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Sample records for affinity propagation clustering

  1. A Poisson-based adaptive affinity propagation clustering for SAGE data.

    PubMed

    Tang, DongMing; Zhu, QingXin; Yang, Fan

    2010-02-01

    Serial analysis of gene expression (SAGE) is a powerful tool to obtain gene expression profiles. Clustering analysis is a valuable technique for analyzing SAGE data. In this paper, we propose an adaptive clustering method for SAGE data analysis, namely, PoissonAPS. The method incorporates a novel clustering algorithm, Affinity Propagation (AP). While AP algorithm has demonstrated good performance on many different data sets, it also faces several limitations. PoissonAPS overcomes the limitations of AP using the clustering validation measure as a cost function of merging and splitting, and as a result, it can automatically cluster SAGE data without user-specified parameters. We evaluated PoissonAPS and compared its performance with other methods on several real life SAGE datasets. The experimental results show that PoissonAPS can produce meaningful and interpretable clusters for SAGE data.

  2. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

    PubMed Central

    Heidelberg, John F.; Tully, Benjamin J.

    2017-01-01

    Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes. PMID:28289564

  3. Classification of neocortical interneurons using affinity propagation.

    PubMed

    Santana, Roberto; McGarry, Laura M; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.

  4. Classification of neocortical interneurons using affinity propagation

    PubMed Central

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, we explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  5. Combining self-organizing mapping and supervised affinity propagation clustering approach to investigate functional brain networks involved in motor imagery and execution with fMRI measurements.

    PubMed

    Zhang, Jiang; Liu, Qi; Chen, Huafu; Yuan, Zhen; Huang, Jin; Deng, Lihua; Lu, Fengmei; Zhang, Junpeng; Wang, Yuqing; Wang, Mingwen; Chen, Liangyin

    2015-01-01

    Clustering analysis methods have been widely applied to identifying the functional brain networks of a multitask paradigm. However, the previously used clustering analysis techniques are computationally expensive and thus impractical for clinical applications. In this study a novel method, called SOM-SAPC that combines self-organizing mapping (SOM) and supervised affinity propagation clustering (SAPC), is proposed and implemented to identify the motor execution (ME) and motor imagery (MI) networks. In SOM-SAPC, SOM was first performed to process fMRI data and SAPC is further utilized for clustering the patterns of functional networks. As a result, SOM-SAPC is able to significantly reduce the computational cost for brain network analysis. Simulation and clinical tests involving ME and MI were conducted based on SOM-SAPC, and the analysis results indicated that functional brain networks were clearly identified with different response patterns and reduced computational cost. In particular, three activation clusters were clearly revealed, which include parts of the visual, ME and MI functional networks. These findings validated that SOM-SAPC is an effective and robust method to analyze the fMRI data with multitasks.

  6. Learning factorizations in estimation of distribution algorithms using affinity propagation.

    PubMed

    Santana, Roberto; Larrañaga, Pedro; Lozano, José A

    2010-01-01

    Estimation of distribution algorithms (EDAs) that use marginal product model factorizations have been widely applied to a broad range of mainly binary optimization problems. In this paper, we introduce the affinity propagation EDA (AffEDA) which learns a marginal product model by clustering a matrix of mutual information learned from the data using a very efficient message-passing algorithm known as affinity propagation. The introduced algorithm is tested on a set of binary and nonbinary decomposable functions and using a hard combinatorial class of problem known as the HP protein model. The results show that the algorithm is a very efficient alternative to other EDAs that use marginal product model factorizations such as the extended compact genetic algorithm (ECGA) and improves the quality of the results achieved by ECGA when the cardinality of the variables is increased.

  7. An Affinity Propagation-Based DNA Motif Discovery Algorithm.

    PubMed

    Sun, Chunxiao; Huo, Hongwei; Yu, Qiang; Guo, Haitao; Sun, Zhigang

    2015-01-01

    The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  8. A multiobjective evolutionary algorithm to find community structures based on affinity propagation

    NASA Astrophysics Data System (ADS)

    Shang, Ronghua; Luo, Shuang; Zhang, Weitong; Stolkin, Rustam; Jiao, Licheng

    2016-07-01

    Community detection plays an important role in reflecting and understanding the topological structure of complex networks, and can be used to help mine the potential information in networks. This paper presents a Multiobjective Evolutionary Algorithm based on Affinity Propagation (APMOEA) which improves the accuracy of community detection. Firstly, APMOEA takes the method of affinity propagation (AP) to initially divide the network. To accelerate its convergence, the multiobjective evolutionary algorithm selects nondominated solutions from the preliminary partitioning results as its initial population. Secondly, the multiobjective evolutionary algorithm finds solutions approximating the true Pareto optimal front through constantly selecting nondominated solutions from the population after crossover and mutation in iterations, which overcomes the tendency of data clustering methods to fall into local optima. Finally, APMOEA uses an elitist strategy, called "external archive", to prevent degeneration during the process of searching using the multiobjective evolutionary algorithm. According to this strategy, the preliminary partitioning results obtained by AP will be archived and participate in the final selection of Pareto-optimal solutions. Experiments on benchmark test data, including both computer-generated networks and eight real-world networks, show that the proposed algorithm achieves more accurate results and has faster convergence speed compared with seven other state-of-art algorithms.

  9. Robust Spectral Clustering Using Statistical Sub-Graph Affinity Model

    PubMed Central

    Eichel, Justin A.; Wong, Alexander; Fieguth, Paul; Clausi, David A.

    2013-01-01

    Spectral clustering methods have been shown to be effective for image segmentation. Unfortunately, the presence of image noise as well as textural characteristics can have a significant negative effect on the segmentation performance. To accommodate for image noise and textural characteristics, this study introduces the concept of sub-graph affinity, where each node in the primary graph is modeled as a sub-graph characterizing the neighborhood surrounding the node. The statistical sub-graph affinity matrix is then constructed based on the statistical relationships between sub-graphs of connected nodes in the primary graph, thus counteracting the uncertainty associated with the image noise and textural characteristics by utilizing more information than traditional spectral clustering methods. Experiments using both synthetic and natural images under various levels of noise contamination demonstrate that the proposed approach can achieve improved segmentation performance when compared to existing spectral clustering methods. PMID:24386111

  10. A Mixed Approach to Similarity Metric Selection in Affinity Propagation-Based WiFi Fingerprinting Indoor Positioning.

    PubMed

    Caso, Giuseppe; de Nardis, Luca; di Benedetto, Maria-Gabriella

    2015-10-30

    The weighted k-nearest neighbors (WkNN) algorithm is by far the most popular choice in the design of fingerprinting indoor positioning systems based on WiFi received signal strength (RSS). WkNN estimates the position of a target device by selecting k reference points (RPs) based on the similarity of their fingerprints with the measured RSS values. The position of the target device is then obtained as a weighted sum of the positions of the k RPs. Two-step WkNN positioning algorithms were recently proposed, in which RPs are divided into clusters using the affinity propagation clustering algorithm, and one representative for each cluster is selected. Only cluster representatives are then considered during the position estimation, leading to a significant computational complexity reduction compared to traditional, flat WkNN. Flat and two-step WkNN share the issue of properly selecting the similarity metric so as to guarantee good positioning accuracy: in two-step WkNN, in particular, the metric impacts three different steps in the position estimation, that is cluster formation, cluster selection and RP selection and weighting. So far, however, the only similarity metric considered in the literature was the one proposed in the original formulation of the affinity propagation algorithm. This paper fills this gap by comparing different metrics and, based on this comparison, proposes a novel mixed approach in which different metrics are adopted in the different steps of the position estimation procedure. The analysis is supported by an extensive experimental campaign carried out in a multi-floor 3D indoor positioning testbed. The impact of similarity metrics and their combinations on the structure and size of the resulting clusters, 3D positioning accuracy and computational complexity are investigated. Results show that the adoption of metrics different from the one proposed in the original affinity propagation algorithm and, in particular, the combination of different

  11. Theoretical calculation of positron affinities of solute clusters in aluminum alloys

    NASA Astrophysics Data System (ADS)

    Mizuno, Masataka; Araki, Hideki; Shirai, Yasuharu

    2016-01-01

    We have performed theoretical calculations of positron states for solute clusters in aluminum alloys to estimate the positron affinity of solute clusters. Positron states of solute clusters in aluminum alloys were calculated under the electronic structures obtained by first- principles molecular orbital calculations using Al158-X13 clusters. We defined the positron affinity of the solute clusters by the difference in the lowest potential sensed by positrons between the solute clusters and Al bulk. With increasing atomic number of 3d metals, the annihilation fraction of the solute clusters rapidly increases at Mn and shows a maximum at Ni. A similar trend is observed for 4d metals. The localization of positron at the solute clusters mainly arises from charge transfer from Al matrix to solute clusters. The positron affinity defined in this work well represents the localization of positron at the solute clusters in aluminum alloys.

  12. Avalanches and clusters in planar crack front propagation.

    PubMed

    Laurson, Lasse; Santucci, Stephane; Zapperi, Stefano

    2010-04-01

    We study avalanches in a model for a planar crack propagating in a disordered medium. Due to long-range interactions, avalanches are formed by a set of spatially disconnected local clusters, the sizes of which are distributed according to a power law with an exponent tau{a}=1.5. We derive a scaling relation tau{a}=2tau-1 between the local cluster exponent tau{a} and the global avalanche exponent tau . For length scales longer than a crossover length proportional to the Larkin length, the aspect ratio of the local clusters scales with the roughness exponent of the line model. Our analysis provides an explanation for experimental results on planar crack avalanches in Plexiglas plates, but the results are applicable also to other systems with long-range interactions.

  13. Reliability Evaluation for Clustered WSNs under Malware Propagation.

    PubMed

    Shen, Shigen; Huang, Longjun; Liu, Jianhua; Champion, Adam C; Yu, Shui; Cao, Qiying

    2016-06-10

    We consider a clustered wireless sensor network (WSN) under epidemic-malware propagation conditions and solve the problem of how to evaluate its reliability so as to ensure efficient, continuous, and dependable transmission of sensed data from sensor nodes to the sink. Facing the contradiction between malware intention and continuous-time Markov chain (CTMC) randomness, we introduce a strategic game that can predict malware infection in order to model a successful infection as a CTMC state transition. Next, we devise a novel measure to compute the Mean Time to Failure (MTTF) of a sensor node, which represents the reliability of a sensor node continuously performing tasks such as sensing, transmitting, and fusing data. Since clustered WSNs can be regarded as parallel-serial-parallel systems, the reliability of a clustered WSN can be evaluated via classical reliability theory. Numerical results show the influence of parameters such as the true positive rate and the false positive rate on a sensor node's MTTF. Furthermore, we validate the method of reliability evaluation for a clustered WSN according to the number of sensor nodes in a cluster, the number of clusters in a route, and the number of routes in the WSN.

  14. Reliability Evaluation for Clustered WSNs under Malware Propagation

    PubMed Central

    Shen, Shigen; Huang, Longjun; Liu, Jianhua; Champion, Adam C.; Yu, Shui; Cao, Qiying

    2016-01-01

    We consider a clustered wireless sensor network (WSN) under epidemic-malware propagation conditions and solve the problem of how to evaluate its reliability so as to ensure efficient, continuous, and dependable transmission of sensed data from sensor nodes to the sink. Facing the contradiction between malware intention and continuous-time Markov chain (CTMC) randomness, we introduce a strategic game that can predict malware infection in order to model a successful infection as a CTMC state transition. Next, we devise a novel measure to compute the Mean Time to Failure (MTTF) of a sensor node, which represents the reliability of a sensor node continuously performing tasks such as sensing, transmitting, and fusing data. Since clustered WSNs can be regarded as parallel-serial-parallel systems, the reliability of a clustered WSN can be evaluated via classical reliability theory. Numerical results show the influence of parameters such as the true positive rate and the false positive rate on a sensor node’s MTTF. Furthermore, we validate the method of reliability evaluation for a clustered WSN according to the number of sensor nodes in a cluster, the number of clusters in a route, and the number of routes in the WSN. PMID:27294934

  15. Structural origin for electron affinity of phenanthrene and ion cores of phenanthrene anion clusters

    NASA Astrophysics Data System (ADS)

    Lee, Sang Hak; Song, Jae Kyu; Kim, Seong Keun

    2015-04-01

    We studied anion clusters of phenanthrene using photoelectron spectra and theoretical calculations. The electron affinity of phenanthrene, which lies between those of naphthalene and anthracene, was explained by the orbital interaction model that reflected the structural differences among these molecules. The spectral feature of the photoelectron spectra indicated strong electron-vibration coupling along two symmetric vibrational modes. Since the spectral features of each ion core structure were uniquely characteristic, we could identify that the pentamer anion had coexisting monomeric and trimeric cores on the basis of the shape of the photoelectron spectra and the size-dependent evolution of the electron affinity.

  16. Identification of piecewise affine systems based on fuzzy PCA-guided robust clustering technique

    NASA Astrophysics Data System (ADS)

    Khanmirza, Esmaeel; Nazarahari, Milad; Mousavi, Alireza

    2016-12-01

    Hybrid systems are a class of dynamical systems whose behaviors are based on the interaction between discrete and continuous dynamical behaviors. Since a general method for the analysis of hybrid systems is not available, some researchers have focused on specific types of hybrid systems. Piecewise affine (PWA) systems are one of the subsets of hybrid systems. The identification of PWA systems includes the estimation of the parameters of affine subsystems and the coefficients of the hyperplanes defining the partition of the state-input domain. In this paper, we have proposed a PWA identification approach based on a modified clustering technique. By using a fuzzy PCA-guided robust k-means clustering algorithm along with neighborhood outlier detection, the two main drawbacks of the well-known clustering algorithms, i.e., the poor initialization and the presence of outliers, are eliminated. Furthermore, this modified clustering technique enables us to determine the number of subsystems without any prior knowledge about system. In addition, applying the structure of the state-input domain, that is, considering the time sequence of input-output pairs, provides a more efficient clustering algorithm, which is the other novelty of this work. Finally, the proposed algorithm has been evaluated by parameter identification of an IGV servo actuator. Simulation together with experiment analysis has proved the effectiveness of the proposed method.

  17. Photoelectron spectra of small LaOn- clusters: decreasing electron affinity upon increasing the number of oxygen atoms

    NASA Astrophysics Data System (ADS)

    Klingeler, R.; Lüttgens, G.; Pontius, N.; Rochow, R.; Bechthold, P. S.; Neeb, M.; Eberhardt, W.

    We present mass selected photoelectron spectra of small lanthanum oxide cluster anions LaOn- (n=1-5) which have been generated in a laser vaporization cluster source. The electron affinity of the lanthanum oxide clusters drops continuously with the number of chemisorbed oxygen atoms as revealed from the anion photoelectron spectra. The decreasing electron affinity behaves contrary to several other metal oxide clusters. The geometry of some of the measured clusters are discussed in comparsion with configuration interaction and density functional calculations using a Gaussian94 program package.

  18. Fatigue damage prognosis of internal delamination in composite plates under cyclic compression loadings using affine arithmetic as uncertainty propagation tool

    NASA Astrophysics Data System (ADS)

    Gbaguidi, Audrey J.-M.

    compressive-buckling loadings is experimentally studied, and the delamination lengths obtained are compared with the predicted values to check the performance of Affine Arithmetic as an uncertainty propagation tool.

  19. Observations of clustering inside oceanic bubble clouds and the effect on short-range acoustic propagation.

    PubMed

    Weber, Thomas C

    2008-11-01

    It has recently been shown [Weber, T. C. et al. (2007). "Acoustic propagation through clustered bubble clouds," IEEE J. Ocean. Eng. 32, 513-523] that gas bubble clustering plays a role in determining the acoustic field characteristics of bubbly fluids. In particular, it has been shown that clustering changes the bubble-induced attenuation as well as the ping-to-ping variability in the acoustic field. The degree to which bubble clustering exists in nature, however, is unknown. This paper describes a method for quantifying bubble clustering using a high frequency (400 kHz) multibeam sonar, and reports on observations of near-surface bubble clustering during a storm (14.6 m/s wind speed) in the Gulf of Maine. The multibeam sonar data are analyzed to estimate the pair correlation function, a measure of bubble clustering. In order to account for clustering in the mean acoustic field, a modification to the effective medium wave number is made. With this modification, the multibeam sonar observations are used to predict the effect of clustering on the attenuation of the mean field for short-range propagation (1 m) at frequencies between 10 and 350 kHz. Results for this specific case show that clustering can cause the attenuation to change by 20%-80% over this frequency range.

  20. Coupled Cluster Studies of Ionization Potentials and Electron Affinities of Single-Walled Carbon Nanotubes.

    PubMed

    Peng, Bo; Govind, Niranjan; Aprà, Edoardo; Klemm, Michael; Hammond, Jeff R; Kowalski, Karol

    2017-02-16

    In this paper, we apply equation-of-motion coupled cluster (EOM-CC) methods in the studies of the vertical ionization potentials (IPs) and electron affinities (EAs) for a series of single-walled carbon nanotubes (SWCNT). The EOM-CC formulations for IPs and EAs employing excitation manifolds spanned by single and double excitations (IP/EA-EOM-CCSD) are used to study the IPs and EAs of the SWCNTs as a function of the nanotube length. Several armchair nanotubes corresponding to C20nH20 models with n = 2-6 have been used in benchmark calculations. In agreement with previous studies, we demonstrate that the electronegativity of C20nH20 systems remains, to a large extent, independent of the nanotube length. We also compare IP/EA-EOM-CCSD results with those obtained with coupled cluster models with single and double excitations corrected by perturbative triples, CCSD(T), and density functional theory (DFT) using global and range-separated hybrid exchange-correlation functionals.

  1. An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility

    NASA Astrophysics Data System (ADS)

    Jamali, Yousef; Jamali, Tahereh; Mofrad, Mohammad R. K.

    2013-07-01

    Integrins are cell-surface protein heterodimers that coordinate cellular responses to mechanochemical cues from the extracellular matrix (ECM) and stimulate the assembly of small adhesion complexes, which are the initial sites of cell-ECM adhesion. Clustering of integrins is known to mediate signaling through a variety of signal transduction pathways. Yet, the molecular mechanisms of integrin clustering are poorly understood. In this paper, we develop computational models, using agent based modeling (ABM) techniques, to explore two key underlying mechanisms of integrin clustering, namely ligand organization and integrin homo-oligomerization. Our models help to shed light on the potential roles ligand clustering and integrin homo-oligomerization may play in controlling integrin clustering. A potential mechanism for the clustering of integrin is discussed and the effects of other parameters such as integrin-ligand affinity, membrane crowdedness and ligand mobility on integrin clustering are examined.

  2. A Novel User Classification Method for Femtocell Network by Using Affinity Propagation Algorithm and Artificial Neural Network

    PubMed Central

    Ahmed, Afaz Uddin; Tariqul Islam, Mohammad; Ismail, Mahamod; Kibria, Salehin; Arshad, Haslina

    2014-01-01

    An artificial neural network (ANN) and affinity propagation (AP) algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation. PMID:25133214

  3. A novel user classification method for femtocell network by using affinity propagation algorithm and artificial neural network.

    PubMed

    Ahmed, Afaz Uddin; Islam, Mohammad Tariqul; Ismail, Mahamod; Kibria, Salehin; Arshad, Haslina

    2014-01-01

    An artificial neural network (ANN) and affinity propagation (AP) algorithm based user categorization technique is presented. The proposed algorithm is designed for closed access femtocell network. ANN is used for user classification process and AP algorithm is used to optimize the ANN training process. AP selects the best possible training samples for faster ANN training cycle. The users are distinguished by using the difference of received signal strength in a multielement femtocell device. A previously developed directive microstrip antenna is used to configure the femtocell device. Simulation results show that, for a particular house pattern, the categorization technique without AP algorithm takes 5 indoor users and 10 outdoor users to attain an error-free operation. While integrating AP algorithm with ANN, the system takes 60% less training samples reducing the training time up to 50%. This procedure makes the femtocell more effective for closed access operation.

  4. Label propagation algorithm based on edge clustering coefficient for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Zhang, Xian-Kun; Tian, Xue; Li, Ya-Nan; Song, Chen

    2014-08-01

    The label propagation algorithm (LPA) is a graph-based semi-supervised learning algorithm, which can predict the information of unlabeled nodes by a few of labeled nodes. It is a community detection method in the field of complex networks. This algorithm is easy to implement with low complexity and the effect is remarkable. It is widely applied in various fields. However, the randomness of the label propagation leads to the poor robustness of the algorithm, and the classification result is unstable. This paper proposes a LPA based on edge clustering coefficient. The node in the network selects a neighbor node whose edge clustering coefficient is the highest to update the label of node rather than a random neighbor node, so that we can effectively restrain the random spread of the label. The experimental results show that the LPA based on edge clustering coefficient has made improvement in the stability and accuracy of the algorithm.

  5. Active learning for semi-supervised clustering based on locally linear propagation reconstruction.

    PubMed

    Chang, Chin-Chun; Lin, Po-Yi

    2015-03-01

    The success of semi-supervised clustering relies on the effectiveness of side information. To get effective side information, a new active learner learning pairwise constraints known as must-link and cannot-link constraints is proposed in this paper. Three novel techniques are developed for learning effective pairwise constraints. The first technique is used to identify samples less important to cluster structures. This technique makes use of a kernel version of locally linear embedding for manifold learning. Samples neither important to locally linear propagation reconstructions of other samples nor on flat patches in the learned manifold are regarded as unimportant samples. The second is a novel criterion for query selection. This criterion considers not only the importance of a sample to expanding the space coverage of the learned samples but also the expected number of queries needed to learn the sample. To facilitate semi-supervised clustering, the third technique yields inferred must-links for passing information about flat patches in the learned manifold to semi-supervised clustering algorithms. Experimental results have shown that the learned pairwise constraints can capture the underlying cluster structures and proven the feasibility of the proposed approach.

  6. A Novel Clustering Methodology Based on Modularity Optimisation for Detecting Authorship Affinities in Shakespearean Era Plays

    PubMed Central

    Craig, Hugh; Berretta, Regina; Moscato, Pablo

    2016-01-01

    In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays. PMID:27571416

  7. A Novel Clustering Methodology Based on Modularity Optimisation for Detecting Authorship Affinities in Shakespearean Era Plays.

    PubMed

    Naeni, Leila M; Craig, Hugh; Berretta, Regina; Moscato, Pablo

    2016-01-01

    In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays.

  8. Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo

    2013-08-01

    Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nɛ positions of the imidazole group to estimate the pKas. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.

  9. Application of a convergent, composite coupled cluster approach to bound state, adiabatic electron affinities in atoms and small molecules.

    PubMed

    Feller, David

    2016-01-07

    Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F(-) value obtained with standard

  10. Application of a convergent, composite coupled cluster approach to bound state, adiabatic electron affinities in atoms and small molecules

    NASA Astrophysics Data System (ADS)

    Feller, David

    2016-01-01

    Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F- value obtained with standard

  11. An Information Theoretic Clustering Approach for Unveiling Authorship Affinities in Shakespearean Era Plays and Poems

    PubMed Central

    Arefin, Ahmed Shamsul; Vimieiro, Renato; Riveros, Carlos; Craig, Hugh; Moscato, Pablo

    2014-01-01

    In this paper we analyse the word frequency profiles of a set of works from the Shakespearean era to uncover patterns of relationship between them, highlighting the connections within authorial canons. We used a text corpus comprising 256 plays and poems from the 16th and 17th centuries, with 17 works of uncertain authorship. Our clustering approach is based on the Jensen-Shannon divergence and a graph partitioning algorithm, and our results show that authors' characteristic styles are very powerful factors in explaining the variation of word use, frequently transcending cross-cutting factors like the differences between tragedy and comedy, early and late works, and plays and poems. Our method also provides an empirical guide to the authorship of plays and poems where this is unknown or disputed. PMID:25347727

  12. Relativistic Coupled Cluster Calculations with Variational Quantum Electrodynamics Resolve the Discrepancy between Experiment and Theory Concerning the Electron Affinity and Ionization Potential of Gold

    NASA Astrophysics Data System (ADS)

    Pašteka, L. F.; Eliav, E.; Borschevsky, A.; Kaldor, U.; Schwerdtfeger, P.

    2017-01-01

    The first ionization potential (IP) and electron affinity (EA) of the gold atom have been determined to an unprecedented accuracy using relativistic coupled cluster calculations up to the pentuple excitation level including the Breit and QED contributions. We reach meV accuracy (with respect to the experimental values) by carefully accounting for all individual contributions beyond the standard relativistic coupled cluster approach. Thus, we are able to resolve the long-standing discrepancy between experimental and theoretical IP and EA of gold.

  13. Relativistic Coupled Cluster Calculations with Variational Quantum Electrodynamics Resolve the Discrepancy between Experiment and Theory Concerning the Electron Affinity and Ionization Potential of Gold.

    PubMed

    Pašteka, L F; Eliav, E; Borschevsky, A; Kaldor, U; Schwerdtfeger, P

    2017-01-13

    The first ionization potential (IP) and electron affinity (EA) of the gold atom have been determined to an unprecedented accuracy using relativistic coupled cluster calculations up to the pentuple excitation level including the Breit and QED contributions. We reach meV accuracy (with respect to the experimental values) by carefully accounting for all individual contributions beyond the standard relativistic coupled cluster approach. Thus, we are able to resolve the long-standing discrepancy between experimental and theoretical IP and EA of gold.

  14. Radio jet propagation and wide-angle tailed radio sources in merging galaxy cluster environments

    NASA Technical Reports Server (NTRS)

    Loken, Chris; Roettiger, Kurt; Burns, Jack O.; Norman, Michael

    1995-01-01

    The intracluster medium (ICM) within merging clusters of galaxies is likely to be in a violent or turbulent dynamical state which may have a significant effect on the evolution of cluster radio sources. We present results from a recent gas + N-body simulation of a cluster merger, suggesting that mergers can result in long-lived, supersonic bulk flows, as well as shocks, within a few hundred kiloparsecs of the core of the dominant cluster. These results have motivated our new two-dimensional and three-dimensional simulations of jet propagation in such environments. The first set of simulations models the ISM/ICM transition as a contact discontinuity with a strong velocity shear. A supersonic (M(sub j) = 6) jet crossing this discontinuity into an ICM with a transverse, supersonic wind bends continuously, becomes 'naked' on the upwind side, and forms a distended cocoon on the downwind side. In the case of a mildly supersonic jet (M(sub j) = 3), however, a shock is driven into the ISM and ISM material is pulled along with the jet into the ICM. Instabilities excited at the ISM/ICM interface result in the jet repeatedly pinching off and reestablishing itself in a series of 'disconnection events.' The second set of simulations deals with a jet encountering a shock in the merging cluster environment. A series of relatively high-resolution two-dimensional calculations is used to confirm earlier analysis predicting that the jet will not disrupt when the jet Mach number is greater than the shock Mach number. A jet which survives the encounter with the shock will decrease in radius and disrupt shortly thereafter as a result of the growth of Kelvin-Helmholtz instabilities. We also find, in disagreement with predictions, that the jet flaring angle decreases with increasing jet density. Finally, a three-dimensional simulation of a jet crossing an oblique shock gives rise to a morphology which resembles a wide-angle tailed radio source with the jet flaring at the shock and

  15. First-principles simulation of light propagation and exciton dynamics in metal cluster nanostructures

    NASA Astrophysics Data System (ADS)

    Lisinetskaya, Polina G.; Röhr, Merle I. S.; Mitrić, Roland

    2016-06-01

    We present a theoretical approach for the simulation of the electric field and exciton propagation in ordered arrays constructed of molecular-sized noble metal clusters bound to organic polymer templates. In order to describe the electronic coupling between individual constituents of the nanostructure we use the ab initio parameterized transition charge method which is more accurate than the usual dipole-dipole coupling. The electronic population dynamics in the nanostructure under an external laser pulse excitation is simulated by numerical integration of the time-dependent Schrödinger equation employing the fully coupled Hamiltonian. The solution of the TDSE gives rise to time-dependent partial point charges for each subunit of the nanostructure, and the spatio-temporal electric field distribution is evaluated by means of classical electrodynamics methods. The time-dependent partial charges are determined based on the stationary partial and transition charges obtained in the framework of the TDDFT. In order to treat large plasmonic nanostructures constructed of many constituents, the approximate self-consistent iterative approach presented in (Lisinetskaya and Mitrić in Phys Rev B 89:035433, 2014) is modified to include the transition-charge-based interaction. The developed methods are used to study the optical response and exciton dynamics of Ag3+ and porphyrin-Ag4 dimers. Subsequently, the spatio-temporal electric field distribution in a ring constructed of ten porphyrin-Ag4 subunits under the action of circularly polarized laser pulse is simulated. The presented methodology provides a theoretical basis for the investigation of coupled light-exciton propagation in nanoarchitectures built from molecular size metal nanoclusters in which quantum confinement effects are important.

  16. Azapeptide analogues of the growth hormone releasing peptide 6 as cluster of differentiation 36 receptor ligands with reduced affinity for the growth hormone secretagogue receptor 1a.

    PubMed

    Proulx, Caroline; Picard, Émilie; Boeglin, Damien; Pohankova, Petra; Chemtob, Sylvain; Ong, Huy; Lubell, William D

    2012-07-26

    The synthetic hexapeptide growth hormone releasing peptide-6 (GHRP-6) exhibits dual affinity for the growth hormone secretagogue receptor 1a (GHS-R1a) and the cluster of differentiation 36 (CD36) receptor. Azapeptide GHRP-6 analogues have been synthesized, exhibiting micromolar affinity to the CD36 receptor with reduced affinity toward the GHS-R1a. A combinatorial split-and-mix approach furnished aza-GHRP-6 leads, which were further examined by alanine scanning. Incorporation of an aza-amino acid residue respectively at the D-Trp(2), Ala(3), or Trp(4) position gave aza-GHRP-6 analogues with reduced affinity toward the GHS-R1a by at least a factor of 100 and in certain cases retained affinity for the CD36 receptor. In the latter cases, the D-Trp(2) residue proved important for CD36 receptor affinity; however, His(1) could be replaced by Ala(1) without considerable loss of binding. In a microvascular sprouting assay using a choroid explant, [azaTyr(4)]-GHRP-6 (15), [Ala(1), azaPhe(2)]-GHRP-6 (16), and [azaLeu(3), Ala(6)]-GHRP-6 (33) all exhibited antiangiogenic activity.

  17. Photo-z with CuBANz: An improved photometric redshift estimator using Clustering aided Back propagation Neural network

    NASA Astrophysics Data System (ADS)

    Samui, Saumyadip; Samui Pal, Shanoli

    2017-02-01

    We present an improved photometric redshift estimator code, CuBANz, that is publicly available at https://goo.gl/fpk90V. It uses the back propagation neural network along with clustering of the training set, which makes it more efficient than existing neural network codes. In CuBANz, the training set is divided into several self learning clusters with galaxies having similar photometric properties and spectroscopic redshifts within a given span. The clustering algorithm uses the color information (i.e. u - g , g - r etc.) rather than the apparent magnitudes at various photometric bands as the photometric redshift is more sensitive to the flux differences between different bands rather than the actual values. Separate neural networks are trained for each cluster using all possible colors, magnitudes and uncertainties in the measurements. For a galaxy with unknown redshift, we identify the closest possible clusters having similar photometric properties and use those clusters to get the photometric redshifts using the particular networks that were trained using those cluster members. For galaxies that do not match with any training cluster, the photometric redshifts are obtained from a separate network that uses entire training set. This clustering method enables us to determine the redshifts more accurately. SDSS Stripe 82 catalog has been used here for the demonstration of the code. For the clustered sources with redshift range zspec < 0.7, the residual error (<(zspec -zphot) 2 > 1 / 2) in the training/testing phase is as low as 0.03 compared to the existing ANNz code that provides residual error on the same test data set of 0.05. Further, we provide a much better estimate of the uncertainty of the derived photometric redshift.

  18. Proper orthogonal decomposition and cluster weighted modeling for sensitivity analysis of sound propagation in the atmospheric surface layer.

    PubMed

    Pettit, Chris L; Wilson, D Keith

    2007-09-01

    Outdoor sound propagation predictions are compromised by uncertainty and error in the atmosphere and terrain representations, and sometimes also by simplified or incorrect physics. A model's predictive power, i.e., its accurate representation of the sound propagation, cannot be assessed without first quantifying the ensemble sound pressure variability and sensitivity to uncertainties in the model's governing parameters. This paper describes fundamental steps toward this goal for a single-frequency point source. The atmospheric surface layer is represented through Monin-Obukhov similarity theory and the acoustic ground properties with a relaxation model. Sound propagation is predicted with the parabolic equation method. Governing parameters are modeled as independent random variables across physically reasonable ranges. Latin hypercube sampling and proper orthogonal decomposition (POD) are employed in conjunction with cluster-weighted models to develop compact representations of the sound pressure random field. Full-field sensitivity of the sound pressure field is computed via the sensitivities of the POD mode coefficients to the system parameters. Ensemble statistics of the full-field sensitivities are computed to illustrate their relative importance at every down range location. The central role of sensitivity analysis in uncertainty quantification of outdoor sound propagation is discussed and pitfalls of sampling-based sensitivity analysis for outdoor sound propagation are described.

  19. The Hueckel Model for Small Metal Clusters. 3. Anion Structures and HMO (Hueckel Molecular Orbital) Electron Affinities.

    DTIC Science & Technology

    1987-04-01

    Electron Affinities by S N Lindsay, Lin Chu, Youqi Wang and Thomas F. George Prepared fur Publication 1in Journal of Chemical Physics 5epartments of...Affinities. 12. PERSONAL AUTIHORiS) D. M. LIndsay, L. Chu, Y. Wang and Thomas F. George 13. TYPE OF REPORT 13b. TIME COVERED vid. OATE OF REPORT fVro .1o...New York, New York 10031 Youqi Wang Department of Chemistry California Institute of Technology Pasadena, Califonia 91125 Thomas IF. Georg Departments

  20. Performance of Analytic Orbit Propagators on a Hypercube and a Workstation Cluster

    DTIC Science & Technology

    1994-01-01

    the maximum e ciency is and is achieved when us ing processors For PSGP the maximum e ciency is over using processors For PSGP and...Computing sub mitted Serial Parallel maxn E maxn E time msec Code Code to propagate an object SGP PSGP SGP PSGP ...Data Figure Estimated Speedup and E ciency of P T for Various Hypercube Sizes Figure Estimated Speedup and E ciency of PSGP for Various Hypercube

  1. The location, clustering, and propagation of massive star formation in giant molecular clouds

    NASA Astrophysics Data System (ADS)

    Ochsendorf, Bram; Meixner, Margaret; Chastenet, Jeremy; Tielens, A. G. G. M.; Roman-Duval, Julia

    2017-01-01

    Massive stars are key players in the evolution of galaxies, yet their formation pathway remains unclear. In this talk, I will highlight results from a project utilizing data from several galaxy-wide surveys to build an unbiased dataset of ~700 massive young stellar objects (MYSOs), ~200 giant molecular clouds (GMCs), and ~100 young (< 10 Myr) optical stellar clusters (SCs) in the Large Magellanic Cloud. We have employed this data to quantitatively study the location and clustering of massive star formation and its relation to the internal structure of GMCs. The main results are as follows: (1) Massive stars do not typically form at the highest column densities nor centers of their parent GMCs. (2) Massive star formation clusters over multiple generations and on size scales much smaller than the size of the parent GMC. (3) The rate of massive star formation is significantly boosted in clouds near SCs. Yet, comparison of molecular clouds associated with SCs with those that are not reveals no significant difference in their global properties. These results reveal a connection between different generations of massive stars on timescales up to 10 Myr. I will compare our findings with Galactic studies and discuss this in terms of GMC collapse, triggered star formation, and a potential dichotomy between low- and high-mass star formation.

  2. The Location, Clustering, and Propagation of Massive Star Formation in Giant Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Ochsendorf, Bram B.; Meixner, Margaret; Chastenet, Jérémy; Tielens, Alexander G. G. M.; Roman-Duval, Julia

    2016-11-01

    Massive stars are key players in the evolution of galaxies, yet their formation pathway remains unclear. In this work, we use data from several galaxy-wide surveys to build an unbiased data set of ∼600 massive young stellar objects, ∼200 giant molecular clouds (GMCs), and ∼100 young (<10 Myr) optical stellar clusters (SCs) in the Large Magellanic Cloud. We employ this data to quantitatively study the location and clustering of massive star formation and its relation to the internal structure of GMCs. We reveal that massive stars do not typically form at the highest column densities nor centers of their parent GMCs at the ∼6 pc resolution of our observations. Massive star formation clusters over multiple generations and on size scales much smaller than the size of the parent GMC. We find that massive star formation is significantly boosted in clouds near SCs. However, whether a cloud is associated with an SC does not depend on either the cloud’s mass or global surface density. These results reveal a connection between different generations of massive stars on timescales up to 10 Myr. We compare our work with Galactic studies and discuss our findings in terms of GMC collapse, triggered star formation, and a potential dichotomy between low- and high-mass star formation.

  3. The roles of the hybrid cluster protein, Hcp and its reductase, Hcr, in high affinity nitric oxide reduction that protects anaerobic cultures of Escherichia coli against nitrosative stress.

    PubMed

    Wang, Jing; Vine, Claire E; Balasiny, Basema K; Rizk, John; Bradley, Charlene L; Tinajero-Trejo, Mariana; Poole, Robert K; Bergaust, Linda L; Bakken, Lars R; Cole, Jeffrey A

    2016-06-01

    The hybrid cluster protein, Hcp, contains a 4Fe-2S-2O iron-sulfur-oxygen cluster that is currently considered to be unique in biology. It protects various bacteria from nitrosative stress, but the mechanism is unknown. We demonstrate that the Escherichia coli Hcp is a high affinity nitric oxide (NO) reductase that is the major enzyme for reducing NO stoichiometrically to N2 O under physiologically relevant conditions. Deletion of hcp results in extreme sensitivity to NO during anaerobic growth and inactivation of the iron-sulfur proteins, aconitase and fumarase, by accumulated cytoplasmic NO. Site directed mutagenesis revealed an essential role in NO reduction for the conserved glutamate 492 that coordinates the hybrid cluster. The second gene of the hcp-hcr operon encodes an NADH-dependent reductase, Hcr. Tight interaction between Hcp and Hcr was demonstrated. Although Hcp and Hcr purified individually were inactive or when recombined, a co-purified preparation reduced NO in vitro with a Km for NO of 500 nM. In an hcr mutant, Hcp is reversibly inactivated by NO concentrations above 200 nM, indicating that Hcr protects Hcp from nitrosylation by its substrate, NO.

  4. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363

    PubMed Central

    2016-01-01

    Lin28A is a post-transcriptional regulator of gene expression that interacts with and negatively regulates the biogenesis of let-7 family miRNAs. Recent data suggested that Lin28A also binds the putative tumor suppressor miR-363, a member of the 106~363 cluster of miRNAs. Affinity for this miRNA and the stoichiometry of the protein–RNA complex are unknown. Characterization of human Lin28’s interaction with RNA has been complicated by difficulties in producing stable RNA-free protein. We have engineered a maltose binding protein fusion with Lin28, which binds let-7 miRNA with a Kd of 54.1 ± 4.2 nM, in agreement with previous data on a murine homologue. We show that human Lin28A binds miR-363 with a 1:1 stoichiometry and with a similar, if not higher, affinity (Kd = 16.6 ± 1.9 nM). Further analysis suggests that the interaction of the N-terminal cold shock domain of Lin28A with RNA is salt-dependent, supporting a model in which the cold shock domain allows the protein to sample RNA substrates through transient electrostatic interactions. PMID:27559824

  5. Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling.

    PubMed

    Li, Xu; Gao, Min; Choi, Jong Min; Kim, Beom-Jun; Zhou, Mao-Tian; Chen, Zhen; Jain, Antrix N; Jung, Sung Yun; Yuan, Jingsong; Wang, Wenqi; Wang, Yi; Chen, Junjie

    2017-04-01

    Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors.

  6. Clustering with shallow trees

    NASA Astrophysics Data System (ADS)

    Bailly-Bechet, M.; Bradde, S.; Braunstein, A.; Flaxman, A.; Foini, L.; Zecchina, R.

    2009-12-01

    We propose a new method for obtaining hierarchical clustering based on the optimization of a cost function over trees of limited depth, and we derive a message-passing method that allows one to use it efficiently. The method and the associated algorithm can be interpreted as a natural interpolation between two well-known approaches, namely that of single linkage and the recently presented affinity propagation. We analyse using this general scheme three biological/medical structured data sets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.

  7. Small copper-doped silicon clusters CuSin (n = 4-10) and their anions: structures, thermochemistry, and electron affinities.

    PubMed

    Lin, Lin; Yang, Jucai

    2015-06-01

    The structures and energies of copper-doped small silicon clusters CuSi n (n = 4-10) and their anions were investigated systematically using CCSD(T)/aug-cc-pVTZ-DK//MP2/6-31G(2df,p), G4//MP2/6-31G(2df,p), and the B3LYP/6-311+G* basis set. The performance of the methods used for the prediction of energetic and thermodynamic properties was evaluated. Comparing experimental [Xu et al. (2012) J Chem Phys 136:104308] and theoretical calculations, it was concluded that the CCSD(T) results are very accurate and exhibit the best performance; the mean absolute deviation from experimental data was 0.043 eV. The excellent agreement of vertical detachment energy (VDE) between experimental results and CCSD(T) calculations indicates that the ground state structures of CuSi n (-) (n = 4-10) presented in this paper are reliable. For CuSi10, assigning 2.90±0.08 eV to the experimental adiabatic electron affinity (AEA) and 3.90±0.08 eV to the VDE is more reasonable than to 3.46±0.08 eV and 3.62±0.08 eV, respectively, based on the CCSD(T) calculations and the previous photoelectron spectrum of CuSi10 (-) (Xu et al., op. cit.). The AEAs of CuSi n (n = 4-10), excluding CuSi7, are in excellent agreement with experimental data, showing that the ground state structures of CuSi n (n = 4-6, 8-10) reported in this paper are reliable. CuSi10 is suggested to be the smallest endohedral ground state structure. However, adding an additional electron to CuSi10 pulls out the Cu atom from the center location, forming an exohedral ground state structure of CuSi10 (-). The charge transfer and dissociation energy of Cu from CuSi n and their anions determined to examine the nature of bonding and their relative stabilities.

  8. Propagation of dynamic nuclear polarization across the xenon cluster boundaries: elucidation of the spin-diffusion bottleneck.

    PubMed

    Pourfathi, M; Kuzma, N N; Kara, H; Ghosh, R K; Shaghaghi, H; Kadlecek, S J; Rizi, R R

    2013-10-01

    Earlier Dynamic Nuclear Polarization (DNP) experiments with frozen xenon/1-propanol/trityl mixtures have demonstrated spontaneous formation of pure xenon clusters above 120 K, enabling spectrally-resolved real-time measurements of (129)Xe nuclear magnetization in the clusters and in the surrounding radical-rich matrix. A spin-diffusion bottleneck was postulated to explain the peculiar time evolution of (129)Xe signals in the clusters as well as the apparent discontinuity of (129)Xe polarization across the cluster boundaries. A self-contained ab initio model of nuclear spin diffusion in heterogeneous systems is developed here, incorporating the intrinsic T1 relaxation towards the temperature-dependent equilibrium polarization and the spin-diffusion coefficients based on the measured NMR line widths and the known atomic densities in each compartment. This simple model provides the physical basis for the observed spin-diffusion bottleneck and is in a good quantitative agreement with the earlier measurements. A simultaneous fit of the model to the time-dependent NMR data at two different DNP frequencies provides excellent estimates of the cluster size, the intrinsic sample temperature, and (129)Xe T1 constants. The model was also applied to the NMR data acquired during relaxation towards the thermal equilibrium after the microwaves were turned off, to estimate T1 relaxation time constants inside and outside the clusters. Fitting the model to the data during and after DNP provides consistent estimates of the cluster size.

  9. Propagation of Dynamic Nuclear Polarization across the Xenon Cluster Boundaries: Elucidation of the Spin-Diffusion Bottleneck

    PubMed Central

    Pourfathi, M.; Kuzma, N. N.; Kara, H.; Ghosh, R. K.; Shaghaghi, H.; Kadlecek, S. J.; Rizi, R. R.

    2013-01-01

    Earlier dynamic nuclear polarization (DNP) experiments with frozen xenon/1-propanol/trityl mixtures have demonstrated spontaneous formation of pure xenon clusters above 120 K, enabling spectrally-resolved real-time measurements of 129Xe nuclear magnetization in the clusters and in the surrounding radical-rich matrix. A spin-diffusion bottleneck was postulated to explain the peculiar time evolution of 129Xe signals in the clusters as well as the apparent discontinuity of 129Xe polarization across the cluster boundaries. A self-contained ab initio model of nuclear spin diffusion in heterogeneous systems is developed here, incorporating the intrinsic T1 relaxation towards the temperature-dependent equilibrium along with the spin-diffusion coefficients based on the measured NMR line widths and the known atomic densities in each compartment. This simple model provides the physical basis for the observed spin-diffusion bottleneck and is in a good quantitative agreement with the earlier measurements. A simultaneous fit of the model to the time-dependent NMR data at two different DNP frequencies provides excellent estimates of the cluster size, the intrinsic sample temperature, and 129Xe T1 constants. The model was also applied to the NMR data acquired during relaxation towards thermal equilibrium after microwaves were turned off to estimate T1 relaxation time constants inside and outside the clusters. Fitting the model to data during and after DNP provides estimates of cluster size that are in complete agreement. PMID:23981341

  10. A Novel Vertex Affinity for Community Detection

    SciTech Connect

    Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot

    2015-10-05

    We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.

  11. Epidemiological Surveillance of HIV-1 Transmitted Drug Resistance in Spain in 2004-2012: Relevance of Transmission Clusters in the Propagation of Resistance Mutations

    PubMed Central

    Vega, Yolanda; Delgado, Elena; Fernández-García, Aurora; Cuevas, Maria Teresa; Thomson, Michael M.; Montero, Vanessa; Sánchez, Monica; Sánchez, Ana Maria; Pérez-Álvarez, Lucia

    2015-01-01

    Our objectives were to carry out an epidemiological surveillance study on transmitted drug resistance (TDR) among individuals newly diagnosed of HIV-1 infection during a nine year period in Spain and to assess the role of transmission clusters (TC) in the propagation of resistant strains. An overall of 1614 newly diagnosed individuals were included in the study from January 2004 through December 2012. Individuals come from two different Spanish regions: Galicia and the Basque Country. Resistance mutations to reverse transcriptase inhibitors (RTI) and protease inhibitors (PI) were analyzed according to mutations included in the surveillance drug-resistance mutations list updated in 2009. TC were defined as those comprising viruses from five or more individuals whose sequences clustered in maximum likelihood phylogenetic trees with a bootstrap value ≥90%. The overall prevalence of TDR to any drug was 9.9%: 4.9% to nucleoside RTIs (NRTIs), 3.6% to non-nucleoside RTIs (NNRTIs), and 2.7% to PIs. A significant decrease of TDR to NRTIs over time was observed [from 10% in 2004 to 2% in 2012 (p=0.01)]. Sixty eight (42.2%) of 161 sequences with TDR were included in 25 TC composed of 5 or more individuals. Of them, 9 clusters harbored TDR associated with high level resistance to antiretroviral drugs. T215D revertant mutation was transmitted in a large cluster comprising 25 individuals. The impact of epidemiological networks on TDR frequency may explain its persistence in newly diagnosed individuals. The knowledge of the populations involved in TC would facilitate the design of prevention programs and public health interventions. PMID:26010948

  12. Epidemiological Surveillance of HIV-1 Transmitted Drug Resistance in Spain in 2004-2012: Relevance of Transmission Clusters in the Propagation of Resistance Mutations.

    PubMed

    Vega, Yolanda; Delgado, Elena; Fernández-García, Aurora; Cuevas, Maria Teresa; Thomson, Michael M; Montero, Vanessa; Sánchez, Monica; Sánchez, Ana Maria; Pérez-Álvarez, Lucia

    2015-01-01

    Our objectives were to carry out an epidemiological surveillance study on transmitted drug resistance (TDR) among individuals newly diagnosed of HIV-1 infection during a nine year period in Spain and to assess the role of transmission clusters (TC) in the propagation of resistant strains. An overall of 1614 newly diagnosed individuals were included in the study from January 2004 through December 2012. Individuals come from two different Spanish regions: Galicia and the Basque Country. Resistance mutations to reverse transcriptase inhibitors (RTI) and protease inhibitors (PI) were analyzed according to mutations included in the surveillance drug-resistance mutations list updated in 2009. TC were defined as those comprising viruses from five or more individuals whose sequences clustered in maximum likelihood phylogenetic trees with a bootstrap value ≥90%. The overall prevalence of TDR to any drug was 9.9%: 4.9% to nucleoside RTIs (NRTIs), 3.6% to non-nucleoside RTIs (NNRTIs), and 2.7% to PIs. A significant decrease of TDR to NRTIs over time was observed [from 10% in 2004 to 2% in 2012 (p=0.01)]. Sixty eight (42.2%) of 161 sequences with TDR were included in 25 TC composed of 5 or more individuals. Of them, 9 clusters harbored TDR associated with high level resistance to antiretroviral drugs. T215D revertant mutation was transmitted in a large cluster comprising 25 individuals. The impact of epidemiological networks on TDR frequency may explain its persistence in newly diagnosed individuals. The knowledge of the populations involved in TC would facilitate the design of prevention programs and public health interventions.

  13. CLAG: an unsupervised non hierarchical clustering algorithm handling biological data

    PubMed Central

    2012-01-01

    Background Searching for similarities in a set of biological data is intrinsically difficult due to possible data points that should not be clustered, or that should group within several clusters. Under these hypotheses, hierarchical agglomerative clustering is not appropriate. Moreover, if the dataset is not known enough, like often is the case, supervised classification is not appropriate either. Results CLAG (for CLusters AGgregation) is an unsupervised non hierarchical clustering algorithm designed to cluster a large variety of biological data and to provide a clustered matrix and numerical values indicating cluster strength. CLAG clusterizes correlation matrices for residues in protein families, gene-expression and miRNA data related to various cancer types, sets of species described by multidimensional vectors of characters, binary matrices. It does not ask to all data points to cluster and it converges yielding the same result at each run. Its simplicity and speed allows it to run on reasonably large datasets. Conclusions CLAG can be used to investigate the cluster structure present in biological datasets and to identify its underlying graph. It showed to be more informative and accurate than several known clustering methods, as hierarchical agglomerative clustering, k-means, fuzzy c-means, model-based clustering, affinity propagation clustering, and not to suffer of the convergence problem proper to this latter. PMID:23216858

  14. Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-Based Model.

    PubMed

    Du, Nan; Knecht, Marc R; Swihart, Mark T; Tang, Zhenghua; Walsh, Tiffany R; Zhang, Aidong

    2015-01-01

    Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins (SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.

  15. Full Text Clustering and Relationship Network Analysis of Biomedical Publications

    PubMed Central

    Guan, Renchu; Yang, Chen; Marchese, Maurizio; Liang, Yanchun; Shi, Xiaohu

    2014-01-01

    Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers. PMID:25250864

  16. Affinity based information diffusion model in social networks

    NASA Astrophysics Data System (ADS)

    Liu, Hongli; Xie, Yun; Hu, Haibo; Chen, Zhigao

    2014-12-01

    There is a widespread intuitive sense that people prefer participating in spreading the information in which they are interested. The affinity of people with information disseminated can affect the information propagation in social networks. In this paper, we propose an information diffusion model incorporating the mechanism of affinity of people with information which considers the fitness of affinity values of people with affinity threshold of the information. We find that the final size of information diffusion is affected by affinity threshold of the information, average degree of the network and the probability of people's losing their interest in the information. We also explore the effects of other factors on information spreading by numerical simulations and find that the probabilities of people's questioning and confirming the information can affect the propagation speed, but not the final scope.

  17. Join-Graph Propagation Algorithms

    PubMed Central

    Mateescu, Robert; Kask, Kalev; Gogate, Vibhav; Dechter, Rina

    2010-01-01

    The paper investigates parameterized approximate message-passing schemes that are based on bounded inference and are inspired by Pearl's belief propagation algorithm (BP). We start with the bounded inference mini-clustering algorithm and then move to the iterative scheme called Iterative Join-Graph Propagation (IJGP), that combines both iteration and bounded inference. Algorithm IJGP belongs to the class of Generalized Belief Propagation algorithms, a framework that allowed connections with approximate algorithms from statistical physics and is shown empirically to surpass the performance of mini-clustering and belief propagation, as well as a number of other state-of-the-art algorithms on several classes of networks. We also provide insight into the accuracy of iterative BP and IJGP by relating these algorithms to well known classes of constraint propagation schemes. PMID:20740057

  18. CONSTRAINED SPECTRAL CLUSTERING FOR IMAGE SEGMENTATION

    PubMed Central

    Sourati, Jamshid; Brooks, Dana H.; Dy, Jennifer G.; Erdogmus, Deniz

    2013-01-01

    Constrained spectral clustering with affinity propagation in its original form is not practical for large scale problems like image segmentation. In this paper we employ novelty selection sub-sampling strategy, besides using efficient numerical eigen-decomposition methods to make this algorithm work efficiently for images. In addition, entropy-based active learning is also employed to select the queries posed to the user more wisely in an interactive image segmentation framework. We evaluate the algorithm on general and medical images to show that the segmentation results will improve using constrained clustering even if one works with a subset of pixels. Furthermore, this happens more efficiently when pixels to be labeled are selected actively. PMID:24466500

  19. A dielectric affinity microbiosensor

    NASA Astrophysics Data System (ADS)

    Huang, Xian; Li, Siqi; Schultz, Jerome S.; Wang, Qian; Lin, Qiao

    2010-01-01

    We present an affinity biosensing approach that exploits changes in dielectric properties of a polymer due to its specific, reversible binding with an analyte. The approach is demonstrated using a microsensor comprising a pair of thin-film capacitive electrodes sandwiching a solution of poly(acrylamide-ran-3-acrylamidophenylboronic acid), a synthetic polymer with specific affinity to glucose. Binding with glucose induces changes in the permittivity of the polymer, which can be measured capacitively for specific glucose detection, as confirmed by experimental results at physiologically relevant concentrations. The dielectric affinity biosensing approach holds the potential for practical applications such as long-term continuous glucose monitoring.

  20. Affinity in electrophoresis.

    PubMed

    Heegaard, Niels H H

    2009-06-01

    The journal Electrophoresis has greatly influenced my approaches to biomolecular affinity studies. The methods that I have chosen as my main tools to study interacting biomolecules--native gel and later capillary zone electrophoresis--have been the topic of numerous articles in Electrophoresis. Below, the role of the journal in the development and dissemination of these techniques and applications reviewed. Many exhaustive reviews on affinity electrophoresis and affinity CE have been published in the last few years and are not in any way replaced by the present deliberations that are focused on papers published by the journal.

  1. Affine dynamics with torsion

    NASA Astrophysics Data System (ADS)

    Gültekin, Kemal

    2016-03-01

    In this study, we give a thorough analysis of a general affine gravity with torsion. After a brief exposition of the affine gravities considered by Eddington and Schrödinger, we construct and analyze different affine gravities based on the determinants of the Ricci tensor, the torsion tensor, the Riemann tensor, and their combinations. In each case we reduce equations of motion to their simplest forms and give a detailed analysis of their solutions. Our analyses lead to the construction of the affine connection in terms of the curvature and torsion tensors. Our solutions of the dynamical equations show that the curvature tensors at different points are correlated via non-local, exponential rescaling factors determined by the torsion tensor.

  2. Lectin affinity electrophoresis.

    PubMed

    Kobayashi, Yuka

    2014-01-01

    An interaction or a binding event typically changes the electrophoretic properties of a molecule. Affinity electrophoresis methods detect changes in the electrophoretic pattern of molecules (mainly macromolecules) that occur as a result of biospecific interactions or complex formation. Lectin affinity electrophoresis is a very effective method for the detection and analysis of trace amounts of glycobiological substances. It is particularly useful for isolating and separating the glycoisomers of target molecules. Here, we describe a sensitive technique for the detection of glycoproteins separated by agarose gel-lectin affinity electrophoresis that uses antibody-affinity blotting. The technique is tested using α-fetoprotein with lectin (Lens culinaris agglutinin and Phaseolus vulgaris agglutinin)-agarose gels.

