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Sample records for affinity propagation clustering

  1. Affinity Propagation Clustering of Measurements for Multiple Extended Target Tracking

    PubMed Central

    Zhang, Tao; Wu, Renbiao

    2015-01-01

    More measurements are generated by the target per observation interval, when the target is detected by a high resolution sensor, or there are more measurement sources on the target surface. Such a target is referred to as an extended target. The probability hypothesis density filter is considered an efficient method for tracking multiple extended targets. However, the crucial problem of how to accurately and effectively partition the measurements of multiple extended targets remains unsolved. In this paper, affinity propagation clustering is introduced into measurement partitioning for extended target tracking, and the elliptical gating technique is used to remove the clutter measurements, which makes the affinity propagation clustering capable of partitioning the measurement in a densely cluttered environment with high accuracy. The Gaussian mixture probability hypothesis density filter is implemented for multiple extended target tracking. Numerical results are presented to demonstrate the performance of the proposed algorithm, which provides improved performance, while obviously reducing the computational complexity. PMID:26370998

  2. 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.

  3. An extended affinity propagation clustering method based on different data density types.

    PubMed

    Zhao, XiuLi; Xu, WeiXiang

    2015-01-01

    Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself.

  4. An Extended Affinity Propagation Clustering Method Based on Different Data Density Types

    PubMed Central

    Zhao, XiuLi; Xu, WeiXiang

    2015-01-01

    Affinity propagation (AP) algorithm, as a novel clustering method, does not require the users to specify the initial cluster centers in advance, which regards all data points as potential exemplars (cluster centers) equally and groups the clusters totally by the similar degree among the data points. But in many cases there exist some different intensive areas within the same data set, which means that the data set does not distribute homogeneously. In such situation the AP algorithm cannot group the data points into ideal clusters. In this paper, we proposed an extended AP clustering algorithm to deal with such a problem. There are two steps in our method: firstly the data set is partitioned into several data density types according to the nearest distances of each data point; and then the AP clustering method is, respectively, used to group the data points into clusters in each data density type. Two experiments are carried out to evaluate the performance of our algorithm: one utilizes an artificial data set and the other uses a real seismic data set. The experiment results show that groups are obtained more accurately by our algorithm than OPTICS and AP clustering algorithm itself. PMID:25685144

  5. 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

  6. 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.

  7. 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. PMID:24348339

  8. Identification of functional networks in resting state fMRI data using adaptive sparse representation and affinity propagation clustering

    PubMed Central

    Li, Xuan; Wang, Haixian

    2015-01-01

    Human brain functional system has been viewed as a complex network. To accurately characterize this brain network, it is important to estimate the functional connectivity between separate brain regions (i.e., association matrix). One common approach to evaluating the connectivity is the pairwise Pearson correlation. However, this bivariate method completely ignores the influence of other regions when computing the pairwise association. Another intractable issue existed in many approaches to further analyzing the network structure is the requirement of applying a threshold to the association matrix. To address these issues, we develop a novel scheme to investigate the brain functional networks. Specifically, we first establish a global functional connection network by using the Adaptive Sparse Representation (ASR), adaptively integrating the sparsity of ℓ1-norm and the grouping effect of ℓ2-norm for linear representation and then identify connectivity patterns with Affinity Propagation (AP) clustering algorithm. Results on both simulated and real data indicate that the proposed scheme is superior to the Pearson correlation in connectivity quality and clustering quality. Our findings suggest that the proposed scheme is an accurate and useful technique to delineate functional network structure for functionally parsimonious and correlated fMRI data with a large number of brain regions. PMID:26528123

  9. 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 Central

    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. PMID:26236217

  10. 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. PMID:26236217

  11. Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis

    PubMed Central

    2011-01-01

    Background Classification and naming is a key step in the analysis, understanding and adequate management of living organisms. However, where to set limits between groups can be puzzling especially in clonal organisms. Within the Mycobacterium tuberculosis complex (MTC), the etiological agent of tuberculosis (TB), experts have first identified several groups according to their pattern at repetitive sequences, especially at the CRISPR locus (spoligotyping), and to their epidemiological relevance. Most groups such as "Beijing" found good support when tested with other loci. However, other groups such as T family and T1 subfamily (belonging to the "Euro-American" lineage) correspond to non-monophyletic groups and still need to be refined. Here, we propose to use a method called Affinity Propagation that has been successfully used in image categorization to identify relevant patterns at the CRISPR locus in MTC. Results To adequately infer the relative divergence time between strains, we used a distance method inspired by the recent evolutionary model by Reyes et al. We first confirm that this method performs better than the Jaccard index commonly used to compare spoligotype patterns. Second, we document the support of each spoligotype family among the previous classification using affinity propagation on the international spoligotyping database SpolDB4. This allowed us to propose a consensus assignation for all SpolDB4 spoligotypes. Third, we propose new signatures to subclassify the T family. Conclusion Altogether, this study shows how the new clustering algorithm Affinity Propagation can help building or refining clonal organims classifications. It also describes well-supported families and subfamilies among M. tuberculosis complex, especially inside the modern "Euro-American" lineage. PMID:21635750

  12. 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.

  13. 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

    2015-01-01

    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

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

    PubMed Central

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

    2015-01-01

    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

  15. 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

  16. Propagation properties of magnetic holes - MMS and Cluster observations

    NASA Astrophysics Data System (ADS)

    Hamrin, Maria; Yao, Shutao; Shi, Quanqi; De Spiegeleer, Alexandre; Pitkänen, Timo; Li, Zeyu; Wang, Xiaogang; Tian, Anmin; Sun, Weijie; Wang, Mengmeng; Burch, Jim

    2016-04-01

    Magnetic holes (MHs) are structures showing a significant decrease in the magnetic field magnitude. Previous investigations suggest that MHs can be excited by the mirror instability, hence implying that they are "frozen" into the plasma flow. Another possible candidate for explaining the observations of LMDs is the soliton wave, which can propagate with respect to the plasma flow. In this study we use multi-spacecraft MMS and Cluster data to investigate MHs in the solar wind, magnetosheath and magnetospheric plasma. Various methods are used to obtain propagation properties of the MHs. Our results are compared with predictions from mirror mode and soliton wave theories. We find that 8 of 10 MH events detected by Cluster in the plasma sheet are propagating in the plasma flow, and they are considered to be generated by soliton waves.

  17. Low affinity binding site clusters confer hox specificity and regulatory robustness.

    PubMed

    Crocker, Justin; Abe, Namiko; Rinaldi, Lucrezia; McGregor, Alistair P; Frankel, Nicolás; Wang, Shu; Alsawadi, Ahmad; Valenti, Philippe; Plaza, Serge; Payre, François; Mann, Richard S; Stern, David L

    2015-01-15

    In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression. PMID:25557079

  18. 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.

  19. Reliability Evaluation for Clustered WSNs under Malware Propagation.

    PubMed

    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

  20. 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

  1. 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.

  2. Affinity Enhancement by Ligand Clustering Effect Inspired by Peptide Dendrimers−Shank PDZ Proteins Interactions

    PubMed Central

    Liu, Jiahui; Liu, Miao; Zheng, Bo; Yao, Zhongping; Xia, Jiang

    2016-01-01

    High-affinity binders are desirable tools to probe the function that specific protein−protein interactions play in cell. In the process of seeking a general strategy to design high-affinity binders, we found a clue from the βPIX (p21-activated kinase interacting exchange factor)−Shank PDZ interaction in synaptic assembly: three PDZ-binding sites are clustered by a parallel coiled-coil trimer but bind to Shank PDZ protein with 1:1 stoichiometry (1 trimer/1 PDZ). Inspired by this architecture, we proposed that peptide dendrimer, mimicking the ligand clustering in βPIX, will also show enhanced binding affinity, yet with 1:1 stoichiometry. This postulation has been proven here, as we synthesized a set of monomeric, dimeric and trimeric peptides and measured their binding affinity and stoichiometry with Shank PDZ domains by isothermal titration calorimetry, native mass spectrometry and surface plasmon resonance. This affinity enhancement, best explained by proximity effect, will be useful to guide the design of high-affinity blockers for protein−protein interactions. PMID:26918521

  3. Propagation of intense short laser pulses in a gas of atomic clusters.

    PubMed

    Gupta, Ayush; Antonsen, T M; Milchberg, H M

    2004-10-01

    We present a model and numerical simulations for the propagation of intense short laser pulses in gases of atomic clusters. As the pulse propagates through the clusters, they absorb energy, expand and explode. The clustered gas thus acts as a medium with time dependent effective dielectric constant. A self-consistent model for the cluster expansion and the laser pulse propagation is developed. Self-focusing of the laser pulse, coupling of laser energy to clusters and the evolution of the pulse spectrum are studied for a laser-cluster system with typical laboratory parameters.

  4. Spatiotemporal Variability and Propagation of Equatorial Noise Observed by Cluster

    NASA Technical Reports Server (NTRS)

    Santolik, O.; Pickett, J. S.; Gurnett, D. A.; Maksimovic, M.; Cornilleau-Wehrlin, N.

    2002-01-01

    We report a multipoint case study of the electromagnetic equatorial noise observed by the Cluster project. High-resolution data were measured in three close points in space located in the morning sector of the outer plasmasphere. We demonstrate a narrow latitudinal extent of the emissions with a typical width of 2 degrees, centered near the minimum-B equator. Power spectra recorded by the different satellites show a complex structure of emission lines whose relative intensities and positions vary at timescales of 1-2 min and/or at spatial scales of tens of wavelengths. These lines do not match harmonics of the local proton cyclotron frequency, as it would be expected if the waves are generated by energetic ions and observed near the source region. We bring observational evidence that the waves propagate with a significant radial component and thus can propagate from a distant generation region located at different radial distances where ion cyclotron frequencies match the observed fine structure.

  5. Electron affinities of d1 transition metal chloride clusters and onset of super halogen behavior

    NASA Astrophysics Data System (ADS)

    Behera, Swayamprabha; Joseph, Jorly; Jena, Purusottam

    2011-03-01

    Geometry, electronic structure, and electron affinity of d1 transition metal chloride clusters (MCl n , M = Sc,Y, La; n = 1--5) have been calculated using density functional theory. Chlorine atoms are chemically bound in all cases except for MCl 5 . The electron affinities of MCl n (n = 1--3) are small and increase only marginally as a function of n until the valence of the metal atom is consumed. Beyond this, they rise sharply and reach a value of 5.96, 6.03 and 5.90 eV for ScCl 4 , YCl 4 and LaCl 4 , respectively and remain high for n = 5. MCl n , (n = 4,5) clusters, therefore, behave as superhalogens. Results are compared with available experimental data

  6. Electron affinities of d1 transition metal chloride clusters and onset of super halogen behavior

    NASA Astrophysics Data System (ADS)

    Joseph, Jorly; Behera, Swayamprabha; Jena, Purusottam

    2010-09-01

    Geometry, electronic structure, and electron affinity of d1 transition metal chloride clusters (MCl n, M = Sc, Y, La; n = 1-5) have been calculated using density functional theory. Chlorine atoms are chemically bound in all cases except for MCl 5. The electron affinities of MCl n ( n = 1-3) are small and increase only marginally as a function of n until the valence of the metal atom is consumed. Beyond this, they rise sharply and reach a value of 5.96, 6.03 and 5.90 eV for ScCl 4, YCl 4 and LaCl 4, respectively and remain high for n = 5. MCl n, ( n = 4,5) clusters, therefore, behave as superhalogens. Results are compared with available experimental data.

  7. 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. PMID:25133214

  8. 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.

  9. 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. PMID:19045766

  10. Azimuthal directions of equatorial noise propagation determined using 10 years of data from the Cluster spacecraft

    NASA Astrophysics Data System (ADS)

    Němec, F.; Santolík, O.; Pickett, J. S.; Hrbáčková, Z.; Cornilleau-Wehrlin, N.

    2013-11-01

    Equatorial noise (EN) emissions are electromagnetic waves at frequencies between the proton cyclotron frequency and the lower hybrid frequency routinely observed within a few degrees of the geomagnetic equator at radial distances from about 2 to 6 RE. They propagate in the extraordinary (fast magnetosonic) mode nearly perpendicularly to the ambient magnetic field. We conduct a systematic analysis of azimuthal directions of wave propagation, using all available Cluster data from 2001 to 2010. Altogether, combined measurements of the Wide-Band Data and Spectrum Analyzer of the Spatio-Temporal Analysis of Field Fluctuations instruments allowed us to determine azimuthal angle of wave propagation for more than 100 EN events. It is found that the observed propagation pattern is mostly related to the plasmapause location. While principally isotropic azimuthal directions of EN propagation were detected inside the plasmasphere, wave propagation in the plasma trough was predominantly found directed to the West or East, perpendicular to the radial direction. The observed propagation pattern can be explained using a simple propagation analysis, assuming that the emissions are generated close to the plasmapause.

  11. 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.

  12. Reconstitution of interactions between tyrosine kinases and the high affinity IgE receptor which are controlled by receptor clustering.

    PubMed Central

    Scharenberg, A M; Lin, S; Cuenod, B; Yamamura, H; Kinet, J P

    1995-01-01

    High affinity IgE receptor (Fc epsilon RI) signaling after contact with antigen occurs in response to receptor clustering. This paper describes methodology, based on vaccinia virus driven protein expression, for probing signaling pathways and its application to Fc epsilon RI interactions with the lyn and syk tyrosine kinases. Reconstitution of the complete tetrameric Fc epsilon RI receptor, lyn and syk in a non-hematopoietic 'null' cell line is sufficient to reconstruct clustering-controlled receptor tyrosine phosphorylation and activation of syk, without apparent requirement for hematopoietic specific phosphatases. The src family kinase lyn phosphorylates Fc epsilon RI in response to receptor clustering, resulting in syk binding to the phosphorylated Fc epsilon RI. Lyn also participates in the tyrosine phosphorylation and activation of syk in a manner which is dependent on phosphorylated Fc epsilon RI. Using overexpression of active and dominant negative syk proteins in a mast cell line which naturally expresses Fc epsilon RI, we corroborate syk's role downstream of receptor phosphorylation, and demonstrate that syk SH2 domains protect receptor ITAMs from ongoing dephosphorylation. Based on these results, we propose that receptor clustering controls lyn-mediated Fc epsilon RI tyrosine phosphorylation by shifting a balance between phosphorylation and dephosphorylation towards accumulation of tyrosine phosphorylated Fc epsilon RI. Fc epsilon RI tyrosine phosphorylation functions to bring syk into a microenvironment where it becomes tyrosine phosphorylated and activated, thereby allowing clustering to indirectly control syk activity. Images PMID:7628439

  13. 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.

  14. Propagation of thermal excitations in a cluster of vortices in superfluid 3He-B

    NASA Astrophysics Data System (ADS)

    Hosio, J. J.; Eltsov, V. B.; de Graaf, R.; Krusius, M.; Mäkinen, J.; Schmoranzer, D.

    2011-12-01

    We describe the first measurement on Andreev scattering of thermal excitations from a vortex configuration with known density, spatial extent, and orientations in 3He-B superfluid. The heat flow from a blackbody radiator in equilibrium rotation at constant angular velocity is measured with two quartz tuning fork oscillators. One oscillator creates a controllable density of excitations at 0.2Tc base temperature and the other records the thermal response. The results are compared to numerical calculations of ballistic propagation of thermal quasiparticles through a cluster of rectilinear vortices. We find good agreement which supports the current understanding of Andreev reflection.

  15. A hybrid algorithm for clustering of time series data based on affinity search technique.

    PubMed

    Aghabozorgi, Saeed; Ying Wah, Teh; Herawan, Tutut; Jalab, Hamid A; Shaygan, Mohammad Amin; Jalali, Alireza

    2014-01-01

    Time series clustering is an important solution to various problems in numerous fields of research, including business, medical science, and finance. However, conventional clustering algorithms are not practical for time series data because they are essentially designed for static data. This impracticality results in poor clustering accuracy in several systems. In this paper, a new hybrid clustering algorithm is proposed based on the similarity in shape of time series data. Time series data are first grouped as subclusters based on similarity in time. The subclusters are then merged using the k-Medoids algorithm based on similarity in shape. This model has two contributions: (1) it is more accurate than other conventional and hybrid approaches and (2) it determines the similarity in shape among time series data with a low complexity. To evaluate the accuracy of the proposed model, the model is tested extensively using syntactic and real-world time series datasets.

  16. 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. PMID:27571416

  17. 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.

  18. 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

  19. Directions of equatorial noise propagation determined using Cluster and DEMETER spacecraft

    NASA Astrophysics Data System (ADS)

    Nemec, Frantisek; Hrbackova, Zuzana; Santolik, Ondrej; Pickett, Jolene S.; Parrot, Michel; Cornilleau-Wehrlin, Nicole

    2013-04-01

    Equatorial noise emissions are electromagnetic waves at frequencies between the proton cyclotron frequency and the lower hybrid frequency routinely observed within a few degrees of the geomagnetic equator at radial distances from about 2 to 6 Re. High resolution data reveal that the emissions are formed by a system of spectral lines, being generated by instabilities of proton distribution functions at harmonics of the proton cyclotron frequency in the source region. The waves propagate in the fast magnetosonic mode nearly perpendicularly to the ambient magnetic field, i.e. the corresponding magnetic field fluctuations are almost linearly polarized along the ambient magnetic field and the corresponding electric field fluctuations are elliptically polarized in the equatorial plane, with the major polarization axis having the same direction as wave and Poynting vectors. We conduct a systematic analysis of azimuthal propagation of equatorial noise. Combined WBD and STAFF-SA measurements performed on the Cluster spacecraft are used to determine not only the azimuthal angle of the wave vector direction, but also to estimate the corresponding beaming angle. It is found that the beaming angle is generally rather large, i.e. the detected waves come from a significant range of directions, and a traditionally used approximation of a single plane wave fails. The obtained results are complemented by a raytracing analysis in order to get a comprehensive picture of equatorial noise propagation in the inner magnetosphere. Finally, high resolution multi-component measurements performed by the low-altitude DEMETER spacecraft are used to demonstrate that equatorial noise emissions can reach altitudes as low as 660 km, and that the observed propagation properties are in agreement with the overall propagation picture.

  20. Propagation characteristics of young hot flow anomalies near the bow shock: Cluster observations

    NASA Astrophysics Data System (ADS)

    Xiao, T.; Zhang, H.; Shi, Q. Q.; Zong, Q.-G.; Fu, S. Y.; Tian, A. M.; Sun, W. J.; Wang, S.; Parks, G. K.; Yao, S. T.; Rème, H.; Dandouras, I.

    2015-06-01

    Based on Cluster observations, the propagation velocities and normal directions of hot flow anomaly (HFA) boundaries upstream the Earth's bow shock are calculated. Twenty-one young HFAs, which have clear leading and trailing boundaries, were selected, and multispacecraft timing method considering errors was employed for the investigation. According to the difference in the propagation velocity of the leading and trailing edges, we categorized these events into three groups, namely, contracting, expanding, and stable events. The contraction speed is a few tens of kilometers per second for the contracting HFAs, and the expansion speed is tens to more than hundred kilometers per second for expanding events. For the stable events, the leading and trailing edges propagate at almost the same speed within the error range. We have further investigated what causes them to contract, expand, or stay stable by carefully calculating the thermal pressure of the young HFAs which have two distinct ion populations (solar wind beam and reflected flow). It is found that the extreme value of the sum of the magnetic and thermal pressure inside the HFAs compared with that of the nearest point outside of the leading edges is higher for expanding events and lower for contracting events, and there is no significant difference for the stable events, and the total pressure (sum of thermal, magnetic, and dynamic pressure) variation has a significant effect on the evolution for most (70%) of the HFAs, which implies that the pressure plays an important role in the evolution of young HFAs.

  1. Transition properties from the Hermitian formulation of the coupled cluster polarization propagator

    SciTech Connect

    Tucholska, Aleksandra M. Modrzejewski, Marcin; Moszynski, Robert

    2014-09-28

    Theory of one-electron transition density matrices has been formulated within the time-independent coupled cluster method for the polarization propagator [R. Moszynski, P. S. Żuchowski, and B. Jeziorski, Coll. Czech. Chem. Commun. 70, 1109 (2005)]. Working expressions have been obtained and implemented with the coupled cluster method limited to single, double, and linear triple excitations (CC3). Selected dipole and quadrupole transition probabilities of the alkali earth atoms, computed with the new transition density matrices are compared to the experimental data. Good agreement between theory and experiment is found. The results obtained with the new approach are of the same quality as the results obtained with the linear response coupled cluster theory. The one-electron density matrices for the ground state in the CC3 approximation have also been implemented. The dipole moments for a few representative diatomic molecules have been computed with several variants of the new approach, and the results are discussed to choose the approximation with the best balance between the accuracy and computational efficiency.

  2. 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

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

    PubMed

    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

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

    PubMed

    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

  5. 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

  6. PROPAGATION OF ULTRAHIGH ENERGY NUCLEI IN CLUSTERS OF GALAXIES: RESULTING COMPOSITION AND SECONDARY EMISSIONS

    SciTech Connect

    Kotera, K.; Allard, D.; Dubois, Y.; Pierog, T.

    2009-12-10

    We study the survival of ultrahigh energy nuclei injected in clusters of galaxies, as well as their secondary neutrino and photon emissions, using a complete numerical propagation method and a realistic modeling of the magnetic, baryonic, and photonic backgrounds. It is found that the survival of heavy nuclei highly depends on the injection position and on the profile of the magnetic field. Taking into account the limited lifetime of the central source could also lead in some cases to the detection of a cosmic-ray afterglow, temporally decorrelated from neutrino and gamma-ray emissions. We calculate that the diffusive neutrino flux around 1 PeV coming from clusters of galaxies may have a chance to be detected by current instruments. The observation of single sources in neutrinos and in gamma rays produced by ultrahigh energy cosmic rays will be more difficult. Signals coming from lower energy cosmic rays (E approx< 1 PeV), if they exist, might however be detected by Fermi, for reasonable sets of parameters.

  7. 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

  8. 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.

  9. The Dipole Potential Modifies the Clustering and Ligand Binding Affinity of ErbB Proteins and Their Signaling Efficiency

    PubMed Central

    Kovács, Tamás; Batta, Gyula; Hajdu, Tímea; Szabó, Ágnes; Váradi, Tímea; Zákány, Florina; Csomós, István; Szöllősi, János; Nagy, Peter

    2016-01-01

    Although activation of the ErbB family of receptor tyrosine kinases (ErbB1-4) is driven by oligomerization mediated by intermolecular interactions between the extracellular, the kinase and the transmembrane domains, the transmembrane domain has been largely neglected in this regard. The largest contributor to the intramembrane electric field, the dipole potential, alters the conformation of transmembrane peptides, but its effect on ErbB proteins is unknown. Here, we show by Förster resonance energy transfer (FRET) and number and brightness (N&B) experiments that the epidermal growth factor (EGF)-induced increase in the homoassociation of ErbB1 and ErbB2 and their heteroassociation are augmented by increasing the dipole potential. These effects were even more pronounced for ErbB2 harboring an activating Val → Glu mutation in the transmembrane domain (NeuT). The signaling capacity of ErbB1 and ErbB2 was also correlated with the dipole potential. Since the dipole potential decreased the affinity of EGF to ErbB1, the augmented growth factor-induced effects at an elevated dipole potential were actually induced at lower receptor occupancy. We conclude that the dipole potential plays a permissive role in the clustering of ErbB receptors and that the effects of lipid rafts on ligand binding and receptor signaling can be partially attributed to the dipole potential. PMID:27775011

  10. Cross-linking of epidermal growth factor receptors in intact cells: detection of initial stages of receptor clustering and determination of molecular weight of high-affinity receptors

    SciTech Connect

    Fanger, B.O.; Austin, K.S.; Earp, H.S.; Cidlowski, J.A.

    1986-10-21

    A method was developed to label epidermal growth factor (EGF) receptors with /sup 125/I-EGF in whole cells using chemical cross-linking reagents. Polyacrylamide gel electrophoresis resolved an M/sub r/ approx. 180,000 EGF-receptor complex and larger M/sub r/ greater than or equal to 360,000 aggregates. The formation of the larger complexes was timed and temperature dependent and appeared to represent the initial events of EGF receptor clustering. Alteration of the ratio of /sup 125/I-EGF-labeled high- and low- affinity complexes by competition with unlabeled EGF or by induction of additional high-affinity sites with dexamethasone suggested that both sites were represented by the M/sub r/ approx. 180,000 /sup 125/I-EGF-receptor complexes. Digestion of cells before cross-linking detected a small population of trypsin-resistant M/sub r/ approx. 180,000 receptors, which could represent previously described cryptic and/or high-affinity receptors. Few of the M/sub r/ approx. 360,000 receptors were trypsin resistant. Glucocorticoid induction of high-affinity EGF receptors failed to induce detectable changes in the microclustering of EGF receptors but did result in a 50% increase in EGF-induced receptor phosphorylation in HeLa S/sub 3/ cell membranes at 4/sup 0/C. Thus, glucocorticoids increase high-affinity EGF binding sites, EGF-induced receptor phosphorylation, and cell growth.

  11. 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. PMID:17927400

  12. High-order finite-element seismic wave propagation modeling with MPI on a large GPU cluster

    SciTech Connect

    Komatitsch, Dimitri; Erlebacher, Gordon; Goeddeke, Dominik; Michea, David

    2010-10-01

    We implement a high-order finite-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 large cluster of NVIDIA Tesla graphics cards using the CUDA programming environment and non-blocking message passing based on MPI. Contrary to many finite-element implementations, ours is implemented successfully in single precision, maximizing the performance of current generation GPUs. We discuss the implementation and optimization of the code and compare it to an existing very optimized 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 non-blocking MPI messages in order to overlap the communications across the network and the data transfer to and from the device via PCIe with calculations on the GPU. 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 depending on how the problem is mapped to the reference CPU cluster, we obtain a speedup of 20x or 12x.

  13. 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. PMID:26879449

  14. Neurally mediated propagating discrete clustered contractions superimposed on myogenic ripples in ex vivo segments of human ileum.

    PubMed

    Kuizenga, Merel H; Sia, Tiong C; Dodds, Kelsi N; Wiklendt, Lukasz; Arkwright, John W; Thomas, A; Brookes, Simon J; Spencer, Nick J; Wattchow, David A; Dinning, Phil G; Costa, Marcello

    2015-01-01

    Narrow muscle strips have been extensively used to study intestinal contractility. Larger specimens from laboratory animals have provided detailed understanding of mechanisms that underlie patterned intestinal motility. Despite progress in animal tissue, investigations of motor patterns in large, intact specimens of human gut ex vivo have been sparse. In this study, we tested whether neurally dependent motor patterns could be detected in isolated specimens of intact human ileum. Specimens (n = 14; 7-30 cm long) of terminal ileum were obtained with prior informed consent from patients undergoing colonic surgery for removal of carcinomas. Preparations were set up in an organ bath with an array of force transducers, a fiberoptic manometry catheter, and a video camera. Spontaneous and distension-evoked motor activity was recorded, and the effects of lidocaine, which inhibits neural activity, were studied. Myogenic contractions (ripples) occurred in all preparations (6.17 ± 0.36/min). They were of low amplitude and formed complex patterns by colliding and propagating in both directions along the specimen at anterograde velocities of 4.1 ± 0.3 mm/s and retrogradely at 4.9 ± 0.6 mm/s. In five specimens, larger amplitude clusters of contractions were seen (discrete clustered contractions), which propagated aborally at 1.05 ± 0.13 mm/s and orally at 1.07 ± 0.09 mm/s. These consisted of two to eight phasic contractions that aligned with ripples. These motor patterns were abolished by addition of lidocaine (0.3 mM). The ripples continued unchanged in the presence of this neural blocking agent. These results demonstrate that both myogenic and neurogenic motor patterns can be studied in isolated specimens of human small intestine.

  15. Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering

    PubMed Central

    Bourguiba, Hedia; Khadari, Bouchaib; Krichen, Lamia; Trifi-Farah, Neila; Santoni, Sylvain

    2010-01-01

    Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated ‘Bargougs’ were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin. PMID:20838857

  16. Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering.

    PubMed

    Bourguiba, Hedia; Khadari, Bouchaib; Krichen, Lamia; Trifi-Farah, Neila; Santoni, Sylvain; Audergon, Jean-Marc

    2010-10-01

    Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated 'Bargougs' were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin. PMID:20838857

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

    PubMed

    Peters, Daniel T; Fung, Herman K H; Levdikov, Vladimir M; Irmscher, Tobias; Warrander, Fiona C; Greive, Sandra J; Kovalevskiy, Oleg; Isaacs, Harry V; Coles, Mark; Antson, Alfred A

    2016-09-13

    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

  18. Feedback control of wave propagation in a rectangular panel, part 2: Experimental realization using clustered velocity and displacement feedback

    NASA Astrophysics Data System (ADS)

    Iwamoto, Hiroyuki; Tanaka, Nobuo; Hill, Simon G.

    2012-10-01

    This study presents the feedback control of flexural waves propagating in a rectangular panel. The objective of this paper (part 2) is to experimentally implement the feedback wave control method which was proposed in part 1 of the two series papers. Firstly, based on the collocation of sensors and actuators, clustered velocity and displacement feedback (C-VDFB) is newly proposed. Next, linking C-VDFB with the active wave control proposed in part 1, it is clarified that the active wave control system can be realized to a limited extent. Then, from a viewpoint of numerical simulations, the characteristics of the feedback gains of C-VDFB and its control performance are clarified. It is shown that C-VDFB enables the inactivation of vibration modes at the target frequencies. Furthermore, it is clarified that even at the non-target frequencies, the proposed method sufficiently reduces the structural vibration. Finally, experiments on the reflected wave absorbing control using clustered direct velocity and displacement feedback are carried out. The experimental results show good agreement with those obtained in the simulation.

  19. Basis set limit electronic excitation energies, ionization potentials, and electron affinities for the 3d transition metal atoms: Coupled cluster and multireference methods

    NASA Astrophysics Data System (ADS)

    Balabanov, Nikolai B.; Peterson, Kirk A.

    2006-08-01

    Recently developed correlation consistent basis sets for the first row transition metal elements Sc-Zn have been utilized to determine complete basis set (CBS) scalar relativistic electron affinities, ionization potentials, and 4s23dn -2-4s1dn -1 electronic excitation energies with single reference coupled cluster methods [CCSD(T), CCSDT, and CCSDTQ] and multireference configuration interaction with three reference spaces: 3d4s, 3d4s4p, and 3d4s4p3d'. The theoretical values calculated with the highest order coupled cluster techniques at the CBS limit, including extrapolations to full configuration interaction, are well within 1kcal/mol of the corresponding experimental data. For the early transition metal elements (Sc-Mn) the internally contracted multireference averaged coupled pair functional method yielded excellent agreement with experiment; however, the atomic properties for the late transition metals (Mn-Zn) proved to be much more difficult to describe with this level of theory, even with the largest reference function of the present work.

  20. Affinity Chromatography.

    ERIC Educational Resources Information Center

    Gray, Gary R.

    1980-01-01

    Presents selected recent advances in immobilization chemistry which have important connections to affinity chromatography. Discusses ligand immobilization and support modification. Cites 51 references. (CS)

  1. 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. PMID:26003428

  2. 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.

  3. Lewis acidities and hydride, fluoride, and X- affinities of the BH(3-n)Xn compounds for (X = F, Cl, Br, I, NH2, OH, and SH) from coupled cluster theory.

    PubMed

    Grant, Daniel J; Dixon, David A; Camaioni, Donald; Potter, Robert G; Christe, Karl O

    2009-09-21

    Atomization energies at 0 K and enthalpies of formation at 0 and 298 K are predicted for the BH(4-n)X(n)(-) and the BH(3-n)X(n)F(-) compounds for (X = F, Cl, Br, I, NH(2), OH, and SH) from coupled cluster theory (CCSD(T)) calculations with correlation-consistent basis sets and with an effective core potential on I. To achieve near chemical accuracy (+/-1.0 kcal/mol), additional corrections were added to the complete basis set binding energies. The hydride, fluoride, and X(-) affinities of the BH(3-n)X(n) compounds were predicted. Although the hydride and fluoride affinities differ somewhat in their magnitudes, they show very similar trends and are both suitable for judging the Lewis acidities of compounds. The only significant differences in their acidity strength orders are found for the boranes substituted with the strongly electron withdrawing and back-donating fluorine and hydroxyl ligands. The highest H(-) and F(-) affinities are found for BI(3) and the lowest ones for B(NH(2))(3). Within the boron trihalide series, the Lewis acidity increases monotonically with increasing atomic weight of the halogen, that is, BI(3) is a considerably stronger Lewis acid than BF(3). For the X(-) affinities in the BX(3), HBX(2), and H(2)BX series, the fluorides show the highest values, whereas the amino and mercapto compounds show the lowest ones. Hydride and fluoride affinities of the BH(3-n)X(n) compounds exhibit linear correlations with the proton affinity of X(-) for most X ligands. Reasons for the correlation are discussed. A detailed analysis of the individual contributions to the Lewis acidities of these substituted boranes shows that the dominant effect in the magnitude of the acidity is the strength of the BX(3)(-)-F bond. The main contributor to the relative differences in the Lewis acidities of BX(3) for X, a halogen, is the electron affinity of BX(3) with a secondary contribution from the distortion energy from planar to pyramidal BX(3). The B-F bond dissociation

  4. A Study of the Orientation, Propagation Speeds, and Thicknesses of Electric Field and Density Structures Observed by Cluster~II in the High-Altitude Auroral Region

    NASA Astrophysics Data System (ADS)

    Hull, A. J.; Bonnell, J. W.; Mozer, F. S.; Andre, M.; Vaivads, A.; Eriksson, A.; Pedersen, A.; Lindqvist, P.; Laakso, H.

    2001-12-01

    The high-altitude auroral region constitues an integral part of the auroral zone electrodynamic system. The high-altitude perpendicular flows and the electric fields associated with those flows are the drivers for the low-altitude flows and mid-altitude acceleration processes that occur in the auroral zone. An interesting open question that the Cluster~II mission is ideally suited to answer is what properties of the generator region and the flows and density structures observed therin are related to the proper motion of the auroral acceleration region and auroral arcs. We will present the results of a study of more than twenty crossings of the high-altitude auroral zone by the Cluster~II spacecraft. The multi-point electric field and density measurements from the Cluster~II constellation will be used to estimate the direction and speed of propagation of structures in the electric fields and plasma density (as inferred from spacecraft floating potential measurements), as well as quantify the thicknesses of those structures. The implications of our observational results on the proper motion of arc systems in the ionosphere will be discussed.

  5. 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.

  6. 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

  7. Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Walters, Rodney R.

    1985-01-01

    Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

  8. Assembly of a Tyr122 Hydrophobic Cluster in Sarcoplasmic Reticulum Ca2+-ATPase Synchronizes Ca2+ Affinity Reduction and Release with Phosphoenzyme Isomerization.

    PubMed

    Yamasaki, Kazuo; Daiho, Takashi; Danko, Stefania; Suzuki, Hiroshi

    2015-11-13

    The mechanism whereby events in and around the catalytic site/head of Ca(2+)-ATPase effect Ca(2+) release to the lumen from the transmembrane helices remains elusive. We developed a method to determine deoccluded bound Ca(2+) by taking advantage of its rapid occlusion upon formation of E1PCa2 and of stabilization afforded by a high concentration of Ca(2+). The assay is applicable to minute amounts of Ca(2+)-ATPase expressed in COS-1 cells. It was validated by measuring the Ca(2+) binding properties of unphosphorylated Ca(2+)-ATPase. The method was then applied to the isomerization of the phosphorylated intermediate associated with the Ca(2+) release process E1PCa2 → E2PCa2 → E2P + 2Ca(2+). In the wild type, Ca(2+) release occurs concomitantly with EP isomerization fitting with rate-limiting isomerization (E1PCa2 → E2PCa2) followed by very rapid Ca(2+) release. In contrast, with alanine mutants of Leu(119) and Tyr(122) on the cytoplasmic part of the second transmembrane helix (M2) and Ile(179) on the A domain, Ca(2+) release in 10 μm Ca(2+) lags EP isomerization, indicating the presence of a transient E2P state with bound Ca(2+). The results suggest that these residues function in Ca(2+) affinity reduction in E2P, likely via a structural rearrangement at the cytoplasmic part of M2 and a resulting association with the A and P domains, therefore leading to Ca(2+) release.

  9. Misty Mountain clustering: application to fast unsupervised flow cytometry gating

    PubMed Central

    2010-01-01

    Background There are many important clustering questions in computational biology for which no satisfactory method exists. Automated clustering algorithms, when applied to large, multidimensional datasets, such as flow cytometry data, prove unsatisfactory in terms of speed, problems with local minima or cluster shape bias. Model-based approaches are restricted by the assumptions of the fitting functions. Furthermore, model based clustering requires serial clustering for all cluster numbers within a user defined interval. The final cluster number is then selected by various criteria. These supervised serial clustering methods are time consuming and frequently different criteria result in different optimal cluster numbers. Various unsupervised heuristic approaches that have been developed such as affinity propagation are too expensive to be applied to datasets on the order of 106 points that are often generated by high throughput experiments. Results To circumvent these limitations, we developed a new, unsupervised density contour clustering algorithm, called Misty Mountain, that is based on percolation theory and that efficiently analyzes large data sets. The approach can be envisioned as a progressive top-down removal of clouds covering a data histogram relief map to identify clusters by the appearance of statistically distinct peaks and ridges. This is a parallel clustering method that finds every cluster after analyzing only once the cross sections of the histogram. The overall run time for the composite steps of the algorithm increases linearly by the number of data points. The clustering of 106 data points in 2D data space takes place within about 15 seconds on a standard laptop PC. Comparison of the performance of this algorithm with other state of the art automated flow cytometry gating methods indicate that Misty Mountain provides substantial improvements in both run time and in the accuracy of cluster assignment. Conclusions Misty Mountain is fast, unbiased

  10. 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.

  11. Full text clustering and relationship network analysis of biomedical publications.

    PubMed

    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.

  12. Full text clustering and relationship network analysis of biomedical publications.

    PubMed

    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

  13. Affine projective Osserman structures

    NASA Astrophysics Data System (ADS)

    Gilkey, P.; Nikčević, S.

    2013-08-01

    By considering the projectivized spectrum of the Jacobi operator, we introduce the concept of projective Osserman manifold in both the affine and in the pseudo-Riemannian settings. If M is an affine projective Osserman manifold, then the deformed Riemannian extension metric on the cotangent bundle is both spacelike and timelike projective Osserman. Since any rank-1-symmetric space is affine projective Osserman, this provides additional information concerning the cotangent bundle of a rank-1 Riemannian symmetric space with the deformed Riemannian extension metric. We construct other examples of affine projective Osserman manifolds where the Ricci tensor is not symmetric and thus the connection in question is not the Levi-Civita connection of any metric. If the dimension is odd, we use methods of algebraic topology to show the Jacobi operator of an affine projective Osserman manifold has only one non-zero eigenvalue and that eigenvalue is real.

  14. Special Report: Affinity Chromatography.

    ERIC Educational Resources Information Center

    Parikh, Indu; Cuatrecasas, Pedro

    1985-01-01

    Describes the nature of affinity chromatography and its use in purifying enzymes, studying cell interactions, exploring hormone receptors, and other areas. The potential the technique may have in treating disease is also considered. (JN)

  15. 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.

  16. Chamber propagation

    SciTech Connect

    Langdon, B.

    1991-01-16

    Propagation of a heavy ion beam to the target appears possible under conditions thought to be realizable by several reactor designs. Beam quality at the lens is believed to provide adequate intensity at the target -- but the beam must pass through chamber debris and its self fields along the way. This paper reviews present consensus on propagation modes and presents recent results on the effects of photoionization of the beam ions by thermal x-rays from the heated target. Ballistic propagation through very low densities is a conservative mode. The more-speculative self-pinched mode, at 1 to 10 Torr, offers reactor advantages and is being re-examined by others. 13 refs.

  17. 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

  18. 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

  19. Affinity driven social networks

    NASA Astrophysics Data System (ADS)

    Ruyú, B.; Kuperman, M. N.

    2007-04-01

    In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.

  20. 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.

  1. 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.

  2. Why do receptor-ligand bonds in cell adhesion cluster into discrete focal-adhesion sites?

    NASA Astrophysics Data System (ADS)

    Gao, Zhiwen; Gao, Yanfei

    2016-10-01

    Cell adhesion often exhibits the clustering of the receptor-ligand bonds into discrete focal-adhesion sites near the contact edge, thus resembling a rosette shape or a contracting membrane anchored by a small number of peripheral forces. The ligands on the extracellular matrix are immobile, and the receptors in the cell plasma membrane consist of two types: high-affinity integrins (that bond to the substrate ligands and are immobile) and low-affinity integrins (that are mobile and not bonded to the ligands). Thus the adhesion energy density is proportional to the high-affinity integrin density. This paper provides a mechanistic explanation for the clustering/assembling of the receptor-ligand bonds from two main points: (1) the cellular contractile force leads to the density evolution of these two types of integrins, and results into a large high-affinity integrin density near the contact edge and (2) the front of a propagating crack into a decreasing toughness field will be unstable and wavy. From this fracture mechanics perspective, the chemomechanical equilibrium is reached when a small number of patches with large receptor-ligand bond density are anticipated to form at the cell periphery, as opposed to a uniform distribution of bonds on the entire interface. Cohesive fracture simulations show that the de-adhesion force can be significantly enhanced by this nonuniform bond density field, but the de-adhesion force anisotropy due to the substrate elastic anisotropy is significantly reduced.

  3. 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.

  4. Affinity chromatography: a historical perspective.

    PubMed

    Hage, David S; Matsuda, Ryan

    2015-01-01

    Affinity chromatography is one of the most selective and versatile forms of liquid chromatography for the separation or analysis of chemicals in complex mixtures. This method makes use of a biologically related agent as the stationary phase, which provides an affinity column with the ability to bind selectively and reversibly to a given target in a sample. This review examines the early work in this method and various developments that have lead to the current status of this technique. The general principles of affinity chromatography are briefly described as part of this discussion. Past and recent efforts in the generation of new binding agents, supports, and immobilization methods for this method are considered. Various applications of affinity chromatography are also summarized, as well as the influence this field has played in the creation of other affinity-based separation or analysis methods. PMID:25749941

  5. 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.

  6. