict avian receptor binding preference, while recombinantly expressed neuraminidases are sensitive to FDA-approved and investigational antivirals. Although H5Nx viruses currently pose a low risk to humans, it is important to maintain surveillance of these circulating viruses and to continually assess future changes that may increase their pandemic potential.

    IMPORTANCEThe H5Nx viruses emerging in North America, Europe, and Asia pose a great public health concern. Here we report a molecular and structural study of the major surface proteins of several H5Nx influenza viruses. Our results improve the understanding of these new viruses and provide important information on their receptor preferences and susceptibilities to antivirals, which are central to pandemic risk assessment.

  4. Inhibition of influenza virus infection and hemagglutinin cleavage by the protease inhibitor HAI-2

    Hamilton, Brian S.; Chung, Changik; Cyphers, Soreen Y.; Rinaldi, Vera D.; Marcano, Valerie C.; Whittaker, Gary R., E-mail: grw7@cornell.edu

    2014-07-25

    Highlights: • Biochemical and cell biological analysis of HAI-2 as an inhibitor of influenza HA cleavage activation. • Biochemical and cell biological analysis of HAI-2 as an inhibitor of influenza virus infection. • Comparative analysis of HAI-2 for vesicular stomatitis virus and human parainfluenza virus type-1. • Analysis of the activity of HAI-2 in a mouse model of influenza. - Abstract: Influenza virus remains a significant concern to public health, with the continued potential for a high fatality pandemic. Vaccination and antiviral therapeutics are effective measures to circumvent influenza virus infection, however, multiple strains have emerged that are resistant to the antiviral therapeutics currently on the market. With this considered, investigation of alternative antiviral therapeutics is being conducted. One such approach is to inhibit cleavage activation of the influenza virus hemagglutinin (HA), which is an essential step in the viral replication cycle that permits viral-endosome fusion. Therefore, targeting trypsin-like, host proteases responsible for HA cleavage in vivo may prove to be an effective therapeutic. Hepatocyte growth factor activator inhibitor 2 (HAI-2) is naturally expressed in the respiratory tract and is a potent inhibitor of trypsin-like serine proteases, some of which have been determined to cleave HA. In this study, we demonstrate that HAI-2 is an effective inhibitor of cleavage of HA from the human-adapted H1 and H3 subtypes. HAI-2 inhibited influenza virus H1N1 infection in cell culture, and HAI-2 administration showed protection in a mouse model of influenza. HAI-2 has the potential to be an effective, alternative antiviral therapeutic for influenza.

  5. Structure of the parainfluenza virus 5 (PIV5 hemagglutinin-neuraminidase (HN ectodomain.

    Brett D Welch

    Full Text Available Paramyxoviruses cause a wide variety of human and animal diseases. They infect host cells using the coordinated action of two surface glycoproteins, the receptor binding protein (HN, H, or G and the fusion protein (F. HN binds sialic acid on host cells (hemagglutinin activity and hydrolyzes these receptors during viral egress (neuraminidase activity, NA. Additionally, receptor binding is thought to induce a conformational change in HN that subsequently triggers major refolding in homotypic F, resulting in fusion of virus and target cell membranes. HN is an oligomeric type II transmembrane protein with a short cytoplasmic domain and a large ectodomain comprising a long helical stalk and large globular head domain containing the enzymatic functions (NA domain. Extensive biochemical characterization has revealed that HN-stalk residues determine F specificity and activation. However, the F/HN interaction and the mechanisms whereby receptor binding regulates F activation are poorly defined. Recently, a structure of Newcastle disease virus (NDV HN ectodomain revealed the heads (NA domains in a "4-heads-down" conformation whereby two of the heads form a symmetrical interaction with two sides of the stalk. The interface includes stalk residues implicated in triggering F, and the heads sterically shield these residues from interaction with F (at least on two sides. Here we report the x-ray crystal structure of parainfluenza virus 5 (PIV5 HN ectodomain in a "2-heads-up/2-heads-down" conformation where two heads (covalent dimers are in the "down position," forming a similar interface as observed in the NDV HN ectodomain structure, and two heads are in an "up position." The structure supports a model in which the heads of HN transition from down to up upon receptor binding thereby releasing steric constraints and facilitating the interaction between critical HN-stalk residues and F.

  6. Shallow Boomerang-shaped Influenza Hemagglutinin G13A Mutant Structure Promotes Leaky Membrane Fusion*

    Lai, Alex L.; Tamm, Lukas K.

    2010-01-01

    Our previous studies showed that an angled boomerang-shaped structure of the influenza hemagglutinin (HA) fusion domain is critical for virus entry into host cells by membrane fusion. Because the acute angle of ∼105° of the wild-type fusion domain promotes efficient non-leaky membrane fusion, we asked whether different angles would still support fusion and thus facilitate virus entry. Here, we show that the G13A fusion domain mutant produces a new leaky fusion phenotype. The mutant fusion domain structure was solved by NMR spectroscopy in a lipid environment at fusion pH. The mutant adopted a boomerang structure similar to that of wild type but with a shallower kink angle of ∼150°. G13A perturbed the structure of model membranes to a lesser degree than wild type but to a greater degree than non-fusogenic fusion domain mutants. The strength of G13A binding to lipid bilayers was also intermediate between that of wild type and non-fusogenic mutants. These membrane interactions provide a clear link between structure and function of influenza fusion domains: an acute angle is required to promote clean non-leaky fusion suitable for virus entry presumably by interaction of the fusion domain with the transmembrane domain deep in the lipid bilayer. A shallower angle perturbs the bilayer of the target membrane so that it becomes leaky and unable to form a clean fusion pore. Mutants with no fixed boomerang angle interacted with bilayers weakly and did not promote any fusion or membrane perturbation. PMID:20826788

  7. Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin.

    Zhou, Yu; Wu, Chao; Zhao, Lifeng; Huang, Niu

    2014-10-01

    Hemagglutinin (HA) mediates the membrane fusion process of influenza virus through its pH-induced conformational change. However, it remains challenging to study its structure reorganization pathways in atomic details. Here, we first applied continuous constant pH molecular dynamics approach to predict the pK(a) values of titratable residues in H2 subtype HA. The calculated net-charges in HA1 globular heads increase from 0e (pH 7.5) to +14e (pH 4.5), indicating that the charge repulsion drives the detrimerization of HA globular domains. In HA2 stem regions, critical pH sensors, such as Glu103(2), His18(1), and Glu89(1), are identified to facilitate the essential structural reorganizations in the fusing pathways, including fusion peptide release and interhelical loop transition. To probe the contribution of identified pH sensors and unveil the early steps of pH-induced conformational change, we carried out conventional molecular dynamics simulations in explicit water with determined protonation state for each titratable residue in different environmental pH conditions. Particularly, energy barriers involving previously uncharacterized hydrogen bonds and hydrophobic interactions are identified in the fusion peptide release pathway. Nevertheless, comprehensive comparisons across HA family members indicate that different HA subtypes might employ diverse pH sensor groups along with different fusion pathways. Finally, we explored the fusion inhibition mechanism of antibody CR6261 and small molecular inhibitor TBHQ, and discovered a novel druggable pocket in H2 and H5 subtypes. Our results provide the underlying mechanism for the pH-driven conformational changes and also novel insight for anti-flu drug development. © 2014 Wiley Periodicals, Inc.

  8. Determinants of glycan receptor specificity of H2N2 influenza A virus hemagglutinin.

    Viswanathan, Karthik; Koh, Xiaoying; Chandrasekaran, Aarthi; Pappas, Claudia; Raman, Rahul; Srinivasan, Aravind; Shriver, Zachary; Tumpey, Terrence M; Sasisekharan, Ram

    2010-10-29

    The H2N2 subtype of influenza A virus was responsible for the Asian pandemic of 1957-58. However, unlike other subtypes that have caused pandemics such as H1N1 and H3N2, which continue to circulate among humans, H2N2 stopped circulating in the human population in 1968. Strains of H2 subtype still continue to circulate in birds and occasionally pigs and could be reintroduced into the human population through antigenic drift or shift. Such an event is a potential global health concern because of the waning population immunity to H2 hemagglutinin (HA). The first step in such a cross-species transmission and human adaptation of influenza A virus is the ability for its surface glycoprotein HA to bind to glycan receptors expressed in the human upper respiratory epithelia. Recent structural and biochemical studies have focused on understanding the glycan receptor binding specificity of the 1957-58 pandemic H2N2 HA. However, there has been considerable HA sequence divergence in the recent avian-adapted H2 strains from the pandemic H2N2 strain. Using a combination of structural modeling, quantitative glycan binding and human respiratory tissue binding methods, we systematically identify mutations in the HA from a recent avian-adapted H2N2 strain (A/Chicken/PA/2004) that make its quantitative glycan receptor binding affinity (defined using an apparent binding constant) comparable to that of a prototypic pandemic H2N2 (A/Albany/6/58) HA.

  9. Determinants of glycan receptor specificity of H2N2 influenza A virus hemagglutinin.

    Karthik Viswanathan

    Full Text Available The H2N2 subtype of influenza A virus was responsible for the Asian pandemic of 1957-58. However, unlike other subtypes that have caused pandemics such as H1N1 and H3N2, which continue to circulate among humans, H2N2 stopped circulating in the human population in 1968. Strains of H2 subtype still continue to circulate in birds and occasionally pigs and could be reintroduced into the human population through antigenic drift or shift. Such an event is a potential global health concern because of the waning population immunity to H2 hemagglutinin (HA. The first step in such a cross-species transmission and human adaptation of influenza A virus is the ability for its surface glycoprotein HA to bind to glycan receptors expressed in the human upper respiratory epithelia. Recent structural and biochemical studies have focused on understanding the glycan receptor binding specificity of the 1957-58 pandemic H2N2 HA. However, there has been considerable HA sequence divergence in the recent avian-adapted H2 strains from the pandemic H2N2 strain. Using a combination of structural modeling, quantitative glycan binding and human respiratory tissue binding methods, we systematically identify mutations in the HA from a recent avian-adapted H2N2 strain (A/Chicken/PA/2004 that make its quantitative glycan receptor binding affinity (defined using an apparent binding constant comparable to that of a prototypic pandemic H2N2 (A/Albany/6/58 HA.

  10. Molecular Evolution and Characterization of Hemagglutinin (H in Peste des Petits Ruminants Virus.

    Zhongxiang Liang

    Full Text Available Peste des Petits Ruminants (PPR is an acute, highly contagious, and febrile viral disease that affects both domestic and wild small ruminants. The disease has become a major obstacle to the development of sustainable Agriculture. Hemagglutinin (H, the envelope glycoprotein of Peste des Petits Ruminants Virus (PPRV, plays a crucial role in regulating viral adsorption and entry, thus determining pathogenicity, and release of newly produced viral particles. In order to accurately understand the epidemic of the disease and the interactions between the virus and host, we launch the work. Here, we examined H gene from all four lineages of the PPRV to investigate evolutionary and epidemiologic dynamics of PPRV by the Bayesian method. In addition, we predicted positive selection sites due to selective pressures. Finally, we studied the interaction between H protein and SLAM receptor based on homology model of the complex. Phylogenetic analysis suggested that H gene can also be used to investigate evolutionary and epidemiologic dynamics of PPRV. Positive selection analysis identified four positive selection sites in H gene, in which only one common site (aa246 was detected by two methods, suggesting strong operation structural and/or functional constraint of changes on the H protein. This target site may be of interest for future mutagenesis studies. The results of homology modeling showed PPRVHv-shSLAM binding interface and MVH-maSLAM binding interface were consistent, wherein the groove in the B4 blade and B5 of the head domain of PPRVHv bound to the AGFCC' β-sheets of the membrane-distal ectodomain of shSLAM. The binding regions could provide insight on the nature of the protein for epitope vaccine design, novel drug discovery, and rational drug design against PPRV.

  11. Quantitative characterization of glycan-receptor binding of H9N2 influenza A virus hemagglutinin.

    Karunya Srinivasan

    Full Text Available Avian influenza subtypes such as H5, H7 and H9 are yet to adapt to the human host so as to establish airborne transmission between humans. However, lab-generated reassorted viruses possessing hemagglutinin (HA and neuraminidase (NA genes from an avian H9 isolate and other genes from a human-adapted (H3 or H1 subtype acquired two amino acid changes in HA and a single amino acid change in NA that confer respiratory droplet transmission in ferrets. We previously demonstrated for human-adapted H1, H2 and H3 subtypes that quantitative binding affinity of their HA to α2→6 sialylated glycan receptors correlates with respiratory droplet transmissibility of the virus in ferrets. Such a relationship remains to be established for H9 HA. In this study, we performed a quantitative biochemical characterization of glycan receptor binding properties of wild-type and mutant forms of representative H9 HAs that were previously used in context of reassorted viruses in ferret transmission studies. We demonstrate here that distinct molecular interactions in the glycan receptor-binding site of different H9 HAs affect the glycan-binding specificity and affinity. Further we show that α2→6 glycan receptor-binding affinity of a mutant H9 HA carrying Thr-189→Ala amino acid change correlates with the respiratory droplet transmission in ferrets conferred by this change. Our findings contribute to a framework for monitoring the evolution of H9 HA by understanding effects of molecular changes in HA on glycan receptor-binding properties.

  12. Technology transfer and scale-up of the Flublok recombinant hemagglutinin (HA) influenza vaccine manufacturing process.

    Buckland, Barry; Boulanger, Robert; Fino, Mireli; Srivastava, Indresh; Holtz, Kathy; Khramtsov, Nikolai; McPherson, Clifton; Meghrous, Jamal; Kubera, Paul; Cox, Manon M J

    2014-09-22

    Multiple different hemagglutinin (HA) protein antigens have been reproducibly manufactured at the 650L scale by Protein Sciences Corporation (PSC) based on an insect cell culture with baculovirus infection. Significantly, these HA protein antigens were produced by the same Universal Manufacturing process as described in the biological license application (BLA) for the first recombinant influenza vaccine approved by the FDA (Flublok). The technology is uniquely designed so that a change in vaccine composition can be readily accommodated from one HA protein antigen to another one. Here we present a vaccine candidate to combat the recently emerged H7N9 virus as an example starting with the genetic sequence for the required HA, creation of the baculovirus and ending with purified protein antigen (or vaccine component) at the 10L scale accomplished within 38 days under GMP conditions. The same process performance is being achieved at the 2L, 10L, 100L, 650L and 2500L scale. An illustration is given of how the technology was transferred from the benchmark 650L scale facility to a retrofitted microbial facility at the 2500L scale within 100 days which includes the time for facility engineering changes. The successful development, technology transfer and scale-up of the Flublok process has major implications for being ready to make vaccine rapidly on a worldwide scale as a defense against pandemic influenza. The technology described does not have the same vulnerability to mutations in the egg adapted strain, and resulting loss in vaccine efficacy, faced by egg based manufacture. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Molecular characterization of the receptor binding structure-activity relationships of influenza B virus hemagglutinin.

    Carbone, V; Kim, H; Huang, J X; Baker, M A; Ong, C; Cooper, M A; Li, J; Rockman, S; Velkov, T

    2013-01-01

    Selectivity of α2,6-linked human-like receptors by B hemagglutinin (HA) is yet to be fully understood. This study integrates binding data with structure-recognition models to examine the impact of regional-specific sequence variations within the receptor-binding pocket on selectivity and structure activity relationships (SAR). The receptor-binding selectivity of influenza B HAs corresponding to either B/Victoria/2/1987 or the B/Yamagata/16/88 lineages was examined using surface plasmon resonance, solid-phase ELISA and gel-capture assays. Our SAR data showed that the presence of asialyl sugar units is the main determinant of receptor preference of α2,6 versus α2,3 receptor binding. Changes to the type of sialyl-glycan linkage present on receptors exhibit only a minor effect upon binding affinity. Homology-based structural models revealed that structural properties within the HA pocket, such as a glyco-conjugate at Asn194 on the 190-helix, sterically interfere with binding to avian receptor analogs by blocking the exit path of the asialyl sugars. Similarly, naturally occurring substitutions in the C-terminal region of the 190-helix and near the N-terminal end of the 140-loop narrows the horizontal borders of the binding pocket, which restricts access of the avian receptor analog LSTa. This study helps bridge the gap between ligand structure and receptor recognition for influenza B HA; and provides a consensus SAR model for the binding of human and avian receptor analogs to influenza B HA.

  14. Inhibition of influenza virus infection and hemagglutinin cleavage by the protease inhibitor HAI-2

    Hamilton, Brian S.; Chung, Changik; Cyphers, Soreen Y.; Rinaldi, Vera D.; Marcano, Valerie C.; Whittaker, Gary R.

    2014-01-01

    Highlights: • Biochemical and cell biological analysis of HAI-2 as an inhibitor of influenza HA cleavage activation. • Biochemical and cell biological analysis of HAI-2 as an inhibitor of influenza virus infection. • Comparative analysis of HAI-2 for vesicular stomatitis virus and human parainfluenza virus type-1. • Analysis of the activity of HAI-2 in a mouse model of influenza. - Abstract: Influenza virus remains a significant concern to public health, with the continued potential for a high fatality pandemic. Vaccination and antiviral therapeutics are effective measures to circumvent influenza virus infection, however, multiple strains have emerged that are resistant to the antiviral therapeutics currently on the market. With this considered, investigation of alternative antiviral therapeutics is being conducted. One such approach is to inhibit cleavage activation of the influenza virus hemagglutinin (HA), which is an essential step in the viral replication cycle that permits viral-endosome fusion. Therefore, targeting trypsin-like, host proteases responsible for HA cleavage in vivo may prove to be an effective therapeutic. Hepatocyte growth factor activator inhibitor 2 (HAI-2) is naturally expressed in the respiratory tract and is a potent inhibitor of trypsin-like serine proteases, some of which have been determined to cleave HA. In this study, we demonstrate that HAI-2 is an effective inhibitor of cleavage of HA from the human-adapted H1 and H3 subtypes. HAI-2 inhibited influenza virus H1N1 infection in cell culture, and HAI-2 administration showed protection in a mouse model of influenza. HAI-2 has the potential to be an effective, alternative antiviral therapeutic for influenza

  15. Epitope Dampening Monotypic Measles Virus Hemagglutinin Glycoprotein Results in Resistance to Cocktail of Monoclonal Antibodies

    Lech, Patrycja J.; Tobin, Gregory J.; Bushnell, Ruth; Gutschenritter, Emily; Pham, Linh D.; Nace, Rebecca; Verhoeyen, Els; Cosset, François-Loïc; Muller, Claude P.; Russell, Stephen J.; Nara, Peter L.

    2013-01-01

    The measles virus (MV) is serologically monotypic. Life-long immunity is conferred by a single attack of measles or following vaccination with the MV vaccine. This is contrary to viruses such as influenza, which readily develop resistance to the immune system and recur. A better understanding of factors that restrain MV to one serotype may allow us to predict if MV will remain monotypic in the future and influence the design of novel MV vaccines and therapeutics. MV hemagglutinin (H) glycoprotein, binds to cellular receptors and subsequently triggers the fusion (F) glycoprotein to fuse the virus into the cell. H is also the major target for neutralizing antibodies. To explore if MV remains monotypic due to a lack of plasticity of the H glycoprotein, we used the technology of Immune Dampening to generate viruses with rationally designed N-linked glycosylation sites and mutations in different epitopes and screened for viruses that escaped monoclonal antibodies (mAbs). We then combined rationally designed mutations with naturally selected mutations to generate a virus resistant to a cocktail of neutralizing mAbs targeting four different epitopes simultaneously. Two epitopes were protected by engineered N-linked glycosylations and two epitopes acquired escape mutations via two consecutive rounds of artificial selection in the presence of mAbs. Three of these epitopes were targeted by mAbs known to interfere with receptor binding. Results demonstrate that, within the epitopes analyzed, H can tolerate mutations in different residues and additional N-linked glycosylations to escape mAbs. Understanding the degree of change that H can tolerate is important as we follow its evolution in a host whose immunity is vaccine induced by genotype A strains instead of multiple genetically distinct wild-type MVs. PMID:23300970

  16. Evolutionary trends of A(H1N1 influenza virus hemagglutinin since 1918.

    Jun Shen

    2009-11-01

    Full Text Available The Pandemic (H1N1 2009 is spreading to numerous countries and causing many human deaths. Although the symptoms in humans are mild at present, fears are that further mutations in the virus could lead to a potentially more dangerous outbreak in subsequent months. As the primary immunity-eliciting antigen, hemagglutinin (HA is the major agent for host-driven antigenic drift in A(H3N2 virus. However, whether and how the evolution of HA is influenced by existing immunity is poorly understood for A(H1N1. Here, by analyzing hundreds of A(H1N1 HA sequences since 1918, we show the first evidence that host selections are indeed present in A(H1N1 HAs. Among a subgroup of human A(H1N1 HAs between 1918 approximately 2008, we found strong diversifying (positive selection at HA(1 156 and 190. We also analyzed the evolutionary trends at HA(1 190 and 225 that are critical determinants for receptor-binding specificity of A(H1N1 HA. Different A(H1N1 viruses appeared to favor one of these two sites in host-driven antigenic drift: epidemic A(H1N1 HAs favor HA(1 190 while the 1918 pandemic and swine HAs favor HA(1 225. Thus, our results highlight the urgency to understand the interplay between antigenic drift and receptor binding in HA evolution, and provide molecular signatures for monitoring future antigenically drifted 2009 pandemic and seasonal A(H1N1 influenza viruses.

  17. Matching with transfer matrices

    Perez-Alvarez, R.; Velasco, V.R.; Garcia-Moliner, F.; Rodriguez-Coppola, H.

    1987-10-01

    An ABC configuration - which corresponds to various systems of physical interest, such as a barrier or a quantum well - is studied by combining a surface Green function matching analysis of the entire system with a description of the intermediate (B) region in terms of a transfer matrix in the sense of Mora et al. (1985). This hybrid approach proves very useful when it is very difficult to construct the corresponding Green function G B . An application is made to the calculation of quantised subband levels in a parabolic quantum well. Further possibilities of extension of this approach are pointed out. (author). 27 refs, 1 tab

  18. Coaxial pulse matching transformer

    Ledenev, V.V.; Khimenko, L.T.

    1986-01-01

    This paper describes a coaxial pulse matching transformer with comparatively simple design, increased mechanical strength, and low stray inductance. The transformer design makes it easy to change the turns ratio. The circuit of the device and an expression for the current multiplication factor are presented; experiments confirm the efficiency of the transformer. Apparatus with a coaxial transformer for producing high-power pulsed magnetic fields is designed (current pulses of 1-10 MA into a load and a natural frequency of 100 kHz)

  19. Identifying antigenicity associated sites in highly pathogenic H5N1 influenza virus hemagglutinin by using sparse learning

    Cai, Zhipeng; Ducatez, Mariette F.; Yang, Jialiang; Zhang, Tong; Long, Li-Ping; Boon, Adrianus C.; Webby, Richard J.; Wan, Xiu-Feng

    2012-01-01

    Since the isolation of A/goose/Guangdong/1/1996 (H5N1) in farmed geese in southern China, highly pathogenic H5N1 avian influenza viruses have posed a continuous threat to both public and animal health. The non-synonymous mutation of the H5 hemagglutinin gene has resulted in antigenic drift, leading to difficulties in both clinical diagnosis and vaccine strain selection. Characterizing H5N1’s antigenic profiles would help resolve these problems. In this study, a novel sparse learning method wa...

  20. Identifying antigenicity-associated sites in highly pathogenic H5N1 influenza virus hemagglutinin by using sparse learning.

    Cai, Zhipeng; Yang, Jialiang; Zhang, Tong; Long, Li-Ping; Boon, Adrianus C; Webby, Richard J; Wan, Xiu-Feng

    2012-01-01

    Since the isolation of A/goose/Guangdong/1/1996 (H5N1) in farmed geese in southern China, highly pathogenic H5N1 avian influenza viruses have posed a continuous threat to both public and animal health. The non-synonymous mutation of the H5 hemagglutinin (HA) gene has resulted in antigenic drift, leading to difficulties in both clinical diagnosis and vaccine strain selection. Characterizing H5N1's antigenic profiles would help resolve these problems. In this study, a novel sparse learning meth...

  1. Plasma focus matching conditions

    Soliman, H.M.; Masoud, M.M.; Elkhalafawy, T.A.

    1988-01-01

    A snow-plough and slug models have been used to obtain the optimum matching conditions of the plasma in the focus. The dimensions of the plasma focus device are, inner electrode radius = 2 cm, outer electrode radius = 5.5 cm, and its length = 8 cm. It was found that the maximum magnetic energy of 12.26 kJ has to be delivered to plasma focus whose density is 10 19 /cm 3 at focusing time of 2.55 μs and with total external inductance of 24.2 n H. The same method is used to evaluate the optimum matching conditions for the previous coaxial discharge system which had inner electrode radius = 1.6 cm, outer electrode radius = 3.3 cm and its length = 31.5 cm. These conditions are charging voltage = 12 kV, capacity of the condenser bank = 430 μf, plasma focus density = 10 19 /cm 3 focusing time = 8 μs and total external inductance = 60.32 n H.3 fig., 2 tab

  2. Comparative study of the hemagglutinin and neuraminidase genes of influenza A virus H3N2, H9N2, and H5N1 subtypes using bioinformatics techniques.

    Ahn, Insung; Son, Hyeon S

    2007-07-01

    To investigate the genomic patterns of influenza A virus subtypes, such as H3N2, H9N2, and H5N1, we collected 1842 sequences of the hemagglutinin and neuraminidase genes from the NCBI database and parsed them into 7 categories: accession number, host species, sampling year, country, subtype, gene name, and sequence. The sequences that were isolated from the human, avian, and swine populations were extracted and stored in a MySQL database for intensive analysis. The GC content and relative synonymous codon usage (RSCU) values were calculated using JAVA codes. As a result, correspondence analysis of the RSCU values yielded the unique codon usage pattern (CUP) of each subtype and revealed no extreme differences among the human, avian, and swine isolates. H5N1 subtype viruses exhibited little variation in CUPs compared with other subtypes, suggesting that the H5N1 CUP has not yet undergone significant changes within each host species. Moreover, some observations may be relevant to CUP variation that has occurred over time among the H3N2 subtype viruses isolated from humans. All the sequences were divided into 3 groups over time, and each group seemed to have preferred synonymous codon patterns for each amino acid, especially for arginine, glycine, leucine, and valine. The bioinformatics technique we introduce in this study may be useful in predicting the evolutionary patterns of pandemic viruses.

  3. Anatomy Ontology Matching Using Markov Logic Networks

    Chunhua Li

    2016-01-01

    Full Text Available The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment.

  4. Body Weight and Matching with a Physically Attractive Romantic Partner

    Carmalt, Julie H.; Cawley, John; Joyner, Kara; Sobal, Jeffery

    2008-01-01

    Matching and attribute trade are two perspectives used to explain mate selection. We investigated patterns of matching and trade, focusing on obesity, using Add Health Romantic Pair data (N = 1,405 couples). Obese individuals, relative to healthy weight individuals, were less likely to have physically attractive partners, with this disadvantage…

  5. Different patterns in the risk of newly developed fatty liver and lipid changes with tamoxifen versus aromatase inhibitors in postmenopausal women with early breast cancer: A propensity score-matched cohort study.

    Hong, Namki; Yoon, Han Gyul; Seo, Da Hea; Park, Seho; Kim, Seung Il; Sohn, Joo Hyuk; Rhee, Yumie

    2017-09-01

    Management of metabolic complications of long-term adjuvant endocrine therapy in early breast cancer remained an unmet need. We aimed to compare the effects of tamoxifen (TMX) and aromatase inhibitors (AIs) on the risk of fatty liver in conjunction with longitudinal changes in the serum lipid parameters. Among 1203 subjects who were taking adjuvant TMX or AI (anastrozole or letrozole) without fatty liver at baseline, those taking TMX or AI were 1:1 matched on the propensity score. The primary outcome was newly developed fatty liver detected on annual liver ultrasonography. Among 328 matched subjects (mean age 53.5 years, body mass index 22.9 kg/m 2 ), 62 cases of fatty liver in the TMX group and 41 cases in the AI group were detected in a total of 987.4 person-years. The incidence rate of fatty liver was higher in the TMX group than in the AI group (128.7 versus 81.1 per 1000 person-years, P = 0.021), particularly within the first 2 years of therapy. TMX was associated with an increased 5-year risk of newly developed fatty liver (adjusted hazard ratio 1.61, P = 0.030) compared with AI independent of obesity and cholesterol level. Subjects who developed fatty liver had higher triglycerides (TGs) and lower high-density lipoprotein cholesterol (HDL-C) level at baseline than those without, which was sustained during follow-up despite the serum cholesterol-lowering effect of TMX. TMX independently increased the 5-year risk of newly developed fatty liver compared with AI in postmenopausal women with early breast cancer. Our findings suggest the need for considering the risk of fatty liver as a different adverse event profile between AI and TMX, particularly in patients with obesity, high TGs and low HDL-C. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Job Searchers, Job Matches and the Elasticity of Matching

    Broersma, L.; van Ours, J.C.

    1998-01-01

    This paper stresses the importance of a specification of the matching function in which the measure of job matches corresponds to the measure of job searchers. In many empirical studies on the matching function this requirement has not been fulfilled because it is difficult to find information about

  7. Kinetics of matching.

    Mark, T A; Gallistel, C R

    1994-01-01

    Rats responded on concurrent variable interval schedules of brain stimulation reward in 2-trial sessions. Between trials, there was a 16-fold reversal in the relative rate of reward. In successive, narrow time windows, the authors compared the ratio of the times spent on the 2 levers to the ratio of the rewards received. Time-allocation ratios tracked wide, random fluctuations in the reward ratio. The adjustment to the midsession reversal in relative rate of reward was largely completed within 1 interreward interval on the leaner schedule. Both results were unaffected by a 16-fold change in the combined rates of reward. The large, rapid, scale-invariant shifts in time-allocation ratios that underlie matching behavior imply that the subjective relative rate of reward can be determined by a very few of the most recent interreward intervals and that this estimate can directly determine the ratio of the expected stay durations.

  8. Electromagnetic wave matching device

    Hirata, Yosuke; Mitsunaka, Yoshika; Hayashi, Ken-ichi; Ito, Yasuyuki.

    1997-01-01

    The present invention provides an electromagnetic wave matching capable of reducing a cost for the transmission system in a system of using electromagnetic waves for plasma heating of a thermonuclear reactor. Namely, incident electromagnetic waves are reflected by using a plurality of phase correction mirrors. The reflected electromagnetic waves are connected to an external transmission system through an exit. The phase correction mirrors have such a shape to receive a plurality of beam-like electromagnetic waves and output electromagnetic waves by the number different from the number of the received electromagnetic wave beams having a predetermined distribution. Further, at least two of the phase correction mirrors have such a shape to change the phase of the electromagnetic waves beams incident to the reflection surface of the phase correction mirrors by a predetermined amount corresponding to the position of the reflection surface. Then, the cost for transmission system can greatly be reduced. (I.S.)

  9. Quantity precommitment and price matching

    Tumennasan, Norovsambuu

    We revisit the question of whether price matching is anti-competitive in a capacity constrained duopoly setting. We show that the effect of price matching depends on capacity. Specifically, price matching has no effect when capacity is relatively low, but it benefits the firms when capacity...... is relatively high. Interestingly, when capacity is in an intermediate range, price matching benefits only the small firm but does not affect the large firm in any way. Therefore, one has to consider capacity seriously when evaluating if price matching is anti-competitive. If the firms choose their capacities...... simultaneously before pricing decisions, then the effect of price matching is either pro-competitive or ambiguous. We show that if the cost of capacity is high, then price matching can only (weakly) decrease the market price. On the other hand, if the cost of capacity is low, then the effect of price matching...

  10. Iris Matching Based on Personalized Weight Map.

    Dong, Wenbo; Sun, Zhenan; Tan, Tieniu

    2011-09-01

    Iris recognition typically involves three steps, namely, iris image preprocessing, feature extraction, and feature matching. The first two steps of iris recognition have been well studied, but the last step is less addressed. Each human iris has its unique visual pattern and local image features also vary from region to region, which leads to significant differences in robustness and distinctiveness among the feature codes derived from different iris regions. However, most state-of-the-art iris recognition methods use a uniform matching strategy, where features extracted from different regions of the same person or the same region for different individuals are considered to be equally important. This paper proposes a personalized iris matching strategy using a class-specific weight map learned from the training images of the same iris class. The weight map can be updated online during the iris recognition procedure when the successfully recognized iris images are regarded as the new training data. The weight map reflects the robustness of an encoding algorithm on different iris regions by assigning an appropriate weight to each feature code for iris matching. Such a weight map trained by sufficient iris templates is convergent and robust against various noise. Extensive and comprehensive experiments demonstrate that the proposed personalized iris matching strategy achieves much better iris recognition performance than uniform strategies, especially for poor quality iris images.

  11. An induced pocket for the binding of potent fusion inhibitor CL-385319 with H5N1 influenza virus hemagglutinin.

    Runming Li

    Full Text Available The influenza glycoprotein hemagglutinin (HA plays crucial roles in the early stage of virus infection, including receptor binding and membrane fusion. Therefore, HA is a potential target for developing anti-influenza drugs. Recently, we characterized a novel inhibitor of highly pathogenic H5N1 influenza virus, CL-385319, which specifically inhibits HA-mediated viral entry. Studies presented here identified the critical binding residues for CL-385319, which clustered in the stem region of the HA trimer by site-directed mutagenesis. Extensive computational simulations, including molecular docking, molecular dynamics simulations, molecular mechanics generalized Born surface area (MM_GBSA calculations, charge density and Laplacian calculations, have been carried out to uncover the detailed molecular mechanism that underlies the binding of CL-385319 to H5N1 influenza virus HA. It was found that the recognition and binding of CL-385319 to HA proceeds by a process of "induced fit" whereby the binding pocket is formed during their interaction. Occupation of this pocket by CL-385319 stabilizes the neutral pH structure of hemagglutinin, thus inhibiting the conformational rearrangements required for membrane fusion. This "induced fit" pocket may be a target for structure-based design of more potent influenza fusion inhibitors.

  12. Spatial competition with intermediated matching

    van Raalte, C.L.J.P.; Webers, H.M.

    1995-01-01

    This paper analyzes the spatial competition in commission fees between two match makers. These match makers serve as middlemen between buyers and sellers who are located uniformly on a circle. The profits of the match makers are determined by their respective market sizes. A limited willingness to

  13. Molecular signatures of hemagglutinin stem-directed heterosubtypic human neutralizing antibodies against influenza A viruses.

    Yuval Avnir

    2014-05-01

    Full Text Available Recent studies have shown high usage of the IGHV1-69 germline immunoglobulin gene for influenza hemagglutinin stem-directed broadly-neutralizing antibodies (HV1-69-sBnAbs. Here we show that a major structural solution for these HV1-69-sBnAbs is achieved through a critical triad comprising two CDR-H2 loop anchor residues (a hydrophobic residue at position 53 (Ile or Met and Phe54, and CDR-H3-Tyr at positions 98±1; together with distinctive V-segment CDR amino acid substitutions that occur in positions sparse in AID/polymerase-η recognition motifs. A semi-synthetic IGHV1-69 phage-display library screen designed to investigate AID/polη restrictions resulted in the isolation of HV1-69-sBnAbs that featured a distinctive Ile52Ser mutation in the CDR-H2 loop, a universal CDR-H3 Tyr at position 98 or 99, and required as little as two additional substitutions for heterosubtypic neutralizing activity. The functional importance of the Ile52Ser mutation was confirmed by mutagenesis and by BCR studies. Structural modeling suggests that substitution of a small amino acid at position 52 (or 52a facilitates the insertion of CDR-H2 Phe54 and CDR-H3-Tyr into adjacent pockets on the stem. These results support the concept that activation and expansion of a defined subset of IGHV1-69-encoded B cells to produce potent HV1-69-sBnAbs does not necessarily require a heavily diversified V-segment acquired through recycling/reentry into the germinal center; rather, the incorporation of distinctive amino acid substitutions by Phase 2 long-patch error-prone repair of AID-induced mutations or by random non-AID SHM events may be sufficient. We propose that these routes of B cell maturation should be further investigated and exploited as a pathway for HV1-69-sBnAb elicitation by vaccination.

  14. Diagnostic potential of recombinant scFv antibodies generated against hemagglutinin protein of influenza A virus

    Roopali eRajput

    2015-09-01

    Full Text Available Human influenza A viruses have been the cause of enormous socio-economic losses worldwide. In order to combat such a notorious pathogen, hemagglutinin protein (HA has been a preferred target for generation of neutralizing-antibodies, as potent therapeutic/ diagnostic agents. In the present study, recombinant anti-HA single chain variable fragment (scFv antibodies were constructed using the phage display technology to aid in diagnosis and treatment of human influenza A virus infections. Spleen cells of mice hyper-immunized with A/New Caledonia/20/99 (H1N1 virus were used as the source for recombinant antibody (rAb production. The antigen-binding phages were quantified after 6 rounds of bio-panning against A/New Caledonia/20/99 (H1N1, A/California/07/2009 (H1N1-like, or A/Udorn/307/72(H3N2 viruses. The phage yield was maximum for the A/New Caledonia/20/99 (H1N1, however, considerable cross-reactivity was observed for the other virus strains as well. The HA-specific polyclonal rAb preparation was subjected to selection of single clones for identification of high reactive relatively conserved epitopes. The high affinity rAbs were tested against certain known conserved HA epitopes by peptide ELISA. Three recombinant mAbs showed reactivity with both the H1N1 strains and one (C5 showed binding with all the three viral strains. The C5 antibody was thus used for development of an ELISA test for diagnosis of influenza virus infection. Based on the sample size in the current analysis, the ELISA test demonstrated 83.9% sensitivity and 100% specificity. Thus, the ELISA, developed in our study, may prove as a cheaper alternative to the presently used real time RT-PCR test for detection of human influenza A viruses in clinical specimens, which will be beneficial, especially in the developing countries. Since, the two antibodies identified in this study are reactive to conserved HA epitopes; these may prove as potential therapeutic agents as well.

  15. Evidence from lateral mobility studies for dynamic interactions of a mutant influenza hemagglutinin with coated pits.

    Fire, E; Zwart, D E; Roth, M G; Henis, Y I

    1991-12-01

    Replacement of cysteine at position 543 by tyrosine in the influenza virus hemagglutinin (HA) protein enables the endocytosis of the mutant protein (Tyr 543) through coated pits (Lazarovits, J., and M. G. Roth. 1988. Cell. 53:743-752). To investigate the interactions between Tyr 543 and the clathrin coats in the plasma membrane of live cells, we performed fluorescence photobleaching recovery measurements comparing the lateral mobilities of Tyr 543 (which enters coated pits) and wild-type HA (HA wt, which is excluded from coated pits), following their expression in CV-1 cells by SV-40 vectors. While both proteins exhibited the same high mobile fractions, the lateral diffusion rate of Tyr 543 was significantly slower than that of HA wt. Incubation of the cells in a sucrose-containing hypertonic medium, a treatment that disperses the membrane-associated coated pits, resulted in similar lateral mobilities for Tyr 543 and HA wt. These findings indicate that the lateral motion of Tyr 543 (but not of HA wt) is inhibited by transient interactions with coated pits (which are essentially immobile on the time scale of the lateral mobility measurements). Acidification of the cytoplasm by prepulsing the cells with NH4Cl (a treatment that arrests the pinching-off of coated vesicles from the plasma membrane and alters the clathrin lattice morphology) led to immobilization of a significant part of the Tyr 543 molecules, presumably due to their entrapment in coated pits for the entire duration of the lateral mobility measurement. Furthermore, in both untreated and cytosol-acidified cells, the restrictions on Tyr 543 mobility were less pronounced in the cold, suggesting that the mobility-restricting interactions are temperature dependent and become weaker at low temperatures. From these studies we conclude the following. (a) Lateral mobility measurements are capable of detecting interactions of transmembrane proteins with coated pits in intact cells. (b) The interactions of Tyr 543

  16. Acid Stability of the Hemagglutinin Protein Regulates H5N1 Influenza Virus Pathogenicity

    DuBois, Rebecca M.; Zaraket, Hassan; Reddivari, Muralidhar; Heath, Richard J.; White, Stephen W.; Russell, Charles J. (Tennessee-HSC); (SJCH)

    2012-12-10

    Highly pathogenic avian influenza viruses of the H5N1 subtype continue to threaten agriculture and human health. Here, we use biochemistry and x-ray crystallography to reveal how amino-acid variations in the hemagglutinin (HA) protein contribute to the pathogenicity of H5N1 influenza virus in chickens. HA proteins from highly pathogenic (HP) A/chicken/Hong Kong/YU562/2001 and moderately pathogenic (MP) A/goose/Hong Kong/437-10/1999 isolates of H5N1 were found to be expressed and cleaved in similar amounts, and both proteins had similar receptor-binding properties. However, amino-acid variations at positions 104 and 115 in the vestigial esterase sub-domain of the HA1 receptor-binding domain (RBD) were found to modulate the pH of HA activation such that the HP and MP HA proteins are activated for membrane fusion at pH 5.7 and 5.3, respectively. In general, an increase in H5N1 pathogenicity in chickens was found to correlate with an increase in the pH of HA activation for mutant and chimeric HA proteins in the observed range of pH 5.2 to 6.0. We determined a crystal structure of the MP HA protein at 2.50 {angstrom} resolution and two structures of HP HA at 2.95 and 3.10 {angstrom} resolution. Residues 104 and 115 that modulate the acid stability of the HA protein are situated at the N- and C-termini of the 110-helix in the vestigial esterase sub-domain, which interacts with the B loop of the HA2 stalk domain. Interactions between the 110-helix and the stalk domain appear to be important in regulating HA protein acid stability, which in turn modulates influenza virus replication and pathogenesis. Overall, an optimal activation pH of the HA protein is found to be necessary for high pathogenicity by H5N1 influenza virus in avian species.

  17. Positive Selection on Hemagglutinin and Neuraminidase Genes of H1N1 Influenza Viruses

    Li, Wenfu

    2011-04-21

    Abstract Background Since its emergence in March 2009, the pandemic 2009 H1N1 influenza A virus has posed a serious threat to public health. To trace the evolutionary path of these new pathogens, we performed a selection-pressure analysis of a large number of hemagglutinin (HA) and neuraminidase (NA) gene sequences of H1N1 influenza viruses from different hosts. Results Phylogenetic analysis revealed that both HA and NA genes have evolved into five distinct clusters, with further analyses indicating that the pandemic 2009 strains have experienced the strongest positive selection. We also found evidence of strong selection acting on the seasonal human H1N1 isolates. However, swine viruses from North America and Eurasia were under weak positive selection, while there was no significant evidence of positive selection acting on the avian isolates. A site-by-site analysis revealed that the positively selected sites were located in both of the cleaved products of HA (HA1 and HA2), as well as NA. In addition, the pandemic 2009 strains were subject to differential selection pressures compared to seasonal human, North American swine and Eurasian swine H1N1 viruses. Conclusions Most of these positively and\\/or differentially selected sites were situated in the B-cell and\\/or T-cell antigenic regions, suggesting that selection at these sites might be responsible for the antigenic variation of the viruses. Moreover, some sites were also associated with glycosylation and receptor-binding ability. Thus, selection at these positions might have helped the pandemic 2009 H1N1 viruses to adapt to the new hosts after they were introduced from pigs to humans. Positive selection on position 274 of NA protein, associated with drug resistance, might account for the prevalence of drug-resistant variants of seasonal human H1N1 influenza viruses, but there was no evidence that positive selection was responsible for the spread of the drug resistance of the pandemic H1N1 strains.

  18. Organizations must match assets

    Carley, G.R.

    1991-01-01

    The unprofitable state of the Canadian oil industry, the adverse economic environment, the difficulty of finding capital, and the diminishing resources of conventional lighter crude oil make it necessary for Canadian oil companies to match their organizations and their financing to their assets. This is illustrated according to the experience of Saskoil, a Saskatchewan oil and gas company. An increasing production of oil and natural gas, and an increasing amount of new oil production as heavy oil, led to organizational changes such as the purchase of an asphalt plant to provide the company with downstream experience, establishing a working group to explore and develop heavy oil resources, and forming a company to manage non-core assets. The latter company, Pasqua Resources, manages assets such as small properties and ownership interests in order to increase the operating efficiency of Saskoil. Pasqua provides Saskoil with a corporate and organizational vehicle to accommodate partnerships and joint venture capital invested in property purchase opportunities, and to manage any of Saskoil's divestiture activities

  19. Examining the hemagglutinin subtype diversity among wild duck-origin influenza A viruses using ethanol-fixed cloacal swabs and a novel RT-PCR method.

    Wang, Ruixue; Soll, Lindsey; Dugan, Vivien; Runstadler, Jonathan; Happ, George; Slemons, Richard D; Taubenberger, Jeffery K

    2008-05-25

    This study presents an interconnected approach for circumventing two inherent limitations associated with studies defining the natural history of influenza A viruses in wild birds. The first limiting factor is the ability to maintain a cold chain from specimen collection to the laboratory when study sites are in more remote locations. The second limiting factor is the ability to identify all influenza A virus HA subtypes present in an original sample. We report a novel method for molecular subtyping of avian influenza A virus hemagglutinin genes using degenerate primers designed to amplify all known hemagglutinin subtypes. It was shown previously that templates larger than 200 bp were not consistently amplifiable from ethanol-fixed cloacal swabs. For this study, new primer sets were designed within these constraints. This method was used to perform subtyping RT-PCR on 191 influenza RNA-positive ethanol-fixed cloacal swabs obtained from 880 wild ducks in central Alaska in 2005. Seven different co-circulating hemagglutinin subtypes were identified in this study set, including H1, H3, H4, H5, H6, H8, and H12. In addition, 16% of original cloacal samples showed evidence of mixed infection, with samples yielding from two-to-five different hemagglutinin subtypes. This study further demonstrates the complex ecobiology of avian influenza A viruses in wild birds.

  20. An Immunosensor Based on Antibody Binding Fragments Attached to Gold Nanoparticles for the Detection of Peptides Derived from Avian Influenza Hemagglutinin H5

    Urszula Jarocka

    2014-08-01

    Full Text Available This paper concerns the development of an immunosensor for detection of peptides derived from avian influenza hemagglutinin H5. Its preparation consists of successive gold electrode modification steps: (i modification with 1,6-hexanedithiol and gold colloidal nanoparticles; (ii immobilization of antibody-binding fragments (Fab’ of anti-hemagglutinin H5 monoclonal antibodies Mab 6-9-1 via S-Au covalent bonds; and (iii covering the remaining free space on the electrode surfaces with bovine serum albumin. The interactions between Fab’ fragments and hemagglutinin (HA variants have been explored with electrochemical impedance spectroscopy (EIS in the presence of [Fe(CN6]3−/4− as an electroactive marker. The immunosensor was able to recognize three different His-tagged variants of recombinant hemagglutinin from H5N1 viruses: H1 subunit (17–340 residues of A/swan/Poland/305-135V08/2006, the long HA (17–530 residues A/Bar-headed Goose/Qinghai/12/2005 and H1 subunit (1–345 residues of A/Vietnam/1194/2004. The strongest response has been observed for the long variant with detection limit of 2.2 pg/mL and dynamic range from 4.0 to 20.0 pg/mL.

  1. DOE Matching Grant Program

    Tsoukalas, L.

    2002-01-01

    Funding used to support a portion of the Nuclear Engineering Educational Activities. Upgrade of teaching labs, student support to attend professional conferences, salary support for graduate students. The US Department of Energy (DOE) has funded Purdue University School of Nuclear Engineering during the period of five academic years covered in this report starting in the academic year 1996-97 and ending in the academic year 2000-2001. The total amount of funding for the grant received from DOE is $416K. In the 1990's, Nuclear Engineering Education in the US experienced a significant slow down. Student enrollment, research support, number of degrees at all levels (BS, MS, and PhD), number of accredited programs, University Research and Training Reactors, all went through a decline to alarmingly low levels. Several departments closed down, while some were amalgamated with other academic units (Mechanical Engineering, Chemical Engineering, etc). The School of Nuclear Engineering at Purdue University faced a major challenge when in the mid 90's our total undergraduate enrollment for the Sophomore, Junior and Senior Years dropped in the low 30's. The DOE Matching Grant program greatly strengthened Purdue's commitment to the Nuclear Engineering discipline and has helped to dramatically improve our undergraduate and graduate enrollment, attract new faculty and raise the School of Nuclear Engineering status within the University and in the National scene (our undergraduate enrollment has actually tripled and stands at an all time high of over 90 students; total enrollment currently exceeds 110 students). In this final technical report we outline and summarize how the grant was expended at Purdue University

  2. Most Recent Match Queries in On-Line Suffix Trees

    Larsson, N. Jesper

    2014-01-01

    A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the problem of locating a most recent match: supporting queries...

  3. Matching theory for wireless networks

    Han, Zhu; Saad, Walid

    2017-01-01

    This book provides the fundamental knowledge of the classical matching theory problems. It builds up the bridge between the matching theory and the 5G wireless communication resource allocation problems. The potentials and challenges of implementing the semi-distributive matching theory framework into the wireless resource allocations are analyzed both theoretically and through implementation examples. Academics, researchers, engineers, and so on, who are interested in efficient distributive wireless resource allocation solutions, will find this book to be an exceptional resource. .

  4. Probability matching and strategy availability

    J. Koehler, Derek; Koehler, Derek J.; James, Greta

    2010-01-01

    Findings from two experiments indicate that probability matching in sequential choice arises from an asymmetry in strategy availability: The matching strategy comes readily to mind, whereas a superior alternative strategy, maximizing, does not. First, compared with the minority who spontaneously engage in maximizing, the majority of participants endorse maximizing as superior to matching in a direct comparison when both strategies are described. Second, when the maximizing strategy is brought...

  5. An Incentive Theory of Matching

    Brown, Alessio J. G.; Merkl, Christian; Snower, Dennis J.

    2010-01-01

    This paper examines the labour market matching process by distinguishing its two component stages: the contact stage, in which job searchers make contact with employers and the selection stage, in which they decide whether to match. We construct a theoretical model explaining two-sided selection through microeconomic incentives. Firms face adjustment costs in responding to heterogeneous variations in the characteristics of workers and jobs. Matches and separations are described through firms'...

  6. Immunization with plasmid DNA encoding the hemagglutinin and the nucleoprotein confers robust protection against a lethal canine distemper virus challenge.

    Dahl, Lotte; Jensen, Trine Hammer; Gottschalck, Elisabeth; Karlskov-Mortensen, Peter; Jensen, Tove Dannemann; Nielsen, Line; Andersen, Mads Klindt; Buckland, Robin; Wild, T Fabian; Blixenkrone-Møller, Merete

    2004-09-09

    We have investigated the protective effect of immunization of a highly susceptible natural host of canine distemper virus (CDV) with DNA plasmids encoding the viral nucleoprotein (N) and hemagglutinin (H). The combined intradermal and intramuscular routes of immunization elicited high virus-neutralizing serum antibody titres in mink (Mustela vison). To mimic natural exposure, we also conducted challenge infection by horizontal transmission from infected contact animals. Other groups received a lethal challenge infection by administration to the mucosae of the respiratory tract and into the muscle. One of the mink vaccinated with N plasmid alone developed severe disease after challenge. In contrast, vaccination with the H plasmid together with the N plasmid conferred solid protection against disease and we were unable to detect CDV infection in PBMCs or in different tissues after challenge. Our findings show that DNA immunization by the combined intradermal and intramuscular routes can confer solid protective immunity against naturally transmitted morbillivirus infection and disease.

  7. Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

    Mochizuki, Yuji; Yamashita, Katsumi; Fukuzawa, Kaori; Takematsu, Kazutomo; Watanabe, Hirofumi; Taguchi, Naoki; Okiyama, Yoshio; Tsuboi, Misako; Nakano, Tatsuya; Tanaka, Shigenori

    2010-06-01

    Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order Møller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore.

  8. Systemic and oral immunogenicity of hemagglutinin protein of rinderpest virus expressed by transgenic peanut plants in a mouse model

    Khandelwal, Abha; Renukaradhya, G.J.; Rajasekhar, M.; Sita, G. Lakshmi; Shaila, M.S.

    2004-01-01

    Rinderpest causes a devastating disease, often fatal, in wild and domestic ruminants. It has been eradicated successfully using a live, attenuated vaccine from most part of the world leaving a few foci of disease in parts of Africa, the Middle East, and South Asia. We have developed transgenic peanut (Arachis hypogaea L.) plants expressing hemagglutinin (H) protein of rinderpest virus (RPV), which is antigenically authentic. In this work, we have evaluated the immunogenicity of peanut-expressed H protein using mouse model, administered parenterally as well as orally. Intraperitoneal immunization of mice with the transgenic peanut extract elicited antibody response specific to H. These antibodies neutralized virus infectivity in vitro. Oral immunization of mice with transgenic peanut induced H-specific serum IgG and IgA antibodies. The systemic and oral immunogenicity of plant-derived H in absence of any adjuvant indicates the potential of edible vaccine for rinderpest

  9. Cell-to-Cell Measles Virus Spread between Human Neurons Is Dependent on Hemagglutinin and Hyperfusogenic Fusion Protein.

    Sato, Yuma; Watanabe, Shumpei; Fukuda, Yoshinari; Hashiguchi, Takao; Yanagi, Yusuke; Ohno, Shinji

    2018-03-15

    Measles virus (MV) usually causes acute infection but in rare cases persists in the brain, resulting in subacute sclerosing panencephalitis (SSPE). Since human neurons, an important target affected in the disease, do not express the known MV receptors (signaling lymphocyte activation molecule [SLAM] and nectin 4), how MV infects neurons and spreads between them is unknown. Recent studies have shown that many virus strains isolated from SSPE patients possess substitutions in the extracellular domain of the fusion (F) protein which confer enhanced fusion activity. Hyperfusogenic viruses with such mutations, unlike the wild-type MV, can induce cell-cell fusion even in SLAM- and nectin 4-negative cells and spread efficiently in human primary neurons and the brains of animal models. We show here that a hyperfusogenic mutant MV, IC323-F(T461I)-EGFP (IC323 with a fusion-enhancing T461I substitution in the F protein and expressing enhanced green fluorescent protein), but not the wild-type MV, spreads in differentiated NT2 cells, a widely used human neuron model. Confocal time-lapse imaging revealed the cell-to-cell spread of IC323-F(T461I)-EGFP between NT2 neurons without syncytium formation. The production of virus particles was strongly suppressed in NT2 neurons, also supporting cell-to-cell viral transmission. The spread of IC323-F(T461I)-EGFP was inhibited by a fusion inhibitor peptide as well as by some but not all of the anti-hemagglutinin antibodies which neutralize SLAM- or nectin-4-dependent MV infection, suggesting the presence of a distinct neuronal receptor. Our results indicate that MV spreads in a cell-to-cell manner between human neurons without causing syncytium formation and that the spread is dependent on the hyperfusogenic F protein, the hemagglutinin, and the putative neuronal receptor for MV. IMPORTANCE Measles virus (MV), in rare cases, persists in the human central nervous system (CNS) and causes subacute sclerosing panencephalitis (SSPE) several

  10. Yeast expressed recombinant Hemagglutinin protein of Novel H1N1 elicits neutralising antibodies in rabbits and mice

    Athmaram TN

    2011-11-01

    Full Text Available Abstract Currently available vaccines for the pandemic Influenza A (H1N1 2009 produced in chicken eggs have serious impediments viz limited availability, risk of allergic reactions and the possible selection of sub-populations differing from the naturally occurring virus, whereas the cell culture derived vaccines are time consuming and may not meet the demands of rapid global vaccination required to combat the present/future pandemic. Hemagglutinin (HA based subunit vaccine for H1N1 requires the HA protein in glycosylated form, which is impossible with the commonly used bacterial expression platform. Additionally, bacterial derived protein requires extensive purification and refolding steps for vaccine applications. For these reasons an alternative heterologous system for rapid, easy and economical production of Hemagglutinin protein in its glycosylated form is required. The HA gene of novel H1N1 A/California/04/2009 was engineered for expression in Pichia pastoris as a soluble secreted protein. The full length HA- synthetic gene having α-secretory tag was integrated into P. pastoris genome through homologous recombination. The resultant Pichia clones having multiple copy integrants of the transgene expressed full length HA protein in the culture supernatant. The Recombinant yeast derived H1N1 HA protein elicited neutralising antibodies both in mice and rabbits. The sera from immunised animals also exhibited Hemagglutination Inhibition (HI activity. Considering the safety, reliability and also economic potential of Pichia expression platform, our preliminary data indicates the feasibility of using this system as an alternative for large-scale production of recombinant influenza HA protein in the face of influenza pandemic threat.

  11. DOE Matching Grant Program; FINAL

    Dr Marvin Adams

    2002-01-01

    OAK 270 - The DOE Matching Grant Program provided$50,000.00 to the Dept of N.E. at TAMU, matching a gift of$50,000.00 from TXU Electric. The$100,000.00 total was spent on scholarships, departmental labs, and computing network

  12. Matching score based face recognition

    Boom, B.J.; Beumer, G.M.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.

    2006-01-01

    Accurate face registration is of vital importance to the performance of a face recognition algorithm. We propose a new method: matching score based face registration, which searches for optimal alignment by maximizing the matching score output of a classifier as a function of the different

  13. Platform pricing in matching markets

    Goos, M.; van Cayseele, P.; Willekens, B.

    2011-01-01

    This paper develops a simple model of monopoly platform pricing accounting for two pertinent features of matching markets. 1) The trading process is characterized by search and matching frictions implying limits to positive cross-side network effects and the presence of own-side congestion.

  14. Statistical methods for history matching

    Johansen, Kent

    Denne afhandling beskriver statistiske metoder til history matching af olieproduktion. History matching er en vigtig del af driften af et oliefelt og er ofte forbundet med problemer relateret til kompleksiteten af reservoiret og selve størrelsen af reservoirsimuleringsmodellen. Begrebet history m...

  15. Role model and prototype matching

    Lykkegaard, Eva; Ulriksen, Lars

    2016-01-01

    ’ meetings with the role models affected their thoughts concerning STEM students and attending university. The regular self-to-prototype matching process was shown in real-life role-models meetings to be extended to a more complex three-way matching process between students’ self-perceptions, prototype...

  16. Efficient line matching with homography

    Shen, Yan; Dai, Yuxing; Zhu, Zhiliang

    2018-03-01

    In this paper, we propose a novel approach to line matching based on homography. The basic idea is to use cheaply obtainable matched points to boost the similarity between two images. Two types of homography method, which are estimated by direct linear transformation, transform images and extract their similar parts, laying a foundation for the use of optical flow tracking. The merit of the similarity is that rapid matching can be achieved by regionalizing line segments and local searching. For multiple homography estimation that can perform better than one global homography, we introduced the rank-one modification method of singular value decomposition to reduce the computation cost. The proposed approach results in point-to-point matches, which can be utilized with state-of-the-art point-match-based structures from motion (SfM) frameworks seamlessly. The outstanding performance and feasible robustness of our approach are demonstrated in this paper.

  17. Haptic spatial matching in near peripersonal space.

    Kaas, Amanda L; Mier, Hanneke I van

    2006-04-01

    Research has shown that haptic spatial matching at intermanual distances over 60 cm is prone to large systematic errors. The error pattern has been explained by the use of reference frames intermediate between egocentric and allocentric coding. This study investigated haptic performance in near peripersonal space, i.e. at intermanual distances of 60 cm and less. Twelve blindfolded participants (six males and six females) were presented with two turn bars at equal distances from the midsagittal plane, 30 or 60 cm apart. Different orientations (vertical/horizontal or oblique) of the left bar had to be matched by adjusting the right bar to either a mirror symmetric (/ \\) or parallel (/ /) position. The mirror symmetry task can in principle be performed accurately in both an egocentric and an allocentric reference frame, whereas the parallel task requires an allocentric representation. Results showed that parallel matching induced large systematic errors which increased with distance. Overall error was significantly smaller in the mirror task. The task difference also held for the vertical orientation at 60 cm distance, even though this orientation required the same response in both tasks, showing a marked effect of task instruction. In addition, men outperformed women on the parallel task. Finally, contrary to our expectations, systematic errors were found in the mirror task, predominantly at 30 cm distance. Based on these findings, we suggest that haptic performance in near peripersonal space might be dominated by different mechanisms than those which come into play at distances over 60 cm. Moreover, our results indicate that both inter-individual differences and task demands affect task performance in haptic spatial matching. Therefore, we conclude that the study of haptic spatial matching in near peripersonal space might reveal important additional constraints for the specification of adequate models of haptic spatial performance.

  18. The urology residency matching program in practice.

    Teichman, J M; Anderson, K D; Dorough, M M; Stein, C R; Optenberg, S A; Thompson, I M

    2000-06-01

    We evaluate behaviors and attitudes among resident applicants and program directors related to the American Urological Association (AUA) residency matching program and recommend changes to improve the match. Written questionnaires were mailed to 519 resident applicants and 112 program directors after the 1999 American Urological Association match. Subjects were asked about their observations, behaviors and opinions towards the match. Questionnaires were returned by 230 resident applicants and 94 program directors (44% and 83% response rates, respectively.) Of the resident applicants 75% spent $1,001 to $5,000 for interviewing. Of the program directors 47% recalled that applicants asked how programs would rank the applicant and 61% of applicants recalled that program directors asked applicants how they would rank programs. Dishonesty was acknowledged by 31% of program directors and 44% of resident applicants. Of program directors 82% thought applicants "lied", while 67% of applicants thought that programs "lied" (quotations indicate questionnaire language). Participants characterized their own dishonesty as "just playing the game" or they "did not feel badly." Of program directors 81% and of applicants 61% were "skeptical" or "did not believe" when informed they were a "high" or "number 1" selection. Being asked about marital status was recalled by 91% of male and 100% of female (p = 0. 02), if they had children by 53% of male and 67% of female, (p = 0. 03), and intent to have children by 25% of male and 62% of female (p match code rules frequently. Program directors and resident applicants are skeptical of each other. Patterns of faculty behavior differ based on applicant gender. Interviews are costly for applicants. We recommend that 1) programs adopt policies to enhance fairness, 2) applications be filed electronically, 3) programs assist resident applicants with interview accommodation to reduce financial burden and 4) a post-interview code of limited or

  19. The match-to-match variation of match-running in elite female soccer.

    Trewin, Joshua; Meylan, César; Varley, Matthew C; Cronin, John

    2018-02-01

    The purpose of this study was to examine the match-to-match variation of match-running in elite female soccer players utilising GPS, using full-match and rolling period analyses. Longitudinal study. Elite female soccer players (n=45) from the same national team were observed during 55 international fixtures across 5 years (2012-2016). Data was analysed using a custom built MS Excel spreadsheet as full-matches and using a rolling 5-min analysis period, for all players who played 90-min matches (files=172). Variation was examined using co-efficient of variation and 90% confidence limits, calculated following log transformation. Total distance per minute exhibited the smallest variation when both the full-match and peak 5-min running periods were examined (CV=6.8-7.2%). Sprint-efforts were the most variable during a full-match (CV=53%), whilst high-speed running per minute exhibited the greatest variation in the post-peak 5-min period (CV=143%). Peak running periods were observed as slightly more variable than full-match analyses, with the post-peak period very-highly variable. Variability of accelerations (CV=17%) and Player Load (CV=14%) was lower than that of high-speed actions. Positional differences were also present, with centre backs exhibiting the greatest variation in high-speed movements (CV=41-65%). Practitioners and researchers should account for within player variability when examining match performances. Identification of peak running periods should be used to assist worst case scenarios. Whilst micro-sensor technology should be further examined as to its viable use within match-analyses. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  20. Speed-up Template Matching through Integral Image based Weak Classifiers

    Wu, t.; Toet, A.

    2014-01-01

    Template matching is a widely used pattern recognition method, especially in industrial inspection. However, the computational costs of traditional template matching increase dramatically with both template-and scene imagesize. This makes traditional template matching less useful for many (e.g.

  1. POOR TEXTURAL IMAGE MATCHING BASED ON GRAPH THEORY

    S. Chen

    2016-06-01

    Full Text Available Image matching lies at the heart of photogrammetry and computer vision. For poor textural images, the matching result is affected by low contrast, repetitive patterns, discontinuity or occlusion, few or homogeneous textures. Recently, graph matching became popular for its integration of geometric and radiometric information. Focused on poor textural image matching problem, it is proposed an edge-weight strategy to improve graph matching algorithm. A series of experiments have been conducted including 4 typical landscapes: Forest, desert, farmland, and urban areas. And it is experimentally found that our new algorithm achieves better performance. Compared to SIFT, doubled corresponding points were acquired, and the overall recall rate reached up to 68%, which verifies the feasibility and effectiveness of the algorithm.

  2. Matching by Monotonic Tone Mapping.

    Kovacs, Gyorgy

    2018-06-01

    In this paper, a novel dissimilarity measure called Matching by Monotonic Tone Mapping (MMTM) is proposed. The MMTM technique allows matching under non-linear monotonic tone mappings and can be computed efficiently when the tone mappings are approximated by piecewise constant or piecewise linear functions. The proposed method is evaluated in various template matching scenarios involving simulated and real images, and compared to other measures developed to be invariant to monotonic intensity transformations. The results show that the MMTM technique is a highly competitive alternative of conventional measures in problems where possible tone mappings are close to monotonic.

  3. MATCHING IN INFORMAL FINANCIAL INSTITUTIONS.

    Eeckhout, Jan; Munshi, Kaivan

    2010-09-01

    This paper analyzes an informal financial institution that brings heterogeneous agents together in groups. We analyze decentralized matching into these groups, and the equilibrium composition of participants that consequently arises. We find that participants sort remarkably well across the competing groups, and that they re-sort immediately following an unexpected exogenous regulatory change. These findings suggest that the competitive matching model might have applicability and bite in other settings where matching is an important equilibrium phenomenon. (JEL: O12, O17, G20, D40).

  4. Toward Practical Secure Stable Matching

    Riazi M. Sadegh

    2017-01-01

    Full Text Available The Stable Matching (SM algorithm has been deployed in many real-world scenarios including the National Residency Matching Program (NRMP and financial applications such as matching of suppliers and consumers in capital markets. Since these applications typically involve highly sensitive information such as the underlying preference lists, their current implementations rely on trusted third parties. This paper introduces the first provably secure and scalable implementation of SM based on Yao’s garbled circuit protocol and Oblivious RAM (ORAM. Our scheme can securely compute a stable match for 8k pairs four orders of magnitude faster than the previously best known method. We achieve this by introducing a compact and efficient sub-linear size circuit. We even further decrease the computation cost by three orders of magnitude by proposing a novel technique to avoid unnecessary iterations in the SM algorithm. We evaluate our implementation for several problem sizes and plan to publish it as open-source.

  5. Probability matching and strategy availability.

    Koehler, Derek J; James, Greta

    2010-09-01

    Findings from two experiments indicate that probability matching in sequential choice arises from an asymmetry in strategy availability: The matching strategy comes readily to mind, whereas a superior alternative strategy, maximizing, does not. First, compared with the minority who spontaneously engage in maximizing, the majority of participants endorse maximizing as superior to matching in a direct comparison when both strategies are described. Second, when the maximizing strategy is brought to their attention, more participants subsequently engage in maximizing. Third, matchers are more likely than maximizers to base decisions in other tasks on their initial intuitions, suggesting that they are more inclined to use a choice strategy that comes to mind quickly. These results indicate that a substantial subset of probability matchers are victims of "underthinking" rather than "overthinking": They fail to engage in sufficient deliberation to generate a superior alternative to the matching strategy that comes so readily to mind.

  6. Computing solutions for matching games

    Biró, Péter; Kern, Walter; Paulusma, Daniël

    2012-01-01

    A matching game is a cooperative game (N, v) defined on a graph G = (N, E) with an edge weighting w : E → R+. The player set is N and the value of a coalition S ⊆ N is defined as the maximum weight of a matching in the subgraph induced by S. First we present an O(nm+n2 log n) algorithm that tests if

  7. Probability Matching, Fast and Slow

    Koehler, Derek J.; James, Greta

    2014-01-01

    A prominent point of contention among researchers regarding the interpretation of probability-matching behavior is whether it represents a cognitively sophisticated, adaptive response to the inherent uncertainty of the tasks or settings in which it is observed, or whether instead it represents a fundamental shortcoming in the heuristics that support and guide human decision making. Put crudely, researchers disagree on whether probability matching is "smart" or "dumb." Here, we consider eviden...

  8. Matching games with partial information

    Laureti, Paolo; Zhang, Yi-Cheng

    2003-06-01

    We analyze different ways of pairing agents in a bipartite matching problem, with regard to its scaling properties and to the distribution of individual “satisfactions”. Then we explore the role of partial information and bounded rationality in a generalized Marriage Problem, comparing the benefits obtained by self-searching and by a matchmaker. Finally we propose a modified matching game intended to mimic the way consumers’ information makes firms to enhance the quality of their products in a competitive market.

  9. Vision-based adaptive cruise control using pattern matching

    Kanjee, R

    2013-10-01

    Full Text Available input generated by the control system does not directly induce a traction force on the car tires. In an electric vehicle, the throttle position is processed by the engine controller and is mapped proportionally to the motor’s angular velocity. For our... simulation, this mapping was obtained from the manufacturer’s datasheet of the electric motor controller being used in the hybrid car. The manufacturer also supplies a speed-torque curve. An approximate equation was obtained using a linear curve fitting...

  10. Computationally Secure Pattern Matching in the Presence of Malicious Adversaries

    Hazay, Carmit; Toft, Tomas

    2010-01-01

    simulation in the presence of malicious, polynomial-time adversaries (assuming that ElGamal encryption is semantically secure) and exhibits computation and communication costs of O(n + m) in a constant round complexity. In addition to the above, we propose a collection of protocols for variations...

  11. The Logical Basis of Evaluation Order and Pattern-Matching

    2009-04-17

    various people in the 1930s, particularly Wittgenstein (“It is what is regarded as the justification of an assertion that constitutes the sense of the...assertion” [ Wittgenstein , 1974, I,§40]), and Brouwer-Heyting-Kolmogorov in their interpretations of intuitionistic logic [Heyting, 1974, Kolmogorov, 1932...Technical Report CMU-CS-02-101, Department of Computer Science, Carnegie Mellon University, 2002. Revised May 2003. Ludwig Wittgenstein

  12. Poor textural image tie point matching via graph theory

    Yuan, Xiuxiao; Chen, Shiyu; Yuan, Wei; Cai, Yang

    2017-07-01

    Feature matching aims to find corresponding points to serve as tie points between images. Robust matching is still a challenging task when input images are characterized by low contrast or contain repetitive patterns, occlusions, or homogeneous textures. In this paper, a novel feature matching algorithm based on graph theory is proposed. This algorithm integrates both geometric and radiometric constraints into an edge-weighted (EW) affinity tensor. Tie points are then obtained by high-order graph matching. Four pairs of poor textural images covering forests, deserts, bare lands, and urban areas are tested. For comparison, three state-of-the-art matching techniques, namely, scale-invariant feature transform (SIFT), speeded up robust features (SURF), and features from accelerated segment test (FAST), are also used. The experimental results show that the matching recall obtained by SIFT, SURF, and FAST varies from 0 to 35% in different types of poor textures. However, through the integration of both geometry and radiometry and the EW strategy, the recall obtained by the proposed algorithm is better than 50% in all four image pairs. The better matching recall improves the number of correct matches, dispersion, and positional accuracy.

  13. Influence of a Prolonged Tennis Match Play on Serve Biomechanics.

    Caroline Martin

    Full Text Available The aim of this study was to quantify kinematic, kinetic and performance changes that occur in the serve throughout a prolonged tennis match play. Serves of eight male advanced tennis players were recorded with a motion capture system before, at mid-match, and after a 3-hour tennis match. Before and after each match, electromyographic data of 8 upper limb muscles obtained during isometric maximal voluntary contraction were compared to determine the presence of muscular fatigue. Vertical ground reaction forces, rating of perceived exertion, ball speed, and ball impact height were measured. Kinematic and upper limb kinetic variables were computed. The results show decrease in mean power frequency values for several upper limb muscles that is an indicator of local muscular fatigue. Decreases in serve ball speed, ball impact height, maximal angular velocities and an increase in rating of perceived exertion were also observed between the beginning and the end of the match. With fatigue, the majority of the upper limb joint kinetics decreases at the end of the match. No change in timing of maximal angular velocities was observed between the beginning and the end of the match. A prolonged tennis match play may induce fatigue in upper limb muscles, which decrease performance and cause changes in serve maximal angular velocities and joint kinetics. The consistency in timing of maximal angular velocities suggests that advanced tennis players are able to maintain the temporal pattern of their serve technique, in spite of the muscular fatigue development.

  14. Diversity of the murine antibody response targeting influenza A(H1N1pdm09) hemagglutinin.

    Wilson, Jason R; Tzeng, Wen-Pin; Spesock, April; Music, Nedzad; Guo, Zhu; Barrington, Robert; Stevens, James; Donis, Ruben O; Katz, Jacqueline M; York, Ian A

    2014-06-01

    We infected mice with the 2009 influenza A pandemic virus (H1N1pdm09), boosted with an inactivated vaccine, and cloned immunoglobulins (Igs) from HA-specific B cells. Based on the redundancy in germline gene utilization, we inferred that between 72-130 unique IgH VDJ and 35 different IgL VJ combinations comprised the anti-HA recall response. The IgH VH1 and IgL VK14 variable gene families were employed most frequently. A representative panel of antibodies were cloned and expressed to confirm reactivity with H1N1pdm09 HA. The majority of the recombinant antibodies were of high avidity and capable of inhibiting H1N1pdm09 hemagglutination. Three of these antibodies were subtype-specific cross-reactive, binding to the HA of A/South Carolina/1/1918(H1N1), and one further reacted with A/swine/Iowa/15/1930(H1N1). These results help to define the genetic diversity of the influenza anti-HA antibody repertoire profile induced following infection and vaccination, which may facilitate the development of influenza vaccines that are more protective and broadly neutralizing. Protection against influenza viruses is mediated mainly by antibodies, and in most cases this antibody response is narrow, only providing protection against closely related viruses. In spite of this limited range of protection, recent findings indicate that individuals immune to one influenza virus may contain antibodies (generally a minority of the overall response) that are more broadly reactive. These findings have raised the possibility that influenza vaccines could induce a more broadly protective response, reducing the need for frequent vaccine strain changes. However, interpretation of these observations is hampered by the lack of quantitative characterization of the antibody repertoire. In this study, we used single-cell cloning of influenza HA-specific B cells to assess the diversity and nature of the antibody response to influenza hemagglutinin in mice. Our findings help to put bounds on the

  15. 76 FR 5235 - Privacy Act of 1974, as Amended; Computer Matching Program (SSA Internal Match)-Match Number 1014

    2011-01-28

    ...; Computer Matching Program (SSA Internal Match)--Match Number 1014 AGENCY: Social Security Administration... regarding protections for such persons. The Privacy Act, as amended, regulates the use of computer matching....C. 552a, as amended, and the provisions of the Computer Matching and Privacy Protection Act of 1988...

  16. Matching faces with emotional expressions

    Wenfeng eChen

    2011-08-01

    Full Text Available There is some evidence that faces with a happy expression are recognized better than faces with other expressions. However, little is known about whether this happy face advantage also applies to perceptual face matching, and whether similar differences exist among other expressions. Using a sequential matching paradigm, we systematically compared the effects of seven basic facial expressions on identity recognition. Identity matching was quickest when a pair of faces had an identical happy/sad/neutral expression, poorer when they had a fearful/surprise/angry expression, and poorest when they had a disgust expression. Faces with a happy/sad/fear/surprise expression were matched faster than those with an anger/disgust expression when the second face in a pair had a neutral expression. These results demonstrate that effects of facial expression on identity recognition are not limited to happy faces when a learned face is immediately tested. The results suggest different influences of expression in perceptual matching and long-term recognition memory.

  17. The Kent Face Matching Test.

    Fysh, Matthew C; Bindemann, Markus

    2018-05-01

    This study presents the Kent Face Matching Test (KFMT), which comprises 200 same-identity and 20 different-identity pairs of unfamiliar faces. Each face pair consists of a photograph from a student ID card and a high-quality portrait that was taken at least three months later. The test is designed to complement existing resources for face-matching research, by providing a more ecologically valid stimulus set that captures the natural variability that can arise in a person's appearance over time. Two experiments are presented to demonstrate that the KFMT provides a challenging measure of face matching but correlates with established tests. Experiment 1 compares a short version of this test with the optimized Glasgow Face Matching Test (GFMT). In Experiment 2, a longer version of the KFMT, with infrequent identity mismatches, is correlated with performance on the Cambridge Face Memory Test (CFMT) and the Cambridge Face Perception Test (CFPT). The KFMT is freely available for use in face-matching research. © 2017 The British Psychological Society.

  18. Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors

    Fengqi Xu

    2018-05-01

    Full Text Available Measles virus (MV causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM, CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH, we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO method. The calculated inter-fragment interaction energies (IFIEs revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4. In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.

  19. Glycosylation of Hemagglutinin and Neuraminidase of Influenza A Virus as Signature for Ecological Spillover and Adaptation among Influenza Reservoirs

    Paul Kim

    2018-04-01

    Full Text Available Glycosylation of the hemagglutinin (HA and neuraminidase (NA of the influenza provides crucial means for immune evasion and viral fitness in a host population. However, the time-dependent dynamics of each glycosylation sites have not been addressed. We monitored the potential N-linked glycosylation (NLG sites of over 10,000 HA and NA of H1N1 subtype isolated from human, avian, and swine species over the past century. The results show a shift in glycosylation sites as a hallmark of 1918 and 2009 pandemics, and also for the 1976 “abortive pandemic”. Co-segregation of particular glycosylation sites was identified as a characteristic of zoonotic transmission from animal reservoirs, and interestingly, of “reverse zoonosis” of human viruses into swine populations as well. After the 2009 pandemic, recent isolates accrued glycosylation at canonical sites in HA, reflecting gradual seasonal adaptation, and a novel glycosylation in NA as an independent signature for adaptation among humans. Structural predictions indicated a remarkably pleiotropic influence of glycans on multiple HA epitopes for immune evasion, without sacrificing the receptor binding of HA or the activity of NA. The results provided the rationale for establishing the ecological niche of influenza viruses among the reservoir and could be implemented for influenza surveillance and improving pandemic preparedness.

  20. A Simple and Robust Method for Culturing Human-Induced Pluripotent Stem Cells in an Undifferentiated State Using Botulinum Hemagglutinin.

    Kim, Mee-Hae; Matsubara, Yoshifumi; Fujinaga, Yukako; Kino-Oka, Masahiro

    2018-02-01

    Clinical and industrial applications of human-induced pluripotent stem cells (hiPSCs) is hindered by the lack of robust culture strategies capable of sustaining a culture in an undifferentiated state. Here, a simple and robust hiPSC-culture-propagation strategy incorporating botulinum hemagglutinin (HA)-mediated selective removal of cells deviating from an undifferentiated state is developed. After HA treatment, cell-cell adhesion is disrupted, and deviated cells detached from the central region of the colony to subsequently form tight monolayer colonies following prolonged incubation. The authors find that the temporal and dose-dependent activity of HA regulated deviated-cell removal and recoverability after disruption of cell-cell adhesion in hiPSC colonies. The effects of HA are confirmed under all culture conditions examined, regardless of hiPSC line and feeder-dependent or -free culture conditions. After routine application of our HA-treatment paradigm for serial passages, hiPSCs maintains expression of pluripotent markers and readily forms embryoid bodies expressing markers for all three germ-cell layers. This method enables highly efficient culturing of hiPSCs and use of entire undifferentiated portions without having to pick deviated cells manually. This simple and readily reproducible culture strategy is a potentially useful tool for improving the robust and scalable maintenance of undifferentiated hiPSC cultures. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Pseudomonas fluorescens filamentous hemagglutinin, an iron-regulated protein, is an important virulence factor that modulates bacterial pathogenicity

    Yuan-yuan Sun

    2016-08-01

    Full Text Available Pseudomonas fluorescens is a common bacterial pathogen to a wide range of aquaculture animals including various species of fish. In this study, we employed proteomic analysis and identified filamentous hemagglutinin (FHA as an iron-responsive protein secreted by TSS, a pathogenic P. fluorescens isolate. In vitro study showed that compared to the wild type, the fha mutant TSSfha (i exhibited a largely similar vegetative growth profile but significantly retarded in the ability of biofilm growth and producing extracellular matrix, (ii displayed no apparent flagella and motility, (iii was defective in the attachment to host cells and unable to form self-aggregation, (iv displayed markedly reduced capacity of hemagglutination and surviving in host serum. In vivo infection analysis revealed that TSSfha was significantly attenuated in the ability of dissemination in fish tissues and inducing host mortality, and that antibody blocking of the natural FHA produced by the wild type TSS impaired the infectivity of the pathogen. Furthermore, when introduced into turbot as a subunit vaccine, recombinant FHA elicited a significant protection against lethal TSS challenge. Taken together, these results indicate for the first time that P. fluorescens FHA is a key virulence factor essential to multiple biological processes associated with pathogenicity.

  2. The recombinant globular head domain of the measles virus hemagglutinin protein as a subunit vaccine against measles.

    Lobanova, Liubov M; Eng, Nelson F; Satkunarajah, Malathy; Mutwiri, George K; Rini, James M; Zakhartchouk, Alexander N

    2012-04-26

    Despite the availability of live attenuated measles virus (MV) vaccines, a large number of measles-associated deaths occur among infants in developing countries. The development of a measles subunit vaccine may circumvent the limitations associated with the current live attenuated vaccines and eventually contribute to global measles eradication. Therefore, the goal of this study was to test the feasibility of producing the recombinant globular head domain of the MV hemagglutinin (H) protein by stably transfected human cells and to examine the ability of this recombinant protein to elicit MV-specific immune responses. The recombinant protein was purified from the culture supernatant of stably transfected HEK293T cells secreting a tagged version of the protein. Two subcutaneous immunizations with the purified recombinant protein alone resulted in the production of MV-specific serum IgG and neutralizing antibodies in mice. Formulation of the protein with adjuvants (polyphosphazene or alum) further enhanced the humoral immune response and in addition resulted in the induction of cell-mediated immunity as measured by the production of MV H-specific interferon gamma (IFN-γ) and interleukin 5 (IL-5) by in vitro re-stimulated splenocytes. Furthermore, the inclusion of polyphosphazene into the vaccine formulation induced a mixed Th1/Th2-type immune response. In addition, the purified recombinant protein retained its immunogenicity even after storage at 37°C for 2 weeks. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Protection against Multiple Subtypes of Influenza Viruses by Virus-Like Particle Vaccines Based on a Hemagglutinin Conserved Epitope

    Shaoheng Chen

    2015-01-01

    Full Text Available We selected the conserved sequence in the stalk region of influenza virus hemagglutinin (HA trimmer, the long alpha helix (LAH, as the vaccine candidate sequence, and inserted it into the major immunodominant region (MIR of hepatitis B virus core protein (HBc, and, by using the E. coli expression system, we prepared a recombinant protein vaccine LAH-HBc in the form of virus-like particles (VLP. Intranasal immunization of mice with this LAH-HBc VLP plus cholera toxin B subunit with 0.2% of cholera toxin (CTB* adjuvant could effectively elicit humoral and cellular immune responses and protect mice against a lethal challenge of homologous influenza viruses (A/Puerto Rico/8/1934 (PR8 (H1N1. In addition, passage of the immune sera containing specific antibodies to naïve mice rendered them resistant against a lethal homologous challenge. Immunization with LAH-HBc VLP vaccine plus CTB* adjuvant could also fully protect mice against a lethal challenge of the 2009 pandemic H1N1 influenza virus or the avian H9N2 virus and could partially protect mice against a lethal challenge of the avian H5N1 influenza virus. This study demonstrated that the LAH-HBc VLP vaccine based on a conserved sequence of the HA trimmer stalk region is a promising candidate vaccine for developing a universal influenza vaccine against multiple influenza viruses infections.

  4. Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses

    Borgwardt, Derek S.; Martin, Aaron D.; van Hemert, Jonathan R.; Yang, Jianyi; Fischer, Carol L.; Recker, Erica N.; Nair, Prashant R.; Vidva, Robinson; Chandrashekaraiah, Shwetha; Progulske-Fox, Ann; Drake, David; Cavanaugh, Joseph E.; Vali, Shireen; Zhang, Yang; Brogden, Kim A.

    2014-01-01

    Histatins are human salivary gland peptides with anti-microbial and anti-inflammatory activities. In this study, we hypothesized that histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and attenuates HagB-induced chemokine responses in human myeloid dendritic cells. Histatin 5 bound to immobilized HagB in a surface plasmon resonance (SPR) spectroscopy-based biosensor system. SPR spectroscopy kinetic and equilibrium analyses, protein microarray studies, and I-TASSER structural modeling studies all demonstrated two histatin 5 binding sites on HagB. One site had a stronger affinity with a KD1 of 1.9 μM and one site had a weaker affinity with a KD2 of 60.0 μM. Binding has biological implications and predictive modeling studies and exposure of dendritic cells both demonstrated that 20.0 μM histatin 5 attenuated (p < 0.05) 0.02 μM HagB-induced CCL3/MIP-1α, CCL4/MIP-1β, and TNFα responses. Thus histatin 5 is capable of attenuating chemokine responses, which may help control oral inflammation.

  5. The Porphyromonas gingivalis hemagglutinins HagB and HagC are major mediators of adhesion and biofilm formation.

    Connolly, E; Millhouse, E; Doyle, R; Culshaw, S; Ramage, G; Moran, G P

    2017-02-01

    Porphyromonas gingivalis is a bacterium associated with chronic periodontitis that possesses a family of genes encoding hemagglutinins required for heme acquisition. In this study we generated ΔhagB and ΔhagC mutants in strain W83 and demonstrate that both hagB and hagC are required for adherence to oral epithelial cells. Unexpectedly, a double ΔhagB/ΔhagC mutant had less severe adherence defects than either of the single mutants, but was found to exhibit increased expression of the gingipain-encoding genes rgpA and kgp, suggesting that a ΔhagB/ΔhagC mutant is only viable in populations of cells that exhibit increased expression of genes involved in heme acquisition. Disruption of hagB in the fimbriated strain ATCC33277 demonstrated that HagB is also required for stable attachment of fimbriated bacteria to oral epithelial cells. Mutants of hagC were also found to form defective single and multi-species biofilms that had reduced biomass relative to biofilms formed by the wild-type strain. This study highlights the hitherto unappreciated importance of these genes in oral colonization and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Protective immunity provided by HLA-A2 epitopes for fusion and hemagglutinin proteins of measles virus

    Oh, Sang Kon; Stegman, Brian; Pendleton, C. David; Ota, Martin O.; Pan, C.-H.; Griffin, Diane E.; Burke, Donald S.; Berzofsky, Jay A.

    2006-01-01

    Natural infection and vaccination with a live-attenuated measles virus (MV) induce CD8 + T-cell-mediated immune responses that may play a central role in controlling MV infection. In this study, we show that newly identified human HLA-A2 epitopes from MV hemagglutinin (H) and fusion (F) proteins induced protective immunity in HLA-A2 transgenic mice challenged with recombinant vaccinia viruses expressing F or H protein. HLA-A2 epitopes were predicted and synthesized. Five and four peptides from H and F, respectively, bound to HLA-A2 molecules in a T2-binding assay, and four from H and two from F could induce peptide-specific CD8 + T cell responses in HLA-A2 transgenic mice. Further experiments proved that three peptides from H (H9-567, H10-250, and H10-516) and one from F protein (F9-57) were endogenously processed and presented on HLA-A2 molecules. All peptides tested in this study are common to 5 different strains of MV including Edmonston. In both A2K b and HHD-2 mice, the identified peptide epitopes induced protective immunity against recombinant vaccinia viruses expressing H or F. Because F and H proteins induce neutralizing antibodies, they are major components of new vaccine strategies, and therefore data from this study will contribute to the development of new vaccines against MV infection

  7. Glycosylation of Hemagglutinin and Neuraminidase of Influenza A Virus as Signature for Ecological Spillover and Adaptation among Influenza Reservoirs

    Kim, Paul; Jang, Yo Han; Kwon, Soon Bin; Lee, Chung Min; Han, Gyoonhee; Seong, Baik Lin

    2018-01-01

    Glycosylation of the hemagglutinin (HA) and neuraminidase (NA) of the influenza provides crucial means for immune evasion and viral fitness in a host population. However, the time-dependent dynamics of each glycosylation sites have not been addressed. We monitored the potential N-linked glycosylation (NLG) sites of over 10,000 HA and NA of H1N1 subtype isolated from human, avian, and swine species over the past century. The results show a shift in glycosylation sites as a hallmark of 1918 and 2009 pandemics, and also for the 1976 “abortive pandemic”. Co-segregation of particular glycosylation sites was identified as a characteristic of zoonotic transmission from animal reservoirs, and interestingly, of “reverse zoonosis” of human viruses into swine populations as well. After the 2009 pandemic, recent isolates accrued glycosylation at canonical sites in HA, reflecting gradual seasonal adaptation, and a novel glycosylation in NA as an independent signature for adaptation among humans. Structural predictions indicated a remarkably pleiotropic influence of glycans on multiple HA epitopes for immune evasion, without sacrificing the receptor binding of HA or the activity of NA. The results provided the rationale for establishing the ecological niche of influenza viruses among the reservoir and could be implemented for influenza surveillance and improving pandemic preparedness. PMID:29642453

  8. Structure, Receptor Binding, and Antigenicity of Influenza Virus Hemagglutinins from the 1957 H2N2 Pandemic

    Xu, Rui; McBride, Ryan; Paulson, James C.; Basler, Christopher F.; Wilson, Ian A. (Sinai); (Scripps)

    2010-03-04

    The hemagglutinin (HA) envelope protein of influenza viruses mediates essential viral functions, including receptor binding and membrane fusion, and is the major viral antigen for antibody neutralization. The 1957 H2N2 subtype (Asian flu) was one of the three great influenza pandemics of the last century and caused 1 million deaths globally from 1957 to 1968. Three crystal structures of 1957 H2 HAs have been determined at 1.60 to 1.75 {angstrom} resolutions to investigate the structural basis for their antigenicity and evolution from avian to human binding specificity that contributed to its introduction into the human population. These structures, which represent the highest resolutions yet recorded for a complete ectodomain of a glycosylated viral surface antigen, along with the results of glycan microarray binding analysis, suggest that a hydrophobicity switch at residue 226 and elongation of receptor-binding sites were both critical for avian H2 HA to acquire human receptor specificity. H2 influenza viruses continue to circulate in birds and pigs and, therefore, remain a substantial threat for transmission to humans. The H2 HA structure also reveals a highly conserved epitope that could be harnessed in the design of a broader and more universal influenza A virus vaccine.

  9. Molecular surveillance of low pathogenic avian influenza viruses in wild birds across the United States: inferences from the hemagglutinin gene.

    Antoinette J Piaggio

    Full Text Available A United States interagency avian influenza surveillance plan was initiated in 2006 for early detection of highly pathogenic avian influenza viruses (HPAIV in wild birds. The plan included a variety of wild bird sampling strategies including the testing of fecal samples from aquatic areas throughout the United States from April 2006 through December 2007. Although HPAIV was not detected through this surveillance effort we were able to obtain 759 fecal samples that were positive for low pathogenic avian influenza virus (LPAIV. We used 136 DNA sequences obtained from these samples along with samples from a public influenza sequence database for a phylogenetic assessment of hemagglutinin (HA diversity in the United States. We analyzed sequences from all HA subtypes except H5, H7, H14 and H15 to examine genetic variation, exchange between Eurasia and North America, and geographic distribution of LPAIV in wild birds in the United States. This study confirms intercontinental exchange of some HA subtypes (including a newly documented H9 exchange event, as well as identifies subtypes that do not regularly experience intercontinental gene flow but have been circulating and evolving in North America for at least the past 20 years. These HA subtypes have high levels of genetic diversity with many lineages co-circulating within the wild birds of North America. The surveillance effort that provided these samples demonstrates that such efforts, albeit labor-intensive, provide important information about the ecology of LPAIV circulating in North America.

  10. The role of filamentous hemagglutinin adhesin in adherence and biofilm formation in Acinetobacter baumannii ATCC19606(T).

    Darvish Alipour Astaneh, Shakiba; Rasooli, Iraj; Mousavi Gargari, Seyed Latif

    2014-09-01

    Filamentous hemagglutinin adhesins (FHA) are key factors for bacterial attachment and subsequent cell accumulation on substrates. Here an FHA-like Outer membrane (OM) adhesin of Acinetobacter baumannii ATCC19606(T) was displayed on Escherichia coli. The candidate autotransporter (AT) genes were identified in A. baumannii ATCC19606(T) genome. The exoprotein (FhaB1) and transporter (FhaC1) were produced independently within the same cell (FhaB1C1). The fhaC1 was mutated. In vitro adherence to epithelial cells of the recombinant FhaB1C1 and the mutant strains were compared with A. baumanni ATCC19606(T). A bivalent chimeric protein (K) composed of immunologically important portions of fhaB1 (B) and fhaC1 (C) was constructed. The mice vaccinated with chimeric protein were challenged with A. baumannii ATCC19606(T) and FhaB1C1 producing recombinant E. coli. Mutations in the fhaC1 resulted in the absence of FhaB1 in the OM. Expression of FhaB1C1 enhanced the adherence of recombinant bacteria to A546 bronchial cell line. The results revealed association of FhaB1 with bacterial adhesion and biofilm formation. Immunization with a combination of recombinant B and K proteins proved protective against A. baumanni ATCC19606(T). The findings may be applied in active and passive immunization strategies against A. baumannii. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Serological characterization of guinea pigs infected with H3N2 human influenza or immunized with hemagglutinin protein

    Bushnell Ruth V

    2010-08-01

    Full Text Available Abstract Background Recent and previous studies have shown that guinea pigs can be infected with, and transmit, human influenza viruses. Therefore guinea pig may be a useful animal model for better understanding influenza infection and assessing vaccine strategies. To more fully characterize the model, antibody responses following either infection/re-infection with human influenza A/Wyoming/03/2003 H3N2 or immunization with its homologous recombinant hemagglutinin (HA protein were studied. Results Serological samples were collected and tested for anti-HA immunoglobulin by ELISA, antiviral antibodies by hemagglutination inhibition (HI, and recognition of linear epitopes by peptide scanning (PepScan. Animals inoculated with infectious virus demonstrated pronounced viral replication and subsequent serological conversion. Animals either immunized with the homologous HA antigen or infected, showed a relatively rapid rise in antibody titers to the HA glycoprotein in ELISA assays. Antiviral antibodies, measured by HI assay, were detectable after the second inoculation. PepScan data identified both previously recognized and newly defined linear epitopes. Conclusions Infection and/or recombinant HA immunization of guinea pigs with H3N2 Wyoming influenza virus resulted in a relatively rapid production of viral-specific antibody thus demonstrating the strong immunogenicity of the major viral structural proteins in this animal model for influenza infection. The sensitivity of the immune response supports the utility of the guinea pig as a useful animal model of influenza infection and immunization.

  12. Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants

    Xueyong Zhu

    2015-11-01

    Full Text Available Avian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA mutants from ferret-transmissible H5N1 viruses of A/Vietnam/1203/2004 and A/Indonesia/5/2005 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6-linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3-linked sialosides. Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogs reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses.

  13. A Phase Matching, Adiabatic Accelerator

    Lemery, Francois [Hamburg U.; Flöttmann, Klaus [DESY; Kärtner, Franz [CFEL, Hamburg; Piot, Philippe [Northern Illinois U.

    2017-05-01

    Tabletop accelerators are a thing of the future. Reducing their size will require scaling down electromagnetic wavelengths; however, without correspondingly high field gradients, particles will be more susceptible to phase-slippage – especially at low energy. We investigate how an adiabatically-tapered dielectric-lined waveguide could maintain phase-matching between the accelerating mode and electron bunch. We benchmark our simple model with CST and implement it into ASTRA; finally we provide a first glimpse into the beam dynamics in a phase-matching accelerator.

  14. Mix-and-match holography

    Peng, Yifan

    2017-11-22

    Computational caustics and light steering displays offer a wide range of interesting applications, ranging from art works and architectural installations to energy efficient HDR projection. In this work we expand on this concept by encoding several target images into pairs of front and rear phase-distorting surfaces. Different target holograms can be decoded by mixing and matching different front and rear surfaces under specific geometric alignments. Our approach, which we call mix-and-match holography, is made possible by moving from a refractive caustic image formation process to a diffractive, holographic one. This provides the extra bandwidth that is required to multiplex several images into pairing surfaces.

  15. Template matching techniques in computer vision theory and practice

    Brunelli, Roberto

    2009-01-01

    The detection and recognition of objects in images is a key research topic in the computer vision community.  Within this area, face recognition and interpretation has attracted increasing attention owing to the possibility of unveiling human perception mechanisms, and for the development of practical biometric systems. This book and the accompanying website, focus on template matching, a subset of object recognition techniques of wide applicability, which has proved to be particularly effective for face recognition applications. Using examples from face processing tasks throughout the book to illustrate more general object recognition approaches, Roberto Brunelli: examines the basics of digital image formation, highlighting points critical to the task of template matching;presents basic and  advanced template matching techniques, targeting grey-level images, shapes and point sets;discusses recent pattern classification paradigms from a template matching perspective;illustrates the development of a real fac...

  16. Vaccine protection of chickens against antigenically diverse H5 highly pathogenic avian influenza isolates with a live HVT vector vaccine expressing the influenza hemagglutinin gene derived from a clade 2.2 avian influenza virus.

    Kapczynski, Darrell R; Esaki, Motoyuki; Dorsey, Kristi M; Jiang, Haijun; Jackwood, Mark; Moraes, Mauro; Gardin, Yannick

    2015-02-25

    Vaccination is an important tool in the protection of poultry against avian influenza (AI). For field use, the overwhelming majority of AI vaccines produced are inactivated whole virus formulated into an oil emulsion. However, recombinant vectored vaccines are gaining use for their ability to induce protection against heterologous isolates and ability to overcome maternal antibody interference. In these studies, we compared protection of chickens provided by a turkey herpesvirus (HVT) vector vaccine expressing the hemagglutinin (HA) gene from a clade 2.2 H5N1 strain (A/swan/Hungary/4999/2006) against homologous H5N1 as well as heterologous H5N1 and H5N2 highly pathogenic (HP) AI challenge. The results demonstrated all vaccinated birds were protected from clinical signs of disease and mortality following homologous challenge. In addition, oral and cloacal swabs taken from challenged birds demonstrated that vaccinated birds had lower incidence and titers of viral shedding compared to sham-vaccinated birds. Following heterologous H5N1 or H5N2 HPAI challenge, 80-95% of birds receiving the HVT vector AI vaccine at day of age survived challenge with fewer birds shedding virus after challenge than sham vaccinated birds. In vitro cytotoxicity analysis demonstrated that splenic T lymphocytes from HVT-vector-AI vaccinated chickens recognized MHC-matched target cells infected with H5, as well as H6, H7, or H9 AI virus. Taken together, these studies provide support for the use of HVT vector vaccines expressing HA to protect poultry against multiple lineages of HPAI, and that both humoral and cellular immunity induced by live vaccines likely contributes to protection. Published by Elsevier Ltd.

  17. Template matching via densities on the roto-translation group

    Bekkers, E.; Loog, M.; Romeny, B. ter Haar; Duits, R.

    2018-01-01

    We propose a template matching method for the detection of 2D image objects that are characterized by orientation patterns. Our method is based on data representations via orientation scores, which are functions on the space of positions and orientations, and which are obtained via a wavelet-type

  18. Rotation-invariant fingerprint matching using radon and DCT

    Sangita Bharkad

    2017-11-20

    Nov 20, 2017 ... [6] Bazen A and Gerez S 2003 Fingerprint matching by thin- plate spline modeling of elastic deformations. Pattern. Recogn. 36(8): 1859–1867. [7] Jain A, Hong L and Bolle R 1997 On-line fingerprint veri- fication. IEEE Trans.

  19. Canonical Skeletons for Shape Matching

    Eede, M. van; Macrini, D.; Telea, A.; Sminchisescu, C.; Dickinson, S.

    2006-01-01

    Skeletal representations of 2-D shape, including shock graphs, have become increasingly popular for shape matching and object recognition. However, it is well known that skeletal structure can be unstable under minor boundary deformation, part articulation, and minor shape deformation (due to, for

  20. Matching Games with Additive Externalities

    Branzei, Simina; Michalak, Tomasz; Rahwan, Talal

    2012-01-01

    Two-sided matchings are an important theoretical tool used to model markets and social interactions. In many real life problems the utility of an agent is influenced not only by their own choices, but also by the choices that other agents make. Such an influence is called an externality. Whereas ...

  1. Monetary Exchange with Multilateral Matching

    Julien, Benoît; Kennes, John; King, Ian

    the results with Kiyotaki and Wright (1993), Trejos and Wright (1995), and Lagos and Wright (2005) respectively. We find that the multilateral matching setting generates very simple and intuitive equilibrium allocations that are similar to those in the other papers, but which have important differences...

  2. An Implementation of Bigraph Matching

    Glenstrup, Arne John; Damgaard, Troels Christoffer; Birkedal, Lars

    We describe a provably sound and complete matching algorithm for bigraphical reactive systems. The algorithm has been implemented in our BPL Tool, a first implementation of bigraphical reactive systems. We describe the tool and present a concrete example of how it can be used to simulate a model...

  3. Myocardium tracking via matching distributions.

    Ben Ayed, Ismail; Li, Shuo; Ross, Ian; Islam, Ali

    2009-01-01

    The goal of this study is to investigate automatic myocardium tracking in cardiac Magnetic Resonance (MR) sequences using global distribution matching via level-set curve evolution. Rather than relying on the pixelwise information as in existing approaches, distribution matching compares intensity distributions, and consequently, is well-suited to the myocardium tracking problem. Starting from a manual segmentation of the first frame, two curves are evolved in order to recover the endocardium (inner myocardium boundary) and the epicardium (outer myocardium boundary) in all the frames. For each curve, the evolution equation is sought following the maximization of a functional containing two terms: (1) a distribution matching term measuring the similarity between the non-parametric intensity distributions sampled from inside and outside the curve to the model distributions of the corresponding regions estimated from the previous frame; (2) a gradient term for smoothing the curve and biasing it toward high gradient of intensity. The Bhattacharyya coefficient is used as a similarity measure between distributions. The functional maximization is obtained by the Euler-Lagrange ascent equation of curve evolution, and efficiently implemented via level-set. The performance of the proposed distribution matching was quantitatively evaluated by comparisons with independent manual segmentations approved by an experienced cardiologist. The method was applied to ten 2D mid-cavity MR sequences corresponding to ten different subjects. Although neither shape prior knowledge nor curve coupling were used, quantitative evaluation demonstrated that the results were consistent with manual segmentations. The proposed method compares well with existing methods. The algorithm also yields a satisfying reproducibility. Distribution matching leads to a myocardium tracking which is more flexible and applicable than existing methods because the algorithm uses only the current data, i.e., does not

  4. Cephalopod dynamic camouflage: bridging the continuum between background matching and disruptive coloration

    Hanlon, R.T.; Chiao, C.-C.; Mäthger, L.M.; Barbosa, A.; Buresch, K.C.; Chubb, C.

    2008-01-01

    Individual cuttlefish, octopus and squid have the versatile capability to use body patterns for background matching and disruptive coloration. We define—qualitatively and quantitatively—the chief characteristics of the three major body pattern types used for camouflage by cephalopods: uniform and mottle patterns for background matching, and disruptive patterns that primarily enhance disruptiveness but aid background matching as well. There is great variation within each of the three body pattern types, but by defining their chief characteristics we lay the groundwork to test camouflage concepts by correlating background statistics with those of the body pattern. We describe at least three ways in which background matching can be achieved in cephalopods. Disruptive patterns in cuttlefish possess all four of the basic components of ‘disruptiveness’, supporting Cott's hypotheses, and we provide field examples of disruptive coloration in which the body pattern contrast exceeds that of the immediate surrounds. Based upon laboratory testing as well as thousands of images of camouflaged cephalopods in the field (a sample is provided on a web archive), we note that size, contrast and edges of background objects are key visual cues that guide cephalopod camouflage patterning. Mottle and disruptive patterns are frequently mixed, suggesting that background matching and disruptive mechanisms are often used in the same pattern. PMID:19008200

  5. 78 FR 73195 - Privacy Act of 1974: CMS Computer Matching Program Match No. 2013-01; HHS Computer Matching...

    2013-12-05

    ... 1974: CMS Computer Matching Program Match No. 2013-01; HHS Computer Matching Program Match No. 1312 AGENCY: Centers for Medicare & Medicaid Services (CMS), Department of Health and Human Services (HHS... Privacy Act of 1974 (5 U.S.C. 552a), as amended, this notice announces the renewal of a CMP that CMS plans...

  6. Matching of equivalent field regions

    Appel-Hansen, Jørgen; Rengarajan, S.B.

    2005-01-01

    In aperture problems, integral equations for equivalent currents are often found by enforcing matching of equivalent fields. The enforcement is made in the aperture surface region adjoining the two volumes on each side of the aperture. In the case of an aperture in a planar perfectly conducting...... screen, having the same homogeneous medium on both sides and an impressed current on one aide, an alternative procedure is relevant. We make use of the fact that in the aperture the tangential component of the magnetic field due to the induced currents in the screen is zero. The use of such a procedure...... shows that equivalent currents can be found by a consideration of only one of the two volumes into which the aperture plane divides the space. Furthermore, from a consideration of an automatic matching at the aperture, additional information about tangential as well as normal field components...

  7. University Reactor Matching Grants Program

    John Valentine; Farzad Rahnema; Said Abdel-Khalik

    2003-01-01

    During the 2002 Fiscal year, funds from the DOE matching grant program, along with matching funds from the industrial sponsors, have been used to support research in the area of thermal-hydraulics. Both experimental and numerical research projects have been performed. Experimental research focused on two areas: (1) Identification of the root cause mechanism for axial offset anomaly in pressurized water reactors under prototypical reactor conditions, and (2) Fluid dynamic aspects of thin liquid film protection schemes for inertial fusion reactor chambers. Numerical research focused on two areas: (1) Multi-fluid modeling of both two-phase and two-component flows for steam conditioning and mist cooling applications, and (2) Modeling of bounded Rayleigh-Taylor instability with interfacial mass transfer and fluid injection through a porous wall simulating the ''wetted wall'' protection scheme in inertial fusion reactor chambers. Details of activities in these areas are given

  8. Mix-and-match holography

    Peng, Yifan; Dun, Xiong; Sun, Qilin; Heidrich, Wolfgang

    2017-01-01

    target images into pairs of front and rear phase-distorting surfaces. Different target holograms can be decoded by mixing and matching different front and rear surfaces under specific geometric alignments. Our approach, which we call mixWe derive a detailed image formation model for the setting of holographic projection displays, as well as a multiplexing method based on a combination of phase retrieval methods and complex matrix factorization. We demonstrate several application scenarios in both simulation and physical prototypes.

  9. Impedance-matched Marx generators

    W. A. Stygar

    2017-04-01

    Full Text Available We have conceived a new class of prime-power sources for pulsed-power accelerators: impedance-matched Marx generators (IMGs. The fundamental building block of an IMG is a brick, which consists of two capacitors connected electrically in series with a single switch. An IMG comprises a single stage or several stages distributed axially and connected in series. Each stage is powered by a single brick or several bricks distributed azimuthally within the stage and connected in parallel. The stages of a multistage IMG drive an impedance-matched coaxial transmission line with a conical center conductor. When the stages are triggered sequentially to launch a coherent traveling wave along the coaxial line, the IMG achieves electromagnetic-power amplification by triggered emission of radiation. Hence a multistage IMG is a pulsed-power analogue of a laser. To illustrate the IMG approach to prime power, we have developed conceptual designs of two ten-stage IMGs with LC time constants on the order of 100 ns. One design includes 20 bricks per stage, and delivers a peak electrical power of 1.05 TW to a matched-impedance 1.22-Ω load. The design generates 113 kV per stage and has a maximum energy efficiency of 89%. The other design includes a single brick per stage, delivers 68 GW to a matched-impedance 19-Ω load, generates 113 kV per stage, and has a maximum energy efficiency of 90%. For a given electrical-power-output time history, an IMG is less expensive and slightly more efficient than a linear transformer driver, since an IMG does not use ferromagnetic cores.

  10. Impedance-matched Marx generators

    Stygar, W. A.; LeChien, K. R.; Mazarakis, M. G.; Savage, M. E.; Stoltzfus, B. S.; Austin, K. N.; Breden, E. W.; Cuneo, M. E.; Hutsel, B. T.; Lewis, S. A.; McKee, G. R.; Moore, J. K.; Mulville, T. D.; Muron, D. J.; Reisman, D. B.; Sceiford, M. E.; Wisher, M. L.

    2017-04-01

    We have conceived a new class of prime-power sources for pulsed-power accelerators: impedance-matched Marx generators (IMGs). The fundamental building block of an IMG is a brick, which consists of two capacitors connected electrically in series with a single switch. An IMG comprises a single stage or several stages distributed axially and connected in series. Each stage is powered by a single brick or several bricks distributed azimuthally within the stage and connected in parallel. The stages of a multistage IMG drive an impedance-matched coaxial transmission line with a conical center conductor. When the stages are triggered sequentially to launch a coherent traveling wave along the coaxial line, the IMG achieves electromagnetic-power amplification by triggered emission of radiation. Hence a multistage IMG is a pulsed-power analogue of a laser. To illustrate the IMG approach to prime power, we have developed conceptual designs of two ten-stage IMGs with L C time constants on the order of 100 ns. One design includes 20 bricks per stage, and delivers a peak electrical power of 1.05 TW to a matched-impedance 1.22 -Ω load. The design generates 113 kV per stage and has a maximum energy efficiency of 89%. The other design includes a single brick per stage, delivers 68 GW to a matched-impedance 19 -Ω load, generates 113 kV per stage, and has a maximum energy efficiency of 90%. For a given electrical-power-output time history, an IMG is less expensive and slightly more efficient than a linear transformer driver, since an IMG does not use ferromagnetic cores.

  11. A spot-matching method using cumulative frequency matrix in 2D gel images

    Han, Chan-Myeong; Park, Joon-Ho; Chang, Chu-Seok; Ryoo, Myung-Chun

    2014-01-01

    A new method for spot matching in two-dimensional gel electrophoresis images using a cumulative frequency matrix is proposed. The method improves on the weak points of the previous method called ‘spot matching by topological patterns of neighbour spots’. It accumulates the frequencies of neighbour spot pairs produced through the entire matching process and determines spot pairs one by one in order of higher frequency. Spot matching by frequencies of neighbour spot pairs shows a fairly better performance. However, it can give researchers a hint for whether the matching results can be trustworthy or not, which can save researchers a lot of effort for verification of the results. PMID:26019609

  12. Transit Matching for International Safeguards

    Gilligan, K.; Whitaker, M.; Oakberg, J.

    2015-01-01

    In 2013 the U.S. Department of Energy / National Nuclear Security Administration Office of Non-proliferation and International Security (NIS) supported a study of the International Atomic Energy Agency's (IAEA) processes and procedures for ensuring that shipments of nuclear material correspond to (match) their receipts (i.e., transit matching). Under Comprehensive Safeguards Agreements, Member States are obliged to declare such information within certain time frames. Nuclear weapons states voluntarily declare such information under INFCIRC/207. This study was funded by the NIS Next Generation Safeguards Initiative (NGSI) Concepts and Approaches program. Oak Ridge National Laboratory led the research, which included collaboration with the U.S. Nuclear Regulatory Commission, the U.S. Nuclear Material Management and Safeguards System (NMMSS), and the IAEA Section for Declared Information Analysis within the Department of Safeguards. The project studied the current transit matching methodologies, identified current challenges (e.g., level of effort and timeliness), and suggested improvements. This paper presents the recommendations that resulted from the study and discussions with IAEA staff. In particular, it includes a recommendation to collaboratively develop a set of best reporting practices for nuclear weapons states under INFCIRC/207. (author)

  13. Deliberate reduction of hemagglutinin and neuraminidase expression of influenza virus leads to an ultraprotective live vaccine in mice.

    Yang, Chen; Skiena, Steven; Futcher, Bruce; Mueller, Steffen; Wimmer, Eckard

    2013-06-04

    A long-held dogma posits that strong presentation to the immune system of the dominant influenza virus glycoprotein antigens neuraminidase (NA) and hemagglutinin (HA) is paramount for inducing protective immunity against influenza virus infection. We have deliberately violated this dogma by constructing a recombinant influenza virus strain of A/PR8/34 (H1N1) in which expression of NA and HA genes was suppressed. We down-regulated NA and HA expression by recoding the respective genes with suboptimal codon pair bias, thereby introducing hundreds of nucleotide changes while preserving their codon use and protein sequence. The variants PR8-NA(Min), PR8-HA(Min), and PR8-(NA+HA)(Min) (Min, minimal expression) were used to assess the contribution of reduced glycoprotein expression to growth in tissue culture and pathogenesis in BALB/c mice. All three variants proliferated in Madin-Darby canine kidney cells to nearly the degree as WT PR8. In mice, however, they expressed explicit attenuation phenotypes, as revealed by their LD50 values: PR8, 32 plaque-forming units (PFU); HA(Min), 1.7 × 10(3) PFU; NA(Min), 2.4 × 10(5) PFU; (NA+HA)(Min), ≥3.16 × 10(6) PFU. Remarkably, (NA+HA)(Min) was attenuated >100,000-fold, with NA(Min) the major contributor to attenuation. In vaccinated mice (NA+HA)(Min) was highly effective in providing long-lasting protective immunity against lethal WT challenge at a median protective dose (PD50) of 2.4 PFU. Moreover, at a PD50 of only 147 or 237, (NA+HA)(Min) conferred protection against heterologous lethal challenges with two mouse-adapted H3N2 viruses. We conclude that the suppression of HA and NA is a unique strategy in live vaccine development.

  14. Chicken galectin-1B inhibits Newcastle disease virus adsorption and replication through binding to hemagglutinin-neuraminidase (HN) glycoprotein.

    Sun, Junfeng; Han, Zongxi; Qi, Tianming; Zhao, Ran; Liu, Shengwang

    2017-12-08

    Galectin-1 is an important immunoregulatory factor and can mediate the host-pathogen interaction via binding glycans on the surface of various viruses. We previously reported that avian respiratory viruses, including lentogenic Newcastle disease virus (NDV), can induce up-regulation of chicken galectin (CG)-1B in the primary target organ. In this study, we investigated whether CG-1B participated in the infectious process of NDV in chickens. We demonstrated that velogenic NDV induced up-regulation of CG-1B in target organs. We also found that CG-1B directly bound to NDV virions and inhibited their hemagglutination activity in vitro We confirmed that CG-1B interacted with NDV hemagglutinin-neuraminidase (HN) glycoprotein, in which the specific G4 N -glycans significantly contributed to the interaction between CG-1B and HN glycoprotein. The presence of extracellular CG-1B, rather than the internalization process, inhibited adsorption of NDV. The interaction between intracellular CG-1B and NDV HN glycoproteins inhibited cell-surface expression of HN glycoprotein and reduced the titer of progeny virus in NDV-infected DF-1 cells. Significantly, the replication of parental and HN glycosylation mutant viruses in CG-1B knockdown and overexpression cells demonstrated that the replication of NDV was correlated with the expression of CG-1B in a specific glycan-dependent manner. Collectively, our results indicate that CG-1B has anti-NDV activity by binding to N -glycans on HN glycoprotein. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Kallistatin Ameliorates Influenza Virus Pathogenesis by Inhibition of Kallikrein-Related Peptidase 1-Mediated Cleavage of Viral Hemagglutinin

    Leu, Chia-Hsing; Yang, Mei-Lin; Chung, Nai-Hui; Huang, Yen-Jang; Su, Yu-Chu; Chen, Yi-Cheng; Lin, Chia-Cheng; Shieh, Gia-Shing; Chang, Meng-Ya; Wang, Shainn-Wei; Chang, Yao; Chao, Julie; Chao, Lee

    2015-01-01

    Proteolytic cleavage of the hemagglutinin (HA) of influenza virus by host trypsin-like proteases is required for viral infectivity. Some serine proteases are capable of cleaving influenza virus HA, whereas some serine protease inhibitors (serpins) inhibit the HA cleavage in various cell types. Kallikrein-related peptidase 1 (KLK1, also known as tissue kallikrein) is a widely distributed serine protease. Kallistatin, a serpin synthesized mainly in the liver and rapidly secreted into the circulation, forms complexes with KLK1 and inhibits its activity. Here, we investigated the roles of KLK1 and kallistatin in influenza virus infection. We show that the levels of KLK1 increased, whereas those of kallistatin decreased, in the lungs of mice during influenza virus infection. KLK1 cleaved H1, H2, and H3 HA molecules and consequently enhanced viral production. In contrast, kallistatin inhibited KLK1-mediated HA cleavage and reduced viral production. Cells transduced with the kallistatin gene secreted kallistatin extracellularly, which rendered them more resistant to influenza virus infection. Furthermore, lentivirus-mediated kallistatin gene delivery protected mice against lethal influenza virus challenge by reducing the viral load, inflammation, and injury in the lung. Taking the data together, we determined that KLK1 and kallistatin contribute to the pathogenesis of influenza virus by affecting the cleavage of the HA peptide and inflammatory responses. This study provides a proof of principle for the potential therapeutic application of kallistatin or other KLK1 inhibitors for influenza. Since proteolytic activation also enhances the infectivity of some other viruses, kallistatin and other kallikrein inhibitors may be explored as antiviral agents against these viruses. PMID:26149981

  16. Pre-clinical evaluation of a replication-competent recombinant adenovirus serotype 4 vaccine expressing influenza H5 hemagglutinin.

    Alexander, Jeff; Ward, Simone; Mendy, Jason; Manayani, Darly J; Farness, Peggy; Avanzini, Jenny B; Guenther, Ben; Garduno, Fermin; Jow, Lily; Snarsky, Victoria; Ishioka, Glenn; Dong, Xin; Vang, Lo; Newman, Mark J; Mayall, Tim

    2012-01-01

    Influenza virus remains a significant health and social concern in part because of newly emerging strains, such as avian H5N1 virus. We have developed a prototype H5N1 vaccine using a recombinant, replication-competent Adenovirus serotype 4 (Ad4) vector, derived from the U.S. military Ad4 vaccine strain, to express the hemagglutinin (HA) gene from A/Vietnam/1194/2004 influenza virus (Ad4-H5-Vtn). Our hypothesis is that a mucosally-delivered replicating Ad4-H5-Vtn recombinant vector will be safe and induce protective immunity against H5N1 influenza virus infection and disease pathogenesis. The Ad4-H5-Vtn vaccine was designed with a partial deletion of the E3 region of Ad4 to accommodate the influenza HA gene. Replication and growth kinetics of the vaccine virus in multiple human cell lines indicated that the vaccine virus is attenuated relative to the wild type virus. Expression of the HA transgene in infected cells was documented by flow cytometry, western blot analysis and induction of HA-specific antibody and cellular immune responses in mice. Of particular note, mice immunized intranasally with the Ad4-H5-Vtn vaccine were protected against lethal H5N1 reassortant viral challenge even in the presence of pre-existing immunity to the Ad4 wild type virus. Several non-clinical attributes of this vaccine including safety, induction of HA-specific humoral and cellular immunity, and efficacy were demonstrated using an animal model to support Phase 1 clinical trial evaluation of this new vaccine.

  17. Centralized Consensus Hemagglutinin Genes Induce Protective Immunity against H1, H3 and H5 Influenza Viruses.

    Richard J Webby

    Full Text Available With the exception of the live attenuated influenza vaccine there have been no substantial changes in influenza vaccine strategies since the 1940's. Here we report an alternative vaccine approach that uses Adenovirus-vectored centralized hemagglutinin (HA genes as vaccine antigens. Consensus H1-Con, H3-Con and H5-Con HA genes were computationally derived. Mice were immunized with Ad vaccines expressing the centralized genes individually. Groups of mice were vaccinated with 1 X 1010, 5 X 107 and 1 X 107 virus particles per mouse to represent high, intermediate and low doses, respectively. 100% of the mice that were vaccinated with the high dose vaccine were protected from heterologous lethal challenges within each subtype. In addition to 100% survival, there were no signs of weight loss and disease in 7 out of 8 groups of high dose vaccinated mice. Lower doses of vaccine showed a reduction of protection in a dose-dependent manner. However, even the lowest dose of vaccine provided significant levels of protection against the divergent influenza strains, especially considering the stringency of the challenge virus. In addition, we found that all doses of H5-Con vaccine were capable of providing complete protection against mortality when challenged with lethal doses of all 3 H5N1 influenza strains. This data demonstrates that centralized H1-Con, H3-Con and H5-Con genes can be effectively used to completely protect mice against many diverse strains of influenza. Therefore, we believe that these Ad-vectored centralized genes could be easily translated into new human vaccines.

  18. Pre-clinical evaluation of a replication-competent recombinant adenovirus serotype 4 vaccine expressing influenza H5 hemagglutinin.

    Jeff Alexander

    Full Text Available Influenza virus remains a significant health and social concern in part because of newly emerging strains, such as avian H5N1 virus. We have developed a prototype H5N1 vaccine using a recombinant, replication-competent Adenovirus serotype 4 (Ad4 vector, derived from the U.S. military Ad4 vaccine strain, to express the hemagglutinin (HA gene from A/Vietnam/1194/2004 influenza virus (Ad4-H5-Vtn. Our hypothesis is that a mucosally-delivered replicating Ad4-H5-Vtn recombinant vector will be safe and induce protective immunity against H5N1 influenza virus infection and disease pathogenesis.The Ad4-H5-Vtn vaccine was designed with a partial deletion of the E3 region of Ad4 to accommodate the influenza HA gene. Replication and growth kinetics of the vaccine virus in multiple human cell lines indicated that the vaccine virus is attenuated relative to the wild type virus. Expression of the HA transgene in infected cells was documented by flow cytometry, western blot analysis and induction of HA-specific antibody and cellular immune responses in mice. Of particular note, mice immunized intranasally with the Ad4-H5-Vtn vaccine were protected against lethal H5N1 reassortant viral challenge even in the presence of pre-existing immunity to the Ad4 wild type virus.Several non-clinical attributes of this vaccine including safety, induction of HA-specific humoral and cellular immunity, and efficacy were demonstrated using an animal model to support Phase 1 clinical trial evaluation of this new vaccine.

  19. Image Segmentation, Registration, Compression, and Matching

    Yadegar, Jacob; Wei, Hai; Yadegar, Joseph; Ray, Nilanjan; Zabuawala, Sakina

    2011-01-01

    A novel computational framework was developed of a 2D affine invariant matching exploiting a parameter space. Named as affine invariant parameter space (AIPS), the technique can be applied to many image-processing and computer-vision problems, including image registration, template matching, and object tracking from image sequence. The AIPS is formed by the parameters in an affine combination of a set of feature points in the image plane. In cases where the entire image can be assumed to have undergone a single affine transformation, the new AIPS match metric and matching framework becomes very effective (compared with the state-of-the-art methods at the time of this reporting). No knowledge about scaling or any other transformation parameters need to be known a priori to apply the AIPS framework. An automated suite of software tools has been created to provide accurate image segmentation (for data cleaning) and high-quality 2D image and 3D surface registration (for fusing multi-resolution terrain, image, and map data). These tools are capable of supporting existing GIS toolkits already in the marketplace, and will also be usable in a stand-alone fashion. The toolkit applies novel algorithmic approaches for image segmentation, feature extraction, and registration of 2D imagery and 3D surface data, which supports first-pass, batched, fully automatic feature extraction (for segmentation), and registration. A hierarchical and adaptive approach is taken for achieving automatic feature extraction, segmentation, and registration. Surface registration is the process of aligning two (or more) data sets to a common coordinate system, during which the transformation between their different coordinate systems is determined. Also developed here are a novel, volumetric surface modeling and compression technique that provide both quality-guaranteed mesh surface approximations and compaction of the model sizes by efficiently coding the geometry and connectivity

  20. Structural differences between the avian and human H7N9 hemagglutinin proteins are attributable to modifications in salt bridge formation: a computational study with implications in viral evolution.

    Cueno, Marni E; Imai, Kenichi; Tamura, Muneaki; Ochiai, Kuniyasu

    2013-01-01

    Influenza A hemagglutinin (HA) is a homotrimeric glycoprotein composed of a fibrous globular stem supporting a globular head containing three sialic acid binding sites responsible for infection. The H7N9 strain has consistently infected an avian host, however, the novel 2013 strain is now capable of infecting a human host which would imply that the HA in both strains structurally differ. A better understanding of the structural differences between the avian and human H7N9 strains may shed light into viral evolution and transmissibility. In this study, we elucidated the structural differences between the avian and human H7N9 strains. Throughout the study, we generated HA homology models, verified the quality of each model, superimposed HA homology models to determine structural differences, and, likewise, elucidated the probable cause for these structural differences. We detected two different types of structural differences between the novel H7N9 human and representative avian strains, wherein, one type (Pattern-1) showed three non-overlapping regions while the other type (Pattern-2) showed only one non-overlapping region. In addition, we found that superimposed HA homology models exhibiting Pattern-1 contain three non-overlapping regions designated as: Region-1 (S1571-A1601); Region-3 (R2621-S2651); and Region-4 (S2701-D2811), whereas, superimposed HA homology models showing Pattern-2 only contain one non-overlapping region designated as Region-2 (S1371-S1451). We attributed the two patterns we observed to either the presence of salt bridges involving the E1141 residue or absence of the R1411:D771 salt bridge. Interestingly, comparison between the human H7N7 and H7N9 HA homology models showed high structural similarity. We propose that the putative absence of the R1411:D771 salt bridge coupled with the putative presence of the E1141:R2621 and E1141:K2641 salt bridges found in the 2013 H7N9 HA homology model is associated to human-type receptor binding. This

  1. Structural differences between the avian and human H7N9 hemagglutinin proteins are attributable to modifications in salt bridge formation: a computational study with implications in viral evolution.

    Marni E Cueno

    Full Text Available Influenza A hemagglutinin (HA is a homotrimeric glycoprotein composed of a fibrous globular stem supporting a globular head containing three sialic acid binding sites responsible for infection. The H7N9 strain has consistently infected an avian host, however, the novel 2013 strain is now capable of infecting a human host which would imply that the HA in both strains structurally differ. A better understanding of the structural differences between the avian and human H7N9 strains may shed light into viral evolution and transmissibility. In this study, we elucidated the structural differences between the avian and human H7N9 strains. Throughout the study, we generated HA homology models, verified the quality of each model, superimposed HA homology models to determine structural differences, and, likewise, elucidated the probable cause for these structural differences. We detected two different types of structural differences between the novel H7N9 human and representative avian strains, wherein, one type (Pattern-1 showed three non-overlapping regions while the other type (Pattern-2 showed only one non-overlapping region. In addition, we found that superimposed HA homology models exhibiting Pattern-1 contain three non-overlapping regions designated as: Region-1 (S1571-A1601; Region-3 (R2621-S2651; and Region-4 (S2701-D2811, whereas, superimposed HA homology models showing Pattern-2 only contain one non-overlapping region designated as Region-2 (S1371-S1451. We attributed the two patterns we observed to either the presence of salt bridges involving the E1141 residue or absence of the R1411:D771 salt bridge. Interestingly, comparison between the human H7N7 and H7N9 HA homology models showed high structural similarity. We propose that the putative absence of the R1411:D771 salt bridge coupled with the putative presence of the E1141:R2621 and E1141:K2641 salt bridges found in the 2013 H7N9 HA homology model is associated to human-type receptor binding

  2. Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators.

    Chiao, Chuan-Chin; Wickiser, J Kenneth; Allen, Justine J; Genter, Brock; Hanlon, Roger T

    2011-05-31

    Camouflage is a widespread phenomenon throughout nature and an important antipredator tactic in natural selection. Many visual predators have keen color perception, and thus camouflage patterns should provide some degree of color matching in addition to other visual factors such as pattern, contrast, and texture. Quantifying camouflage effectiveness in the eyes of the predator is a challenge from the perspectives of both biology and optical imaging technology. Here we take advantage of hyperspectral imaging (HSI), which records full-spectrum light data, to simultaneously visualize color match and pattern match in the spectral and the spatial domains, respectively. Cuttlefish can dynamically camouflage themselves on any natural substrate and, despite their colorblindness, produce body patterns that appear to have high-fidelity color matches to the substrate when viewed directly by humans or with RGB images. Live camouflaged cuttlefish on natural backgrounds were imaged using HSI, and subsequent spectral analysis revealed that most reflectance spectra of individual cuttlefish and substrates were similar, rendering the color match possible. Modeling color vision of potential di- and trichromatic fish predators of cuttlefish corroborated the spectral match analysis and demonstrated that camouflaged cuttlefish show good color match as well as pattern match in the eyes of fish predators. These findings (i) indicate the strong potential of HSI technology to enhance studies of biological coloration and (ii) provide supporting evidence that cuttlefish can produce color-coordinated camouflage on natural substrates despite lacking color vision.

  3. A human monoclonal antibody derived from a vaccinated volunteer recognizes heterosubtypically a novel epitope on the hemagglutinin globular head of H1 and H9 influenza A viruses

    Boonsathorn, Naphatsawan; Panthong, Sumolrat; Koksunan, Sarawut; Chittaganpitch, Malinee; Phuygun, Siripaporn; Waicharoen, Sunthareeya; Prachasupap, Apichai; Sasaki, Tadahiro; Kubota-Koketsu, Ritsuko; Yasugi, Mayo; Ono, Ken-ichiro; Arai, Yasuha

    2014-01-01

    Highlights: • A human monoclonal antibody against influenza virus was produced from a volunteer. • The antibody was generated from the PBMCs of the volunteer using the fusion method. • The antibody neutralized heterosubtypically group 1 influenza A viruses (H1 and H9). • The antibody targeted a novel epitope in globular head region of the hemagglutinin. • Sequences of the identified epitope are highly conserved among H1 and H9 subtypes. - Abstract: Most neutralizing antibodies elicited during influenza virus infection or by vaccination have a narrow spectrum because they usually target variable epitopes in the globular head region of hemagglutinin (HA). In this study, we describe a human monoclonal antibody (HuMAb), 5D7, that was prepared from the peripheral blood lymphocytes of a vaccinated volunteer using the fusion method. The HuMAb heterosubtypically neutralizes group 1 influenza A viruses, including seasonal H1N1, 2009 pandemic H1N1 (H1N1pdm) and avian H9N2, with a strong hemagglutinin inhibition activity. Selection of an escape mutant showed that the HuMAb targets a novel conformational epitope that is located in the HA head region but is distinct from the receptor binding site. Furthermore, Phe114Ile substitution in the epitope made the HA unrecognizable by the HuMAb. Amino acid residues in the predicted epitope region are also highly conserved in the HAs of H1N1 and H9N2. The HuMAb reported here may be a potential candidate for the development of therapeutic/prophylactic antibodies against H1 and H9 influenza viruses

  4. A human monoclonal antibody derived from a vaccinated volunteer recognizes heterosubtypically a novel epitope on the hemagglutinin globular head of H1 and H9 influenza A viruses

    Boonsathorn, Naphatsawan; Panthong, Sumolrat [Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Muang, Nonthaburi (Thailand); Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo (Japan); Koksunan, Sarawut [Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Muang, Nonthaburi (Thailand); Chittaganpitch, Malinee; Phuygun, Siripaporn; Waicharoen, Sunthareeya [National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Muang, Nonthaburi (Thailand); Prachasupap, Apichai [Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health, Muang, Nonthaburi (Thailand); Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo (Japan); Sasaki, Tadahiro [Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka (Japan); Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo (Japan); Kubota-Koketsu, Ritsuko [Kanonji Institute, The Research Foundation for Microbial Diseases of Osaka University, Kanonji, Kagawa (Japan); Yasugi, Mayo [Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka (Japan); Ono, Ken-ichiro [Ina Laboratory, Medical and Biological Laboratories Corporation, Ltd., Ina, Nagano (Japan); Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo (Japan); Arai, Yasuha [Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka (Japan); and others

    2014-09-26

    Highlights: • A human monoclonal antibody against influenza virus was produced from a volunteer. • The antibody was generated from the PBMCs of the volunteer using the fusion method. • The antibody neutralized heterosubtypically group 1 influenza A viruses (H1 and H9). • The antibody targeted a novel epitope in globular head region of the hemagglutinin. • Sequences of the identified epitope are highly conserved among H1 and H9 subtypes. - Abstract: Most neutralizing antibodies elicited during influenza virus infection or by vaccination have a narrow spectrum because they usually target variable epitopes in the globular head region of hemagglutinin (HA). In this study, we describe a human monoclonal antibody (HuMAb), 5D7, that was prepared from the peripheral blood lymphocytes of a vaccinated volunteer using the fusion method. The HuMAb heterosubtypically neutralizes group 1 influenza A viruses, including seasonal H1N1, 2009 pandemic H1N1 (H1N1pdm) and avian H9N2, with a strong hemagglutinin inhibition activity. Selection of an escape mutant showed that the HuMAb targets a novel conformational epitope that is located in the HA head region but is distinct from the receptor binding site. Furthermore, Phe114Ile substitution in the epitope made the HA unrecognizable by the HuMAb. Amino acid residues in the predicted epitope region are also highly conserved in the HAs of H1N1 and H9N2. The HuMAb reported here may be a potential candidate for the development of therapeutic/prophylactic antibodies against H1 and H9 influenza viruses.

  5. Application of four different football match analysis systems

    Randers, Morten B; Mujika, Inigo; Hewitt, Adam

    2010-01-01

    Using a video-based time-motion analysis system, a semi-automatic multiple-camera system, and two commercially available GPS systems (GPS-1; 5 Hz and GPS-2; 1 Hz), we compared activity pattern and fatigue development in the same football match. Twenty football players competing in the Spanish...... a football game and can be used to study game-induced fatigue. Rather large between-system differences were present in the determination of the absolute distances covered, meaning that any comparisons of results between different match analysis systems should be done with caution....

  6. Compressed Subsequence Matching and Packed Tree Coloring

    Bille, Philip; Cording, Patrick Hagge; Gørtz, Inge Li

    2017-01-01

    We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size n compressing a string of size N and a pattern string of size m over an alphabet of size \\(\\sigma \\), our algorithm uses \\(O(n+\\frac{n\\sigma }{w})\\) space and \\(O(n+\\frac{n\\sigma }{w}+m\\log N\\log...... w\\cdot occ)\\) or \\(O(n+\\frac{n\\sigma }{w}\\log w+m\\log N\\cdot occ)\\) time. Here w is the word size and occ is the number of minimal occurrences of the pattern. Our algorithm uses less space than previous algorithms and is also faster for \\(occ=o(\\frac{n}{\\log N})\\) occurrences. The algorithm uses...... a new data structure that allows us to efficiently find the next occurrence of a given character after a given position in a compressed string. This data structure in turn is based on a new data structure for the tree color problem, where the node colors are packed in bit strings....

  7. Matchings with Externalities and Attitudes

    Branzei, Simina; Michalak, Tomasz; Rahwan, Talal

    2013-01-01

    Two-sided matchings are an important theoretical tool used to model markets and social interactions. In many real-life problems the utility of an agent is influenced not only by their own choices, but also by the choices that other agents make. Such an influence is called an externality. Whereas ...... where agents take different attitudes when reasoning about the actions of others. In particular, we study optimistic, neutral and pessimistic attitudes and provide both computational hardness results and polynomial-time algorithms for computing stable outcomes....

  8. Modeling Architectural Patterns Using Architectural Primitives

    Zdun, Uwe; Avgeriou, Paris

    2005-01-01

    Architectural patterns are a key point in architectural documentation. Regrettably, there is poor support for modeling architectural patterns, because the pattern elements are not directly matched by elements in modeling languages, and, at the same time, patterns support an inherent variability that

  9. Analysis of shots on target and goals scored in soccer matches ...

    The aim of this study was to analyse the characteristics and patterns of shots on target and goals scored during the 2012-European Championship. The broadcasted matches were recorded and converted into electronic video files for a computerbased analysis. This quantitative study examined 31 matches of the ...

  10. Canine distemper virus neutralization activity is low in human serum and it is sensitive to an amino acid substitution in the hemagglutinin protein

    Zhang, Xinsheng; Wallace, Olivia L.; Domi, Arban; Wright, Kevin J.; Driscoll, Jonathan; Anzala, Omu; Sanders, Eduard J.; Kamali, Anatoli; Karita, Etienne; Allen, Susan; Fast, Pat; Gilmour, Jill; Price, Matt A.; Parks, Christopher L.

    2015-01-01

    Serum was analyzed from 146 healthy adult volunteers in eastern Africa to evaluate measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb) prevalence and potency. MV plaque reduction neutralization test (PRNT) results indicated that all sera were positive for MV nAbs. Furthermore, the 50% neutralizing dose (ND50) for the majority of sera corresponded to antibody titers induced by MV vaccination. CDV nAbs titers were low and generally were detected in sera with high MV nAb titers. A mutant CDV was generated that was less sensitive to neutralization by human serum. The mutant virus genome had 10 nucleotide substitutions, which coded for single amino acid substitutions in the fusion (F) and hemagglutinin (H) glycoproteins and two substitutions in the large polymerase (L) protein. The H substitution occurred in a conserved region involved in receptor interactions among morbilliviruses, implying that this region is a target for cross-reactive neutralizing antibodies. - Highlights: • Screened 146 serum samples for measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb). • MV nAb is prevalent in the sera. • CDV neutralizing activity is generally low or absent and when detected it is present in sera with high MV nAb titers. • A neutralization-resistant CDV mutant was isolated using human serum selection. • A mutation was identified in the receptor-binding region of CDV hemagglutinin protein that confers the neutralization resistance

  11. Canine distemper virus neutralization activity is low in human serum and it is sensitive to an amino acid substitution in the hemagglutinin protein

    Zhang, Xinsheng, E-mail: xzhang@iavi.org [AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative (IAVI), Brooklyn, NY (United States); Molecular and Cellular Biology Program, State University of New York, Brooklyn, NY (United States); Wallace, Olivia L.; Domi, Arban; Wright, Kevin J.; Driscoll, Jonathan [AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative (IAVI), Brooklyn, NY (United States); Anzala, Omu [Kenya AIDS Vaccine Initiative (KAVI)-Institute of Clinical Research, Nairobi (Kenya); Sanders, Eduard J. [Centre for Geographic Medicine Research, Kenya Medical Research Institute (KEMRI), Kilifi, Kenya & Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Headington (United Kingdom); Kamali, Anatoli [MRC/UVRI Uganda Virus Research Unit on AIDS, Masaka and Entebbe (Uganda); Karita, Etienne [Projet San Francisco, Kigali (Rwanda); Allen, Susan [Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA (United States); Fast, Pat [Department of Medical Affairs, International AIDS Vaccine Initiative, NY, NY (United States); Gilmour, Jill [Human Immunology Laboratory, International AIDS Vaccine Initiative, London (United Kingdom); Price, Matt A. [Department of Medical Affairs, International AIDS Vaccine Initiative, NY, NY (United States); Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA (United States); Parks, Christopher L. [AIDS Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative (IAVI), Brooklyn, NY (United States); Molecular and Cellular Biology Program, State University of New York, Brooklyn, NY (United States)

    2015-08-15

    Serum was analyzed from 146 healthy adult volunteers in eastern Africa to evaluate measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb) prevalence and potency. MV plaque reduction neutralization test (PRNT) results indicated that all sera were positive for MV nAbs. Furthermore, the 50% neutralizing dose (ND50) for the majority of sera corresponded to antibody titers induced by MV vaccination. CDV nAbs titers were low and generally were detected in sera with high MV nAb titers. A mutant CDV was generated that was less sensitive to neutralization by human serum. The mutant virus genome had 10 nucleotide substitutions, which coded for single amino acid substitutions in the fusion (F) and hemagglutinin (H) glycoproteins and two substitutions in the large polymerase (L) protein. The H substitution occurred in a conserved region involved in receptor interactions among morbilliviruses, implying that this region is a target for cross-reactive neutralizing antibodies. - Highlights: • Screened 146 serum samples for measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb). • MV nAb is prevalent in the sera. • CDV neutralizing activity is generally low or absent and when detected it is present in sera with high MV nAb titers. • A neutralization-resistant CDV mutant was isolated using human serum selection. • A mutation was identified in the receptor-binding region of CDV hemagglutinin protein that confers the neutralization resistance.

  12. Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

    Hauck, Nastasja C.; Kirpach, Josiane; Kiefer, Christina; Farinelle, Sophie; Morris, Stephen A.; Muller, Claude P.; Lu, I-Na

    2018-01-01

    To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA) long alpha helix (LAH). Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants. PMID:29587397

  13. Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

    Nastasja C. Hauck

    2018-03-01

    Full Text Available To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA long alpha helix (LAH. Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants.

  14. Transient expression of hemagglutinin antigen from low pathogenic avian influenza A (H7N7 in Nicotiana benthamiana.

    Selvaraju Kanagarajan

    Full Text Available The influenza A virus is of global concern for the poultry industry, especially the H5 and H7 subtypes as they have the potential to become highly pathogenic for poultry. In this study, the hemagglutinin (HA of a low pathogenic avian influenza virus of the H7N7 subtype isolated from a Swedish mallard Anas platyrhynchos was sequenced, characterized and transiently expressed in Nicotiana benthamiana. Recently, plant expression systems have gained interest as an alternative for the production of vaccine antigens. To examine the possibility of expressing the HA protein in N. benthamiana, a cDNA fragment encoding the HA gene was synthesized de novo, modified with a Kozak sequence, a PR1a signal peptide, a C-terminal hexahistidine (6×His tag, and an endoplasmic retention signal (SEKDEL. The construct was cloned into a Cowpea mosaic virus (CPMV-based vector (pEAQ-HT and the resulting pEAQ-HT-HA plasmid, along with a vector (pJL3:p19 containing the viral gene-silencing suppressor p19 from Tomato bushy stunt virus, was agro-infiltrated into N. benthamiana. The highest gene expression of recombinant plant-produced, uncleaved HA (rHA0, as measured by quantitative real-time PCR was detected at 6 days post infiltration (dpi. Guided by the gene expression profile, rHA0 protein was extracted at 6 dpi and subsequently purified utilizing the 6×His tag and immobilized metal ion adsorption chromatography. The yield was 0.2 g purified protein per kg fresh weight of leaves. Further molecular characterizations showed that the purified rHA0 protein was N-glycosylated and its identity confirmed by liquid chromatography-tandem mass spectrometry. In addition, the purified rHA0 exhibited hemagglutination and hemagglutination inhibition activity indicating that the rHA0 shares structural and functional properties with native HA protein of H7 influenza virus. Our results indicate that rHA0 maintained its native antigenicity and specificity, providing a good source of

  15. H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets.

    Marion Russier

    2017-03-01

    Full Text Available A pandemic-capable influenza virus requires a hemagglutinin (HA surface glycoprotein that is immunologically unseen by most people and is capable of supporting replication and transmission in humans. HA stabilization has been linked to 2009 pH1N1 pandemic potential in humans and H5N1 airborne transmissibility in the ferret model. Swine have served as an intermediate host for zoonotic influenza viruses, yet the evolutionary pressure exerted by this host on HA stability was unknown. For over 70 contemporary swine H1 and H3 isolates, we measured HA activation pH to range from pH 5.1 to 5.9 for H1 viruses and pH 5.3 to 5.8 for H3 viruses. Thus, contemporary swine isolates vary widely in HA stability, having values favored by both avian (pH >5.5 and human and ferret (pH ≤5.5 species. Using an early 2009 pandemic H1N1 (pH1N1 virus backbone, we generated three viruses differing by one HA residue that only altered HA stability: WT (pH 5.5, HA1-Y17H (pH 6.0, and HA2-R106K (pH 5.3. All three replicated in pigs and transmitted from pig-to-pig and pig-to-ferret. WT and R106 viruses maintained HA genotype and phenotype after transmission. Y17H (pH 6.0 acquired HA mutations that stabilized the HA protein to pH 5.8 after transmission to pigs and 5.5 after transmission to ferrets. Overall, we found swine support a broad range of HA activation pH for contact transmission and many recent swine H1N1 and H3N2 isolates have stabilized (human-like HA proteins. This constitutes a heightened pandemic risk and underscores the importance of ongoing surveillance and control efforts for swine viruses.

  16. Reducing the likelihood of long tennis matches.

    Barnett, Tristan; Alan, Brown; Pollard, Graham

    2006-01-01

    Long matches can cause problems for tournaments. For example, the starting times of subsequent matches can be substantially delayed causing inconvenience to players, spectators, officials and television scheduling. They can even be seen as unfair in the tournament setting when the winner of a very long match, who may have negative aftereffects from such a match, plays the winner of an average or shorter length match in the next round. Long matches can also lead to injuries to the participating players. One factor that can lead to long matches is the use of the advantage set as the fifth set, as in the Australian Open, the French Open and Wimbledon. Another factor is long rallies and a greater than average number of points per game. This tends to occur more frequently on the slower surfaces such as at the French Open. The mathematical method of generating functions is used to show that the likelihood of long matches can be substantially reduced by using the tiebreak game in the fifth set, or more effectively by using a new type of game, the 50-40 game, throughout the match. Key PointsThe cumulant generating function has nice properties for calculating the parameters of distributions in a tennis matchA final tiebreaker set reduces the length of matches as currently being used in the US OpenA new 50-40 game reduces the length of matches whilst maintaining comparable probabilities for the better player to win the match.

  17. Ontology Matching with Semantic Verification.

    Jean-Mary, Yves R; Shironoshita, E Patrick; Kabuka, Mansur R

    2009-09-01

    ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies.

  18. Fast matching of sensor data with manual observations.

    Jit, Biswas; Maniyeri, Jayachandran; Louis, Shue; Philip, Yap Lin Kiat

    2009-01-01

    In systems and trials concerning wearable sensors and devices used for medical data collection, the validation of sensor data with respect to manual observations is very important. However, this is often problematic because of feigned behavior, errors in manual recording (misclassification), gaps in recording (missing readings), missed observations and timing mismatch between manual observations and sensor data due to a difference in time granularity. Using sleep activity pattern monitoring as an example we present a fast algorithm for matching sensor data with manual observations. Major components include a) signal analysis to classify states of sleep activity pattern, b) matching of states with Sleep Diary (SD) and c) automated detection of anomalies and reconciliation of mismatches between the SD and the sensor data.

  19. Using crosswell data to enhance history matching

    Ravanelli, Fabio M.; Hoteit, Ibrahim

    2014-01-01

    of the reality. This problem is mitigated by conditioning the model with data through data assimilation, a process known in the oil industry as history matching. Several recent advances are being used to improve history matching reliability, notably the use

  20. A multiscale approach to mutual information matching

    Pluim, J.P.W.; Maintz, J.B.A.; Viergever, M.A.; Hanson, K.M.

    1998-01-01

    Methods based on mutual information have shown promising results for matching of multimodal brain images. This paper discusses a multiscale approach to mutual information matching, aiming for an acceleration of the matching process while considering the accuracy and robustness of the method. Scaling

  1. Connections between the matching and chromatic polynomials

    E. J. Farrell

    1992-01-01

    Full Text Available The main results established are (i a connection between the matching and chromatic polynomials and (ii a formula for the matching polynomial of a general complement of a subgraph of a graph. Some deductions on matching and chromatic equivalence and uniqueness are made.

  2. Database crime to crime match rate calculation.

    Buckleton, John; Bright, Jo-Anne; Walsh, Simon J

    2009-06-01

    Guidance exists on how to count matches between samples in a crime sample database but we are unable to locate a definition of how to estimate a match rate. We propose a method that does not proceed from the match counting definition but which has a strong logic.

  3. Efficient Aho-Corasick String Matching on Emerging Multicore Architectures

    Tumeo, Antonino; Villa, Oreste; Secchi, Simone; Chavarría-Miranda, Daniel

    2013-12-12

    String matching algorithms are critical to several scientific fields. Beside text processing and databases, emerging applications such as DNA protein sequence analysis, data mining, information security software, antivirus, ma- chine learning, all exploit string matching algorithms [3]. All these applica- tions usually process large quantity of textual data, require high performance and/or predictable execution times. Among all the string matching algorithms, one of the most studied, especially for text processing and security applica- tions, is the Aho-Corasick algorithm. 1 2 Book title goes here Aho-Corasick is an exact, multi-pattern string matching algorithm which performs the search in a time linearly proportional to the length of the input text independently from pattern set size. However, depending on the imple- mentation, when the number of patterns increase, the memory occupation may raise drastically. In turn, this can lead to significant variability in the performance, due to the memory access times and the caching effects. This is a significant concern for many mission critical applications and modern high performance architectures. For example, security applications such as Network Intrusion Detection Systems (NIDS), must be able to scan network traffic against very large dictionaries in real time. Modern Ethernet links reach up to 10 Gbps, and malicious threats are already well over 1 million, and expo- nentially growing [28]. When performing the search, a NIDS should not slow down the network, or let network packets pass unchecked. Nevertheless, on the current state-of-the-art cache based processors, there may be a large per- formance variability when dealing with big dictionaries and inputs that have different frequencies of matching patterns. In particular, when few patterns are matched and they are all in the cache, the procedure is fast. Instead, when they are not in the cache, often because many patterns are matched and the caches are

  4. Geographic Trends in the Plastic Surgery Match.

    Silvestre, Jason; Lin, Ines C; Serletti, Joseph M; Chang, Benjamin

    2016-01-01

    The integrated plastic surgery match is among the most competitive residency matches in recent years. Although previous studies have correlated applicant characteristics with successful match outcomes, none have comprehensively investigated the role of geography in the match. This study elucidates regional biases in the match. Plastic surgery residents who matched during 2011-2015 were eligible for study inclusion. Names of residents were obtained from official residency program websites and cross-referenced with data obtained from the Student Doctor Network. For each resident, region of residency program and medical school were compared. From 67 programs, 622 residents were identified. Most graduated from US medical schools (97.9%). A total of 94 residents matched at a home institution (15.1%). Half of the residents matched in the same region as their medical school (48.9%). Programs in the South matched the greatest number of residents from the same region (60.8%), whereas West programs matched the least (30.8%, p < 0.001). No regional differences existed regarding residents matching at their home institution (p = 0.268). More women matched at West programs (43.1%) versus East programs (30.6%, p < 0.05). A significant number of residents matched at their home institution. Roughly, half matched at a program in the same region as their medical school. Whether this regional phenomenon stems from applicant or program factors remains unknown. Yet, given the limited number of interviews and the high costs of interviewing, applicants and programs can use these data to help optimize the match process. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

  5. Image matching navigation based on fuzzy information

    田玉龙; 吴伟仁; 田金文; 柳健

    2003-01-01

    In conventional image matching methods, the image matching process is mostly based on image statistic information. One aspect neglected by all these methods is that there is much fuzzy information contained in these images. A new fuzzy matching algorithm based on fuzzy similarity for navigation is presented in this paper. Because the fuzzy theory is of the ability of making good description of the fuzzy information contained in images, the image matching method based on fuzzy similarity would look forward to producing good performance results. Experimental results using matching algorithm based on fuzzy information also demonstrate its reliability and practicability.

  6. Best Practices for NPT Transit Matching

    Gilligan, Kimberly V.; Whitaker, J. Michael; Oakberg, John A.; Snow, Catherine

    2016-01-01

    Transit matching is the process for relating or matching reports of shipments and receipts submitted to the International Atomic Energy Agency (IAEA). Transit matching is a component used by the IAEA in drawing safeguards conclusions and performing investigative analysis. Transit matching is part of IAEA safeguards activities and the State evaluation process, and it is included in the annual Safeguards Implementation Report (SIR). Annually, the IAEA currently receives reports of ~900,000 nuclear material transactions, of which ~500,000 are for domestic and foreign transfers. Of these the IAEA software can automatically match (i.e., machine match) about 95% of the domestic transfers and 25% of the foreign transfers. Given the increasing demands upon IAEA resources, it is highly desirable for the machine-matching process to match as many transfers as possible. Researchers at Oak Ridge National Laboratory (ORNL) have conducted an investigation funded by the National Nuclear Security Administration through the Next Generation Safeguards Initiative to identify opportunities to strengthen IAEA transit matching. Successful matching, and more specifically machine matching, is contingent on quality data from the reporting States. In February 2016, ORNL hosted representatives from three States, the IAEA, and Euratom to share results from past studies and to discuss the processes, policies, and procedures associated with State reporting for transit matching. Drawing on each entity's experience and knowledge, ORNL developed a best practices document to be shared with the international safeguards community to strengthen transit matching. This paper shares the recommendations that resulted from this strategic meeting and the next steps being taken to strengthen transit matching.

  7. Probabilistic seismic history matching using binary images

    Davolio, Alessandra; Schiozer, Denis Jose

    2018-02-01

    Currently, the goal of history-matching procedures is not only to provide a model matching any observed data but also to generate multiple matched models to properly handle uncertainties. One such approach is a probabilistic history-matching methodology based on the discrete Latin Hypercube sampling algorithm, proposed in previous works, which was particularly efficient for matching well data (production rates and pressure). 4D seismic (4DS) data have been increasingly included into history-matching procedures. A key issue in seismic history matching (SHM) is to transfer data into a common domain: impedance, amplitude or pressure, and saturation. In any case, seismic inversions and/or modeling are required, which can be time consuming. An alternative to avoid these procedures is using binary images in SHM as they allow the shape, rather than the physical values, of observed anomalies to be matched. This work presents the incorporation of binary images in SHM within the aforementioned probabilistic history matching. The application was performed with real data from a segment of the Norne benchmark case that presents strong 4D anomalies, including softening signals due to pressure build up. The binary images are used to match the pressurized zones observed in time-lapse data. Three history matchings were conducted using: only well data, well and 4DS data, and only 4DS. The methodology is very flexible and successfully utilized the addition of binary images for seismic objective functions. Results proved the good convergence of the method in few iterations for all three cases. The matched models of the first two cases provided the best results, with similar well matching quality. The second case provided models presenting pore pressure changes according to the expected dynamic behavior (pressurized zones) observed on 4DS data. The use of binary images in SHM is relatively new with few examples in the literature. This work enriches this discussion by presenting a new

  8. Best Practices for NPT Transit Matching

    Gilligan, Kimberly V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Whitaker, J. Michael [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Oakberg, John A. [Tetra Tech, Inc., Oak Ridge, TN (United States); Snow, Catherine [Sno Consulting, LLC, Sandy, UT (United States)

    2016-09-01

    Transit matching is the process for relating or matching reports of shipments and receipts submitted to the International Atomic Energy Agency (IAEA). Transit matching is a component used by the IAEA in drawing safeguards conclusions and performing investigative analysis. Transit matching is part of IAEA safeguards activities and the State evaluation process, and it is included in the annual Safeguards Implementation Report (SIR). Annually, the IAEA currently receives reports of ~900,000 nuclear material transactions, of which ~500,000 are for domestic and foreign transfers. Of these the IAEA software can automatically match (i.e., machine match) about 95% of the domestic transfers and 25% of the foreign transfers. Given the increasing demands upon IAEA resources, it is highly desirable for the machine-matching process to match as many transfers as possible. Researchers at Oak Ridge National Laboratory (ORNL) have conducted an investigation funded by the National Nuclear Security Administration through the Next Generation Safeguards Initiative to identify opportunities to strengthen IAEA transit matching. Successful matching, and more specifically machine matching, is contingent on quality data from the reporting States. In February 2016, ORNL hosted representatives from three States, the IAEA, and Euratom to share results from past studies and to discuss the processes, policies, and procedures associated with State reporting for transit matching. Drawing on each entity's experience and knowledge, ORNL developed a best practices document to be shared with the international safeguards community to strengthen transit matching. This paper shares the recommendations that resulted from this strategic meeting and the next steps being taken to strengthen transit matching.

  9. Matching energy sources to demand

    Hendry, A.

    1979-01-01

    Diagrams show the current pattern of energy usage in Scotland; primary energy inputs; the various classes of user; the disposition of input energy in terms of useful and waste energy; an energy flow diagram showing the proportions of primary fuels taken by the various user groups and the proportions of useful energy derived by each. Within the S.S.E.B. area, installed capacity and maximum demand are shown for the present and projected future to the year 2000. A possible energy flow diagram for Scotland in 1996 is shown. The more efficient use of energy is discussed, with particular reference to the use of electricity. The primary energy inputs considered are oil, coal, nuclear, hydro and gas. (U.K.)

  10. Influenza A Virus Hemagglutinin is Required for the Assembly of Viral Components Including Bundled vRNPs at the Lipid Raft

    Naoki Takizawa

    2016-09-01

    Full Text Available The influenza glycoproteins, hemagglutinin (HA and neuraminidase (NA, which are associated with the lipid raft, have the potential to initiate virion budding. However, the role of these viral proteins in infectious virion assembly is still unclear. In addition, it is not known how the viral ribonucleoprotein complex (vRNP is tethered to the budding site. Here, we show that HA is necessary for the efficient progeny virion production and vRNP packaging in the virion. We also found that the level of HA does not affect the bundling of the eight vRNP segments, despite reduced virion production. Detergent solubilization and a subsequent membrane flotation analysis indicated that the accumulation of nucleoprotein, viral polymerases, NA, and matrix protein 1 (M1 in the lipid raft fraction was delayed without HA. Based on our results, we inferred that HA plays a role in the accumulation of viral components, including bundled vRNPs, at the lipid raft.

  11. Neuraminidase stalk length and additional glycosylation of the hemagglutinin influence the virulence of influenza H5N1 viruses for mice.

    Matsuoka, Yumiko; Swayne, David E; Thomas, Colleen; Rameix-Welti, Marie-Anne; Naffakh, Nadia; Warnes, Christine; Altholtz, Melanie; Donis, Ruben; Subbarao, Kanta

    2009-05-01

    Following circulation of avian influenza H5 and H7 viruses in poultry, the hemagglutinin (HA) can acquire additional glycosylation sites, and the neuraminidase (NA) stalk becomes shorter. We investigated whether these features play a role in the pathogenesis of infection in mammalian hosts. From 1996 to 2007, H5N1 viruses with a short NA stalk have become widespread in several avian species. Compared to viruses with a long-stalk NA, viruses with a short-stalk NA showed a decreased capacity to elute from red blood cells and an increased virulence in mice, but not in chickens. The presence of additional HA glycosylation sites had less of an effect on virulence than did NA stalk length. The short-stalk NA of H5N1 viruses circulating in Asia may contribute to virulence in humans.

  12. Neuraminidase Stalk Length and Additional Glycosylation of the Hemagglutinin Influence the Virulence of Influenza H5N1 Viruses for Mice▿

    Matsuoka, Yumiko; Swayne, David E.; Thomas, Colleen; Rameix-Welti, Marie-Anne; Naffakh, Nadia; Warnes, Christine; Altholtz, Melanie; Donis, Ruben; Subbarao, Kanta

    2009-01-01

    Following circulation of avian influenza H5 and H7 viruses in poultry, the hemagglutinin (HA) can acquire additional glycosylation sites, and the neuraminidase (NA) stalk becomes shorter. We investigated whether these features play a role in the pathogenesis of infection in mammalian hosts. From 1996 to 2007, H5N1 viruses with a short NA stalk have become widespread in several avian species. Compared to viruses with a long-stalk NA, viruses with a short-stalk NA showed a decreased capacity to elute from red blood cells and an increased virulence in mice, but not in chickens. The presence of additional HA glycosylation sites had less of an effect on virulence than did NA stalk length. The short-stalk NA of H5N1 viruses circulating in Asia may contribute to virulence in humans. PMID:19225004

  13. Influenza A Virus Hemagglutinin is Required for the Assembly of Viral Components Including Bundled vRNPs at the Lipid Raft.

    Takizawa, Naoki; Momose, Fumitaka; Morikawa, Yuko; Nomoto, Akio

    2016-09-10

    The influenza glycoproteins, hemagglutinin (HA) and neuraminidase (NA), which are associated with the lipid raft, have the potential to initiate virion budding. However, the role of these viral proteins in infectious virion assembly is still unclear. In addition, it is not known how the viral ribonucleoprotein complex (vRNP) is tethered to the budding site. Here, we show that HA is necessary for the efficient progeny virion production and vRNP packaging in the virion. We also found that the level of HA does not affect the bundling of the eight vRNP segments, despite reduced virion production. Detergent solubilization and a subsequent membrane flotation analysis indicated that the accumulation of nucleoprotein, viral polymerases, NA, and matrix protein 1 (M1) in the lipid raft fraction was delayed without HA. Based on our results, we inferred that HA plays a role in the accumulation of viral components, including bundled vRNPs, at the lipid raft.

  14. Fractional Order Element Based Impedance Matching

    Radwan, Ahmed Gomaa

    2014-06-24

    Disclosed are various embodiments of methods and systems related to fractional order element based impedance matching. In one embodiment, a method includes aligning a traditional Smith chart (|.alpha.|=1) with a fractional order Smith chart (|.alpha.|.noteq.1). A load impedance is located on the traditional Smith chart and projected onto the fractional order Smith chart. A fractional order matching element is determined by transitioning along a matching circle of the fractional order Smith chart based at least in part upon characteristic line impedance. In another embodiment, a system includes a fractional order impedance matching application executed in a computing device. The fractional order impedance matching application includes logic that obtains a first set of Smith chart coordinates at a first order, determines a second set of Smith chart coordinates at a second order, and determines a fractional order matching element from the second set of Smith chart coordinates.

  15. Recombinant Parainfluenza Virus 5 Expressing Hemagglutinin of Influenza A Virus H5N1 Protected Mice against Lethal Highly Pathogenic Avian Influenza Virus H5N1 Challenge

    Li, Zhuo; Mooney, Alaina J.; Gabbard, Jon D.; Gao, Xiudan; Xu, Pei; Place, Ryan J.; Hogan, Robert J.; Tompkins, S. Mark

    2013-01-01

    A safe and effective vaccine is the best way to prevent large-scale highly pathogenic avian influenza virus (HPAI) H5N1 outbreaks in the human population. The current FDA-approved H5N1 vaccine has serious limitations. A more efficacious H5N1 vaccine is urgently needed. Parainfluenza virus 5 (PIV5), a paramyxovirus, is not known to cause any illness in humans. PIV5 is an attractive vaccine vector. In our studies, a single dose of a live recombinant PIV5 expressing a hemagglutinin (HA) gene of H5N1 (rPIV5-H5) from the H5N1 subtype provided sterilizing immunity against lethal doses of HPAI H5N1 infection in mice. Furthermore, we have examined the effect of insertion of H5N1 HA at different locations within the PIV5 genome on the efficacy of a PIV5-based vaccine. Interestingly, insertion of H5N1 HA between the leader sequence, the de facto promoter of PIV5, and the first viral gene, nucleoprotein (NP), did not lead to a viable virus. Insertion of H5N1 HA between NP and the next gene, V/phosphorprotein (V/P), led to a virus that was defective in growth. We have found that insertion of H5N1 HA at the junction between the small hydrophobic (SH) gene and the hemagglutinin-neuraminidase (HN) gene gave the best immunity against HPAI H5N1 challenge: a dose as low as 1,000 PFU was sufficient to protect against lethal HPAI H5N1 challenge in mice. The work suggests that recombinant PIV5 expressing H5N1 HA has great potential as an HPAI H5N1 vaccine. PMID:23077314

  16. Broadly-Reactive Neutralizing and Non-neutralizing Antibodies Directed against the H7 Influenza Virus Hemagglutinin Reveal Divergent Mechanisms of Protection.

    Gene S Tan

    2016-04-01

    Full Text Available In the early spring of 2013, Chinese health authorities reported several cases of H7N9 influenza virus infections in humans. Since then the virus has established itself at the human-animal interface in Eastern China and continues to cause several hundred infections annually. In order to characterize the antibody response to the H7N9 virus we generated several mouse monoclonal antibodies against the hemagglutinin of the A/Shanghai/1/13 (H7N9 virus. Of particular note are two monoclonal antibodies, 1B2 and 1H5, that show broad reactivity to divergent H7 hemagglutinins. Monoclonal antibody 1B2 binds to viruses of the Eurasian and North American H7 lineages and monoclonal antibody 1H5 reacts broadly to virus isolates of the Eurasian lineage. Interestingly, 1B2 shows broad hemagglutination inhibiting and neutralizing activity, while 1H5 fails to inhibit hemagglutination and demonstrates no neutralizing activity in vitro. However, both monoclonal antibodies were highly protective in an in vivo passive transfer challenge model in mice, even at low doses. Experiments using mutant antibodies that lack the ability for Fc/Fc-receptor and Fc/complement interactions suggest that the protection provided by mAb 1H5 is, at least in part, mediated by the Fc-fragment of the mAb. These findings highlight that a protective response to a pathogen may not only be due to neutralizing antibodies, but can also be the result of highly efficacious non-neutralizing antibodies not readily detected by classical in vitro neutralization or hemagglutination inhibition assays. This is of interest because H7 influenza virus vaccines induce only low hemagglutination inhibiting antibody titers while eliciting robust antibody titers as measured by ELISA. Our data suggest that these binding but non-neutralizing antibodies contribute to protection in vivo.

  17. Fast and compact regular expression matching

    Bille, Philip; Farach-Colton, Martin

    2008-01-01

    We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized words to be manipulated in constant time. We show how...... to improve the space and/or remove a dependency on the alphabet size for each problem using either an improved tabulation technique of an existing algorithm or by combining known algorithms in a new way....

  18. Matching fields and lattice points of simplices

    Loho, Georg; Smith, Ben

    2018-01-01

    We show that the Chow covectors of a linkage matching field define a bijection of lattice points and we demonstrate how one can recover the linkage matching field from this bijection. This resolves two open questions from Sturmfels & Zelevinsky (1993) on linkage matching fields. For this, we give an explicit construction that associates a bipartite incidence graph of an ordered partition of a common set to all lattice points in a dilated simplex. Given a triangulation of a product of two simp...

  19. Online Job Search and Matching Quality

    Constantin Mang

    2012-01-01

    The Internet has fundamentally changed the way workers and firms are matched on the job market. Compared to newspapers and other traditional employment resources, online job boards presumably lead to better matches by providing a wider choice of job advertisements and more sophisticated methods for finding suitable vacancies. This study investigates the association of online job search and matching quality using individual-level data from the German Socio-Economic Panel (SOEP). My results sho...

  20. Polyhedral patterns

    Jiang, Caigui; Tang, Chengcheng; Vaxman, Amir; Wonka, Peter; Pottmann, Helmut

    2015-01-01

    We study the design and optimization of polyhedral patterns, which are patterns of planar polygonal faces on freeform surfaces. Working with polyhedral patterns is desirable in architectural geometry and industrial design. However, the classical

  1. Matching and correlation computations in stereoscopic depth perception.

    Doi, Takahiro; Tanabe, Seiji; Fujita, Ichiro

    2011-03-02

    A fundamental task of the visual system is to infer depth by using binocular disparity. To encode binocular disparity, the visual cortex performs two distinct computations: one detects matched patterns in paired images (matching computation); the other constructs the cross-correlation between the images (correlation computation). How the two computations are used in stereoscopic perception is unclear. We dissociated their contributions in near/far discrimination by varying the magnitude of the disparity across separate sessions. For small disparity (0.03°), subjects performed at chance level to a binocularly opposite-contrast (anti-correlated) random-dot stereogram (RDS) but improved their performance with the proportion of contrast-matched (correlated) dots. For large disparity (0.48°), the direction of perceived depth reversed with an anti-correlated RDS relative to that for a correlated one. Neither reversed nor normal depth was perceived when anti-correlation was applied to half of the dots. We explain the decision process as a weighted average of the two computations, with the relative weight of the correlation computation increasing with the disparity magnitude. We conclude that matching computation dominates fine depth perception, while both computations contribute to coarser depth perception. Thus, stereoscopic depth perception recruits different computations depending on the disparity magnitude.

  2. Anomalous dispersion enhanced Cerenkov phase-matching

    Kowalczyk, T.C.; Singer, K.D. [Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Physics; Cahill, P.A. [Sandia National Labs., Albuquerque, NM (United States)

    1993-11-01

    The authors report on a scheme for phase-matching second harmonic generation in polymer waveguides based on the use of anomalous dispersion to optimize Cerenkov phase matching. They have used the theoretical results of Hashizume et al. and Onda and Ito to design an optimum structure for phase-matched conversion. They have found that the use of anomalous dispersion in the design results in a 100-fold enhancement in the calculated conversion efficiency. This technique also overcomes the limitation of anomalous dispersion phase-matching which results from absorption at the second harmonic. Experiments are in progress to demonstrate these results.

  3. The Gastroenterology Fellowship Match: A Decade Later.

    Huang, Robert J; Triadafilopoulos, George; Limsui, David

    2017-06-01

    Following a period of uncertainty and disorganization, the gastroenterology (GI) national leadership decided to reinstitute the fellowship match (the Match) under the auspices of the National Residency Matching Program (NRMP) in 2006. Although it has now been a decade since the rebirth of the Match, there have been limited data published regarding progress made. In this piece, we discuss reasons for the original collapse of the GI Match, including most notably a perceived oversupply of GI physicians and a poor job market. We discuss the negative impacts the absence of the Match had on programs and on applicants, as well as the impetus to reorganize the Match under the NRMP. We then utilize data published annually by the NRMP to demonstrate that in the decade since its rebirth, the GI Match has been remarkably successful in terms of attracting the participation of applicants and programs. We show that previous misguided concerns of an oversupply of GI physicians were not realized, and that GI fellowship positions remain highly competitive for internal medicine applicants. Finally, we discuss possible implications of recent changes in the healthcare landscape on the GI Match.

  4. Genetic structure of human A/H1N1 and A/H3N2 influenza virus on Corsica Island: phylogenetic analysis and vaccine strain match, 2006-2010.

    Alessandra Falchi

    Full Text Available BACKGROUND: The aim of this study was to analyse the genetic patterns of Hemagglutinin (HA genes of influenza A strains circulating on Corsica Island during the 2006-2009 epidemic seasons and the 2009-2010 pandemic season. METHODS: Nasopharyngeal samples from 371 patients with influenza-like illness (ILI were collected by General Practitioners (GPs of the Sentinelles Network through a randomised selection routine. RESULTS: Phylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006-2007 to 2008-2009. Seasonal Corsican influenza A/H1N1 isolated during the 2007-2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008-2009 season. The A/H1N1 2009 (A/H1N1pdm strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E. The percentages of the perfect match vaccine efficacy, estimated by using the p(epitope model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene. CONCLUSION: The molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006-2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.

  5. Natural Cytotoxicity Receptors: Pattern Recognition and Involvement of Carbohydrates

    Angel Porgador

    2005-01-01

    Full Text Available Natural cytotoxicity receptors (NCRs, expressed by natural killer (NK cells, trigger NK lysis of tumor and virus-infected cells on interaction with cell-surface ligands of these target cells. We have determined that viral hemagglutinins expressed on the surface of virus-infected cells are involved in the recognition by the NCRs, NKp44 and NKp46. Recognition of tumor cells by the NCRs NKp30 and NKp46 involves heparan sulfate epitopes expressed on the tumor cell membrane. Our studies provide new evidence for the identity of the ligands for NCRs and indicate that a broader definition should be applied to pathological patterns recognized by innate immune receptors. Since nonmicrobial endogenous carbohydrate structures contribute significantly to this recognition, there is an imperative need to develop appropriate tools for the facile sequencing of carbohydrate moieties.

  6. Scanless multitarget-matching multiphoton excitation fluorescence microscopy

    Junpeng Qiu

    2018-03-01

    Full Text Available Using the combination of a reflective blazed grating and a reflective phase-only diffractive spatial light modulator (SLM, scanless multitarget-matching multiphoton excitation fluorescence microscopy (SMTM-MPM was achieved. The SLM shaped an incoming mode-locked, near-infrared Ti:sapphire laser beam into an excitation pattern with addressable shapes and sizes that matched the samples of interest in the field of view. Temporal and spatial focusing were simultaneously realized by combining an objective lens and a blazed grating. The fluorescence signal from illuminated areas was recorded by a two-dimensional sCMOS camera. Compared with a conventional temporal focusing multiphoton microscope, our microscope achieved effective use of the laser power and decreased photodamage with higher axial resolution.

  7. On Tree-Constrained Matchings and Generalizations

    S. Canzar (Stefan); K. Elbassioni; G.W. Klau (Gunnar); J. Mestre

    2011-01-01

    htmlabstractWe consider the following \\textsc{Tree-Constrained Bipartite Matching} problem: Given two rooted trees $T_1=(V_1,E_1)$, $T_2=(V_2,E_2)$ and a weight function $w: V_1\\times V_2 \\mapsto \\mathbb{R}_+$, find a maximum weight matching $\\mathcal{M}$ between nodes of the two trees, such that

  8. Matching of Tore Supra ICRH antennas

    Ladurelle, L.; Beaumont, B.; Kuus, H.; Lombard, G.

    1994-01-01

    An automatic matching method is described for Tore Supra ICRH antennas based on impedance variations seen at their feed points. Error signals derived from directional voltage and phase measurements in the feeder allow to control the matching capacitors values for optimal power transmission. (author) 5 refs.; 9 figs

  9. DOE/Industry Matching Grant Program

    Lee, John C.

    2003-01-01

    For the academic year 2001-2002, the Department of Nuclear Engineering and Radiological Sciences received $50,000 of industrial contributions, matched by a DOE grant of $35,000. We used the combined DOE/Industry Matching Grant of $85,000 toward (a) undergraduate merit scholarships and research support, (b) graduate student support, and (c) partial support of a research scientist

  10. Object-based connectedness facilitates matching

    Koning, A.R.; Lier, R.J. van

    2003-01-01

    In two matching tasks, participants had to match two images of object pairs. Image-based (113) connectedness refers to connectedness between the objects in an image. Object-based (OB) connectedness refers to connectedness between the interpreted objects. In Experiment 1, a monocular depth cue

  11. On solution concepts for matching games

    Biro, Peter; Kern, Walter; Paulusma, Daniël; Kratochvil, J.; Li, A.; Fiala, J.; Kolman, P.

    A matching game is a cooperative game $(N,v)$ defined on a graph $G = (N,E)$ with an edge weighting $\\omega : E \\to {\\Bbb R}_+$ . The player set is $N$ and the value of a coalition $S \\subseteq  N$ is defined as the maximum weight of a matching in the subgraph induced by $S$. First we present an

  12. Equilibrium and matching under price controls

    Herings, P.J.J.

    2015-01-01

    The paper considers a one-to-one matching with contracts model in the presence of price controls. This set-up contains two important streams in the matching literature, those with and those without monetary transfers, as special cases and allows for intermediate cases with some restrictions on the

  13. Competence Matching Tool - Explanations and Implementation

    Herder, Eelco; Kärger, Philipp

    2010-01-01

    Herder, E., Kärger, P. (2009) Competence Matching Tool - Explanations and Implementation. The document contains the technical specification of the competence matching tool. The tool can be found at http://tencompetence.cvs.sourceforge.net/viewvc/tencompetence/wp7/CompetenceMatcher/ and the location

  14. Matching Two-dimensional Gel Electrophoresis' Spots

    Dos Anjos, António; AL-Tam, Faroq; Shahbazkia, Hamid Reza

    2012-01-01

    This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches. This ar...

  15. Local Stereo Matching Using Adaptive Local Segmentation

    Damjanovic, S.; van der Heijden, Ferdinand; Spreeuwers, Lieuwe Jan

    We propose a new dense local stereo matching framework for gray-level images based on an adaptive local segmentation using a dynamic threshold. We define a new validity domain of the fronto-parallel assumption based on the local intensity variations in the 4-neighborhood of the matching pixel. The

  16. Dynamic Matchings in Convex Bipartite Graphs

    Brodal, Gerth Stølting; Georgiadis, Loukas; Hansen, Kristoffer Arnsfelt

    2007-01-01

    We consider the problem of maintaining a maximum matching in a convex bipartite graph G = (V,E) under a set of update operations which includes insertions and deletions of vertices and edges. It is not hard to show that it is impossible to maintain an explicit representation of a maximum matching...

  17. Gender differences in game responses during badminton match play.

    Fernandez-Fernandez, Jaime; de la Aleja Tellez, Jose G; Moya-Ramon, Manuel; Cabello-Manrique, David; Mendez-Villanueva, Alberto

    2013-09-01

    The aim of this study was to evaluate possible gender differences in match play activity pattern [rally duration, rest time between rallies, effective playing time, and strokes performed during a rally] and exercise intensity (heart rate [HR], blood lactate [La], and subjective ratings of perceived exertion [RPE]) during 9 simulated badminton matches in male (n = 8) and female (n = 8) elite junior (16.0 ± 1.4 years) players. Results showed significant differences (all p 0.05; ES = -0.33 to 0.08) were observed between female or male players in average HR (174 ± 7 vs. 170 ± 9 b·min(-1)), %HRmax (89.2 ± 4.0% vs. 85.9 ± 4.3%), La (2.5 ± 1.3 vs. 3.2 ± 1.8 mmol·L(-1)), and RPE values (14.2 ± 1.9 vs. 14.6 ± 1.8) during match play, although male players spent more time (moderate effect sizes) at intensities between 81 and 90% HRmax (35.3 ± 17.9 vs. 25.3 ± 13.6; p < 0.05; ES = 0.64) in the second game. There seemed to be a trend toward an increased playing intensity (i.e., higher HR, La, and RPE) from the first to the second game, highlighting the higher exercise intensity experienced during the last part of the match. The clear between-gender differences in activity patterns induced only slightly different physiological responses.

  18. Technical performance and match-to-match variation in elite football teams.

    Liu, Hongyou; Gómez, Miguel-Angel; Gonçalves, Bruno; Sampaio, Jaime

    2016-01-01

    Recent research suggests that match-to-match variation adds important information to performance descriptors in team sports, as it helps measure how players fine-tune their tactical behaviours and technical actions to the extreme dynamical environments. The current study aims to identify the differences in technical performance of players from strong and weak teams and to explore match-to-match variation of players' technical match performance. Performance data of all the 380 matches of season 2012-2013 in the Spanish First Division Professional Football League were analysed. Twenty-one performance-related match actions and events were chosen as variables in the analyses. Players' technical performance profiles were established by unifying count values of each action or event of each player per match into the same scale. Means of these count values of players from Top3 and Bottom3 teams were compared and plotted into radar charts. Coefficient of variation of each match action or event within a player was calculated to represent his match-to-match variation of technical performance. Differences in the variation of technical performances of players across different match contexts (team and opposition strength, match outcome and match location) were compared. All the comparisons were achieved by the magnitude-based inferences. Results showed that technical performances differed between players of strong and weak teams from different perspectives across different field positions. Furthermore, the variation of the players' technical performance is affected by the match context, with effects from team and opposition strength greater than effects from match location and match outcome.

  19. Stereo Matching Based On Election Campaign Algorithm

    Xie Qing Hua

    2016-01-01

    Full Text Available Stereo matching is one of the significant problems in the study of the computer vision. By getting the distance information through pixels, it is possible to reproduce a three-dimensional stereo. In this paper, the edges are the primitives for matching, the grey values of the edges and the magnitude and direction of the edge gradient were figured out as the properties of the edge feature points, according to the constraints for stereo matching, the energy function was built for finding the route minimizing by election campaign optimization algorithm during the process of stereo matching was applied to this problem the energy function. Experiment results show that this algorithm is more stable and it can get the matching result with better accuracy.

  20. Fiber cavities with integrated mode matching optics.

    Gulati, Gurpreet Kaur; Takahashi, Hiroki; Podoliak, Nina; Horak, Peter; Keller, Matthias

    2017-07-17

    In fiber based Fabry-Pérot Cavities (FFPCs), limited spatial mode matching between the cavity mode and input/output modes has been the main hindrance for many applications. We have demonstrated a versatile mode matching method for FFPCs. Our novel design employs an assembly of a graded-index and large core multimode fiber directly spliced to a single mode fiber. This all-fiber assembly transforms the propagating mode of the single mode fiber to match with the mode of a FFPC. As a result, we have measured a mode matching of 90% for a cavity length of ~400 μm. This is a significant improvement compared to conventional FFPCs coupled with just a single mode fiber, especially at long cavity lengths. Adjusting the parameters of the assembly, the fundamental cavity mode can be matched with the mode of almost any single mode fiber, making this approach highly versatile and integrable.

  1. Semantic Data Matching: Principles and Performance

    Deaton, Russell; Doan, Thao; Schweiger, Tom

    Automated and real-time management of customer relationships requires robust and intelligent data matching across widespread and diverse data sources. Simple string matching algorithms, such as dynamic programming, can handle typographical errors in the data, but are less able to match records that require contextual and experiential knowledge. Latent Semantic Indexing (LSI) (Berry et al. ; Deerwester et al. is a machine intelligence technique that can match data based upon higher order structure, and is able to handle difficult problems, such as words that have different meanings but the same spelling, are synonymous, or have multiple meanings. Essentially, the technique matches records based upon context, or mathematically quantifying when terms occur in the same record.

  2. Evaluation of goal kicking performance in international rugby union matches.

    Quarrie, Kenneth L; Hopkins, Will G

    2015-03-01

    Goal kicking is an important element in rugby but has been the subject of minimal research. To develop and apply a method to describe the on-field pattern of goal-kicking and rank the goal kicking performance of players in international rugby union matches. Longitudinal observational study. A generalized linear mixed model was used to analyze goal-kicking performance in a sample of 582 international rugby matches played from 2002 to 2011. The model adjusted for kick distance, kick angle, a rating of the importance of each kick, and venue-related conditions. Overall, 72% of the 6769 kick attempts were successful. Forty-five percent of points scored during the matches resulted from goal kicks, and in 5.7% of the matches the result of the match hinged on the outcome of a kick attempt. There was an extremely large decrease in success with increasing distance (odds ratio for two SD distance 0.06, 90% confidence interval 0.05-0.07) and a small decrease with increasingly acute angle away from the mid-line of the goal posts (odds ratio for 2 SD angle, 0.44, 0.39-0.49). Differences between players were typically small (odds ratio for 2 between-player SD 0.53, 0.45-0.65). The generalized linear mixed model with its random-effect solutions provides a tool for ranking the performance of goal kickers in rugby. This modelling approach could be applied to other performance indicators in rugby and in other sports in which discrete outcomes are measured repeatedly on players or teams. Copyright © 2015. Published by Elsevier Ltd.

  3. Towards a Next-Generation Catalogue Cross-Match Service

    Pineau, F.; Boch, T.; Derriere, S.; Arches Consortium

    2015-09-01

    We have been developing in the past several catalogue cross-match tools. On one hand the CDS XMatch service (Pineau et al. 2011), able to perform basic but very efficient cross-matches, scalable to the largest catalogues on a single regular server. On the other hand, as part of the European project ARCHES1, we have been developing a generic and flexible tool which performs potentially complex multi-catalogue cross-matches and which computes probabilities of association based on a novel statistical framework. Although the two approaches have been managed so far as different tracks, the need for next generation cross-match services dealing with both efficiency and complexity is becoming pressing with forthcoming projects which will produce huge high quality catalogues. We are addressing this challenge which is both theoretical and technical. In ARCHES we generalize to N catalogues the candidate selection criteria - based on the chi-square distribution - described in Pineau et al. (2011). We formulate and test a number of Bayesian hypothesis which necessarily increases dramatically with the number of catalogues. To assign a probability to each hypotheses, we rely on estimated priors which account for local densities of sources. We validated our developments by comparing the theoretical curves we derived with the results of Monte-Carlo simulations. The current prototype is able to take into account heterogeneous positional errors, object extension and proper motion. The technical complexity is managed by OO programming design patterns and SQL-like functionalities. Large tasks are split into smaller independent pieces for scalability. Performances are achieved resorting to multi-threading, sequential reads and several tree data-structures. In addition to kd-trees, we account for heterogeneous positional errors and object's extension using M-trees. Proper-motions are supported using a modified M-tree we developed, inspired from Time Parametrized R-trees (TPR

  4. The Interaction Between Schema Matching and Record Matching in Data Integration

    Gu, Binbin; Li, Zhixu; Zhang, Xiangliang; Liu, An; Liu, Guanfeng; Zheng, Kai; Zhao, Lei; Zhou, Xiaofang

    2016-01-01

    Schema Matching (SM) and Record Matching (RM) are two necessary steps in integrating multiple relational tables of different schemas, where SM unifies the schemas and RM detects records referring to the same real-world entity. The two processes have

  5. Distortion analysis on binary representation of minutiae based fingerprint matching for match-on-card

    Mlambo, CS

    2016-12-01

    Full Text Available The fingerprint matching on the smart card has long been developed and recognized faster method than fingerprint matching on a computer or large capacity systems. There has been much research and activities concerned with improving the accuracy...

  6. MR angiography with a matched filter

    De Castro, J.B.; Riederer, S.J.; Lee, J.N.

    1987-01-01

    The technique of matched filtering was applied to a series of cine MR images. The filter was devised to yield a subtraction angiographic image in which direct current components present in the cine series are removed and the signal-to-noise ratio (S/N) of the vascular structures is optimized. The S/N of a matched filter was compared with that of a simple subtraction, in which an image with high flow is subtracted from one with low flow. Experimentally, a range of results from minimal improvement to significant (60%) improvement in S/N was seen in the comparisons of matched filtered subtraction with simple subtraction

  7. State of otolaryngology match: has competition increased since the "early" match?

    Cabrera-Muffly, Cristina; Sheeder, Jeanelle; Abaza, Mona

    2015-05-01

    To examine fluctuations in supply and demand of otolaryngology residency positions after the shift from an "early match" coordinated by the San Francisco match to a "conventional" matching process through the National Residency Matching Program (NRMP). To determine whether competition among otolaryngology residency positions have changed during this time frame. Database analysis. Matching statistics from 1998 to 2013 were obtained for all first-year residency positions through the NRMP. Matching statistics from 1998 to 2005 were obtained for otolaryngology residency positions through the San Francisco match. Univariate analysis was performed, with a P value less than .05 determined as significant. The number of otolaryngology positions and applicants remained proportional to the overall number of positions and applicants in the NRMP match. Otolaryngology applicants per position and the matching rate of all applicants did not change between the 2 time periods studied. The overall match rate of US seniors applying to otolaryngology did not change, while the match rate of non-US seniors decreased significantly following initiation of the conventional match. There was no significant change in United States Medical Licensing Exam step 1 scores or percentage of unfilled otolaryngology residency positions between the 2 time periods. When comparing the early versus conventional otolaryngology match time periods, the only major change was the decreased percentage of matching among non-US senior applicants. Despite a significant shift in match timing after 2006, the supply, demand, and competitiveness of otolaryngology residency positions have not changed significantly. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015.

  8. Polyhedral patterns

    Jiang, Caigui

    2015-10-27

    We study the design and optimization of polyhedral patterns, which are patterns of planar polygonal faces on freeform surfaces. Working with polyhedral patterns is desirable in architectural geometry and industrial design. However, the classical tiling patterns on the plane must take on various shapes in order to faithfully and feasibly approximate curved surfaces. We define and analyze the deformations these tiles must undertake to account for curvature, and discover the symmetries that remain invariant under such deformations. We propose a novel method to regularize polyhedral patterns while maintaining these symmetries into a plethora of aesthetic and feasible patterns.

  9. Shape-matching soft mechanical metamaterials

    Mirzaali Mazandarani, M.; Janbaz, S.; Strano, M.; Vergani, L.; Zadpoor, A.A.

    2018-01-01

    Architectured materials with rationally designed geometries could be used to create mechanical metamaterials with unprecedented or rare properties and functionalities. Here, we introduce "shape-matching" metamaterials where the geometry of cellular structures comprising auxetic and conventional

  10. The Effectiveness of Advertising Matching Purchase Motivation

    J. Loef (Joost); G. Antonides (Gerrit); W.F. van Raaij (Fred)

    2001-01-01

    textabstractSeveral authors have proposed frameworks to help advertisers predict and plan advertising effectiveness. Rossiter and Percy's advertising grid (1997) recommends that the ad appeal should match the purchase motivation or attitude base. They suggest that for utilitarian brands

  11. Personalized Medicine: Matching Treatments to Your Genes

    ... Issues Subscribe December 2013 Print this issue Personalized Medicine Matching Treatments to Your Genes Send us your ... for disease, and the ways you respond to medicines are also unique. Medicines that work well for ...

  12. Mobile Application for Pesticide Label Matching

    The label matching application will give inspectors the ability to instantly compare pesticide product labels against state and federal label databases via their cell phone, tablet or other mobile device.

  13. Study of matching between HIRFL and CSR

    Tang Jingyu; Li Haohu; Yuan Youjin

    2001-01-01

    'HIRFL-CSR Cooler Storage Ring' makes use of existing HIRFL as its pre-accelerator. In order to take the full capability of HIRFL, the authors have studied in detailed the matching modes between HIRFL and CSR. It is proposed to use two matching modes; direct matching between SFC (HIRFL injector cyclotron) and CSRm (CSR main ring); three-cascade matching of SFC, SSC (HIRFL main cyclotron) and CSRm. With these combinations, better beam transmission efficiency, better beam utilization efficiency of HIRFL-CSR accelerator complex and better operation efficiency of HIRFL can be obtained. In the first case, SSC can be used simultaneously in other purposes, either to accelerate medium energy heavy ions or to accelerate protons combined with another small cyclotron

  14. Matching modes between HIRFL and CSR

    Tang, J.Y.; Li, H.H.; Yuan, Y.J.

    2001-01-01

    National key scientific project 'HIRFL-CSR Cooler Storage Ring' makes use of existing HIRFL as its pre-accelerator. In order to take the full capability of HIRFL, we have studied in detailed the matching modes between HIRFL and CSR. It is proposed to use two matching modes: direct matching between SFC (HIRFL injector cyclotron) and CSRm (CSR main ring), three-cascade matching of SFC, SSC (HIRFL main cyclotron) and CSRm. With these combinations, better beam transmission efficiency, better beam utilization efficiency of HIRFL-CSR accelerator complex and better operation efficiency of HIRFL can be obtained. In the first case, SSC can be used simultaneously in other purposes, either to accelerate medium energy heavy ions or to accelerate protons combined with another small cyclotron

  15. Fractional Order Element Based Impedance Matching

    Radwan, Ahmed Gomaa; Salama, Khaled N.; Shamim, Atif

    2014-01-01

    Disclosed are various embodiments of methods and systems related to fractional order element based impedance matching. In one embodiment, a method includes aligning a traditional Smith chart (|.alpha.|=1) with a fractional order Smith chart (|.alpha

  16. Reliability of visual and instrumental color matching.

    Igiel, Christopher; Lehmann, Karl Martin; Ghinea, Razvan; Weyhrauch, Michael; Hangx, Ysbrand; Scheller, Herbert; Paravina, Rade D

    2017-09-01

    The aim of this investigation was to evaluate intra-rater and inter-rater reliability of visual and instrumental shade matching. Forty individuals with normal color perception participated in this study. The right maxillary central incisor of a teaching model was prepared and restored with 10 feldspathic all-ceramic crowns of different shades. A shade matching session consisted of the observer (rater) visually selecting the best match by using VITA classical A1-D4 (VC) and VITA Toothguide 3D Master (3D) shade guides and the VITA Easyshade Advance intraoral spectrophotometer (ES) to obtain both VC and 3D matches. Three shade matching sessions were held with 4 to 6 weeks between sessions. Intra-rater reliability was assessed based on the percentage of agreement for the three sessions for the same observer, whereas the inter-rater reliability was calculated as mean percentage of agreement between different observers. The Fleiss' Kappa statistical analysis was used to evaluate visual inter-rater reliability. The mean intra-rater reliability for the visual shade selection was 64(11) for VC and 48(10) for 3D. The corresponding ES values were 96(4) for both VC and 3D. The percentages of observers who matched the same shade with VC and 3D were 55(10) and 43(12), respectively, while corresponding ES values were 88(8) for VC and 92(4) for 3D. The results for visual shade matching exhibited a high to moderate level of inconsistency for both intra-rater and inter-rater comparisons. The VITA Easyshade Advance intraoral spectrophotometer exhibited significantly better reliability compared with visual shade selection. This study evaluates the ability of observers to consistently match the same shade visually and with a dental spectrophotometer in different sessions. The intra-rater and inter-rater reliability (agreement of repeated shade matching) of visual and instrumental tooth color matching strongly suggest the use of color matching instruments as a supplementary tool in

  17. Specialization Patterns

    Schultz, Ulrik Pagh; Lawall, Julia Laetitia; Consel, Charles

    2000-01-01

    Design patterns offer many advantages for software development, but can introduce inefficiency into the final program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose that these concepts...... are complementary. Program specialization can optimize programs written using design patterns, and design patterns provide information about the program structure that can guide specialization. Concretely, we propose specialization patterns, which describe how to apply program specialization to optimize uses...... of design patterns. In this paper, we analyze the specialization opportunities provided by specific uses of design patterns. Based on the analysis of each design pattern, we define the associated specialization pattern. These specialization opportunities can be declared using the specialization classes...

  18. Modelling relationships between match events and match outcome in elite football.

    Liu, Hongyou; Hopkins, Will G; Gómez, Miguel-Angel

    2016-08-01

    Identifying match events that are related to match outcome is an important task in football match analysis. Here we have used generalised mixed linear modelling to determine relationships of 16 football match events and 1 contextual variable (game location: home/away) with the match outcome. Statistics of 320 close matches (goal difference ≤ 2) of season 2012-2013 in the Spanish First Division Professional Football League were analysed. Relationships were evaluated with magnitude-based inferences and were expressed as extra matches won or lost per 10 close matches for an increase of two within-team or between-team standard deviations (SD) of the match event (representing effects of changes in team values from match to match and of differences between average team values, respectively). There was a moderate positive within-team effect from shots on target (3.4 extra wins per 10 matches; 99% confidence limits ±1.0), and a small positive within-team effect from total shots (1.7 extra wins; ±1.0). Effects of most other match events were related to ball possession, which had a small negative within-team effect (1.2 extra losses; ±1.0) but a small positive between-team effect (1.7 extra wins; ±1.4). Game location showed a small positive within-team effect (1.9 extra wins; ±0.9). In analyses of nine combinations of team and opposition end-of-season rank (classified as high, medium, low), almost all between-team effects were unclear, while within-team effects varied depending on the strength of team and opposition. Some of these findings will be useful to coaches and performance analysts when planning training sessions and match tactics.

  19. Fingerprint Recognition Using Minutia Score Matching

    J, Ravi.; Raja, K. B.; R, Venugopal. K.

    2010-01-01

    The popular Biometric used to authenticate a person is Fingerprint which is unique and permanent throughout a person’s life. A minutia matching is widely used for fingerprint recognition and can be classified as ridge ending and ridge bifurcation. In this paper we projected Fingerprint Recognition using Minutia Score Matching method (FRMSM). For Fingerprint thinning, the Block Filter is used, which scans the image at the boundary to preserves the quality of the image and extract the minutiae ...

  20. Parikh Matching in the Streaming Model

    Lee, Lap-Kei; Lewenstein, Moshe; Zhang, Qin

    2012-01-01

    Let S be a string over an alphabet Σ = {σ1, σ2, …}. A Parikh-mapping maps a substring S′ of S to a |Σ|-length vector that contains, in location i of the vector, the count of σi in S′. Parikh matching refers to the problem of finding all substrings of a text T which match to a given input |Σ|-leng...

  1. THE Economics of Match-Fixing

    Caruso, Raul

    2007-01-01

    The phenomenon of match-fixing does constitute a constant element of sport contests. This paper presents a simple formal model in order to explain it. The intuition behind is that an asymmetry in the evaluation of the stake is the key factor leading to match-fixing. In sum, this paper considers a partial equilibrium model of contest where two asymmetric, rational and risk-neutral opponents evaluate differently a contested stake. Differently from common contest models, agents have the option ...

  2. INFORMATION SYSTEMS AUDIT CURRICULA CONTENT MATCHING

    Vasile-Daniel CARDOȘ; Ildikó Réka CARDOȘ

    2014-01-01

    Financial and internal auditors must cope with the challenge of performing their mission in technology enhanced environment. In this article we match the information technology description found in the International Federation of Accountants (IFAC) and the Institute of Internal Auditors (IIA) curricula against the Model Curriculum issued by the Information Systems Audit and Control Association (ISACA). By reviewing these three curricula, we matched the content in the ISACA Model Curriculum wi...

  3. Women match men when learning a spatial skill.

    Spence, Ian; Yu, Jingjie Jessica; Feng, Jing; Marshman, Jeff

    2009-07-01

    Meta-analytic studies have concluded that although training improves spatial cognition in both sexes, the male advantage generally persists. However, because some studies run counter to this pattern, a closer examination of the anomaly is warranted. The authors investigated the acquisition of a basic skill (spatial selective attention) using a matched-pair two-wave longitudinal design. Participants were screened with the use of an attentional visual field task, with the objective of selecting and matching 10 male-female pairs, over a wide range (30% to 57% correct). Subsequently, 20 participants 17-23 years of age (selected from 43 screened) were trained for 10 hr (distributed over several sessions) by playing a first-person shooter video game. This genre is known to be highly effective in enhancing spatial skills. All 20 participants improved, with matched members of the male-female pairs achieving very similar gains, independent of starting level. This is consistent with the hypothesis that the learning trajectory of women is not inferior to that of men when acquiring a basic spatial skill. Training methods that develop basic spatial skills may be essential to achieve gender parity in both basic and complex spatial tasks.

  4. Robust, Efficient Depth Reconstruction With Hierarchical Confidence-Based Matching.

    Sun, Li; Chen, Ke; Song, Mingli; Tao, Dacheng; Chen, Gang; Chen, Chun

    2017-07-01

    In recent years, taking photos and capturing videos with mobile devices have become increasingly popular. Emerging applications based on the depth reconstruction technique have been developed, such as Google lens blur. However, depth reconstruction is difficult due to occlusions, non-diffuse surfaces, repetitive patterns, and textureless surfaces, and it has become more difficult due to the unstable image quality and uncontrolled scene condition in the mobile setting. In this paper, we present a novel hierarchical framework with multi-view confidence-based matching for robust, efficient depth reconstruction in uncontrolled scenes. Particularly, the proposed framework combines local cost aggregation with global cost optimization in a complementary manner that increases efficiency and accuracy. A depth map is efficiently obtained in a coarse-to-fine manner by using an image pyramid. Moreover, confidence maps are computed to robustly fuse multi-view matching cues, and to constrain the stereo matching on a finer scale. The proposed framework has been evaluated with challenging indoor and outdoor scenes, and has achieved robust and efficient depth reconstruction.

  5. Fast group matching for MR fingerprinting reconstruction.

    Cauley, Stephen F; Setsompop, Kawin; Ma, Dan; Jiang, Yun; Ye, Huihui; Adalsteinsson, Elfar; Griswold, Mark A; Wald, Lawrence L

    2015-08-01

    MR fingerprinting (MRF) is a technique for quantitative tissue mapping using pseudorandom measurements. To estimate tissue properties such as T1 , T2 , proton density, and B0 , the rapidly acquired data are compared against a large dictionary of Bloch simulations. This matching process can be a very computationally demanding portion of MRF reconstruction. We introduce a fast group matching algorithm (GRM) that exploits inherent correlation within MRF dictionaries to create highly clustered groupings of the elements. During matching, a group specific signature is first used to remove poor matching possibilities. Group principal component analysis (PCA) is used to evaluate all remaining tissue types. In vivo 3 Tesla brain data were used to validate the accuracy of our approach. For a trueFISP sequence with over 196,000 dictionary elements, 1000 MRF samples, and image matrix of 128 × 128, GRM was able to map MR parameters within 2s using standard vendor computational resources. This is an order of magnitude faster than global PCA and nearly two orders of magnitude faster than direct matching, with comparable accuracy (1-2% relative error). The proposed GRM method is a highly efficient model reduction technique for MRF matching and should enable clinically relevant reconstruction accuracy and time on standard vendor computational resources. © 2014 Wiley Periodicals, Inc.

  6. Hybrid-Based Dense Stereo Matching

    Chuang, T. Y.; Ting, H. W.; Jaw, J. J.

    2016-06-01

    Stereo matching generating accurate and dense disparity maps is an indispensable technique for 3D exploitation of imagery in the fields of Computer vision and Photogrammetry. Although numerous solutions and advances have been proposed in the literature, occlusions, disparity discontinuities, sparse texture, image distortion, and illumination changes still lead to problematic issues and await better treatment. In this paper, a hybrid-based method based on semi-global matching is presented to tackle the challenges on dense stereo matching. To ease the sensitiveness of SGM cost aggregation towards penalty parameters, a formal way to provide proper penalty estimates is proposed. To this end, the study manipulates a shape-adaptive cross-based matching with an edge constraint to generate an initial disparity map for penalty estimation. Image edges, indicating the potential locations of occlusions as well as disparity discontinuities, are approved by the edge drawing algorithm to ensure the local support regions not to cover significant disparity changes. Besides, an additional penalty parameter 𝑃𝑒 is imposed onto the energy function of SGM cost aggregation to specifically handle edge pixels. Furthermore, the final disparities of edge pixels are found by weighting both values derived from the SGM cost aggregation and the U-SURF matching, providing more reliable estimates at disparity discontinuity areas. Evaluations on Middlebury stereo benchmarks demonstrate satisfactory performance and reveal the potency of the hybrid-based dense stereo matching method.

  7. A Frequency Matching Method for Generation of a Priori Sample Models from Training Images

    Lange, Katrine; Cordua, Knud Skou; Frydendall, Jan

    2011-01-01

    This paper presents a Frequency Matching Method (FMM) for generation of a priori sample models based on training images and illustrates its use by an example. In geostatistics, training images are used to represent a priori knowledge or expectations of models, and the FMM can be used to generate...... new images that share the same multi-point statistics as a given training image. The FMM proceeds by iteratively updating voxel values of an image until the frequency of patterns in the image matches the frequency of patterns in the training image; making the resulting image statistically...... indistinguishable from the training image....

  8. K-Line Patterns’ Predictive Power Analysis Using the Methods of Similarity Match and Clustering

    Lv Tao

    2017-01-01

    Full Text Available Stock price prediction based on K-line patterns is the essence of candlestick technical analysis. However, there are some disputes on whether the K-line patterns have predictive power in academia. To help resolve the debate, this paper uses the data mining methods of pattern recognition, pattern clustering, and pattern knowledge mining to research the predictive power of K-line patterns. The similarity match model and nearest neighbor-clustering algorithm are proposed for solving the problem of similarity match and clustering of K-line series, respectively. The experiment includes testing the predictive power of the Three Inside Up pattern and Three Inside Down pattern with the testing dataset of the K-line series data of Shanghai 180 index component stocks over the latest 10 years. Experimental results show that (1 the predictive power of a pattern varies a great deal for different shapes and (2 each of the existing K-line patterns requires further classification based on the shape feature for improving the prediction performance.

  9. Protection of chickens against H5N1 highly pathogenic avian influenza virus infection by live vaccination with infectious laryngotracheitis virus recombinants expressing H5 hemagglutinin and N1 neuraminidase.

    Pavlova, Sophia P; Veits, Jutta; Keil, Günther M; Mettenleiter, Thomas C; Fuchs, Walter

    2009-01-29

    Attenuated vaccine strains of the alphaherpesvirus causing infectious laryngotracheitis of chickens (ILTV, gallid herpesvirus 1) can be used for mass application. Previously, we showed that live virus vaccination with recombinant ILTV expressing hemagglutinin of highly pathogenic avian influenza viruses (HPAIV) protected chickens against ILT and fowl plague caused by HPAIV carrying the corresponding hemagglutinin subtypes [Lüschow D, Werner O, Mettenleiter TC, Fuchs W. Protection of chickens from lethal avian influenza A virus infection by live-virus vaccination with infectious laryngotracheitis virus recombinants expressing the hemagglutinin (H5) gene. Vaccine 2001;19(30):4249-59; Veits J, Lüschow D, Kindermann K, Werner O, Teifke JP, Mettenleiter TC, et al. Deletion of the non-essential UL0 gene of infectious laryngotracheitis (ILT) virus leads to attenuation in chickens, and UL0 mutants expressing influenza virus haemagglutinin (H7) protect against ILT and fowl plague. J Gen Virol 2003;84(12):3343-52]. However, protection against H5N1 HPAIV was not satisfactory. Therefore, a newly designed dUTPase-negative ILTV vector was used for rapid insertion of the H5-hemagglutinin, or N1-neuraminidase genes of a recent H5N1 HPAIV isolate. Compared to our previous constructs, protein expression was considerably enhanced by insertion of synthetic introns downstream of the human cytomegalovirus immediate-early promoter within the 5'-nontranslated region of the transgenes. Deletion of the viral dUTPase gene did not affect in vitro replication of the ILTV recombinants, but led to sufficient attenuation in vivo. After a single ocular immunization, all chickens developed H5- or N1-specific serum antibodies. Nevertheless, animals immunized with N1-ILTV died after subsequent H5N1 HPAIV challenge, although survival times were prolonged compared to non-vaccinated controls. In contrast, all chickens vaccinated with either H5-ILTV alone, or H5- and N1-ILTV simultaneously, survived

  10. MATCH: An Atom- Typing Toolset for Molecular Mechanics Force Fields

    Yesselman, Joseph D.; Price, Daniel J.; Knight, Jennifer L.; Brooks, Charles L.

    2011-01-01

    We introduce a toolset of program libraries collectively titled MATCH (Multipurpose Atom-Typer for CHARMM) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion from multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges and force field parameters is achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In the present work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM CGENFF force field (Vanommeslaeghe, et al., JCC., 2010, 31, 671–690), one million molecules from the PubChem database of small molecules are typed, parameterized and minimized. PMID:22042689

  11. Preimplantation genetic diagnosis with HLA matching.

    Rechitsky, Svetlana; Kuliev, Anver; Tur-Kaspa, Illan; Morris, Randy; Verlinsky, Yury

    2004-08-01

    Preimplantation genetic diagnosis (PGD) has recently been offered in combination with HLA typing, which allowed a successful haematopoietic reconstitution in affected siblings with Fanconi anaemia by transplantation of stem cells obtained from the HLA-matched offspring resulting from PGD. This study presents the results of the first PGD practical experience performed in a group of couples at risk for producing children with genetic disorders. These parents also requested preimplantation HLA typing for treating the affected children in the family, who required HLA-matched stem cell transplantation. Using a standard IVF procedure, oocytes or embryos were tested for causative gene mutations simultaneously with HLA alleles, selecting and transferring only those unaffected embryos, which were HLA matched to the affected siblings. The procedure was performed for patients with children affected by Fanconi anaemia (FANC) A and C, different thalassaemia mutations, Wiscott-Aldrich syndrome, X-linked adrenoleukodystrophy, X-linked hyperimmunoglobulin M syndrome and X-linked hypohidrotic ectodermal displasia with immune deficiency. Overall, 46 PGD cycles were performed for 26 couples, resulting in selection and transfer of 50 unaffected HLA-matched embryos in 33 cycles, yielding six HLA-matched clinical pregnancies and the birth of five unaffected HLA-matched children. Despite the controversy of PGD use for HLA typing, the data demonstrate the usefulness of this approach for at-risk couples, not only to avoid the birth of affected children with an inherited disease, but also for having unaffected children who may also be potential HLA-matched donors of stem cells for treatment of affected siblings.

  12. Effects of plant density on recombinant hemagglutinin yields in an Agrobacterium-mediated transient gene expression system using Nicotiana benthamiana plants.

    Fujiuchi, Naomichi; Matsuda, Ryo; Matoba, Nobuyuki; Fujiwara, Kazuhiro

    2017-08-01

    Agrobacterium-mediated transient expression systems enable plants to rapidly produce a wide range of recombinant proteins. To achieve economically feasible upstream production and downstream processing, it is beneficial to obtain high levels of two yield-related quantities of upstream production: recombinant protein content per fresh mass of harvested biomass (g gFM -1 ) and recombinant protein productivity per unit area-time (g m -2 /month). Here, we report that the density of Nicotiana benthamiana plants during upstream production had significant impacts on the yield-related quantities of recombinant hemagglutinin (HA). The two quantities were smaller at a high plant density of 400 plants m -2 than at a low plant density of 100 plants m -2 . The smaller quantities at the high plant density were attributed to: (i) a lower HA content in young leaves, which usually have high HA accumulation potentials; (ii) a lower biomass allocation to the young leaves; and (iii) a high area-time requirement for plants. Thus, plant density is a key factor for improving upstream production in Agrobacterium-mediated transient expression systems. Biotechnol. Bioeng. 2017;114: 1762-1770. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. New Orf virus (Parapoxvirus) recombinant expressing H5 hemagglutinin protects mice against H5N1 and H1N1 influenza A virus.

    Rohde, Jörg; Amann, Ralf; Rziha, Hanns-Joachim

    2013-01-01

    Previously we demonstrated the versatile utility of the Parapoxvirus Orf virus (ORFV) as a vector platform for the development of potent recombinant vaccines. In this study we present the generation of new ORFV recombinants expressing the hemagglutinin (HA) or nucleoprotein (NP) of the highly pathogenic avian influenza virus (HPAIV) H5N1. Correct foreign gene expression was examined in vitro by immunofluorescence, Western blotting and flow cytometry. The protective potential of both recombinants was evaluated in the mouse challenge model. Despite adequate expression of NP, the recombinant D1701-V-NPh5 completely failed to protect mice from lethal challenge. However, the H5 HA-expressing recombinant D1701-V-HAh5n mediated solid protection in a dose-dependent manner. Two intramuscular (i.m.) injections of the HA-expressing recombinant protected all animals from lethal HPAIV infection without loss of body weight. Notably, the immunized mice resisted cross-clade H5N1 and heterologous H1N1 (strain PR8) influenza virus challenge. In vivo antibody-mediated depletion of CD4-positive and/or CD8-posititve T-cell subpopulations during immunization and/or challenge infection implicated the relevance of CD4-positive T-cells for induction of protective immunity by D1701-V-HAh5n, whereas the absence of CD8-positive T-cells did not significantly influence protection. In summary, this study validates the potential of the ORFV vectored vaccines also to combat HPAIV.

  14. Both CD4+ and CD8+ Lymphocytes Participate in the IFN-γ Response to Filamentous Hemagglutinin from Bordetella pertussis in Infants, Children, and Adults

    Violette Dirix

    2012-01-01

    Full Text Available Infant CD4+ T-cell responses to bacterial infections or vaccines have been extensively studied, whereas studies on CD8+ T-cell responses focused mainly on viral and intracellular parasite infections. Here we investigated CD8+ T-cell responses upon Bordetella pertussis infection in infants, children, and adults and pertussis vaccination in infants. Filamentous hemagglutinin-specific IFN-γ secretion by circulating lymphocytes was blocked by anti-MHC-I or -MHC-II antibodies, suggesting that CD4+ and CD8+ T lymphocytes are involved in IFN-γ production. Flow cytometry analyses confirmed that both cell types synthesized antigen-specific IFN-γ, although CD4+ lymphocytes were the major source of this cytokine. IFN-γ synthesis by CD8+ cells was CD4+ T cell dependent, as evidenced by selective depletion experiments. Furthermore, IFN-γ synthesis by CD4+ cells was sometimes inhibited by CD8+ lymphocytes, suggesting the presence of CD8+ regulatory T cells. The role of this dual IFN-γ secretion by CD4+ and CD8+ T lymphocytes in pertussis remains to be investigated.

  15. Stable lentiviral transformation of CHO cells for the expression of the hemagglutinin H5 of avian influenza virus in suspension culture

    Alaín González Pose

    2014-09-01

    Full Text Available Avian influenza virus H5N1 has caused extensive damage worldwide among poultry and humans. Effective expression systems are needed for the production of viral proteins required for monitoring this devastating disease. The present study deals with the establishment of a stable expression system for the hemagglutinin H5 (HAH5 of avian influenza virus using CHO cells in suspension culture transduced with a recombinant lentiviral vector. The synthetic gene coding the HAH5 protein was inserted in a lentiviral vector with the aim of performing a stable transduction of CHO cells. After the selection of recombinant clones, the one with the highest expression level was adapted to suspension culture and the HAH5 protein was purified by immunoaffinity chromatography from the culture supernatant. There were no significant differences when this protein, purified or direct from the culture supernatant of CHO or SiHa cells, was utilized in an immunologic assay using positive and negative sera as reference. It was also demonstrated that the HAH5 protein in its purified form is able to bind anti-HAH5 antibodies generated with proper and non-proper folded proteins. The results demonstrate that the CHO cell line stably transduced with a lentiviral vector coding the sequence of the HAH5 protein and cultured in suspension can be a suitable expression system to obtain this protein for diagnostic purpose in a consistent and reliable manner.

  16. Establishment of the cross-clade antigen detection system for H5 subtype influenza viruses using peptide monoclonal antibodies specific for influenza virus H5 hemagglutinin.

    Takahashi, Hitoshi; Nagata, Shiho; Odagiri, Takato; Kageyama, Tsutomu

    2018-04-15

    The H5 subtype of highly pathogenic avian influenza (H5 HPAI) viruses is a threat to both animal and human public health and has the potential to cause a serious future pandemic in humans. Thus, specific and rapid detection of H5 HPAI viruses is required for infection control in humans. To develop a simple and rapid diagnostic system to detect H5 HPAI viruses with high specificity and sensitivity, we attempted to prepare monoclonal antibodies (mAbs) that specifically recognize linear epitopes in hemagglutinin (HA) of H5 subtype viruses. Nine mAb clones were obtained from mice immunized with a synthetic partial peptide of H5 HA molecules conserved among various H5 HPAI viruses. The antigen-capture enzyme-linked immunosorbent assay using the most suitable combination of these mAbs, which bound specifically to lysed H5 HA under an optimized detergent condition, was specific for H5 viruses and could broadly detect H5 viruses in multiple different clades. Taken together, these peptide mAbs, which recognize linear epitopes in a highly conserved region of H5 HA, may be useful for specific and highly sensitive detection of H5 HPAI viruses and can help in the rapid diagnosis of human, avian, and animal H5 virus infections. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Induction of Robust B Cell Responses after Influenza mRNA Vaccination Is Accompanied by Circulating Hemagglutinin-Specific ICOS+ PD-1+ CXCR3+ T Follicular Helper Cells

    Gustaf Lindgren

    2017-11-01

    Full Text Available Modified mRNA vaccines have developed into an effective and well-tolerated vaccine platform that offers scalable and precise antigen production. Nevertheless, the immunological events leading to strong antibody responses elicited by mRNA vaccines are largely unknown. In this study, we demonstrate that protective levels of antibodies to hemagglutinin were induced after two immunizations of modified non-replicating mRNA encoding influenza H10 encapsulated in lipid nanoparticles (LNP in non-human primates. While both intradermal (ID and intramuscular (IM administration induced protective titers, ID delivery generated this response more rapidly. Circulating H10-specific memory B cells expanded after each immunization, along with a transient appearance of plasmablasts. The memory B cell pool waned over time but remained detectable throughout the 25-week study. Following prime immunization, H10-specific plasma cells were found in the bone marrow and persisted over time. Germinal centers were formed in vaccine-draining lymph nodes along with an increase in circulating H10-specific ICOS+ PD-1+ CXCR3+ T follicular helper cells, a population shown to correlate with high avidity antibody responses after seasonal influenza vaccination in humans. Collectively, this study demonstrates that mRNA/LNP vaccines potently induce an immunological repertoire associated with the generation of high magnitude and quality antibodies.

  18. Immunomodulatory Effects of Hemagglutinin- (HA- Modified A20 B-Cell Lymphoma Expanded as a Brain Tumor on Adoptively Transferred HA-Specific CD4+ T Cells

    Valentin P. Shichkin

    2014-01-01

    Full Text Available Previously, the mouse A20 B-cell lymphoma engineered to express hemagglutinin (HA antigen (A20HA was used as a systemic tumor model. In this work, we used the A20HA cells as a brain tumor. HA-specific CD4+ T cells were transferred intravenously in a tail vein 5 days after A20HA intracranial inoculation and analyzed on days 2, 9, and 16 after the adoptive transfer by different methods. The transferred cells demonstrated state of activation as early as day 2 after the adoptive transfer and most the of viable HA-specific cells became anergic on day 16. Additionally, symptoms of systemic immunosuppression were observed in mice with massive brain tumors at a late stage of the brain tumor progression (days 20–24 after the A20HA inoculation. Despite that, a deal of HA-specific CD4+ T cells kept the functional activity even at the late stage of A20HA tumor growth. The activated HA-specific CD4+ T cells were found also in the brain of brain-tumor-bearing mice. These cells were still responding to reactivation with HA-peptide in vitro. Our data support an idea about sufficient role of both the tumor-specific and -nonspecific mechanisms inducing immunosuppression in cancer patients.

  19. Single Dose of Consensus Hemagglutinin-Based Virus-Like Particles Vaccine Protects Chickens against Divergent H5 Subtype Influenza Viruses

    Peipei Wu

    2017-11-01

    Full Text Available The H5 subtype highly pathogenic avian influenza (HPAI virus is one of the greatest threats to global poultry industry. To develop broadly protective H5 subunit vaccine, a recombinant consensus HA sequence (rHA was constructed and expressed in virus-like particles (rHA VLPs in the baculovirus-insect cell system. The efficacy of the rHA VLPs vaccine with or without immunopotentiator (CVCVA5 was assessed in chickens. Compared to the commercial Re6 or Re6-CVCVA5 vaccines, single dose immunization of chickens with rHA VLPs or rHA-CVCVA5 vaccines induced higher levels of serum hemagglutinin inhibition titers and neutralization titers, mucosal antibodies, IFN-γ and IL-4 cytokines in sera, and cytotoxic T lymphocyte responses. The rHA VLPs vaccine was superior to the commercial Re6 vaccine in conferring cross-protection against different clades of H5 subtype viruses. This study reports that H5 subtype consensus HA VLP single dose vaccination provides broad protection against HPAI virus in chickens.

  20. Mucosal and systemic immune responses elicited by recombinant Lactococcus lactis expressing a fusion protein composed of pertussis toxin and filamentous hemagglutinin from Bordetella pertussis.

    Torkashvand, Ali; Bahrami, Fariborz; Adib, Minoo; Ajdary, Soheila

    2018-05-05

    We constructed a food-grade expression system harboring a F1S1 fusion protein of Bordetella pertussis to be produced in Lactococcus lactis NZ3900 as a new oral vaccine model against whooping cough, caused by B. pertussis. F1S1 was composed of N-terminally truncated S1 subunit of pertussis toxin and type I immunodominant domain of filamentous hemagglutinin which are both known as protective immunogens against pertussis. The recombinant L. lactis was administered via oral or intranasal routes to BALB/c mice and the related specific systemic and mucosal immune responses were then evaluated. The results indicated significantly higher levels of specific IgA in the lung extracts and IgG in sera of mucosally-immunized mice, compared to their controls. It was revealed that higher levels of IgG2a, compared to IgG1, were produced in all mucosally-immunized mice. Moreover, immunized mice developed Th1 responses with high levels of IFN-γ production by the spleen cells. These findings provide evidence for L. lactis to be used as a suitable vehicle for expression and delivery of F1S1 fusion protein to mucosa and induction of appropriate systemic and mucosal immune responses against pertussis. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. A single base-pair change in 2009 H1N1 hemagglutinin increases human receptor affinity and leads to efficient airborne viral transmission in ferrets.

    Akila Jayaraman

    2011-03-01

    Full Text Available The 2009 H1N1 influenza A virus continues to circulate among the human population as the predominant H1N1 subtype. Epidemiological studies and airborne transmission studies using the ferret model have shown that the transmission efficiency of 2009 H1N1 viruses is lower than that of previous seasonal strains and the 1918 pandemic H1N1 strain. We recently correlated this reduced transmission efficiency to the lower binding affinity of the 2009 H1N1 hemagglutinin (HA to α2→6 sialylated glycan receptors (human receptors. Here we report that a single point mutation (Ile219→Lys; a base pair change in the glycan receptor-binding site (RBS of a representative 2009 H1N1 influenza A virus, A/California/04/09 or CA04/09, quantitatively increases its human receptor-binding affinity. The increased human receptor-affinity is in the same range as that of the HA from highly transmissible seasonal and 1918 pandemic H1N1 viruses. Moreover, a 2009 H1N1 virus carrying this mutation in the RBS (generated using reverse genetics transmits efficiently in ferrets by respiratory droplets thereby reestablishing our previously observed correlation between human receptor-binding affinity and transmission efficiency. These findings are significant in the context of monitoring the evolution of the currently circulating 2009 H1N1 viruses.

  2. Viral hemagglutinin is involved in promoting the internalisation of Staphylococcus aureus into human pneumocytes during influenza A H1N1 virus infection.

    Passariello, Claudio; Nencioni, Lucia; Sgarbanti, Rossella; Ranieri, Danilo; Torrisi, Maria Rosaria; Ripa, Sandro; Garaci, Enrico; Palamara, Anna Teresa

    2011-02-01

    Secondary pneumonia caused by Staphylococcus aureus is reemerging as a primary cause of excess mortality associated with infection by the influenza A virus. We have investigated in vitro the cellular and molecular mechanisms underlying this synergism. Experimental data show a significant increase in the efficiency of internalisation of S. aureus into cultured pneumocytes during the early phases of viral infection, while a relevant increase in the efficiency of adhesion is evident only later during viral infection, suggesting that the 2 effects are based on different molecular mechanisms. Data reported in this paper show that S. aureus cells can bind the viral hemagglutinin (HA) and that this binding promotes enhanced bacterial internalisation by 2 mechanisms: binding to HA exposed at the surface of infected cells and binding to free extracellular virions, enabling internalisation at high efficiency also in cells that are not infected by the virus. The affinity of binding that involves S. aureus and HA was shown to be enhanced by the reducing extracellular environment that the virus can generate. Copyright © 2010 Elsevier GmbH. All rights reserved.

  3. Structures of Receptor Complexes of a North American H7N2 Influenza Hemagglutinin with a Loop Deletion in the Receptor Binding Site

    Yang, Hua; Chen, Li-Mei; Carney, Paul J.; Donis, Ruben O.; Stevens, James (CDC)

    2012-02-21

    Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107), including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN) and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb). Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering) are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type ({alpha}2-3) receptor binding profile, with only moderate binding to human-type ({alpha}2-6) receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

  4. Canine distemper virus neutralization activity is low in human serum and it is sensitive to an amino acid substitution in the hemagglutinin protein.

    Zhang, Xinsheng; Wallace, Olivia L; Domi, Arban; Wright, Kevin J; Driscoll, Jonathan; Anzala, Omu; Sanders, Eduard J; Kamali, Anatoli; Karita, Etienne; Allen, Susan; Fast, Pat; Gilmour, Jill; Price, Matt A; Parks, Christopher L

    2015-08-01

    Serum was analyzed from 146 healthy adult volunteers in eastern Africa to evaluate measles virus (MV) and canine distemper virus (CDV) neutralizing antibody (nAb) prevalence and potency. MV plaque reduction neutralization test (PRNT) results indicated that all sera were positive for MV nAbs. Furthermore, the 50% neutralizing dose (ND50) for the majority of sera corresponded to antibody titers induced by MV vaccination. CDV nAbs titers were low and generally were detected in sera with high MV nAb titers. A mutant CDV was generated that was less sensitive to neutralization by human serum. The mutant virus genome had 10 nucleotide substitutions, which coded for single amino acid substitutions in the fusion (F) and hemagglutinin (H) glycoproteins and two substitutions in the large polymerase (L) protein. The H substitution occurred in a conserved region involved in receptor interactions among morbilliviruses, implying that this region is a target for cross-reactive neutralizing antibodies. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Computational Identification of Antigenicity-Associated Sites in the Hemagglutinin Protein of A/H1N1 Seasonal Influenza Virus.

    Xiaowei Ren

    Full Text Available The antigenic variability of influenza viruses has always made influenza vaccine development challenging. The punctuated nature of antigenic drift of influenza virus suggests that a relatively small number of genetic changes or combinations of genetic changes may drive changes in antigenic phenotype. The present study aimed to identify antigenicity-associated sites in the hemagglutinin protein of A/H1N1 seasonal influenza virus using computational approaches. Random Forest Regression (RFR and Support Vector Regression based on Recursive Feature Elimination (SVR-RFE were applied to H1N1 seasonal influenza viruses and used to analyze the associations between amino acid changes in the HA1 polypeptide and antigenic variation based on hemagglutination-inhibition (HI assay data. Twenty-three and twenty antigenicity-associated sites were identified by RFR and SVR-RFE, respectively, by considering the joint effects of amino acid residues on antigenic drift. Our proposed approaches were further validated with the H3N2 dataset. The prediction models developed in this study can quantitatively predict antigenic differences with high prediction accuracy based only on HA1 sequences. Application of the study results can increase understanding of H1N1 seasonal influenza virus antigenic evolution and accelerate the selection of vaccine strains.

  6. Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1 Viruses.

    William T Harvey

    2016-04-01

    Full Text Available Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1 virus isolates (1997-2009 and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens.

  7. Screening of random peptide library of hemagglutinin from pandemic 2009 A(H1N1 influenza virus reveals unexpected antigenically important regions.

    Wanghui Xu

    Full Text Available The antigenic structure of the membrane protein hemagglutinin (HA from the 2009 A(H1N1 influenza virus was dissected with a high-throughput screening method using complex antisera. The approach involves generating yeast cell libraries displaying a pool of random peptides of controllable lengths on the cell surface, followed by one round of fluorescence-activated cell sorting (FACS against antisera from mouse, goat and human, respectively. The amino acid residue frequency appearing in the antigenic peptides at both the primary sequence and structural level was determined and used to identify "hot spots" or antigenically important regions. Unexpectedly, different antigenic structures were seen for different antisera. Moreover, five antigenic regions were identified, of which all but one are located in the conserved HA stem region that is responsible for membrane fusion. Our findings are corroborated by several recent studies on cross-neutralizing H1 subtype antibodies that recognize the HA stem region. The antigenic peptides identified may provide clues for creating peptide vaccines with better accessibility to memory B cells and better induction of cross-neutralizing antibodies than the whole HA protein. The scheme used in this study enables a direct mapping of the antigenic regions of viral proteins recognized by antisera, and may be useful for dissecting the antigenic structures of other viral proteins.

  8. Enhanced effect of BCG vaccine against pulmonary Mycobacterium tuberculosis infection in mice with lung Th17 response to mycobacterial heparin-binding hemagglutinin adhesin antigen.

    Fukui, Masayuki; Shinjo, Kikuko; Umemura, Masayuki; Shigeno, Satoko; Harakuni, Tetsuya; Arakawa, Takeshi; Matsuzaki, Goro

    2015-12-01

    Although the BCG vaccine can prevent tuberculosis (TB) in infants, its ability to prevent adult pulmonary TB is reportedly limited. Therefore, development of a novel effective vaccine against pulmonary TB has become an international research priority. We have previously reported that intranasal vaccination of mice with a mycobacterial heparin-binding hemagglutinin adhesin (HBHA) plus mucosal adjuvant cholera toxin (CT) enhances production of IFN-γ and anti-HBHA antibody and suppresses extrapulmonary bacterial dissemination after intranasal infection with BCG. In the present study, the effects of intranasal HBHA + CT vaccine on murine pulmonary Mycobacterium tuberculosis (Mtb) infection were examined. Intranasal HBHA + CT vaccination alone failed to reduce the bacterial burden in the infected lung. However, a combination vaccine consisting of s.c. BCG priming and an intranasal HBHA + CT booster significantly enhanced protective immunity against pulmonary Mtb infection on day 14 compared with BCG vaccine alone. Further, it was found that intranasal HBHA + CT vaccine enhanced not only IFN-γ but also IL-17A production by HBHA-specific T cells in the lung after pulmonary Mtb infection. Therefore, this combination vaccine may be a good candidate for a new vaccine strategy against pulmonary TB. © 2015 The Societies and Wiley Publishing Asia Pty Ltd.

  9. Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses

    Harvey, William T.; Benton, Donald J.; Gregory, Victoria; Hall, James P. J.; Daniels, Rodney S.; Bedford, Trevor; Haydon, Daniel T.; Hay, Alan J.; McCauley, John W.; Reeve, Richard

    2016-01-01

    Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI) assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA) glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1) virus isolates (1997–2009) and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens. PMID:27057693

  10. Structures of receptor complexes of a North American H7N2 influenza hemagglutinin with a loop deletion in the receptor binding site.

    Hua Yang

    2010-09-01

    Full Text Available Human infections with subtype H7 avian influenza viruses have been reported as early as 1979. In 1996, a genetically stable 24-nucleotide deletion emerged in North American H7 influenza virus hemagglutinins, resulting in an eight amino acid deletion in the receptor-binding site. The continuous circulation of these viruses in live bird markets, as well as its documented ability to infect humans, raises the question of how these viruses achieve structural stability and functionality. Here we report a detailed molecular analysis of the receptor binding site of the North American lineage subtype H7N2 virus A/New York/107/2003 (NY107, including complexes with an avian receptor analog (3'-sialyl-N-acetyllactosamine, 3'SLN and two human receptor analogs (6'-sialyl-N-acetyllactosamine, 6'SLN; sialyllacto-N-tetraose b, LSTb. Structural results suggest a novel mechanism by which residues Arg220 and Arg229 (H3 numbering are used to compensate for the deletion of the 220-loop and form interactions with the receptor analogs. Glycan microarray results reveal that NY107 maintains an avian-type (alpha2-3 receptor binding profile, with only moderate binding to human-type (alpha2-6 receptor. Thus despite its dramatically altered receptor binding site, this HA maintains functionality and confirms a need for continued influenza virus surveillance of avian and other animal reservoirs to define their zoonotic potential.

  11. Family Patterns Associated with Anorexia Nervosa.

    Grigg, Darryl N.; And Others

    1989-01-01

    Used family systems perspective to explore familial transactional patterns related to anorexia nervosa among 22 families with an anorexic child and 22 matched control families. Identified 7 family groups with unique family dynamics differentiating one from another. With no single family pattern characterizing families of anorexics, results…

  12. Content Based Image Matching for Planetary Science

    Deans, M. C.; Meyer, C.

    2006-12-01

    Planetary missions generate large volumes of data. With the MER rovers still functioning on Mars, PDS contains over 7200 released images from the Microscopic Imagers alone. These data products are only searchable by keys such as the Sol, spacecraft clock, or rover motion counter index, with little connection to the semantic content of the images. We have developed a method for matching images based on the visual textures in images. For every image in a database, a series of filters compute the image response to localized frequencies and orientations. Filter responses are turned into a low dimensional descriptor vector, generating a 37 dimensional fingerprint. For images such as the MER MI, this represents a compression ratio of 99.9965% (the fingerprint is approximately 0.0035% the size of the original image). At query time, fingerprints are quickly matched to find images with similar appearance. Image databases containing several thousand images are preprocessed offline in a matter of hours. Image matches from the database are found in a matter of seconds. We have demonstrated this image matching technique using three sources of data. The first database consists of 7200 images from the MER Microscopic Imager. The second database consists of 3500 images from the Narrow Angle Mars Orbital Camera (MOC-NA), which were cropped into 1024×1024 sub-images for consistency. The third database consists of 7500 scanned archival photos from the Apollo Metric Camera. Example query results from all three data sources are shown. We have also carried out user tests to evaluate matching performance by hand labeling results. User tests verify approximately 20% false positive rate for the top 14 results for MOC NA and MER MI data. This means typically 10 to 12 results out of 14 match the query image sufficiently. This represents a powerful search tool for databases of thousands of images where the a priori match probability for an image might be less than 1%. Qualitatively, correct

  13. Optimally matching support and perceived spousal sensitivity.

    Cutrona, Carolyn E; Shaffer, Philip A; Wesner, Kristin A; Gardner, Kelli A

    2007-12-01

    Partner sensitivity is an important antecedent of both intimacy (H. T. Reis & P. Shaver, 1988) and attachment (M. D. S. Ainsworth, 1989). On the basis of the optimal matching model of social support (C. E. Cutrona & D. Russell, 1990), support behaviors that "matched" the support goals of the stressed individual were predicted to lead to the perception of partner sensitivity. Predictions were tested with 59 married couples, who engaged in a videotaped self-disclosure task. Matching support was defined as the disclosure of emotions followed by emotional support or a request for information followed by informational support. Partial evidence was found for the predictions. Matching support following the disclosure of emotions was predictive of perceived partner sensitivity. Mismatched support following the disclosure of emotions predicted lower marital satisfaction, through the mediation of partner sensitivity. Matching support following a request for information was not predictive of perceived partner sensitivity, but negative partner responses (e.g., criticism or sarcasm) following a request for information negatively predicted perceptions of partner sensitivity. The importance of considering the context of support transactions is discussed.

  14. Unsupervised image matching based on manifold alignment.

    Pei, Yuru; Huang, Fengchun; Shi, Fuhao; Zha, Hongbin

    2012-08-01

    This paper challenges the issue of automatic matching between two image sets with similar intrinsic structures and different appearances, especially when there is no prior correspondence. An unsupervised manifold alignment framework is proposed to establish correspondence between data sets by a mapping function in the mutual embedding space. We introduce a local similarity metric based on parameterized distance curves to represent the connection of one point with the rest of the manifold. A small set of valid feature pairs can be found without manual interactions by matching the distance curve of one manifold with the curve cluster of the other manifold. To avoid potential confusions in image matching, we propose an extended affine transformation to solve the nonrigid alignment in the embedding space. The comparatively tight alignments and the structure preservation can be obtained simultaneously. The point pairs with the minimum distance after alignment are viewed as the matchings. We apply manifold alignment to image set matching problems. The correspondence between image sets of different poses, illuminations, and identities can be established effectively by our approach.

  15. Match Analysis in Volleyball: a systematic review

    Miguel Silva

    2016-03-01

    Full Text Available The present article aims to review the available literature on match analysis in adult male Volleyball. Specific key words "performance analysis", "match analysis", "game analysis", "notational analysis", "tactical analysis", "technical analysis", "outcome" and "skills" were used to search relevant databases (PubMed, Web of Science, SportDiscus, Academic Search Complete and the International Journal of Performance Analysis in Sport. The research was conducted according to PRISMA (Preferred Reporting Items for Systematic reviews and Meta analyses guidelines. Of 3407 studies initially identified, only 34 were fully reviewed, and their outcome measures extracted and analyzed. Studies that fit all inclusion criteria were organized into two levels of analysis, according to their research design (comparative or predictive and depending on the type of variables analyzed (skills and their relationship with success, play position and match phase. Results show that from a methodological point of view, comparative studies where currently complemented with some predictive studies. This predictive approach emerged with the aim to identify the relationship between variables, considering their possible interactions and consequently its effect on team performance, contributing to a better understanding of Volleyball game performance through match analysis. Taking into account the limitations of the reviewed studies, future research should provide comprehensive operational definitions for the studied variables, using more recent samples, and consider integrating the player positions and match phase contexts into the analysis of Volleyball.

  16. PREDICTING THE MATCH OUTCOME IN ONE DAY INTERNATIONAL CRICKET MATCHES, WHILE THE GAME IS IN PROGRESS

    Michael Bailey

    2006-12-01

    Full Text Available Millions of dollars are wagered on the outcome of one day international (ODI cricket matches, with a large percentage of bets occurring after the game has commenced. Using match information gathered from all 2200 ODI matches played prior to January 2005, a range of variables that could independently explain statistically significant proportions of variation associated with the predicted run totals and match outcomes were created. Such variables include home ground advantage, past performances, match experience, performance at the specific venue, performance against the specific opposition, experience at the specific venue and current form. Using a multiple linear regression model, prediction variables were numerically weighted according to statistical significance and used to predict the match outcome. With the use of the Duckworth-Lewis method to determine resources remaining, at the end of each completed over, the predicted run total of the batting team could be updated to provide a more accurate prediction of the match outcome. By applying this prediction approach to a holdout sample of matches, the efficiency of the "in the run" wagering market could be assessed. Preliminary results suggest that the market is prone to overreact to events occurring throughout the course of the match, thus creating brief inefficiencies in the wagering market

  17. Shape-matching soft mechanical metamaterials.

    Mirzaali, M J; Janbaz, S; Strano, M; Vergani, L; Zadpoor, A A

    2018-01-17

    Architectured materials with rationally designed geometries could be used to create mechanical metamaterials with unprecedented or rare properties and functionalities. Here, we introduce "shape-matching" metamaterials where the geometry of cellular structures comprising auxetic and conventional unit cells is designed so as to achieve a pre-defined shape upon deformation. We used computational models to forward-map the space of planar shapes to the space of geometrical designs. The validity of the underlying computational models was first demonstrated by comparing their predictions with experimental observations on specimens fabricated with indirect additive manufacturing. The forward-maps were then used to devise the geometry of cellular structures that approximate the arbitrary shapes described by random Fourier's series. Finally, we show that the presented metamaterials could match the contours of three real objects including a scapula model, a pumpkin, and a Delft Blue pottery piece. Shape-matching materials have potential applications in soft robotics and wearable (medical) devices.

  18. Achromatic hues matching in graphic printing

    Martinia Ira Glogar

    2015-05-01

    Full Text Available Some problems in process of dark achromatic hues reproduction and matching in graphic industry, where requests on colour matching are very high, are discussed. When achromatic hues is concerned, in terms of high requests on colour parameter matching, right on time production, quick response and high quality standards requests, the production and moreover the reproduction is subject to many variables and represent the manufacturing process of high complexity. The aim is to achieve a graphic reproduction with defined colour parameters and remission characteristics as close as possible to a standard. In this paper, black and grey hues characterized with average lightness value L*≤ 20, were analysed. Subjective as well as objective colour evaluation have been performed and results of colour differences obtained by two colour difference formulae, CIELAB and CMC(l:c have been compared.

  19. Improved Stereo Matching With Boosting Method

    Shiny B

    2015-06-01

    Full Text Available Abstract This paper presents an approach based on classification for improving the accuracy of stereo matching methods. We propose this method for occlusion handling. This work employs classification of pixels for finding the erroneous disparity values. Due to the wide applications of disparity map in 3D television medical imaging etc the accuracy of disparity map has high significance. An initial disparity map is obtained using local or global stereo matching methods from the input stereo image pair. The various features for classification are computed from the input stereo image pair and the obtained disparity map. Then the computed feature vector is used for classification of pixels by using GentleBoost as the classification method. The erroneous disparity values in the disparity map found by classification are corrected through a completion stage or filling stage. A performance evaluation of stereo matching using AdaBoostM1 RUSBoost Neural networks and GentleBoost is performed.

  20. Covariant diagrams for one-loop matching

    Zhang, Zhengkang

    2016-10-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  1. 6d, Coulomb branch anomaly matching

    Intriligator, Kenneth

    2014-10-01

    6d QFTs are constrained by the analog of 't Hooft anomaly matching: all anomalies for global symmetries and metric backgrounds are constants of RG flows, and for all vacua in moduli spaces. We discuss an anomaly matching mechanism for 6d theories on their Coulomb branch. It is a global symmetry analog of Green-Schwarz-West-Sagnotti anomaly cancellation, and requires the apparent anomaly mismatch to be a perfect square, . Then Δ I 8 is cancelled by making X 4 an electric/magnetic source for the tensor multiplet, so background gauge field instantons yield charged strings. This requires the coefficients in X 4 to be integrally quantized. We illustrate this for theories. We also consider the SCFTs from N small E8 instantons, verifying that the recent result for its anomaly polynomial fits with the anomaly matching mechanism.

  2. Matching to Openly Innovate with Suppliers

    Laursen, Linda Nhu

    2017-01-01

    heterogeneous suppliers with the internal organisation in order to openly innovate. More specifically, it focuses on a governance mode, recently emerged in practice, by which firms summon their suppliers and their own internal organisation at an event to match them for open innovation activities – innovation......When large firms choose to involve their many suppliers in open innovation, they are faced with a set of challenges pertaining to the governance of several suppliers. Suppliers are heterogeneous, offering heterogeneous materials, products, information, services, and knowledge, which are differently...... organized across functions and hierarchies. To make use of such heterogeneous resources, a critical challenge for open innovation is to pair a supplier resource with a suitable opportunity-for-use from within the firm – a challenge of matching. This dissertation addresses the challenge of matching...

  3. INFORMATION SYSTEMS AUDIT CURRICULA CONTENT MATCHING

    Vasile-Daniel CARDOȘ

    2014-11-01

    Full Text Available Financial and internal auditors must cope with the challenge of performing their mission in technology enhanced environment. In this article we match the information technology description found in the International Federation of Accountants (IFAC and the Institute of Internal Auditors (IIA curricula against the Model Curriculum issued by the Information Systems Audit and Control Association (ISACA. By reviewing these three curricula, we matched the content in the ISACA Model Curriculum with the IFAC International Education Practice Statement 2 and the IIAs’ Global Model Internal Audit Curriculum. In the IFAC and IIA Curriculum there are 16 content elements, out of 19 possible, which match, in their description, the ISACA Model Curriculum’s content. We noticed that a candidate who graduates an IFAC or IIA compliant program acquire IS auditing competences similar to the specific content of the ISACA model curriculum but less than the requirements for a professional information systems auditor.

  4. Covariant diagrams for one-loop matching

    Zhang, Zhengkang [Michigan Center for Theoretical Physics (MCTP), University of Michigan,450 Church Street, Ann Arbor, MI 48109 (United States); Deutsches Elektronen-Synchrotron (DESY),Notkestraße 85, 22607 Hamburg (Germany)

    2017-05-30

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  5. A medium resolution fingerprint matching system

    Ayman Mohammad Bahaa-Eldin

    2013-09-01

    Full Text Available In this paper, a novel minutiae based fingerprint matching system is proposed. The system is suitable for medium resolution fingerprint images obtained by low cost commercial sensors. The paper presents a new thinning algorithm, a new features extraction and representation, and a novel feature distance matching algorithm. The proposed system is rotation and translation invariant and is suitable for complete or partial fingerprint matching. The proposed algorithms are optimized to be executed on low resource environments both in CPU power and memory space. The system was evaluated using a standard fingerprint dataset and good performance and accuracy were achieved under certain image quality requirements. In addition, the proposed system was compared favorably to that of the state of the art systems.

  6. Covariant diagrams for one-loop matching

    Zhang, Zhengkang [Michigan Univ., Ann Arbor, MI (United States). Michigan Center for Theoretical Physics; Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2016-10-15

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gaugecovariant quantities and are thus dubbed ''covariant diagrams.'' The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  7. Matching of ion sources to cyclotron inflectors

    Baartman, R.

    1988-06-01

    In general, cyclotron inflectors strongly couple the two transverse subspaces. This leads to a growth in emittance projections for a beam with no initial correlation between the two transverse subspaces. Only in the case of the Mueller (hyperboloid) inflector is there no emittance growth. We have made calculations using an optimization routine to match a given beam through the axial injection system. We find that in the limit where all the emittance is due to a beam's axial angular momentum (for example, from an ECR source), matching with no emittance growth is possible even in the case of mirror or spiral inflectors. Moreover, any one of the two transverse emittances circulating in the cyclotron can be made smaller than the source emittance while maintaining the sum of the emittances constant. This is achieved by rotating the matching quadrupoles with respect to the inflector and retuning

  8. Covariant diagrams for one-loop matching

    Zhang, Zhengkang

    2017-01-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed “covariant diagrams.” The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  9. Surface Area Distribution Descriptor for object matching

    Mohamed F. Gafar

    2010-07-01

    Full Text Available Matching 3D objects by their similarity is a fundamental problem in computer vision, computer graphics and many other fields. The main challenge in object matching is to find a suitable shape representation that can be used to accurately and quickly discriminate between similar and dissimilar shapes. In this paper we present a new volumetric descriptor to represent 3D objects. The proposed descriptor is used to match objects under rigid transformations including uniform scaling. The descriptor represents the object by dividing it into shells, acquiring the area distribution of the object through those shells. The computed areas are normalised to make the descriptor scale-invariant in addition to rotation and translation invariant. The effectiveness and stability of the proposed descriptor to noise and variant sampling density as well as the effectiveness of the similarity measures are analysed and demonstrated through experimental results.

  10. Specialization Patterns

    Schultz , Ulrik Pagh; Lawall , Julia ,; Consel , Charles

    1999-01-01

    Design patterns offer numerous advantages for software development, but can introduce inefficiency into the finished program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose to consider program specialization and design patterns as complementary concepts. On the one hand, program specialization can optimize object-oriented programs written using design patterns. On the other hand, design pat...

  11. Using crosswell data to enhance history matching

    Ravanelli, Fabio M.

    2014-01-01

    One of the most challenging tasks in the oil industry is the production of reliable reservoir forecast models. Due to different sources of uncertainties in the numerical models and inputs, reservoir simulations are often only crude approximations of the reality. This problem is mitigated by conditioning the model with data through data assimilation, a process known in the oil industry as history matching. Several recent advances are being used to improve history matching reliability, notably the use of time-lapse data and advanced data assimilation techniques. One of the most promising data assimilation techniques employed in the industry is the ensemble Kalman filter (EnKF) because of its ability to deal with non-linear models at reasonable computational cost. In this paper we study the use of crosswell seismic data as an alternative to 4D seismic surveys in areas where it is not possible to re-shoot seismic. A synthetic reservoir model is used in a history matching study designed better estimate porosity and permeability distributions and improve the quality of the model to predict future field performance. This study is divided in three parts: First the use of production data only is evaluated (baseline for benchmark). Second the benefits of using production and 4D seismic data are assessed. Finally, a new conceptual idea is proposed to obtain time-lapse information for history matching. The use of crosswell time-lapse seismic tomography to map velocities in the interwell region is demonstrated as a potential tool to ensure survey reproducibility and low acquisition cost when compared with full scale surface surveys. Our numerical simulations show that the proposed method provides promising history matching results leading to similar estimation error reductions when compared with conventional history matched surface seismic data.

  12. Physiological characteristics of badminton match play.

    Faude, Oliver; Meyer, Tim; Rosenberger, Friederike; Fries, Markus; Huber, Günther; Kindermann, Wilfried

    2007-07-01

    The present study aimed at examining the physiological characteristics and metabolic demands of badminton single match play. Twelve internationally ranked badminton players (eight women and four men) performed an incremental treadmill test [VO(2peak = )50.3 +/- 4.1 ml min(-1) kg(-1) (women) and 61.8 +/- 5.9 ml min(-1) kg(-1) (men), respectively]. On a separate day, they played a simulated badminton match of two 15 min with simultaneous gas exchange (breath-by-breath) and heart rate measurements. Additionally, blood lactate concentrations were determined before, after 15 min and at the end of the match. Furthermore, the duration of rallies and rests in between, the score as well as the number of shots per rally were recorded. A total of 630 rallies was analysed. Mean rally and rest duration were 5.5 +/- 4.4 s and 11.4 +/- 6.0 s, respectively, with an average 5.1 +/- 3.9 shots played per rally. Mean oxygen uptake (VO(2)), heart rate (HR), and blood lactate concentrations during badminton matches were 39.6 +/- 5.7 ml min(-1) kg(-1) (73.3% VO(2peak)), 169 +/- 9 min(-1) (89.0% HR(peak)) and 1.9 +/- 0.7 mmol l(-1), respectively. For a single subject 95% confidence intervals for VO(2) and HR during match play were on average 45.7-100.9% VO(2peak) and 78.3-99.8% HR(peak). High average intensity of badminton match play and considerable variability of several physiological variables demonstrate the importance of anaerobic alactacid and aerobic energy production in competitive badminton. A well-developed aerobic endurance capacity seems necessary for fast recovery between rallies or intensive training workouts.

  13. Pattern recognition

    Theodoridis, Sergios

    2003-01-01

    Pattern recognition is a scientific discipline that is becoming increasingly important in the age of automation and information handling and retrieval. Patter Recognition, 2e covers the entire spectrum of pattern recognition applications, from image analysis to speech recognition and communications. This book presents cutting-edge material on neural networks, - a set of linked microprocessors that can form associations and uses pattern recognition to ""learn"" -and enhances student motivation by approaching pattern recognition from the designer's point of view. A direct result of more than 10

  14. History Matching: Towards Geologically Reasonable Models

    Melnikova, Yulia; Cordua, Knud Skou; Mosegaard, Klaus

    This work focuses on the development of a new method for history matching problem that through a deterministic search finds a geologically feasible solution. Complex geology is taken into account evaluating multiple point statistics from earth model prototypes - training images. Further a function...... that measures similarity between statistics of a training image and statistics of any smooth model is introduced and its analytical gradient is computed. This allows us to apply any gradientbased method to history matching problem and guide a solution until it satisfies both production data and complexity...

  15. Faster and Simpler Approximation of Stable Matchings

    Katarzyna Paluch

    2014-04-01

    Full Text Available We give a 3 2 -approximation algorithm for finding stable matchings that runs in O(m time. The previous most well-known algorithm, by McDermid, has the same approximation ratio but runs in O(n3/2m time, where n denotes the number of people andm is the total length of the preference lists in a given instance. In addition, the algorithm and the analysis are much simpler. We also give the extension of the algorithm for computing stable many-to-many matchings.

  16. Famous face recognition, face matching, and extraversion.

    Lander, Karen; Poyarekar, Siddhi

    2015-01-01

    It has been previously established that extraverts who are skilled at interpersonal interaction perform significantly better than introverts on a face-specific recognition memory task. In our experiment we further investigate the relationship between extraversion and face recognition, focusing on famous face recognition and face matching. Results indicate that more extraverted individuals perform significantly better on an upright famous face recognition task and show significantly larger face inversion effects. However, our results did not find an effect of extraversion on face matching or inverted famous face recognition.

  17. A Novel Fast and Robust Binary Affine Invariant Descriptor for Image Matching

    Xiujie Qu

    2014-01-01

    Full Text Available As the current binary descriptors have disadvantages of high computational complexity, no affine invariance, and the high false matching rate with viewpoint changes, a new binary affine invariant descriptor, called BAND, is proposed. Different from other descriptors, BAND has an irregular pattern, which is based on local affine invariant region surrounding a feature point, and it has five orientations, which are obtained by LBP effectively. Ultimately, a 256 bits binary string is computed by simple random sampling pattern. Experimental results demonstrate that BAND has a good matching result in the conditions of rotating, image zooming, noising, lighting, and small-scale perspective transformation. It has better matching performance compared with current mainstream descriptors, while it costs less time.

  18. An improved principal component analysis based region matching method for fringe direction estimation

    He, A.; Quan, C.

    2018-04-01

    The principal component analysis (PCA) and region matching combined method is effective for fringe direction estimation. However, its mask construction algorithm for region matching fails in some circumstances, and the algorithm for conversion of orientation to direction in mask areas is computationally-heavy and non-optimized. We propose an improved PCA based region matching method for the fringe direction estimation, which includes an improved and robust mask construction scheme, and a fast and optimized orientation-direction conversion algorithm for the mask areas. Along with the estimated fringe direction map, filtered fringe pattern by automatic selective reconstruction modification and enhanced fast empirical mode decomposition (ASRm-EFEMD) is used for Hilbert spiral transform (HST) to demodulate the phase. Subsequently, windowed Fourier ridge (WFR) method is used for the refinement of the phase. The robustness and effectiveness of proposed method are demonstrated by both simulated and experimental fringe patterns.

  19. Effects of a lighter, smaller football on Acute match injuries in adolescent female football

    Zebis, Mette K.; Thorborg, Kristian; Andersen, Lars L.

    2018-01-01

    BACKGROUND: The high injury incidence during match-play in female adolescent football is a major concern. In football, males and females play matches with the same football size. No studies have investigated the effect of football size on injury incidence in female adolescent football. Thus......, the aim of the present study was to investigate the effects of introducing a lighter, smaller football on the injury pattern in female adolescent football. METHODS We conducted a pilot cluster randomized controlled trial including 26 football teams representing 346 adolescent female football players (age...... 15-18 years). The teams were randomized to a new lighter, smaller football (INT, N.=12 teams) or a traditional FIFA size 5 football (CON, N.=14 teams) during a full match-season. Acute time-loss injuries and football-exposure during match-play were reported weekly by text-message questions...

  20. Actors with Multi-Headed Message Receive Patterns

    Sulzmann, Martin; Lam, Edmund Soon Lee; Van Weert, Peter

    2008-01-01

    style actors with receive clauses containing multi-headed message patterns. Patterns may be non-linear and constrained by guards. We provide a number of examples to show the usefulness of the extension. We also explore the design space for multi-headed message matching semantics, for example first-match......The actor model provides high-level concurrency abstractions to coordinate simultaneous computations by message passing. Languages implementing the actor model such as Erlang commonly only support single-headed pattern matching over received messages. We propose and design an extension of Erlang...... and rule priority-match semantics. The various semantics are inspired by the multi-set constraint matching semantics found in Constraint Handling Rules. This provides us with a formal model to study actors with multi-headed message receive patterns. The system can be implemented efficiently and we have...

  1. Pigeons ("Columba Livia") Approach Nash Equilibrium in Experimental Matching Pennies Competitions

    Sanabria, Federico; Thrailkill, Eric

    2009-01-01

    The game of Matching Pennies (MP), a simplified version of the more popular Rock, Papers, Scissors, schematically represents competitions between organisms with incentives to predict each other's behavior. Optimal performance in iterated MP competitions involves the production of random choice patterns and the detection of nonrandomness in the…

  2. Gait impairment in cervical spondylotic myelopathy: comparison with age- and gender-matched healthy controls.

    Malone, Ailish

    2012-12-01

    Gait impairment is a primary symptom of cervical spondylotic myelopathy (CSM); however, little is known about specific kinetic and kinematic gait parameters. The objectives of the study were: (1) to compare gait patterns of people with untreated CSM to those of age- and gender-matched healthy controls; (2) to examine the effect of gait speed on kinematic and kinetic parameters.

  3. Dispersion and betatron matching into the linac

    Decker, F.J.; Adolphsen, C.; Corbett, W.J.; Emma, P.; Hsu, I.; Moshammer, H.; Seeman, J.T.; Spence, W.L.

    1991-05-01

    In high energy linear colliders, the low emittance beam from a damping ring has to be preserved all the way to the linac, in the linac and to the interaction point. In particular, the Ring-To-Linac (RTL) section of the SLAC Linear Collider (SLC) should provide an exact betatron and dispersion match from the damping ring to the linac. A beam with a non-zero dispersion shows up immediately as an increased emittance, while with a betatron mismatch the beam filaments in the linac. Experimental tests and tuning procedures have shown that the linearized beta matching algorithms are insufficient if the actual transport line has some unknown errors not included in the model. Also, adjusting quadrupole strengths steers the beam if it is offset in the quadrupole magnets. These and other effects have lead to a lengthy tuning process, which in the end improves the matching, but is not optimal. Different ideas will be discussed which should improve this matching procedure and make it a more reliable, faster and simpler process. 5 refs., 2 figs

  4. Photon signature analysis using template matching

    Bradley, D.A., E-mail: d.a.bradley@surrey.ac.uk [Department of Physics, University of Surrey, Guildford GU2 7XH (United Kingdom); Hashim, S., E-mail: suhairul@utm.my [Department of Physics, Universiti Teknologi Malaysia, 81310 Skudai, Johor (Malaysia); Saripan, M.I. [Faculty of Engineering, Universiti Putra Malaysia, 43400 Serdang, Selangor (Malaysia); Wells, K. [Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford GU2 7XH (United Kingdom); Dunn, W.L. [Department of Mechanical and Nuclear Engineering, Kansas State University, 3002 Rathbone Hall, Manhattan, KS 66506 (United States)

    2011-10-01

    We describe an approach to detect improvised explosive devices (IEDs) by using a template matching procedure. This approach relies on the signature due to backstreaming {gamma} photons from various targets. In this work we have simulated cylindrical targets of aluminum, iron, copper, water and ammonium nitrate (nitrogen-rich fertilizer). We simulate 3.5 MeV source photons distributed on a plane inside a shielded area using Monte Carlo N-Particle (MCNP{sup TM}) code version 5 (V5). The 3.5 MeV source gamma rays yield 511 keV peaks due to pair production and scattered gamma rays. In this work, we simulate capture of those photons that backstream, after impinging on the target element, toward a NaI detector. The captured backstreamed photons are expected to produce a unique spectrum that will become part of a simple signal processing recognition system based on the template matching method. Different elements were simulated using different sets of random numbers in the Monte Carlo simulation. To date, the sum of absolute differences (SAD) method has been used to match the template. In the examples investigated, template matching was found to detect all elements correctly.

  5. Probabilistic evaluation of process model matching techniques

    Kuss, Elena; Leopold, Henrik; van der Aa, Han; Stuckenschmidt, Heiner; Reijers, Hajo A.

    2016-01-01

    Process model matching refers to the automatic identification of corresponding activities between two process models. It represents the basis for many advanced process model analysis techniques such as the identification of similar process parts or process model search. A central problem is how to

  6. Decentralized trade with bargaining and voluntary matching

    Tranæs, Torben; Sloth, Birgitte; Hendon, Ebbe

    1994-01-01

    Rubinstein and Wolinsky (1990) study a market with one seller, two buyers, and voluntary matching. Both the competitive outcomepc and the bilateral bargaining outcomepb are possible in subgame perfect equilibrium. We consider two variations. First, if there is a cost larger thanpc−pc to the seller...

  7. Regular Expression Matching and Operational Semantics

    Asiri Rathnayake

    2011-08-01

    Full Text Available Many programming languages and tools, ranging from grep to the Java String library, contain regular expression matchers. Rather than first translating a regular expression into a deterministic finite automaton, such implementations typically match the regular expression on the fly. Thus they can be seen as virtual machines interpreting the regular expression much as if it were a program with some non-deterministic constructs such as the Kleene star. We formalize this implementation technique for regular expression matching using operational semantics. Specifically, we derive a series of abstract machines, moving from the abstract definition of matching to increasingly realistic machines. First a continuation is added to the operational semantics to describe what remains to be matched after the current expression. Next, we represent the expression as a data structure using pointers, which enables redundant searches to be eliminated via testing for pointer equality. From there, we arrive both at Thompson's lockstep construction and a machine that performs some operations in parallel, suitable for implementation on a large number of cores, such as a GPU. We formalize the parallel machine using process algebra and report some preliminary experiments with an implementation on a graphics processor using CUDA.

  8. Secure matching of Dutch car license plates

    Sunil, A.B.; Erkiny, Z.; Veugenyz, T.

    2016-01-01

    License plate matching plays an important role in applications like law enforcement, traffic management and road pricing, where the plate is first recognized and then compared to a database of authorized vehicle registration plates. Unfortunately, there are several privacy related issues that should

  9. 7 CFR 3430.906 - Matching requirements.

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Matching requirements. 3430.906 Section 3430.906 Agriculture Regulations of the Department of Agriculture (Continued) COOPERATIVE STATE RESEARCH, EDUCATION, AND EXTENSION SERVICE, DEPARTMENT OF AGRICULTURE COMPETITIVE AND NONCOMPETITIVE NON-FORMULA FEDERAL...

  10. Symmetric Circular Matchings and RNA Folding

    Hofacker, Ivo L.; Reidys, Christian; Stadler, Peter F.

    2012-01-01

    RNA secondary structures can be computed as optimal solutions of certain circular matching problems. An accurate treatment of this energy minimization problem has to account for the small --- but non-negligible --- entropic destabilization of secondary structures with non-trivial automorphisms. S...

  11. 13 CFR 130.450 - Matching funds.

    2010-01-01

    ... in the budget proposal. Cash sources shall be identified by name and account. All applicants must... agreement. The account containing such cash must be under the direct management of the SBDC Director, or, if... received by the SBDC during the budget period, as long as the total Cash Match provided by the SBDC is 50...

  12. 13 CFR 108.2030 - Matching requirements.

    2010-01-01

    ... Section 108.2030 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS VENTURE CAPITAL... resources raised by the NMVC Company or SSBIC. (b) Allowable sources. (1) Any source other than SBA is an... this part. (3) A portion of Private Capital may be designated as matching resources if the designated...

  13. Performance Evaluation of Tree Object Matching

    Somchaipeng, Kerawit; Sporring, Jon; Kreiborg, Sven

    2005-01-01

    Multi-Scale Singularity Trees (MSSTs) represents the deep structure of images in scale-space and provide both the connections between image features at different scales and their strengths. In this report we present and evaluate an algorithm that exploits the MSSTs for image matching. Two versions...

  14. Language style matching and police interrogation outcomes

    Richardson, Beth H.; Taylor, Paul J; Snook, Brent; Conchie, Stacey M.; Bennell, Craig

    2014-01-01

    This research examined the coordination of interrogator and suspects’ verbal behavior in interrogations. Sixty-four police interrogations were examined at the aggregate and utterance level using a measure of verbal mimicry known as Language Style Matching. Analyses revealed an interaction between

  15. Sidescan Sonar Image Matching Using Cross Correlation

    Thisen, Erik; Sørensen, Helge Bjarup Dissing; Stage, Bjarne

    2003-01-01

    When surveying an area for sea mines with a sidescan sonar, the ability to find the same object in two different sonar images is helpful to determine the nature of the object. The main problem with matching two sidescan sonar images is that a scene changes appearance when viewed from different vi...

  16. Matching Expectations for Successful University Student Volunteering

    Paull, Megan; Omari, Maryam; MacCallum, Judith; Young, Susan; Walker, Gabrielle; Holmes, Kirsten; Haski-Leventha, Debbie; Scott, Rowena

    2017-01-01

    Purpose: The purpose of this paper is to demonstrate the importance of expectation formation and matching for university student volunteers and their hosts. Design/methodology/approach: This research involved a multi-stage data collection process including interviews with student volunteers, and university and host representatives from six…

  17. 7 CFR 3419.2 - Matching funds.

    2010-01-01

    ... Regulations of the Department of Agriculture (Continued) COOPERATIVE STATE RESEARCH, EDUCATION, AND EXTENSION SERVICE, DEPARTMENT OF AGRICULTURE MATCHING FUNDS REQUIREMENT FOR AGRICULTURAL RESEARCH AND EXTENSION FORMULA FUNDS AT 1890 LAND-GRANT INSTITUTIONS, INCLUDING TUSKEGEE UNIVERSITY, AND AT 1862 LAND-GRANT...

  18. Nonlinear soliton matching between optical fibers

    Agger, Christian; Sørensen, Simon Toft; Thomsen, Carsten L.

    2011-01-01

    In this Letter, we propose a generic nonlinear coupling coefficient, η2 NL ¼ ηjγ=β2jfiber2=jγ=β2jfiber1, which gives a quantitative measure for the efficiency of nonlinear matching of optical fibers by describing how a fundamental soliton couples from one fiber into another. Specifically, we use η...

  19. The Match Quality Gains from Unemployment Insurance

    Centeno, Mario

    2004-01-01

    The benefits of unemployment insurance (UI) by measuring its effect in match quality are assessed. The relationship between post-unemployment job tenure and measures of the state level UI generosity and the unemployment rate at the time of the job is analyzed, using NLSY data.

  20. History Matching in Parallel Computational Environments

    Steven Bryant; Sanjay Srinivasan; Alvaro Barrera; Sharad Yadav

    2004-08-31

    In the probabilistic approach for history matching, the information from the dynamic data is merged with the prior geologic information in order to generate permeability models consistent with the observed dynamic data as well as the prior geology. The relationship between dynamic response data and reservoir attributes may vary in different regions of the reservoir due to spatial variations in reservoir attributes, fluid properties, well configuration, flow constrains on wells etc. This implies probabilistic approach should then update different regions of the reservoir in different ways. This necessitates delineation of multiple reservoir domains in order to increase the accuracy of the approach. The research focuses on a probabilistic approach to integrate dynamic data that ensures consistency between reservoir models developed from one stage to the next. The algorithm relies on efficient parameterization of the dynamic data integration problem and permits rapid assessment of the updated reservoir model at each stage. The report also outlines various domain decomposition schemes from the perspective of increasing the accuracy of probabilistic approach of history matching. Research progress in three important areas of the project are discussed: {lg_bullet}Validation and testing the probabilistic approach to incorporating production data in reservoir models. {lg_bullet}Development of a robust scheme for identifying reservoir regions that will result in a more robust parameterization of the history matching process. {lg_bullet}Testing commercial simulators for parallel capability and development of a parallel algorithm for history matching.

  1. Cash Management/Data Matching. Training Guide.

    Office of Student Financial Assistance (ED), Washington, DC.

    This training guide for financial aid staff explains the process of direct loan reconciliation and suggests appropriate cash management accounting practices. Chapter 1 explains the importance of cash management, the role of data matching, and reviews basic reconciliation concepts and terms and direct loan reporting requirements. Chapter 2 reviews…

  2. Fingerprint matching on smart card: A review

    Baruni, Kedimotse P

    2016-12-01

    Full Text Available Fingerprint Match-on-Card (MoC) offers the highest degree of privacy and security to cardholders as the fingerprint never leaves the secure environment of a smart card. The level of security of a biometric system is evaluated by the location where...

  3. On a special case of model matching

    Zagalak, Petr

    2004-01-01

    Roč. 77, č. 2 (2004), s. 164-172 ISSN 0020-7179 R&D Projects: GA ČR GA102/01/0608 Institutional research plan: CEZ:AV0Z1075907 Keywords : linear systems * state feedback * model matching Subject RIV: BC - Control Systems Theory Impact factor: 0.702, year: 2004

  4. The Brown-Servranckx matching transformer for simultaneous RFQ to DTL H+ and H- matching

    Wadlinger, E.A.; Garnett, R.W.

    1996-01-01

    The issue involved in the simultaneous matching of H + and H - beams between an RFQ and DTL lies in the fact that both beams experience the same electric-field forces at a given position in the RFQ. Hence, the two beams are focused to the same correlation. However, matching to a DTL requires correlation of the opposite sign. The Brown-Servranckx quarter-wave (λ / 4) matching transformer system, which requires four quadrupoles, provides a method to simultaneously match H + and H - beams between an RFQ and a DTL. The method requires the use of a special RFQ section to obtain the Twiss parameter conditions β x = β y and α x = α y = 0 at the exit of the RFQ. This matching between the RFQ and DTL is described. (author)

  5. The Brown-Servranckx matching transformer for simultaneous RFQ to DTL H+ and H- matching

    Wadlinger, E.A.; Garnett, R.W.

    1996-01-01

    The issue involved in simultaneous matching of H + and H - beams between an RFQ and DTL lies in the fact that both beams experience the same electric-field forces at a given position in the RFQ. Hence, the two beams are focused to the same correlation. However, matching to a DTL requires correlation of the opposite sign. The Brown-Servranckx quarter-wave (λ/4) matching transformer system, which requires four quadrupoles, provides a method to simultaneously match H + and H - beams between an RFQ and a DTL. The method requires the use of a special RFQ section to obtain the Twiss parameter conditions β x =β y and α x =α y =0 at the exit of the RFQ. This matching between the RFQ and DTL is described

  6. Geodesic patterns

    Pottmann, Helmut; Huang, Qixing; Deng, Bailin; Schiftner, Alexander; Kilian, Martin; Guibas, Leonidas J.; Wallner, Johannes

    2010-01-01

    Geodesic curves in surfaces are not only minimizers of distance, but they are also the curves of zero geodesic (sideways) curvature. It turns out that this property makes patterns of geodesics the basic geometric entity when dealing with the cladding of a freeform surface with wooden panels which do not bend sideways. Likewise a geodesic is the favored shape of timber support elements in freeform architecture, for reasons of manufacturing and statics. Both problem areas are fundamental in freeform architecture, but so far only experimental solutions have been available. This paper provides a systematic treatment and shows how to design geodesic patterns in different ways: The evolution of geodesic curves is good for local studies and simple patterns; the level set formulation can deal with the global layout of multiple patterns of geodesics; finally geodesic vector fields allow us to interactively model geodesic patterns and perform surface segmentation into panelizable parts. © 2010 ACM.

  7. Foam patterns

    Chaudhry, Anil R; Dzugan, Robert; Harrington, Richard M; Neece, Faurice D; Singh, Nipendra P; Westendorf, Travis

    2013-11-26

    A method of creating a foam pattern comprises mixing a polyol component and an isocyanate component to form a liquid mixture. The method further comprises placing a temporary core having a shape corresponding to a desired internal feature in a cavity of a mold and inserting the mixture into the cavity of the mold so that the mixture surrounds a portion of the temporary core. The method optionally further comprises using supporting pins made of foam to support the core in the mold cavity, with such pins becoming integral part of the pattern material simplifying subsequent processing. The method further comprises waiting for a predetermined time sufficient for a reaction from the mixture to form a foam pattern structure corresponding to the cavity of the mold, wherein the foam pattern structure encloses a portion of the temporary core and removing the temporary core from the pattern independent of chemical leaching.

  8. Geodesic patterns

    Pottmann, Helmut

    2010-07-26

    Geodesic curves in surfaces are not only minimizers of distance, but they are also the curves of zero geodesic (sideways) curvature. It turns out that this property makes patterns of geodesics the basic geometric entity when dealing with the cladding of a freeform surface with wooden panels which do not bend sideways. Likewise a geodesic is the favored shape of timber support elements in freeform architecture, for reasons of manufacturing and statics. Both problem areas are fundamental in freeform architecture, but so far only experimental solutions have been available. This paper provides a systematic treatment and shows how to design geodesic patterns in different ways: The evolution of geodesic curves is good for local studies and simple patterns; the level set formulation can deal with the global layout of multiple patterns of geodesics; finally geodesic vector fields allow us to interactively model geodesic patterns and perform surface segmentation into panelizable parts. © 2010 ACM.

  9. New Orf virus (Parapoxvirus recombinant expressing H5 hemagglutinin protects mice against H5N1 and H1N1 influenza A virus.

    Jörg Rohde

    Full Text Available Previously we demonstrated the versatile utility of the Parapoxvirus Orf virus (ORFV as a vector platform for the development of potent recombinant vaccines. In this study we present the generation of new ORFV recombinants expressing the hemagglutinin (HA or nucleoprotein (NP of the highly pathogenic avian influenza virus (HPAIV H5N1. Correct foreign gene expression was examined in vitro by immunofluorescence, Western blotting and flow cytometry. The protective potential of both recombinants was evaluated in the mouse challenge model. Despite adequate expression of NP, the recombinant D1701-V-NPh5 completely failed to protect mice from lethal challenge. However, the H5 HA-expressing recombinant D1701-V-HAh5n mediated solid protection in a dose-dependent manner. Two intramuscular (i.m. injections of the HA-expressing recombinant protected all animals from lethal HPAIV infection without loss of body weight. Notably, the immunized mice resisted cross-clade H5N1 and heterologous H1N1 (strain PR8 influenza virus challenge. In vivo antibody-mediated depletion of CD4-positive and/or CD8-posititve T-cell subpopulations during immunization and/or challenge infection implicated the relevance of CD4-positive T-cells for induction of protective immunity by D1701-V-HAh5n, whereas the absence of CD8-positive T-cells did not significantly influence protection. In summary, this study validates the potential of the ORFV vectored vaccines also to combat HPAIV.

  10. Protection of pigs against pandemic swine origin H1N1 influenza A virus infection by hemagglutinin- or neuraminidase-expressing attenuated pseudorabies virus recombinants.

    Klingbeil, Katharina; Lange, Elke; Blohm, Ulrike; Teifke, Jens P; Mettenleiter, Thomas C; Fuchs, Walter

    2015-03-02

    Influenza is an important respiratory disease of pigs, and may lead to novel human pathogens like the 2009 pandemic H1N1 swine-origin influenza virus (SoIV). Therefore, improved influenza vaccines for pigs are required. Recently, we demonstrated that single intranasal immunization with a hemagglutinin (HA)-expressing pseudorabies virus recombinant of vaccine strain Bartha (PrV-Ba) protected pigs from H1N1 SoIV challenge (Klingbeil et al., 2014). Now we investigated enhancement of efficacy by prime-boost vaccination and/or intramuscular administration. Furthermore, a novel PrV-Ba recombinant expressing codon-optimized N1 neuraminidase (NA) was included. In vitro replication of this virus was only slightly affected compared to parental virus. Unlike HA, the abundantly expressed NA was efficiently incorporated into PrV particles. Immunization of pigs with the two PrV recombinants, either singly or in combination, induced B cell proliferation and the expected SoIV-specific antibodies, whose titers increased substantially after boost vaccination. After immunization of animals with either PrV recombinant H1N1 SoIV challenge virus replication was significantly reduced compared to PrV-Ba vaccinated or naïve controls. Protective efficacy of HA-expressing PrV was higher than of NA-expressing PrV, and not significantly enhanced by combination. Despite higher serum antibody titers obtained after intramuscular immunization, transmission of challenge virus to naïve contact animals was only prevented after intranasal prime-boost vaccination with HA-expressing PrV-Ba. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Preexisting Salmonella-specific immunity interferes with the subsequent development of immune responses against the Salmonella strains delivering H9N2 hemagglutinin.

    Hajam, Irshad Ahmed; Lee, John Hwa

    2017-06-01

    Recombinant Salmonella strains expressing foreign heterologous antigens have been extensively studied as promising live vaccine delivery vehicles. In this study, we constructed attenuated smooth (S-HA) and rough (R-HA) Salmonella strains expressing hemagglutinin (HA) of H9N2, a low pathogenic avian influenza A virus. We then investigated the HA-specific immune responses following oral immunization with either S-HA or R-HA strain in chicken model. We further examined the effects of the preexisting anti-Salmonella immunity on the subsequent elicitation of the HA and the Salmonella ompA specific immune responses. Our results showed that primary immunization with either the S-HA or the R-HA strain elicited comparable HA-specific immune responses and the responses were significantly (pSalmonella vector control. When chickens were pre-immunized with the smooth Salmonella carrier alone and then vaccinated with either S-HA or R-HA strain 3, 6 and 9 weeks later, respectively, significant reductions were seen for HA-specific immune responses at week 6, a point which corresponded to the peak of the primary Salmonella-specific antibody responses. No reductions were seen at week 3 and 9, albeit, the HA-specific immune responses were boosted at week 9, a point which corresponded to the lowest primary Salmonella-specific antibody responses. The ompA recall responses remain refractory at week 3 and 6 following deliberate immunization with the carrier strain, but were significantly (pSalmonella immunity inhibits antigen-specific immune responses and this effect could be avoided by carefully selecting the time point when carrier-specific immune responses are relatively low. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. A novel eight amino acid insertion contributes to the hemagglutinin cleavability and the virulence of a highly pathogenic avian influenza A (H7N3) virus in mice

    Sun, Xiangjie; Belser, Jessica A.; Tumpey, Terrence M., E-mail: tft9@cdc.gov

    2016-01-15

    In 2012, an avian influenza A H7N3 (A/Mexico/InDRE7218/2012; Mx/7218) virus was responsible for two confirmed cases of human infection and led to the death or culling of more than 22 million chickens in Jalisco, Mexico. Interestingly, this virus acquired an 8-amino acid (aa)-insertion (..PENPK-DRKSRHRR-TR/GLF) near the hemagglutinin (HA) cleavage site by nonhomologous recombination with host rRNA. It remains unclear which specific residues at the cleavage site contribute to the virulence of H7N3 viruses in mammals. Using loss-of-function approaches, we generated a series of cleavage site mutant viruses by reverse genetics and characterized the viruses in vitro and in vivo. We found that the 8-aa insertion and the arginine at position P4 of the Mx/7218 HA cleavage site are essential for intracellular HA cleavage in 293T cells, but have no effect on the pH of membrane fusion. However, we identified a role for the histidine residue at P5 position in viral fusion pH. In mice, the 8-aa insertion is required for Mx/7218 virus virulence; however, the basic residues upstream of the P4 position are dispensable for virulence. Overall, our study provides the first line of evidence that the insertion in the Mx/7218 virus HA cleavage site confers its intracellular cleavability, and consequently contributes to enhanced virulence in mice. - Highlights: • An avian influenza H7N3 virus acquired a unique 8-amino acid (aa) insertion. • The role of specific basic residues in the HA insertion in viral pathogenesis was determined. • In mice, the 8-aa insertion is required for H7N3 virus virulence. • The R residue at position P4 is essential for HA intracellular cleavage and virus virulence.

  13. Measles Virus Hemagglutinin epitopes immunogenic in natural infection and vaccination are targeted by broad or genotype-specific neutralizing monoclonal antibodies.

    Muñoz-Alía, Miguel Angel; Casasnovas, José M; Celma, María Luisa; Carabaña, Juan; Liton, Paloma B; Fernandez-Muñoz, Rafael

    2017-05-15

    Measles virus (MV) remains a leading cause of vaccine-preventable deaths in children. Protection against MV is associated with neutralizing antibodies that preferentially recognize the viral hemagglutinin (MV-H), and to a lesser extent, the fusion protein (MV-F). Although MV is serologically monotypic, 24 genotypes have been identified. Here we report three neutralization epitopes conserved in the more prevalent circulating MV genotypes, two located in the MV-H receptor binding site (RBS) (antigenic site III) and a third in MV-H/MV-F interphase (antigenic site Ia) which are essential for MV multiplication. In contrast, two MV-H neutralization epitopes, showed a genotype-specific neutralization escape due to a single amino acid change, that we mapped in the "noose" antigenic site, or an enhanced neutralization epitope (antigenic site IIa). The monoclonal antibody (mAb) neutralization potency correlated with its binding affinity and was mainly driven by kinetic dissociation rate (k off ). We developed an immunoassay for mAb binding to MV-H in its native hetero-oligomeric structure with MV-F on the surface of a MV productive steady-state persistently infected (p.i.) human cell lines, and a competitive-binding assay with serum from individuals with past infection by different MV genotypes. Binding assays revealed that a broad neutralization epitope, in RBS antigenic site, a genotype specific neutralization epitopes, in noose and IIa sites, were immunogenic in natural infection and vaccination and may elicit long-lasting humoral immunity that might contribute to explain MV immunogenic stability. These results support the design of improved measles vaccines, broad-spectrum prophylactic or therapeutic antibodies and MV-used in oncolytic therapies. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. A novel eight amino acid insertion contributes to the hemagglutinin cleavability and the virulence of a highly pathogenic avian influenza A (H7N3) virus in mice

    Sun, Xiangjie; Belser, Jessica A.; Tumpey, Terrence M.

    2016-01-01

    In 2012, an avian influenza A H7N3 (A/Mexico/InDRE7218/2012; Mx/7218) virus was responsible for two confirmed cases of human infection and led to the death or culling of more than 22 million chickens in Jalisco, Mexico. Interestingly, this virus acquired an 8-amino acid (aa)-insertion (..PENPK-DRKSRHRR-TR/GLF) near the hemagglutinin (HA) cleavage site by nonhomologous recombination with host rRNA. It remains unclear which specific residues at the cleavage site contribute to the virulence of H7N3 viruses in mammals. Using loss-of-function approaches, we generated a series of cleavage site mutant viruses by reverse genetics and characterized the viruses in vitro and in vivo. We found that the 8-aa insertion and the arginine at position P4 of the Mx/7218 HA cleavage site are essential for intracellular HA cleavage in 293T cells, but have no effect on the pH of membrane fusion. However, we identified a role for the histidine residue at P5 position in viral fusion pH. In mice, the 8-aa insertion is required for Mx/7218 virus virulence; however, the basic residues upstream of the P4 position are dispensable for virulence. Overall, our study provides the first line of evidence that the insertion in the Mx/7218 virus HA cleavage site confers its intracellular cleavability, and consequently contributes to enhanced virulence in mice. - Highlights: • An avian influenza H7N3 virus acquired a unique 8-amino acid (aa) insertion. • The role of specific basic residues in the HA insertion in viral pathogenesis was determined. • In mice, the 8-aa insertion is required for H7N3 virus virulence. • The R residue at position P4 is essential for HA intracellular cleavage and virus virulence.

  15. Impact of Mutations in the Hemagglutinin of H10N7 Viruses Isolated from Seals on Virus Replication in Avian and Human Cells.

    Dittrich, Anne; Scheibner, David; Salaheldin, Ahmed H; Veits, Jutta; Gischke, Marcel; Mettenleiter, Thomas C; Abdelwhab, Elsayed M

    2018-02-14

    Wild birds are the reservoir for low-pathogenic avian influenza viruses, which are frequently transmitted to domestic birds and occasionally to mammals. In 2014, an H10N7 virus caused severe mortality in harbor seals in northeastern Europe. Although the hemagglutinin (HA) of this virus was closely related to H10 of avian H10N4 virus, it possessed unique nonsynonymous mutations, particularly in the HA1 subunit in or adjacent to the receptor binding domain and proteolytic cleavage site. Here, the impact of these mutations on virus replication was studied in vitro. Using reverse genetics, an avian H10N4 virus was cloned, and nine recombinant viruses carrying one of eight unique mutations or the complete HA from the seal virus were rescued. Receptor binding affinity, replication in avian and mammalian cell cultures, cell-to-cell spread, and HA cleavability of these recombinant viruses were studied. Results show that wild-type recombinant H10N4 virus has high affinity to avian-type sialic acid receptors and no affinity to mammalian-type receptors. The H10N7 virus exhibits dual receptor binding affinity. Interestingly, Q220L (H10 numbering) in the rim of the receptor binding pocket increased the affinity of the H10N4 virus to mammal-type receptors and completely abolished the affinity to avian-type receptors. No remarkable differences in cell-to-cell spread or HA cleavability were observed. All viruses, including the wild-type H10N7 virus, replicated at higher levels in chicken cells than in human cells. These results indicate that H10N7 acquired adaptive mutations (e.g., Q220L) to enhance replication in mammals and retained replication efficiency in the original avian host.

  16. Hemagglutinin-based polyanhydride nanovaccines against H5N1 influenza elicit protective virus neutralizing titers and cell-mediated immunity

    Ross KA

    2014-12-01

    Full Text Available Kathleen A Ross,1 Hyelee Loyd,2 Wuwei Wu,2 Lucas Huntimer,3 Shaheen Ahmed,4 Anthony Sambol,5 Scott Broderick,6 Zachary Flickinger,2 Krishna Rajan,6 Tatiana Bronich,4 Surya Mallapragada,1 Michael J Wannemuehler,3 Susan Carpenter,2 Balaji Narasimhan1 1Chemical and Biological Engineering, Iowa State University, Ames, IA, USA; 2Animal Science, Iowa State University, Ames, IA, USA; 3Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA; 4Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA; 5Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA; 6Materials Science and Engineering, Iowa State University, Ames, IA, USA Abstract: H5N1 avian influenza is a significant global concern with the potential to become the next pandemic threat. Recombinant subunit vaccines are an attractive alternative for pandemic vaccines compared to traditional vaccine technologies. In particular, polyanhydride nanoparticles encapsulating subunit proteins have been shown to enhance humoral and cell-mediated immunity and provide protection upon lethal challenge. In this work, a recombinant H5 hemagglutinin trimer (H53 was produced and encapsulated into polyanhydride nanoparticles. The studies performed indicated that the recombinant H53 antigen was a robust immunogen. Immunizing mice with H53 encapsulated into polyanhydride nanoparticles induced high neutralizing antibody titers and enhanced CD4+ T cell recall responses in mice. Finally, the H53-based polyanhydride nanovaccine induced protective immunity against a low-pathogenic H5N1 viral challenge. Informatics analyses indicated that mice receiving the nanovaccine formulations and subsequently challenged with virus were similar to naïve mice that were not challenged. The current studies provide a basis to further exploit the advantages of polyanhydride nanovaccines in pandemic scenarios. Keywords: polymer, nanoparticle, vaccine, subunit

  17. Impact of Mutations in the Hemagglutinin of H10N7 Viruses Isolated from Seals on Virus Replication in Avian and Human Cells

    Anne Dittrich

    2018-02-01

    Full Text Available Wild birds are the reservoir for low-pathogenic avian influenza viruses, which are frequently transmitted to domestic birds and occasionally to mammals. In 2014, an H10N7 virus caused severe mortality in harbor seals in northeastern Europe. Although the hemagglutinin (HA of this virus was closely related to H10 of avian H10N4 virus, it possessed unique nonsynonymous mutations, particularly in the HA1 subunit in or adjacent to the receptor binding domain and proteolytic cleavage site. Here, the impact of these mutations on virus replication was studied in vitro. Using reverse genetics, an avian H10N4 virus was cloned, and nine recombinant viruses carrying one of eight unique mutations or the complete HA from the seal virus were rescued. Receptor binding affinity, replication in avian and mammalian cell cultures, cell-to-cell spread, and HA cleavability of these recombinant viruses were studied. Results show that wild-type recombinant H10N4 virus has high affinity to avian-type sialic acid receptors and no affinity to mammalian-type receptors. The H10N7 virus exhibits dual receptor binding affinity. Interestingly, Q220L (H10 numbering in the rim of the receptor binding pocket increased the affinity of the H10N4 virus to mammal-type receptors and completely abolished the affinity to avian-type receptors. No remarkable differences in cell-to-cell spread or HA cleavability were observed. All viruses, including the wild-type H10N7 virus, replicated at higher levels in chicken cells than in human cells. These results indicate that H10N7 acquired adaptive mutations (e.g., Q220L to enhance replication in mammals and retained replication efficiency in the original avian host.

  18. Immunization with gingipain A hemagglutinin domain of Porphyromonas gingivalis induces IgM antibodies binding to malondialdehyde-acetaldehyde modified low-density lipoprotein.

    Mikael Kyrklund

    Full Text Available Treatment of periodontitis has beneficial effects on systemic inflammation markers that relate to progression of atherosclerosis. We aimed to investigate whether immunization with A hemagglutinin domain (Rgp44 of Porphyromonas gingivalis (Pg, a major etiologic agent of periodontitis, would lead to an antibody response cross-reacting with oxidized low-density lipoprotein (OxLDL and how it would affect the progression of atherosclerosis in low-density lipoprotein receptor-deficient (LDLR-/- mice. The data revealed a prominent IgM but not IgG response to malondialdehyde-acetaldehyde modified LDL (MAA-LDL after Rgp44 and Pg immunizations, implying that Rgp44/Pg and MAA adducts may share cross-reactive epitopes that prompt IgM antibody production and consequently confer atheroprotection. A significant negative association was observed between atherosclerotic lesion and plasma IgA to Rgp44 in Rgp44 immunized mice, supporting further the anti-atherogenic effect of Rgp44 immunization. Plasma IgA levels to Rgp44 and to Pg in both Rgp44- and Pg-immunized mice were significantly higher than those in saline control, suggesting that IgA to Rgp44 could be a surrogate marker of immunization in Pg-immunized mice. Distinct antibody responses in plasma IgA levels to MAA-LDL, to Pg lipopolysaccharides (Pg-LPS, and to phosphocholine (PCho were observed after Rgp44 and Pg immunizations, indicating that different immunogenic components between Rpg44 and Pg may behave differently in regard of their roles in the development of atherosclerosis. Immunization with Rgp44 also displayed atheroprotective features in modulation of plaque size through association with plasma levels of IL-1α whereas whole Pg bacteria achieved through regulation of anti-inflammatory cytokine levels of IL-5 and IL-10. The present study may contribute to refining therapeutic approaches aiming to modulate immune responses and inflammatory/anti-inflammatory processes in atherosclerosis.

  19. Attenuated Salmonella enterica serovar Typhi and Shigella flexneri 2a strains mucosally deliver DNA vaccines encoding measles virus hemagglutinin, inducing specific immune responses and protection in cotton rats.

    Pasetti, Marcela F; Barry, Eileen M; Losonsky, Genevieve; Singh, Mahender; Medina-Moreno, Sandra M; Polo, John M; Ulmer, Jeffrey; Robinson, Harriet; Sztein, Marcelo B; Levine, Myron M

    2003-05-01

    Measles remains a leading cause of child mortality in developing countries. Residual maternal measles antibodies and immunologic immaturity dampen immunogenicity of the current vaccine in young infants. Because cotton rat respiratory tract is susceptible to measles virus (MV) replication after intranasal (i.n.) challenge, this model can be used to assess the efficacy of MV vaccines. Pursuing a new measles vaccine strategy that might be effective in young infants, we used attenuated Salmonella enterica serovar Typhi CVD 908-htrA and Shigella flexneri 2a CVD 1208 vaccines to deliver mucosally to cotton rats eukaryotic expression plasmid pGA3-mH and Sindbis virus-based DNA replicon pMSIN-H encoding MV hemagglutinin (H). The initial i.n. dose-response with bacterial vectors alone identified a well-tolerated dosage (1 x 10(9) to 7 x 10(9) CFU) and a volume (20 micro l) that elicited strong antivector immune responses. Animals immunized i.n. on days 0, 28, and 76 with bacterial vectors carrying DNA plasmids encoding MV H or immunized parenterally with these naked DNA vaccine plasmids developed MV plaque reduction neutralizing antibodies and proliferative responses against MV antigens. In a subsequent experiment of identical design, cotton rats were challenged with wild-type MV 1 month after the third dose of vaccine or placebo. MV titers were significantly reduced in lung tissue of animals immunized with MV DNA vaccines delivered either via bacterial live vectors or parenterally. Since attenuated serovar Typhi and S. flexneri can deliver measles DNA vaccines mucosally in cotton rats, inducing measles immune responses (including neutralizing antibodies) and protection, boosting strategies can now be evaluated in animals primed with MV DNA vaccines.

  20. H3N2 influenza infection elicits more cross-reactive and less clonally expanded anti-hemagglutinin antibodies than influenza vaccination.

    M Anthony Moody

    Full Text Available BACKGROUND: During the recent H1N1 influenza pandemic, excess morbidity and mortality was seen in young but not older adults suggesting that prior infection with influenza strains may have protected older subjects. In contrast, a history of recent seasonal trivalent vaccine in younger adults was not associated with protection. METHODS AND FINDINGS: To study hemagglutinin (HA antibody responses in influenza immunization and infection, we have studied the day 7 plasma cell repertoires of subjects immunized with seasonal trivalent inactivated influenza vaccine (TIV and compared them to the plasma cell repertoires of subjects experimentally infected (EI with influenza H3N2 A/Wisconsin/67/2005. The majority of circulating plasma cells after TIV produced influenza-specific antibodies, while most plasma cells after EI produced antibodies that did not react with influenza HA. While anti-HA antibodies from TIV subjects were primarily reactive with single or few HA strains, anti-HA antibodies from EI subjects were isolated that reacted with multiple HA strains. Plasma cell-derived anti-HA antibodies from TIV subjects showed more evidence of clonal expansion compared with antibodies from EI subjects. From an H3N2-infected subject, we isolated a 4-member clonal lineage of broadly cross-reactive antibodies that bound to multiple HA subtypes and neutralized both H1N1 and H3N2 viruses. This broad reactivity was not detected in post-infection plasma suggesting this broadly reactive clonal lineage was not immunodominant in this subject. CONCLUSION: The presence of broadly reactive subdominant antibody responses in some EI subjects suggests that improved vaccine designs that make broadly reactive antibody responses immunodominant could protect against novel influenza strains.