  3. Accelerating a 3D finite-difference wave propagation code by a factor of 50 and a spectral-element code by a factor of 25 using a cluster of GPU graphics cards

    NASA Astrophysics Data System (ADS)

    Komatitsch, Dimitri; Michéa, David; Erlebacher, Gordon; Göddeke, Dominik

    2010-05-01

    We first accelerate a three-dimensional finite-difference in the time domain (FDTD) wave propagation code by a factor of about 50 using Graphics Processing Unit (GPU) computing on a cheap NVIDIA graphics card with the CUDA programming language. We implement the code in CUDA in the case of the fully heterogeneous elastic wave equation. We also implement Convolution Perfectly Matched Layers (CPMLs) on the graphics card to efficiently absorb outgoing waves on the fictitious edges of the grid. We show that the code that runs on the graphics card gives the expected results by comparing our results to those obtained by running the same simulation on a classical processor core. The methodology that we present can be used for Maxwell's equations as well because their form is similar to that of the seismic wave equation written in velocity vector and stress tensor. We then implement a high-order finite-element (spectral-element) application, which performs the numerical simulation of seismic wave propagation resulting for instance from earthquakes at the scale of a continent or from active seismic acquisition experiments in the oil industry, on a cluster of NVIDIA Tesla graphics cards using the CUDA programming language and non blocking message passing based on MPI. We compare it to the implementation in C language and MPI on a classical cluster of CPU nodes. We use mesh coloring to efficiently handle summation operations over degrees of freedom on an unstructured mesh, and we exchange information between nodes using non blocking MPI messages. Using non-blocking communications allows us to overlap the communications across the network and the data transfer between the GPU card and the CPU node on which it is installed with calculations on that GPU card. We perform a number of numerical tests to validate the single-precision CUDA and MPI implementation and assess its accuracy. We then analyze performance measurements and in average we obtain a speedup of 20x to 25x.

  4. Atmospheric Propagation

    NASA Technical Reports Server (NTRS)

    Embleton, Tony F. W.; Daigle, Gilles A.

    1991-01-01

    Reviewed here is the current state of knowledge with respect to each basic mechanism of sound propagation in the atmosphere and how each mechanism changes the spectral or temporal characteristics of the sound received at a distance from the source. Some of the basic processes affecting sound wave propagation which are present in any situation are discussed. They are geometrical spreading, molecular absorption, and turbulent scattering. In geometrical spreading, sound levels decrease with increasing distance from the source; there is no frequency dependence. In molecular absorption, sound energy is converted into heat as the sound wave propagates through the air; there is a strong dependence on frequency. In turbulent scattering, local variations in wind velocity and temperature induce fluctuations in phase and amplitude of the sound waves as they propagate through an inhomogeneous medium; there is a moderate dependence on frequency.

  5. Natural Microbial Community Compositions Compared by a Back-Propagating Neural Network and Cluster Analysis of 5S rRNA

    PubMed Central

    Noble, P. A.; Bidle, K. D.; Fletcher, M.

    1997-01-01

    The community compositions of free-living and particle-associated bacteria in the Chesapeake Bay estuary were analyzed by comparing banding patterns of stable low-molecular-weight RNA (SLMW RNA) which include 5S rRNA and tRNA molecules. By analyzing images of autoradiographs of SLMW RNAs on polyacrylamide gels, band intensities of 5S rRNA were converted to binary format for transmission to a back-propagating neural network (NN). The NN was trained to relate binary input to sample stations, collection times, positions in the water column, and sample types (e.g., particle-associated versus free-living communities). Dendrograms produced by using Euclidean distance and average and Ward's linkage methods on data of three independently trained NNs yielded the following results. (i) Community compositions of Chesapeake Bay water samples varied both seasonally and spatially. (ii) Although there was no difference in the compositions of free-living and particle-associated bacteria in the summer, these community types differed significantly in the winter. (iii) In the summer, most bay samples had a common 121-nucleotide 5S rRNA molecule. Although this band occurred in the top water of midbay samples, it did not occur in particle-associated communities of bottom-water samples. (iv) Regardless of the season, midbay samples had the greatest variety of 5S rRNA sizes. The utility of NNs for interpreting complex banding patterns in electrophoresis gels was demonstrated. PMID:16535593

  6. Data Clustering

    NASA Astrophysics Data System (ADS)

    Wagstaff, Kiri L.

    2012-03-01

    particular application involves considerations of the kind of data being analyzed, algorithm runtime efficiency, and how much prior knowledge is available about the problem domain, which can dictate the nature of clusters sought. Fundamentally, the clustering method and its representations of clusters carries with it a definition of what a cluster is, and it is important that this be aligned with the analysis goals for the problem at hand. In this chapter, I emphasize this point by identifying for each algorithm the cluster representation as a model, m_j , even for algorithms that are not typically thought of as creating a “model.” This chapter surveys a basic collection of clustering methods useful to any practitioner who is interested in applying clustering to a new data set. The algorithms include k-means (Section 25.2), EM (Section 25.3), agglomerative (Section 25.4), and spectral (Section 25.5) clustering, with side mentions of variants such as kernel k-means and divisive clustering. The chapter also discusses each algorithm’s strengths and limitations and provides pointers to additional in-depth reading for each subject. Section 25.6 discusses methods for incorporating domain knowledge into the clustering process. This chapter concludes with a brief survey of interesting applications of clustering methods to astronomy data (Section 25.7). The chapter begins with k-means because it is both generally accessible and so widely used that understanding it can be considered a necessary prerequisite for further work in the field. EM can be viewed as a more sophisticated version of k-means that uses a generative model for each cluster and probabilistic item assignments. Agglomerative clustering is the most basic form of hierarchical clustering and provides a basis for further exploration of algorithms in that vein. Spectral clustering permits a departure from feature-vector-based clustering and can operate on data sets instead represented as affinity, or similarity

  7. Affine Sphere Relativity

    NASA Astrophysics Data System (ADS)

    Minguzzi, E.

    2017-03-01

    We investigate spacetimes whose light cones could be anisotropic. We prove the equivalence of the structures: (a) Lorentz-Finsler manifold for which the mean Cartan torsion vanishes, (b) Lorentz-Finsler manifold for which the indicatrix (observer space) at each point is a convex hyperbolic affine sphere centered on the zero section, and (c) pair given by a spacetime volume and a sharp convex cone distribution. The equivalence suggests to describe (affine sphere) spacetimes with this structure, so that no algebraic-metrical concept enters the definition. As a result, this work shows how the metric features of spacetime emerge from elementary concepts such as measure and order. Non-relativistic spacetimes are obtained replacing proper spheres with improper spheres, so the distinction does not call for group theoretical elements. In physical terms, in affine sphere spacetimes the light cone distribution and the spacetime measure determine the motion of massive and massless particles (hence the dispersion relation). Furthermore, it is shown that, more generally, for Lorentz-Finsler theories non-differentiable at the cone, the lightlike geodesics and the transport of the particle momentum over them are well defined, though the curve parametrization could be undefined. Causality theory is also well behaved. Several results for affine sphere spacetimes are presented. Some results in Finsler geometry, for instance in the characterization of Randers spaces, are also included.

  8. Affinity+: Semi-Structured Brainstorming on Large Displays

    SciTech Connect

    Burtner, Edwin R.; May, Richard A.; Scarberry, Randall E.; LaMothe, Ryan R.; Endert, Alexander

    2013-04-27

    Affinity diagraming is a powerful method for encouraging and capturing lateral thinking in a group environment. The Affinity+ Concept was designed to improve the collaborative brainstorm process through the use of large display surfaces in conjunction with mobile devices like smart phones and tablets. The system works by capturing the ideas digitally and allowing users to sort and group them on a large touch screen manually. Additionally, Affinity+ incorporates theme detection, topic clustering, and other processing algorithms that help bring structured analytic techniques to the process without requiring explicit leadership roles and other overhead typically involved in these activities.

  9. On constructing purely affine theories with matter

    NASA Astrophysics Data System (ADS)

    Cervantes-Cota, Jorge L.; Liebscher, D.-E.

    2016-08-01

    We explore ways to obtain the very existence of a space-time metric from an action principle that does not refer to it a priori. Although there are reasons to believe that only a non-local theory can viably achieve this goal, we investigate here local theories that start with Schrödinger's purely affine theory (Schrödinger in Space-time structure. Cambridge UP, Cambridge, 1950), where he gave reasons to set the metric proportional to the Ricci curvature aposteriori. When we leave the context of unified field theory, and we couple the non-gravitational matter using some weak equivalence principle, we can show that the propagation of shock waves does not define a lightcone when the purely affine theory is local and avoids the explicit use of the Ricci tensor in realizing the weak equivalence principle. When the Ricci tensor is substituted for the metric, the equations seem to have only a very limited set of solutions. This backs the conviction that viable purely affine theories have to be non-local.

  10. Hybrid fuzzy cluster ensemble framework for tumor clustering from biomolecular data.

    PubMed

    Yu, Zhiwen; Chen, Hantao; You, Jane; Han, Guoqiang; Li, Le

    2013-01-01

    Cancer class discovery using biomolecular data is one of the most important tasks for cancer diagnosis and treatment. Tumor clustering from gene expression data provides a new way to perform cancer class discovery. Most of the existing research works adopt single-clustering algorithms to perform tumor clustering is from biomolecular data that lack robustness, stability, and accuracy. To further improve the performance of tumor clustering from biomolecular data, we introduce the fuzzy theory into the cluster ensemble framework for tumor clustering from biomolecular data, and propose four kinds of hybrid fuzzy cluster ensemble frameworks (HFCEF), named as HFCEF-I, HFCEF-II, HFCEF-III, and HFCEF-IV, respectively, to identify samples that belong to different types of cancers. The difference between HFCEF-I and HFCEF-II is that they adopt different ensemble generator approaches to generate a set of fuzzy matrices in the ensemble. Specifically, HFCEF-I applies the affinity propagation algorithm (AP) to perform clustering on the sample dimension and generates a set of fuzzy matrices in the ensemble based on the fuzzy membership function and base samples selected by AP. HFCEF-II adopts AP to perform clustering on the attribute dimension, generates a set of subspaces, and obtains a set of fuzzy matrices in the ensemble by performing fuzzy c-means on subspaces. Compared with HFCEF-I and HFCEF-II, HFCEF-III and HFCEF-IV consider the characteristics of HFCEF-I and HFCEF-II. HFCEF-III combines HFCEF-I and HFCEF-II in a serial way, while HFCEF-IV integrates HFCEF-I and HFCEF-II in a concurrent way. HFCEFs adopt suitable consensus functions, such as the fuzzy c-means algorithm or the normalized cut algorithm (Ncut), to summarize generated fuzzy matrices, and obtain the final results. The experiments on real data sets from UCI machine learning repository and cancer gene expression profiles illustrate that 1) the proposed hybrid fuzzy cluster ensemble frameworks work well on real

  11. Kernel Affine Projection Algorithms

    NASA Astrophysics Data System (ADS)

    Liu, Weifeng; Príncipe, José C.

    2008-12-01

    The combination of the famed kernel trick and affine projection algorithms (APAs) yields powerful nonlinear extensions, named collectively here, KAPA. This paper is a follow-up study of the recently introduced kernel least-mean-square algorithm (KLMS). KAPA inherits the simplicity and online nature of KLMS while reducing its gradient noise, boosting performance. More interestingly, it provides a unifying model for several neural network techniques, including kernel least-mean-square algorithms, kernel adaline, sliding-window kernel recursive-least squares (KRLS), and regularization networks. Therefore, many insights can be gained into the basic relations among them and the tradeoff between computation complexity and performance. Several simulations illustrate its wide applicability.

  12. Adjoint affine fusion and tadpoles

    NASA Astrophysics Data System (ADS)

    Urichuk, Andrew; Walton, Mark A.

    2016-06-01

    We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.

  13. First Genome Data from Uncultured Upland Soil Cluster Alpha Methanotrophs Provide Further Evidence for a Close Phylogenetic Relationship to Methylocapsa acidiphila B2 and for High-Affinity Methanotrophy Involving Particulate Methane Monooxygenase

    PubMed Central

    Ricke, Peter; Kube, Michael; Nakagawa, Satoshi; Erkel, Christoph; Reinhardt, Richard; Liesack, Werner

    2005-01-01

    Members of upland soil cluster alpha (USCα) are assumed to be methanotrophic bacteria (MB) adapted to the trace level of atmospheric methane. So far, these MB have eluded all cultivation attempts. While the 16S rRNA phylogeny of USCα members is still not known, phylogenies constructed for the active-site polypeptide (encoded by pmoA) of particulate methane monooxygenase (pMMO) placed USCα next to the alphaproteobacterial Methylocapsa acidiphila B2. To assess whether the pmoA tree reflects the evolutionary identity of USCα, a 42-kb genomic contig of a USCα representative was obtained from acidic forest soil by screening a metagenomic fosmid library of 250,000 clones using pmoA-targeted PCR. For comparison, a 101-kb genomic contig from M. acidiphila was analyzed, including the pmo operon. The following three lines of evidence confirmed a close phylogenetic relationship between USCα and M. acidiphila: (i) tetranucleotide frequency patterns of 5-kb genomic subfragments, (ii) annotation and comparative analysis of the genomic fragments against all completely sequenced genomes available in public domain databases, and (iii) three single gene phylogenies constructed using the deduced amino acid sequences of a putative prephenate dehydratase, a staphylococcal-like nuclease, and a putative zinc metalloprotease. A comparative analysis of the pmo operons of USCα and M. acidiphila corroborated previous reports that both the pmo operon structure and the predicted secondary structure of deduced pMMO are highly conserved among all MB. PMID:16269789

  14. Electron Affinity Calculations for Thioethers

    NASA Technical Reports Server (NTRS)

    Sulton, Deley L.; Boothe, Michael; Ball, David W.; Morales, Wilfredo

    1997-01-01

    Previous work indicated that polyphenyl thioethers possessed chemical properties, related to their electron affinities, which could allow them to function as vapor phase lubricants (VPL). Indeed, preliminary tribological tests revealed that the thioethers could function as vapor phase lubricants but not over a wide temperature and hertzian pressure range. Increasing the electron affinity of the thioethers may improve their VPL properties over this range. Adding a substituent group to the thioether will alter its electron affinity in many cases. Molecular orbital calculations were undertaken to determine the effect of five different substituent groups on the electron affinity of polyphenyl thioethers. It was found that the NO2, F, and I groups increased the thioethers electron affinity by the greatest amount. Future work will involve the addition of these groups to the thioethers followed by tribological testing to assess their VPL properties.

  15. Fatigue damage prognosis using affine arithmetic

    NASA Astrophysics Data System (ADS)

    Gbaguidi, Audrey; Kim, Daewon

    2014-02-01

    Among the essential steps to be taken in structural health monitoring systems, damage prognosis would be the field that is least investigated due to the complexity of the uncertainties. This paper presents the possibility of using Affine Arithmetic for uncertainty propagation of crack damage in damage prognosis. The structures examined are thin rectangular plates made of titanium alloys with central mode I cracks and a composite plate with an internal delamination caused by mixed mode I and II fracture modes, under a harmonic uniaxial loading condition. The model-based method for crack growth rates are considered using the Paris Erdogan law model for the isotropic plates and the delamination growth law model proposed by Kardomateas for the composite plate. The parameters for both models are randomly taken and their uncertainties are considered as defined by an interval instead of a probability distribution. A Monte Carlo method is also applied to check whether Affine Arithmetic (AA) leads to tight bounds on the lifetime of the structure.

  16. Contractions of affine spherical varieties

    SciTech Connect

    Arzhantsev, I V

    1999-08-31

    The language of filtrations and contractions is used to describe the class of G-varieties obtainable as the total spaces of the construction of contraction applied to affine spherical varieties, which is well-known in invariant theory. These varieties are local models for arbitrary affine G-varieties of complexity 1 with a one-dimensional categorical quotient. As examples, reductive algebraic semigroups and three-dimensional SL{sub 2}-varieties are considered.

  17. Enhancing Community Detection By Affinity-based Edge Weighting Scheme

    SciTech Connect

    Yoo, Andy; Sanders, Geoffrey; Henson, Van; Vassilevski, Panayot

    2015-10-05

    Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is ideal for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.

  18. Cloning and functional characterization of the high-affinity K+ transporter HAK1 of pepper.

    PubMed

    Martínez-Cordero, M Angeles; Martínez, Vicente; Rubio, Francisco

    2004-10-01

    High-affinity K+ uptake in plants plays a crucial role in K+ nutrition and different systems have been postulated to contribute to the high-affinity K+ uptake. The results presented here with pepper (Capsicum annum) demonstrate that a HAK1-type transporter greatly contributes to the high-affinity K+ uptake observed in roots. Pepper plants starved of K+ for 3 d showed high-affinity K+ uptake (Km of 6 microM K+) that was very sensitive to NH and their roots expressed a high-affinity K+ transporter, CaHAK1, which clusters in group I of the KT/HAK/KUP family of transporters. When expressed in yeast ( Saccharomyces cerevisiae ), CaHAK1 mediated high-affinity K+ and Rb+ uptake with Km values of 3.3 and 1.9 microM, respectively. Rb+ uptake was competitively inhibited by micromolar concentrations of NH and Cs+, and by millimolar concentrations of Na+.

  19. Cluster Headache

    MedlinePlus

    Cluster headache Overview By Mayo Clinic Staff Cluster headaches, which occur in cyclical patterns or clusters, are one of the most painful types of headache. A cluster headache commonly awakens you ...

  20. Electro-Optic Propagation

    DTIC Science & Technology

    2003-09-30

    Electro - Optic Propagation Stephen Doss-Hammel SPAWARSYSCEN San Diego code 2858 49170 Propagation Path San Diego, CA 92152-7385 phone: (619...scenarios to extend the capabilities of TAWS to surface and low altitude situations. OBJECTIVES The electro - optical propagation objectives are: 1...development of a new propagation assessment tool called EOSTAR ( Electro - Optical Signal Transmission and Ranging). The goal of the EOSTAR project is to

  1. Chemical binding affinity estimation using MSB

    NASA Astrophysics Data System (ADS)

    Weaver, John B.; Rauwerdink, Adam M.

    2011-03-01

    Binding affinity can be estimated in several ways in the laboratory but there is no viable way to estimate binding affinity in vivo without assumptions on the number of binding sites. Magnetic spectroscopy of nanoparticle Brownian motion, MSB, measures the rotational Brownian motion. The MSB signal is affected by nanoparticle binding affinity so it provides a mechanism to measure the chemical binding affinity. We present a possible mechanism to quantify the binding affinity and test that mechanism using viscous solutions.

  2. Affine Contractions on the Plane

    ERIC Educational Resources Information Center

    Celik, D.; Ozdemir, Y.; Ureyen, M.

    2007-01-01

    Contractions play a considerable role in the theory of fractals. However, it is not easy to find contractions which are not similitudes. In this study, it is shown by counter examples that an affine transformation of the plane carrying a given triangle onto another triangle may not be a contraction even if it contracts edges, heights or medians.…

  3. Affinity-aware checkpoint restart

    SciTech Connect

    Saini, Ajay; Rezaei, Arash; Mueller, Frank; Hargrove, Paul; Roman, Eric

    2014-12-08

    Current checkpointing techniques employed to overcome faults for HPC applications result in inferior application performance after restart from a checkpoint for a number of applications. This is due to a lack of page and core affinity awareness of the checkpoint/restart (C/R) mechanism, i.e., application tasks originally pinned to cores may be restarted on different cores, and in case of non-uniform memory architectures (NUMA), quite common today, memory pages associated with tasks on a NUMA node may be associated with a different NUMA node after restart. Here, this work contributes a novel design technique for C/R mechanisms to preserve task-to-core maps and NUMA node specific page affinities across restarts. Experimental results with BLCR, a C/R mechanism, enhanced with affinity awareness demonstrate significant performance benefits of 37%-73% for the NAS Parallel Benchmark codes and 6-12% for NAMD with negligible overheads instead of up to nearly four times longer an execution times without affinity-aware restarts on 16 cores.

  4. Affinity-aware checkpoint restart

    DOE PAGES

    Saini, Ajay; Rezaei, Arash; Mueller, Frank; ...

    2014-12-08

    Current checkpointing techniques employed to overcome faults for HPC applications result in inferior application performance after restart from a checkpoint for a number of applications. This is due to a lack of page and core affinity awareness of the checkpoint/restart (C/R) mechanism, i.e., application tasks originally pinned to cores may be restarted on different cores, and in case of non-uniform memory architectures (NUMA), quite common today, memory pages associated with tasks on a NUMA node may be associated with a different NUMA node after restart. Here, this work contributes a novel design technique for C/R mechanisms to preserve task-to-core mapsmore » and NUMA node specific page affinities across restarts. Experimental results with BLCR, a C/R mechanism, enhanced with affinity awareness demonstrate significant performance benefits of 37%-73% for the NAS Parallel Benchmark codes and 6-12% for NAMD with negligible overheads instead of up to nearly four times longer an execution times without affinity-aware restarts on 16 cores.« less

  5. ELECTRON AFFINITIES OF INORGANIC RADICALS.

    DTIC Science & Technology

    energy in the latter compound is 110 kcals/mole, distinctly higher than in ammonia. Cyanogen (CN)2 and hydrocyanic acid (HCN) yield values for the...ions very readily, and the electron affinity is 49 kcals/mole. A comparison with the results from thiocyanic acid (HNCS) indicates that the H-N bond

  6. Structural origins of high-affinity biotin binding to streptavidin.

    PubMed

    Weber, P C; Ohlendorf, D H; Wendoloski, J J; Salemme, F R

    1989-01-06

    The high affinity of the noncovalent interaction between biotin and streptavidin forms the basis for many diagnostic assays that require the formation of an irreversible and specific linkage between biological macromolecules. Comparison of the refined crystal structures of apo and a streptavidin:biotin complex shows that the high affinity results from several factors. These factors include the formation of multiple hydrogen bonds and van der Waals interactions between biotin and the protein, together with the ordering of surface polypeptide loops that bury the biotin in the protein interior. Structural alterations at the biotin binding site produce quaternary changes in the streptavidin tetramer. These changes apparently propagate through cooperative deformations in the twisted beta sheets that link tetramer subunits.

  7. Theoretical proton affinity and fluoride affinity of nerve agent VX.

    PubMed

    Bera, Narayan C; Maeda, Satoshi; Morokuma, Keiji; Viggiano, Al A

    2010-12-23

    Proton affinity and fluoride affinity of nerve agent VX at all of its possible sites were calculated at the RI-MP2/cc-pVTZ//B3LYP/6-31G* and RI-MP2/aug-cc-pVTZ//B3LYP/6-31+G* levels, respectively. The protonation leads to various unique structures, with H(+) attached to oxygen, nitrogen, and sulfur atoms; among which the nitrogen site possesses the highest proton affinity of -ΔE ∼ 251 kcal/mol, suggesting that this is likely to be the major product. In addition some H(2), CH(4) dissociation as well as destruction channels have been found, among which the CH(4) + [Et-O-P(═O)(Me)-S-(CH(2))(2)-N(+)(iPr)═CHMe] product and the destruction product forming Et-O-P(═O)(Me)-SMe + CH(2)═N(+)(iPr)(2) are only 9 kcal/mol less stable than the most stable N-protonated product. For fluoridization, the S-P destruction channel to give Et-O-P(═O)(Me)(F) + [S-(CH(2))(2)-N-(iPr)(2)](-) is energetically the most favorable, with a fluoride affinity of -ΔE ∼ 44 kcal. Various F(-) ion-molecule complexes are also found, with the one having F(-) interacting with two hydrogen atoms in different alkyl groups to be only 9 kcal/mol higher than the above destruction product. These results suggest VX behaves quite differently from surrogate systems.

  8. Affinity learning with diffusion on tensor product graph.

    PubMed

    Yang, Xingwei; Prasad, Lakshman; Latecki, Longin Jan

    2013-01-01

    In many applications, we are given a finite set of data points sampled from a data manifold and represented as a graph with edge weights determined by pairwise similarities of the samples. Often the pairwise similarities (which are also called affinities) are unreliable due to noise or due to intrinsic difficulties in estimating similarity values of the samples. As observed in several recent approaches, more reliable similarities can be obtained if the original similarities are diffused in the context of other data points, where the context of each point is a set of points most similar to it. Compared to the existing methods, our approach differs in two main aspects. First, instead of diffusing the similarity information on the original graph, we propose to utilize the tensor product graph (TPG) obtained by the tensor product of the original graph with itself. Since TPG takes into account higher order information, it is not a surprise that we obtain more reliable similarities. However, it comes at the price of higher order computational complexity and storage requirement. The key contribution of the proposed approach is that the information propagation on TPG can be computed with the same computational complexity and the same amount of storage as the propagation on the original graph. We prove that a graph diffusion process on TPG is equivalent to a novel iterative algorithm on the original graph, which is guaranteed to converge. After its convergence we obtain new edge weights that can be interpreted as new, learned affinities. We stress that the affinities are learned in an unsupervised setting. We illustrate the benefits of the proposed approach for data manifolds composed of shapes, images, and image patches on two very different tasks of image retrieval and image segmentation. With learned affinities, we achieve the bull's eye retrieval score of 99.99 percent on the MPEG-7 shape dataset, which is much higher than the state-of-the-art algorithms. When the data

  9. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  10. Propagation research in Japan

    NASA Technical Reports Server (NTRS)

    Wakana, Hiromitsu

    1991-01-01

    L-band propagation measurements for land-mobile, maritime, and aeronautical satellite communications have been carried out by using the Japanese Engineering Test Satellite-Five (ETS-5) which was launched in Aug. 1987. This paper presents propagation characteristics for each of the mobile satellite communication channels.

  11. NASA Propagation Information Center

    NASA Technical Reports Server (NTRS)

    Smith, Ernest K.; Flock, Warren L.

    1989-01-01

    The NASA Propagation Information Center became formally operational in July 1988. It is located in the Department of Electrical and Computer Engineering of the University of Colorado at Boulder. The Center is several things: a communications medium for the propagation with the outside world, a mechanism for internal communication within the program, and an aid to management.

  12. Shallow-Water Propagation

    DTIC Science & Technology

    2016-06-07

    Shallow- Water Propagation William L. Siegmann Rensselaer Polytechnic Institute 110 Eighth Street Troy, New York 12180-3590 phone: (518) 276...ocean_acoustics LONG-TERM GOALS Develop methods for propagation and coherence calculations in complex shallow- water environments, determine...intensity and coherence. APPROACH (A) Develop high accuracy PE techniques for applications to shallow- water sediments, accounting for

  13. Millimeter wavelength propagation studies

    NASA Technical Reports Server (NTRS)

    Hodge, D. B.

    1974-01-01

    The investigations conducted for the Millimeter Wavelength Propagation Studies during the period December, 1966, to June 1974 are reported. These efforts included the preparation for the ATS-5 Millimeter Wavelength Propagation Experiment and the subsequent data acquisition and data analysis. The emphasis of the OSU participation in this experiment was placed on the determination of reliability improvement resulting from the use of space diversity on a millimeter wavelength earth-space communication link. Related measurements included the determination of the correlation between radiometric temperature and attenuation along the earth-space propagation path. Along with this experimental effort a theoretical model was developed for the prediction of attenuation statistics on single and spatially separated earth space propagation paths. A High Resolution Radar/Radiometer System and Low Resolution Radar System were developed and implemented for the study of intense rain cells in preparation for the ATS-6 Millimeter Wavelength Propagation Experiment.

  14. Gear crack propagation investigations

    NASA Technical Reports Server (NTRS)

    Lewicki, David G.; Ballarini, Roberto

    1996-01-01

    Analytical and experimental studies were performed to investigate the effect of gear rim thickness on crack propagation life. The FRANC (FRacture ANalysis Code) computer program was used to simulate crack propagation. The FRANC program used principles of linear elastic fracture mechanics, finite element modeling, and a unique re-meshing scheme to determine crack tip stress distributions, estimate stress intensity factors, and model crack propagation. Various fatigue crack growth models were used to estimate crack propagation life based on the calculated stress intensity factors. Experimental tests were performed in a gear fatigue rig to validate predicted crack propagation results. Test gears were installed with special crack propagation gages in the tooth fillet region to measure bending fatigue crack growth. Good correlation between predicted and measured crack growth was achieved when the fatigue crack closure concept was introduced into the analysis. As the gear rim thickness decreased, the compressive cyclic stress in the gear tooth fillet region increased. This retarded crack growth and increased the number of crack propagation cycles to failure.

  15. Gear Crack Propagation Investigation

    NASA Technical Reports Server (NTRS)

    1995-01-01

    Reduced weight is a major design goal in aircraft power transmissions. Some gear designs incorporate thin rims to help meet this goal. Thin rims, however, may lead to bending fatigue cracks. These cracks may propagate through a gear tooth or into the gear rim. A crack that propagates through a tooth would probably not be catastrophic, and ample warning of a failure could be possible. On the other hand, a crack that propagates through the rim would be catastrophic. Such cracks could lead to disengagement of a rotor or propeller from an engine, loss of an aircraft, and fatalities. To help create and validate tools for the gear designer, the NASA Lewis Research Center performed in-house analytical and experimental studies to investigate the effect of rim thickness on gear-tooth crack propagation. Our goal was to determine whether cracks grew through gear teeth (benign failure mode) or through gear rims (catastrophic failure mode) for various rim thicknesses. In addition, we investigated the effect of rim thickness on crack propagation life. A finite-element-based computer program simulated gear-tooth crack propagation. The analysis used principles of linear elastic fracture mechanics, and quarter-point, triangular elements were used at the crack tip to represent the stress singularity. The program had an automated crack propagation option in which cracks were grown numerically via an automated remeshing scheme. Crack-tip stress-intensity factors were estimated to determine crack-propagation direction. Also, various fatigue crack growth models were used to estimate crack-propagation life. Experiments were performed in Lewis' Spur Gear Fatigue Rig to validate predicted crack propagation results. Gears with various backup ratios were tested to validate crack-path predictions. Also, test gears were installed with special crack-propagation gages in the tooth fillet region to measure bending-fatigue crack growth. From both predictions and tests, gears with backup ratios

  16. Star clusters in the Magellanic Clouds - I. Parametrization and classification of 1072 clusters in the LMC

    NASA Astrophysics Data System (ADS)

    Nayak, P. K.; Subramaniam, A.; Choudhury, S.; Indu, G.; Sagar, Ram

    2016-12-01

    We have introduced a semi-automated quantitative method to estimate the age and reddening of 1072 star clusters in the Large Magellanic Cloud (LMC) using the Optical Gravitational Lensing Experiment III survey data. This study brings out 308 newly parametrized clusters. In a first of its kind, the LMC clusters are classified into groups based on richness/mass as very poor, poor, moderate and rich clusters, similar to the classification scheme of open clusters in the Galaxy. A major cluster formation episode is found to happen at 125 ± 25 Myr in the inner LMC. The bar region of the LMC appears prominently in the age range 60-250 Myr and is found to have a relatively higher concentration of poor and moderate clusters. The eastern and the western ends of the bar are found to form clusters initially, which later propagates to the central part. We demonstrate that there is a significant difference in the distribution of clusters as a function of mass, using a movie based on the propagation (in space and time) of cluster formation in various groups. The importance of including the low-mass clusters in the cluster formation history is demonstrated. The catalogue with parameters, classification, and cleaned and isochrone fitted colour-magnitude diagrams of 1072 clusters, which are available as online material, can be further used to understand the hierarchical formation of clusters in selected regions of the LMC.

  17. Affinity membrane introduction mass spectrometry

    SciTech Connect

    Xu, C.; Patrick, J.S.; Cooks, R.G. )

    1995-02-15

    A new technique, affinity membrane introduction mass spectrometry, is described. In this method, a chemically modified membrane is used to selectively adsorb analytes bearing a particular functional group and concentrate them from solution. Release of the bound analyte results in its transfer across the membrane and allows it to be monitored mass spectrometrically, using, in the present case, a benchtop ion trap instrument. Alkylamine-modified cellulose membranes are used to bind substituted benzaldehydes through imine formation at high pH. Release of the bound aldehyde is achieved by acid hydrolysis of the surface-bound imine. Benzaldehyde is detected with excellent specificity at 10 ppm in a complex mixture using this method. Using the enrichment capability of the membrane, a full mass spectrum of benzaldehyde can be measured at a concentration of 10 ppb. The behavior of a variety of other aldehydes is also discussed to illustrate the capabilities of the method. 21 refs., 5 figs., 2 tabs.

  18. Cluster headache

    MedlinePlus

    Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... be related to the body's sudden release of histamine (chemical in the body released during an allergic ...

  19. Propagation of Environmental Noise

    ERIC Educational Resources Information Center

    Lyon, R. H.

    1973-01-01

    Solutions for environmental noise pollution lie in systematic study of many basic processes such as reflection, scattering, and spreading. Noise propagation processes should be identified in different situations and assessed for their relative importance. (PS)

  20. Wave Propagation Program

    SciTech Connect

    McCandless, Kathleen; Petersson, Anders; Nilsson, Stefan; Sjogreen, Bjorn

    2007-01-08

    WPP is a massively parallel, 3D, C++, finite-difference elastodynamic wave propagation code. Typical applications for wave propagation with WPP include: evaluation of seismic event scenarios and damage from earthquakes, non-destructive evaluation of materials, underground facility detection, oil and gas exploration, predicting the electro-magnetic fields in accelerators, and acoustic noise generation. For more information, see User’s Manual [1].

  1. Antisymmetric tensor generalizations of affine vector fields

    PubMed Central

    Morisawa, Yoshiyuki; Tomoda, Kentaro

    2016-01-01

    Tensor generalizations of affine vector fields called symmetric and antisymmetric affine tensor fields are discussed as symmetry of spacetimes. We review the properties of the symmetric ones, which have been studied in earlier works, and investigate the properties of the antisymmetric ones, which are the main theme in this paper. It is shown that antisymmetric affine tensor fields are closely related to one-lower-rank antisymmetric tensor fields which are parallelly transported along geodesics. It is also shown that the number of linear independent rank-p antisymmetric affine tensor fields in n-dimensions is bounded by (n + 1)!/p!(n − p)!. We also derive the integrability conditions for antisymmetric affine tensor fields. Using the integrability conditions, we discuss the existence of antisymmetric affine tensor fields on various spacetimes. PMID:26858463

  2. Conformal field theory on affine Lie groups

    SciTech Connect

    Clubok, Kenneth Sherman

    1996-04-01

    Working directly on affine Lie groups, we construct several new formulations of the WZW model, the gauged WZW model, and the generic affine-Virasoro action. In one formulation each of these conformal field theories (CFTs) is expressed as a one-dimensional mechanical system whose variables are coordinates on the affine Lie group. When written in terms of the affine group element, this formulation exhibits a two-dimensional WZW term. In another formulation each CFT is written as a two-dimensional field theory, with a three- dimensional WZW term, whose fields are coordinates on the affine group. On the basis of these equivalent formulations, we develop a translation dictionary in which the new formulations on the affine Lie group are understood as mode formulations of the conventional formulations on the Lie group. Using this dictionary, we also express each CFT as a three-dimensional field theory on the Lie group with a four-dimensional WZW term. 36 refs.

  3. Meaningful Clusters

    SciTech Connect

    Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2004-05-26

    We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

  4. Structural determinants of sigma receptor affinity

    SciTech Connect

    Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.

    1987-12-01

    The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.

  5. Structure of Greyhound hemoglobin: origin of high oxygen affinity.

    PubMed

    Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F

    2011-05-01

    This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure.

  6. About the Clusters Program

    EPA Pesticide Factsheets

    The Environmental Technology Innovation Clusters Program advises cluster organizations, encourages collaboration between clusters, tracks U.S. environmental technology clusters, and connects EPA programs to cluster needs.

  7. Parallel Splash Belief Propagation

    DTIC Science & Technology

    2010-08-01

    Dean and S. Ghemawat. MapReduce : simplified data processing on large clusters . Commun. ACM, (1). P. Domingos. Uw-cse mlns, 2009. URL... Distributed Memory and Cluster Computing . . . . . . . . . . . . . . . . . . . . . 3 3 Graphical Models 4 3.1 Factor Graphs...passing messages across a reliable but typically slow communication network. . . . . . . . 3 2 The factor graph corresponding to the factorized distribution

  8. Structure of classical affine and classical affine fractional W-algebras

    SciTech Connect

    Suh, Uhi Rinn

    2015-01-15

    We introduce a classical BRST complex (See Definition 3.2.) and show that one can construct a classical affine W-algebra via the complex. This definition clarifies that classical affine W-algebras can be considered as quasi-classical limits of quantum affine W-algebras. We also give a definition of a classical affine fractional W-algebra as a Poisson vertex algebra. As in the classical affine case, a classical affine fractional W-algebra has two compatible λ-brackets and is isomorphic to an algebra of differential polynomials as a differential algebra. When a classical affine fractional W-algebra is associated to a minimal nilpotent, we describe explicit forms of free generators and compute λ-brackets between them. Provided some assumptions on a classical affine fractional W-algebra, we find an infinite sequence of integrable systems related to the algebra, using the generalized Drinfel’d and Sokolov reduction.

  9. DROMO Propagator Revisited

    NASA Astrophysics Data System (ADS)

    Urrutxua, H.; Sanjurjo-Rivo, M.; Peláez, J.

    2013-12-01

    In year 2000 a house-made orbital propagator was developed by the SDGUPM (former Grupo de Dinámica de Tethers) based in a set of redundant variables including Euler parameters. This propagator was called DROMO. and it was mainly used in numerical simulations of electrodynamic tethers. It was presented for the first time in the international meeting V Jornadas de Trabajo en Mecánica Celeste, held in Albarracín, Spain, in 2002 (see reference 1). The special perturbation method associated with DROMO can be consulted in the paper.2 In year 1975, Andre Deprit in reference 3 proposes a propagation scheme very similar to the one in which DROMO is based, by using the ideal frame concept of Hansen. The different approaches used in references 3 and 2 gave rise to a small controversy. In this paper we carried out a different deduction of the DROMO propagator, underlining its close relation with the Hansen ideal frame concept, and also the similarities and the differences with the theory carried out by Deprit in 3. Simultaneously we introduce some improvements in the formulation that leads to a more synthetic propagator.

  10. Self-affine and ARX-models zonation of well logging data

    NASA Astrophysics Data System (ADS)

    Shiri, Yousef; Tokhmechi, Behzad; Zarei, Zeinab; Koneshloo, Mohammad

    2012-11-01

    Zonation of time series into models which their parameters are piecewise constant are important and well-studied problems. Geophysical well logging data often show a complex pattern due to their multifractal nature. In a multifractal system, any pieces of it are established by a distinct exponent that can characterize them. This feature has the capability to cluster them. Self-affine zonation by Auto Regressive model with exogenous inputs (ARX) is a new approach which places well logging segments in the clusters which are more self-affine against the other clusters. This approach was performed and compared with a conventional ARX zonation in the well logging data of three different oilfields in southern parts of Iran. The results showed a good accuracy for detecting homogeneous lithological segments and led to a precise interpretation process to update the reservoir architecture.

  11. Elevated Temperature Crack Propagation

    NASA Technical Reports Server (NTRS)

    Orange, Thomas W.

    1994-01-01

    This paper is a summary of two NASA contracts on high temperature fatigue crack propagation in metals. The first evaluated the ability of fairly simple nonlinear fracture parameters to correlate crack propagation. Hastelloy-X specimens were tested under isothermal and thermomechanical cycling at temperatures up to 980 degrees C (1800 degrees F). The most successful correlating parameter was the crack tip opening displacement derived from the J-integral. The second evaluated the ability of several path-independent integrals to correlate crack propagation behavior. Inconel 718 specimens were tested under isothermal, thermomechanical, temperature gradient, and creep conditions at temperatures up to 650 degrees C (1200 degrees F). The integrals formulated by Blackburn and by Kishimoto correlated the data reasonably well under all test conditions.

  12. Elevated temperature crack propagation

    SciTech Connect

    Orange, T.W.

    1994-02-01

    This paper is a summary of two NASA contracts on high temperature fatigue crack propagation in metals. The first evaluated the ability of fairly simple nonlinear fracture parameters to correlate crack propagation. Hastelloy-X specimens were tested under isothermal and thermomechanical cycling at temperatures up to 980 degrees C (1800 degrees F). The most successful correlating parameter was the crack tip opening displacement derived from the J-integral. The second evaluated the ability of several path-independent integrals to correlate crack propagation behavior. Inconel 718 specimens were tested under isothermal, thermomechanical, temperature gradient, and creep conditions at temperatures up to 650 degrees C (1200 degrees F). The integrals formulated by Blackburn and by Kishimoto correlated the data reasonably well under all test conditions.

  13. Improving image segmentation by learning region affinities

    SciTech Connect

    Prasad, Lakshman; Yang, Xingwei; Latecki, Longin J

    2010-11-03

    We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

  14. Turbofan Duct Propagation Model

    NASA Technical Reports Server (NTRS)

    Lan, Justin H.; Posey, Joe W. (Technical Monitor)

    2001-01-01

    The CDUCT code utilizes a parabolic approximation to the convected Helmholtz equation in order to efficiently model acoustic propagation in acoustically treated, complex shaped ducts. The parabolic approximation solves one-way wave propagation with a marching method which neglects backwards reflected waves. The derivation of the parabolic approximation is presented. Several code validation cases are given. An acoustic lining design process for an example aft fan duct is discussed. It is noted that the method can efficiently model realistic three-dimension effects, acoustic lining, and flow within the computational capabilities of a typical computer workstation.

  15. Delimiting affinity zones as a basis for air pollution mapping in Europe.

    PubMed

    Vienneau, Danielle; Briggs, David J

    2013-01-01

    Affinity zones are defined as areas within which air quality displays consistent behaviour over space and time. Constructed using multivariate statistical techniques and physiographic and landscape variables reflecting underlying sources and spatial patterns of air pollution, affinity zones provide a spatial structure suited to exploring the representativity of monitoring networks and as a basis for air pollution mapping and exposure assessment. The affinity zone method is demonstrated using European air pollution monitoring sites, and environmental data compiled within a 1 km GIS. Organised into three main stages, this method involves: (i) indicator selection, using principal components analysis, (ii) zonation by cluster analysis to classify areas into distinct types, and (iii) site allocation, to confirm similarity within affinity zones in terms of monitored air pollution concentrations. Ten interpretable and coherent air pollution affinity zones were constructed for Europe, including two rural zones and eight related to different types of densely populated and built up environments. Concentrations between affinity zones differed significantly for NO(2) background and traffic sites and for PM(10) traffic sites only. Not all zones, however, were found to be sufficiently represented by monitoring sites, illustrating the importance of affinity zones in identifying deficiencies in monitoring networks. Spatial modelling within affinity zones is also demonstrated, showing that simple kriging of background NO(2) concentrations within zones (compared to kriging ignoring zones) produced a ca. 22% reduction in errors and increased R(2) by 0.25 at reserved validation monitoring sites. The affinity zone method developed here is a robust, statistical approach that can be used for evaluating the representativity of routine monitoring networks often used in continental level environmental and health risk assessments.

  16. Rac recruits high-affinity integrin alphavbeta3 to lamellipodia in endothelial cell migration.

    PubMed

    Kiosses, W B; Shattil, S J; Pampori, N; Schwartz, M A

    2001-03-01

    Integrin alphavbeta3 has an important role in the proliferation, survival, invasion and migration of vascular endothelial cells. Like other integrins, alphavbeta3 can exist in different functional states with respect to ligand binding. These changes involve both affinity modulation, by which conformational changes in the integrin heterodimer govern affinity for individual extracellular matrix proteins, and avidity modulation, by which changes in lateral mobility and integrin clustering affect the binding of cells to multivalent matrices. Here we have used an engineered monoclonal antibody Fab (antigen-binding fragment) named WOW-1, which binds to activated integrins alphavbeta3 and alphavbeta5 from several species, to investigate the role of alphavbeta3 activation in endothelial cell behaviour. Because WOW-1 is monovalent, it is insensitive to changes in integrin clustering and therefore reports only changes in affinity. WOW-1 contains an RGD tract in its variable region and binds only to unoccupied, high-affinity integrins. By using WOW-1, we have identified the selective recruitment of high-affinity integrins as a mechanism by which lamellipodia promote formation of new adhesions at the leading edge in cell migration.

  17. DROMO propagator revisited

    NASA Astrophysics Data System (ADS)

    Urrutxua, Hodei; Sanjurjo-Rivo, Manuel; Peláez, Jesús

    2016-01-01

    In the year 2000 an in-house orbital propagator called DROMO (Peláez et al. in Celest Mech Dyn Astron 97:131-150, 2007. doi: 10.1007/s10569-006-9056-3) was developed by the Space Dynamics Group of the Technical University of Madrid, based in a set of redundant variables including Euler-Rodrigues parameters. An original deduction of the DROMO propagator is carried out, underlining its close relation with the ideal frame concept introduced by Hansen (Abh der Math-Phys Cl der Kon Sachs Ges der Wissensch 5:41-218, 1857). Based on the very same concept, Deprit (J Res Natl Bur Stand Sect B Math Sci 79B(1-2):1-15, 1975) proposed a formulation for orbit propagation. In this paper, similarities and differences with the theory carried out by Deprit are analyzed. Simultaneously, some improvements are introduced in the formulation, that lead to a more synthetic and better performing propagator. Also, the long-term effect of the oblateness of the primary is studied in terms of DROMO variables, and new numerical results are presented to evaluate the performance of the method.

  18. PROPER: Optical propagation routines

    NASA Astrophysics Data System (ADS)

    Krist, John E.

    2014-05-01

    PROPER simulates the propagation of light through an optical system using Fourier transform algorithms (Fresnel, angular spectrum methods). Distributed as IDL source code, it includes routines to create complex apertures, aberrated wavefronts, and deformable mirrors. It is especially useful for the simulation of high contrast imaging telescopes (extrasolar planet imagers like TPF).

  19. GRC RF Propagation Studies

    NASA Technical Reports Server (NTRS)

    Nessel, James

    2013-01-01

    NASA Glenn Research Center has been involved in the characterization of atmospheric effects on space communications links operating at Ka-band and above for the past 20 years. This presentation reports out on the most recent activities of propagation characterization that NASA is currently involved in.

  20. The Cutting Edge of Affinity Electrophoresis Technology

    PubMed Central

    Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

    2015-01-01

    Affinity electrophoresis is an important technique that is widely used to separate and analyze biomolecules in the fields of biology and medicine. Both quantitative and qualitative information can be gained through affinity electrophoresis. Affinity electrophoresis can be applied through a variety of strategies, such as mobility shift electrophoresis, charge shift electrophoresis or capillary affinity electrophoresis. These strategies are based on changes in the electrophoretic patterns of biological macromolecules that result from interactions or complex-formation processes that induce changes in the size or total charge of the molecules. Nucleic acid fragments can be characterized through their affinity to other molecules, for example transcriptional factor proteins. Hydrophobic membrane proteins can be identified by means of a shift in the mobility induced by a charged detergent. The various strategies have also been used in the estimation of association/disassociation constants. Some of these strategies have similarities to affinity chromatography, in that they use a probe or ligand immobilized on a supported matrix for electrophoresis. Such methods have recently contributed to profiling of major posttranslational modifications of proteins, such as glycosylation or phosphorylation. Here, we describe advances in analytical techniques involving affinity electrophoresis that have appeared during the last five years. PMID:28248262

  1. An Empirical Approach to Logical Clustering of Software Failure Regions

    DTIC Science & Technology

    1994-03-01

    that study was quite preliminary and local in its investigation. This thesis examines clustering from two other perspectives, taxonomical (type of...clustering was cross-examined across the perspectives. The results show that the studied failure regions have a strong tendency to form taxonornical...propagation of the fault (structural clustering). However, that study was quite preliminary and local in its investigation. This thesis examines clustering

  2. Approximate Bruechner orbitals in electron propagator calculations

    SciTech Connect

    Ortiz, J.V.

    1999-12-01

    Orbitals and ground-state correlation amplitudes from the so-called Brueckner doubles approximation of coupled-cluster theory provide a useful reference state for electron propagator calculations. An operator manifold with hold, particle, two-hole-one-particle and two-particle-one-hole components is chosen. The resulting approximation, third-order algebraic diagrammatic construction [2ph-TDA, ADC (3)] and 3+ methods. The enhanced versatility of this approximation is demonstrated through calculations on valence ionization energies, core ionization energies, electron detachment energies of anions, and on a molecule with partial biradical character, ozone.

  3. A Database for Propagation Models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Rucker, James

    1997-01-01

    The Propagation Models Database is designed to allow the scientists and experimenters in the propagation field to process their data through many known and accepted propagation models. The database is an Excel 5.0 based software that houses user-callable propagation models of propagation phenomena. It does not contain a database of propagation data generated out of the experiments. The database not only provides a powerful software tool to process the data generated by the experiments, but is also a time- and energy-saving tool for plotting results, generating tables and producing impressive and crisp hard copy for presentation and filing.

  4. Reaction of anionic and cationic silicon clusters with tungsten hexafluoride studied by fourier transform ion cyclotron resonance mass spectrometry

    NASA Astrophysics Data System (ADS)

    Reents, W. D., Jr.; Mandich, M. L.; Bondybey, V. E.

    1986-10-01

    Anionic and cationic silicon clusters react exothermically with WF 6 to give a variety of tungsten and silicon fluorides. All the silicon anionic clusters transfer their charge to WF 6. The electron affinities of Si 2-6 are estimated to be less than the electron affinity of WF 6 (350 kJ/mole (3.6 eV)).

  5. Propagating Instabilities in Solids

    NASA Astrophysics Data System (ADS)

    Kyriakides, Stelios

    1998-03-01

    Instability is one of the factors which limit the extent to which solids can be loaded or deformed and plays a pivotal role in the design of many structures. Such instabilities often result in localized deformation which precipitates catastrophic failure. Some materials have the capacity to recover their stiffness following a certain amount of localized deformation. This local recovery in stiffness arrests further local deformation and spreading of the instability to neighboring material becomes preferred. Under displacement controlled loading the propagation of the transition fronts can be achieved in a steady-state manner at a constant stress level known as the propagation stress. The stresses in the transition fronts joining the highly deformed zone to the intact material overcome the instability nucleation stresses and, as a result, the propagation stress is usually much lower than the stress required to nucleate the instability. The classical example of this class of material instabilities is L/"uders bands which tend to affect mild steels and other metals. Recent work has demonstrated that propagating instabilities occur in several other materials. Experimental and analytical results from four examples will be used to illustrate this point: First the evolution of L=FCders bands in mild steel strips will be revisited. The second example involves the evolution of stress induced phase transformations (austenite to martensite phases and the reverse) in a shape memory alloy under displacement controlled stretching. The third example is the crushing behavior of cellular materials such as honeycombs and foams made from metals and polymers. The fourth example involves the axial broadening/propagation of kink bands in aligned fiber/matrix composites under compression. The microstructure and, as a result, the micromechanisms governing the onset, localization, local arrest and propagation of instabilities in each of the four materials are vastly different. Despite this

  6. Visualizing Antibody Affinity Maturation in Germinal Centers

    PubMed Central

    Tas, Jeroen M.J.; Mesin, Luka; Pasqual, Giulia; Targ, Sasha; Jacobsen, Johanne T.; Mano, Yasuko M.; Chen, Casie S.; Weill, Jean-Claude; Reynaud, Claude-Agnès; Browne, Edward P.; Meyer-Hermann, Michael; Victora, Gabriel D.

    2016-01-01

    Antibodies somatically mutate to attain high affinity in germinal centers (GCs). There, competition between B cell clones and among somatic mutants of each clone drives an increase in average affinity across the population. The extent to which higher-affinity cells eliminating competitors restricts clonal diversity is unknown. By combining multiphoton microscopy and sequencing, we show that tens to hundreds of distinct B cell clones seed each GC, and that GCs lose clonal diversity at widely disparate rates. Furthermore, efficient affinity maturation can occur in the absence of homogenizing selection, ensuring that many clones can mature in parallel within the same GC. Our findings have implications for development of vaccines in which antibodies with non-immunodominant specificities must be elicited, as is the case for HIV-1 and influenza. PMID:26912368

  7. PRINCIPLES OF AFFINITY-BASED BIOSENSORS

    EPA Science Inventory

    Despite the amount of resources that have been invested by national and international academic, government, and commercial sectors to develop affinity-based biosensor products, little obvious success has been realized through commercialization of these devices for specific applic...

  8. Protein purification using PDZ affinity chromatography.

    PubMed

    Walkup, Ward G; Kennedy, Mary B

    2015-04-01

    PDZ domains function in nature as protein-binding domains within scaffold and membrane-associated proteins. They comprise approximately 90 residues and undergo specific, high-affinity interactions with complementary C-terminal peptide sequences, other PDZ domains, and/or phospholipids. We have previously shown that the specific, strong interactions of PDZ domains with their ligands make them well suited for use in affinity chromatography. This unit provides protocols for the PDZ affinity chromatography procedure that are applicable for the purification of proteins that contain PDZ domains or PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We detail the preparation of affinity resins composed of PDZ domains or PDZ domain peptide ligands coupled to solid supports. These resins can be used to purify proteins containing endogenous or genetically introduced PDZ domains or ligands, eluting the proteins with free PDZ domain peptide ligands.

  9. Quintuplet Cluster

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Penetrating 25,000 light-years of obscuring dust and myriad stars, NASA's Hubble Space Telescope has provided the clearest view yet of one of the largest young clusters of stars inside our Milky Way galaxy, located less than 100 light-years from the very center of the Galaxy. Having the equivalent mass greater than 10,000 stars like our sun, the monster cluster is ten times larger than typical young star clusters scattered throughout our Milky Way. It is destined to be ripped apart in just a few million years by gravitational tidal forces in the galaxy's core. But in its brief lifetime it shines more brightly than any other star cluster in the Galaxy. Quintuplet Cluster is 4 million years old. It has stars on the verge of blowing up as supernovae. It is the home of the brightest star seen in the galaxy, called the Pistol star. This image was taken in infrared light by Hubble's NICMOS camera in September 1997. The false colors correspond to infrared wavelengths. The galactic center stars are white, the red stars are enshrouded in dust or behind dust, and the blue stars are foreground stars between us and the Milky Way's center. The cluster is hidden from direct view behind black dust clouds in the constellation Sagittarius. If the cluster could be seen from earth it would appear to the naked eye as a 3rd magnitude star, 1/6th of a full moon's diameter apart.

  10. Affinity Electrophoresis Using Ligands Attached To Polymers

    NASA Technical Reports Server (NTRS)

    Van Alstine, James M.; Snyder, Robert S.; Harris, J. M.; Brooks, D. E.

    1990-01-01

    In new technique, reduction of electrophoretic mobilities by addition of polyethylene glycol to ligands increases electrophoretic separabilities. In immuno-affinity electrophoresis, modification of ligands extends specificity of electrophoretic separation to particles having surface electric-charge structures otherwise making them electrophoretically inseparable. Modification of antibodies by polyethylene glycol greatly reduces ability to aggregate while enhancing ability to affect electrophoretic mobilities of cells. In hydrophobic-affinity electrophoresis, addition of polyethylene glycol reduces tendency toward aggregation of cells or macromolecules.

  11. Atmospheric sound propagation

    NASA Technical Reports Server (NTRS)

    Cook, R. K.

    1969-01-01

    The propagation of sound waves at infrasonic frequencies (oscillation periods 1.0 - 1000 seconds) in the atmosphere is being studied by a network of seven stations separated geographically by distances of the order of thousands of kilometers. The stations measure the following characteristics of infrasonic waves: (1) the amplitude and waveform of the incident sound pressure, (2) the direction of propagation of the wave, (3) the horizontal phase velocity, and (4) the distribution of sound wave energy at various frequencies of oscillation. Some infrasonic sources which were identified and studied include the aurora borealis, tornadoes, volcanos, gravity waves on the oceans, earthquakes, and atmospheric instability waves caused by winds at the tropopause. Waves of unknown origin seem to radiate from several geographical locations, including one in the Argentine.

  12. Florida's propagation report

    NASA Technical Reports Server (NTRS)

    Helmken, Henry; Henning, Rudolf

    1994-01-01

    One of the key goals of the Florida Center is to obtain a maximum of useful information on propagation behavior unique to its subtropical weather and subtropical climate. Such weather data is of particular interest when it is (or has the potential to become) useful for developing and implementing techniques to compensate for adverse weather effects. Also discussed are data observations, current challenges, CDF's, sun movement, and diversity experiments.

  13. Transionospheric Propagation Code (TIPC)

    SciTech Connect

    Roussel-Dupre, R.; Kelley, T.A.

    1990-10-01

    The Transionospheric Propagation Code is a computer program developed at Los Alamos National Lab to perform certain tasks related to the detection of vhf signals following propagation through the ionosphere. The code is written in Fortran 77, runs interactively and was designed to be as machine independent as possible. A menu format in which the user is prompted to supply appropriate parameters for a given task has been adopted for the input while the output is primarily in the form of graphics. The user has the option of selecting from five basic tasks, namely transionospheric propagation, signal filtering, signal processing, DTOA study, and DTOA uncertainty study. For the first task a specified signal is convolved against the impulse response function of the ionosphere to obtain the transionospheric signal. The user is given a choice of four analytic forms for the input pulse or of supplying a tabular form. The option of adding Gaussian-distributed white noise of spectral noise to the input signal is also provided. The deterministic ionosphere is characterized to first order in terms of a total electron content (TEC) along the propagation path. In addition, a scattering model parameterized in terms of a frequency coherence bandwidth is also available. In the second task, detection is simulated by convolving a given filter response against the transionospheric signal. The user is given a choice of a wideband filter or a narrowband Gaussian filter. It is also possible to input a filter response. The third task provides for quadrature detection, envelope detection, and three different techniques for time-tagging the arrival of the transionospheric signal at specified receivers. The latter algorithms can be used to determine a TEC and thus take out the effects of the ionosphere to first order. Task four allows the user to construct a table of delta-times-of-arrival (DTOAs) vs TECs for a specified pair of receivers.

  14. Nonlinear Wave Propagation

    DTIC Science & Technology

    2009-02-09

    of parameters. Hence one expects that the solutions of the two equations , PES and NLS, are comparable. In Fig. 3 we plot the two solutions for...power saturated term, in the PES equation ) have stable soliton solutions or mode-locking evolution. In general the solitons are found to be unstable...literature. Generally speaking, the above lattice equations omitting nonlinear terms have solutions propagating along z direction, i.e., ψ(r, z) = e−iµzϕ(r

  15. Olympus propagation experiments

    NASA Technical Reports Server (NTRS)

    Arbesser-Rastburg, Bertram

    1994-01-01

    A summary of the activities of the OPEX (Olympus Propagation EXperimenters) group is given and some of the recent findings are presented. OLYMPUS, a telecommunication satellite owned by the European Space Agency, was launched on 12 June 1989. After the in-orbit tests were completed (in September 1989) the first propagation experiments started. Throughout 1990 the spacecraft functioned very well and a large number of experimenters received the beacon signals. On 29 May 1991 the spacecraft became inoperational after a major technical problem. With a series of complicated procedures OLYMPUS was recovered on 15 August 1991 - the first time in history that a civilian telecommunications satellite was brought back to service after losing power and telemetry. The propagation experiments were back on track. However, the recovery had used up so much fuel that the North-South station keeping had to be abandoned, which led to a natural increase of inclination at a rate of about 0.8 deg per year. On 10 October 1992 the second 30 GHz beacon tube failed, causing a loss of this beacon signal. The other two beacon frequencies continued to deliver a stable signal for more than two years. On 12 August 1993 the spacecraft experienced another problem with the altitude control, but this time there was not enough fuel left for a recovery maneuver and thus the mission came to an end.

  16. Spitzer Clusters

    NASA Astrophysics Data System (ADS)

    Krick, Kessica

    This proposal is a specific response to the strategic goal of NASA's research program to "discover how the universe works and explore how the universe evolved into its present form." Towards this goal, we propose to mine the Spitzer archive for all observations of galaxy groups and clusters for the purpose of studying galaxy evolution in clusters, contamination rates for Sunyaev Zeldovich cluster surveys, and to provide a database of Spitzer observed clusters to the broader community. Funding from this proposal will go towards two years of support for a Postdoc to do this work. After searching the Spitzer Heritage Archive, we have found 194 unique galaxy groups and clusters that have data from both the Infrared array camera (IRAC; Fazio et al. 2004) at 3.6 - 8 microns and the multiband imaging photometer for Spitzer (MIPS; Rieke et al. 2004) at 24microns. This large sample will add value beyond the individual datasets because it will be a larger sample of IR clusters than ever before and will have sufficient diversity in mass, redshift, and dynamical state to allow us to differentiate amongst the effects of these cluster properties. An infrared sample is important because it is unaffected by dust extinction while at the same time is an excellent measure of both stellar mass (IRAC wavelengths) and star formation rate (MIPS wavelengths). Additionally, IRAC can be used to differentiate star forming galaxies (SFG) from active galactic nuclei (AGN), due to their different spectral shapes in this wavelength regime. Specifically, we intend to identify SFG and AGN in galaxy groups and clusters. Groups and clusters differ from the field because the galaxy densities are higher, there is a large potential well due mainly to the mass of the dark matter, and there is hot X-ray gas (the intracluster medium; ICM). We will examine the impact of these differences in environment on galaxy formation by comparing cluster properties of AGN and SFG to those in the field. Also, we will

  17. Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Miller, Christopher J. Miller

    2012-03-01

    There are many examples of clustering in astronomy. Stars in our own galaxy are often seen as being gravitationally bound into tight globular or open clusters. The Solar System's Trojan asteroids cluster at the gravitational Langrangian in front of Jupiter’s orbit. On the largest of scales, we find gravitationally bound clusters of galaxies, the Virgo cluster (in the constellation of Virgo at a distance of ˜50 million light years) being a prime nearby example. The Virgo cluster subtends an angle of nearly 8◦ on the sky and is known to contain over a thousand member galaxies. Galaxy clusters play an important role in our understanding of theUniverse. Clusters exist at peaks in the three-dimensional large-scale matter density field. Their sky (2D) locations are easy to detect in astronomical imaging data and their mean galaxy redshifts (redshift is related to the third spatial dimension: distance) are often better (spectroscopically) and cheaper (photometrically) when compared with the entire galaxy population in large sky surveys. Photometric redshift (z) [Photometric techniques use the broad band filter magnitudes of a galaxy to estimate the redshift. Spectroscopic techniques use the galaxy spectra and emission/absorption line features to measure the redshift] determinations of galaxies within clusters are accurate to better than delta_z = 0.05 [7] and when studied as a cluster population, the central galaxies form a line in color-magnitude space (called the the E/S0 ridgeline and visible in Figure 16.3) that contains galaxies with similar stellar populations [15]. The shape of this E/S0 ridgeline enables astronomers to measure the cluster redshift to within delta_z = 0.01 [23]. The most accurate cluster redshift determinations come from spectroscopy of the member galaxies, where only a fraction of the members need to be spectroscopically observed [25,42] to get an accurate redshift to the whole system. If light traces mass in the Universe, then the locations

  18. Self-affine crossover length in a layered silicate deposit.

    PubMed

    Fossum, J O; Bergene, H H; Hansen, Alex; O'Rourke, B; Manificat, G

    2004-03-01

    Self-affine dehydrated colloidal deposits on fresh mica surfaces of the synthetic layered silicate 2:1 smectite clay laponite have been studied by means of atomic force microscopy (AFM). AFM images of these prepared assemblies of sol and gel aggregates have been analyzed both by means of standard AFM Fourier software and a wavelet method. The deposited surfaces show a persistence to antipersistent crossover with a clay concentration dependent crossover length. It is concluded that the crossover length is associated with aggregate size, and further that the persistent roughness at small length scales signals near compact clusters of fractal dimension three, whereas the antipersistent roughness at large length scales signals a sedimentation process.

  19. Self-affine crossover length in a layered silicate deposit

    NASA Astrophysics Data System (ADS)

    Fossum, J. O.; Bergene, H. H.; Hansen, Alex; O'Rourke, B.; Manificat, G.

    2004-03-01

    Self-affine dehydrated colloidal deposits on fresh mica surfaces of the synthetic layered silicate 2:1 smectite clay laponite have been studied by means of atomic force microscopy (AFM). AFM images of these prepared assemblies of sol and gel aggregates have been analyzed both by means of standard AFM Fourier software and a wavelet method. The deposited surfaces show a persistence to antipersistent crossover with a clay concentration dependent crossover length. It is concluded that the crossover length is associated with aggregate size, and further that the persistent roughness at small length scales signals near compact clusters of fractal dimension three, whereas the antipersistent roughness at large length scales signals a sedimentation process.

  20. Star clusters

    NASA Astrophysics Data System (ADS)

    Labhardt, Lukas; Binggeli, Bruno

    Star clusters are at the heart of astronomy, being key objects for our understanding of stellar evolution and galactic structure. Observations with the Hubble Space Telescope and other modern equipment have revealed fascinating new facts about these galactic building blocks. This book provides two comprehensive and up-to-date, pedagogically designed reviews on star clusters by two well-known experts in the field. Bruce Carney presents our current knowledge of the relative and absolute ages of globular clusters and the chemical history of our Galaxy. Bill Harris addresses globular clusters in external galaxies and their use as tracers of galaxy formation and cosmic distance indicators. The book is written for graduate students as well as professionals in astronomy and astrophysics.

  1. Occupational Clusters.

    ERIC Educational Resources Information Center

    Pottawattamie County School System, Council Bluffs, IA.

    The 15 occupational clusters (transportation, fine arts and humanities, communications and media, personal service occupations, construction, hospitality and recreation, health occupations, marine science occupations, consumer and homemaking-related occupations, agribusiness and natural resources, environment, public service, business and office…

  2. Cluster generator

    DOEpatents

    Donchev, Todor I.; Petrov, Ivan G.

    2011-05-31

    Described herein is an apparatus and a method for producing atom clusters based on a gas discharge within a hollow cathode. The hollow cathode includes one or more walls. The one or more walls define a sputtering chamber within the hollow cathode and include a material to be sputtered. A hollow anode is positioned at an end of the sputtering chamber, and atom clusters are formed when a gas discharge is generated between the hollow anode and the hollow cathode.

  3. Gas-phase nitronium ion affinities.

    PubMed Central

    Cacace, F; de Petris, G; Pepi, F; Angelelli, F

    1995-01-01

    Evaluation of nitronium ion-transfer equilibria, L1NO2+ + L2 = L2NO2+ + L1 (where L1 and L2 are ligands 1 and 2, respectively) by Fourier-transform ion cyclotron resonance mass spectrometry and application of the kinetic method, based on the metastable fragmentation of L1(NO2+)L2 nitronium ion-bound dimers led to a scale of relative gas-phase nitronium ion affinities. This scale, calibrated to a recent literature value for the NO2+ affinity of water, led for 18 ligands, including methanol, ammonia, representative ketones, nitriles, and nitroalkanes, to absolute NO2+ affinities, that fit a reasonably linear general correlation when plotted vs. the corresponding proton affinities (PAs). The slope of the plot depends to a certain extent on the specific nature of the ligands and, hence, the correlations between the NO2+ affinities, and the PAs of a given class of compounds display a better linearity than the general correlation and may afford a useful tool for predicting the NO2+ affinity of a molecule based on its PA. The NO2+ binding energies are considerably lower than the corresponding PAs and well below the binding energies of related polyatomic cations, such as NO+, a trend consistent with the available theoretical results on the structure and the stability of simple NO2+ complexes. The present study reports an example of extension of the kinetic method to dimers, such as L1(NO2+)L2, bound by polyatomic ions, which may considerably widen its scope. Finally, measurement of the NO2+ affinity of ammonia allowed evaluation of the otherwise inaccessible PA of the amino group of nitramide and, hence, direct experimental verification of previous theoretical estimates. PMID:11607578

  4. Characterization of the Chemokine CXCL11-Heparin Interaction Suggests Two Different Affinities for Glycosaminoglycans*

    PubMed Central

    Severin, India C.; Gaudry, Jean-Philippe; Johnson, Zoë; Kungl, Andreas; Jansma, Ariane; Gesslbauer, Bernd; Mulloy, Barbara; Power, Christine; Proudfoot, Amanda E. I.; Handel, Tracy

    2010-01-01

    Chemokines orchestrate the migration of leukocytes in the context of homeostasis and inflammation. In addition to interactions of chemokines with receptors on migrating cells, these processes require interactions of chemokines with glycosaminoglycans (GAGs) for cell surface localization. Most chemokines are basic proteins with Arg/Lys/His residue clusters functioning as recognition epitopes for GAGs. In this study we characterized the GAG-binding epitopes of the chemokine I-TAC/CXCL11. Four separate clusters of basic residues were mutated to alanine and tested for their ability to bind to GAGs in vitro and to activate the receptor, CXCR3. Mutation of a set of basic residues in the C-terminal helix (the 50s cluster, 57KSKQAR62) along with Lys17, significantly impaired heparin binding in vitro, identifying these residues as components of the dominant epitope. However, this GAG mutant retained nearly wild type receptor binding affinity, and its ability to induce cell migration in vitro was only mildly perturbed. Nevertheless, the mutant was unable to induce cell migration in vivo, establishing a requirement of CXCL11 for GAG binding for in vivo function. These studies also led to some interesting findings. First, CXCL11 exhibits conformational heterogeneity, as evidenced by the doubling of peaks in its HSQC spectra. Second, it exhibits more than one affinity state for both heparin and CXCR3, which may be related to its structural plasticity. Finally, although the binding affinities of chemokines for GAGs are typically weaker than interactions with receptors, the high affinity GAG binding state of CXCL11 is comparable with typical receptor binding affinities, suggesting some unique properties of this chemokine. PMID:20363748

  5. Temporal scaling in information propagation

    NASA Astrophysics Data System (ADS)

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-01

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  6. Temporal scaling in information propagation.

    PubMed

    Huang, Junming; Li, Chao; Wang, Wen-Qiang; Shen, Hua-Wei; Li, Guojie; Cheng, Xue-Qi

    2014-06-18

    For the study of information propagation, one fundamental problem is uncovering universal laws governing the dynamics of information propagation. This problem, from the microscopic perspective, is formulated as estimating the propagation probability that a piece of information propagates from one individual to another. Such a propagation probability generally depends on two major classes of factors: the intrinsic attractiveness of information and the interactions between individuals. Despite the fact that the temporal effect of attractiveness is widely studied, temporal laws underlying individual interactions remain unclear, causing inaccurate prediction of information propagation on evolving social networks. In this report, we empirically study the dynamics of information propagation, using the dataset from a population-scale social media website. We discover a temporal scaling in information propagation: the probability a message propagates between two individuals decays with the length of time latency since their latest interaction, obeying a power-law rule. Leveraging the scaling law, we further propose a temporal model to estimate future propagation probabilities between individuals, reducing the error rate of information propagation prediction from 6.7% to 2.6% and improving viral marketing with 9.7% incremental customers.

  7. Crack propagation modeling using Peridynamic theory

    NASA Astrophysics Data System (ADS)

    Hafezi, M. H.; Alebrahim, R.; Kundu, T.

    2016-04-01

    Crack propagation and branching are modeled using nonlocal peridynamic theory. One major advantage of this nonlocal theory based analysis tool is the unifying approach towards material behavior modeling - irrespective of whether the crack is formed in the material or not. No separate damage law is needed for crack initiation and propagation. This theory overcomes the weaknesses of existing continuum mechanics based numerical tools (e.g. FEM, XFEM etc.) for identifying fracture modes and does not require any simplifying assumptions. Cracks grow autonomously and not necessarily along a prescribed path. However, in some special situations such as in case of ductile fracture, the damage evolution and failure depend on parameters characterizing the local stress state instead of peridynamic damage modeling technique developed for brittle fracture. For brittle fracture modeling the bond is simply broken when the failure criterion is satisfied. This simulation helps us to design more reliable modeling tool for crack propagation and branching in both brittle and ductile materials. Peridynamic analysis has been found to be very demanding computationally, particularly for real-world structures (e.g. vehicles, aircrafts, etc.). It also requires a very expensive visualization process. The goal of this paper is to bring awareness to researchers the impact of this cutting-edge simulation tool for a better understanding of the cracked material response. A computer code has been developed to implement the peridynamic theory based modeling tool for two-dimensional analysis. A good agreement between our predictions and previously published results is observed. Some interesting new results that have not been reported earlier by others are also obtained and presented in this paper. The final objective of this investigation is to increase the mechanics knowledge of self-similar and self-affine cracks.

  8. Stability of flavin semiquinones in the gas phase: the electron affinity, proton affinity, and hydrogen atom affinity of lumiflavin.

    PubMed

    Zhang, Tianlan; Papson, Kaitlin; Ochran, Richard; Ridge, Douglas P

    2013-11-07

    Examination of electron transfer and proton transfer reactions of lumiflavin and proton transfer reactions of the lumiflavin radical anion by Fourier transform ion cyclotron resonance mass spectrometry is described. From the equilibrium constant determined for electron transfer between 1,4-naphthoquinone and lumiflavin the electron affinity of lumiflavin is deduced to be 1.86 ± 0.1 eV. Measurements of the rate constants and efficiencies for proton transfer reactions indicate that the proton affinity of the lumiflavin radical anion is between that of difluoroacetate (331.0 kcal/mol) and p-formyl-phenoxide (333.0 kcal/mol). Combining the electron affinity of lumiflavin with the proton affinity of the lumiflavin radical anion gives a lumiflavin hydrogen atom affinity of 59.7 ± 2.2 kcal/mol. The ΔG298 deduced from these results for adding an H atom to gas phase lumiflavin, 52.1 ± 2.2 kcal/mol, is in good agreement with ΔG298 for adding an H atom to aqueous lumiflavin from electrochemical measurements in the literature, 51.0 kcal/mol, and that from M06-L density functional calculations in the literature, 51.2 kcal/mol, suggesting little, if any, solvent effect on the H atom addition. The proton affinity of lumiflavin deduced from the equilibrium constant for the proton transfer reaction between lumiflavin and 2-picoline is 227.3 ± 2.0 kcal mol(-1). Density functional theory calculations on isomers of protonated lumiflavin provide a basis for assigning the most probable site of protonation as position 1 on the isoalloxazine ring and for estimating the ionization potentials of lumiflavin neutral radicals.

  9. Ganglioside embedded in reconstituted lipoprotein binds cholera toxin with elevated affinity.

    PubMed

    Bricarello, Daniel A; Mills, Emily J; Petrlova, Jitka; Voss, John C; Parikh, Atul N

    2010-09-01

    The ability to exogenously present cell-surface receptors in high-affinity conformations in a synthetic system offers an opportunity to provide host cells with protection from pathogenic toxins. This strategy requires improvement of the synthetic receptor binding affinity against its native counterpart, particularly with polyvalent toxins where clustering of membrane receptors can hinder binding. Here we demonstrate that reconstituted lipoprotein, nanometer-sized discoidal lipid bilayers bounded by apolipoprotein and functionalized by incorporation of pathogen receptors, provides a means to enhance toxin-receptor binding through molecular-level control over the receptor microenvironment (specifically, its rigidity, composition, and heterogeneity). Using a Foerster Resonance Energy Transfer (FRET)-based assay, we found that reconstituted lipoprotein incorporating low concentrations of ganglioside monosialotetrahexosylganglioside (GM1) binds polymeric cholera toxin with significantly higher affinity than liposomes or supported lipid bilayers, most likely a result of the enhanced control over receptor clustering provided by the lipoprotein platform. Using wide-area epifluorescence, we found that this enhanced binding capacity can be effectively utilized to divert cholera toxin away from populations of healthy mammalian cells. In summary, we found that reconstitutions of high-density lipoprotein can be engineered to include specific pathogen receptors; that their pathogen binding affinity is altered, presumably due to attenuation of receptor aggregation; and that these assemblies are effective at protecting cells from biological toxins.

  10. Transport with Feynman propagators

    SciTech Connect

    White, R.H.

    1990-11-06

    Richard Feynman's formulation of quantum electrodynamics suggests a Monte Carlo algorithm for calculating wave propagation. We call this the Sum Over All Paths (SOAP) method. The method is applied to calculate diffraction by double slits of finite width and by a reflection grating. Calculations of reflection by plane and parabolic mirrors of finite aperture and from several figured surfaces are shown. An application to a one-dimensional scattering problem is discussed. A variation of SOAP can be applied to the diffusion equation. 2 refs., 8 figs.

  11. Beam Propagation Experimental Study.

    DTIC Science & Technology

    1982-03-01

    30- -40- -50 I 0 100 200 300 Time (ns) Figure 2. FX-100 diode voltage and current. The gas- insulated coax was charged to 4.2 MV in order to produce...limit the usable gradient. The voltage standoff capability will be further limited by electron bombardment of the insulators , which may lead to flashover ...the low-pressure window for stable propagation has been inferred from measurements of the time delay for the beam arrival at a given axial position. 8

  12. Proton Affinity Calculations with High Level Methods.

    PubMed

    Kolboe, Stein

    2014-08-12

    Proton affinities, stretching from small reference compounds, up to the methylbenzenes and naphthalene and anthracene, have been calculated with high accuracy computational methods, viz. W1BD, G4, G3B3, CBS-QB3, and M06-2X. Computed and the currently accepted reference proton affinities are generally in excellent accord, but there are deviations. The literature value for propene appears to be 6-7 kJ/mol too high. Reported proton affinities for the methylbenzenes seem 4-5 kJ/mol too high. G4 and G3 computations generally give results in good accord with the high level W1BD. Proton affinity values computed with the CBS-QB3 scheme are too low, and the error increases with increasing molecule size, reaching nearly 10 kJ/mol for the xylenes. The functional M06-2X fails markedly for some of the small reference compounds, in particular, for CO and ketene, but calculates methylbenzene proton affinities with high accuracy.

  13. Collective thermoregulation in bee clusters.

    PubMed

    Ocko, Samuel A; Mahadevan, L

    2014-02-06

    Swarming is an essential part of honeybee behaviour, wherein thousands of bees cling onto each other to form a dense cluster that may be exposed to the environment for several days. This cluster has the ability to maintain its core temperature actively without a central controller. We suggest that the swarm cluster is akin to an active porous structure whose functional requirement is to adjust to outside conditions by varying its porosity to control its core temperature. Using a continuum model that takes the form of a set of advection-diffusion equations for heat transfer in a mobile porous medium, we show that the equalization of an effective 'behavioural pressure', which propagates information about the ambient temperature through variations in density, leads to effective thermoregulation. Our model extends and generalizes previous models by focusing the question of mechanism on the form and role of the behavioural pressure, and allows us to explain the vertical asymmetry of the cluster (as a consequence of buoyancy-driven flows), the ability of the cluster to overpack at low ambient temperatures without breaking up at high ambient temperatures, and the relative insensitivity to large variations in the ambient temperature. Our theory also makes testable hypotheses for the response of the cluster to external temperature inhomogeneities and suggests strategies for biomimetic thermoregulation.

  14. Identity, Affinity, Reality: Making the Case for Affinity Groups in Elementary School

    ERIC Educational Resources Information Center

    Parsons, Julie; Ridley, Kimberly

    2012-01-01

    Affinity groups are places where students build connections and process "ouch" moments from their classes. Children talk about the isolation they sometimes feel. The relationships students gain through race-based affinity groups enable them to feel less alone with their emotions and help them build a stronger sense of self. At the same…

  15. Stepparents' Affinity-Seeking and Affinity-Maintaining Strategies with Stepchildren.

    ERIC Educational Resources Information Center

    Ganong, Lawrence; Coleman, Marilyn; Fine, Mark; Martin, Patricia

    1999-01-01

    Examines the strategies that stepparents use to develop and maintain affinity with stepchildren and the effects that these strategies have on the development of stepparent-stepchildren relationships. Thirty-one affinity-seeking strategies are identified. Results show that dyadic activities worked best, but it is important that stepchildren…

  16. Desertification by front propagation?

    PubMed

    Zelnik, Yuval R; Uecker, Hannes; Feudel, Ulrike; Meron, Ehud

    2017-04-07

    Understanding how desertification takes place in different ecosystems is an important step in attempting to forecast and prevent such transitions. Dryland ecosystems often exhibit patchy vegetation, which has been shown to be an important factor on the possible regime shifts that occur in arid regions in several model studies. In particular, both gradual shifts that occur by front propagation, and abrupt shifts where patches of vegetation vanish at once, are a possibility in dryland ecosystems due to their emergent spatial heterogeneity. However, recent theoretical work has suggested that the final step of desertification - the transition from spotted vegetation to bare soil - occurs only as an abrupt shift, but the generality of this result, and its underlying origin, remain unclear. We investigate two models that detail the dynamics of dryland vegetation using a markedly different functional structure, and find that in both models the final step of desertification can only be abrupt. Using a careful numerical analysis, we show that this behavior is associated with the disappearance of confined spot-pattern domains as stationary states, and identify the mathematical origin of this behavior. Our findings show that a gradual desertification to bare soil due to a front propagation process can not occur in these and similar models, and opens the question of whether these dynamics can take place in nature.

  17. Bolt beam propagation analysis

    NASA Astrophysics Data System (ADS)

    Shokair, I. R.

    BOLT (Beam on Laser Technology) is a rocket experiment to demonstrate electron beam propagation on a laser ionized plasma channel across the geomagnetic field in the ion focused regime (IFR). The beam parameters for BOLT are: beam current I(sub b) = 100 Amps, beam energy of 1--1.5 MeV (gamma =3-4), and a Gaussian beam and channel of radii r(sub b) = r(sub c) = 1.5 cm. The N+1 ionization scheme is used to ionize atomic oxygen in the upper atmosphere. This scheme utilizes 130 nm light plus three IR lasers to excite and then ionize atomic oxygen. The limiting factor for the channel strength is the energy of the 130 nm laser, which is assumed to be 1.6 mJ for BOLT. At a fixed laser energy and altitude (fixing the density of atomic oxygen), the range can be varied by adjusting the laser tuning, resulting in a neutralization fraction axial profile of the form: f(z) = f(sub 0) e(exp minus z)/R, where R is the range. In this paper we consider the propagation of the BOLT beam and calculate the range of the electron beam taking into account the fact that the erosion rates (magnetic and inductive) vary with beam length as the beam and channel dynamically respond to sausage and hose instabilities.

  18. Affine coherent states and Toeplitz operators

    NASA Astrophysics Data System (ADS)

    Hutníková, Mária; Hutník, Ondrej

    2012-06-01

    We study a parameterized family of Toeplitz operators in the context of affine coherent states based on the Calderón reproducing formula (= resolution of unity on L_2( {R})) and the specific admissible wavelets (= affine coherent states in L_2( {R})) related to Laguerre functions. Symbols of such Calderón-Toeplitz operators as individual coordinates of the affine group (= upper half-plane with the hyperbolic geometry) are considered. In this case, a certain class of pseudo-differential operators, their properties and their operator algebras are investigated. As a result of this study, the Fredholm symbol algebras of the Calderón-Toeplitz operator algebras for these particular cases of symbols are described. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’.

  19. Non-affine elasticity in jammed systems

    NASA Astrophysics Data System (ADS)

    Maloney, Craig

    2006-03-01

    Symmetry dictates that perfect crystals should deform homogeneously, or affinely, under external load, and computing the elastic moduli from the underlying interaction potential is then straightforward. For disordered materials no such simple procedure exists, and recent numerical works have demonstrated that non-affine corrections can dramatically reduce the naive expectation for the shear modulus in a broad class of disordered systems and may control rigidity loss in the zero pressure limit in purely repulsive systems, i.e. the unjamming transition (c.f. [O'Hern et. al. PRE 68, 011306 (2003)]). We present numerical results and an analytical framework for the study of these non-affine corrections to the elastic response of disordered packings.

  20. Biomimetic affinity ligands for protein purification.

    PubMed

    Sousa, Isabel T; Taipa, M Angela

    2014-01-01

    The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins and are designated as "biomimetic ligands." A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogues of amino acids side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

  1. Use of Affinity Diagrams as Instructional Tools in Inclusive Classrooms.

    ERIC Educational Resources Information Center

    Haselden, Polly G.

    2003-01-01

    This article describes how the affinity diagram, a tool for gathering information and organizing it into natural groupings, can be used in inclusive classrooms. It discusses how students can be taught to use an affinity diagram, how affinity diagrams can be used to reflect many voices, and how affinity diagrams can be used to plan class projects.…

  2. Cation affinity numbers of Lewis bases.

    PubMed

    Lindner, Christoph; Tandon, Raman; Maryasin, Boris; Larionov, Evgeny; Zipse, Hendrik

    2012-01-01

    Using selected theoretical methods the affinity of a large range of Lewis bases towards model cations has been quantified. The range of model cations includes the methyl cation as the smallest carbon-centered electrophile, the benzhydryl and trityl cations as models for electrophilic substrates encountered in Lewis base-catalyzed synthetic procedures, and the acetyl cation as a substrate model for acyl-transfer reactions. Affinities towards these cationic electrophiles are complemented by data for Lewis-base addition to Michael acceptors as prototypical neutral electrophiles.

  3. New unitary affine-Virasoro constructions

    SciTech Connect

    Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M. ); Yamron, J.P. )

    1990-06-20

    This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g.

  4. On the electron affinity of B2

    SciTech Connect

    Glezakou, Vanda A.; Taylor, Peter

    2009-02-02

    We present the results of high-level ab initio calculations on the electron affinity of B2. Our new best estimate of 1.93±0.03 eV is in agreement with previous calculations as well as the sole existing experimental estimate of 1.8 eV, as derived from quantities with an uncertainty of 0.4 eV. The electron affinity of atomic boron, which is much smaller, is also calculated for comparison, and again found to be in good agreement with experiment. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  5. Negative Electron Affinity Mechanism for Diamond Surfaces

    NASA Technical Reports Server (NTRS)

    Krainsky, I. L.; Asnin, V. M.

    1998-01-01

    The energy distribution of the secondary electrons for chemical vacuum deposited diamond films with Negative Electron Affinity (NEA) was investigated. It was found that while for completely hydrogenated diamond surfaces the negative electron affinity peak in the energy spectrum of the secondary electrons is present for any energy of the primary electrons, for partially hydrogenated diamond surfaces there is a critical energy above which the peak is present in the spectrum. This critical energy increases sharply when hydrogen coverage of the diamond surface diminishes. This effect was explained by the change of the NEA from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surfaces.

  6. Evidence of multi-affinity in the Japanese stock market

    NASA Astrophysics Data System (ADS)

    Katsuragi, Hiroaki

    2000-04-01

    Fluctuations of the Japanese stock market (Tokyo Stock Price Index: TOPIX) are analyzed using a multi-affine analysis method. In the research to date, only some simulated self-affine models have shown multi-affinity. In most experiments using observations of self-affine fractal profiles, multi-affinity has not been found. However, we find evidence of multi-affinity in fluctuations of the Japanese stock market (TOPIX). The qth-order Hurst exponent Hq varies with changes in q. This multi-affinity indicates that there are plural mechanisms that affect the same time scale as stock market price fluctuation dynamics.

  7. ACTS propagation experiment discussion: Ka-band propagation measurements using the ACTS propagation terminal and the CSU-CHILL and Space Communications Technology Center Florida propagation program

    NASA Technical Reports Server (NTRS)

    Bringi, V. N.; Chandrasekar, V.; Mueller, Eugene A.; Turk, Joseph; Beaver, John; Helmken, Henry F.; Henning, Rudy

    1993-01-01

    Papers on Ka-band propagation measurements using the ACTS propagation terminal and the Colorado State University CHILL multiparameter radar and on Space Communications Technology Center Florida Propagation Program are discussed. Topics covered include: microwave radiative transfer and propagation models; NASA propagation terminal status; ACTS channel characteristics; FAU receive only terminal; FAU terminal status; and propagation testbed.

  8. Linear connections with a propagating spin-3 field in gravity

    SciTech Connect

    Baekler, Peter; Boulanger, Nicolas; Hehl, Friedrich W.

    2006-12-15

    We show that Fronsdal's Lagrangian for a free massless spin-3 gauge field in Minkowski spacetime is contained in a general Yang-Mills-like Lagrangian of metric-affine gravity (MAG), the gauge theory of the general affine group in the presence of a metric. Because of the geometric character of MAG, this can best be seen by using Vasiliev's frame formalism for higher-spin gauge fields in which the spin-3 frame is identified with the tracefree nonmetricity one-form associated with the shear generators of GL(n,R). Furthermore, for specific gravitational gauge models in the framework of full nonlinear MAG, exact solutions are constructed, featuring propagating massless and massive spin-3 fields.

  9. Direct Delta-MBPT(2) method for ionization potentials, electron affinities, and excitation energies using fractional occupation numbers

    SciTech Connect

    Beste, Ariana; Vazquez-Mayagoitia, Alvaro; Ortiz, J. Vincent

    2013-01-01

    A direct method (D-Delta-MBPT(2)) to calculate second-order ionization potentials (IPs), electron affinities (EAs), and excitation energies is developed. The Delta-MBPT(2) method is defined as the correlated extension of the Delta-HF method. Energy differences are obtained by integrating the energy derivative with respect to occupation numbers over the appropriate parameter range. This is made possible by writing the second-order energy as a function of the occupation numbers. Relaxation effects are fully included at the SCF level. This is in contrast to linear response theory, which makes the D-Delta-MBPT(2) applicable not only to single excited but also higher excited states. We show the relationship of the D-Delta-MBPT(2) method for IPs and EAs to a second-order approximation of the effective Fock-space coupled-cluster Hamiltonian and a second-order electron propagator method. We also discuss the connection between the D-Delta-MBPT(2) method for excitation energies and the CIS-MP2 method. Finally, as a proof of principle, we apply our method to calculate ionization potentials and excitation energies of some small molecules. For IPs, the Delta-MBPT(2) results compare well to the second-order solution of the Dyson equation. For excitation energies, the deviation from EOM-CCSD increases when correlation becomes more important. When using the numerical integration technique, we encounter difficulties that prevented us from reaching the Delta-MBPT(2) values. Most importantly, relaxation beyond the Hartree Fock level is significant and needs to be included in future research.

  10. Retroelements: propagation and adaptation.

    PubMed

    Hull, R; Covey, S N

    1995-01-01

    Retroelements are genetic entities that exist in both DNA and RNA forms generated by cyclic alternation of transcription and reverse transcription. They have in common a genetic core (the gag-pol core), encoding conserved functions of a structural protein and a replicase. These are supplemented with a variety of cis-acting nucleic acid sequences controlling transcription and reverse transcription. Most retroelements have additional genes with regulatory or adaptive roles, both within the cell and for movement between cells and organisms. These features reflect the variety of mechanisms that have developed to ensure propagation of the elements and their ability to adapt to specific niches in their hosts with which they co-evolve.

  11. Gauge engineering and propagators

    NASA Astrophysics Data System (ADS)

    Maas, Axel

    2017-03-01

    Beyond perturbation theory gauge-fixing becomes more involved due to the Gribov-Singer ambiguity: The appearance of additional gauge copies requires to define a procedure how to handle them. For the case of Landau gauge the structure and properties of these additional gauge copies will be investigated. Based on these properties gauge conditions are constructed to account for these gauge copies. The dependence of the propagators on the choice of these complete gauge-fixings will then be investigated using lattice gauge theory for Yang-Mills theory. It is found that the implications for the infrared, and to some extent mid-momentum behavior, can be substantial. In going beyond the Yang-Mills case it turns out that the influence of matter can generally not be neglected. This will be briefly discussed for various types of matter.

  12. ACTS mobile propagation campaign

    NASA Technical Reports Server (NTRS)

    Goldhirsh, Julius; Vogel, Wolfhard J.; Torrence, Geoffrey W.

    1994-01-01

    Preliminary results are presented for three propagation measurement campaigns involving a mobile receiving laboratory and 20 GHz transmissions from the Advanced Communications Technology Satellite (ACTS). Four 1994 campaigns were executed during weekly periods in and around Austin, Texas in February and May, in Central Maryland during March, and in Fairbanks, Alaska and environs in June. Measurements tested the following effects at 20 GHz: (1) attenuation due to roadside trees with and without foliage, (2) multipath effects for scenarios in which line-of-sight paths were unshadowed, (3) fades due to terrain and roadside obstacles, (4) fades due to structures in urban environs, (5) single tree attenuation, and (6) effects of fading at low elevation angles (8 deg in Fairbanks, Alaska) and high elevation angles (55 deg in Austin, Texas). Results presented here cover sampled measurements in Austin, Texas for foliage and non-foliage cases and in Central Maryland for non-foliage runs.

  13. Propagation Terminal Design and Measurements

    NASA Technical Reports Server (NTRS)

    Nessel, James

    2015-01-01

    The NASA propagation terminal has been designed and developed by the Glenn Research Center and is presently deployed at over 5 NASA and partner ground stations worldwide collecting information on the effects of the atmosphere on Ka-band and millimeter wave communications links. This lecture provides an overview of the fundamentals and requirements of the measurement of atmospheric propagation effects and, specifically, the types of hardware and digital signal processing techniques employed by current state-of-the-art propagation terminal systems.

  14. Interferometric Propagation Delay

    NASA Technical Reports Server (NTRS)

    Goldstein, Richard

    1999-01-01

    Radar interferometry based on (near) exact repeat passes has lately been used by many groups of scientists, worldwide, to achieve state of the art measurements of topography, glacier and ice stream motion, earthquake displacements, oil field subsidence, lava flows, crop-induced surface decorrelation, and other effects. Variations of tropospheric and ionospheric propagation delays limit the accuracy of all such measurements. We are investigating the extent of this limitation, using data from the Shuttle radar flight, SIR-C, which is sensitive to the troposphere, and the Earth Resources Satellites, ERS-1/2, which are sensitive to both the troposphere and the ionosphere. We are presently gathering statistics of the delay variations over selected, diverse areas to determine the best accuracy possible for repeat track interferometry. The phases of an interferogram depend on both the topography of the scene and variations in propagation delay. The delay variations can be caused by movement of elements in the scene, by changes in tropospheric water vapor and by changes of the charge concentrations in the ionosphere. We plan to separate these causes by using the data from a third satellite visit (three-pass interferometry). The figure gives the geometry of the three-pass observations. The page of the figure is taken to be perpendicular to the spacecraft orbits. The three observational locations are marked on the figure, giving baselines B-12 and B-13, separated by the angle alpha. These parameters are almost constant over the whole scene. However, each pixel has an individual look angle, theta, which is related to the topography, rho is the slant range. A possible spurious time delay is shown. Additional information is contained in the original.

  15. On modality and complexity of affine embeddings

    SciTech Connect

    Arzhantsev, I V

    2001-08-31

    Let G be a reductive algebraic group and let H be a reductive subgroup of G. The modality of a G-variety X is the largest number of the parameters in a continuous family of G-orbits in X. A precise formula for the maximum value of the modality over all affine embeddings of the homogeneous space G/H is obtained.

  16. Modern affinity reagents: Recombinant antibodies and aptamers.

    PubMed

    Groff, Katherine; Brown, Jeffrey; Clippinger, Amy J

    2015-12-01

    Affinity reagents are essential tools in both basic and applied research; however, there is a growing concern about the reproducibility of animal-derived monoclonal antibodies. The need for higher quality affinity reagents has prompted the development of methods that provide scientific, economic, and time-saving advantages and do not require the use of animals. This review describes two types of affinity reagents, recombinant antibodies and aptamers, which are non-animal technologies that can replace the use of animal-derived monoclonal antibodies. Recombinant antibodies are protein-based reagents, while aptamers are nucleic-acid-based. In light of the scientific advantages of these technologies, this review also discusses ways to gain momentum in the use of modern affinity reagents, including an update to the 1999 National Academy of Sciences monoclonal antibody production report and federal incentives for recombinant antibody and aptamer efforts. In the long-term, these efforts have the potential to improve the overall quality and decrease the cost of scientific research.

  17. Validation of affinity reagents using antigen microarrays.

    PubMed

    Sjöberg, Ronald; Sundberg, Mårten; Gundberg, Anna; Sivertsson, Asa; Schwenk, Jochen M; Uhlén, Mathias; Nilsson, Peter

    2012-06-15

    There is a need for standardised validation of affinity reagents to determine their binding selectivity and specificity. This is of particular importance for systematic efforts that aim to cover the human proteome with different types of binding reagents. One such international program is the SH2-consortium, which was formed to generate a complete set of renewable affinity reagents to the SH2-domain containing human proteins. Here, we describe a microarray strategy to validate various affinity reagents, such as recombinant single-chain antibodies, mouse monoclonal antibodies and antigen-purified polyclonal antibodies using a highly multiplexed approach. An SH2-specific antigen microarray was designed and generated, containing more than 6000 spots displayed by 14 identical subarrays each with 406 antigens, where 105 of them represented SH2-domain containing proteins. Approximately 400 different affinity reagents of various types were analysed on these antigen microarrays carrying antigens of different types. The microarrays revealed not only very detailed specificity profiles for all the binders, but also showed that overlapping target sequences of spotted antigens were detected by off-target interactions. The presented study illustrates the feasibility of using antigen microarrays for integrative, high-throughput validation of various types of binders and antigens.

  18. Stabilization of the Motion of Affine Systems

    NASA Astrophysics Data System (ADS)

    Babenko, E. A.; Martynyuk, A. A.

    2016-07-01

    Sufficient conditions for the stability of a nonlinear affine system subject to interval initial conditions are established. These conditions are based on new estimates of the norms of the solutions of the systems of perturbed equations of motion. This stabilization method is used to analyze an electromechanical system with permanent magnet

  19. Fan Affinity Laws from a Collision Model

    ERIC Educational Resources Information Center

    Bhattacharjee, Shayak

    2012-01-01

    The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour…

  20. Vygotsky's and Buber's Pedagogical Perspectives: Some Affinities

    ERIC Educational Resources Information Center

    Bartholo, Roberto; Tunes, Elizabeth; Tacca, Maria Carmen Villela Rosa

    2010-01-01

    The purpose of this paper is to examine the dialogical and creative character of pedagogic work by analyzing the affinities between Martin Buber's "I-Thou relation" and Lev Semenovich Vygotsky's "Zone of Proximal Development". Backed up by empirical studies on the teacher-student relation, we understand that education can only result in students'…

  1. A global/local affinity graph for image segmentation.

    PubMed

    Xiaofang Wang; Yuxing Tang; Masnou, Simon; Liming Chen

    2015-04-01

    Construction of a reliable graph capturing perceptual grouping cues of an image is fundamental for graph-cut based image segmentation methods. In this paper, we propose a novel sparse global/local affinity graph over superpixels of an input image to capture both short- and long-range grouping cues, and thereby enabling perceptual grouping laws, including proximity, similarity, continuity, and to enter in action through a suitable graph-cut algorithm. Moreover, we also evaluate three major visual features, namely, color, texture, and shape, for their effectiveness in perceptual segmentation and propose a simple graph fusion scheme to implement some recent findings from psychophysics, which suggest combining these visual features with different emphases for perceptual grouping. In particular, an input image is first oversegmented into superpixels at different scales. We postulate a gravitation law based on empirical observations and divide superpixels adaptively into small-, medium-, and large-sized sets. Global grouping is achieved using medium-sized superpixels through a sparse representation of superpixels' features by solving a ℓ0-minimization problem, and thereby enabling continuity or propagation of local smoothness over long-range connections. Small- and large-sized superpixels are then used to achieve local smoothness through an adjacent graph in a given feature space, and thus implementing perceptual laws, for example, similarity and proximity. Finally, a bipartite graph is also introduced to enable propagation of grouping cues between superpixels of different scales. Extensive experiments are carried out on the Berkeley segmentation database in comparison with several state-of-the-art graph constructions. The results show the effectiveness of the proposed approach, which outperforms state-of-the-art graphs using four different objective criteria, namely, the probabilistic rand index, the variation of information, the global consistency error, and the

  2. High-frequency affine mechanics and nonaffine relaxation in a model cytoskeleton.

    PubMed

    Head, David A; Ikebe, Emi; Nakamasu, Akiko; Zhang, Peijuan; Villaruz, Lara Gay; Kinoshita, Suguru; Ando, Shoji; Mizuno, Daisuke

    2014-04-01

    The cytoskeleton is a network of crosslinked, semiflexible filaments, and it has been suggested that it has properties of a glassy state. Here we employ optical-trap-based microrheology to apply forces to a model cytoskeleton and measure the high-bandwidth response at an anterior point. Simulating the highly nonlinear and anisotropic stress-strain propagation assuming affinity, we found that theoretical predictions for the quasistatic response of semiflexible polymers are only realized at high frequencies inaccessible to conventional rheometers. We give a theoretical basis for determining the frequency when both affinity and quasistaticity are valid, and we discuss with experimental evidence that the relaxations at lower frequencies can be characterized by the experimentally obtained nonaffinity parameter.

  3. Photoelectron spectroscopy of nitromethane anion clusters

    NASA Astrophysics Data System (ADS)

    Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

    2016-08-01

    Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

  4. Cluster bulleticity

    NASA Astrophysics Data System (ADS)

    Massey, Richard; Kitching, Thomas; Nagai, Daisuke

    2011-05-01

    The unique properties of dark matter are revealed during collisions between clusters of galaxies, such as the bullet cluster (1E 0657-56) and baby bullet (MACS J0025-12). These systems provide evidence for an additional, invisible mass in the separation between the distributions of their total mass, measured via gravitational lensing, and their ordinary 'baryonic' matter, measured via its X-ray emission. Unfortunately, the information available from these systems is limited by their rarity. Constraints on the properties of dark matter, such as its interaction cross-section, are therefore restricted by uncertainties in the individual systems' impact velocity, impact parameter and orientation with respect to the line of sight. Here we develop a complementary, statistical measurement in which every piece of substructure falling into every massive cluster is treated as a bullet. We define 'bulleticity' as the mean separation between dark matter and ordinary matter, and we measure the signal in hydrodynamical simulations. The phase space of substructure orbits also exhibits symmetries that provide an equivalent control test. Any detection of bulleticity in real data would indicate a difference in the interaction cross-sections of baryonic and dark matter that may rule out hypotheses of non-particulate dark matter that are otherwise able to model individual systems. A subsequent measurement of bulleticity could constrain the dark matter cross-section. Even with conservative estimates, the existing Hubble Space Telescope archive should yield an independent constraint tighter than that from the bullet cluster. This technique is then trivially extendable to and benefits enormously from larger, future surveys.

  5. Analysis of Network Clustering Algorithms and Cluster Quality Metrics at Scale

    PubMed Central

    Kobourov, Stephen; Gallant, Mike; Börner, Katy

    2016-01-01

    Overview Notions of community quality underlie the clustering of networks. While studies surrounding network clustering are increasingly common, a precise understanding of the realtionship between different cluster quality metrics is unknown. In this paper, we examine the relationship between stand-alone cluster quality metrics and information recovery metrics through a rigorous analysis of four widely-used network clustering algorithms—Louvain, Infomap, label propagation, and smart local moving. We consider the stand-alone quality metrics of modularity, conductance, and coverage, and we consider the information recovery metrics of adjusted Rand score, normalized mutual information, and a variant of normalized mutual information used in previous work. Our study includes both synthetic graphs and empirical data sets of sizes varying from 1,000 to 1,000,000 nodes. Cluster Quality Metrics We find significant differences among the results of the different cluster quality metrics. For example, clustering algorithms can return a value of 0.4 out of 1 on modularity but score 0 out of 1 on information recovery. We find conductance, though imperfect, to be the stand-alone quality metric that best indicates performance on the information recovery metrics. Additionally, our study shows that the variant of normalized mutual information used in previous work cannot be assumed to differ only slightly from traditional normalized mutual information. Network Clustering Algorithms Smart local moving is the overall best performing algorithm in our study, but discrepancies between cluster evaluation metrics prevent us from declaring it an absolutely superior algorithm. Interestingly, Louvain performed better than Infomap in nearly all the tests in our study, contradicting the results of previous work in which Infomap was superior to Louvain. We find that although label propagation performs poorly when clusters are less clearly defined, it scales efficiently and accurately to large

  6. Fluctuation-controlled front propagation

    NASA Astrophysics Data System (ADS)

    Ridgway, Douglas Thacher

    1997-09-01

    the symmetry of the absorbing state, but which is unsuccessful at capturing the behavior of diffusion-limited growth. In an effort to find a simpler model system, we turned to modelling fitness increases in evolution. The work was motivated by an experiment on vesicular stomatitis virus, a short (˜9600bp) single-stranded RNA virus. A highly bottlenecked viral population increases in fitness rapidly until a certain point, after which the fitness increases at a slower rate. This is well modeled by a constant population reproducing and mutating on a smooth fitness landscape. Mean field theory of this system displays the same infinite propagation velocity blowup as mean field diffusion-limited aggregation. However, we have been able to make progress on a number of fronts. One is solving systems of moment equations, where a hierarchy of moments is truncated arbitrarily at some level. Good results for front propagation velocity are found with just two moments, corresponding to inclusion of the basic finite population clustering effect ignored by mean field theory. In addition, for small mutation rates, most of the population will be entirely on a single site or two adjacent sites, and the density of these cases can be described and solved. (Abstract shortened by UMI.)

  7. Modeling turbulent flame propagation

    SciTech Connect

    Ashurst, W.T.

    1994-08-01

    Laser diagnostics and flow simulation techniques axe now providing information that if available fifty years ago, would have allowed Damkoehler to show how turbulence generates flame area. In the absence of this information, many turbulent flame speed models have been created, most based on Kolmogorov concepts which ignore the turbulence vortical structure, Over the last twenty years, the vorticity structure in mixing layers and jets has been shown to determine the entrainment and mixing behavior and these effects need to be duplicated by combustion models. Turbulence simulations reveal the intense vorticity structure as filaments and simulations of passive flamelet propagation show how this vorticity Creates flame area and defines the shape of the expected chemical reaction surface. Understanding how volume expansion interacts with flow structure should improve experimental methods for determining turbulent flame speed. Since the last decade has given us such powerful new tools to create and see turbulent combustion microscopic behavior, it seems that a solution of turbulent combustion within the next decade would not be surprising in the hindsight of 2004.

  8. Directed HK propagator.

    PubMed

    Kocia, Lucas; Heller, Eric J

    2015-09-28

    We offer a more formal justification for the successes of our recently communicated "directed Heller-Herman-Kluk-Kay" (DHK) time propagator by examining its performance in one-dimensional bound systems which exhibit at least quasi-periodic motion. DHK is distinguished by its single one-dimensional integral--a vast simplification over the usual 2N-dimensional integral in full Heller-Herman-Kluk-Kay (for an N-dimensional system). We find that DHK accurately captures particular coherent state autocorrelations when its single integral is chosen to lie along these states' fastest growing manifold, as long as it is not perpendicular to their action gradient. Moreover, the larger the action gradient, the better DHK will perform. We numerically examine DHK's accuracy in a one-dimensional quartic oscillator and illustrate that these conditions are frequently satisfied such that the method performs well. This lends some explanation for why DHK frequently seems to work so well and suggests that it may be applicable to systems exhibiting quite strong anharmonicity.

  9. Directed HK propagator

    NASA Astrophysics Data System (ADS)

    Kocia, Lucas; Heller, Eric J.

    2015-09-01

    We offer a more formal justification for the successes of our recently communicated "directed Heller-Herman-Kluk-Kay" (DHK) time propagator by examining its performance in one-dimensional bound systems which exhibit at least quasi-periodic motion. DHK is distinguished by its single one-dimensional integral—a vast simplification over the usual 2N-dimensional integral in full Heller-Herman-Kluk-Kay (for an N-dimensional system). We find that DHK accurately captures particular coherent state autocorrelations when its single integral is chosen to lie along these states' fastest growing manifold, as long as it is not perpendicular to their action gradient. Moreover, the larger the action gradient, the better DHK will perform. We numerically examine DHK's accuracy in a one-dimensional quartic oscillator and illustrate that these conditions are frequently satisfied such that the method performs well. This lends some explanation for why DHK frequently seems to work so well and suggests that it may be applicable to systems exhibiting quite strong anharmonicity.

  10. Optimal Affine-Invariant Point Matching

    NASA Astrophysics Data System (ADS)

    Costa, Mauro S.; Haralick, Robert M.; Phillips, Tsaiyun I.; Shapiro, Linda G.

    1989-03-01

    The affine-transformation matching scheme proposed by Hummel and Wolfson (1988) is very efficient in a model-based matching system, not only in terms of the computational complexity involved, but also in terms of the simplicity of the method. This paper addresses the implementation of the affine-invariant point matching, applied to the problem of recognizing and determining the pose of sheet metal parts. It points out errors that can occur with this method due to quantization, stability, symmetry, and noise problems. By beginning with an explicit noise model which the Hummel and Wolfson technique lacks, we can derive an optimal approach which overcomes these problems. We show that results obtained with the new algorithm are clearly better than the results from the original method.

  11. Affinity Chromatography in Nonionic Detergent Solutions

    NASA Astrophysics Data System (ADS)

    Robinson, Jack B.; Strottmann, James M.; Wick, Donald G.; Stellwagen, Earle

    1980-10-01

    Anionic dye affinity chromatography is commonly unproductive in the presence of nonionic detergents used to extract particulate proteins. Using lactate dehydrogenase as a model protein, Cibacron blue F3GA as a model dye, and Triton X-100 as a model detergent, we find that the dye is encapsulated in nonionic detergent micelles, rendering the dye incapable of ligation with the enzyme. However, the dye can be liberated from the micelles without altering the nonionic detergent concentration by addition of an anionic detergent, such as deoxycholate or sodium dodecyl sulfate, forming mixed anionic/nonionic micelles that displace the anionic dye. Encapsulation of the anionic detergents prevents their activity as protein denaturants. These observations have been successfully translated to the dye affinity chromatography of a detergent extract of brain particulate cyclic nucleotide phosphodiesterase.

  12. Negative affinity X-ray photocathodes

    NASA Technical Reports Server (NTRS)

    Vanspeybroeck, L.; Kellogg, E.; Murray, S.; Duckett, S.

    1974-01-01

    A new X-ray image intensifier is described. The device should eventually have a quantum efficiency which is an order of magnitude greater than that of presently available high spatial resolution X-ray detectors, such as microchannel plates. The new intesifier is based upon a GaAs crystal photocathode which is activated to achieve negative electron affinity. Details concerning the detector concept are discussed together with the theoretical relations involved, X-ray data, and optical data.

  13. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture.

  14. Dike Propagation Near Drifts

    SciTech Connect

    NA

    2002-03-04

    The purpose of this Analysis and Model Report (AMR) supporting the Site Recommendation/License Application (SR/LA) for the Yucca Mountain Project is the development of elementary analyses of the interactions of a hypothetical dike with a repository drift (i.e., tunnel) and with the drift contents at the potential Yucca Mountain repository. This effort is intended to support the analysis of disruptive events for Total System Performance Assessment (TSPA). This AMR supports the Process Model Report (PMR) on disruptive events (CRWMS M&O 2000a). This purpose is documented in the development plan (DP) ''Coordinate Modeling of Dike Propagation Near Drifts Consequences for TSPA-SR/LA'' (CRWMS M&O 2000b). Evaluation of that Development Plan and the work to be conducted to prepare Interim Change Notice (ICN) 1 of this report, which now includes the design option of ''Open'' drifts, indicated that no revision to that DP was needed. These analyses are intended to provide reasonable bounds for a number of expected effects: (1) Temperature changes to the waste package from exposure to magma; (2) The gas flow available to degrade waste containers during the intrusion; (3) Movement of the waste package as it is displaced by the gas, pyroclasts and magma from the intruding dike (the number of packages damaged); (4) Movement of the backfill (Backfill is treated here as a design option); (5) The nature of the mechanics of the dike/drift interaction. These analyses serve two objectives: to provide preliminary analyses needed to support evaluation of the consequences of an intrusive event and to provide a basis for addressing some of the concerns of the Nuclear Regulatory Commission (NRC) expressed in the Igneous Activity Issue Resolution Status Report.

  15. Engineering of Bispecific Affinity Proteins with High Affinity for ERBB2 and Adaptable Binding to Albumin

    PubMed Central

    Nilvebrant, Johan; Åstrand, Mikael; Georgieva-Kotseva, Maria; Björnmalm, Mattias; Löfblom, John; Hober, Sophia

    2014-01-01

    The epidermal growth factor receptor 2, ERBB2, is a well-validated target for cancer diagnostics and therapy. Recent studies suggest that the over-expression of this receptor in various cancers might also be exploited for antibody-based payload delivery, e.g. antibody drug conjugates. In such strategies, the full-length antibody format is probably not required for therapeutic effect and smaller tumor-specific affinity proteins might be an alternative. However, small proteins and peptides generally suffer from fast excretion through the kidneys, and thereby require frequent administration in order to maintain a therapeutic concentration. In an attempt aimed at combining ERBB2-targeting with antibody-like pharmacokinetic properties in a small protein format, we have engineered bispecific ERBB2-binding proteins that are based on a small albumin-binding domain. Phage display selection against ERBB2 was used for identification of a lead candidate, followed by affinity maturation using second-generation libraries. Cell surface display and flow-cytometric sorting allowed stringent selection of top candidates from pools pre-enriched by phage display. Several affinity-matured molecules were shown to bind human ERBB2 with sub-nanomolar affinity while retaining the interaction with human serum albumin. Moreover, parallel selections against ERBB2 in the presence of human serum albumin identified several amino acid substitutions that dramatically modulate the albumin affinity, which could provide a convenient means to control the pharmacokinetics. The new affinity proteins competed for ERBB2-binding with the monoclonal antibody trastuzumab and recognized the native receptor on a human cancer cell line. Hence, high affinity tumor targeting and tunable albumin binding were combined in one small adaptable protein. PMID:25089830

  16. High intensity laser interactions with atomic clusters

    SciTech Connect

    Ditmire, T

    2000-08-07

    The development of ultrashort pulse table top lasers with peak pulse powers in excess of 1 TW has permitted an access to studies of matter subject to unprecedented light intensities. Such interactions have accessed exotic regimes of multiphoton atomic and high energy-density plasma physics. Very recently, the nature of the interactions between these very high intensity laser pulses and atomic clusters of a few hundred to a few thousand atoms has come under study. Such studies have found some rather unexpected results, including the striking finding that these interactions appear to be more energetic than interactions with either single atoms or solid density plasmas. Recent experiments have shown that the explosion of such clusters upon intense irradiation can expel ions from the cluster with energies from a few keV to nearly 1 MeV. This phenomenon has recently been exploited to produce DD fusion neutrons in a gas of exploding deuterium clusters. Under this project, we have undertaken a general study of the intense femtosecond laser cluster interaction. Our goal is to understand the macroscopic and microscopic coupling between the laser and the clusters with the aim of optimizing high flux fusion neutron production from the exploding deuterium clusters or the x-ray yield in the hot plasmas that are produced in this interaction. In particular, we are studying the physics governing the cluster explosions. The interplay between a traditional Coulomb explosion description of the cluster disassembly and a plasma-like hydrodynamic explosion is not entirely understood, particularly for small to medium sized clusters (<1000 atoms) and clusters composed of low-Z atoms. We are focusing on experimental studies of the ion and electron energies resulting from such explosions through various experimental techniques. We are also examining how an intense laser pulse propagates through a dense medium containing these clusters.

  17. Experimental measurements of ultrasonic propagation velocity and attenuation in a magnetic fluid.

    PubMed

    Motozawa, M; Iizuka, Y; Sawada, T

    2008-05-21

    The ultrasonic propagation velocity and attenuation in a magnetic fluid subjected to magnetic field are measured precisely. Various characteristic properties of ultrasonic propagation in magnetic fluid such as hysteresis and anisotropy are observed. These results show that the ultrasonic propagation velocity and attenuation are dependent upon the intensity and the length of time for which the magnetic field is applied. When the magnetic field is applied, some of the magnetic particles in the magnetic fluid form clustering structures that influence ultrasonic propagation in a magnetic fluid. Our results indicate that the inner structure of a magnetic fluid can be analysed experimentally and we discuss the application of this non-contact inspection of the clustering structures in a magnetic fluid by ultrasonic techniques.

  18. Hydrodynamic model for picosecond propagation of laser-created nanoplasmas

    NASA Astrophysics Data System (ADS)

    Saxena, Vikrant; Jurek, Zoltan; Ziaja, Beata; Santra, Robin

    2015-06-01

    The interaction of a free-electron-laser pulse with a moderate or large size cluster is known to create a quasi-neutral nanoplasma, which then expands on hydrodynamic timescale, i.e., > 1 ps. To have a better understanding of ion and electron data from experiments derived from laser-irradiated clusters, one needs to simulate cluster dynamics on such long timescales for which the molecular dynamics approach becomes inefficient. We therefore propose a two-step Molecular Dynamics-Hydrodynamic scheme. In the first step we use molecular dynamics code to follow the dynamics of an irradiated cluster until all the photo-excitation and corresponding relaxation processes are finished and a nanoplasma, consisting of ground-state ions and thermalized electrons, is formed. In the second step we perform long-timescale propagation of this nanoplasma with a computationally efficient hydrodynamic approach. In the present paper we examine the feasibility of a hydrodynamic two-fluid approach to follow the expansion of spherically symmetric nanoplasma, without accounting for the impact ionization and three-body recombination processes at this stage. We compare our results with the corresponding molecular dynamics simulations. We show that all relevant information about the nanoplasma propagation can be extracted from hydrodynamic simulations at a significantly lower computational cost when compared to a molecular dynamics approach. Finally, we comment on the accuracy and limitations of our present model and discuss possible future developments of the two-step strategy.

  19. Integrin avidity regulation: are changes in affinity and conformation underemphasized?

    PubMed

    Carman, Christopher V; Springer, Timothy A

    2003-10-01

    Integrins play critical roles in development, wound healing, immunity and cancer. Central to their function is their unique ability to modulate dynamically their adhesiveness through both affinity- and valency-based mechanisms. Recent advances have shed light on the structural basis for affinity regulation and on the signaling mechanisms responsible for both affinity and valency modes of regulation.

  20. Review of aircraft noise propagation

    NASA Technical Reports Server (NTRS)

    Putnam, T. W.

    1975-01-01

    The current state of knowledge about the propagation of aircraft noise was reviewed. The literature on the subject is surveyed and methods for predicting the most important and best understood propagation effects are presented. Available empirical data are examined and the data's general validity is assessed. The methods used to determine the loss of acoustic energy due to uniform spherical spreading, absorption in a homogeneous atmosphere, and absorption due to ground cover are presented. A procedure for determining ground induced absorption as a function of elevation angle between source and receiver is recommended. Other factors that affect propagation, such as refraction and scattering due to turbulence, which were found to be less important for predicting the propagation of aircraft noise, are also evaluated.

  1. Photon propagator for axion electrodynamics

    SciTech Connect

    Itin, Yakov

    2007-10-15

    The axion modified electrodynamics is usually used as a model for description of possible violation of Lorentz invariance in field theory. The low-energy manifestation of Lorentz violation can hopefully be observed in experiments with electromagnetic waves. It justifies the importance of studying how a small axion addition can modify the wave propagation. Although a constant axion does not contribute to the dispersion relation at all, even a slowly varying axion field destroys the light cone structure. In this paper, we study the wave propagation in the axion modified electrodynamics in the framework of the premetric approach. In addition to the modified dispersion relation, we derive the axion generalization of the photon propagator in Feynman and Landau gauge. Our consideration is free of the usual restriction to the constant gradient axion field. It is remarkable that the axion modified propagator is Hermitian. Consequently, the dissipation effects are absent even in the phenomenological model considered here.

  2. Propagation Limitations in Remote Sensing.

    DTIC Science & Technology

    Contents: Multi-sensors and systems in remote sensing ; Radar sensing systems over land; Remote sensing techniques in oceanography; Influence of...propagation media and background; Infrared techniques in remote sensing ; Photography in remote sensing ; Analytical studies in remote sensing .

  3. A database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Suwitra, Krisjani S.

    1992-01-01

    In June 1991, a paper at the fifteenth NASA Propagation Experimenters Meeting (NAPEX 15) was presented outlining the development of a database for propagation models. The database is designed to allow the scientists and experimenters in the propagation field to process their data through any known and accepted propagation model. The architecture of the database also incorporates the possibility of changing the standard models in the database to fit the scientist's or the experimenter's needs. The database not only provides powerful software to process the data generated by the experiments, but is also a time- and energy-saving tool for plotting results, generating tables, and producing impressive and crisp hard copy for presentation and filing.

  4. Reconstruction of nonlinear wave propagation

    DOEpatents

    Fleischer, Jason W; Barsi, Christopher; Wan, Wenjie

    2013-04-23

    Disclosed are systems and methods for characterizing a nonlinear propagation environment by numerically propagating a measured output waveform resulting from a known input waveform. The numerical propagation reconstructs the input waveform, and in the process, the nonlinear environment is characterized. In certain embodiments, knowledge of the characterized nonlinear environment facilitates determination of an unknown input based on a measured output. Similarly, knowledge of the characterized nonlinear environment also facilitates formation of a desired output based on a configurable input. In both situations, the input thus characterized and the output thus obtained include features that would normally be lost in linear propagations. Such features can include evanescent waves and peripheral waves, such that an image thus obtained are inherently wide-angle, farfield form of microscopy.

  5. Propagating plasmons on silver nanowires

    NASA Astrophysics Data System (ADS)

    He, Weidong; Wei, Hong; Li, Zhipeng; Huang, Yingzhou; Fang, Yurui; Li, Ping; Xu, Hongxing

    2010-08-01

    Chemically synthesized Ag nanowires (NWs) can serve as waveguides to support propagating surface plasmons (SPs). By using the propagating SPs on Ag NWs, the surface-enhanced Raman scattering of molecules, located in the nanowire-nanoparticle junction a few microns away from the laser spot on one end of the NW, was excited. The propagating SPs can excite the excitons in quantum dots, and in reverse, the decay of excitons can generate SPs. The direction and polarization of the light emitted through the Ag NW waveguide. The emission polarization depends strongly on the shape of the NW terminals. In branched NW structures, the SPs can be switched between the main NW and the branch NW, by tuning the incident polarization. The light of different wavelength can also be controlled to propagate along different ways. Thus, the branched NW structure can serve as controllable plasmonic router and multiplexer.

  6. Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids.

    PubMed

    Carlin, Caleb; Gordon, Mark S

    2015-04-05

    Developing a better understanding of the bulk properties of ionic liquids requires accurate measurements of the underlying molecular properties that help to determine the bulk behavior. Two computational methods are used in this work: second-order perturbation theory (MP2) and completely renormalized coupled cluster theory [CR-CC(2,3)], to calculate the proton affinity and ionization potential of a set of anions that are of interest for use in protic, energetic ionic liquids. Compared with experimental values, both methods predict similarly accurate proton affinities, but CR-CC(2,3) predicts significantly more accurate ionization potentials. It is concluded that more time intensive methods like CR-CC(2,3) are required in calculations involving open shell states like the ionization potential.

  7. Propagating rifts on midocean ridges

    NASA Astrophysics Data System (ADS)

    Hey, Richard; Duennebier, Frederick K.; Morgan, W. Jason

    1980-07-01

    Spreading center jumps identified west of the Galapagos Islands near 95°W occur in a pattern consistent with the propagating rift hypothesis. A new rift is gradually breaking through the Cocos plate. Each successive jump is slightly longer than the preceding jump. The new spreading center grows at a new azimuth toward the west as the old one dies. The jumps are a manifestation of rift propagation. We extend the analysis of propagating rifts to the case of continuous propagation and predict patterns of magnetic anomalies and bathymetry consistent with the observed patterns. In particular, we correctly predict the trends of fossil spreading centers and V patterns of magnetic anomaly offsets required by the propagating rift hypothesis. Similar V patterns have been observed on many other spreading centers and have been interpreted in various ways. The propagating rift hypothesis appears to offer a simple explanation, consistent with rigid plate tectonics, for each of these patterns. This hypothesis may also have important implications for continental rifting.

  8. Dual-Metal Centered Zirconium-Organic Framework: A Metal-Affinity Probe for Highly Specific Interaction with Phosphopeptides.

    PubMed

    Peng, Jiaxi; Zhang, Hongyan; Li, Xin; Liu, Shengju; Zhao, Xingyun; Wu, Jing; Kang, Xiaohui; Qin, Hongqiang; Pan, Zaifa; Wu, Ren'an

    2016-12-28

    The highly specific affinity between probes and phosphopeptides is the fundamental interaction for selective identification of phosphoproteomes that uncover the mechanisms of signal transduction, cell cycle, enzymatic regulation, and gene expression in biological systems. In this study, a metal-affinity probe possessing both interactions of metal oxide affinity chromatography (MOAC) and immobilized metal ion affinity chromatography (IMAC) was facilely prepared by immobilizing zirconium(IV) on a zirconium-organic framework of UiO-66-NH2, which holds dual-metal centers of not only the inherent Zr-O cluster but also the immobilized Zr(IV) center. This dual-metal centered zirconium-organic framework (DZMOF) demonstrates as a highly specific metal-affinity probe toward the extraction of phosphopeptides due to the metal-affinity interactions of MOAC and IMAC toward either mono-phosphorylated or multi-phosphorylated peptides. The binding energies of zirconium 3d5/2 and 3d3/2 in this DZMOF are 183.07 and 185.47 eV, respectively, which are higher than those of the intact UiO-66-NH2 (182.84 and 185.17 eV, respectively), confirming the higher metal-affinity interaction between the DZMOF and phosphopeptides. This high metal-affinity probe presents an unprecedented strong performance in anti-nonspecific interference during the capturing of phosphopeptides of β-casein with the molar ratio of β-casein vs bovine serum albumin up to ca. 1:5000. The enrichment of phosphopeptides from a human saliva sample by DZMOF further confirms the great potential of DZMOF in the extraction of low-abundance phosphopeptides for real complex biological samples.

  9. Latest European coelacanth shows Gondwanan affinities.

    PubMed

    Cavin, Lionel; Forey, Peter L; Buffetaut, Eric; Tong, Haiyan

    2005-06-22

    The last European fossil occurrence of a coelacanth is from the Mid-Cretaceous of the English Chalk (Turonian, 90 million years ago). Here, we report the discovery of a coelacanth from Late Cretaceous non-marine rocks in southern France. It consists of a left angular bone showing structures that imply close phylogenetic affinities with some extinct Mawsoniidae. The closest relatives are otherwise known from Cretaceous continental deposits of southern continents and suggest that the dispersal of freshwater organisms from Africa to Europe occurred in the Late Cretaceous.

  10. On the electron affinity of Be2

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Partridge, H.

    1984-01-01

    Calculations of the electron affinity (EA) of Be2 using a large Slater-type orbital basis set and extensive correlation based upon a CASSCF reference are reported. The adiabatic EAs are estimated to be 0.44 eV for the 2Sigma sub g(+) state and 0.56 eV for the 2Pi sub u state. The extra electron attaches into an empty bonding orbital, causing a shortening of the bond length and an increase in omega(e). The D(e) of the 2Pi sub u state of Be2 is six times as large as the D(e) of Be2.

  11. On the structure of self-affine convex bodies

    SciTech Connect

    Voynov, A S

    2013-08-31

    We study the structure of convex bodies in R{sup d} that can be represented as a union of their affine images with no common interior points. Such bodies are called self-affine. Vallet's conjecture on the structure of self-affine bodies was proved for d = 2 by Richter in 2011. In the present paper we disprove the conjecture for all d≥3 and derive a detailed description of self-affine bodies in R{sup 3}. Also we consider the relation between properties of self-affine bodies and functional equations with a contraction of an argument. Bibliography: 10 titles.

  12. Affinity filtration coupled with capillary-based affinity purification for the isolation of protein complexes.

    PubMed

    Qureshi, M S; Sheikh, Q I; Hill, R; Brown, P E; Dickman, M J; Tzokov, S B; Rice, D W; Gjerde, D T; Hornby, D P

    2013-08-01

    The isolation of complex macromolecular assemblies at the concentrations required for structural analysis represents a major experimental challenge. Here we present a method that combines the genetic power of site-specific recombination in order to selectively "tag" one or more components of a protein complex with affinity-based rapid filtration and a final step of capillary-based enrichment. This modified form of tandem affinity purification produces highly purified protein complexes at high concentrations in a highly efficient manner. The application of the method is demonstrated for the yeast Arp2/3 heptameric protein complex involved in mediating reorganization of the actin cytoskeleton.

  13. The physical theory and propagation model of THz atmospheric propagation

    NASA Astrophysics Data System (ADS)

    Wang, R.; Yao, J. Q.; Xu, D. G.; Wang, J. L.; Wang, P.

    2011-02-01

    Terahertz (THz) radiation is extensively applied in diverse fields, such as space communication, Earth environment observation, atmosphere science, remote sensing and so on. And the research on propagation features of THz wave in the atmosphere becomes more and more important. This paper firstly illuminates the advantages and outlook of THz in space technology. Then it introduces the theoretical framework of THz atmospheric propagation, including some fundamental physical concepts and processes. The attenuation effect (especially the absorption of water vapor), the scattering of aerosol particles and the effect of turbulent flow mainly influence THz atmosphere propagation. Fundamental physical laws are illuminated as well, such as Lamber-beer law, Mie scattering theory and radiative transfer equation. The last part comprises the demonstration and comparison of THz atmosphere propagation models like Moliere(V5), SARTre and AMATERASU. The essential problems are the deep analysis of physical mechanism of this process, the construction of atmospheric propagation model and databases of every kind of material in the atmosphere, and the standardization of measurement procedures.

  14. Structures and energetics of neutral and ionic silicon-germanium clusters: density functional theory and coupled cluster studies.

    PubMed

    Wang, Yi-Siang; Chao, Sheng D

    2011-03-10

    We have calculated the structural and energetic properties of neutral and ionic (singly charged anionic and cationic) semiconductor binary silicon-germanium clusters Si(m)Ge(n) for s = m + n ≤ 12 using the density functional theory (DFT-B3LYP) and coupled cluster [CCSD(T)] methods with Pople's 6-311++G(3df, 3pd) basis set. Neutral and anionic clusters share similar ground state structures for s = 3-7, independent of the stoichiometry and atom locations, but start to deviate at s = 8. The relative energetic stability of the calculated ground state structures among possible isomers has been analyzed through a bond strength propensity model where the pair interactions of Si-Si, Si-Ge, and Ge-Ge are competing. Electron affinities, ionization potentials, energy gaps between the highest and lowest occupied molecular orbitals (HOMO-LUMO gaps), and cluster mixing energies were calculated and analyzed. Overall, for a fixed s, the vertical ionization potential increases as the number of silicon atoms m increases, while the vertical electron affinity shows a dip at m = 2. As s increases, the ionization potentials increase from s = 2 to s = 3 and then decrease slowly to s = 8. The mixing energies for neutral and ionic clusters are all negative, indicating that the binary clusters are more stable than pure elemental clusters. Except for s = 4 and 8, cationic clusters are more stable than anionic ones and, thus, are more likely to be observed in experiments.

  15. Extraction of haemoglobin from human blood by affinity precipitation using a haptoglobin-based stimuli-responsive affinity macroligand.

    PubMed

    Stocker-Majd, Gisela; Hilbrig, Frank; Freitag, Ruth

    2008-06-13

    Affinity precipitation was compared to affinity chromatography and batch adsorption as the final purification step in a protocol for the isolation of haemoglobin from human blood. Haptoglobin was the affinity ligand. The first steps on the process were realized by traditional methods (lyses of red blood cells followed by ammonium sulphate precipitation). For affinity chromatography (and batch adsorption) the ligand was linked to Sepharose, for affinity precipitation to a thermoresponsive polymer, namely poly(N-isopropylacrylamide). Five haptoglobin-poly(N-isopropylacrylamide) bioconjugates (affinity macroligands) were constructed with different polymer: haptoglobin-coupling ratios. Conjugation of haptoglobin to the soluble poly(N-isopropylacrylamide) apparently does not change the interaction thermodynamics with haemoglobin, as the haemoglobin binding constants calculated by a Scatchard analysis for the affinity macroligand were of the same order of magnitude as those described in the literature for the haemoglobin-haptoglobin complex in solution. Two elution protocols were used for haemoglobin release from the various affinity materials, one at pH 2, the other with 5 M urea at pH 11. Both affinity chromatography and affinity precipitation yielded a pure haemoglobin of high quality. Compared to the affinity chromatography, affinity precipitation showed a significantly higher ligand efficiency (ratio of the experimental capacity to the theoretical one). The method thus makes better use of the expensive affinity ligands. As affinity precipitation only requires small temperature changes to bring about precipitation/redissolution of the affinity complexes and a centrifugation step for recovery of the precipitate, the method in addition has advantages in term of scalability and simplicity.

  16. Quantification of hydrophobic interaction affinity of colloids

    NASA Astrophysics Data System (ADS)

    Saini, G.; Nasholm, N.; Wood, B. D.

    2009-12-01

    Colloids play an important role in a wide variety of disciplines, including water and wastewater treatment, subsurface transport of metals and organic contaminants, migration of fines in oil reservoirs, biocolloid (virus and bacteria) transport in subsurface, and are integral to laboratory transport studies. Although the role of hydrophobicity in adhesion and transport of colloids, particularly bacteria, is well known; there is scarcity of literature regarding hydrophobicity measurement of non-bacterial colloids and other micron-sized particles. Here we detail an experimental approach based on differential partitioning of colloids between two liquid phases (hydrocarbon and buffer) as a measure of the hydrophobic interaction affinity of colloids. This assay, known as Microbial adhesion to hydrocarbons or MATH, is frequently used in microbiology and bacteriology for quantifying the hydrophobicity of microbes. Monodispersed colloids and particles, with sizes ranging from 1 micron to 33 micron, were used for the experiments. A range of hydrophobicity values were observed for different particles. The hydrophobicity results are also verified against water contact angle measurements of these particles. This liquid-liquid partitioning assay is quick, easy-to-perform and requires minimal instrumentation. Estimation of the hydrophobic interaction affinity of colloids would lead to a better understanding of their adhesion to different surfaces and subsequent transport in porous media.

  17. Affinity-based target deconvolution of safranal

    PubMed Central

    2013-01-01

    Background and the purpose of the study Affinity-based target deconvolution is an emerging method for the identification of interactions between drugs/drug candidates and cellular proteins, and helps to predict potential activities and side effects of a given compound. In the present study, we hypothesized that a part of safranal pharmacological effects, one of the major constituent of Crocus sativus L., relies on its physical interaction with target proteins. Methods Affinity chromatography solid support was prepared by covalent attachment of safranal to agarose beads. After passing tissue lysate through the column, safranal-bound proteins were isolated and separated on SDS-PAGE or two-dimensional gel electrophoresis. Proteins were identified using MALDI-TOF/TOF mass spectrometry and Mascot software. Results and major conclusion Data showed that safranal physically binds to beta actin, cytochrome b-c1 complex sub-unit 1, trifunctional enzyme sub-unit beta and ATP synthase sub-unit alpha and beta. These interactions may explain part of safranal’s pharmacological effects. However, phenotypic and/or biological relevance of these interactions remains to be elucidated by future pharmacological studies. PMID:23514587

  18. Affine conformal vectors in space-time

    NASA Astrophysics Data System (ADS)

    Coley, A. A.; Tupper, B. O. J.

    1992-05-01

    All space-times admitting a proper affine conformal vector (ACV) are found. By using a theorem of Hall and da Costa, it is shown that such space-times either (i) admit a covariantly constant vector (timelike, spacelike, or null) and the ACV is the sum of a proper affine vector and a conformal Killing vector or (ii) the space-time is 2+2 decomposable, in which case it is shown that no ACV can exist (unless the space-time decomposes further). Furthermore, it is proved that all space-times admitting an ACV and a null covariantly constant vector (which are necessarily generalized pp-wave space-times) must have Ricci tensor of Segré type {2,(1,1)}. It follows that, among space-times admitting proper ACV, the Einstein static universe is the only perfect fluid space-time, there are no non-null Einstein-Maxwell space-times, and only the pp-wave space-times are representative of null Einstein-Maxwell solutions. Otherwise, the space-times can represent anisotropic fluids and viscous heat-conducting fluids, but only with restricted equations of state in each case.

  19. Partial coherence and imperfect optics at a synchrotron radiation source modeled by wavefront propagation

    NASA Astrophysics Data System (ADS)

    Laundy, David; Alcock, Simon G.; Alianelli, Lucia; Sutter, John P.; Sawhney, Kawal J. S.; Chubar, Oleg

    2014-09-01

    A full wave propagation of X-rays from source to sample at a storage ring beamline requires simulation of the electron beam source and optical elements in the beamline. The finite emittance source causes the appearance of partial coherence in the wave field. Consequently, the wavefront cannot be treated exactly with fully coherent wave propagation or fully incoherent ray tracing. We have used the wavefront code Synchrotron Radiation Workshop (SRW) to perform partially coherent wavefront propagation using a parallel computing cluster at the Diamond Light Source. Measured mirror profiles have been used to correct the wavefront for surface errors.

  20. Application of Epidemiology Model on Complex Networks in Propagation Dynamics of Airspace Congestion.

    PubMed

    Dai, Xiaoxu; Hu, Minghua; Tian, Wen; Xie, Daoyi; Hu, Bin

    2016-01-01

    This paper presents a propagation dynamics model for congestion propagation in complex networks of airspace. It investigates the application of an epidemiology model to complex networks by comparing the similarities and differences between congestion propagation and epidemic transmission. The model developed satisfies the constraints of actual motion in airspace, based on the epidemiology model. Exploiting the constraint that the evolution of congestion cluster in the airspace is always dynamic and heterogeneous, the SIR epidemiology model (one of the classical models in epidemic spreading) with logistic increase is applied to congestion propagation and shown to be more accurate in predicting the evolution of congestion peak than the model based on probability, which is common to predict the congestion propagation. Results from sample data show that the model not only predicts accurately the value and time of congestion peak, but also describes accurately the characteristics of congestion propagation. Then, a numerical study is performed in which it is demonstrated that the structure of the networks have different effects on congestion propagation in airspace. It is shown that in regions with severe congestion, the adjustment of dissipation rate is more significant than propagation rate in controlling the propagation of congestion.

  1. Cluster headache

    PubMed Central

    Leroux, Elizabeth; Ducros, Anne

    2008-01-01

    Cluster headache (CH) is a primary headache disease characterized by recurrent short-lasting attacks (15 to 180 minutes) of excruciating unilateral periorbital pain accompanied by ipsilateral autonomic signs (lacrimation, nasal congestion, ptosis, miosis, lid edema, redness of the eye). It affects young adults, predominantly males. Prevalence is estimated at 0.5–1.0/1,000. CH has a circannual and circadian periodicity, attacks being clustered (hence the name) in bouts that can occur during specific months of the year. Alcohol is the only dietary trigger of CH, strong odors (mainly solvents and cigarette smoke) and napping may also trigger CH attacks. During bouts, attacks may happen at precise hours, especially during the night. During the attacks, patients tend to be restless. CH may be episodic or chronic, depending on the presence of remission periods. CH is associated with trigeminovascular activation and neuroendocrine and vegetative disturbances, however, the precise cautive mechanisms remain unknown. Involvement of the hypothalamus (a structure regulating endocrine function and sleep-wake rhythms) has been confirmed, explaining, at least in part, the cyclic aspects of CH. The disease is familial in about 10% of cases. Genetic factors play a role in CH susceptibility, and a causative role has been suggested for the hypocretin receptor gene. Diagnosis is clinical. Differential diagnoses include other primary headache diseases such as migraine, paroxysmal hemicrania and SUNCT syndrome. At present, there is no curative treatment. There are efficient treatments to shorten the painful attacks (acute treatments) and to reduce the number of daily attacks (prophylactic treatments). Acute treatment is based on subcutaneous administration of sumatriptan and high-flow oxygen. Verapamil, lithium, methysergide, prednisone, greater occipital nerve blocks and topiramate may be used for prophylaxis. In refractory cases, deep-brain stimulation of the hypothalamus and

  2. Formation of Cluster Complexes by Cluster-Cluster-Collisions

    NASA Astrophysics Data System (ADS)

    Ichihashi, Masahiko; Odaka, Hideho

    2015-03-01

    Multi-element clusters are interested in their chemical and physical properties, and it is expected that they are utilized as catalysts, for example. Their properties critically depend on the size, composition and atomic ordering, and it should be important to adjust the above parameters for their functionality. One of the ways to form a multi-element cluster is to employ a low-energy collision between clusters. Here, we show characteristic results obtained in the collision between a neutral Ar cluster and a size-selected Co cluster ion. Low-energy collision experiment was accomplished by using a newly developed merging-beam apparatus. Cobalt cluster ions were produced by laser ablation, and mass-selected. On the other hand, argon clusters were prepared by the supersonic expansion of Ar gas. Both cluster beams were merged together in an ion guide, and ionic cluster complexes were mass-analyzed. In the collision of Co2+ and ArN, Co2Arn+ (n = 1 - 30) were observed, and the total intensity of Co2Arn+ (n >= 1) is inversely proportional to the relative velocity between Co2+ and ArN. This suggests that the charge-induced dipole interaction between Co2+ and a neutral Ar cluster is dominant in the formation of the cluster complex, Co2+Arn.

  3. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

    PubMed

    Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter

    2016-08-26

    Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

  4. The geometry of propagating rifts

    NASA Astrophysics Data System (ADS)

    McKenzie, Dan

    1986-03-01

    The kinematics of two different processes are investigated, both of which have been described as rift propagation. Courtillot uses this term to describe the change from distributed to localised extension which occurs during the early development of an ocean basin. The term localisation is instead used here to describe this process, to distinguish it from Hey's type of propagation. Localisation generally leads to rotation of the direction of magnetisation. To Hey propagation means the extension of a rift into the undeformed plate beyond a transform fault. Detail surveys of the Galapagos rift have shown that the propagating and failing rifts are not connected by a single transform fault, but by a zone which is undergoing shear. The principal deformation is simple shear, and the kinematics of this deformation are investigated in some detail. The strike of most of the lineations observed in the area can be produced by such deformation. The mode of extension on the propagating rift appears to be localised for some periods but to be distributed for others. Neither simple kinematic arguments nor stretching of the lithosphere with conservation of crust can account for the observed variations in water depth.

  5. User needs for propagation data

    NASA Technical Reports Server (NTRS)

    Sullivan, Thomas M.

    1993-01-01

    New and refined models of radio signal propagation phenomena are needed to support studies of evolving satellite services and systems. Taking an engineering perspective, applications for propagation measurements and models in the context of various types of analyses that are of ongoing interest are reviewed. Problems that were encountered in the signal propagation aspects of these analyses are reviewed, and potential solutions to these problems are discussed. The focus is on propagation measurements and models needed to support design and performance analyses of systems in the Mobile-Satellite Service (MSS) operating in the 1-3 GHz range. These systems may use geostationary or non-geostationary satellites and Frequency Division Multiple Access (FDMA), Time Division Multiple Access Digital (TDMA), or Code Division Multiple Access (CDMA) techniques. Many of the propagation issues raised in relation to MSS are also pertinent to other services such as broadcasting-satellite (sound) at 2310-2360 MHz. In particular, services involving mobile terminals or terminals with low gain antennas are of concern.

  6. Structure of a High-Affinity

    SciTech Connect

    Saphire, E.O.; Montero, M.; Menendez, A.; Houten, N.E.van; Irving, M.B.; Pantophlet, R.; Swick, M.B.; Parren, P.W.H.I.; Burton, D.R.; Scott, J.K.; Wilson, I.A.; /Scripps Res. Inst. /Simon Fraser U. /British Columbia U.

    2007-07-13

    The human antibody b12 recognizes a discontinuous epitope on gp120 and is one of the rare monoclonal antibodies that neutralize a broad range of primary human immunodeficiency virus type 1 (HIV-1) isolates. We previously reported the isolation of B2.1, a dimeric peptide that binds with high specificity to b12 and competes with gp120 for b12 antibody binding. Here, we show that the affinity of B2.1 was improved 60-fold over its synthetic-peptide counterpart by fusing it to the N terminus of a soluble protein. This affinity, which is within an order of magnitude of that of gp120, probably more closely reflects the affinity of the phage-borne peptide. The crystal structure of a complex between Fab of b12 and B2.1 was determined at 1.8 Angstrom resolution. The structural data allowed the differentiation of residues that form critical contacts with b12 from those required for maintenance of the antigenic structure of the peptide, and revealed that three contiguous residues mediate B2.1's critical contacts with b12. This single region of critical contact between the B2.1 peptide and the b12 paratope is unlikely to mimic the discontinuous key binding residues involved in the full b12 epitope for gp120, as previously identified by alanine scanning substitutions on the gp120 surface. These structural observations are supported by experiments that demonstrate that B2.1 is an ineffective immunogenic mimic of the b12 epitope on gp120. Indeed, an extensive series of immunizations with B2.1 in various forms failed to produce gp120 cross-reactive sera. The functional and structural data presented here, however, suggest that the mechanism by which b12 recognizes the two antigens is very different. Here, we present the first crystal structure of peptide bound to an antibody that was originally raised against a discontinuous protein epitope. Our results highlight the challenge of producing immunogens that mimic discontinuous protein epitopes, and the necessity of combining

  7. Wave propagation in ballistic gelatine.

    PubMed

    Naarayan, Srinivasan S; Subhash, Ghatu

    2017-01-23

    Wave propagation characteristics in long cylindrical specimens of ballistic gelatine have been investigated using a high speed digital camera and hyper elastic constitutive models. The induced transient deformation is modelled with strain rate dependent Mooney-Rivlin parameters which are determined by modelling the stress-strain response of gelatine at a range of strain rates. The varying velocity of wave propagation through the gelatine cylinder is derived as a function of prestress or stretch in the gelatine specimen. A finite element analysis is conducted using the above constitutive model by suitably defining the impulse imparted by the polymer bar into the gelatine specimen. The model results are found to capture the experimentally observed wave propagation characteristics in gelatine effectively.

  8. Ultra-Intense Laser Pulse Propagation in Gas and Plasma

    SciTech Connect

    Antonsen, T. M.

    2004-10-26

    identified theoretically and experimentally in the group, and (6) studies of propagation in cluster plasmas. New models will be developed for the harmonic generation of radiation and these will be incorporated in the modeling and simulation.

  9. Dynamical Realism and Uncertainty Propagation

    NASA Astrophysics Data System (ADS)

    Park, Inkwan

    In recent years, Space Situational Awareness (SSA) has become increasingly important as the number of tracked Resident Space Objects (RSOs) continues their growth. One of the most significant technical discussions in SSA is how to propagate state uncertainty in a consistent way with the highly nonlinear dynamical environment. In order to keep pace with this situation, various methods have been proposed to propagate uncertainty accurately by capturing the nonlinearity of the dynamical system. We notice that all of the methods commonly focus on a way to describe the dynamical system as precisely as possible based on a mathematical perspective. This study proposes a new perspective based on understanding dynamics of the evolution of uncertainty itself. We expect that profound insights of the dynamical system could present the possibility to develop a new method for accurate uncertainty propagation. These approaches are naturally concluded in goals of the study. At first, we investigate the most dominant factors in the evolution of uncertainty to realize the dynamical system more rigorously. Second, we aim at developing the new method based on the first investigation enabling orbit uncertainty propagation efficiently while maintaining accuracy. We eliminate the short-period variations from the dynamical system, called a simplified dynamical system (SDS), to investigate the most dominant factors. In order to achieve this goal, the Lie transformation method is introduced since this transformation can define the solutions for each variation separately. From the first investigation, we conclude that the secular variations, including the long-period variations, are dominant for the propagation of uncertainty, i.e., short-period variations are negligible. Then, we develop the new method by combining the SDS and the higher-order nonlinear expansion method, called state transition tensors (STTs). The new method retains advantages of the SDS and the STTs and propagates

  10. Wave equations for pulse propagation

    SciTech Connect

    Shore, B.W.

    1987-06-24

    Theoretical discussions of the propagation of pulses of laser radiation through atomic or molecular vapor rely on a number of traditional approximations for idealizing the radiation and the molecules, and for quantifying their mutual interaction by various equations of propagation (for the radiation) and excitation (for the molecules). In treating short-pulse phenomena it is essential to consider coherent excitation phenomena of the sort that is manifest in Rabi oscillations of atomic or molecular populations. Such processes are not adequately treated by rate equations for excitation nor by rate equations for radiation. As part of a more comprehensive treatment of the coupled equations that describe propagation of short pulses, this memo presents background discussion of the equations that describe the field. This memo discusses the origin, in Maxwell's equations, of the wave equation used in the description of pulse propagation. It notes the separation into lamellar and solenoidal (or longitudinal and transverse) and positive and negative frequency parts. It mentions the possibility of separating the polarization field into linear and nonlinear parts, in order to define a susceptibility or index of refraction and, from these, a phase and group velocity. The memo discusses various ways of characterizing the polarization characteristics of plane waves, that is, of parameterizing a transverse unit vector, such as the Jones vector, the Stokes vector, and the Poincare sphere. It discusses the connection between macroscopically defined quantities, such as the intensity or, more generally, the Stokes parameters, and microscopic field amplitudes. The material presented here is a portion of a more extensive treatment of propagation to be presented separately. The equations presented here have been described in various books and articles. They are collected here as a summary and review of theory needed when treating pulse propagation.

  11. Gap soliton propagation in optical fiber gratings

    NASA Astrophysics Data System (ADS)

    Mohideen, U.; Slusher, R. E.; Mizrahi, V.; Erdogan, T.; Kuwata-Gonokami, M.; Lemaire, P. J.; Sipe, J. E.; Martijn de Sterke, C.; Broderick, Neil G. R.

    1995-08-01

    Intense optical pulse propagation in a GeO2 -doped silica glass fiber grating results in nonlinear pulse propagation velocities and increased transmission at wavelengths where the grating reflects light in the linear limit. These nonlinear pulse propagation effects are predicted by numerical simulations of gap soliton propagation. The large linear refractive-index variations used for the fiber gratings in these experiments permit the propagation of gap solitons in short lengths of fiber.

  12. The affine cohomology spaces and its applications

    NASA Astrophysics Data System (ADS)

    Fraj, Nizar Ben; Laraiedh, Ismail

    2016-12-01

    We compute the nth cohomology space of the affine Lie superalgebra 𝔞𝔣𝔣(1) on the (1,1)-dimensional real superspace with coefficient in a large class of 𝔞𝔣𝔣(1)-modules M. We apply our results to the module of weight densities and the module of linear differential operators acting on a superspace of weighted densities. This work is the generalization of a result by Basdouri et al. [The linear 𝔞𝔣𝔣(n|1)-invariant differential operators on weighted densities on the superspace ℝ1|n and 𝔞𝔣𝔣(n|1)-relative cohomology, Int. J. Geom. Meth. Mod. Phys. 10 (2013), Article ID: 1320004, 9 pp.

  13. Automatic gesture analysis using constant affine velocity.

    PubMed

    Cifuentes, Jenny; Boulanger, Pierre; Pham, Minh Tu; Moreau, Richard; Prieto, Flavio

    2014-01-01

    Hand human gesture recognition has been an important research topic widely studied around the world, as this field offers the ability to identify, recognize, and analyze human gestures in order to control devices or to interact with computer interfaces. In particular, in medical training, this approach is an important tool that can be used to obtain an objective evaluation of a procedure performance. In this paper, some obstetrical gestures, acquired by a forceps, were studied with the hypothesis that, as the scribbling and drawing movements, they obey the one-sixth power law, an empirical relationship which connects path curvature, torsion, and euclidean velocity. Our results show that obstetrical gestures have a constant affine velocity, which is different for each type of gesture and based on this idea this quantity is proposed as an appropriate classification feature in the hand human gesture recognition field.

  14. Dynamic friction of self-affine surfaces

    NASA Astrophysics Data System (ADS)

    Schmittbuhl, Jean; Vilotte, Jean-Pierre; Roux, Stéphane

    1994-02-01

    We investigate the velocity dependence of the friction between two rigid blocks limited by a self-affine surface such as the one generated by a crack. The upper solid is subjected either to gravity or to an external elastic stiffness, and is driven horizontally at constant velocity, V, while the lower solid is fixed. For low velocities, the apparent friction coefficient is constant. For high velocities, the apparent friction is shown to display a velocity weakening. The weakening can be related to the variation of the mean contact time due to the occurrence of jumps during the motions. The cross-over between these two regimes corresponds to a characteristic velocity which depends on the geometry of the surfaces and on the mean normal force. In the case of simple gravity loading, the velocity dependence of the apparent friction at high velocities is proportional to 1/V^2 where V is the imposed tangential velocity. In the case of external elastic stiffness, two velocity weakening regimes can be identified, the first is identical to the gravity case with a 1/V^2 dependence, the second appears at higher velocities and is characterized by a 1/V variation. The characteristic velocity of this second cross-over depends on the roughness and the elastic stiffness. The statistical distribution of ballistic flight distances is analysed, and is shown to reveal in all cases the self-affinity of the contacting surfaces. Nous analysons la dépendence en vitesse du frottement entre deux solides limités par une surface rugueuse auto-affine comme celle d'une surface de fracture. Le solide supérieur est soumis soit à la gravité, soit à une raideur élastique externe, et est entraîné à vitesse horizontale constante V sur le solide inférieur fixe. A faible vitesse, le coefficient de friction apparent, est constant. A forte vitesse, le coefficient de friction apparent devient inversement proportionnel à la vitesse. Cette dépendance peut être reliée à la variation du temps

  15. Propagation of elastic waves through textured polycrystals: application to ice.

    PubMed

    Maurel, Agnès; Lund, Fernando; Montagnat, Maurine

    2015-05-08

    The propagation of elastic waves in polycrystals is revisited, with an emphasis on configurations relevant to the study of ice. Randomly oriented hexagonal single crystals are considered with specific, non-uniform, probability distributions for their major axis. Three typical textures or fabrics (i.e. preferred grain orientations) are studied in detail: one cluster fabric and two girdle fabrics, as found in ice recovered from deep ice cores. After computing the averaged elasticity tensor for the considered textures, wave propagation is studied using a wave equation with elastic constants c=〈c〉+δc that are equal to an average plus deviations, presumed small, from that average. This allows for the use of the Voigt average in the wave equation, and velocities are obtained solving the appropriate Christoffel equation. The velocity for vertical propagation, as appropriate to interpret sonic logging measurements, is analysed in more details. Our formulae are shown to be accurate at the 0.5% level and they provide a rationale for previous empirical fits to wave propagation velocities with a quantitative agreement at the 0.07-0.7% level. We conclude that, within the formalism presented here, it is appropriate to use, with confidence, velocity measurements to characterize ice fabrics.

  16. Propagation of elastic waves through textured polycrystals: application to ice

    PubMed Central

    Maurel, Agnès; Lund, Fernando; Montagnat, Maurine

    2015-01-01

    The propagation of elastic waves in polycrystals is revisited, with an emphasis on configurations relevant to the study of ice. Randomly oriented hexagonal single crystals are considered with specific, non-uniform, probability distributions for their major axis. Three typical textures or fabrics (i.e. preferred grain orientations) are studied in detail: one cluster fabric and two girdle fabrics, as found in ice recovered from deep ice cores. After computing the averaged elasticity tensor for the considered textures, wave propagation is studied using a wave equation with elastic constants c=〈c〉+δc that are equal to an average plus deviations, presumed small, from that average. This allows for the use of the Voigt average in the wave equation, and velocities are obtained solving the appropriate Christoffel equation. The velocity for vertical propagation, as appropriate to interpret sonic logging measurements, is analysed in more details. Our formulae are shown to be accurate at the 0.5% level and they provide a rationale for previous empirical fits to wave propagation velocities with a quantitative agreement at the 0.07–0.7% level. We conclude that, within the formalism presented here, it is appropriate to use, with confidence, velocity measurements to characterize ice fabrics. PMID:27547099

  17. Excitation wave propagation in a patterned multidomain cardiac tissue

    NASA Astrophysics Data System (ADS)

    Kudryashova, N. N.; Teplenin, A. S.; Orlova, Y. V.; Agladze, K. I.

    2015-06-01

    Electrospun fibrous mats are widely used in the contemporary cardiac tissue engineering as the substrates for growing cardiac cells. The substrate with chaotically oriented nanofibers leads to the growth of cardiac tissue with randomly oriented, but internally morphologically anisotropic clusters or domains. The domain structure affects the stability of the excitation propagation and we studied the stability of the propagating excitation waves versus the average size of the domains and the externally applied excitation rate. In an experimental model based on neonatal rat cardiac tissue monolayers, as well as in the computer simulations, we have found that an increase in domain sizes leads to the decrease in the critical stimulation frequencies, thus evidencing that larger domains are having a higher arrhythmogenic effect.

  18. Fourier-transform light scattering of individual colloidal clusters.

    PubMed

    Yu, HyeonSeung; Park, HyunJoo; Kim, Youngchan; Kim, Mahn Won; Park, YongKeun

    2012-07-01

    We present measurements of the scalar-field light scattering of individual dimer, trimer, and tetrahedron shapes among colloidal clusters. By measuring the electric field with quantitative phase imaging at the sample plane and then numerically propagating to the far-field scattering plane, the two-dimensional light-scattering patterns from individual colloidal clusters are effectively and precisely retrieved. The measured scattering patterns are consistent with simulated patterns calculated from the generalized multiparticle Mie solution.

  19. Propagators in polymer quantum mechanics

    NASA Astrophysics Data System (ADS)

    Flores-González, Ernesto; Morales-Técotl, Hugo A.; Reyes, Juan D.

    2013-09-01

    Polymer Quantum Mechanics is based on some of the techniques used in the loop quantization of gravity that are adapted to describe systems possessing a finite number of degrees of freedom. It has been used in two ways: on one hand it has been used to represent some aspects of the loop quantization in a simpler context, and, on the other, it has been applied to each of the infinite mechanical modes of other systems. Indeed, this polymer approach was recently implemented for the free scalar field propagator. In this work we compute the polymer propagators of the free particle and a particle in a box; amusingly, just as in the non polymeric case, the one of the particle in a box may be computed also from that of the free particle using the method of images. We verify the propagators hereby obtained satisfy standard properties such as: consistency with initial conditions, composition and Green's function character. Furthermore they are also shown to reduce to the usual Schrödinger propagators in the limit of small parameter μ0, the length scale introduced in the polymer dynamics and which plays a role analog of that of Planck length in Quantum Gravity.

  20. Microwave Propagation in Dielectric Fluids.

    ERIC Educational Resources Information Center

    Lonc, W. P.

    1980-01-01

    Describes an undergraduate experiment designed to verify quantitatively the effect of a dielectric fluid's dielectric constant on the observed wavelength of microwave radiation propagating through the fluid. The fluid used is castor oil, and results agree with the expected behavior within 5 percent. (Author/CS)

  1. Smooth affine shear tight frames: digitization and applications

    NASA Astrophysics Data System (ADS)

    Zhuang, Xiaosheng

    2015-08-01

    In this paper, we mainly discuss one of the recent developed directional multiscale representation systems: smooth affine shear tight frames. A directional wavelet tight frame is generated by isotropic dilations and translations of directional wavelet generators, while an affine shear tight frame is generated by anisotropic dilations, shears, and translations of shearlet generators. These two tight frames are actually connected in the sense that the affine shear tight frame can be obtained from a directional wavelet tight frame through subsampling. Consequently, an affine shear tight frame indeed has an underlying filter bank from the MRA structure of its associated directional wavelet tight frame. We call such filter banks affine shear filter banks, which can be designed completely in the frequency domain. We discuss the digitization of affine shear filter banks and their implementations: the forward and backward digital affine shear transforms. Redundancy rate and computational complexity of digital affine shear transforms are also investigated in this paper. Numerical experiments and comparisons in image/video processing show the advantages of digital affine shear transforms over many other state-of-art directional multiscale representation systems.

  2. Evolution of promoter affinity for transcription factors in the human lineage.

    PubMed

    Molineris, Ivan; Grassi, Elena; Ala, Ugo; Di Cunto, Ferdinando; Provero, Paolo

    2011-08-01

    Changes in gene regulation are believed to play an important role in the evolution of animals. It has been suggested that changes in cis-regulatory regions are responsible for many or most of the anatomical and behavioral differences between humans and apes. However, the study of the evolution of cis-regulatory regions is made problematic by the degeneracy of transcription factor (TF) binding sites and the shuffling of their positions. In this work, we use the predicted total affinity of a promoter for a large collection of TFs as the basis for studying the evolution of cis-regulatory regions in mammals. We introduce the human specificity of a promoter, measuring the divergence between the affinity profile of a human promoter and its orthologous promoters in other mammals. The promoters of genes involved in functional categories such as neural processes and signal transduction, among others, have higher human specificity compared with the rest of the genome. Clustering of the human-specific affinities (HSAs) of neural genes reveals patterns of promoter evolution associated with functional categories such as synaptic transmission and brain development and to diseases such as bipolar disorder and autism.

  3. First molecular and biochemical analysis of in vivo affinity maturation in an ectothermic vertebrate.

    PubMed

    Dooley, Helen; Stanfield, Robyn L; Brady, Rebecca A; Flajnik, Martin F

    2006-02-07

    The cartilaginous fish are the oldest phylogenetic group in which Igs have been found. Sharks produce a unique Ig isotype, IgNAR, a heavy-chain homodimer that does not associate with light chains. Instead, the variable (V) regions of IgNAR bind antigen as soluble single domains. Our group has shown that IgNAR plays an integral part in the humoral response of nurse sharks (Ginglymostoma cirratum) upon antigen challenge. Here, we generated phage-displayed libraries of IgNAR V regions from an immunized animal and found a family of clones derived from the same rearrangement event but differentially mutated during expansion. Because of the cluster organization of shark Ig genes and the paucicopy nature of IgNAR, we were able to construct the putative ancestor of this family. By studying mutations in the context of clone affinities, we found evidence that affinity maturation occurs for this isotype. Subsequently, we were able to identify mutations important in the affinity improvement of this family. Because the family clones were all obtained after immunization, they provide insight into the in vivo maturation mechanisms, in general, and for single-domain antibody fragments.

  4. A study of electron affinities using the initiator approach to full configuration interaction quantum Monte Carlo.

    PubMed

    Cleland, D M; Booth, George H; Alavi, Ali

    2011-01-14

    For the atoms with Z ≤ 11, energies obtained using the "initiator" extension to full configuration interaction quantum Monte Carlo (i-FCIQMC) come to within statistical errors of the FCIQMC results. As these FCIQMC values have been shown to converge onto FCI results, the i-FCIQMC method allows similar accuracy to be achieved while significantly reducing the scaling with the size of the Slater determinant space. The i-FCIQMC electron affinities of the Z ≤ 11 atoms in the aug-cc-pVXZ basis sets are presented here. In every case, values are obtained to well within chemical accuracy [the mean absolute deviation (MAD) from the relativistically corrected experimental values is 0.41 mE(h)], and significantly improve on coupled cluster with singles, doubles and perturbative triples [CCSD(T)] results. Since the only remaining source of error is basis set incompleteness, we have investigated using CCSD(T)-F12 contributions to correct the i-FCIQMC results. By doing so, much faster convergence with respect to basis set size may be achieved for both the electron affinities and the FCIQMC ionization potentials presented in a previous paper. With this F12 correction, the MAD can be further reduced to 0.13 mE(h) for the electron affinities and 0.31 mE(h) for the ionization potentials.

  5. Nanostar clustering improves the sensitivity of plasmonic assays

    PubMed Central

    Park, Yong; Im, Hyungsoon; Weissleder, Ralph; Lee, Hakho

    2017-01-01

    Star-shaped Au nanoparticles (Au nanostars, AuNS) have been developed to improve the plasmonic sensitivity, but their application has largely been limited to single-particle probes. We herein describe a AuNS clustering assay based on nanoscale self-assembly of multiple AuNS and which further increases detection sensitivity. We show that each cluster contains multiple nanogaps to concentrate electric fields, thereby amplifying the signal via plasmon coupling. Numerical simulation indicated that AuNS clusters assume up to 460-fold higher field density than Au nanosphere clusters of similar mass. The results were validated in model assays of protein biomarker detection. The AuNS clustering assay showed higher sensitivity than Au nanosphere. Minimizing the size of affinity ligand was found important to tightly confine electric fields and improve the sensitivity. The resulting assay is simple and fast, and can be readily applied to point-of-care molecular detection schemes. PMID:26102604

  6. Noncompetitive affinity assays of glucagon and amylin using mirror-image aptamers as affinity probes.

    PubMed

    Yi, Lian; Wang, Xue; Bethge, Lucas; Klussmann, Sven; Roper, Michael G

    2016-03-21

    The ability to detect picomolar concentrations of glucagon and amylin using fluorescently labeled mirror-image aptamers, so-called Spiegelmers, is demonstrated. Spiegelmers rival the specificity of antibodies and overcome the problem of biostability of natural aptamers in a biological matrix. Using Spiegelmers as affinity probes, noncompetitive capillary electrophoresis affinity assays of glucagon and murine amylin were developed and optimized. The detection limit for glucagon was 6 pM and for amylin was 40 pM. Glucagon-like peptide-1 and -2 did not interfere with the glucagon assay, while the amylin assay showed cross-reactivity to calcitonin gene related peptide. The developed assays were combined with a competitive immunoassay for insulin to measure glucagon, amylin, and insulin secretion from batches of islets after incubation with different glucose concentrations. The development of these assays is an important step towards incorporation into an online measurement system for monitoring dynamic secretion from single islets.

  7. Effects of shear rate on propagation of blood clotting determined using microfluidics and numerical simulations.

    PubMed

    Runyon, Matthew K; Kastrup, Christian J; Johnson-Kerner, Bethany L; Ha, Thuong G Van; Ismagilov, Rustem F

    2008-03-19

    This paper describes microfluidic experiments with human blood plasma and numerical simulations to determine the role of fluid flow in the regulation of propagation of blood clotting. We demonstrate that propagation of clotting can be regulated by different mechanisms depending on the volume-to-surface ratio of a channel. In small channels, propagation of clotting can be prevented by surface-bound inhibitors of clotting present on vessel walls. In large channels, where surface-bound inhibitors are ineffective, propagation of clotting can be prevented by a shear rate above a threshold value, in agreement with predictions of a simple reaction-diffusion mechanism. We also demonstrate that propagation of clotting in a channel with a large volume-to-surface ratio and a shear rate below a threshold shear rate can be slowed by decreasing the production of thrombin, an activator of clotting. These in vitro results make two predictions, which should be experimentally tested in vivo. First, propagation of clotting from superficial veins to deep veins may be regulated by shear rate, which might explain the correlation between superficial thrombosis and the development of deep vein thrombosis (DVT). Second, nontoxic thrombin inhibitors with high binding affinities could be locally administered to prevent recurrent thrombosis after a clot has been removed. In addition, these results demonstrate the utility of simplified mechanisms and microfluidics for generating and testing predictions about the dynamics of complex biochemical networks.

  8. Pressure wave propagation studies for oscillating cascades

    NASA Technical Reports Server (NTRS)

    Huff, Dennis L.

    1992-01-01

    The unsteady flowfield around an oscillating cascade of flat plates is studied using a time marching Euler code. Exact solutions based on linear theory serve as model problems to study pressure wave propagation in the numerical solution. The importance of using proper unsteady boundary conditions, grid resolution, and time step is demonstrated. Results show that an approximate non-reflecting boundary condition based on linear theory does a good job of minimizing reflections from the inflow and outflow boundaries and allows the placement of the boundaries to be closer than cases using reflective boundary conditions. Stretching the boundary to dampen the unsteady waves is another way to minimize reflections. Grid clustering near the plates does a better job of capturing the unsteady flowfield than cases using uniform grids as long as the CFL number is less than one for a sufficient portion of the grid. Results for various stagger angles and oscillation frequencies show good agreement with linear theory as long as the grid is properly resolved.

  9. Pressure wave propagation studies for oscillating cascades

    NASA Technical Reports Server (NTRS)

    Huff, Dennis L.

    1992-01-01

    The unsteady flow field around an oscillating cascade of flat plates is studied using a time marching Euler code. Exact solutions based on linear theory serve as model problems to study pressure wave propagation in the numerical solution. The importance of using proper unsteady boundary conditions, grid resolution, and time step is demonstrated. Results show that an approximate non-reflecting boundary condition based on linear theory does a good job of minimizing reflections from the inflow and outflow boundaries and allows the placement of the boundaries to be closer than cases using reflective boundary conditions. Stretching the boundary to dampen the unsteady waves is another way to minimize reflections. Grid clustering near the plates does a better job of capturing the unsteady flow field than cases using uniform grids as long as the CFL number is less than one for a sufficient portion of the grid. Results for various stagger angles and oscillation frequencies show good agreement with linear theory as long as the grid is properly resolved.

  10. Simulation of MAD Cow Disease Propagation

    NASA Astrophysics Data System (ADS)

    Magdoń-Maksymowicz, M. S.; Maksymowicz, A. Z.; Gołdasz, J.

    Computer simulation of dynamic of BSE disease is presented. Both vertical (to baby) and horizontal (to neighbor) mechanisms of the disease spread are considered. The game takes place on a two-dimensional square lattice Nx×Ny = 1000×1000 with initial population randomly distributed on the net. The disease may be introduced either with the initial population or by a spontaneous development of BSE in an item, at a small frequency. Main results show a critical probability of the BSE transmission above which the disease is present in the population. This value is vulnerable to possible spatial clustering of the population and it also depends on the mechanism responsible for the disease onset, evolution and propagation. A threshold birth rate below which the population is extinct is seen. Above this threshold the population is disease free at equilibrium until another birth rate value is reached when the disease is present in population. For typical model parameters used for the simulation, which may correspond to the mad cow disease, we are close to the BSE-free case.

  11. A quaternion-based spectral clustering method for color image segmentation

    NASA Astrophysics Data System (ADS)

    Li, Xiang; Jin, Lianghai; Liu, Hong; He, Zeng

    2011-11-01

    Spectral clustering method has been widely used in image segmentation. A key issue in spectral clustering is how to build the affinity matrix. When it is applied to color image segmentation, most of the existing methods either use Euclidean metric to define the affinity matrix, or first converting color-images into gray-level images and then use the gray-level images to construct the affinity matrix (component-wise method). However, it is known that Euclidean distances can not represent the color differences well and the component-wise method does not consider the correlation between color channels. In this paper, we propose a new method to produce the affinity matrix, in which the color images are first represented in quaternion form and then the similarities between color pixels are measured by quaternion rotation (QR) mechanism. The experimental results show the superiority of the new method.

  12. Affine connection form of Regge calculus

    NASA Astrophysics Data System (ADS)

    Khatsymovsky, V. M.

    2016-12-01

    Regge action is represented analogously to how the Palatini action for general relativity (GR) as some functional of the metric and a general connection as independent variables represents the Einstein-Hilbert action. The piecewise flat (or simplicial) spacetime of Regge calculus is equipped with some world coordinates and some piecewise affine metric which is completely defined by the set of edge lengths and the world coordinates of the vertices. The conjugate variables are the general nondegenerate matrices on the three-simplices which play the role of a general discrete connection. Our previous result on some representation of the Regge calculus action in terms of the local Euclidean (Minkowsky) frame vectors and orthogonal connection matrices as independent variables is somewhat modified for the considered case of the general linear group GL(4, R) of the connection matrices. As a result, we have some action invariant w.r.t. arbitrary change of coordinates of the vertices (and related GL(4, R) transformations in the four-simplices). Excluding GL(4, R) connection from this action via the equations of motion we have exactly the Regge action for the considered spacetime.

  13. [Separation of osteoclasts by lectin affinity chromatography].

    PubMed

    Itokazu, M; Tan, A; Tanaka, S

    1991-09-01

    Newborn rat calvaria bone cells obtained by digestion were fractionated on columns of wheat-germ agglutinin (WGA) sepharose 6MB for osteoclast isolation. The initial nonspecific binding cells which were passed through the WGA sepharose column by a buffer acquired a high enzyme activity of alkaline phosphatase, but not that of acid phosphatase. However, elution of cells using a buffer with the addition of N-acetyl-D-glucosamine resulted in a high acid phosphatase activity but no alkaline phosphatase activity. The former WGA binding negative fraction enriched osteoblasts averaging 30 microns in size. The latter WGA binding positive fraction enriched osteoclasts ranging from 20 microns to 60 microns in size. The electron-microscope clearly demonstrated the cellular details of osteoclasts. Isolated cell counts showed a ratio of six to four. These results indicate that our method of osteoclast isolation is simple and useful in lectin affinity chromatography because all cells have sugar moieties on their surface and the binding of osteoclasts can be reversed by the addition of specific lectin-binding sugars to the eluting buffer.

  14. Prostate Cancer and Bone: The Elective Affinities

    PubMed Central

    2014-01-01

    The onset of metastases dramatically changes the prognosis of prostate cancer patients, determining increased morbidity and a drastic fall in survival expectancy. Bone is a common site of metastases in few types of cancer, and it represents the most frequent metastatic site in prostate cancer. Of note, the prevalence of tumor relapse to the bone appears to be increasing over the years, likely due to a longer overall survival of prostate cancer patients. Bone tropism represents an intriguing challenge for researchers also because the preference of prostate cancer cells for the bone is the result of a sequential series of targetable molecular events. Many factors have been associated with the peculiar ability of prostate cancer cells to migrate in bone marrow and to determine mixed osteoblastic/osteolytic lesions. As anticipated by the success of current targeted therapy aimed to block bone resorption, a better understanding of molecular affinity between prostate cancer and bone microenvironment will permit us to cure bone metastasis and to improve prognosis of prostate cancer patients. PMID:24971315

  15. Multiplexed protein profiling by sequential affinity capture

    PubMed Central

    Ayoglu, Burcu; Birgersson, Elin; Mezger, Anja; Nilsson, Mats; Uhlén, Mathias; Nilsson, Peter

    2016-01-01

    Antibody microarrays enable parallelized and miniaturized analysis of clinical samples, and have proven to provide novel insights for the analysis of different proteomes. However, there are concerns that the performance of such direct labeling and single antibody assays are prone to off‐target binding due to the sample context. To improve selectivity and sensitivity while maintaining the possibility to conduct multiplexed protein profiling, we developed a multiplexed and semi‐automated sequential capture assay. This novel bead‐based procedure encompasses a first antigen capture, labeling of captured protein targets on magnetic particles, combinatorial target elution and a read‐out by a secondary capture bead array. We demonstrate in a proof‐of‐concept setting that target detection via two sequential affinity interactions reduced off‐target contribution, while lowered background and noise levels, improved correlation to clinical values compared to single binder assays. We also compared sensitivity levels with single binder and classical sandwich assays, explored the possibility for DNA‐based signal amplification, and demonstrate the applicability of the dual capture bead‐based antibody microarray for biomarker analysis. Hence, the described concept enhances the possibilities for antibody array assays to be utilized for protein profiling in body fluids and beyond. PMID:26935855

  16. Cambrian trilobites with Siberian affinities, southwestern Alaska

    SciTech Connect

    Palmer, A.R.; Egbert, R.M.; Sullivan, R.; Knoth, J.S.

    1985-02-01

    Cambrian trilobites occur in two levels (about 7 m apart) in the core of a large, complex anticlinal structure in the area between the Taylor Mountains and the Hoholitna River in southwestern Alaska. The lower collection contains Erbia, Macannaia (a species close to Soviet forms described as Pagetia ferox Lermontova), two species of Kootenia (including one perhaps cospecific with forms from the central Brooks range), and several species of ptychoparioid trilobites. It is clear that biogeographic affinities are with the transitional facies of the eastern Siberian platform and the south Siberian foldbelt. In Soviet terms, the age of the collection falls in a disputed interval called latest Early Cambrian (Tojonian) by some authors, and earliest Middle Cambrian (Amgan) by others. In North American terms, Macannaia is known only from early Middle Cambrian beds. The younger collection contains abundant agnostids, a variety of conocoryphids, Paradoxides, and several species of ptychoparioid trilobites. This is an assemblage of undoubted late Middle Cambrian age, comparable to faunas described from the Maya State of the Siberian platform and the Paradoxides paradoxissimus Stage of the Baltic region. Both faunas are from ocean-facing or outer shelf environments. None of the key non-agnostid or non-pagetiid elements have been seen previously in deposits of Cambrian North America.

  17. Affinity of guanosine derivatives for polycytidylate revisited

    NASA Technical Reports Server (NTRS)

    Kanavarioti, A.; Hurley, T. B.; Baird, E. E.

    1995-01-01

    Evidence is presented for complexation of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) with polycytidylate (poly(C)) at pH 8.0 and 23 degrees C in the presence of 1.0 M NaCl2 and 0.2 M MgCl2 in water. The association of 2-MeImpG with poly(C) was investigated using UV-vis spectroscopy as well as by monitoring the kinetics of the nucleophilic substitution reaction of the imidazole moiety by amines. The results of both methods are consistent with moderately strong poly(C) 2-MeImpG complexation and the spectrophotometric measurements allowed the construction of a binding isotherm with a concentration of 2-MeImpG equal to 5.55 +/- 0.15 mM at half occupancy. UV spectroscopy was employed to establish the binding of other guanosine derivatives on poly(C). These derivatives are guanosine 5'-monophosphate (5'GMP), guanosine 5'-monophosphate imidazolide (ImpG), and guanosine 5'-monophosphate morpholidate (morpG). Within experimental error these guanosine derivatives exhibit the same affinity for poly(C) as 2-MeImpG.

  18. Macroporous chitin affinity membranes for lysozyme separation.

    PubMed

    Ruckenstein, E; Zeng, X

    1997-12-20

    Macroporous chitin membranes with high, controlled porosity and good mechanical properties have been prepared using a technique developed in this laboratory based on silica particles as porogen. They were employed for the affinity separation of lysozyme. Chitin membranes (1 mm thickness) can be operated at high fluxes (>/=1.1 mL/min/cm(2)) corresponding to pressure drops >/=2 psi. Their adsorption capacity for lysozyme ( approximately 50 mg/mL membrane) is by an order of magnitude higher than that of the chitin beads employed in column separation. In a binary mixture of lysozyme and ovalbumin, the membranes showed very high selectivity towards lysozyme. The effect of some important operation parameters, such as the flow rates during loading and elution were investigated. Lysozyme of very high purity (>98%) was obtained from a mixture of lysozyme and ovalbumin, and from egg white. The results indicate that the macroporous chitin membranes can be used for the separation, purification, and recovery of lysozyme at large scale. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 610-617, 1997.

  19. Lightning location with variable radio wave propagation velocity

    NASA Astrophysics Data System (ADS)

    Liu, Zhongjian; Koh, Kuang Liang; Mezentsev, Andrew; Sugier, Jacqueline; Fullekrug, Martin

    2016-04-01

    Lightning discharges can be located by triangulation of their broadband electromagnetic pulses in long-baseline (~500 km) radio receiver networks. Here we apply the time of arrival difference (TOA) method to electric field recordings with a low frequency radio receiver array consisting of four stations in western Europe. The electromagnetic wave propagation velocity at low radio frequencies is an important input parameter for the TOA calculation and it is normally assumed to be equal to the speed of light. However, the radio wave propagation depends for example on the frequency, ground conductivity and the ionospheric height and small variations can cause location differences from hundreds to thousands of meters, as demonstrated in this study. The radio wave propagation from two VLF transmissions at 20.9 kHz and 23.4 kHz are compared. The results show that the apparent phase velocities are 0.6% slower and 0.5% faster than the speed of light respectively. As a result, a variable velocity is implemented in the TOA method using continuously recorded data on the 8th August 2014, when a mesoscale convective system developed over central France. The lightning locations inferred with a variable wave propagation velocity are more clustered than those using a fixed velocity. The distribution of the lightning velocities in a given geographic area fits a normal distribution that is not centred at the speed of light. As a result, representative velocities can be calculated for smaller regions to generate a velocity map over a larger area of enhanced lightning activity. These results suggest a connection with the ground elevation and/or surface conductivity that might have an impact on the observed wave propagation velocities.

  20. Germinal center reaction: antigen affinity and presentation explain it all.

    PubMed

    Oropallo, Michael A; Cerutti, Andrea

    2014-07-01

    The selection and expansion of B cells undergoing affinity maturation in the germinal center is a hallmark of humoral immunity. A recent paper in Nature provides new insights into the relationships between the affinity of the immunoglobulin receptor for antigen, the ability of B cells to present antigen to T cells, and the processes of selection, mutation, and clonal expansion in the germinal center.

  1. Striving for Empathy: Affinities, Alliances and Peer Sexuality Educators

    ERIC Educational Resources Information Center

    Fields, Jessica; Copp, Martha

    2015-01-01

    Peer sexuality educators' accounts of their work reveal two approaches to empathy with their students: affinity and alliance. "Affinity-based empathy" rests on the idea that the more commonalities sexuality educators and students share (or perceive they share), the more they will be able to empathise with one another, while…

  2. Conformational kinetics reveals affinities of protein conformational states.

    PubMed

    Daniels, Kyle G; Suo, Yang; Oas, Terrence G

    2015-07-28

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

  3. Affine group formulation of the Standard Model coupled to gravity

    SciTech Connect

    Chou, Ching-Yi; Ita, Eyo; Soo, Chopin

    2014-04-15

    In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant.

  4. Tending to Change: Toward a Situated Model of Affinity Spaces

    ERIC Educational Resources Information Center

    Bommarito, Dan

    2014-01-01

    The concept of affinity spaces, a theoretical construct used to analyze literate activity from a spatial perspective, has gained popularity among scholars of literacy studies and, particularly, video-game studies. This article seeks to expand current notions of affinity spaces by identifying key assumptions that have limited researchers'…

  5. PREFACE: Nuclear Cluster Conference; Cluster'07

    NASA Astrophysics Data System (ADS)

    Freer, Martin

    2008-05-01

    The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

  6. Sound propagation in choked ducts

    NASA Technical Reports Server (NTRS)

    Hersh, A. S.; Liu, C. Y.

    1976-01-01

    The linearized equations describing the propagation of sound in variable area ducts containing flow are shown to be singular when the duct mean flow is sonic. The singularity is removed when previously ignored nonlinear terms are retained. The results of a numerical study, for the case of plane waves propagating in a one-dimensional converging-diverging duct, show that the sound field is adequately described by the linearized equations only when the axial mean flow Mach number at the duct throat M sub th 0.6. For M sub th 0.6, the numerical results showed that acoustic energy flux was not conserved. An attempt was made to extend the study to include the nonlinear behavior of the sound field. Meaningful results were not obtained due, primarily, to numerical difficulties.

  7. Exact propagators in harmonic superspace

    NASA Astrophysics Data System (ADS)

    Kuzenko, Sergei M.

    2004-10-01

    Within the background field formulation in harmonic superspace for quantum N = 2 super-Yang-Mills theories, the propagators of the matter, gauge and ghost superfields possess a complicated dependence on the SU(2) harmonic variables via the background vector multiplet. This dependence is shown to simplify drastically in the case of an on-shell vector multiplet. For a covariantly constant background vector multiplet, we exactly compute all the propagators. In conjunction with the covariant multi-loop scheme developed in arxiv:hep-th/0302205, these results provide an efficient (manifestly N = 2 supersymmetric) technical setup for computing multi-loop quantum corrections to effective actions in N = 2 supersymmetric gauge theories, including the N = 4 super-Yang-Mills theory.

  8. Atmospheric propagation of THz radiation.

    SciTech Connect

    Wanke, Michael Clement; Mangan, Michael A.; Foltynowicz, Robert J.

    2005-11-01

    In this investigation, we conduct a literature study of the best experimental and theoretical data available for thin and thick atmospheres on THz radiation propagation from 0.1 to 10 THz. We determined that for thick atmospheres no data exists beyond 450 GHz. For thin atmospheres data exists from 0.35 to 1.2 THz. We were successful in using FASE code with the HITRAN database to simulate the THz transmission spectrum for Mauna Kea from 0.1 to 2 THz. Lastly, we successfully measured the THz transmission spectra of laboratory atmospheres at relative humidities of 18 and 27%. In general, we found that an increase in the water content of the atmosphere led to a decrease in the THz transmission. We identified two potential windows in an Albuquerque atmosphere for THz propagation which were the regions from 1.2 to 1.4 THz and 1.4 to 1.6 THz.

  9. Fracture propagation, pipe deformation study

    SciTech Connect

    Aloe, A.; Di Candia, A.; Bramante, M.

    1983-04-15

    Shear fracture propagation has become an important research subject connected with design aspects of gas pipelines. Difficulties involved in predicting safe service conditions from pure theoretical studies require 1:1 scale experiments. Through these tests, semiempirical design criteria was formulated where the minimum level of material quality, indicated by Charpy V energy in the ductile range, is determined as a function of pipe geometry and hoop stress. Disagreements exist among these criteria. Different arrest energy predictions at high hoop stresses and different effects ascribed to the thickness have called for further research in the field. Some interesting indications were obtained about shape and size of the plastic zone ahead of the propagating crack. Burst tests have been conducted and are discussed.

  10. Special Topics in HF Propagation

    DTIC Science & Technology

    1979-11-01

    data for the prediction of auroral absorption experienced by high-frequency radio waves: Basler (1965), Gorbushina et al. (1969), Agy (1970), Vargas ...Thomas (1959), Studies in polar blackout morphology, URSI-AGI, Com- mittee Report. Vargas -Vila, R. (1972), Auroral absorption predictions for high...cuide wa]ls in mho/m permeability of the propagation medium in henry /m E. permittivity of the propagat.on medium iiu fa-ad/m. For TE. modes, thi-s

  11. A database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Suwitra, Krisjani; Le, Chuong

    1995-01-01

    A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel software under Windows environment or a Macintosh using Excel software for Macintosh. All the steps necessary to use the software are easy and many times self explanatory.

  12. A database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.; Suwitra, Krisjani; Le, Choung

    1994-01-01

    A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel software under Windows environment or a Macintosh using Excel software for Macintosh. All the steps necessary to use the software are easy and many times self-explanatory; however, a sample run of the CCIR rain attenuation model is presented.

  13. A database for propagation models

    NASA Astrophysics Data System (ADS)

    Kantak, Anil V.; Suwitra, Krisjani; Le, Chuong

    1995-08-01

    A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel software under Windows environment or a Macintosh using Excel software for Macintosh. All the steps necessary to use the software are easy and many times self explanatory.

  14. UHF Radiowave Propagation through Forests

    DTIC Science & Technology

    1982-09-01

    sde It nece sary and Identify b block number) " A model for UHF radiowave propagation thzough a forest of tree trunks, branches, and leaves is...all having prescribed location and orientation statistics. Tree trunks are modelled as infinitely-long, circular, lossy-di- electric cylinders...results. An anisotropic half-space model of the forest is developed based upon the effective dyadic susceptibility and the direct-, reflected-, and

  15. GOES dynamic propagation of attitude

    NASA Technical Reports Server (NTRS)

    Markley, F. Landis; Seidewitz, ED; Chu, Don; Rowe, John N.

    1988-01-01

    The spacecraft in the next series of Geostationary Operational Environmental Satellites (GOES-Next) are Earth pointing and have 5-year mission lifetimes. Because gyros can be depended on only for a few years of continuous use, they will be turned off during routine operations. This means attitude must, at times, be determined without benefit of gyros and, often, using only Earth sensor data. To minimize the interruption caused by dumping angular momentum, these spacecraft have been designed to reduce the environmental torque acting on them and incorporate an adjustable solar trim tab for fine adjustment. A new support requirement for GOES-Next is that of setting the solar trim tab. Optimizing its setting requires an estimate of the unbalanced torque on the spacecraft. These two requirements, determining attitude without gyros and estimating the external torque, are addressed by replacing or supplementing the gyro propagation with a dynamic one, that is, one that integrates the rigid body equations of motion. By processing quarter-orbit or longer batches, this approach takes advantage of roll-yaw coupling to observe attitude completely without Sun sensor data. Telemetered momentum wheel speeds are used as observations of the unbalanced external torques. GOES-Next provides a unique opportunity to study dynamic attitude propagation. The geosynchronous altitude and adjustable trim tab minimize the external torque and its uncertainty, making long-term dynamic propagation feasible. This paper presents the equations for dynamic propagation, an analysis of the environmental torques, and an estimate of the accuracies obtainable with the proposed method.

  16. Camelid VHH affinity ligands enable separation of closely related biopharmaceuticals

    PubMed Central

    Pabst, Timothy M.; Wendeler, Michaela; Wang, Xiangyang; Bezemer, Sandra; Hermans, Pim

    2016-01-01

    Abstract Interest in new and diverse classes of molecules such as recombinant toxins, enzymes, and blood factors continues to grow for use a biotherapeutics. Compared to monoclonal antibodies, these novel drugs typically lack a commercially available affinity chromatography option, which leads to greater process complexity, longer development timelines, and poor platformability. To date, for both monoclonal antibodies and novel molecules, affinity chromatography has been mostly reserved for separation of process‐related impurities such as host cell proteins and DNA. Reports of affinity purification of closely related product variants and modified forms are much rarer. In this work we describe custom affinity chromatography development using camelid VHH antibody fragments as "tunable" immunoaffinity ligands for separation of product‐related impurities. One example demonstrates high selectivity for a recombinant immunotoxin where no binding was observed for an undesired deamidated species. Also discussed is affinity purification of a coagulation factor through specific recognition of the gamma‐carboxylglutamic acid domain. PMID:27677057

  17. Affinity Monolith-Integrated Microchips for Protein Purification and Concentration.

    PubMed

    Gao, Changlu; Sun, Xiuhua; Wang, Huaixin; Qiao, Wei; Hu, Bo

    2016-01-01

    Affinity chromatography is a valuable method to purify and concentrate minute amount of proteins. Monoliths with epoxy groups for affinity immobilization were prepared by direct in-situ photopolymerization of glycidyl methacrylate and ethylene glycol dimethacrylate in porogenic solvents consisting of 1-dodecanol and cyclohexanol. By integrating affinity monoliths onto a microfluidic system, targeted biomolecules can be captured and retained on affinity column, while other biomolecules having no specific interactions toward the immobilized ligands flow through the microchannel. Therefore, proteins which remain on the affinity column are purified and concentrated, and then eluted by appropriate solutions and finally, separated by microchip capillary electrophoresis. This integrated microfluidic device has been applied to the purification and separation of specific proteins (FITC-labeled human serum albumin and IgG) in a mixture.

  18. Optimal T-cell receptor affinity for inducing autoimmunity

    PubMed Central

    Koehli, Sabrina; Naeher, Dieter; Galati-Fournier, Virginie; Zehn, Dietmar; Palmer, Ed

    2014-01-01

    T-cell receptor affinity for self-antigen has an important role in establishing self-tolerance. Three transgenic mouse strains expressing antigens of variable affinity for the OVA transgenic-I T-cell receptor were generated to address how TCR affinity affects the efficiency of negative selection, the ability to prime an autoimmune response, and the elimination of the relevant target cell. Mice expressing antigens with an affinity just above the negative selection threshold exhibited the highest risk of developing experimental autoimmune diabetes. The data demonstrate that close to the affinity threshold for negative selection, sufficient numbers of self-reactive T cells escape deletion and create an increased risk for the development of autoimmunity. PMID:25411315

  19. Detection of protein-protein interactions using tandem affinity purification.

    PubMed

    Goodfellow, Ian; Bailey, Dalan

    2014-01-01

    Tandem affinity purification (TAP) is an invaluable technique for identifying interaction partners for an affinity tagged bait protein. The approach relies on the fusion of dual tags to the bait before separate rounds of affinity purification and precipitation. Frequently two specific elution steps are also performed to increase the specificity of the overall technique. In the method detailed here, the two tags used are protein G and a short streptavidin binding peptide; however, many variations can be employed. In our example the tags are separated by a cleavable tobacco etch virus protease target sequence, allowing for specific elution after the first round of affinity purification. Proteins isolated after the final elution step in this process are concentrated before being identified by mass spectrometry. The use of dual affinity tags and specific elution in this technique dramatically increases both the specificity and stringency of the pull-downs, ensuring a low level of background nonspecific interactions.

  20. Affinity Regulates Spatial Range of EGF Receptor Autocrine Ligand Binding

    SciTech Connect

    Dewitt, Ann; Iida, Tomoko; Lam, Ho-Yan; Hill, Virginia; Wiley, H S.; Lauffenburger, Douglas A.

    2002-08-08

    Proper spatial localization of EGFR signaling activated by autocrine ligands represents a critical factor in embryonic development as well as tissue organization and function, and ligand/receptor binding affinity is among the molecular and cellular properties suggested to play a role in governing this localization. The authors employ a computational model to predict how receptor-binding affinity affects local capture of autocrine ligand vis-a-vis escape to distal regions, and provide experimental test by constructing cell lines expressing EGFR along with either wild-type EGF or a low-affinity mutant, EGF{sup L47M}. The model predicts local capture of a lower affinity autocrine ligand to be less efficient when the ligand production rate is small relative to receptor appearance rate. The experimental data confirm this prediction, demonstrating that cells can use ligand/receptor binding affinity to regulate ligand spatial distribution when autocrine ligand production is limiting for receptor signaling.

  1. Jet propagation through energetic materials

    SciTech Connect

    Pincosy, P; Poulsen, P

    2004-01-08

    In applications where jets propagate through energetic materials, they have been observed to become sufficiently perturbed to reduce their ability to effectively penetrate subsequent material. Analytical calculations of the jet Bernoulli flow provides an estimate of the onset and extent of such perturbations. Although two-dimensional calculations show the back-flow interaction pressure pulses, the symmetry dictates that the flow remains axial. In three dimensions the same pressure impulses can be asymmetrical if the jet is asymmetrical. The 3D calculations thus show parts of the jet having a significant component of radial velocity. On the average the downstream effects of this radial flow can be estimated and calculated by a 2D code by applying a symmetrical radial component to the jet at the appropriate position as the jet propagates through the energetic material. We have calculated the 3D propagation of a radio graphed TOW2 jet with measured variations in straightness and diameter. The resultant three-dimensional perturbations on the jet result in radial flow, which eventually tears apart the coherent jet flow. This calculated jet is compared with jet radiographs after passage through the energetic material for various material thickness and plate thicknesses. We noted that confinement due to a bounding metal plate on the energetic material extends the pressure duration and extent of the perturbation.

  2. Turbofan Acoustic Propagation and Radiation

    NASA Technical Reports Server (NTRS)

    Eversman, Walter

    2000-01-01

    This document describes progress in the development of finite element codes for the prediction of near and far field acoustic radiation from the inlet and aft fan ducts of turbofan engines. The report consists of nine papers which have appeared in archival journals and conference proceedings, or are presently in review for publication. Topics included are: 1. Aft Fan Duct Acoustic Radiation; 2. Mapped Infinite Wave Envelope Elements for Acoustic Radiation in a Uniformly Moving Medium; 3. A Reflection Free Boundary Condition for Propagation in Uniform Flow Using Mapped Infinite Wave Envelope Elements; 4. A Numerical Comparison Between Multiple-Scales and FEM Solution for Sound Propagation in Lined Flow Ducts; 5. Acoustic Propagation at High Frequencies in Ducts; 6. The Boundary Condition at an Impedance Wall in a Nonuniform Duct with Potential Flow; 7. A Reverse Flow Theorem and Acoustic Reciprocity in Compressible Potential Flows; 8. Reciprocity and Acoustics Power in One Dimensional Compressible Potential Flows; and 9. Numerical Experiments on Acoustic Reciprocity in Compressible Potential Flows.

  3. Sound Propagation in the Atmosphere

    NASA Astrophysics Data System (ADS)

    Attenborough, Keith

    Propagation of sound close to the ground outdoors involves geometric spreading, air absorption, interaction with the ground, barriers, vegetation and refraction associated with wind and temperature gradients. After a brief survey of historical aspects of the study of outdoor sound and its applications, this chapter details the physical principles associated with various propagation effects, reviews data that demonstrate them and methods for predicting them. The discussion is concerned primarily with the relatively short ranges and spectra of interest when predicting and assessing community noise rather than the frequencies and long ranges of concern, for example, in infrasonic global monitoring or used for remote sensing of the atmosphere. Specific phenomena that are discussed include spreading losses, atmospheric absorption, diffraction by barriers and buildings, interaction of sound with the ground (ground waves, surface waves, ground impedance associated with porosity and roughness, and elasticity effects), propagation through crops, shrubs and trees, wind and temperature gradient effects, shadow zones and incoherence due to atmospheric turbulence. The chapter concludes by suggesting a few areas that require further research.

  4. Transequatorial Propagation and Depletion Precursors

    NASA Astrophysics Data System (ADS)

    Miller, E. S.; Bust, G. S.; Kaeppler, S. R.; Frissell, N. A.; Paxton, L. J.

    2014-12-01

    The bottomside equatorial ionosphere in the afternoon and evening sector frequently evolves rapidly from smoothly stratified to violently unstable with large wedges of depleted plasma growing through to the topside on timescales of a few tens of minutes. These depletions have numerous practical impacts on radio propagation, including amplitude scintillation, field-aligned irregularity scatter, HF blackouts, and long-distance transequatorial propagation at frequencies above the MUF. Practical impacts notwithstanding, the pathways and conditions under which depletions form remain a topic of vigorous inquiry some 80 years after their first report. Structuring of the pre-sunset ionosphere---morphology of the equatorial anomalies and long-wavelength undulations of the isodensity contours on the bottomside---are likely to hold some clues to conditions that are conducive to depletion formation. The Conjugate Depletion Experiment is an upcoming transequatorial forward-scatter HF/VHF experiment to investigate pre-sunset undulations and their connection with depletion formation. We will present initial results from the Conjugate Depletion Experiment, as well as a companion analysis of a massive HF propagation data set.

  5. Ordered Subspace Clustering With Block-Diagonal Priors.

    PubMed

    Wu, Fei; Hu, Yongli; Gao, Junbin; Sun, Yanfeng; Yin, Baocai

    2016-12-01

    Many application scenarios involve sequential data, but most existing clustering methods do not well utilize the order information embedded in sequential data. In this paper, we study the subspace clustering problem for sequential data and propose a new clustering method, namely ordered sparse clustering with block-diagonal prior (BD-OSC). Instead of using the sparse normalizer in existing sparse subspace clustering methods, a quadratic normalizer for the data sparse representation is adopted to model the correlation among the data sparse coefficients. Additionally, a block-diagonal prior for the spectral clustering affinity matrix is integrated with the model to improve clustering accuracy. To solve the proposed BD-OSC model, which is a complex optimization problem with quadratic normalizer and block-diagonal prior constraint, an efficient algorithm is proposed. We test the proposed clustering method on several types of databases, such as synthetic subspace data set, human face database, video scene clips, motion tracks, and dynamic 3-D face expression sequences. The experiments show that the proposed method outperforms state-of-the-art subspace clustering methods.

  6. Calculations of precursor propagation in dispersive dielectrics.

    SciTech Connect

    Bacon, Larry Donald

    2003-08-01

    The present study is a numerical investigation of the propagation of electromagnetic transients in dispersive media. It considers propagation in water using Debye and composite Rocard-Powles-Lorentz models for the complex permittivity. The study addresses this question: For practical transmitted spectra, does precursor propagation provide any features that can be used to advantage over conventional signal propagation in models of dispersive media of interest? A companion experimental study is currently in progress that will attempt to measure the effects studied here.

  7. Confining crack propagation in defective graphene.

    PubMed

    López-Polín, Guillermo; Gómez-Herrero, Julio; Gómez-Navarro, Cristina

    2015-03-11

    Crack propagation in graphene is essential to understand mechanical failure in 2D materials. We report a systematic study of crack propagation in graphene as a function of defect content. Nanoindentations and subsequent images of graphene membranes with controlled induced defects show that while tears in pristine graphene span microns length, crack propagation is strongly reduced in the presence of defects. Accordingly, graphene oxide exhibits minor crack propagation. Our work suggests controlled defect creation as an approach to avoid catastrophic failure in graphene.

  8. Value, Cost, and Sharing: Open Issues in Constrained Clustering

    NASA Technical Reports Server (NTRS)

    Wagstaff, Kiri L.

    2006-01-01

    Clustering is an important tool for data mining, since it can identify major patterns or trends without any supervision (labeled data). Over the past five years, semi-supervised (constrained) clustering methods have become very popular. These methods began with incorporating pairwise constraints and have developed into more general methods that can learn appropriate distance metrics. However, several important open questions have arisen about which constraints are most useful, how they can be actively acquired, and when and how they should be propagated to neighboring points. This position paper describes these open questions and suggests future directions for constrained clustering research.

  9. Chasing polys: Interdisciplinary affinity and its connection to physics identity

    NASA Astrophysics Data System (ADS)

    Scott, Tyler D.

    This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a student sees themselves in relation to physics. By understanding how physics identity is developed, researchers and educators can identify factors that increase interest and engagement in physics classrooms. Therefore, physics identity was used in conjunction with interdisciplinary affinity. Using a mixed methods approach, this research used quantitative data to identify the relationships interdisciplinary affinity has with physics identity and the physics classroom. These connections were explored in more detail using a case study of three students in a high school physics class. Results showed significant and positive relationships between interdisciplinary affinity and physics identity, including the individual interest and recognition components of identity. It also identified characteristics of physics classrooms that had a significant, positive relationship with interdisciplinary affinity. The qualitative case study highlighted the importance of student interest to the relationship between interdisciplinary affinity and physics identity. It also identified interest and mastery orientation as key to understanding the link between interdisciplinary affinity and the physics classroom. These results are a positive sign that by understanding interdisciplinary affinity and physics identity

  10. Enzyme- and affinity biomolecule-mediated polymerization systems for biological signal amplification and cell screening.

    PubMed

    Malinowska, Klara H; Nash, Michael A

    2016-06-01

    Enzyme-mediated polymerization and polymerization-based signal amplification have emerged as two closely related techniques that are broadly applicable in the nanobio sciences. We review recent progress on polymerization systems mediated by biological molecules (e.g., affinity molecules and enzymes), and highlight newly developed formats and configurations of these systems to perform such tasks as non-instrumented biodetection, synthesis of core-shell nanomaterials, isolation of rare cells, and high-throughput screening. We discuss useful features of biologically mediated polymerization systems, such as multiple mechanisms of amplification (e.g., enzymatic, radical chain propagation), and the ability to localize structures at interfaces and at cell surfaces with microscopic spatial confinement. We close with a perspective on desirable improvements that need to be addressed to adapt these molecular systems to future applications.

  11. Japanese propagation experiments with ETS-5

    NASA Technical Reports Server (NTRS)

    Ikegami, Tetsushi

    1989-01-01

    Propagation experiments for maritime, aeronautical, and land mobile satellite communications were performed using Engineering Test Satellite-Five (ETS-5). The propagation experiments are one of major mission of Experimental Mobile Satellite System (EMSS) which is aimed for establishing basic technology for future general mobile satellite communication systems. A brief introduction is presented for the experimental results on propagation problems of ETS-5/EMSS.

  12. Understanding and Predicting Urban Propagation Losses

    DTIC Science & Technology

    2009-09-01

    available, the vast variety of physical cond Propagation Loss Tool will also be entered into a variety of examples, to test a few of the propagation loss...Model for Urban Areas. Rep. Silva, Junior, Edgar, and Gilberto A. Carrijo. "A Vectorial Istanbul: Bogazici University. Analysis of UHF Propagation

  13. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  14. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  15. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 3 2013-10-01 2013-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  16. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation....

  17. 49 CFR 195.111 - Fracture propagation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false Fracture propagation. 195.111 Section 195.111... PIPELINE Design Requirements § 195.111 Fracture propagation. A carbon dioxide pipeline system must be designed to mitigate the effects of fracture propagation. [Amdt. 195-45, 56 FR 26926, June 12, 1991]...

  18. Affinity capillary electrophoresis: the theory of electromigration.

    PubMed

    Dubský, Pavel; Dvořák, Martin; Ansorge, Martin

    2016-12-01

    We focus on the state-of-the-art theory of electromigration under single and multiple complexation equilibrium. Only 1:1 complexation stoichiometry is discussed because of its unique status in the field of affinity capillary electrophoresis (ACE). First, we summarize the formulas for the effective mobility in various ACE systems as they appeared since the pioneering days in 1992 up to the most recent theories till 2015. Disturbing phenomena that do not alter the mobility of the analyte directly but cause an unexpected peak broadening have been studied only recently and are also discussed in this paper. Second, we turn our attention to the viscosity effects in ACE. Change in the background electrolyte viscosity is unavoidable in ACE but numerous observations scattered throughout the literature have not been reviewed previously. This leads to an uncritical employment of correction factors that may or may not be appropriate in practice. Finally, we consider the ionic strength effects in ACE, too. Limitations of the current theories are also discussed and the tasks identified where open problems still prevail. Graphical Abstract A weak base (A) undergoes an acidic-basic equilibria (in blue) and migrates with an electrophoretic mobility of [Formula: see text]. Simultaneously, it interacts with a selector (sel) while the analyte-selector complex migrates with an electrophoretic mobility of [Formula: see text]. The strength of the interaction (in orange) is governed by the binding constant, K A , and the concentration of the selector, c sel . This all gives the analyte an effective mobility of [Formula: see text] and moves it out of the zero position (EOF; right top insert). The interaction of the positively charged analyte with the neutral selector slows down the analyte with increasing selector concentration (right bottom insert).

  19. Cluster Physics with Merging Galaxy Clusters

    NASA Astrophysics Data System (ADS)

    Molnar, Sandor

    Collisions between galaxy clusters provide a unique opportunity to study matter in a parameter space which cannot be explored in our laboratories on Earth. In the standard ΛCDM model, where the total density is dominated by the cosmological constant (Λ) and the matter density by cold dark matter (CDM), structure formation is hierarchical, and clusters grow mostly by merging. Mergers of two massive clusters are the most energetic events in the universe after the Big Bang, hence they provide a unique laboratory to study cluster physics. The two main mass components in clusters behave differently during collisions: the dark matter is nearly collisionless, responding only to gravity, while the gas is subject to pressure forces and dissipation, and shocks and turbulence are developed during collisions. In the present contribution we review the different methods used to derive the physical properties of merging clusters. Different physical processes leave their signatures on different wavelengths, thus our review is based on a multifrequency analysis. In principle, the best way to analyze multifrequency observations of merging clusters is to model them using N-body/HYDRO numerical simulations. We discuss the results of such detailed analyses. New high spatial and spectral resolution ground and space based telescopes will come online in the near future. Motivated by these new opportunities, we briefly discuss methods which will be feasible in the near future in studying merging clusters.

  20. Gold-bismuth clusters.

    PubMed

    Martínez, Ana

    2014-08-07

    Metal clusters have interesting characteristics, such as the relationship between properties and size of the cluster. This is not always apparent, so theoretical studies can provide relevant information. In this report, optimized structures and electron donor-acceptor properties of AunBim clusters are reported (n + m = 2-7, 20). Density functional theory calculations were performed to obtain optimized structures. The ground states of gold clusters formed with up to seven atoms are planar. The presence of Bi modifies the structure, and the clusters become 3-D. Several optimized geometries have at least one Bi atom bonded to gold or bismuth atoms and form structures similar to NH3. This fragment is also present in clusters with 20 atoms, where the formation of Au3Bi stabilizes the structures. Bismuth clusters are better electron donors and worse electron acceptors than gold clusters. Mixed clusters fall in between these two extremes. The presence of Bi atoms in gold clusters modifies the electron donor-acceptor properties of the clusters, but there is no correlation between the number of Bi atoms present in the cluster and the capacity for donating electrons. The effect of planarity in Au19Bi clusters is the same as that in Au20 clusters. The properties of pure gold clusters are certainly interesting, but clusters formed by Bi and Au are more important because the introduction of different atoms modifies the geometry, the stability, and consequently the physical and chemical properties. Apparently, the presence of Bi may increase the reactivity of gold clusters, but further studies are necessary to corroborate this hypothesis.

  1. Cutting line determination for plant propagation

    NASA Astrophysics Data System (ADS)

    Lo, Li-Yun; Hsia, Chi-Chun; Sun, Hua-Hong; Chen, Hsiang-Ju; Wu, Xin-Ting; Hu, Min-Chun

    2014-01-01

    Investigating an efficient method for plant propagation can help not only prevent extinction of plants but also facilitate the development of botanical industries. In this paper, we propose to use image processing techniques to determine the cutting-line for the propagation of two kinds of plants, i.e. Melaleuca alternifolia Cheel and Cinnamomum kanehirai Hay, which have quite different characteristics in terms of shape, structure, and propagation way (e.g. propagation by seeding and rooting, respectively). The proposed cutting line determination methods can be further applied to develop an automatic control system to reduce labor cost and increase the effectiveness of plant propagation.

  2. Analysis of biomolecular interactions using affinity microcolumns: A review

    PubMed Central

    Zheng, Xiwei; Li, Zhao; Beeram, Sandya; Podariu, Maria; Matsuda, Ryan; Pfaunmiller, Erika L.; White, Christopher J.; Carter, NaTasha; Hage, David S.

    2014-01-01

    Affinity chromatography has become an important tool for characterizing biomolecular interactions. The use of affinity microcolumns, which contain immobilized binding agents and have volumes in the mid-to-low microliter range, has received particular attention in recent years. Potential advantages of affinity microcolumns include the many analysis and detection formats that can be used with these columns, as well as the need for only small amounts of supports and immobilized binding agents. This review examines how affinity microcolumns have been used to examine biomolecular interactions. Both capillary-based microcolumns and short microcolumns are considered. The use of affinity microcolumns with zonal elution and frontal analysis methods are discussed. The techniques of peak decay analysis, ultrafast affinity extraction, split-peak analysis, and band-broadening studies are also explored. The principles of these methods are examined and various applications are provided to illustrate the use of these methods with affinity microcolumns. It is shown how these techniques can be utilized to provide information on the binding strength and kinetics of an interaction, as well as on the number and types of binding sites. It is further demonstrated how information on competition or displacement effects can be obtained by these methods. PMID:24572459

  3. The paranodal cytoskeleton clusters Na(+) channels at nodes of Ranvier.

    PubMed

    Amor, Veronique; Zhang, Chuansheng; Vainshtein, Anna; Zhang, Ao; Zollinger, Daniel R; Eshed-Eisenbach, Yael; Brophy, Peter J; Rasband, Matthew N; Peles, Elior

    2017-01-30

    A high density of Na(+) channels at nodes of Ranvier is necessary for rapid and efficient action potential propagation in myelinated axons. Na+ channel clustering is thought to depend on two axonal cell adhesion molecules that mediate interactions between the axon and myelinating glia at the nodal gap (i.e., NF186) and the paranodal junction (i.e., Caspr). Here we show that while Na(+) channels cluster at nodes in the absence of NF186, they fail to do so in double conditional knockout mice lacking both NF186 and the paranodal cell adhesion molecule Caspr, demonstrating that a paranodal junction-dependent mechanism can cluster Na(+) channels at nodes. Furthermore, we show that paranode-dependent clustering of nodal Na(+) channels requires axonal βII spectrin which is concentrated at paranodes. Our results reveal that the paranodal junction-dependent mechanism of Na(+)channel clustering is mediated by the spectrin-based paranodal axonal cytoskeleton.

  4. Wave Propagation in Bimodular Geomaterials

    NASA Astrophysics Data System (ADS)

    Kuznetsova, Maria; Pasternak, Elena; Dyskin, Arcady; Pelinovsky, Efim

    2016-04-01

    Observations and laboratory experiments show that fragmented or layered geomaterials have the mechanical response dependent on the sign of the load. The most adequate model accounting for this effect is the theory of bimodular (bilinear) elasticity - a hyperelastic model with different elastic moduli for tension and compression. For most of geo- and structural materials (cohesionless soils, rocks, concrete, etc.) the difference between elastic moduli is such that their modulus in compression is considerably higher than that in tension. This feature has a profound effect on oscillations [1]; however, its effect on wave propagation has not been comprehensively investigated. It is believed that incorporation of bilinear elastic constitutive equations within theory of wave dynamics will bring a deeper insight to the study of mechanical behaviour of many geomaterials. The aim of this paper is to construct a mathematical model and develop analytical methods and numerical algorithms for analysing wave propagation in bimodular materials. Geophysical and exploration applications and applications in structural engineering are envisaged. The FEM modelling of wave propagation in a 1D semi-infinite bimodular material has been performed with the use of Marlow potential [2]. In the case of the initial load expressed by a harmonic pulse loading strong dependence on the pulse sign is observed: when tension is applied before compression, the phenomenon of disappearance of negative (compressive) strains takes place. References 1. Dyskin, A., Pasternak, E., & Pelinovsky, E. (2012). Periodic motions and resonances of impact oscillators. Journal of Sound and Vibration, 331(12), 2856-2873. 2. Marlow, R. S. (2008). A Second-Invariant Extension of the Marlow Model: Representing Tension and Compression Data Exactly. In ABAQUS Users' Conference.

  5. Nuclear Clusters in Astrophysics

    NASA Astrophysics Data System (ADS)

    Kubono, S.; Binh, Dam N.; Hayakawa, S.; Hashimoto, H.; Kahl, D.; Wakabayashi, Y.; Yamaguchi, H.; Teranishi, T.; Iwasa, N.; Komatsubara, T.; Kato, S.; Khiem, Le H.

    2010-03-01

    The role of nuclear clustering is discussed for nucleosynthesis in stellar evolution with Cluster Nucleosynthesis Diagram (CND) proposed before. Special emphasis is placed on α-induced stellar reactions together with molecular states for O and C burning.

  6. Matlab Cluster Ensemble Toolbox

    SciTech Connect

    Sapio, Vincent De; Kegelmeyer, Philip

    2009-04-27

    This is a Matlab toolbox for investigating the application of cluster ensembles to data classification, with the objective of improving the accuracy and/or speed of clustering. The toolbox divides the cluster ensemble problem into four areas, providing functionality for each. These include, (1) synthetic data generation, (2) clustering to generate individual data partitions and similarity matrices, (3) consensus function generation and final clustering to generate ensemble data partitioning, and (4) implementation of accuracy metrics. With regard to data generation, Gaussian data of arbitrary dimension can be generated. The kcenters algorithm can then be used to generate individual data partitions by either, (a) subsampling the data and clustering each subsample, or by (b) randomly initializing the algorithm and generating a clustering for each initialization. In either case an overall similarity matrix can be computed using a consensus function operating on the individual similarity matrices. A final clustering can be performed and performance metrics are provided for evaluation purposes.

  7. Binding Affinities Controlled by Shifting Conformational Equilibria: Opportunities and Limitations

    PubMed Central

    Michielssens, Servaas; de Groot, Bert L.; Grubmüller, Helmut

    2015-01-01

    Conformational selection is an established mechanism in molecular recognition. Despite its power to explain binding events, it is hardly used in protein/ligand design to modulate molecular recognition. Here, we explore the opportunities and limitations of design by conformational selection. Using appropriate thermodynamic cycles, our approach predicts the effects of a conformational shift on binding affinity and also allows one to disentangle the effects induced by a conformational shift from other effects influencing the binding affinity. The method is assessed and applied to explain the contribution of a conformational shift on the binding affinity of six ubiquitin mutants showing different conformational shifts in six different complexes. PMID:25992736

  8. SPECTRAL IMAGING OF GALAXY CLUSTERS WITH PLANCK

    SciTech Connect

    Bourdin, H.; Mazzotta, P.; Rasia, E.

    2015-12-20

    The Sunyaev–Zeldovich (SZ) effect is a promising tool for detecting the presence of hot gas out to the galaxy cluster peripheries. We developed a spectral imaging algorithm dedicated to the SZ observations of nearby galaxy clusters with Planck, with the aim of revealing gas density anisotropies related to the filamentary accretion of materials, or pressure discontinuities induced by the propagation of shock fronts. To optimize an unavoidable trade-off between angular resolution and precision of the SZ flux measurements, the algorithm performs a multi-scale analysis of the SZ maps as well as of other extended components, such as the cosmic microwave background (CMB) anisotropies and the Galactic thermal dust. The demixing of the SZ signal is tackled through kernel-weighted likelihood maximizations. The CMB anisotropies are further analyzed through a wavelet analysis, while the Galactic foregrounds and SZ maps are analyzed via a curvelet analysis that best preserves their anisotropic details. The algorithm performance has been tested against mock observations of galaxy clusters obtained by simulating the Planck High Frequency Instrument and by pointing at a few characteristic positions in the sky. These tests suggest that Planck should easily allow us to detect filaments in the cluster peripheries and detect large-scale shocks in colliding galaxy clusters that feature favorable geometry.

  9. Coupled cluster Green function: Model involving single and double excitations

    SciTech Connect

    Bhaskaran-Nair, Kiran; Kowalski, Karol; Shelton, William A.

    2016-04-14

    In this paper we report on the parallel implementation of the coupled-cluster (CC) Green function formulation (GF-CC) employing single and double excitations in the cluster operator (GF-CCSD). The detailed description of the underlying algorithm is provided, including the structure of ionization-potential- and electron-affinity-type intermediate tensors which enable to formulate GF-CC approach in a computationally feasible form. Several examples including calculations of ionization-potentials and electron a*ffinities for benchmark systems, which are juxtaposed against the experimental values, provide an illustration of the accuracies attainable in the GFCCSD simulations. We also discuss the structure of the CCSD self energies and discuss approximation that are geared to reduce the computational cost while maintaining the pole structure of the full GF-CCSD approach.

  10. Energy propagation throughout chemical networks.

    PubMed

    Le Saux, Thomas; Plasson, Raphaël; Jullien, Ludovic

    2014-06-14

    In order to maintain their metabolism from an energy source, living cells rely on chains of energy transfer involving functionally identified components and organizations. However, propagation of a sustained energy flux through a cascade of reaction cycles has only been recently reproduced at a steady state in simple chemical systems. As observed in living cells, the spontaneous onset of energy-transfer chains notably drives local generation of singular dissipative chemical structures: continuous matter fluxes are dynamically maintained at boundaries between spatially and chemically segregated zones but in the absence of any membrane or predetermined material structure.

  11. LCMV: Propagation, quantitation, and storage

    PubMed Central

    Seedhom, Mina O.

    2011-01-01

    Lymphocytic choriomeningitis virus (LCMV) is an enveloped ambisense RNA virus and the prototypic virus of the arenavirus group. It can cause viral meningitis and other ailments in humans, but it's natural host is the mouse. The LCMV/mouse model has been useful for examining mechanisms of viral persistence and basic concepts of virus-induced immunity and immunopathology. Here we discuss strain differences and biosafety containment issues for LCMV. Recommendations are made for techniques to propagate LCMV to high titers, to quantify it by plaque assay and PCR techniques, and to preserve its infectivity by appropriate storage. PMID:18770534

  12. ACTS and OLYMPUS propagation experiments

    NASA Technical Reports Server (NTRS)

    Bostian, Charles W.; Baker, Kenneth R.

    1988-01-01

    The OLYMPUS and ACTS satellites both provide opportunities for 10 to 30 GHz propagation measurements. The spacecraft are sufficiently alike that OLYMPUS can be used to test some prototype ACTS equipment and experiments. Data are particularly needed on short term signal behavior and in support of uplink power control and adaptive forward error correction (FEC) techniques. The Virginia Tech Satellite Communications Group has proposed a set of OLYMPUS experiments including attenuation and fade rate measurements, data communications, uplink power control, rain scatter interference, and small-scale site diversity operation. A digital signal processing receiver for the OLYMPUS and ACTS beacon signals is being developed.

  13. Mode II fatigue crack propagation.

    NASA Technical Reports Server (NTRS)

    Roberts, R.; Kibler, J. J.

    1971-01-01

    Fatigue crack propagation rates were obtained for 2024-T3 bare aluminum plates subjected to in-plane, mode I, extensional loads and transverse, mode II, bending loads. These results were compared to the results of Iida and Kobayashi for in-plane mode I-mode II extensional loads. The engineering significance of mode I-mode II fatigue crack growth is considered in view of the present results. A fatigue crack growth equation for handling mode I-mode II fatigue crack growth rates from existing mode I data is also discussed.

  14. Modeling of Transionospheric Radio Propagation

    DTIC Science & Technology

    1975-08-01

    sin cpj dcp dq (17) where and VXz = Fresnel-zone radius at scattering layer 2 2 7 (0,0’) = [l + tan e cos (0 - «(*)] ß...y /nai, - 7 «T MODELING OF JRANSIONOSPHKir RADIO PROPAGATION RADI ^ja By: E. J. TREMOUW C L. RINO (£>. Augm IB?5 Prepared for: ROME A|R...following three relationships arise from Eqs. (1) and (2) 2 Ro cos (26) ( 7 ) R [ r. 2 o 0 = y ^ll + ^^cos (26) 2 L

  15. Ultrasound propagation measurements and applications

    NASA Technical Reports Server (NTRS)

    Lynnworth, L. C.; Papadakis, E. P.; Fowler, K. A.

    1977-01-01

    This paper reviews three systems designed for accurately measuring the propagation of ultrasonic pulses. The three systems are presented in order of velocity-measuring precision: + or - 100 ns, + or - 1 ns, + or - 0.2 ns. Also included is a brief discussion of phase and group velocities, with reference to dispersive, highly attenuating materials. Measurement of attenuation by pulse-echo buffer rod techniques is described briefly. These techniques and instruments have been used to measure sound velocity and attenuation in a variety of materials and shapes, over a wide temperature range.

  16. Propagation modelling in microcellular environments

    NASA Astrophysics Data System (ADS)

    Sharples, P. A.; Mehler, M. J.

    This paper describes a microcellular model, based on ray tracing techniques. Ray tracing is a stationary phase technique which relies on the quasi-optical properties of radio waves in regions where any obstacles are large in terms of a wavelength. The model described is a very versatile implementation which can be used to study both indoor and outdoor propagation phenomena for a number of different types of service. In its fullest form it requires input data of a sophistication that is not commercially available. However, this allows the model to be used to assess the implications in terms of the achievable accuracy when using commercial building databases.

  17. Light Propagation through Anisotropic Turbulence

    DTIC Science & Technology

    2011-03-01

    Kolmogorov stratospheric turbulence on star image motion,” Proc. SPIE 3126, 113–123 (1997). 5. B. E . Stribling, B. M . Welsh, and M . C. Roggemann...746407 (2009). 10. M . Chang, C. O. Font, F. Santiago, Y. Luna, E . Roura, and S. Restaino, “Marine environment optical propagation measure- ments,” Proc...Anisotropic factor as a function of alpha for several zeta values. Toselli et al. Vol. 28, No. 3 / March 2011 / J. Opt. Soc. Am. A 487 14. M . S

  18. Continuous propagation of microalgae. III.

    NASA Technical Reports Server (NTRS)

    Hanson, D. T.; Fredrickson, A. G.; Tsuchiya, H. M.

    1971-01-01

    Data are presented which give the specific photosynthetic rate and the specific utilization rates of urea and carbon dioxide as functions of specific growth rate for Chlorella. A mathematical model expresses a set of mass balance relations between biotic and environmental materials. Criteria of validity are used to test this model. Predictive procedures are complemented by a particular model of microbial growth. Methods are demonstrated for predicting substrate utilization rates, production rates of extracellular metabolites, growth limiting conditions, and photosynthetic quotients from propagator variables.

  19. LogDet Rank Minimization with Application to Subspace Clustering.

    PubMed

    Kang, Zhao; Peng, Chong; Cheng, Jie; Cheng, Qiang

    2015-01-01

    Low-rank matrix is desired in many machine learning and computer vision problems. Most of the recent studies use the nuclear norm as a convex surrogate of the rank operator. However, all singular values are simply added together by the nuclear norm, and thus the rank may not be well approximated in practical problems. In this paper, we propose using a log-determinant (LogDet) function as a smooth and closer, though nonconvex, approximation to rank for obtaining a low-rank representation in subspace clustering. Augmented Lagrange multipliers strategy is applied to iteratively optimize the LogDet-based nonconvex objective function on potentially large-scale data. By making use of the angular information of principal directions of the resultant low-rank representation, an affinity graph matrix is constructed for spectral clustering. Experimental results on motion segmentation and face clustering data demonstrate that the proposed method often outperforms state-of-the-art subspace clustering algorithms.

  20. [Pathophysiology of cluster headache].

    PubMed

    Donnet, Anne

    2015-11-01

    The aetiology of cluster headache is partially unknown. Three areas are involved in the pathogenesis of cluster headache: the trigeminal nociceptive pathways, the autonomic system and the hypothalamus. The cluster headache attack involves activation of the trigeminal autonomic reflex. A dysfunction located in posterior hypothalamic gray matter is probably pivotal in the process. There is a probable association between smoke exposure, a possible genetic predisposition and the development of cluster headache.

  1. Electronic and magnetic properties of CrGen (15 ⩽ n ⩽ 29) clusters: A DFT study

    NASA Astrophysics Data System (ADS)

    Mahtout, Sofiane; Tariket, Yacine

    2016-06-01

    We report ab initio calculations of electronic and magnetic properties of medium-sized CrGen (15 ⩽ n ⩽ 29) clusters using density functional theory. The encapsulation of Cr atoms within Gen clusters leads to stable Cr encapsulated Gen clusters. The binding energies generally increase while the differences between the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO gaps) generally decrease with the increasing of cluster size. The clusters of CrGen at size 16, 17, 19, 22, 24 and 29 exhibit high stabilities when compared to their neighbors. This has been discussed in terms of their structures, energies and the effect of the position of doping atom. Doping of Gen clusters with one Cr atom leads to CrGen clusters with magnetic moment depending on the structure of the clusters and the position of Cr atom in the clusters. Moreover, vertical ionization potential, vertical electronic affinity, and chemical hardness are also analyzed.

  2. Clustering algorithm studies

    NASA Astrophysics Data System (ADS)

    Graf, Norman A.

    2001-07-01

    An object-oriented framework for undertaking clustering algorithm studies has been developed. We present here the definitions for the abstract Cells and Clusters as well as the interface for the algorithm. We intend to use this framework to investigate the interplay between various clustering algorithms and the resulting jet reconstruction efficiency and energy resolutions to assist in the design of the calorimeter detector.

  3. Light propagation through anisotropic turbulence.

    PubMed

    Toselli, Italo; Agrawal, Brij; Restaino, Sergio

    2011-03-01

    A wealth of experimental data has shown that atmospheric turbulence can be anisotropic; in this case, a Kolmogorov spectrum does not describe well the atmospheric turbulence statistics. In this paper, we show a quantitative analysis of anisotropic turbulence by using a non-Kolmogorov power spectrum with an anisotropic coefficient. The spectrum we use does not include the inner and outer scales, it is valid only inside the inertial subrange, and it has a power-law slope that can be different from a Kolmogorov one. Using this power spectrum, in the weak turbulence condition, we analyze the impact of the power-law variations α on the long-term beam spread and scintillation index for several anisotropic coefficient values ς. We consider only horizontal propagation across the turbulence cells, assuming circular symmetry is maintained on the orthogonal plane to the propagation direction. We conclude that the anisotropic coefficient influences both the long-term beam spread and the scintillation index by the factor ς(2-α).

  4. OPEX propagation measurements and studies

    NASA Technical Reports Server (NTRS)

    Arbesser-Rastburg, Bertram

    1990-01-01

    With the launch of the telecommunications Olympus satellite a new area began for the Olympus Propagation Experiments (OPEX) group. The years of preparations are now paying off - the experiments are underway and the co-operative effort is now turning its attention to the processing and analysis of data and to the interpretation of results. The aim here is to give a short review of the accomplishments made since NAPEX 13 and the work planned for the future. When ESA's Olympus was launched in summer of 1989 it carried a payload producing three unmodulated beacons at 12.5, 19.8, and 29.7 GHz. The main purpose of these beacons is to enable scientists to carry out long term slant path propagation experiments at these frequencies. The OPEX group, which was set up under ESA auspices in 1980, had been preparing for this event very carefully. The specifications for the equipment to be used and the elaboration of standard procedures for data processing and analysis have been worked out jointly. Today the OPEX community includes approximately 30 groups of experimenters. Immediately after achieving platform stability at the orbital location at 341 degrees east, ESA performed the In-Orbit Tests. Most measurements were carried out in Belgium using terminals specially developed for this purpose. A summary of the test results is given.

  5. Simplified propagation of standard uncertainties

    SciTech Connect

    Shull, A.H.

    1997-06-09

    An essential part of any measurement control program is adequate knowledge of the uncertainties of the measurement system standards. Only with an estimate of the standards` uncertainties can one determine if the standard is adequate for its intended use or can one calculate the total uncertainty of the measurement process. Purchased standards usually have estimates of uncertainty on their certificates. However, when standards are prepared and characterized by a laboratory, variance propagation is required to estimate the uncertainty of the standard. Traditional variance propagation typically involves tedious use of partial derivatives, unfriendly software and the availability of statistical expertise. As a result, the uncertainty of prepared standards is often not determined or determined incorrectly. For situations meeting stated assumptions, easier shortcut methods of estimation are now available which eliminate the need for partial derivatives and require only a spreadsheet or calculator. A system of simplifying the calculations by dividing into subgroups of absolute and relative uncertainties is utilized. These methods also incorporate the International Standards Organization (ISO) concepts for combining systematic and random uncertainties as published in their Guide to the Expression of Measurement Uncertainty. Details of the simplified methods and examples of their use are included in the paper.

  6. Joint Acoustic Propagation Experiment (JAPE)

    NASA Technical Reports Server (NTRS)

    Carnes, Benny L.; Olsen, Robert O.; Kennedy, Bruce W.

    1993-01-01

    The Joint Acoustic Propagation Experiment (JAPE), performed under the auspices of NATO and the Acoustics Working Group, was conducted at White Sands Missile Range, New Mexico, USA, during the period 11-28 Jul. 1991. JAPE consisted of 220 trials using various acoustic sources including speakers, propane cannon, various types of military vehicles, helicopters, a 155mm howitzer, and static high explosives. Of primary importance to the performance of these tests was the intensive characterization of the atmosphere before and during the trials. Because of the wide range of interests on the part of the participants, JAPE was organized in such a manner to provide a broad cross section of test configurations. These included short and long range propagation from fixed and moving vehicles, terrain masking, and vehicle detection. A number of independent trials were also performed by individual participating agencies using the assets available during JAPE. These tests, while not documented in this report, provided substantial and important data to those groups. Perhaps the most significant feature of JAPE is the establishment of a permanent data base which can be used by not only the participants but by others interested in acoustics. A follow-on test was performed by NASA LaRC during the period 19-29 Aug. 1991 at the same location. These trials consisted of 59 overflights of supersonic aircraft in order to establish the relationship between atmospheric turbulence and the received sonic boom energy at the surface.

  7. Microwave propagation on acupuncture channels.

    PubMed

    Krevsky, Michael A; Zinina, Ekaterina S; Koshurinov, Yuri; Ovechkin, Aleck M; Tkachenko, Yuri A; Han, Wantaek; Lee, Sang-Min; Yoon, Gilwon

    2006-01-01

    Quantitative studies on functional state of acupuncture points and meridians have been done mostly by electrical measurement that requires the contact of the electrode on skin and is subject to pressure, humidity, etc. In this study, a new modality of using microwave was investigated. Microwave energy in the frequency range of 250 approximately 550MHz was irradiated on an acupuncture point. Transmitted microwave energy along the meridian was measured at the next acupuncture point of the same meridian. Diabetic and cancer patients were compared with healthy persons. Normal group consisted of 50 healthy persons. Diabetic group included 50 diabetic patients. Breast cancer group had also 50 patients. All 12 meridians on both right and left hands and feet were measured. For the diabetic group, the microwave energy propagation in this frequency range was 1.417 dB lower along Lung channel and 1.601 dB higher along Spleen channel compared with the normal group regardless of sex and diabetic types. For cancer patients, the propagation was 1.620 dB lower along Liver channel and 1.245 dB higher along Kidney channel compared with the normal group. Microwave energy proved to be a potential diagnostic method.

  8. Bidirectional elastic image registration using B-spline affine transformation.

    PubMed

    Gu, Suicheng; Meng, Xin; Sciurba, Frank C; Ma, Hongxia; Leader, Joseph; Kaminski, Naftali; Gur, David; Pu, Jiantao

    2014-06-01

    A registration scheme termed as B-spline affine transformation (BSAT) is presented in this study to elastically align two images. We define an affine transformation instead of the traditional translation at each control point. Mathematically, BSAT is a generalized form of the affine transformation and the traditional B-spline transformation (BST). In order to improve the performance of the iterative closest point (ICP) method in registering two homologous shapes but with large deformation, a bidirectional instead of the traditional unidirectional objective/cost function is proposed. In implementation, the objective function is formulated as a sparse linear equation problem, and a sub-division strategy is used to achieve a reasonable efficiency in registration. The performance of the developed scheme was assessed using both two-dimensional (2D) synthesized dataset and three-dimensional (3D) volumetric computed tomography (CT) data. Our experiments showed that the proposed B-spline affine model could obtain reasonable registration accuracy.

  9. Bidirectional Elastic Image Registration Using B-Spline Affine Transformation

    PubMed Central

    Gu, Suicheng; Meng, Xin; Sciurba, Frank C.; Wang, Chen; Kaminski, Naftali; Pu, Jiantao

    2014-01-01

    A registration scheme termed as B-spline affine transformation (BSAT) is presented in this study to elastically align two images. We define an affine transformation instead of the traditional translation at each control point. Mathematically, BSAT is a generalized form of the affine transformation and the traditional B-Spline transformation (BST). In order to improve the performance of the iterative closest point (ICP) method in registering two homologous shapes but with large deformation, a bi-directional instead of the traditional unidirectional objective / cost function is proposed. In implementation, the objective function is formulated as a sparse linear equation problem, and a sub-division strategy is used to achieve a reasonable efficiency in registration. The performance of the developed scheme was assessed using both two-dimensional (2D) synthesized dataset and three-dimensional (3D) volumetric computed tomography (CT) data. Our experiments showed that the proposed B-spline affine model could obtain reasonable registration accuracy. PMID:24530210

  10. A thermodynamic approach to the affinity optimization of drug candidates.

    PubMed

    Freire, Ernesto

    2009-11-01

    High throughput screening and other techniques commonly used to identify lead candidates for drug development usually yield compounds with binding affinities to their intended targets in the mid-micromolar range. The affinity of these molecules needs to be improved by several orders of magnitude before they become viable drug candidates. Traditionally, this task has been accomplished by establishing structure activity relationships to guide chemical modifications and improve the binding affinity of the compounds. As the binding affinity is a function of two quantities, the binding enthalpy and the binding entropy, it is evident that a more efficient optimization would be accomplished if both quantities were considered and improved simultaneously. Here, an optimization algorithm based upon enthalpic and entropic information generated by Isothermal Titration Calorimetry is presented.

  11. Antibody Affinity Maturation in Fishes—Our Current Understanding

    PubMed Central

    Magor, Brad G.

    2015-01-01

    It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. PMID:26264036

  12. Étude statistique et dynamique de la propagation d'épidémies dans un réseau de petit mondeStatistical and dynamical study of the epidemics propagation in a small world network

    NASA Astrophysics Data System (ADS)

    Zekri, Nouredine; Clerc, Jean Pierre

    We study numerically in this work the statistical and dynamical properties of the clusters in a one dimensional small world model. The parameters chosen correspond to a realistic network of children of school age where a disease like measles can propagate. Extensive results on the statistical behavior of the clusters around the percolation threshold, as well as the evoltion with time, are discussed. To cite this article: N. Zekri, J.P. Clerc, C. R. Physique 3 (2002) 741-747.

  13. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters

    NASA Astrophysics Data System (ADS)

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-08-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1–12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms.

  14. Insights into the structural, electronic and magnetic properties of V-doped copper clusters: comparison with pure copper clusters

    PubMed Central

    Die, Dong; Zheng, Ben-Xia; Zhao, Lan-Qiong; Zhu, Qi-Wen; Zhao, Zheng-Quan

    2016-01-01

    The structural, electronic and magnetic properties of Cun+1 and CunV (n = 1–12) clusters have been investigated by using density functional theory. The growth behaviors reveal that V atom in low-energy CunV isomer favors the most highly coordinated position and changes the geometry of the three-dimensional host clusters. The vibrational spectra are predicted and can be used to identify the ground state. The relative stability and chemical activity of the ground states are analyzed through the binding energy per atom, energy second-order difference and energy gap. It is found that that the stability of CunV (n ≥ 8) is higher than that of Cun+1. The substitution of a V atom for a Cu atom in copper clusters alters the odd-even oscillations of stability and activity of the host clusters. The vertical ionization potential, electron affinity and photoelectron spectrum are calculated and simulated for all of the most stable clusters. Compare with the experimental data, we determine the ground states of pure copper clusters. The magnetism analyses show that the magnetic moments of CunV clusters are mainly localized on the V atom and decease with the increase of cluster size. The magnetic change is closely related to the charge transfer between V and Cu atoms. PMID:27534599

  15. Electrospun polyethersulfone affinity membrane: membrane preparation and performance evaluation.

    PubMed

    Ma, Zuwei; Lan, Zhengwei; Matsuura, Takeshi; Ramakrishna, Seeram

    2009-11-01

    Non-woven polyethersulfone (PES) membranes were prepared by electrospinning. After heat treatment and surface activation, the membranes were covalently functionalized with ligands to be used as affinity membranes. The membranes were characterized in terms of fiber diameter, porosity, specific area, pore size, ligand density and binding capacities. To evaluate the binding efficiency of the membrane, dynamic adsorption of bovine serum albumin (BSA) on the Cibacron blue F3GA (CB) functionalized PES membrane was studied. Experimental breakthrough curves were fitted with the theoretical curves based on the plate model to estimate plate height (H(p)) of the affinity membrane. The high value of H(p) (1.6-8 cm) of the affinity membrane implied a poor dynamic binding efficiency, which can be explained by the intrinsic microstructures of the material. Although the electrospun membrane might not be an ideal candidate for the preparative affinity membrane chromatography for large-scale production, it still can be used for fast small-scale protein purification in which a highly efficient binding is not required. Spin columns packed with protein A/G immobilized PES membranes were demonstrated to be capable of binding IgG specifically. SDS-PAGE results demonstrated that the PES affinity membrane had high specific binding selectivity for IgG molecules and low non-specific protein adsorption. Compared with other reported affinity membranes, the PES affinity membrane had a comparable IgG binding capacity of 4.5 mg/ml, and had a lower flow through pressure drop due to its larger pore size. In conclusion, the novel PES affinity membrane is an ideal spin column packing material for fast protein purification.

  16. Considering affinity: an ethereal conversation (part two of three).

    PubMed

    Winsor, Mary P

    2015-06-01

    In 1840 Hugh Strickland published a diagram showing the relationships of genera of birds in the kingfisher family. Three years later he applied this mapping idea to genera of birds of prey and songbirds, creating a large wall chart that he displayed to colleagues but never published. Both of his diagrams featured a scale of degrees of affinity. The meaning of taxonomic affinity was something Darwin thought about deeply. Details in the chart undermine Strickland's claim that his method was purely inductive.

  17. Proton affinity of methyl nitrate - Less than proton affinity of nitric acid

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    Several state-of-the-art ab initio quantum mechanical methods were used to investigate the equilibrium structure, dipole moments, harmonic vibrational frequencies, and IR intensities of methyl nitrate, methanol, and several structures of protonated methyl nitrate, using the same theoretical methods as in an earlier study (Lee and Rice, 1992) of nitric acid. The ab initio results for methyl nitrate and methanol were found to be in good agreement with available experimental data. The proton affinity (PA) of methyl nitrate was calculated to be 176.9 +/-5 kcal/mol, in excellent agreement with the experimental value 176 kcal/mol obtained by Attina et al. (1987) and less than the PA value of nitric acid. An explanation of the discrepancy of the present results with those of an earlier study on protonated nitric acid is proposed.

  18. A new clustering strategy

    NASA Astrophysics Data System (ADS)

    Feng, Jian-xin; Tang, Jia-fu; Wang, Guang-xing

    2007-04-01

    On the basis of the analysis of clustering algorithm that had been proposed for MANET, a novel clustering strategy was proposed in this paper. With the trust defined by statistical hypothesis in probability theory and the cluster head selected by node trust and node mobility, this strategy can realize the function of the malicious nodes detection which was neglected by other clustering algorithms and overcome the deficiency of being incapable of implementing the relative mobility metric of corresponding nodes in the MOBIC algorithm caused by the fact that the receiving power of two consecutive HELLO packet cannot be measured. It's an effective solution to cluster MANET securely.

  19. Star cluster dynamics.

    PubMed

    Vesperini, Enrico

    2010-02-28

    Dynamical evolution plays a key role in shaping the current properties of star clusters and star cluster systems. A detailed understanding of the effects of evolutionary processes is essential to be able to disentangle the properties that result from dynamical evolution from those imprinted at the time of cluster formation. In this review, I focus my attention on globular clusters, and review the main physical ingredients driving their early and long-term evolution, describe the possible evolutionary routes and show how cluster structure and stellar content are affected by dynamical evolution.

  20. Light propagation beyond the mean-field theory of standard optics.

    PubMed

    Javanainen, Juha; Ruostekoski, Janne

    2016-01-25

    With ready access to massive computer clusters we may now study light propagation in a dense cold atomic gas by means of basically exact numerical simulations. We report on a direct comparison between traditional optics, that is, electrodynamics of a polarizable medium, and numerical simulations in an elementary problem of light propagating through a slab of matter. The standard optics fails already at quite low atom densities, and the failure becomes dramatic when the average interatomic separation is reduced to around k(-1), where k is the wave number of resonant light. The difference between the two solutions originates from correlations between the atoms induced by light-mediated dipole-dipole interactions.

  1. Direct measurement of equilibrium constants for high-affinity hemoglobins.

    PubMed

    Kundu, Suman; Premer, Scott A; Hoy, Julie A; Trent, James T; Hargrove, Mark S

    2003-06-01

    The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (K(D) < 1 micro M) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and approximately 100 micro M(-1) respectively, indicate that they are not capable of facilitating oxygen transport.

  2. Functionalized multi-walled carbon nanotubes as affinity ligands

    NASA Astrophysics Data System (ADS)

    Yu, L.; Li, C. M.; Zhou, Q.; Gan, Y.; Bao, Q. L.

    2007-03-01

    Functionalization of carbon nanotubes is very challenging for their applications. The paper here describes a new method to functionalize multi-walled carbon nanotubes (MWCNTs) as specific affinity adsorbents. MWCNTs were acid purified and pretreated with (3-aminopropyl)-triethoxysilane (APTES) in order to introduce abundant amino groups on the surface of MWCNTs. After the conversion of amino groups to carboxyl groups by succinic acid anhydride, MWCNTs were attached to protein A or aminodextran using 1-ethyl-3,3' (dimethylamion)-propylcarbodiimide as a biofunctional crosslinker. The incorporation of aminodextran as a spacer arm noticeably increased the binding capacity of the APTES-modified MWCNTs for protein A. The application of affinity MWCNTs for purification of immunoglobulin G was then evaluated. The affinity of MWCNTs with AMD spacer exhibited a high adsorption capacity of ~361 µg IgG/mg MWCNT (wet basis). About 75% of bound IgG was eluted from affinity MWCNTs (ANT-I and ANT-II) and ELISA confirmed that the biological activity of IgG was well preserved during the course of affinity separation. The functionalized MWCNTs could be potentially used in affinity chromatography.

  3. Unconventional methods for clustering

    NASA Astrophysics Data System (ADS)

    Kotyrba, Martin

    2016-06-01

    Cluster analysis or clustering is a task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters). It is the main task of exploratory data mining and a common technique for statistical data analysis used in many fields, including machine learning, pattern recognition, image analysis, information retrieval, and bioinformatics. The topic of this paper is one of the modern methods of clustering namely SOM (Self Organising Map). The paper describes the theory needed to understand the principle of clustering and descriptions of algorithm used with clustering in our experiments.

  4. SHOCK HEATING OF THE MERGING GALAXY CLUSTER A521

    SciTech Connect

    Bourdin, H.; Mazzotta, P.; Markevitch, M.; Giacintucci, S.; Brunetti, G.

    2013-02-10

    A521 is an interacting galaxy cluster located at z = 0.247, hosting a low-frequency radio halo connected to an eastern radio relic. Previous Chandra observations hinted at the presence of an X-ray brightness edge at the position of the relic, which may be a shock front. We analyze a deep observation of A521 recently performed with XMM-Newton in order to probe the cluster structure up to the outermost regions covered by the radio emission. The cluster atmosphere exhibits various brightness and temperature anisotropies. In particular, two cluster cores appear to be separated by two cold fronts. We find two shock fronts, one that was suggested by Chandra and that is propagating to the east, and another to the southwestern cluster outskirt. The two main interacting clusters appear to be separated by a shock-heated region, which exhibits a spatial correlation with the radio halo. The outer edge of the radio relic coincides spatially with a shock front, suggesting that this shock is responsible for the generation of cosmic-ray electrons in the relic. The propagation direction and Mach number of the shock front derived from the gas density jump, M = 2.4 {+-} 0.2, are consistent with expectations from the radio spectral index, under the assumption of Fermi I acceleration mechanism.

  5. Shock Heating of the Merging Galaxy Cluster A521

    NASA Technical Reports Server (NTRS)

    Bourdin, H.; Mazzotta, P.; Markevitch, M.; Giacintucci, S.; Brunetti, G.

    2013-01-01

    A521 is an interacting galaxy cluster located at z = 0.247, hosting a low-frequency radio halo connected to an eastern radio relic. Previous Chandra observations hinted at the presence of an X-ray brightness edge at the position of the relic, which may be a shock front. We analyze a deep observation of A521 recently performed with XMM-Newton in order to probe the cluster structure up to the outermost regions covered by the radio emission. The cluster atmosphere exhibits various brightness and temperature anisotropies. In particular, two cluster cores appear to be separated by two cold fronts. We find two shock fronts, one that was suggested by Chandra and that is propagating to the east, and another to the southwestern cluster outskirt. The two main interacting clusters appear to be separated by a shock-heated region, which exhibits a spatial correlation with the radio halo. The outer edge of the radio relic coincides spatially with a shock front, suggesting that this shock is responsible for the generation of cosmic-ray electrons in the relic. The propagation direction and Mach number of the shock front derived from the gas density jump, M = 2.4 +/- 0.2, are consistent with expectations from the radio spectral index, under the assumption of Fermi I acceleration mechanism.

  6. Local BLyS production by T follicular cells mediates retention of high affinity B cells during affinity maturation

    PubMed Central

    Goenka, Radhika; Matthews, Andrew H.; Zhang, Bochao; O’Neill, Patrick J.; Scholz, Jean L.; Migone, Thi-Sau; Leonard, Warren J.; Stohl, William; Hershberg, Uri

    2014-01-01

    We have assessed the role of B lymphocyte stimulator (BLyS) and its receptors in the germinal center (GC) reaction and affinity maturation. Despite ample BLyS retention on B cells in follicular (FO) regions, the GC microenvironment lacks substantial BLyS. This reflects IL-21–mediated down-regulation of the BLyS receptor TACI (transmembrane activator and calcium modulator and cyclophilin ligand interactor) on GC B cells, thus limiting their capacity for BLyS binding and retention. Within the GC, FO helper T cells (TFH cells) provide a local source of BLyS. Whereas T cell–derived BLyS is dispensable for normal GC cellularity and somatic hypermutation, it is required for the efficient selection of high affinity GC B cell clones. These findings suggest that during affinity maturation, high affinity clones rely on TFH-derived BLyS for their persistence. PMID:24367004

  7. Nanoparticles Self-Assembly Driven by High Affinity Repeat Protein Pairing.

    PubMed

    Gurunatha, Kargal L; Fournier, Agathe C; Urvoas, Agathe; Valerio-Lepiniec, Marie; Marchi, Valérie; Minard, Philippe; Dujardin, Erik

    2016-03-22

    Proteins are the most specific yet versatile biological self-assembling agents with a rich chemistry. Nevertheless, the design of new proteins with recognition capacities is still in its infancy and has seldom been exploited for the self-assembly of functional inorganic nanoparticles. Here, we report on the protein-directed assembly of gold nanoparticles using purpose-designed artificial repeat proteins having a rigid but modular 3D architecture. αRep protein pairs are selected for their high mutual affinity from a library of 10(9) variants. Their conjugation onto gold nanoparticles drives the massive colloidal assembly of free-standing, one-particle thick films. When the average number of proteins per nanoparticle is lowered, the extent of self-assembly is limited to oligomeric particle clusters. Finally, we demonstrate that the aggregates are reversibly disassembled by an excess of one free protein. Our approach could be optimized for applications in biosensing, cell targeting, or functional nanomaterials engineering.

  8. Vibration Propagation in Spider Webs

    NASA Astrophysics Data System (ADS)

    Hatton, Ross; Otto, Andrew; Elias, Damian

    Due to their poor eyesight, spiders rely on web vibrations for situational awareness. Web-borne vibrations are used to determine the location of prey, predators, and potential mates. The influence of web geometry and composition on web vibrations is important for understanding spider's behavior and ecology. Past studies on web vibrations have experimentally measured the frequency response of web geometries by removing threads from existing webs. The full influence of web structure and tension distribution on vibration transmission; however, has not been addressed in prior work. We have constructed physical artificial webs and computer models to better understand the effect of web structure on vibration transmission. These models provide insight into the propagation of vibrations through the webs, the frequency response of the bare web, and the influence of the spider's mass and stiffness on the vibration transmission patterns. Funded by NSF-1504428.

  9. Light propagation in nanorod arrays

    NASA Astrophysics Data System (ADS)

    Rahachou, A. I.; Zozoulenko, I. V.

    2007-03-01

    We study the propagation of TM- and TE-polarized light in two-dimensional arrays of silver nanorods of various diameters in a gelatin background. We calculate the transmittance, reflectance and absorption of arranged and disordered nanorod arrays and compare the exact numerical results with the predictions of the Maxwell-Garnett effective-medium theory. We show that interactions between nanorods, multipole contributions and formations of photonic gaps affect strongly the transmittance spectra that cannot be accounted for in terms of the conventional effective-medium theory. We also demonstrate and explain the degradation of the transmittance in arrays with randomly located rods as well as the weak influence of their fluctuating diameter. For TM modes we outline the importance of the skin effect, which causes the full reflection of the incoming light. We then illustrate the possibility of using periodic arrays of nanorods as high-quality polarizers.

  10. Light propagation in inhomogeneous universes

    NASA Technical Reports Server (NTRS)

    Schneider, Peter; Weiss, Achim

    1988-01-01

    Refsdal's (1970) method is generalized to study the propagation of light rays through an inhomogeneous universe. The probability distribution for the linear component of the cumulative shear (CS) along light rays is derived, and it is shown that the CS can be dominated by nonlinear components, espcially for light rays in empty cones. The amplification tail of the amplification probability distribution is compared with analytic results; these linear investigations are shown to underestimate the high-amplification probability and hence the importance of the amplification bias in source counts. The distribution of the ellipticity of images of infinitesimal circular sources is derived, and it is shown that this can be dominated by the nonlinear contributions to the CS.

  11. ETS-V propagation experiments in Japan

    NASA Technical Reports Server (NTRS)

    Ohmori, Shingo

    1988-01-01

    Propagation experiments on ship, aircraft, and land mobile earth stations were carried out using the Engineering Test Satellite-V (ETS-V), which was launched in August 1987. The propagation experiments are one of the missions of the Experimental Mobile Satellite System (EMSS). Initial experimental results of ETS-V/EMSS on propagation using ship, aircraft, and land mobiles with ETS-V are given.

  12. Multipath Propagation over Snow at Millimeter Wavelengths,

    DTIC Science & Technology

    1980-02-01

    Propagation Branch Electromagnetic Sciences Division APPROVED: ALLAN C. SCHELL , Chief Electromagnetic Sciences Division FOR THE COMANDER: JOHN P...type of snow cover. A computer program was developed in order to model the reflection as a specular process, with the underlying terrain represented...data. 2,B’ 3II Contents 1. INTRODUCTION 9 2. ANALYSIS OF MULTIPATH PROPAGATION 10 2. 1 Propagation Mechanisms 12 2.2 Model Calculations for Flat Terrain

  13. 25. Steenbock symposium -- Biosynthesis and function of metal clusters for enzymes: Proceedings

    SciTech Connect

    1997-12-31

    This symposium was held June 10--14, 1997 in Madison, Wisconsin. The purpose of this conference was to provide a multidisciplinary forum for exchange of state-of-the-art information on biochemistry of enzymes that have an affinity for metal clusters. Attention is focused on the following: metal clusters involved in energy conservation and remediation; tungsten, molybdenum, and cobalt-containing enzymes; Fe proteins, and Mo-binding proteins; nickel enzymes; and nitrogenase.

  14. Emergence of coexisting percolating clusters in networks

    NASA Astrophysics Data System (ADS)

    Faqeeh, Ali; Melnik, Sergey; Colomer-de-Simón, Pol; Gleeson, James P.

    2016-06-01

    It is commonly assumed in percolation theories that at most one percolating cluster can exist in a network. We show that several coexisting percolating clusters (CPCs) can emerge in networks due to limited mixing, i.e., a finite and sufficiently small number of interlinks between network modules. We develop an approach called modular message passing (MMP) to describe and verify these observations. We demonstrate that the appearance of CPCs is an important source of inaccuracy in previously introduced percolation theories, such as the message passing (MP) approach, which is a state-of-the-art theory based on the belief propagation method. Moreover, we show that the MMP theory improves significantly over the predictions of MP for percolation on synthetic networks with limited mixing and also on several real-world networks. These findings have important implications for understanding the robustness of networks and in quantifying epidemic outbreaks in the susceptible-infected-recovered (SIR) model of disease spread.

  15. Correlation between the linguistic affinity and genetic diversity of Chinese ethnic groups.

    PubMed

    Sun, Hao; Zhou, Chi; Huang, Xiaoqin; Liu, Shuyuan; Lin, Keqin; Yu, Liang; Huang, Kai; Chu, Jiayou; Yang, Zhaoqing

    2013-10-01

    As the world's most populous nation, China exhibits a population with 56 nationalities. We already know the associations between genetic relationship of these ethnic groups in China and their geographic distributions are closely. However, the correlations between genetic diversity and linguistic affinities have still not been fully revealed in China. To investigate these correlations, 31 populations and 1527 samples were chosen, and the languages of this population covered all of the languages spoken in mainland China (including 8 main linguistic families and 16 subfamilies). The genetic polymorphisms of the populations were investigated using 10 autosomal microsatellites. Five ethnic groups, which included 234 samples, were genotyped in this survey, and the data collected from the other 26 populations were obtained from our previous study. An analysis of molecular variance, principal coordinate analysis, clustering analysis using the STRUCTURE and the Mantel test were used to investigate the correlations between genetic diversity and linguistic affinity. These analyses indicated that most populations who speak the same language demonstrate a similar genetic composition, although a few populations deviated from this linkage between genetics and language. The demographic histories of these populations who deviated from this linkage were investigated. Obvious reasons for why evolutionary processes of genetics and linguistics separated in these populations included geographic isolation, gene replacement, language replacement and intermarriage. Thus, we proposed that the consistency of genetic and linguistic evolution is still present in most populations in China; however, this consistency can be broken by many factors, such as isolation, language replacement or intermarriage.

  16. Ionization potentials and electron affinities of the superheavy elements 115-117 and their sixth-row homologues Bi, Po, and At

    NASA Astrophysics Data System (ADS)

    Borschevsky, A.; Pašteka, L. F.; Pershina, V.; Eliav, E.; Kaldor, U.

    2015-02-01

    Calculations of the first and second ionization potentials and electron affinities of superheavy elements 115-117 are presented. The calculations are performed in the framework of the Dirac-Coulomb Hamiltonian, and the results are corrected for the Breit and QED contributions. Correlation is treated by the relativistic coupled cluster approach with single, double, and perturbative triple excitations [CCSD(T)]. The same approach is used to calculate the ionization potentials and electron affinities of the lighter homologues, Bi, Po, and At. Comparison of the available experimental values for these atoms, namely, the first ionization potentials (IPs) of Bi, Po, and At and the second IP and EA of Bi, with our results shows excellent agreement, within a few hundredths of an eV, lending credence to our predictions for their superheavy homologues. High-accuracy predictions are also made for the second ionization potentials and electron affinities of Po and At, where no experiment is available.

  17. GALPROP: New Developments in CR Propagation Code

    NASA Technical Reports Server (NTRS)

    Moskalenko, I. V.; Jones, F. C.; Mashnik, S. G.; Strong, A. W.; Ptuskin, V. S.

    2003-01-01

    The numerical Galactic CR propagation code GALPROP has been shown to reproduce simultaneously observational data of many kinds related to CR origin and propagation. It has been validated on direct measurements of nuclei, antiprotons, electrons, positrons as well as on astronomical measurements of gamma rays and synchrotron radiation. Such data provide many independent constraints on model parameters while revealing some contradictions in the conventional view of Galactic CR propagation. Using a new version of GALPROP we study new effects such as processes of wave-particle interactions in the interstellar medium. We also report about other developments in the CR propagation code.

  18. ACTS Propagation Measurements in Maryland and Virginia

    NASA Technical Reports Server (NTRS)

    Dissanayake, Asoka; Lin, Kuan-Ting

    1996-01-01

    Rapid growth in new satellite services incorporating very small aperture terminals (VSAT) and ultra small aperture terminals (USAT) is expected in the coming years. Small size terminals allow for widespread use of satellite services in small business and domestic applications. Due to congestion of lower frequency bands such as C and Ku, most of these services will use Ka-band (2/20 GHz) frequencies. Propagation impairments produced by the troposphere is a limiting factor for the effective use of the 20/30 GHz band and the use of smaller Earth terminals makes it difficult to provide sufficient link margins for propagation related outages. In this context, reliable prediction of propagation impairments for low margin systems becomes important. Due to the complexity of propagation phenomena propagation modeling is mainly attempted on an empirical basis. As such, the availability of reliable measured data that extend to probability levels well in excess of the traditional limit of 1 percent is of great importance in the development, validation, and refinement of propagation models. The beacon payload on the Advanced Communications Technology Satellite (ACTS) together with the propagation measurement terminals developed under the NASA ACTS propagation program provide an excellent opportunity to collect such data on a long-term basis. This paper presents the results of ACTS propagation measurements conducted in the Washington, DC metropolitan area by COMSAT Laboratories.

  19. A stochastic model for propagation through tissue.

    PubMed

    Lacaze, Bernard

    2009-10-01

    Attenuation of ultrasonic waves is often assumed linear with respect to frequency in biological applications whereas it is considered quadratic when the propagation occurs in the atmosphere or the water. In the latter case, other studies show that a Gaussian propagation duration can explain this attenuation behavior and provide a model for the energy loss in the stationary limit. The present paper defines an equivalent random propagation duration with Cauchy distribution, which is appropriate for the propagation of ultrasound through tissue. The model adds an unobserved noise that represents the signal deterioration. In addition, the model agrees with the mode downshift in the case of a narrowband signal.

  20. Quench propagation velocity for highly stabilized conductors

    SciTech Connect

    Mints, R.G. |; Ogitsu, T. |; Devred, A.

    1995-05-01

    Quench propagation velocity in conductors having a large amount of stabilizer outside the multifilamentary area is considered. It is shown that the current redistribution process between the multifilamentary area and the stabilizer can strongly effect the quench propagation. A criterion is derived determining the conditions under which the current redistribution process becomes significant, and a model of effective stabilizer area is suggested to describe its influence on the quench propagation velocity. As an illustration, the model is applied to calculate the adiabatic quench propagation velocity for a conductor geometry with a multifilamentary area embedded inside the stabilizer.

  1. Fuzzy Subspace Clustering

    NASA Astrophysics Data System (ADS)

    Borgelt, Christian

    In clustering we often face the situation that only a subset of the available attributes is relevant for forming clusters, even though this may not be known beforehand. In such cases it is desirable to have a clustering algorithm that automatically weights attributes or even selects a proper subset. In this paper I study such an approach for fuzzy clustering, which is based on the idea to transfer an alternative to the fuzzifier (Klawonn and Höppner, What is fuzzy about fuzzy clustering? Understanding and improving the concept of the fuzzifier, In: Proc. 5th Int. Symp. on Intelligent Data Analysis, 254-264, Springer, Berlin, 2003) to attribute weighting fuzzy clustering (Keller and Klawonn, Int J Uncertain Fuzziness Knowl Based Syst 8:735-746, 2000). In addition, by reformulating Gustafson-Kessel fuzzy clustering, a scheme for weighting and selecting principal axes can be obtained. While in Borgelt (Feature weighting and feature selection in fuzzy clustering, In: Proc. 17th IEEE Int. Conf. on Fuzzy Systems, IEEE Press, Piscataway, NJ, 2008) I already presented such an approach for a global selection of attributes and principal axes, this paper extends it to a cluster-specific selection, thus arriving at a fuzzy subspace clustering algorithm (Parsons, Haque, and Liu, 2004).

  2. Spatiotemporal Mapping of Interictal Spike Propagation: A Novel Methodology Applied to Pediatric Intracranial EEG Recordings.

    PubMed

    Tomlinson, Samuel B; Bermudez, Camilo; Conley, Chiara; Brown, Merritt W; Porter, Brenda E; Marsh, Eric D

    2016-01-01

    Synchronized cortical activity is implicated in both normative cognitive functioning and many neurologic disorders. For epilepsy patients with intractable seizures, irregular synchronization within the epileptogenic zone (EZ) is believed to provide the network substrate through which seizures initiate and propagate. Mapping the EZ prior to epilepsy surgery is critical for detecting seizure networks in order to achieve postsurgical seizure control. However, automated techniques for characterizing epileptic networks have yet to gain traction in the clinical setting. Recent advances in signal processing and spike detection have made it possible to examine the spatiotemporal propagation of interictal spike discharges across the epileptic cortex. In this study, we present a novel methodology for detecting, extracting, and visualizing spike propagation and demonstrate its potential utility as a biomarker for the EZ. Eighteen presurgical intracranial EEG recordings were obtained from pediatric patients ultimately experiencing favorable (i.e., seizure-free, n = 9) or unfavorable (i.e., seizure-persistent, n = 9) surgical outcomes. Novel algorithms were applied to extract multichannel spike discharges and visualize their spatiotemporal propagation. Quantitative analysis of spike propagation was performed using trajectory clustering and spatial autocorrelation techniques. Comparison of interictal propagation patterns revealed an increase in trajectory organization (i.e., spatial autocorrelation) among Sz-Free patients compared with Sz-Persist patients. The pathophysiological basis and clinical implications of these findings are considered.

  3. Spatiotemporal Mapping of Interictal Spike Propagation: A Novel Methodology Applied to Pediatric Intracranial EEG Recordings

    PubMed Central

    Tomlinson, Samuel B.; Bermudez, Camilo; Conley, Chiara; Brown, Merritt W.; Porter, Brenda E.; Marsh, Eric D.

    2016-01-01

    Synchronized cortical activity is implicated in both normative cognitive functioning and many neurologic disorders. For epilepsy patients with intractable seizures, irregular synchronization within the epileptogenic zone (EZ) is believed to provide the network substrate through which seizures initiate and propagate. Mapping the EZ prior to epilepsy surgery is critical for detecting seizure networks in order to achieve postsurgical seizure control. However, automated techniques for characterizing epileptic networks have yet to gain traction in the clinical setting. Recent advances in signal processing and spike detection have made it possible to examine the spatiotemporal propagation of interictal spike discharges across the epileptic cortex. In this study, we present a novel methodology for detecting, extracting, and visualizing spike propagation and demonstrate its potential utility as a biomarker for the EZ. Eighteen presurgical intracranial EEG recordings were obtained from pediatric patients ultimately experiencing favorable (i.e., seizure-free, n = 9) or unfavorable (i.e., seizure-persistent, n = 9) surgical outcomes. Novel algorithms were applied to extract multichannel spike discharges and visualize their spatiotemporal propagation. Quantitative analysis of spike propagation was performed using trajectory clustering and spatial autocorrelation techniques. Comparison of interictal propagation patterns revealed an increase in trajectory organization (i.e., spatial autocorrelation) among Sz-Free patients compared with Sz-Persist patients. The pathophysiological basis and clinical implications of these findings are considered. PMID:28066315

  4. Nanoparticle multivalency counterbalances the ligand affinity loss upon PEGylation.

    PubMed

    Hennig, Robert; Pollinger, Klaus; Veser, Anika; Breunig, Miriam; Goepferich, Achim

    2014-11-28

    The conjugation of receptor ligands to shielded nanoparticles is a widely used strategy to precisely control nanoparticle-cell interactions. However, it is often overlooked that a ligand's affinity can be severely impaired by its attachment to the polyethylene glycol (PEG) chains that are frequently used to protect colloids from serum protein adsorption. Using the model ligand EXP3174, a small-molecule antagonist for the angiotensin II receptor type 1 (AT1R), we investigated the ligand's affinity before and after its PEGylation and when attached to PEGylated nanoparticles. The PEGylated ligand displayed a 580-fold decreased receptor affinity compared to the native ligand. Due to their multivalency, the nanoparticles regained a low nanomolar receptor affinity, which is in the range of the affinity of the native ligand. Moreover, a four orders of magnitude higher concentration of free ligand was required to displace PEGylated nanoparticles carrying EXP3174 from the receptor. On average, one nanoparticle was decorated with 11.2 ligand molecules, which led to a multivalent enhancement factor of 22.5 compared to the monovalent PEGylated ligand. The targeted nanoparticles specifically bound the AT1R and showed no interaction to receptor negative cells. Our study shows that the attachment of a small-molecule ligand to a PEG chain can severely affect its receptor affinity. Concomitantly, when the ligand is tethered to nanoparticles, the immense avidity greatly increases the ligand-receptor interaction. Based on our results, we highly recommend the affinity testing of receptor ligands before and after PEGylation to identify potent molecules for active nanoparticle targeting.

  5. Protein Complex Affinity Capture from Cryomilled Mammalian Cells.

    PubMed

    LaCava, John; Jiang, Hua; Rout, Michael P

    2016-12-09

    Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets.

  6. Protein Complex Affinity Capture from Cryomilled Mammalian Cells

    PubMed Central

    LaCava, John; Jiang, Hua; Rout, Michael P.

    2016-01-01

    Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets. PMID:28060343

  7. Numerical models of jet disruption in cluster cooling flows

    NASA Technical Reports Server (NTRS)

    Loken, Chris; Burns, Jack O.; Roettiger, Kurt; Norman, Mike

    1993-01-01

    We present a coherent picture for the formation of the observed diverse radio morphological structures in dominant cluster galaxies based on the jet Mach number. Realistic, supersonic, steady-state cooling flow atmospheres are evolved numerically and then used as the ambient medium through which jets of various properties are propagated. Low Mach number jets effectively stagnate due to the ram pressure of the cooling flow atmosphere while medium Mach number jets become unstable and disrupt in the cooling flow to form amorphous structures. High Mach number jets manage to avoid disruption and are able to propagate through the cooling flow.

  8. Alkali Metal Cluster Theory.

    NASA Astrophysics Data System (ADS)

    Chen, Jian

    Available from UMI in association with The British Library. Requires signed TDF. In this thesis, we apply the tight-binding Hubbard model to alkali metal clusters with Hartree-Fock self-consistent methods and perturbation methods for the numerical calculations. We have studied the relation between the equilibrium structures and the range of the hopping matrix elements in the Hubbard Hamiltonian. The results show that the structures are not sensitive to the interaction range but are determined by the number of valence electrons each atom has. Inertia tensors are used to analyse the symmetries of the clusters. The principal axes of the clusters are determined and they are the axes of rotational symmetries of clusters if the clusters have any. The eigenvalues of inertia tensors which are the indication of the deformation of clusters are compared between our model and the ellipsoidal jellium model. The agreement is good for large clusters. At a finite temperature, the thermal motion fluctuates the structures. We defined a fluctuation function with the distance matrix of a cluster. The fluctuation has been studied with the Monte-Carlo simulation method. Our studies show that the clusters remain in the solid state when temperature is low. The small values of fluctuation functions indicates the thermal vibration of atoms around their equilibrium positions. If the temperature is high, the atoms are delocalized. The cluster melts and enters the liquid region. The cluster melting is simulated by the Monte-Carlo simulation with the fluctuation function we defined. Energy levels of clusters are calculated from the Hubbard model. Ionization potentials and magic numbers are also obtained from these energy levels. The results confirm that the Hubbard model is a good approximation for a small cluster. The excitation energy is presented by the difference between the original level and excited level, and the electron-hole interactions. We also have studied cooling of clusters

  9. Fullerene Molecules and Other Clusters of III-V Compounds

    NASA Astrophysics Data System (ADS)

    Hira, Ajit; Auxier, John, II; Lucero, Melinda

    2010-03-01

    The goal of the our work is to derive geometries of fullerene-like cages and other clusters of atoms from groups III and V of the periodic table. Our previous research focused on Carbon Fullerenes and on GanAsn clusters (n = 1 thru 12). Our research group has made an original discovery about GanAsn clusters. In our work on nanotechnology to date, we used the hybrid ab initio methods of quantum chemistry to derive the different geometries for the clusters of interest. We also calculated binding energies, bond-lengths, ionization potentials, electron affinities and HOMO-LUMO gaps, and IR spectra for these geometries. Of particular significance was the magic number for GaAs cluster stability that we found at n = 8. This is important because materials containing controlled III-V nanostructures provide the capability of preparing new classes of materials with enhanced optical, magnetic, chemical sensor and photo-catalytic properties. The second phase of the investigation will examine the effects of confinement on the optical properties the clusters. It will be interesting to observe novel linear as well as nonlinear optical processes in them. The third phase of the investigation will focus on the improved design of solar cells based on the optical properties of the clusters.

  10. Information-based clustering

    PubMed Central

    Slonim, Noam; Atwal, Gurinder Singh; Tkačik, Gašper; Bialek, William

    2005-01-01

    In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster “prototype,” does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures. PMID:16352721

  11. Clusters of galaxies

    NASA Astrophysics Data System (ADS)

    Vikhlinin, A. A.; Kravtsov, A. V.; Markevich, M. L.; Sunyaev, R. A.; Churazov, E. M.

    2014-04-01

    Galaxy clusters are formed via nonlinear growth of primordial density fluctuations and are the most massive gravitationally bound objects in the present Universe. Their number density at different epochs and their properties depend strongly on the properties of dark matter and dark energy, making clusters a powerful tool for observational cosmology. Observations of the hot gas filling the gravitational potential well of a cluster allows studying gasdynamic and plasma effects and the effect of supermassive black holes on the heating and cooling of gas on cluster scales. The work of Yakov Borisovich Zeldovich has had a profound impact on virtually all cosmological and astrophysical studies of galaxy clusters, introducing concepts such as the Harrison-Zeldovich spectrum, the Zeldovich approximation, baryon acoustic peaks, and the Sunyaev-Zeldovich effect. Here, we review the most basic properties of clusters and their role in modern astrophysics and cosmology.

  12. Nonstructural 5A Protein of Hepatitis C Virus Interacts with Pyruvate Carboxylase and Modulates Viral Propagation

    PubMed Central

    Kim, Jong-Wook; Hwang, Soon B.

    2013-01-01

    Hepatitis C virus (HCV) is highly dependent on cellular factors for its own propagation. By employing tandem affinity purification method, we identified pyruvate carboxylase (PC) as a cellular partner for NS5A protein. NS5A interacted with PC through the N-terminal region of NS5A and the biotin carboxylase domain of PC. PC expression was decreased in cells expressing NS5A and HCV-infected cells. Promoter activity of PC was also decreased by NS5A protein. However, FAS expression was increased in cells expressing NS5A and cell culture grown HCV (HCVcc)-infected cells. Silencing of PC promoted fatty acid synthase (FAS) expression level. These data suggest HCV may modulate PC via NS5A protein for its own propagation. PMID:23861867

  13. Explosion propagation in inert porous media.

    PubMed

    Ciccarelli, G

    2012-02-13

    Porous media are often used in flame arresters because of the high surface area to volume ratio that is required for flame quenching. However, if the flame is not quenched, the flow obstruction within the porous media can promote explosion escalation, which is a well-known phenomenon in obstacle-laden channels. There are many parallels between explosion propagation through porous media and obstacle-laden channels. In both cases, the obstructions play a duel role. On the one hand, the obstruction enhances explosion propagation through an early shear-driven turbulence production mechanism and then later by shock-flame interactions that occur from lead shock reflections. On the other hand, the presence of an obstruction can suppress explosion propagation through momentum and heat losses, which both impede the unburned gas flow and extract energy from the expanding combustion products. In obstacle-laden channels, there are well-defined propagation regimes that are easily distinguished by abrupt changes in velocity. In porous media, the propagation regimes are not as distinguishable. In porous media the entire flamefront is affected, and the effects of heat loss, turbulence and compressibility are smoothly blended over most of the propagation velocity range. At low subsonic propagation speeds, heat loss to the porous media dominates, whereas at higher supersonic speeds turbulence and compressibility are important. This blending of the important phenomena results in no clear transition in propagation mechanism that is characterized by an abrupt change in propagation velocity. This is especially true for propagation velocities above the speed of sound where many experiments performed with fuel-air mixtures show a smooth increase in the propagation velocity with mixture reactivity up to the theoretical detonation wave velocity.

  14. Visualizing the Propagation of Acute Lung Injury

    PubMed Central

    Cereda, Maurizio; Xin, Yi; Meeder, Natalie; Zeng, Johnathan; Jiang, YunQing; Hamedani, Hooman; Profka, Harrilla; Kadlecek, Stephen; Clapp, Justin; Deshpande, Charuhas G.; Wu, Jue; Gee, James C.; Kavanagh, Brian P.; Rizi, Rahim R.

    2015-01-01

    Background Mechanical ventilation worsens acute respiratory distress syndrome (ARDS), but this secondary ‘ventilator-associated’ injury is variable and difficult to predict. We aimed to visualize the propagation of such ventilator-induced injury, in the presence (and absence) of a primary underlying lung injury, and to determine the predictors of propagation. Methods Anesthetized rats (n=20) received acid aspiration (HCl) followed by ventilation with moderate tidal volume (VT). In animals surviving ventilation for at least two hours, propagation of injury was quantified using serial computed tomography (CT). Baseline lung status was assessed by oxygenation, lung weight, and lung strain (VT/expiratory lung volume). Separate groups of rats without HCl aspiration were ventilated with large (n=10) or moderate (n=6) VT. Results In 15 rats surviving longer than two hours, CT opacities spread outwards from the initial site of injury. Propagation was associated with higher baseline strain (propagation vs. no propagation, mean ± SD: 1.52 ± 0.13 vs. 1.16 ± 0.20, p<0.01), but similar oxygenation and lung weight. Propagation did not occur where baseline strain <1.29. In healthy animals, large VT caused injury that was propagated inwards from the lung periphery; in the absence of preexisting injury, propagation did not occur where strain was <2.0. Conclusions Compared with healthy lungs, underlying injury causes propagation to occur at a lower strain threshold and, it originates at the site of injury; this suggests that tissue around the primary lesion is more sensitive. Understanding how injury is propagated may ultimately facilitate a more individualized monitoring or management. PMID:26536308

  15. Gradient-based habitat affinities predict species vulnerability to drought.

    PubMed

    Debinski, Diane M; Caruthers, Jennet C; Cook, Dianne; Crowley, Jason; Wickham, Hadley

    2013-05-01

    Ecological fingerprints of climate change are becoming increasingly evident at broad geographical scales as measured by species range shifts and changes in phenology. However, finer-scale species-level responses to environmental fluctuations may also provide an important bellwether of impending future community responses. Here we examined changes in abundance of butterfly species along a hydrological gradient of six montane meadow habitat types in response to drought. Our data collection began prior to the drought, and we were able to track changes for 11 years, of which eight were considered mild to extreme drought conditions. We separated the species into those that had an affinity for hydric vs. xeric habitats. We suspected that drought would favor species with xeric habitat affinities, but that there could be variations in species-level responses along the hydrological gradient. We also suspected that mesic meadows would be most sensitive to drought conditions. Temporal trajectories were modeled for both species groups (hydric vs. xeric affinity) and individual species. Abundances of species with affinity for xeric habitats increased in virtually all meadow types. Conversely, abundances of species with affinity for hydric habitats decreased, particularly in mesic and xeric meadows. Mesic meadows showed the most striking temporal abundance trajectory: Increasing abundances of species with xeric habitat affinity were offset by decreasing or stable abundances of species with hydric habitat affinity. The one counterintuitive finding was that, in some hydric meadows, species with affinity for hydric habitats increased. In these cases, we suspect that decreasing moisture conditions in hydric meadows actually increased habitat suitability because sites near the limit of moisture extremes for some species became more acceptable. Thus, species responses were relatively predictable based upon habitat affinity and habitat location along the hydrological gradient, and

  16. Chemistry Within Molecular Clusters

    DTIC Science & Technology

    1990-01-01

    DME )nCH3OCH 2 +). We speculate that this is due to the fragments being consumed by an ion-molecule reaction within the cluster. One likely candidate is...the ion-molecule reaction of the fragment cations with a neutral DME , within the bulk cluster to form a trimethyloxonlum cation intermediate. This...the observed products. We therefore speculate that the DME cluster reactions leading to the same products, should involve the same mechanism found to

  17. Chemistry Within Molecular Clusters

    DTIC Science & Technology

    1992-06-01

    and ( DME ).CH 3OCH2+). We speculate that this is due to the fragments being consumed by an ion-molecule reaction within the cluster. A likely candidate...is the ion-molecule reaction of the fragment cations with a neutral DME within the bulk cluster, to form a trimethyloxonium cation intermediate...a trimethyloxonium intermediate as the common intermediate for the observed products. We therefore speculate that the DME cluster reactions leading to

  18. Cluster State Quantum Computation

    DTIC Science & Technology

    2014-02-01

    nearest neighbor cluster state has been shown to be a universal resource for MBQC thus we can say our quantum computer is universal. We note that...CLUSTER STATE QUANTUM COMPUTATION FEBRUARY 2014 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED STINFO COPY AIR FORCE...TITLE AND SUBTITLE CLUSTER STATE QUANTUM COMPUTATION 5a. CONTRACT NUMBER IN-HOUSE 5b. GRANT NUMBER N/A 5c. PROGRAM ELEMENT NUMBER 62788F 6

  19. Chemical Reactions in Clusters

    DTIC Science & Technology

    1992-11-04

    NH 3)n, n _> 4, clusters has been attributed to the (solvated) naphtholate anion.3a A single picosecond decay measurement has been reported which...vibrational energy in the cluster Sl state. The data are summarized in Table I. A model to explain these decay results can be constructed based on a proton...11 TITLE (Include Security Classification) Chemical Reactions in Clusters 12 PERSONAL AUTHOR(S) Elliot R. Bernstein 13a TYPE OF REPORT 13b TIME COVERED

  20. Coenzyme-like ligands for affinity isolation of cholesterol oxidase.

    PubMed

    Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu

    2016-05-15

    Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%.

  1. The proton affinities of saturated and unsaturated heterocyclic molecules

    NASA Astrophysics Data System (ADS)

    Kabli, Samira; van Beelen, Eric S. E.; Ingemann, Steen; Henriksen, Lars; Hammerum, Steen

    2006-03-01

    The proton affinities derived from G3-calculations of 23 five-membered ring heteroaromatic molecules agree well with the experimentally determined values available in the literature. The calculated local proton affinities show that the principal site of protonation of the heteroaromatic compounds examined is an atom of the ring, carbon when there is only one heteroatom in the ring, and nitrogen where there are two or more heteroatoms. The experimental proton affinities of non-aromatic cyclic ethers, amines and thioethers are also in excellent agreement with the calculated values, with two exceptions (oxetane, N-methylazetidine). The literature proton affinities of the four simple cyclic ethers, oxetane, tetrahydrofuran, tetrahydropyran and oxepane were confirmed by Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry, in order to examine the disagreement between the values predicted by extrapolation or additivity for tetrahydrofuran and tetrahydropyran and those determined by experiment and by calculation. The proton affinity differences between the pairs tetrahydropyran/1,4-dioxane, piperidine/morpholine and related compounds show that introduction of an additional oxygen atom in the ring considerably lowers the basicity.

  2. Improving antibody binding affinity and specificity for therapeutic development.

    PubMed

    Bostrom, Jenny; Lee, Chingwei V; Haber, Lauric; Fuh, Germaine

    2009-01-01

    Affinity maturation is an important part of the therapeutic antibody development process as in vivo activity often requires high binding affinity. Here, we describe a targeted approach for affinity improvement of therapeutic antibodies. Sets of CDR residues that are solvent accessible and relatively diverse in natural antibodies are targeted for diversification. Degenerate oligonucleotides are used to generate combinatorial phage-displayed antibody libraries with varying degree of diversity at randomized positions from which high-affinity antibodies can be selected. An advantage of using antibodies for therapy is their exquisite target specificity, which enables selective antigen binding and reduces off-target effects. However, it can be useful, and often it is necessary, to generate cross-reactive antibodies binding to not only the human antigen but also the corresponding non-human primate or rodent orthologs. Such cross-reactive antibodies can be used to validate the therapeutic targeting and examine the safety profile in preclinical animal models before committing to a costly development track. We show how affinity improvement and cross-species binding can be achieved in a one-step process.

  3. High-affinity K+ uptake in pepper plants.

    PubMed

    Martínez-Cordero, M Angeles; Martínez, Vicente; Rubio, Francisco

    2005-06-01

    High-affinity K+ uptake is an essential process for plant nutrition under K+-limiting conditions. The results presented here demonstrate that pepper (Capsicum annuum) plants grown in the absence of NH4+ and starved of K+ show an NH4+-sensitive high-affinity K+ uptake that allows plant roots to deplete external K+ to values below 1 microM. When plants are grown in the presence of NH4+, high-affinity K+ uptake is not inhibited by NH4+. Although NH4+-grown plants deplete external K+ below 1 microM in the absence of NH4+, when 1 mM NH4+ is present they do not deplete external K+ below 10 microM. A K+ transporter of the HAK family, CaHAK1, is very likely mediating the NH4+-sensitive component of the high-affinity K+ uptake in pepper roots. CaHAK1 is strongly induced in the roots that show the NH4+-sensitive high-affinity K+ uptake and its induction is reduced in K+-starved plants grown in the presence of NH4+. The NH4+-insensitive K+ uptake may be mediated by an AKT1-like K+ channel.

  4. Affine kinematics in planar fibrous connective tissues: an experimental investigation.

    PubMed

    Jayyosi, C; Affagard, J-S; Ducourthial, G; Bonod-Bidaud, C; Lynch, B; Bancelin, S; Ruggiero, F; Schanne-Klein, M-C; Allain, J-M; Bruyère-Garnier, K; Coret, M

    2017-03-29

    The affine transformation hypothesis is usually adopted in order to link the tissue scale with the fibers scale in structural constitutive models of fibrous tissues. Thanks to the recent advances in imaging techniques, such as multiphoton microscopy, the microstructural behavior and kinematics of fibrous tissues can now be monitored at different stretching within the same sample. Therefore, the validity of the affine hypothesis can be investigated. In this paper, the fiber reorientation predicted by the affine assumption is compared to experimental data obtained during mechanical tests on skin and liver capsule coupled with microstructural imaging using multiphoton microscopy. The values of local strains and the collagen fibers orientation measured at increasing loading levels are used to compute a theoretical estimation of the affine reorientation of collagen fibers. The experimentally measured reorientation of collagen fibers during loading could not be successfully reproduced with this simple affine model. It suggests that other phenomena occur in the stretching process of planar fibrous connective tissues, which should be included in structural constitutive modeling approaches.

  5. Biphasic Affinity Chromatographic Approach for Deep Tyrosine Phosphoproteome Analysis.

    PubMed

    Deng, Zhenzhen; Dong, Mingming; Wang, Yan; Dong, Jing; Li, Shawn S-C; Zou, Hanfa; Ye, Mingliang

    2017-02-21

    Tyrosine phosphorylation (pTyr) is important for normal physiology and implicated in many human diseases, particularly cancer. Identification of pTyr sites is critical to dissecting signaling pathways and understanding disease pathologies. However, compared with serine/threonine phosphorylation (pSer/pThr), the analysis of pTyr at the proteome level is more challenging due to its low abundance. Here, we developed a biphasic affinity chromatographic approach where Src SH2 superbinder was coupled with NeutrAvidin affinity chromatography, for tyrosine phosphoproteome analysis. With the use of competitive elution agent biotin-pYEEI, this strategy can distinguish high-affinity phosphotyrosyl peptides from low-affinity ones, while the excess competitive agent is readily removed by using NeutrAvidin agarose resin in an integrated tip system. The excellent performance of this system was demonstrated by analyzing tyrosine phosphoproteome of Jurkat cells from which 3,480 unique pTyr sites were identified. The biphasic affinity chromatography method for deep Tyr phosphoproteome analysis is rapid, sensitive, robust, and cost-effective. It is widely applicable to the global analysis of the tyrosine phosphoproteome associated with tyrosine kinase signal transduction.

  6. Protein purification by aminosquarylium cyanine dye-affinity chromatography.

    PubMed

    Silva, M S; Graça, V C; Reis, L V; Santos, P F; Almeida, P; Queiroz, J A; Sousa, F

    2013-12-01

    The most selective purification method for proteins and other biomolecules is affinity chromatography. This method is based on the unique biological-based specificity of the biomolecule-ligand interaction and commonly uses biological ligands. However, these ligands may present some drawbacks, mainly because of their cost and lability. Dye-affinity chromatography overcomes the limitations of biological ligands and is widely used owing to the low cost of synthetic dyes and to their resistance to biological and chemical degradation. In this work, immobilized aminosquarylium cyanine dyes are used in order to exploit affinity interactions with standard proteins such as lysozyme, α-chymotrypsin and trypsin. These studies evaluate the affinity interactions occurring between the immobilized ligand and the different proteins, as a reflection of the sum of several molecular interactions, namely ionic, hydrophobic and van der Waals, spread throughout the structure, in a defined spatial manner. The results show the possibility of using an aminosquarylium cyanine dye bearing a N-hexyl pendant chain, with a ligand density of 1.8 × 10(-2) mmol of dye/g of chromatographic support, to isolate lysozyme, α-chymotrypsin and trypsin from a mixture. The application of a decreasing ammonium sulfate gradient resulted in the recovery of lysozyme in the flowthrough. On the other hand, α-chymotrypsin and trypsin were retained, involving different interactions with the ligand. In conclusion, this study demonstrates the potential applicability of ligands such as aminosquarylium cyanine dyes for the separation and purification of proteins by affinity chromatography.

  7. Energetics of Al13 Keggin cluster compounds

    PubMed Central

    Armstrong, Christopher R.; Casey, William H.; Navrotsky, Alexandra

    2011-01-01

    The ϵ-Al13 Keggin aluminum hydroxide clusters are essential models in establishing molecular pathways for geochemical reactions. Enthalpies of formation are reported for two salts of aluminum centered ϵ-Keggin clusters, Al13 selenate, (Na(AlO4)Al12(OH)24(SeO4)4•12H2O) and Al13 sulfate, (NaAlO4Al12(OH)24(SO4)4•12H2O). The measured enthalpies of solution, ΔHsol, at 28 °C in 5 N HCl for the ε-Al13 selenate and sulfate are −924.57 (± 3.83) and −944.30 ( ± 5.66) kJ·mol-1, respectively. The enthalpies of formation from the elements, ΔHf,el, for Al13 selenate and sulfate are −19,656.35 ( ± 67.30) kJ·mol-1, and −20,892.39 ( ± 70.01) kJ·mol-1, respectively. In addition, ΔHf,el for sodium selenate decahydrate was calculated using data from high temperature oxide melt solution calorimetry measurements: −4,006.39 ( ± 11.91) kJ·mol-1. The formation of both ε-Al13 Keggin cluster compounds is exothermic from oxide-based components but energetically unfavorable with respect to a gibbsite-based assemblage. To understand the relative affinity of the ϵ-Keggin clusters for selenate and sulfate, the enthalpy associated with two S-Se exchange reactions was calculated. In the solid state, selenium is favored in the Al13 compound relative to the binary chalcogenate, while in 5 N HCl, sulfur is energetically favored in the cluster compound compared to the aqueous solution. This contribution represents the first thermodynamic study of ε-Al13 cluster compounds and establishes a method for other such molecules, including the substituted versions that have been created for kinetic studies. Underscoring the importance of ε-Al13 clusters in natural and anthropogenic systems, these data provide conclusive thermodynamic evidence that the Al13 Keggin cluster is a crucial intermediate species in the formation pathway from aqueous aluminum monomers to aluminum hydroxide precipitates. PMID:21852572

  8. Star Clusters within FIRE

    NASA Astrophysics Data System (ADS)

    Perez, Adrianna; Moreno, Jorge; Naiman, Jill; Ramirez-Ruiz, Enrico; Hopkins, Philip F.

    2017-01-01

    In this work, we analyze the environments surrounding star clusters of simulated merging galaxies. Our framework employs Feedback In Realistic Environments (FIRE) model (Hopkins et al., 2014). The FIRE project is a high resolution cosmological simulation that resolves star forming regions and incorporates stellar feedback in a physically realistic way. The project focuses on analyzing the properties of the star clusters formed in merging galaxies. The locations of these star clusters are identified with astrodendro.py, a publicly available dendrogram algorithm. Once star cluster properties are extracted, they will be used to create a sub-grid (smaller than the resolution scale of FIRE) of gas confinement in these clusters. Then, we can examine how the star clusters interact with these available gas reservoirs (either by accreting this mass or blowing it out via feedback), which will determine many properties of the cluster (star formation history, compact object accretion, etc). These simulations will further our understanding of star formation within stellar clusters during galaxy evolution. In the future, we aim to enhance sub-grid prescriptions for feedback specific to processes within star clusters; such as, interaction with stellar winds and gas accretion onto black holes and neutron stars.

  9. Melting of nickel clusters

    SciTech Connect

    Garzon, I.L.; Jellinek, J.

    1991-12-31

    The meltinglike phenomenon in Ni{sub n}, n = 19,20,55, clusters is studied using microcanonical molecular dynamics simulations. The interaction between the atoms in the clusters is modelled by a size-dependent Gupta-like potential that incorporates many-body effects. The clusters display the ``usual`` stages in their meltinglike transition, which characterize also Lennard-Jones (e.g., noble gas) and ionic clusters. In addition, Ni{sub 20} passes through a so-called premelting stage found earlier also for Ni{sub 14}. 11 ref., 3 figs.

  10. Melting of nickel clusters

    SciTech Connect

    Garzon, I.L. . Inst. de Fisica); Jellinek, J. )

    1991-01-01

    The meltinglike phenomenon in Ni{sub n}, n = 19,20,55, clusters is studied using microcanonical molecular dynamics simulations. The interaction between the atoms in the clusters is modelled by a size-dependent Gupta-like potential that incorporates many-body effects. The clusters display the usual'' stages in their meltinglike transition, which characterize also Lennard-Jones (e.g., noble gas) and ionic clusters. In addition, Ni{sub 20} passes through a so-called premelting stage found earlier also for Ni{sub 14}. 11 ref., 3 figs.

  11. Mini-clusters

    NASA Technical Reports Server (NTRS)

    Chinellato, J. A.; Dobrigkeit, C.; Bellandifilho, J.; Lattes, C. M. G.; Menon, M. J.; Navia, C. E.; Pamilaju, A.; Sawayanagi, K.; Shibuya, E. H.; Turtelli, A., Jr.

    1985-01-01

    Experimental results of mini-clusters observed in Chacaltaya emulsion chamber no.19 are summarized. The study was made on 54 single core shower upper and 91 shower clusters of E(gamma) 10 TeV from 30 families which are visible energy greater than 80 TeV and penetrate through both upper and lower detectors of the two-story chamber. The association of hadrons in mini-cluster is made clear from their penetrative nature and microscopic observation of shower continuation in lower chamber. Small P sub t (gamma) of hadrons in mini-clusters remained in puzzle.

  12. Clustering versus non-clustering phase synchronizations

    SciTech Connect

    Liu, Shuai; Zhan, Meng

    2014-03-15

    Clustering phase synchronization (CPS) is a common scenario to the global phase synchronization of coupled dynamical systems. In this work, a novel scenario, the non-clustering phase synchronization (NPS), is reported. It is found that coupled systems do not transit to the global synchronization until a certain sufficiently large coupling is attained, and there is no clustering prior to the global synchronization. To reveal the relationship between CPS and NPS, we further analyze the noise effect on coupled phase oscillators and find that the coupled oscillator system can change from CPS to NPS with the increase of noise intensity or system disorder. These findings are expected to shed light on the mechanism of various intriguing self-organized behaviors in coupled systems.

  13. Wiggler magnetic field assisted second harmonic generation in clusters

    NASA Astrophysics Data System (ADS)

    Aggarwal, Munish; Vij, Shivani; Kant, Niti

    2015-06-01

    Wiggler magnetic field assisted second harmonic generation in clusters has been investigated theoretically. An intense short-pulse laser propagating through a gas embedded with atomic clusters, converts it into hot plasma balls. For clusters with radius less than one tenth of the laser wavelength, the nonlinear restoration force dominates, which leads to second harmonic generation. The magnetic wiggler provides the uncompensated momentum to second harmonic photon, to make the process of harmonic generation resonant. We explore the impact of laser intensity and cluster size on the efficiency of second harmonic generation. Pulse slippage of second harmonic pulse out of the domain of fundamental laser pulse has been observed on account of group velocity mismatch between the fundamental and second harmonic pulse. Enhancement in the efficiency of the second harmonic is seen for the optimum values of wiggler magnetic field.

  14. Rapid vegetative propagation method for carob

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many fruit species are propagated by vegetative methods such as budding, grafting, cutting, suckering, layering etc. to avoid heterozygosity. Carob trees (Ceratonia siliqua L.) are of highly economical value and it is among the most difficult-to-propagate fruit species. In this study, air-layering p...

  15. Propagation of major plant-virus hosts.

    PubMed

    Hull, Roger

    2009-08-01

    Plant viruses are propagated in host plants, which are usually grown in glasshouses, screen houses, or growth cabinets. In most cases, the plants are grown from seed; in some cases, they are propagated as cuttings. This unit describes the basic techniques of growing suitable plants from seed and cuttings.

  16. Nondestructive evaluation of pyroshock propagation using hydrocodes

    NASA Astrophysics Data System (ADS)

    Lee, Juho; Hwang, Dae-Hyeon; Jang, Jae-Kyeong; Lee, Jung-Ryul; Han, Jae-Hung

    2016-04-01

    Pyroshock or pyrotechnic shock generated by explosive events of pyrotechnic devices can induce fatal failures in electronic payloads. Therefore, understanding and estimation of pyroshock propagation through complex structures are necessary. However, an experimental approach using real pyrotechnic devices is quite burdensome because pyrotechnic devices can damage test structures and newly manufactured test structures are necessary for each experiment. Besides, pyrotechnic experiments are quite expensive, time-consuming, and dangerous. Consequently, nondestructive evaluation (NDE) of pyroshock propagation without using real pyrotechnic devices is necessary. In this study, nondestructive evaluation technique for pyroshock propagation estimation using hydrocodes is proposed. First, pyroshock propagation is numerically analyzed using AUTODYN, a commercial hydrocodes. Hydrocodes can handle stress wave propagation including elastic, plastic, and shock wave in the time domain. Test structures are modeled and pyroshock time history is applied to where the pyroshock propagation originates. Numerical NDE results of pyroshock propagation on test structures are analyzed in terms of acceleration time histories and acceleration shock response spectra (SRS) results. To verify the proposed numerical methodology, impact tests using airsoft gun are performed. The numerical analysis results for the impact tests are compared with experimental results and they show good agreements. The proposed numerical techniques enable us to nondestructively characterize pyroshock propagation.

  17. Vehicular sources in acoustic propagation experiments

    NASA Technical Reports Server (NTRS)

    Prado, Gervasio; Fitzgerald, James; Arruda, Anthony; Parides, George

    1990-01-01

    One of the most important uses of acoustic propagation models lies in the area of detection and tracking of vehicles. Propagation models are used to compute transmission losses in performance prediction models and to analyze the results of past experiments. Vehicles can also provide the means for cost effective experiments to measure acoustic propagation conditions over significant ranges. In order to properly correlate the information provided by the experimental data and the propagation models, the following issues must be taken into consideration: the phenomenology of the vehicle noise sources must be understood and characterized; the vehicle's location or 'ground truth' must be accurately reproduced and synchronized with the acoustic data; and sufficient meteorological data must be collected to support the requirements of the propagation models. The experimental procedures and instrumentation needed to carry out propagation experiments are discussed. Illustrative results are presented for two cases. First, a helicopter was used to measure propagation losses at a range of 1 to 10 Km. Second, a heavy diesel-powered vehicle was used to measure propagation losses in the 300 to 2200 m range.

  18. Propagation testing multi-cell batteries.

    SciTech Connect

    Orendorff, Christopher J.; Lamb, Joshua; Steele, Leigh Anna Marie; Spangler, Scott Wilmer

    2014-10-01

    Propagation of single point or single cell failures in multi-cell batteries is a significant concern as batteries increase in scale for a variety of civilian and military applications. This report describes the procedure for testing failure propagation along with some representative test results to highlight the potential outcomes for different battery types and designs.

  19. PROPHET: An applicaton of propagation forecasting principles

    NASA Technical Reports Server (NTRS)

    Argo, P. E.; Rothmuller, I. J.

    1979-01-01

    A propagation assessment and forecasting terminal, PROPHET, is described. The terminal is a key element of the environmental prediction and assessment system which uses real time solar/geophysical data to provide real time knowledge of propagation conditions. The terminal uses models to translate data from satellite and ground based sources into performance predictions for specific systems.

  20. Uncertainty Propagation in an Ecosystem Nutrient Budget.

    EPA Science Inventory

    New aspects and advancements in classical uncertainty propagation methods were used to develop a nutrient budget with associated error for a northern Gulf of Mexico coastal embayment. Uncertainty was calculated for budget terms by propagating the standard error and degrees of fr...

  1. Propagation of almond rootstocks and trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Millions of almond trees in production in California and elsewhere were propagated by nurseries using the grafting technique called budding. This gives a uniform orchard and allows the grower to select nut cultivar (scion) and rootstock combinations. Grafting is a form of clonal propagation and resu...

  2. Propagation and Damping of Kinetic Alfven Waves Generated During Magnetic Reconnection

    NASA Astrophysics Data System (ADS)

    Sharma, P.; Shay, M. A.; Haggerty, C. C.; Parashar, T.

    2015-12-01

    Magnetospheric waves have the potential to convert to Kinetic Alfven Waves (KAW) at scales close to the ion larmor radius and the electron inertial length. At this length scale, it is observed that KAW generated at reconnection propagates super-Alfvenically and the wave is responsible for the parallel propagation of the Hall magnetic field near the separatrice from the magnetotial region. The pointing flux associated with this Hall magnetic field is also consistent with observed Cluster data observations [1]. An important question is whether this KAW energy will be able to propagate all the way to the Earth, creating aurora associated with a substorm. If this KAW propagation can be well understood, then this will provide valuable insight as to the relative timing of substorm onset versus reconnection onset in the magnetotail. The difficulty currently is that the nonlinear damping of KAW is not well understood even in a homogenous system, let alone more realistic magnetotail geometries including changes to density, magnetic field strength, and magnetic orientation. We study the propagation, dispersion, and damping of these KAWs using P3D, a kinetic particle-in-cell (PIC) simulation code. Travelling waves are initialized based on a fluid model and allowed to propagate for substantial time periods. Damping of the waves are compared with Landau damping predictions. The waves are simulated in both homogenous and varying equilibrium meant to determine the effect on propagation. Implications for energetic electron production and Poynting flux input into the ionosphere are discussed. [1] Shay, M. A., J. F. Drake, J. P. Eastwood, and T. D. Phan, Super-Alfvenic propagation of substorm reconnection signatures and Poynting flux,, Physics Review Letters, Vol. 107, 065001, 2011.

  3. Density-Aware Clustering Based on Aggregated Heat Kernel and Its Transformation

    SciTech Connect

    Huang, Hao; Yoo, Shinjae; Yu, Dantong; Qin, Hong

    2015-06-01

    Current spectral clustering algorithms suffer from the sensitivity to existing noise, and parameter scaling, and may not be aware of different density distributions across clusters. If these problems are left untreated, the consequent clustering results cannot accurately represent true data patterns, in particular, for complex real world datasets with heterogeneous densities. This paper aims to solve these problems by proposing a diffusion-based Aggregated Heat Kernel (AHK) to improve the clustering stability, and a Local Density Affinity Transformation (LDAT) to correct the bias originating from different cluster densities. AHK statistically\\ models the heat diffusion traces along the entire time scale, so it ensures robustness during clustering process, while LDAT probabilistically reveals local density of each instance and suppresses the local density bias in the affinity matrix. Our proposed framework integrates these two techniques systematically. As a result, not only does it provide an advanced noise-resisting and density-aware spectral mapping to the original dataset, but also demonstrates the stability during the processing of tuning the scaling parameter (which usually controls the range of neighborhood). Furthermore, our framework works well with the majority of similarity kernels, which ensures its applicability to many types of data and problem domains. The systematic experiments on different applications show that our proposed algorithms outperform state-of-the-art clustering algorithms for the data with heterogeneous density distributions, and achieve robust clustering performance with respect to tuning the scaling parameter and handling various levels and types of noise.

  4. Density-Aware Clustering Based on Aggregated Heat Kernel and Its Transformation

    DOE PAGES

    Huang, Hao; Yoo, Shinjae; Yu, Dantong; ...

    2015-06-01

    Current spectral clustering algorithms suffer from the sensitivity to existing noise, and parameter scaling, and may not be aware of different density distributions across clusters. If these problems are left untreated, the consequent clustering results cannot accurately represent true data patterns, in particular, for complex real world datasets with heterogeneous densities. This paper aims to solve these problems by proposing a diffusion-based Aggregated Heat Kernel (AHK) to improve the clustering stability, and a Local Density Affinity Transformation (LDAT) to correct the bias originating from different cluster densities. AHK statistically\\ models the heat diffusion traces along the entire time scale, somore » it ensures robustness during clustering process, while LDAT probabilistically reveals local density of each instance and suppresses the local density bias in the affinity matrix. Our proposed framework integrates these two techniques systematically. As a result, not only does it provide an advanced noise-resisting and density-aware spectral mapping to the original dataset, but also demonstrates the stability during the processing of tuning the scaling parameter (which usually controls the range of neighborhood). Furthermore, our framework works well with the majority of similarity kernels, which ensures its applicability to many types of data and problem domains. The systematic experiments on different applications show that our proposed algorithms outperform state-of-the-art clustering algorithms for the data with heterogeneous density distributions, and achieve robust clustering performance with respect to tuning the scaling parameter and handling various levels and types of noise.« less

  5. Density functional study of hydrogen binding on gold and silver-gold clusters.

    PubMed

    Zhao, Shuang; Ren, YunLi; Ren, YunLai; Wang, JianJi; Yin, WeiPing

    2010-04-15

    A theoretical study was carried out on the binding of hydrogen on small bimetallic Ag(m)Au(n) (m + n < or = 5) and pure Au(n) (n < or = 5) clusters with neutral, negative, and positive charge state. It is found that the composition and charge state of clusters have strong influence on the most favorable binding site. The adiabatic ionization potentials, electron affinities, and hydrogen binding energies of cluster hydrides increase with the Au content increasing for the given cluster size. The cationic silver-gold cluster hydrides prefer ejection of Au-containing products whereas the anionic silver-gold cluster hydrides prefer ejection of Ag-containing products. The magnitude of metal-H frequency in combination with the metal-H bond length indicates that, with the same type of the binding site, the Au-H interaction is stronger than the Ag-H interaction.

  6. Do anionic titanium dioxide nano-clusters reach bulk band gap? A density functional theory study.

    PubMed

    Qu, Zheng-Wang; Zhu, Hui

    2010-07-30

    The electronic properties of both neutral and anionic (TiO(2))(n) (n = 1-10) clusters are investigated by extensive density functional theory calculations. The predicted electron detachment energies and excitation gaps of anionic clusters agree well with the original experimental anion photoelectron spectra (APES). It is shown that the old way to analyze APES tends to overestimate vertical excitation gaps (VGA) of large anionic clusters, due to the nature of multiple electronic origins for the higher APES bands. Moreover, the VGA of anionic TiO(2) clusters are evidently smaller than those of neutral clusters, which may also be the case for other metal oxide clusters with high electron affinity.

  7. EVOLUTION OF SHOCKS AND TURBULENCE IN MAJOR CLUSTER MERGERS

    SciTech Connect

    Paul, S.; Mannheim, K.; Iapichino, L.; Miniati, F.; Bagchi, J.

    2011-01-01

    We performed a set of cosmological simulations of major mergers in galaxy clusters, in order to study the evolution of merger shocks and the subsequent injection of turbulence in the post-shock region and in the intra-cluster medium (ICM). The computations have been performed with the grid-based, adaptive mesh refinement hydrodynamical code Enzo, using a refinement criterion especially designed for refining turbulent flows in the vicinity of shocks. When a major merger event occurs, a substantial amount of turbulence energy is injected in the ICM of the newly formed cluster. Our simulations show that the shock launched after a major merger develops an ellipsoidal shape and gets broken by the interaction with the filamentary cosmic web around the merging cluster. The size of the post-shock region along the direction of shock propagation is of the order of 300 kpc h{sup -1}, and the turbulent velocity dispersion in this region is larger than 100 km s{sup -1}. We performed a scaling analysis of the turbulence energy within our cluster sample. The best fit for the scaling of the turbulence energy with the cluster mass is consistent with M{sup 5/3}, which is also the scaling law for the thermal energy in the self-similar cluster model. This clearly indicates the close relation between virialization and injection of turbulence in the cluster evolution. As for the turbulence in the cluster core, we found that within 2 Gyr after the major merger (the timescale for the shock propagation in the ICM), the ratio of the turbulent to total pressure is larger than 10%, and after about 4 Gyr it is still larger than 5%, a typical value for nearly relaxed clusters. Turbulence at the cluster center is thus sustained for several gigayears, which is substantially longer than typically assumed in the turbulent re-acceleration models, invoked to explain the statistics of observed radio halos. Striking similarities in the morphology and other physical parameters between our simulations

  8. Crack propagation driven by crystal growth

    SciTech Connect

    A. Royne; Paul Meaking; A. Malthe-Sorenssen; B. Jamtveit; D. K. Dysthe

    2011-10-01

    Crystals that grow in confinement may exert a force on their surroundings and thereby drive crack propagation in rocks and other materials. We describe a model of crystal growth in an idealized crack geometry in which the crystal growth and crack propagation are coupled through the stress in the surrounding bulk solid. Subcritical crack propagation takes place during a transient period, which may be very long, during which the crack velocity is limited by the kinetics of crack propagation. When the crack is sufficiently large, the crack velocity becomes limited by the kinetics of crystal growth. The duration of the subcritical regime is determined by two non-dimensional parameters, which relate the kinetics of crack propagation and crystal growth to the supersaturation of the fluid and the elastic properties of the surrounding material.

  9. The affine structure of gravitational theories: Symplectic groups and geometry

    NASA Astrophysics Data System (ADS)

    Capozziello, Salvatore; Cirilo-Lombardo, D. J.; de Laurentis, Mariafelicia

    2014-09-01

    We give a geometrical description of gravitational theories from the viewpoint of symmetries and affine structure. We show how gravity, considered as a gauge theory, can be consistently achieved by the nonlinear realization of the conformal-affine group in an indirect manner: due to the partial isomorphism between CA(3, 1) and the centrally extended Sp( 8), we perform a nonlinear realization of the centrally extended (CE)Sp( 8) in its semi-simple version. In particular, starting from the bundle structure of gravity, we derive the conformal-affine Lie algebra and then, by the nonlinear realization, we define the coset field transformations, the Cartan forms and the inverse Higgs constraints. Finally, we discuss the geometrical Lagrangians where all the information on matter fields and their interactions can be contained.

  10. Affinity maturation of antibodies requires integrity of the adult thymus.

    PubMed

    AbuAttieh, Mouhammed; Bender, Diane; Liu, Esther; Wettstein, Peter; Platt, Jeffrey L; Cascalho, Marilia

    2012-02-01

    The generation of B-cell responses to proteins requires a functional thymus to produce CD4(+) T cells which helps in the activation and differentiation of B cells. Because the mature T-cell repertoire has abundant cells with the helper phenotype, one might predict that in mature individuals, the generation of B-cell memory would proceed independently of the thymus. Contrary to that prediction, we show here that the removal of the thymus after the establishment of the T-cell compartment or sham surgery without removal of the thymus impairs the affinity maturation of antibodies. Because removal or manipulation of the thymus did not decrease the frequency of mutation of the Ig variable heavy chain exons encoding antigen-specific antibodies, we conclude that the thymus controls affinity maturation of antibodies in the mature individual by facilitating the selection of B cells with high-affinity antibodies.

  11. A fast quantum algorithm for the affine Boolean function identification

    NASA Astrophysics Data System (ADS)

    Younes, Ahmed

    2015-02-01

    Bernstein-Vazirani algorithm (the one-query algorithm) can identify a completely specified linear Boolean function using a single query to the oracle with certainty. The first aim of the paper is to show that if the provided Boolean function is affine, then one more query to the oracle (the two-query algorithm) is required to identify the affinity of the function with certainty. The second aim of the paper is to show that if the provided Boolean function is incompletely defined, then the one-query and the two-query algorithms can be used as bounded-error quantum polynomial algorithms to identify certain classes of incompletely defined linear and affine Boolean functions respectively with probability of success at least 2/3.

  12. On the electron affinity of the oxygen atom

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Langhoff, S. R.; Partridge, H.; Taylor, P. R.

    1986-01-01

    The electron affinity (EA) of oxygen is computed to be 1.287 eV, using 2p electron full configuration-interaction (CI) wave functions expanded in a 6s5p3d2f Slater-type orbital basis. The best complete active space self-consistent field - multireference CI (CASSCF-MRCI) result including only 2p correlation is 1.263 eV. However, inclusion of 2s intrashell and 2s2p intershell correlation increases the computed EA to 1.290 at the CASSCF-MRCI level. At the full CI basis set limit, the 2s contribution to the electron affinity is estimated to be as large as 0.1 eV. This study clearly establishes the synergistic effect between the higher excitations and basis set completeness on the electron affinity when the 2s electrons are correlated.

  13. On the electron affinity of the oxygen atom

    NASA Technical Reports Server (NTRS)

    Bauschlicher, C. W., Jr.; Langhoff, S. R.; Partridge, H.; Taylor, P. R.

    1986-01-01

    The electron affinity of oxygen is computed to be 1.287 eV, at the full CI level using a 6s5p3d 2f Slater-type orbital basis and correlating only the 2p electrons. The best CASSCF-MRCI result including only 2p correlation is 1.263 eV. However, inclusion of 2s intrashell and 2s2p intershell coorelation increases the computed EA to 1.290 eV at the CASSCF-MRCI level. At the full CI basis set limit, the 2s contribution to the electron affinity is estimated to be as large as 0.1 eV. The higher excitation contribution to the electron affinity is found to increase substantially with basis set completeness, especially when the 2s electrons are correlated. Relativistic effects are shown to make a small (less than 0.01 eV) change in the EA.

  14. AMPK beta subunits display isoform specific affinities for carbohydrates.

    PubMed

    Koay, Ann; Woodcroft, Ben; Petrie, Emma J; Yue, Helen; Emanuelle, Shane; Bieri, Michael; Bailey, Michael F; Hargreaves, Mark; Park, Jong-Tae; Park, Kwan-Hwa; Ralph, Stuart; Neumann, Dietbert; Stapleton, David; Gooley, Paul R

    2010-08-04

    AMP-activated protein kinase (AMPK) is a heterotrimer of catalytic (alpha) and regulatory (beta and gamma) subunits with at least two isoforms for each subunit. AMPK beta1 is widely expressed whilst AMPK beta2 is highly expressed in muscle and both beta isoforms contain a mid-molecule carbohydrate-binding module (beta-CBM). Here we show that beta2-CBM has evolved to contain a Thr insertion and increased affinity for glycogen mimetics with a preference for oligosaccharides containing a single alpha-1,6 branched residue. Deletion of Thr-101 reduces affinity for single alpha-1,6 branched oligosaccharides by 3-fold, while insertion of this residue into the equivalent position in the beta1-CBM sequence increases affinity by 3-fold, confirming the functional importance of this residue.

  15. Uncertainty propagation in nuclear forensics.

    PubMed

    Pommé, S; Jerome, S M; Venchiarutti, C

    2014-07-01

    Uncertainty propagation formulae are presented for age dating in support of nuclear forensics. The age of radioactive material in this context refers to the time elapsed since a particular radionuclide was chemically separated from its decay product(s). The decay of the parent radionuclide and ingrowth of the daughter nuclide are governed by statistical decay laws. Mathematical equations allow calculation of the age of specific nuclear material through the atom ratio between parent and daughter nuclides, or through the activity ratio provided that the daughter nuclide is also unstable. The derivation of the uncertainty formulae of the age may present some difficulty to the user community and so the exact solutions, some approximations, a graphical representation and their interpretation are presented in this work. Typical nuclides of interest are actinides in the context of non-proliferation commitments. The uncertainty analysis is applied to a set of important parent-daughter pairs and the need for more precise half-life data is examined.

  16. S-Band propagation measurements

    NASA Technical Reports Server (NTRS)

    Briskman, Robert D.

    1994-01-01

    A geosynchronous satellite system capable of providing many channels of digital audio radio service (DARS) to mobile platforms within the contiguous United States using S-band radio frequencies is being implemented. The system is designed uniquely to mitigate both multipath fading and outages from physical blockage in the transmission path by use of satellite spatial diversity in combination with radio frequency and time diversity. The system also employs a satellite orbital geometry wherein all mobile platforms in the contiguous United States have elevation angles greater than 20 deg to both of the diversity satellites. Since implementation of the satellite system will require three years, an emulation has been performed using terrestrial facilities in order to allow evaluation of DARS capabilities in advance of satellite system operations. The major objective of the emulation was to prove the feasibility of broadcasting from satellites 30 channels of CD quality programming using S-band frequencies to an automobile equipped with a small disk antenna and to obtain quantitative performance data on S-band propagation in a satellite spatial diversity system.

  17. VPSim: Variance propagation by simulation

    SciTech Connect

    Burr, T.; Coulter, C.A.; Prommel, J.

    1997-12-01

    One of the fundamental concepts in a materials control and accountability system for nuclear safeguards is the materials balance (MB). All transfers into and out of a material balance area are measured, as are the beginning and ending inventories. The resulting MB measures the material loss, MB = T{sub in} + I{sub B} {minus} T{sub out} {minus} I{sub E}. To interpret the MB, the authors must estimate its measurement error standard deviation, {sigma}{sub MB}. When feasible, they use a method usually known as propagation of variance (POV) to estimate {sigma}{sub MB}. The application of POV for estimating the measurement error variance of an MB is straightforward but tedious. By applying POV to individual measurement error standard deviations they can estimate {sigma}{sub MB} (or more generally, they can estimate the variance-covariance matrix, {Sigma}, of a sequence of MBs). This report describes a new computer program (VPSim) that uses simulation to estimate the {Sigma} matrix of a sequence of MBs. Given the proper input data, VPSim calculates the MB and {sigma}{sub MB}, or calculates a sequence of n MBs and the associated n-by-n covariance matrix, {Sigma}. The covariance matrix, {Sigma}, contains the variance of each MB in the diagonal entries and the covariance between pairs of MBs in the off-diagonal entries.

  18. Twist Propagation in Dinucleosome Arrays

    PubMed Central

    Dobrovolskaia, Irina V.; Kenward, Martin; Arya, Gaurav

    2010-01-01

    We present a Monte Carlo simulation study of the distribution and propagation of twist from one DNA linker to another for a two-nucleosome array subjected to externally applied twist. A mesoscopic model of the array that incorporates nucleosome geometry along with the bending and twisting mechanics of the linkers is employed and external twist is applied in stepwise increments to mimic quasistatic twisting of chromatin fibers. Simulation results reveal that the magnitude and sign of the imposed and induced twist on contiguous linkers depend strongly on their relative orientation. Remarkably, the relative direction of the induced and applied twist can become inverted for a subset of linker orientations—a phenomenon we refer to as “twist inversion”. We characterize the twist inversion, as a function of relative linker orientation, in a phase diagram and explain its key features using a simple model based on the geometry of the nucleosome/linker complex. In addition to twist inversion, our simulations reveal “nucleosome flipping”, whereby nucleosomes may undergo sudden flipping in response to applied twist, causing a rapid bending of the linker and a significant change in the overall twist and writhe of the array. Our findings shed light on the underlying mechanisms by which torsional stresses impact chromatin organization. PMID:21081084

  19. A nonparametric clustering technique which estimates the number of clusters

    NASA Technical Reports Server (NTRS)

    Ramey, D. B.

    1983-01-01

    In applications of cluster analysis, one usually needs to determine the number of clusters, K, and the assignment of observations to each cluster. A clustering technique based on recursive application of a multivariate test of bimodality which automatically estimates both K and the cluster assignments is presented.

  20. Dynamical quorum sensing and clustering dynamics in a population of spatially distributed active rotators

    NASA Astrophysics Data System (ADS)

    Sakaguchi, Hidetsugu; Maeyama, Satomi

    2013-02-01

    A model of clustering dynamics is proposed for a population of spatially distributed active rotators. A transition from excitable to oscillatory dynamics is induced by the increase of the local density of active rotators. It is interpreted as dynamical quorum sensing. In the oscillation regime, phase waves propagate without decay, which generates an effectively long-range interaction in the clustering dynamics. The clustering process becomes facilitated and only one dominant cluster appears rapidly as a result of the dynamical quorum sensing. An exact localized solution is found to a simplified model equation, and the competitive dynamics between two localized states is studied numerically.

  1. Statistical analysis of loopy belief propagation in random fields

    NASA Astrophysics Data System (ADS)

    Yasuda, Muneki; Kataoka, Shun; Tanaka, Kazuyuki

    2015-10-01

    Loopy belief propagation (LBP), which is equivalent to the Bethe approximation in statistical mechanics, is a message-passing-type inference method that is widely used to analyze systems based on Markov random fields (MRFs). In this paper, we propose a message-passing-type method to analytically evaluate the quenched average of LBP in random fields by using the replica cluster variation method. The proposed analytical method is applicable to general pairwise MRFs with random fields whose distributions differ from each other and can give the quenched averages of the Bethe free energies over random fields, which are consistent with numerical results. The order of its computational cost is equivalent to that of standard LBP. In the latter part of this paper, we describe the application of the proposed method to Bayesian image restoration, in which we observed that our theoretical results are in good agreement with the numerical results for natural images.

  2. A small change in neuronal network topology can induce explosive synchronization transition and activity propagation in the entire network.

    PubMed

    Wang, Zhenhua; Tian, Changhai; Dhamala, Mukesh; Liu, Zonghua

    2017-04-03

    We here study explosive synchronization transitions and network activity propagation in networks of coupled neurons to provide a new understanding of the relationship between network topology and explosive dynamical transitions as in epileptic seizures and their propagations in the brain. We model local network motifs and configurations of coupled neurons and analyze the activity propagations between a group of active neurons to their inactive neuron neighbors in a variety of network configurations. We find that neuronal activity propagation is limited to local regions when network is highly clustered with modular structures as in the normal brain networks. When the network cluster structure is slightly changed, the activity propagates to the entire network, which is reminiscent of epileptic seizure propagation in the brain. Finally, we analyze intracranial electroencephalography (IEEG) recordings of a seizure episode from a epilepsy patient and uncover that explosive synchronization-like transition occurs around the clinically defined onset of seizure. These findings may provide a possible mechanism for the recurrence of epileptic seizures, which are known to be the results of aberrant neuronal network structure and/or function in the brain.

  3. Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment

    PubMed Central

    Levay, Agata; Brenneman, Randall; Hoinka, Jan; Sant, David; Cardone, Marco; Trinchieri, Giorgio; Przytycka, Teresa M.; Berezhnoy, Alexey

    2015-01-01

    Oligonucleotide aptamers represent a novel platform for creating ligands with desired specificity, and they offer many potentially significant advantages over monoclonal antibodies in terms of feasibility, cost, and clinical applicability. However, the isolation of high-affinity aptamer ligands from random oligonucleotide pools has been challenging. Although high-throughput sequencing (HTS) promises to significantly facilitate systematic evolution of ligands by exponential enrichment (SELEX) analysis, the enormous datasets generated in the process pose new challenges for identifying those rare, high-affinity aptamers present in a given pool. We show that emulsion PCR preserves library diversity, preventing the loss of rare high-affinity aptamers that are difficult to amplify. We also demonstrate the importance of using reference targets to eliminate binding candidates with reduced specificity. Using a combination of bioinformatics and functional analyses, we show that the rate of amplification is more predictive than prevalence with respect to binding affinity and that the mutational landscape within a cluster of related aptamers can guide the identification of high-affinity aptamer ligands. Finally, we demonstrate the power of this selection process for identifying cross-species aptamers that can bind human receptors and cross-react with their murine orthologs. PMID:26007661

  4. Solid support resins and affinity purification mass spectrometry.

    PubMed

    Havis, Spencer; Moree, Wilna J; Mali, Sujina; Bark, Steven J

    2017-02-28

    Co-affinity purification-mass spectrometry (CoAP-MS) is a primary technology for elucidating the protein-protein interactions that form the basis of all biological processes. A critical component of CoAP-MS is the affinity purification (AP) of the bait protein, usually by immobilization of an antibody to a solid-phase resin. This Minireview discusses common resins, reagents, tagging methods, and their consideration for successful AP of tagged proteins. We discuss our experiences with different solid supports, their impact in AP experiments, and propose areas where chemistry can advance this important technology.

  5. Affine generalization of the Komar complex of general relativity

    NASA Astrophysics Data System (ADS)

    Mielke, Eckehard W.

    2001-02-01

    On the basis of the ``on shell'' Noether identities of the metric-affine gauge approach of gravity, an affine superpotential is derived which comprises the energy- and angular-momentum content of exact solutions. In the special case of general relativity (GR) or its teleparallel equivalent, the Komar or Freud complex, respectively, are recovered. Applying this to the spontaneously broken anti-de Sitter gauge model of McDowell and Mansouri with an induced Euler term automatically yields the correct mass and spin of the Kerr-AdS solution of GR with a (induced) cosmological constant without the factor two discrepancy of the Komar formula.

  6. A quantum affine algebra for the deformed Hubbard chain

    NASA Astrophysics Data System (ADS)

    Beisert, Niklas; Galleas, Wellington; Matsumoto, Takuya

    2012-09-01

    The integrable structure of the one-dimensional Hubbard model is based on Shastry's R-matrix and the Yangian of a centrally extended \\mathfrak {sl}(2|2) superalgebra. Alcaraz and Bariev have shown that the model admits an integrable deformation whose R-matrix has recently been found. This R-matrix is of trigonometric type and here we derive its underlying exceptional quantum affine algebra. We also show how the algebra reduces to the above-mentioned Yangian and to the conventional quantum affine \\mathfrak {sl}(2|2) algebra in two special limits.

  7. Scalable Prediction of Energy Consumption using Incremental Time Series Clustering

    SciTech Connect

    Simmhan, Yogesh; Noor, Muhammad Usman

    2013-10-09

    Time series datasets are a canonical form of high velocity Big Data, and often generated by pervasive sensors, such as found in smart infrastructure. Performing predictive analytics on time series data can be computationally complex, and requires approximation techniques. In this paper, we motivate this problem using a real application from the smart grid domain. We propose an incremental clustering technique, along with a novel affinity score for determining cluster similarity, which help reduce the prediction error for cumulative time series within a cluster. We evaluate this technique, along with optimizations, using real datasets from smart meters, totaling ~700,000 data points, and show the efficacy of our techniques in improving the prediction error of time series data within polynomial time.

  8. Propagating Waves of Directionality and Coordination Orchestrate Collective Cell Migration

    PubMed Central

    Zaritsky, Assaf; Kaplan, Doron; Hecht, Inbal; Natan, Sari; Wolf, Lior; Gov, Nir S.; Ben-Jacob, Eshel; Tsarfaty, Ilan

    2014-01-01

    The ability of cells to coordinately migrate in groups is crucial to enable them to travel long distances during embryonic development, wound healing and tumorigenesis, but the fundamental mechanisms underlying intercellular coordination during collective cell migration remain elusive despite considerable research efforts. A novel analytical framework is introduced here to explicitly detect and quantify cell clusters that move coordinately in a monolayer. The analysis combines and associates vast amount of spatiotemporal data across multiple experiments into transparent quantitative measures to report the emergence of new modes of organized behavior during collective migration of tumor and epithelial cells in wound healing assays. First, we discovered the emergence of a wave of coordinated migration propagating backward from the wound front, which reflects formation of clusters of coordinately migrating cells that are generated further away from the wound edge and disintegrate close to the advancing front. This wave emerges in both normal and tumor cells, and is amplified by Met activation with hepatocyte growth factor/scatter factor. Second, Met activation was found to induce coinciding waves of cellular acceleration and stretching, which in turn trigger the emergence of a backward propagating wave of directional migration with about an hour phase lag. Assessments of the relations between the waves revealed that amplified coordinated migration is associated with the emergence of directional migration. Taken together, our data and simplified modeling-based assessments suggest that increased velocity leads to enhanced coordination: higher motility arises due to acceleration and stretching that seems to increase directionality by temporarily diminishing the velocity components orthogonal to the direction defined by the monolayer geometry. Spatial and temporal accumulation of directionality thus defines coordination. The findings offer new insight and suggest a basic

  9. Photoionization of molecular clusters

    NASA Astrophysics Data System (ADS)

    Andres, R. P.; Calo, J. M.

    1981-12-01

    An experimental apparatus consisting of a novel multiple expansion cluster source coupled with a molecular beam system and photoionization mass spectrometer has been designed and constructed. This apparatus has been thoroughly tested and preliminary measurements of the growth kinetics of water clusters and the photoionization cross section of the water dimer have been carried out.

  10. Probability and Cancer Clusters

    ERIC Educational Resources Information Center

    Hamilton-Keene, Rachael; Lenard, Christoper T.; Mills, Terry M.

    2009-01-01

    Recently there have been several news items about possible cancer clusters in the Australian media. The term "cancer cluster" is used when an unusually large number of people in one geographic area, often a workplace, are diagnosed with cancer in a short space of time. In this paper the authors explore this important health issue using…

  11. Coma cluster of galaxies

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Atlas Image mosaic, covering 34' x 34' on the sky, of the Coma cluster, aka Abell 1656. This is a particularly rich cluster of individual galaxies (over 1000 members), most prominently the two giant ellipticals, NGC 4874 (right) and NGC 4889 (left). The remaining members are mostly smaller ellipticals, but spiral galaxies are also evident in the 2MASS image. The cluster is seen toward the constellation Coma Berenices, but is actually at a distance of about 100 Mpc (330 million light years, or a redshift of 0.023) from us. At this distance, the cluster is in what is known as the 'Hubble flow,' or the overall expansion of the Universe. As such, astronomers can measure the Hubble Constant, or the universal expansion rate, based on the distance to this cluster. Large, rich clusters, such as Coma, allow astronomers to measure the 'missing mass,' i.e., the matter in the cluster that we cannot see, since it gravitationally influences the motions of the member galaxies within the cluster. The near-infrared maps the overall luminous mass content of the member galaxies, since the light at these wavelengths is dominated by the more numerous older stellar populations. Galaxies, as seen by 2MASS, look fairly smooth and homogeneous, as can be seen from the Hubble 'tuning fork' diagram of near-infrared galaxy morphology. Image mosaic by S. Van Dyk (IPAC).

  12. Mixed-Initiative Clustering

    ERIC Educational Resources Information Center

    Huang, Yifen

    2010-01-01

    Mixed-initiative clustering is a task where a user and a machine work collaboratively to analyze a large set of documents. We hypothesize that a user and a machine can both learn better clustering models through enriched communication and interactive learning from each other. The first contribution or this thesis is providing a framework of…

  13. Cluster Guide. Accounting Occupations.

    ERIC Educational Resources Information Center

    Beaverton School District 48, OR.

    Based on a recent task inventory of key occupations in the accounting cluster taken in the Portland, Oregon, area, this curriculum guide is intended to assist administrators and teachers in the design and implementation of high school accounting cluster programs. The guide is divided into four major sections: program organization and…

  14. Marketing Occupations. Cluster Guide.

    ERIC Educational Resources Information Center

    Oregon State Dept. of Education, Salem.

    This cluster guide, which is designed to show teachers what specific knowledge and skills qualify high school students for entry-level employment (or postsecondary training) in marketing occupations, is organized into three sections: (1) cluster organization and implementation, (2) instructional emphasis areas, and (3) assessment. The first…

  15. Ultrametric Hierarchical Clustering Algorithms.

    ERIC Educational Resources Information Center

    Milligan, Glenn W.

    1979-01-01

    Johnson has shown that the single linkage and complete linkage hierarchical clustering algorithms induce a metric on the data known as the ultrametric. Johnson's proof is extended to four other common clustering algorithms. Two additional methods also produce hierarchical structures which can violate the ultrametric inequality. (Author/CTM)

  16. [Cluster headache differential diagnosis].

    PubMed

    Guégan-Massardier, Evelyne; Laubier, Cécile

    2015-11-01

    Cluster headache is characterized by disabling stereotyped headache. Early diagnosis allows appropriate treatment, unfortunately diagnostic errors are frequent. The main differential diagnoses are other primary or essential headaches. Migraine, more frequent and whose diagnosis is carried by excess, trigeminal neuralgia or other trigemino-autonomic cephalgia. Vascular or tumoral underlying condition can mimic cluster headache, neck and brain imaging is recommended, ideally MRI.

  17. Targeting Clusters, Achieving Excellence.

    ERIC Educational Resources Information Center

    Rosenfeld, Stuart; Jacobs, Jim; Liston, Cynthia

    2003-01-01

    Suggests that groups, or clusters, of industries form partnerships with community colleges in order to positively impact economic development. Asserts that a cluster-oriented community college system requires innovation, specialized resources and expertise, knowledge of trends, and links to industry. Offers suggestions for developing such a…

  18. Multiple frame cluster tracking

    NASA Astrophysics Data System (ADS)

    Gadaleta, Sabino; Klusman, Mike; Poore, Aubrey; Slocumb, Benjamin J.

    2002-08-01

    Tracking large number of closely spaced objects is a challenging problem for any tracking system. In missile defense systems, countermeasures in the form of debris, chaff, spent fuel, and balloons can overwhelm tracking systems that track only individual objects. Thus, tracking these groups or clusters of objects followed by transitions to individual object tracking (if and when individual objects separate from the groups) is a necessary capability for a robust and real-time tracking system. The objectives of this paper are to describe the group tracking problem in the context of multiple frame target tracking and to formulate a general assignment problem for the multiple frame cluster/group tracking problem. The proposed approach forms multiple clustering hypotheses on each frame of data and base individual frame clustering decisions on the information from multiple frames of data in much the same way that MFA or MHT work for individual object tracking. The formulation of the assignment problem for resolved object tracking and candidate clustering methods for use in multiple frame cluster tracking are briefly reviewed. Then, three different formulations are presented for the combination of multiple clustering hypotheses on each frame of data and the multiple frame assignments of clusters between frames.

  19. Brightest Cluster Galaxy Identification

    NASA Astrophysics Data System (ADS)

    Leisman, Luke; Haarsma, D. B.; Sebald, D. A.; ACCEPT Team

    2011-01-01

    Brightest cluster galaxies (BCGs) play an important role in several fields of astronomical research. The literature includes many different methods and criteria for identifying the BCG in the cluster, such as choosing the brightest galaxy, the galaxy nearest the X-ray peak, or the galaxy with the most extended profile. Here we examine a sample of 75 clusters from the Archive of Chandra Cluster Entropy Profile Tables (ACCEPT) and the Sloan Digital Sky Survey (SDSS), measuring masked magnitudes and profiles for BCG candidates in each cluster. We first identified galaxies by hand; in 15% of clusters at least one team member selected a different galaxy than the others.We also applied 6 other identification methods to the ACCEPT sample; in 30% of clusters at least one of these methods selected a different galaxy than the other methods. We then developed an algorithm that weighs brightness, profile, and proximity to the X-ray peak and centroid. This algorithm incorporates the advantages of by-hand identification (weighing multiple properties) and automated selection (repeatable and consistent). The BCG population chosen by the algorithm is more uniform in its properties than populations selected by other methods, particularly in the relation between absolute magnitude (a proxy for galaxy mass) and average gas temperature (a proxy for cluster mass). This work supported by a Barry M. Goldwater Scholarship and a Sid Jansma Summer Research Fellowship.

  20. Mutation at Expanding Front of Self-Replicating Colloidal Clusters

    NASA Astrophysics Data System (ADS)

    Tanaka, Hidenori; Zeravcic, Zorana; Brenner, Michael P.

    2016-12-01

    We construct a scheme for self-replicating square clusters of particles in two spatial dimensions, and validate it with computer simulations in a finite-temperature heat bath. We find that the self-replication reactions propagate through the bath in the form of Fisher waves. Our model reflects existing colloidal systems, but is simple enough to allow simulation of many generations and thereby the first study of evolutionary dynamics in an artificial system. By introducing spatially localized mutations in the replication rules, we show that the mutated cluster population can survive and spread with the expanding front in circular sectors of the colony.

  1. Fast left ventricle tracking in CMR images using localized anatomical affine optical flow

    NASA Astrophysics Data System (ADS)

    Queirós, Sandro; Vilaça, João. L.; Morais, Pedro; Fonseca, Jaime C.; D'hooge, Jan; Barbosa, Daniel

    2015-03-01

    In daily cardiology practice, assessment of left ventricular (LV) global function using non-invasive imaging remains central for the diagnosis and follow-up of patients with cardiovascular diseases. Despite the different methodologies currently accessible for LV segmentation in cardiac magnetic resonance (CMR) images, a fast and complete LV delineation is still limitedly available for routine use. In this study, a localized anatomically constrained affine optical flow method is proposed for fast and automatic LV tracking throughout the full cardiac cycle in short-axis CMR images. Starting from an automatically delineated LV in the end-diastolic frame, the endocardial and epicardial boundaries are propagated by estimating the motion between adjacent cardiac phases using optical flow. In order to reduce the computational burden, the motion is only estimated in an anatomical region of interest around the tracked boundaries and subsequently integrated into a local affine motion model. Such localized estimation enables to capture complex motion patterns, while still being spatially consistent. The method was validated on 45 CMR datasets taken from the 2009 MICCAI LV segmentation challenge. The proposed approach proved to be robust and efficient, with an average distance error of 2.1 mm and a correlation with reference ejection fraction of 0.98 (1.9 +/- 4.5%). Moreover, it showed to be fast, taking 5 seconds for the tracking of a full 4D dataset (30 ms per image). Overall, a novel fast, robust and accurate LV tracking methodology was proposed, enabling accurate assessment of relevant global function cardiac indices, such as volumes and ejection fraction

  2. Hybridization schemes for clusters

    NASA Astrophysics Data System (ADS)

    Wales, David J.

    The concept of an optimum hybridization scheme for cluster compounds is developed with particular reference to electron counting. The prediction of electron counts for clusters and the interpretation of the bonding is shown to depend critically upon the presumed hybridization pattern of the cluster vertex atoms. This fact has not been properly appreciated in previous work, particularly in applications of Stone's tensor surface harmonic (TSH) theory, but is found to be a useful tool when dealt with directly. A quantitative definition is suggested for the optimum cluster hybridization pattern based directly upon the ease of interpretation of the molecular orbitals, and results are given for a range of species. The relationship of this scheme to the detailed cluster geometry is described using Löwdin's partitioned perturbation theory, and the success and range of application of TSH theory are discussed.

  3. Cool Cluster Correctly Correlated

    SciTech Connect

    Varganov, Sergey Aleksandrovich

    2005-01-01

    Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, since empirical and semiempirical methods rely on simple models with many parameters, it is often difficult to estimate the quantitative and even qualitative accuracy of the results. On the other hand, because of significant advances in quantum chemical methods and computer capabilities, it is now possible to do high quality ab-initio calculations not only on systems of few atoms but on clusters of practical interest as well. In addition to accurate results for specific clusters, such methods can be used for benchmarking of different empirical and semiempirical approaches. The atomic clusters studied in this work contain from a few atoms to

  4. Water propagation in two-dimensional petroleum reservoirs

    NASA Astrophysics Data System (ADS)

    Najafi, M. N.; Ghaedi, M.; Moghimi-Araghi, Saman

    2016-03-01

    In the present paper we investigate the problem of water propagation in 2 dimensional (2D) petroleum reservoir in which each site has the probability p of being occupied. We first analyze this propagation pattern described by Darcy equations by focusing on its geometrical features. We find that the domain-walls of this model at p =pc ≃ 0.59 are Schramm-Loewner evolution (SLE) curves with κ = 3.05 ∓ 0.1 consistent with the Ising universality class. We also numerically show that the fractal dimension of these domain-walls at p =pc is Df ≃ 1.38 consistent with SLEκ=3. Along with this analysis, we introduce a self-organized critical (SOC) model in which the water movement is modeled by a chain of topplings taking place when the water saturation exceeds the critical value. We present strong indications that it coincides with the reservoir simulation described by Darcy equation. We further analyze the SOC model and show numerically that for this model the spanning cluster probability has a maximum around p = 0.65.

  5. Impact of coronary bifurcation morphology on wave propagation

    PubMed Central

    Rivolo, Simone; Hadjilucas, Lucas; Sinclair, Matthew; van Horssen, Pepijn; van den Wijngaard, Jeroen; Wesolowski, Roman; Chiribiri, Amedeo; Smith, Nicolas P.

    2016-01-01

    The branching pattern of the coronary vasculature is a key determinant of its function and plays a crucial role in shaping the pressure and velocity wave forms measured for clinical diagnosis. However, although multiple scaling laws have been proposed to characterize the branching pattern, the implications they have on wave propagation remain unassessed to date. To bridge this gap, we have developed a new theoretical framework by combining the mathematical formulation of scaling laws with the wave propagation theory in the pulsatile flow regime. This framework was then validated in multiple species using high-resolution cryomicrotome images of porcine, canine, and human coronary networks. Results demonstrate that the forward well-matchedness (no reflection for pressure/flow waves traveling from the coronary stem toward the microcirculation) is a salient feature in the coronary vasculature, and this result remains robust under many scenarios of the underlying pulse wave speed distribution assumed in the network. This result also implies a significant damping of the backward traveling waves, especially for smaller vessels (radius, <0.3 mm). Furthermore, the theoretical prediction of increasing area ratios (ratio between the area of the mother and daughter vessels) in more symmetric bifurcations found in the distal circulation was confirmed by experimental measurements. No differences were observed by clustering the vessel segments in terms of transmurality (from epicardium to endocardium) or perfusion territories (left anterior descending, left circumflex, and right coronary artery). PMID:27402665

  6. Galaxy cluster's rotation

    NASA Astrophysics Data System (ADS)

    Manolopoulou, M.; Plionis, M.

    2017-03-01

    We study the possible rotation of cluster galaxies, developing, testing, and applying a novel algorithm which identifies rotation, if such does exist, as well as its rotational centre, its axis orientation, rotational velocity amplitude, and, finally, the clockwise or counterclockwise direction of rotation on the plane of the sky. To validate our algorithms we construct realistic Monte Carlo mock rotating clusters and confirm that our method provides robust indications of rotation. We then apply our methodology on a sample of Abell clusters with z ≲ 0.1 with member galaxies selected from the Sloan Digital Sky Survey DR10 spectroscopic data base. After excluding a number of substructured clusters, which could provide erroneous indications of rotation, and taking into account the expected fraction of misidentified coherent substructure velocities for rotation, provided by our Monte Carlo simulation analysis, we find that ∼23 per cent of our clusters are rotating under a set of strict criteria. Loosening the strictness of the criteria, on the expense of introducing spurious rotation indications, we find this fraction increasing to ∼28 per cent. We correlate our rotation indicators with the cluster dynamical state, provided either by their Bautz-Morgan type or by their X-ray isophotal shape and find for those clusters showing rotation within 1.5 h^{-1}_{70} Mpc that the significance of their rotation is related to the dynamically younger phases of cluster formation but after the initial anisotropic accretion and merging has been completed. Finally, finding rotational modes in galaxy clusters could lead to the necessity of correcting the dynamical cluster mass calculations.

  7. MPPE (Multiple Pulse Propagation Experiment) results

    SciTech Connect

    Chambers, F.W.; Caporaso, G.J.; Chong, Y.P.; Deadrick, F.J.; Guethlein, G.; Fawley, W.M.; Orzechowski, T.J.; Renbarger, V.L.; Rogers, D. Jr.; Weir, J.T. ); Lee, P. ); Struve, K.W. ); Hubbard, R. ); Feinstein, L.; Keeley, D. (Science Applicatio

    1990-10-01

    The Multiple Pulse Propagation Experiment (MPPE) was conducted by the Beam Research Group of the Lawrence Livermore National Laboratory from September 1989, through January 1990, using the Advanced Test Accelerator (ATA). This experiment represents the culmination of the three previous beam propagation experiments conducted at the ATA over the past half decade. Highlights of this experiment were the multiple pulse operation of ATA, and the diagnosis of the beam propagation, and channel production at the higher repetition rates. A large database was collected on beam propagation in uniform gas and channels including m = 0 beam size and net current measurements; and m = 1 hose measurements. The generation and evolution of the electron beam driven channels was well documented. A key result of this experiment was that the beam was dominated by hose instability which limited propagation ranges. This report is organized into five sections. The experimental layout and beam parameters have been detailed in previous reports. First the beam initial conditions will be discussed in detail. Since beam injection parameters are ultimately the only variables one can specify in an atmospheric application, the control and documentation of the beam at the entrance to the gas is crucial. Next the beam lead pulse propagation in gas will be reported. Lead pulse results will be compared with past experiments. The density channel production and evolution will be briefly reported; an additional reference is available. Beam propagation in the channel will then be examined. Finally, conclusions will be presented.

  8. The accuracy of dynamic attitude propagation

    NASA Technical Reports Server (NTRS)

    Harvie, E.; Chu, D.; Woodard, M.

    1990-01-01

    Propagating attitude by integrating Euler's equation for rigid body motion has long been suggested for the Earth Radiation Budget Satellite (ERBS) but until now has not been implemented. Because of limited Sun visibility, propagation is necessary for yaw determination. With the deterioration of the gyros, dynamic propagation has become more attractive. Angular rates are derived from integrating Euler's equation with a stepsize of 1 second, using torques computed from telemetered control system data. The environmental torque model was quite basic. It included gravity gradient and unshadowed aerodynamic torques. Knowledge of control torques is critical to the accuracy of dynamic modeling. Due to their coarseness and sparsity, control actuator telemetry were smoothed before integration. The dynamic model was incorporated into existing ERBS attitude determination software. Modeled rates were then used for attitude propagation in the standard ERBS fine-attitude algorithm. In spite of the simplicity of the approach, the dynamically propagated attitude matched the attitude propagated with good gyros well for roll and yaw but diverged up to 3 degrees for pitch because of the very low resolution in pitch momentum wheel telemetry. When control anomalies significantly perturb the nominal attitude, the effect of telemetry granularity is reduced and the dynamically propagated attitudes are accurate on all three axes.

  9. Potential of ZrO clusters as replacement Pd catalyst

    SciTech Connect

    Behera, Swayamprabha; King, Nicholas; Jena, Puru; Samanta, Devleena

    2014-07-21

    Atomic clusters with specific size and composition and mimicking the chemistry of elements in the periodic table are commonly known as superatoms. It has been suggested that superatoms could be used to replace elements that are either scarce or expensive. Based on a photoelectron spectroscopy experiment of negatively charged ions, Castleman and co-workers [Proc. Natl. Acad. Sci. U.S.A. 107, 975 (2010)] have recently shown that atoms of Ni, Pd, and Pt which are well known for their catalytic properties, have the same electronic structure as their counterpart isovalent diatomic species, TiO, ZrO, and WC, respectively. Based on this similarity they have suggested that ZrO, for example, could be a replacement catalyst for Pd. Since catalysts are seldom single isolated atoms, one has to demonstrate that clusters of ZrO also have the same electronic structure as same sized Pd clusters. To examine if this is indeed the case, we have calculated the geometries, electronic structure, electron affinity, ionization potential, and hardness of Pd{sub n} and (ZrO){sub n} clusters (n = 1-5). We further studied the reaction of these clusters in neutral and charged forms with H{sub 2}, O{sub 2}, and CO and found it to be qualitatively different in most cases. These results obtained using density functional theory with hybrid B3LYP functional do not support the view that ZrO clusters can replace Pd as a catalyst.

  10. Potential of ZrO clusters as replacement Pd catalyst.

    PubMed

    Behera, Swayamprabha; King, Nicholas; Samanta, Devleena; Jena, Puru

    2014-07-21

    Atomic clusters with specific size and composition and mimicking the chemistry of elements in the periodic table are commonly known as superatoms. It has been suggested that superatoms could be used to replace elements that are either scarce or expensive. Based on a photoelectron spectroscopy experiment of negatively charged ions, Castleman and co-workers [Proc. Natl. Acad. Sci. U.S.A. 107, 975 (2010)] have recently shown that atoms of Ni, Pd, and Pt which are well known for their catalytic properties, have the same electronic structure as their counterpart isovalent diatomic species, TiO, ZrO, and WC, respectively. Based on this similarity they have suggested that ZrO, for example, could be a replacement catalyst for Pd. Since catalysts are seldom single isolated atoms, one has to demonstrate that clusters of ZrO also have the same electronic structure as same sized Pd clusters. To examine if this is indeed the case, we have calculated the geometries, electronic structure, electron affinity, ionization potential, and hardness of Pdn and (ZrO)n clusters (n = 1-5). We further studied the reaction of these clusters in neutral and charged forms with H2, O2, and CO and found it to be qualitatively different in most cases. These results obtained using density functional theory with hybrid B3LYP functional do not support the view that ZrO clusters can replace Pd as a catalyst.

  11. Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

    DOEpatents

    Sanfilippo, Antonio; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

    2009-12-22

    Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

  12. Electromagnetic Propagation Prediction Inside Aircraft Cabins

    NASA Technical Reports Server (NTRS)

    Hankins, Genevieve; Vahala, Linda; Beggs, John H.

    2004-01-01

    Electromagnetic propagation models for signal strength prediction within aircraft cabins are essential for evaluating and designing a wireless communication system to be implemented onboard aircraft. A model was developed using Wireless Valley's SitePlanner; which is commercial grade software intended for predictions within office buildings. The performance of the model was evaluated through a comparison with test data measurements taken on several aircraft. The comparison concluded that the model can accurately predict power propagation within the cabin. This model can enhance researchers understanding of power propagation within aircraft cabins and will aid in future research.

  13. Propagation considerations in land mobile satellite transmission

    NASA Technical Reports Server (NTRS)

    Vogel, W. J.; Smith, E. K.

    1985-01-01

    It appears likely that the Land Mobile Satellite Services (LMSS) will be authorized by the FCC for operation in the 800 to 900 MHz (UHF) and possibly near 1500 MHz (L-band). Propagation problems are clearly an important factor in the effectiveness of this service, but useful measurements are few, and produced contradictory interpretations. A first order overview of existing measurements is presented with particular attention to the first two NASA balloon to mobile vehicle propagation experiments. Some physical insight into the interpretation of propagation effects in LMSS transmissions is provided.

  14. Asymmetric counter propagation of domain walls

    NASA Astrophysics Data System (ADS)

    Andrade-Silva, I.; Clerc, M. G.; Odent, V.

    2016-07-01

    Far from equilibrium systems show different states and domain walls between them. These walls, depending on the type of connected equilibria, exhibit a rich spatiotemporal dynamics. Here, we investigate the asymmetrical counter propagation of domain walls in an in-plane-switching cell filled with a nematic liquid crystal. Experimentally, we characterize the shape and speed of the domain walls. Based on the molecular orientation, we infer that the counter propagative walls have different elastic deformations. These deformations are responsible of the asymmetric counter propagating fronts. Theoretically, based on symmetry arguments, we propose a simple bistable model under the influence of a nonlinear gradient, which qualitatively describes the observed dynamics.

  15. Photon propagator in light-shell gauge

    NASA Astrophysics Data System (ADS)

    Georgi, Howard; Kestin, Greg; Sajjad, Aqil

    2016-05-01

    We derive the photon propagator in light-shell gauge (LSG) vμAμ=0 , where vμ=(1,r ^ ) μ . This gauge is an important ingredient of the light-shell effective theory—an effective theory for describing high energy jet processes on a 2-dimensional spherical shell expanding at the speed of light around the point of the initial collision producing the jets. Since LSG is a noncovariant gauge, we cannot calculate the LSG propagator by using the standard procedure for covariant gauges. We therefore employ a new technique for computing the propagator, which we hope may be of relevance in other gauges as well.

  16. Propagation of Light Elements in the Galaxy

    NASA Technical Reports Server (NTRS)

    Moskalenko, I. V.; Strong, A. W.; Mashnik, S. G.; Jones, F. C.

    2003-01-01

    The origin and evolution of isotopes of the lightest elements d, He-3, Li, Be, and B in the universe is a key problem in such fields as astrophysics of CR, Galactic evolution, non-thermal nucleosynthesis, and cosmological studies. One of the major sources of these species is spallation by CR nuclei in the interstellar medium. On the other hand, it is the Boron/Carbon ratio in CR and Be-10 abundance which are used to fix the propagation parameters and thus spallation rate. We study production and Galactic propagation of these species using the numerical propagation code GALPROP and updated production cross sections.

  17. Propagation of sound through a sheared flow

    NASA Technical Reports Server (NTRS)

    Woolley, J. P.; Smith, C. A.; Karamcheti, K.

    1978-01-01

    Sound generated in a moving fluid must propagate through a shear layer in order to be measured by a fixed instrument. These propagation effects were evaluated for noise sources typically associated with single and co-flowing subsonic jets and for subcritical flow over airfoils in such jets. The techniques for describing acoustic propagation fall into two categories: geometric acoustics and wave acoustics. Geometric acoustics is most convenient and accurate for high frequency sound. In the frequency range of interest to the present study (greater than 150 Hz), the geometric acoustics approach was determined to be most useful and practical.

  18. Inward propagating chemical waves in Taylor vortices

    NASA Astrophysics Data System (ADS)

    Thompson, Barnaby W.; Novak, Jan; Wilson, Mark C. T.; Britton, Melanie M.; Taylor, Annette F.

    2010-04-01

    Advection-reaction-diffusion (ARD) waves in the Belousov-Zhabotinsky reaction in steady Taylor-Couette vortices have been visualized using magnetic-resonance imaging and simulated using an adapted Oregonator model. We show how propagating wave behavior depends on the ratio of advective, chemical and diffusive time scales. In simulations, inward propagating spiral flamelets are observed at high Damköhler number (Da). At low Da, the reaction distributes itself over several vortices and then propagates inwards as contracting ring pulses—also observed experimentally.

  19. Propagating confined states in phase dynamics

    NASA Technical Reports Server (NTRS)

    Brand, Helmut R.; Deissler, Robert J.

    1992-01-01

    Theoretical treatment is given to the possibility of the existence of propagating confined states in the nonlinear phase equation by generalizing stationary confined states. The nonlinear phase equation is set forth for the case of propagating patterns with long wavelengths and low-frequency modulation. A large range of parameter values is shown to exist for propagating confined states which have spatially localized regions which travel on a background with unique wavelengths. The theoretical phenomena are shown to correspond to such physical systems as spirals in Taylor instabilities, traveling waves in convective systems, and slot-convection phenomena for binary fluid mixtures.

  20. Surface acoustic wave propagation in graphene

    NASA Astrophysics Data System (ADS)

    Thalmeier, Peter; Dóra, Balázs; Ziegler, Klaus

    2010-01-01

    Surface acoustic wave (SAW) propagation is a powerful method to investigate two-dimensional (2D) electron systems. We show how SAW observables are influenced by coupling to the 2D massless Dirac electrons of graphene and argue that Landau oscillations in SAW propagation can be observed as function of gate voltage for constant field. Contrary to other transport measurements, the zero-field SAW propagation gives the wave-vector dependence of graphene conductivity for small wave numbers. We predict a crossover from Schrödinger to Dirac-like behavior as a function of gate voltage, with no attenuation in the latter for clean samples.

  1. Inward propagating chemical waves in Taylor vortices.

    PubMed

    Thompson, Barnaby W; Novak, Jan; Wilson, Mark C T; Britton, Melanie M; Taylor, Annette F

    2010-04-01

    Advection-reaction-diffusion (ARD) waves in the Belousov-Zhabotinsky reaction in steady Taylor-Couette vortices have been visualized using magnetic-resonance imaging and simulated using an adapted Oregonator model. We show how propagating wave behavior depends on the ratio of advective, chemical and diffusive time scales. In simulations, inward propagating spiral flamelets are observed at high Damköhler number (Da). At low Da, the reaction distributes itself over several vortices and then propagates inwards as contracting ring pulses--also observed experimentally.

  2. Computing Propagation Of Sound In Engine Ducts

    NASA Technical Reports Server (NTRS)

    Saylor, Silvia

    1995-01-01

    Frequency Domain Propagation Model (FREDOM) computer program accounts for acoustic loads applied to components of engines. Models propagation of noise through fluids in ducts between components and through passages within components. Used not only to analyze hardware problems, but also for design purposes. Updated version of FREQPL program easier to use. Devised specifically for use in analyzing acoustic loads in rocket engines. Underlying physical and mathematical concepts implemented also applicable to acoustic propagation in other enclosed spaces; analyzing process plumbing and ducts in industrial buildings with view toward reducing noise in work areas.

  3. Student Engagement and Neoliberalism: Mapping an Elective Affinity

    ERIC Educational Resources Information Center

    Zepke, Nick

    2015-01-01

    The purpose of this article is to argue that student engagement, an important area for research about learning and teaching in formal higher education, has an elective affinity with neoliberalism, a hegemonic ideology in many countries of the developed world. The paper first surveys an extensive research literature examining student engagement and…

  4. "The Hunger Games": Literature, Literacy, and Online Affinity Spaces

    ERIC Educational Resources Information Center

    Curwood, Jen Scott

    2013-01-01

    This article examines adolescent literacy practices related to "The Hunger Games," a young adult novel and the first of a trilogy. By focusing on the interaction of social identities, discourses, and media paratexts within an online affinity space, this ethnographic study offers insight into how young adults engage with contemporary…

  5. Affinities and beyond! Developing Ways of Seeing in Online Spaces

    ERIC Educational Resources Information Center

    Davies, Julia

    2006-01-01

    This article presents an insider view of an online community of adults involved in sharing digital photography through a host website, Flickr. It describes how reciprocal teaching and learning partnerships in a dynamic multimodal environment are achieved through the creation of a "Third Space" or "Affinity Space", where "Funds of Knowledge" are…

  6. Electrochemical affinity biosensors for detection of mycotoxins: A review.

    PubMed

    Vidal, Juan C; Bonel, Laura; Ezquerra, Alba; Hernández, Susana; Bertolín, Juan R; Cubel, Carlota; Castillo, Juan R

    2013-11-15

    This review discusses the current state of electrochemical biosensors in the determination of mycotoxins in foods. Mycotoxins are highly toxic secondary metabolites produced by molds. The acute toxicity of these results in serious human and animal health problems, although it has been only since early 1960s when the first studied aflatoxins were found to be carcinogenic. Mycotoxins affect a broad range of agricultural products, most important cereals and cereal-based foods. A majority of countries, mentioning especially the European Union, have established preventive programs to control contamination and strict laws of the permitted levels in foods. Official methods of analysis of mycotoxins normally requires sophisticated instrumentation, e.g. liquid chromatography with fluorescence or mass detectors, combined with extraction procedures for sample preparation. For about sixteen years, the use of simpler and faster analytical procedures based on affinity biosensors has emerged in scientific literature as a very promising alternative, particularly electrochemical (i.e., amperometric, impedance, potentiometric or conductimetric) affinity biosensors due to their simplicity and sensitivity. Typically, electrochemical biosensors for mycotoxins use specific antibodies or aptamers as affinity ligands, although recombinant antibodies, artificial receptors and molecular imprinted polymers show potential utility. This article deals with recent advances in electrochemical affinity biosensors for mycotoxins and covers complete literature from the first reports about sixteen years ago.

  7. Toward an Affinity Space Methodology: Considerations for Literacy Research

    ERIC Educational Resources Information Center

    Lammers, Jayne C.; Curwood, Jen Scott; Magnifico, Alecia Marie

    2012-01-01

    As researchers seek to make sense of young people's online literacy practices and participation, questions of methodology are important to consider. In our work to understand the culture of physical, virtual and blended spheres that adolescents inhabit, we find it necessary to expand Gee's (2004) notion of affinity spaces. In this article, we draw…

  8. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

    PubMed Central

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-01-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6. PMID:27291418

  9. Kinetic Studies of Biological Interactions By Affinity Chromatography

    PubMed Central

    Schiel, John E.; Hage, David S.

    2009-01-01

    The rates at which biological interactions occur can provide important information on the mechanism and behavior of such processes in living systems. This review will discuss how affinity chromatography can be used as a tool to examine the kinetics of biological interactions. This approach, referred to here as biointeraction chromatography, uses a column with an immobilized binding agent to examine the association or dissociation of this agent with other compounds. The use of HPLC-based affinity columns in kinetic studies has received particular attention in recent years. Advantages of using HPLC with affinity chromatography for this purpose include the ability to reuse the same ligand within a column for a large number of experiments, and the good precision and accuracy of this approach. A number of techniques are available for kinetic studies through the use of affinity columns and biointeraction chromatography. These approaches include plate height measurements, peak profiling, peak fitting, split-peak measurements, and peak decay analysis. The general principles for each of these methods are discussed in this review and some recent applications of these techniques are presented. The advantages and potential limitations of each approach are also considered. PMID:19391173

  10. Affinity of cefoperazone for penicillin-binding proteins.

    PubMed Central

    Matsubara, N; Minami, S; Matsuhashi, M; Takaoka, M; Mitsuhashi, S

    1980-01-01

    Cefoperazone (T-1551, CFP) a new semisynthetic cephalosporin, has a broad spectrum of antibacterial activity. We investigated the affinity of CFP to penicillin-binding proteins (PBPs) and the inhibition of peptidoglycan synthesis by CFP. CFP had high affinities for Escherichia coli PBP-3, -1Bs, -2, and -1A, in descending order, and low affinities for PBP-4, -5, and -6. Similarly, CFP showed high affinity for Pseudomonas aeruginosa PBP-3, -1A, -1B, -2, and -4, in descending order. It is known that E. coli PBP-3 and P. aeruginosa PBP-3 participate in cell division. These results are in good agreement with the formation of filamentous cells of E. coli and P. aeruginosa treated with CFP. CFP had lower inhibitory activities on D-alanine carboxypeptidase IA and IB of E. coli than that of penicillin G, but its inhibitory activities on the cross-link formation in peptidoglycan synthesis were the same as those of penicillin G and higher than those of ampicillin. Images PMID:6448021

  11. A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

    NASA Astrophysics Data System (ADS)

    Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

    2016-06-01

    Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6.

  12. Limit measures for affine cellular automata on topological Markov subgroups

    NASA Astrophysics Data System (ADS)

    Maass, Alejandro; Martínez, Servet; Sobottka, Marcelo

    2006-09-01

    Consider a topological Markov subgroup which is ps-torsion (with p prime) and an affine cellular automaton defined on it. We show that the Cesàro mean of the iterates, by the automaton of a probability measure with complete connections and summable memory decay that is compatible with the topological Markov subgroup, converges to the Haar measure.

  13. Affinity through Mathematical Activity: Cultivating Democratic Learning Communities

    ERIC Educational Resources Information Center

    Sengupta-Irving, Tesha

    2014-01-01

    In this article, the author demonstrates how a broader view of what shapes affinity is ideologically and practically linked to creating democratic learning communities. Specifically, the author explores how a teacher employed complex instruction (an equity pedagogy) with her ethnically and racially diverse students in the "lowest track"…

  14. Evolution Properties of Clusters and AXAF Contributions to understanding Clusters

    NASA Technical Reports Server (NTRS)

    Jones, Christine

    1998-01-01

    Our ROSAT survey for distant clusters of galaxies contains the largest solid angle of all ROSAT pointed surveying and thus has sufficient area to test the previously reported cluster evolution. We find significant negative cluster evolution, i.e,, at high redshifts there are fewer luminous clusters than at present. We compare optical cluster properties for the most distant clusters in the ROSAT survey with those measured for nearby clusters. We also present AXAF capabilities and show how AXAF will significantly extend our understanding of cluster properties and their cosmological evolution.

  15. Anion photoelectron spectroscopy of radicals and clusters

    SciTech Connect

    Travis, Taylor R.

    1999-12-01

    Anion photoelectron spectroscopy is used to study free radicals and clusters. The low-lying 2Σ and 2π states of C2nH (n = 1--4) have been studied. The anion photoelectron spectra yielded electron affinities, term values, and vibrational frequencies for these combustion and astrophysically relevant species. Photoelectron angular distributions allowed the author to correctly assign the electronic symmetry of the ground and first excited states and to assess the degree of vibronic coupling in C2H and C4H. Other radicals studied include NCN and I3. The author was able to observe the low-lying singlet and triplet states of NCN for the first time. Measurement of the electron affinity of I3 revealed that it has a bound ground state and attachment of an argon atom to this moiety enabled him to resolve the symmetric stretching progression.

  16. Comparing halo bias from abundance and clustering

    NASA Astrophysics Data System (ADS)

    Hoffmann, K.; Bel, J.; Gaztañaga, E.

    2015-06-01

    We model the abundance of haloes in the ˜(3 Gpc h-1)3 volume of the MICE Grand Challenge simulation by fitting the universal mass function with an improved Jackknife error covariance estimator that matches theory predictions. We present unifying relations between different fitting models and new predictions for linear (b1) and non-linear (c2 and c3) halo clustering bias. Different mass function fits show strong variations in their performance when including the low mass range (Mh ≲ 3 × 1012 M⊙ h-1) in the analysis. Together with fits from the literature, we find an overall variation in the amplitudes of around 10 per cent in the low mass and up to 50 per cent in the high mass (galaxy cluster) range (Mh > 1014 M⊙ h-1). These variations propagate into a 10 per cent change in b1 predictions and a 50 per cent change in c2 or c3. Despite these strong variations, we find universal relations between b1 and c2 or c3 for which we provide simple fits. Excluding low-mass haloes, different models fitted with reasonable goodness in this analysis, show per cent level agreement in their b1 predictions, but are systematically 5-10 per cent lower than the bias directly measured with two-point halo-mass clustering. This result confirms previous findings derived from smaller volumes (and smaller masses). Inaccuracies in the bias predictions lead to 5-10 per cent errors in growth measurements. They also affect any halo occupation distribution fitting or (cluster) mass calibration from clustering measurements.

  17. Thermodynamics of the Coma Cluster Outskirts

    NASA Astrophysics Data System (ADS)

    Simionescu, A.; Werner, N.; Urban, O.; Allen, S. W.; Fabian, A. C.; Mantz, A.; Matsushita, K.; Nulsen, P. E. J.; Sanders, J. S.; Sasaki, T.; Sato, T.; Takei, Y.; Walker, S. A.

    2013-09-01

    We present results from a large mosaic of Suzaku observations of the Coma Cluster, the nearest and X-ray brightest hot (~8 keV), dynamically active, non-cool core system, focusing on the thermodynamic properties of the intracluster medium on large scales. For azimuths not aligned with an infalling subcluster toward the southwest, our measured temperature and X-ray brightness profiles exhibit broadly consistent radial trends, with the temperature decreasing from about 8.5 keV at the cluster center to about 2 keV at a radius of 2 Mpc, which is the edge of our detection limit. The southwest merger significantly boosts the surface brightness, allowing us to detect X-ray emission out to ~2.2 Mpc along this direction. Apart from the southwestern infalling subcluster, the surface brightness profiles show multiple edges around radii of 30-40 arcmin. The azimuthally averaged temperature profile, as well as the deprojected density and pressure profiles, all show a sharp drop consistent with an outwardly-propagating shock front located at 40 arcmin, corresponding to the outermost edge of the giant radio halo observed at 352 MHz with the Westerbork Synthesis Radio Telescope. The shock front may be powering this radio emission. A clear entropy excess inside of r 500 reflects the violent merging events linked with these morphological features. Beyond r 500, the entropy profiles of the Coma Cluster along the relatively relaxed directions are consistent with the power-law behavior expected from simple models of gravitational large-scale structure formation. The pressure is also in agreement at these radii with the expected values measured from Sunyaev-Zel'dovich data from the Planck satellite. However, due to the large uncertainties associated with the Coma Cluster measurements, we cannot yet exclude an entropy flattening in this system consistent with that seen in more relaxed cool core clusters.

  18. THERMODYNAMICS OF THE COMA CLUSTER OUTSKIRTS

    SciTech Connect

    Simionescu, A.; Werner, N.; Urban, O.; Allen, S. W.; Fabian, A. C.; Sanders, J. S.; Walker, S. A.; Mantz, A.; Matsushita, K.; Sasaki, T.; Sato, T.; Nulsen, P. E. J.; Takei, Y.

    2013-09-20

    We present results from a large mosaic of Suzaku observations of the Coma Cluster, the nearest and X-ray brightest hot ({approx}8 keV), dynamically active, non-cool core system, focusing on the thermodynamic properties of the intracluster medium on large scales. For azimuths not aligned with an infalling subcluster toward the southwest, our measured temperature and X-ray brightness profiles exhibit broadly consistent radial trends, with the temperature decreasing from about 8.5 keV at the cluster center to about 2 keV at a radius of 2 Mpc, which is the edge of our detection limit. The southwest merger significantly boosts the surface brightness, allowing us to detect X-ray emission out to {approx}2.2 Mpc along this direction. Apart from the southwestern infalling subcluster, the surface brightness profiles show multiple edges around radii of 30-40 arcmin. The azimuthally averaged temperature profile, as well as the deprojected density and pressure profiles, all show a sharp drop consistent with an outwardly-propagating shock front located at 40 arcmin, corresponding to the outermost edge of the giant radio halo observed at 352 MHz with the Westerbork Synthesis Radio Telescope. The shock front may be powering this radio emission. A clear entropy excess inside of r{sub 500} reflects the violent merging events linked with these morphological features. Beyond r{sub 500}, the entropy profiles of the Coma Cluster along the relatively relaxed directions are consistent with the power-law behavior expected from simple models of gravitational large-scale structure formation. The pressure is also in agreement at these radii with the expected values measured from Sunyaev-Zel'dovich data from the Planck satellite. However, due to the large uncertainties associated with the Coma Cluster measurements, we cannot yet exclude an entropy flattening in this system consistent with that seen in more relaxed cool core clusters.

  19. Structures and Stabilities of the Metal Doped Gold Nano-Clusters: M@Au10 (M = W, Mo, Ru, Co).

    PubMed

    Hossain, Delwar; Pittman, Charles U; Gwaltney, Steven R

    2014-01-01

    The structures and stabilities of a series of endohedral gold clusters containing ten gold atoms M@Au10 (M = W, Mo, Ru, Co) have been determined using density functional theory. The gradient-corrected functional BP86, the Tao-Perdew-Staroverov-Scuseria TPSS meta-GGA functional, and the hybrid density functionals B3LYP and PBE1PBE were employed to calculate the structures, binding energies, adiabatic ionization potentials, and adiabatic electron affinities for these clusters. The LanL2DZ effective core potentials and the corresponding valence basis sets were employed. The M@Au10 (M = W, Mo, Ru, Co) clusters have higher binding energies than an empty Au10 cluster. In addition, the large HOMO-LUMO gaps suggest that the M@Au10 (M = W, Mo, Ru, Co) clusters are all likely to be stable chemically. The ionization potentials and electron affinities for these clusters are very high, and the W@Au10 and Mo@Au10 clusters have electron affinities similar to the super-halogen Al13.

  20. Structures and Stabilities of the Metal Doped Gold Nano-Clusters: M@Au10 (M = W, Mo, Ru, Co)

    PubMed Central

    Hossain, Delwar; Pittman, Charles U.; Gwaltney, Steven R.

    2014-01-01

    The structures and stabilities of a series of endohedral gold clusters containing ten gold atoms M@Au10 (M = W, Mo, Ru, Co) have been determined using density functional theory. The gradient-corrected functional BP86, the Tao-Perdew-Staroverov-Scuseria TPSS meta-GGA functional, and the hybrid density functionals B3LYP and PBE1PBE were employed to calculate the structures, binding energies, adiabatic ionization potentials, and adiabatic electron affinities for these clusters. The LanL2DZ effective core potentials and the corresponding valence basis sets were employed. The M@Au10 (M = W, Mo, Ru, Co) clusters have higher binding energies than an empty Au10 cluster. In addition, the large HOMO–LUMO gaps suggest that the M@Au10 (M = W, Mo, Ru, Co) clusters are all likely to be stable chemically. The ionization potentials and electron affinities for these clusters are very high, and the W@Au10 and Mo@Au10 clusters have electron affinities similar to the super-halogen Al13. PMID:24611036

  1. Studies in clustering theory

    NASA Astrophysics Data System (ADS)

    Stell, George

    In recent years the properties of percolation models have been studied intensively. The purpose of our project was to develop a general theory of percolation and clustering between particles of arbitrary size and shape, with arbitrary correlations between them. The goal of such a theory includes the treatment of continuum percolation as well as a novel treatment of lattice percolation. We made substantial progress toward this goal. The quantities basic to a description of clustering, the mean cluster size, mean number of clusters, etc., were developed. Concise formulas were given for the terms in such series, and proved, at least for sufficiently low densities, that the series are absolutely convergent. These series can now be used to construct Pade approximants that will allow one to probe the percolation transition. A scaled-particle theory of percolation was developed which gives analytic approximants for the mean number of clusters in a large class of two and three dimensional percolation models. Although this quantity is essential in many applications, e.g., explaining colligative properties, and interpreting low-angle light-scattering data, no systematic studies of it have been done before this work. Recently carried out detailed computer simulations show that the mean number of clusters is given to high accuracy by several of there approximations. Extensions of this work will allow calculation of the complete cluster size distribution.

  2. Nuclear Star Clusters

    NASA Astrophysics Data System (ADS)

    Neumayer, Nadine

    2017-03-01

    The centers of galaxies host two distinct, compact components: massive black holes and nuclear star clusters. Nuclear star clusters are the densest stellar systems in the universe, with masses of ~ 107M⊙ and sizes of ~ 5pc. They are almost ubiquitous at the centres of nearby galaxies with masses similar to, or lower than the Milky Way. Their occurrence both in spirals and dwarf elliptical galaxies appears to be a strong function of total galaxy light or mass. Nucleation fractions are up to 100% for total galaxy magnitudes of M B = -19mag or total galaxy luminosities of about L B = 1010 L ⊙ and falling nucleation fractions for both smaller and higher galaxy masses. Although nuclear star clusters are so common, their formation mechanisms are still under debate. The two main formation scenarios proposed are the infall and subsequent merging of star clusters and the in-situ formation of stars at the center of a galaxy. Here, I review the state-of-the-art of nuclear star cluster observations concerning their structure, stellar populations and kinematics. These observations are used to constrain the proposed formation scenarios for nuclear star clusters. Constraints from observations show, that likely both cluster infall and in-situ star formation are at work. The relative importance of these two mechanisms is still subject of investigation.

  3. Allodynia in Cluster Headache.

    PubMed

    Wilbrink, Leopoldine A; Louter, Mark A; Teernstra, Onno Pm; van Zwet, Erik W; Huygen, Frank Jpm; Haan, Joost; Ferrari, Michel D; Terwindt, Gisela M

    2017-03-04

    Cutaneous allodynia is an established marker for central sensitization in migraine. There is debate whether cutaneous allodynia may also occur in cluster headache, another episodic headache disorder. Here we examined the presence and severity of allodynia in a large well-defined nation-wide population of people with cluster headache.Using validated questionnaires we assessed, cross-sectionally, ictal allodynia and comorbid depression and migraine in the nation-wide "Leiden University Cluster headache neuro-Analysis" (LUCA) study. Participants with cluster headache were diagnosed according to the International Classification of Headache Disorders criteria. Multivariate regression models were used, with correction for demographic factors and cluster headache subtype (chronic vs. episodic; recent attacks < 1 month vs. no recent attacks).In total 606/798 (75.9%) participants with cluster headache responded of whom 218/606 (36%) had allodynia during attacks. Female gender (OR 2.05, 95% CI 1.28-3.29), low age at onset (OR 0.98, 95% CI 0.96- 0.99), lifetime depression (OR 1.63; 95% CI 1.06-2.50), comorbid migraine (OR 1.96; 95% CI 1.02-3.79), and having recent attacks (OR 1.80; 95% CI 1.13-2.86), but not duration of attacks and chronic cluster headache, were independent risk factors for allodynia.The high prevalence of cutaneous allodynia with similar risk factors for allodynia as found for migraine suggests that central sensitization, like in migraine, also occurs in cluster headache. In clinical practice, awareness that people with cluster headache may suffer from allodynia can in the future be an important feature in treatment options.

  4. Simulations of ultrasound propagation in random arrangements of elliptic scatterers: occurrence of two longitudinal waves.

    PubMed

    Mézière, Fabien; Muller, Marie; Dobigny, Blandine; Bossy, Emmanuel; Derode, Arnaud

    2013-02-01

    Ultrasound propagation in clusters of elliptic (two-dimensional) or ellipsoidal (three-dimensional) scatterers randomly distributed in a fluid is investigated numerically. The essential motivation for the present work is to gain a better understanding of ultrasound propagation in trabecular bone. Bone microstructure exhibits structural anisotropy and multiple wave scattering. Some phenomena remain partially unexplained, such as the propagation of two longitudinal waves. The objective of this study was to shed more light on the occurrence of these two waves, using finite-difference simulations on a model medium simpler than bone. Slabs of anisotropic, scattering media were randomly generated. The coherent wave was obtained through spatial and ensemble-averaging of the transmitted wavefields. When varying relevant medium parameters, four of them appeared to play a significant role for the observation of two waves: (i) the solid fraction, (ii) the direction of propagation relatively to the scatterers orientation, (iii) the ability of scatterers to support shear waves, and (iv) a continuity of the solid matrix along the propagation. These observations are consistent with the hypothesis that fast waves are guided by the locally plate/bar-like solid matrix. If confirmed, this interpretation could significantly help developing approaches for a better understanding of trabecular bone micro-architecture using ultrasound.

  5. Novel trends in affinity biosensors: current challenges and perspectives

    NASA Astrophysics Data System (ADS)

    Arugula, Mary A.; Simonian, Aleksandr

    2014-03-01

    Molecular biorecognition processes facilitate physical and biochemical interactions between molecules in all crucial metabolic pathways. Perhaps the target analyte and the biorecognition element interactions have the most impactful use in biosensing applications. Traditional analytical sensing systems offer excellent biorecognition elements with the ability to detect and determine the presence of analytes. High affinity antibodies and DNA play an important role in the development of affinity biosensors based on electrochemical, optical and mass sensitive approaches. Advancements in this area routinely employ labels, label free, nanoparticles, multifunctional matrices, carbon nanotubes and other methods to meet the requirements of its own application. However, despite increasing affinity ceilings for conventional biosensors, the field draws back in meeting specifically important demands, such as long-term stability, ultrasensitivity, rapid detection, extreme selectivity, strong biological base, calibration, in vivo measurements, regeneration, satisfactory performance and ease of production. Nevertheless, recent efforts through this line have produced novel high-tech nanosensing systems such as ‘aptamers’ and ‘phages’ which exhibit high-throughput sensing. Aptamers and phages are powerful tools that excel over antibodies in sensibility, stability, multi-detection, in vivo measurements and regeneration. Phages are superior in stability, screening for affinity-based target molecules ranging from small to proteins and even cells, and easy production. In this review, we focus mainly on recent developments in affinity-based biosensors such as immunosensors, DNA sensors, emphasizing aptasensors and phage-based biosensors basing on novel electrochemical, optical and mass sensitive detection techniques. We also address enzyme inhibition-based biosensors and the current problems associated with the above sensors and their future perspectives.

  6. Semiempirical Theories of the Affinities of Negative Atomic Ions

    NASA Technical Reports Server (NTRS)

    Edie, John W.

    1961-01-01

    The determination of the electron affinities of negative atomic ions by means of direct experimental investigation is limited. To supplement the meager experimental results, several semiempirical theories have been advanced. One commonly used technique involves extrapolating the electron affinities along the isoelectronic sequences, The most recent of these extrapolations Is studied by extending the method to Include one more member of the isoelectronic sequence, When the results show that this extension does not increase the accuracy of the calculations, several possible explanations for this situation are explored. A different approach to the problem is suggested by the regularities appearing in the electron affinities. Noting that the regular linear pattern that exists for the ionization potentials of the p electrons as a function of Z, repeats itself for different degrees of ionization q, the slopes and intercepts of these curves are extrapolated to the case of the negative Ion. The method is placed on a theoretical basis by calculating the Slater parameters as functions of q and n, the number of equivalent p-electrons. These functions are no more than quadratic in q and n. The electron affinities are calculated by extending the linear relations that exist for the neutral atoms and positive ions to the negative ions. The extrapolated. slopes are apparently correct, but the intercepts must be slightly altered to agree with experiment. For this purpose one or two experimental affinities (depending on the extrapolation method) are used in each of the two short periods. The two extrapolation methods used are: (A) an isoelectronic sequence extrapolation of the linear pattern as such; (B) the same extrapolation of a linearization of this pattern (configuration centers) combined with an extrapolation of the other terms of the ground configurations. The latter method Is preferable, since it requires only experimental point for each period. The results agree within

  7. Affine Covariant Features for Fisheye Distortion Local Modelling.

    PubMed

    Furnari, Antonino; Farinella, Giovanni; Bruna, Arcangelo; Battiato, Sebastiano

    2016-11-10

    Perspective cameras are the most popular imaging sensors used in Computer Vision. However, many application fields including automotive, surveillance and robotics, require the use of wide angle cameras (e.g., fisheye), which allow to acquire a larger portion of the scene using a single device at the cost of the introduction of noticeable radial distortion in the images. Affine covariant feature detectors have proven successful in a variety of Computer Vision applications including object recognition, image registration and visual search. Moreover, their robustness to a series of variabilities related to both the scene and the image acquisition process has been thoroughly studied in the literature. In this paper, we investigate their effectiveness on fisheye images providing both theoretical and experimental analyses. As theoretical outcome, we show that the inherently non-linear radial distortion can be locally approximated by linear functions with a reasonably small error. The experimental analysis builds on Mikolajczyk's benchmark to assess the robustness of three popular affine region detectors (i.e., Maximally Stable Extremal Regions (MSER), Harris and Hessian affine region detectors), with respect to different variabilities as well as to radial distortion. To support the evaluations, we rely on the Oxford dataset and introduce a novel benchmark dataset comprising 50 images depicting different scene categories. Experiments are carried out on rectilinear images to which radial distortion is artificially added, and on real-world images acquired using fisheye lenses. Our analysis points out that affine region detectors can be effectively employed directly on fisheye images and that the radial distortion is locally modelled as an additional affine variability.

  8. Debris Flow Distributed Propagation Model

    NASA Astrophysics Data System (ADS)

    Gregoretti, C.

    The debris flow distributed propagation model is a DEM-based model. The fan is dis- cretized by square cells and each cell is assigned an altitude on the sea level. The cells of the catchment are distinguished in two categories: the source cells and the stripe cells. The source cells receive the input hydograph: the cells close to the torrent which are flooded by the debris flow overflowing the torrent embankment are source cells. The stripes cells are the cells flooded by debris flow coming from the surrounding cells. At the first time step only the source cells are flooded by debris flow coming from the torrent. At the second time step a certain number of cells are flooded by de- bris flow coming from the source cells. These cells constitute a stripe of cells and are assigned order two. At the third time step another group of cells are flooded by the debris flow coming from the cells whose order is two. These cells constitute another stripe and are assigned order three. The cell order of a stripe is the time step number corresponding to the transition from dry to flooded state. The mass transfer or mo- mentum exchange between cells is governed by two different mechanisms. The mass transfer is allowed only by a positive or equal to zero flow level difference between the drained cell and the receiving cell. The mass transfer is limited by a not negative final flow level difference between the drained cell and the receiving cells. This limitation excludes the case of possible oscillations in the mass transfer. Another limitation is that the mass drained by a cell should be less than the available mass in that cell. This last condition provides the respect of mass conservation. The first mechanism of mass transfer is the gravity. The mass in a cell is transferred to the neighbouring cells with lower altitude and flow level according to an uniform flow law: The second mecha- nism of mass transfer is the broad crested weir. The mass in a cell is transferred to the

  9. Extending Beowulf Clusters

    USGS Publications Warehouse

    Steinwand, Daniel R.; Maddox, Brian; Beckmann, Tim; Hamer, George

    2003-01-01

    Beowulf clusters can provide a cost-effective way to compute numerical models and process large amounts of remote sensing image data. Usually a Beowulf cluster is designed to accomplish a specific set of processing goals, and processing is very efficient when the problem remains inside the constraints of the original design. There are cases, however, when one might wish to compute a problem that is beyond the capacity of the local Beowulf system. In these cases, spreading the problem to multiple clusters or to other machines on the network may provide a cost-effective solution.

  10. Dwarfs in Coma Cluster

    NASA Technical Reports Server (NTRS)

    2007-01-01

    [figure removed for brevity, see original site] Click on image for larger poster version

    This false-color mosaic of the central region of the Coma cluster combines infrared and visible-light images to reveal thousands of faint objects (green). Follow-up observations showed that many of these objects, which appear here as faint green smudges, are dwarf galaxies belonging to the cluster. Two large elliptical galaxies, NGC 4889 and NGC 4874, dominate the cluster's center. The mosaic combines visible-light data from the Sloan Digital Sky Survey (color coded blue) with long- and short-wavelength infrared views (red and green, respectively) from NASA's Spitzer Space Telescope.

  11. Magnetization of ferromagnetic clusters

    SciTech Connect

    Onishi, Naoki; Bertsch, G.; Yabana, Kazuhiro

    1995-02-01

    The magnetization and deflection profiles of magnetic clusters in a Stern-Gerlach magnet are calculated for conditions under which the magnetic moment is fixed in the intrinsic frame of the cluster, and the clusters enter the magnetic field adiabatically. The predicted magnetization is monotonic in the Langevin parameter, the ratio of magnetic energy {mu}{sub 0}B to thermal energy k{sub B}T. In low field the average magnetization is 2/3 of the Langevin function. The high-field moment approaches saturation asymptotically as B{sup {minus}1/2} instead of the B{sup {minus}1} dependence in the Langevin function.

  12. H-cluster stars

    NASA Astrophysics Data System (ADS)

    Lai, X. Y.; Gao, C. Y.; Xu, R. X.

    2013-06-01

    The study of dense matter at ultrahigh density has a very long history, which is meaningful for us to understand not only cosmic events in extreme circumstances but also fundamental laws of physics. It is well known that the state of cold matter at supranuclear density depends on the non-perturbative nature of quantum chromodynamics (QCD) and is essential for modelling pulsars. A so-called H-cluster matter is proposed in this paper as the nature of dense matter in reality. In compact stars at only a few nuclear densities but low temperature, quarks could be interacting strongly with each other there. That might render quarks grouped in clusters, although the hypothetical quark clusters in cold dense matter have not been confirmed due to the lack of both theoretical and experimental evidence. Motivated by recent lattice QCD simulations of the H-dibaryons (with structure uuddss), we therefore consider here a possible kind of quark clusters, H-clusters, that could emerge inside compact stars during their initial cooling as the dominant components inside (the degree of freedom could then be H-clusters there). Taking into account the in-medium stiffening effect, we find that at baryon densities of compact stars H-cluster matter could be more stable than nuclear matter. We also find that for the H-cluster matter with lattice structure, the equation of state could be so stiff that it would seem to be `superluminal' in the most dense region. However, the real sound speed for H-cluster matter is in fact difficult to calculate, so at this stage we do not put constraints on our model from the usual requirement of causality. We study the stars composed of H-clusters, i.e. H-cluster stars, and derive the dependence of their maximum mass on the in-medium stiffening effect, showing that the maximum mass could be well above 2 M⊙ as observed and that the resultant mass-radius relation fits the measurement of the rapid burster under reasonable parameters. Besides a general

  13. Atomic cluster collisions

    NASA Astrophysics Data System (ADS)

    Korol, Andrey V.; Solov'yov, Andrey

    2013-01-01

    Atomic cluster collisions are a field of rapidly emerging research interest by both experimentalists and theorists. The international symposium on atomic cluster collisions (ISSAC) is the premier forum to present cutting-edge research in this field. It was established in 2003 and the most recent conference was held in Berlin, Germany in July of 2011. This Topical Issue presents original research results from some of the participants, who attended this conference. This issues specifically focuses on two research areas, namely Clusters and Fullerenes in External Fields and Nanoscale Insights in Radiation Biodamage.

  14. Partially supervised speaker clustering.

    PubMed

    Tang, Hao; Chu, Stephen Mingyu; Hasegawa-Johnson, Mark; Huang, Thomas S

    2012-05-01

    Content-based multimedia indexing, retrieval, and processing as well as multimedia databases demand the structuring of the media content (image, audio, video, text, etc.), one significant goal being to associate the identity of the content to the individual segments of the signals. In this paper, we specifically address the problem of speaker clustering, the task of assigning every speech utterance in an audio stream to its speaker. We offer a complete treatment to the idea of partially supervised speaker clustering, which refers to the use of our prior knowledge of speakers in general to assist the unsupervised speaker clustering process. By means of an independent training data set, we encode the prior knowledge at the various stages of the speaker clustering pipeline via 1) learning a speaker-discriminative acoustic feature transformation, 2) learning a universal speaker prior model, and 3) learning a discriminative speaker subspace, or equivalently, a speaker-discriminative distance metric. We study the directional scattering property of the Gaussian mixture model (GMM) mean supervector representation of utterances in the high-dimensional space, and advocate exploiting this property by using the cosine distance metric instead of the euclidean distance metric for speaker clustering in the GMM mean supervector space. We propose to perform discriminant analysis based on the cosine distance metric, which leads to a novel distance metric learning algorithm—linear spherical discriminant analysis (LSDA). We show that the proposed LSDA formulation can be systematically solved within the elegant graph embedding general dimensionality reduction framework. Our speaker clustering experiments on the GALE database clearly indicate that 1) our speaker clustering methods based on the GMM mean supervector representation and vector-based distance metrics outperform traditional speaker clustering methods based on the “bag of acoustic features” representation and statistical

  15. Size-restricted proton transfer within toluene-methanol cluster ions.

    PubMed

    Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek; Furlani, Thomas; DeLeon, Robert L; Garvey, James F

    2008-11-20

    To understand the interaction between toluene and methanol, the chemical reactivity of [(C6H5CH3)(CH3OH) n=1-7](+) cluster ions has been investigated via tandem quadrupole mass spectrometry and through calculations. Collision Induced Dissociation (CID) experiments show that the dissociated intracluster proton transfer reaction from the toluene cation to methanol clusters, forming protonated methanol clusters, only occurs for n = 2-4. For n = 5-7, CID spectra reveal that these larger clusters have to sequentially lose methanol monomers until they reach n = 4 to initiate the deprotonation of the toluene cation. Metastable decay data indicate that for n = 3 and n = 4 (CH3OH)3H(+) is the preferred fragment ion. The calculational results reveal that both the gross proton affinity of the methanol subcluster and the structure of the cluster itself play an important role in driving this proton transfer reaction. When n = 3, the cooperative effect of the methanols in the subcluster provides the most important contribution to allow the intracluster proton transfer reaction to occur with little or no energy barrier. As n >or= 4, the methanol subcluster is able to form ring structures to stabilize the cluster structures so that direct proton transfer is not a favored process. The preferred reaction product, the (CH3OH)3H(+) cluster ion, indicates that this size-restricted reaction is driven by both the proton affinity and the enhanced stability of the resulting product.

  16. F+ and F⁻ affinities of simple N(x)F(y) and O(x)F(y) compounds.

    PubMed

    Grant, Daniel J; Wang, Tsang-Hsiu; Vasiliu, Monica; Dixon, David A; Christe, Karl O

    2011-03-07

    Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for the neutral and ionic N(x)F(y) and O(x)F(y) systems using coupled cluster theory with single and double excitations and including a perturbative triples correction (CCSD(T)) method with correlation consistent basis sets extrapolated to the complete basis set (CBS) limit. To achieve near chemical accuracy (±1 kcal/mol), three corrections to the electronic energy were added to the frozen core CCSD(T)/CBS binding energies: corrections for core-valence, scalar relativistic, and first order atomic spin-orbit effects. Vibrational zero point energies were computed at the CCSD(T) level of theory where possible. The calculated heats of formation are in good agreement with the available experimental values, except for FOOF because of the neglect of higher order correlation corrections. The F(+) affinity in the N(x)F(y) series increases from N(2) to N(2)F(4) by 63 kcal/mol, while that in the O(2)F(y) series decreases by 18 kcal/mol from O(2) to O(2)F(2). Neither N(2) nor N(2)F(4) is predicted to bind F(-), and N(2)F(2) is a very weak Lewis acid with an F(-) affinity of about 10 kcal/mol for either the cis or trans isomer. The low F(-) affinities of the nitrogen fluorides explain why, in spite of the fact that many stable nitrogen fluoride cations are known, no nitrogen fluoride anions have been isolated so far. For example, the F(-) affinity of NF is predicted to be only 12.5 kcal/mol which explains the numerous experimental failures to prepare NF(2)(-) salts from the well-known strong acid HNF(2). The F(-) affinity of O(2) is predicted to have a small positive value and increases for O(2)F(2) by 23 kcal/mol, indicating that the O(2)F(3)(-) anion might be marginally stable at subambient temperatures. The calculated adiabatic ionization potentials and electron affinities are in good agreement with experiment considering that many of the experimental values are for vertical processes.

  17. Combining cluster number counts and galaxy clustering

    NASA Astrophysics Data System (ADS)

    Lacasa, Fabien; Rosenfeld, Rogerio

    2016-08-01

    The abundance of clusters and the clustering of galaxies are two of the important cosmological probes for current and future large scale surveys of galaxies, such as the Dark Energy Survey. In order to combine them one has to account for the fact that they are not independent quantities, since they probe the same density field. It is important to develop a good understanding of their correlation in order to extract parameter constraints. We present a detailed modelling of the joint covariance matrix between cluster number counts and the galaxy angular power spectrum. We employ the framework of the halo model complemented by a Halo Occupation Distribution model (HOD). We demonstrate the importance of accounting for non-Gaussianity to produce accurate covariance predictions. Indeed, we show that the non-Gaussian covariance becomes dominant at small scales, low redshifts or high cluster masses. We discuss in particular the case of the super-sample covariance (SSC), including the effects of galaxy shot-noise, halo second order bias and non-local bias. We demonstrate that the SSC obeys mathematical inequalities and positivity. Using the joint covariance matrix and a Fisher matrix methodology, we examine the prospects of combining these two probes to constrain cosmological and HOD parameters. We find that the combination indeed results in noticeably better constraints, with improvements of order 20% on cosmological parameters compared to the best single probe, and even greater improvement on HOD parameters, with reduction of error bars by a factor 1.4-4.8. This happens in particular because the cross-covariance introduces a synergy between the probes on small scales. We conclude that accounting for non-Gaussian effects is required for the joint analysis of these observables in galaxy surveys.

  18. In vitro propagation of Paphiopedilum orchids.

    PubMed

    Zeng, Songjun; Huang, Weichang; Wu, Kunlin; Zhang, Jianxia; da Silva, Jaime A Teixeira; Duan, Jun

    2016-01-01

    Paphiopedilum is one of the most popular and rare orchid genera. Members of the genus are sold and exhibited as pot plants and cut flowers. Wild populations of Paphiopedilum are under the threat of extinction due to over-collection and loss of suitable habitats. A reduction in their commercial value through large-scale propagation in vitro is an option to reduce pressure from illegal collection, to attempt to meet commercial needs and to re-establish threatened species back into the wild. Although they are commercially propagated via asymbiotic seed germination, Paphiopedilum are considered to be difficult to propagate in vitro, especially by plant regeneration from tissue culture. This review aims to cover the most important aspects and to provide an up-to-date research progress on in vitro propagation of Paphiopedilum and to emphasize the importance of further improving tissue culture protocols for ex vitro-derived explants.

  19. Noise propagation in urban and industrial areas

    NASA Technical Reports Server (NTRS)

    Davies, H. G.

    1976-01-01

    Noise propagation in streets and the discrepancies between theoretical analyses and field measurements are discussed. A cell-model is used to estimate the general background level of noise due to vehicular sources distributed over the urban area.

  20. The ghost propagator in Coulomb gauge

    NASA Astrophysics Data System (ADS)

    Watson, P.; Reinhardt, H.

    2011-05-01

    We present results for a numerical study of the ghost propagator in Coulomb gauge whereby lattice results for the spatial gluon propagator are used as input to solving the ghost Dyson-Schwinger equation. We show that in order to solve completely, the ghost equation must be supplemented by a boundary condition (the value of the inverse ghost propagator dressing function at zero momentum) which determines if the solution is critical (zero value for the boundary condition) or subcritical (finite value). The various solutions exhibit a characteristic behavior where all curves follow the same (critical) solution when going from high to low momenta until `forced' to freeze out in the infrared to the value of the boundary condition. The boundary condition can be interpreted in terms of the Gribov gauge-fixing ambiguity; we also demonstrate that this is not connected to the renormalization. Further, the connection to the temporal gluon propagator and the infrared slavery picture of confinement is discussed.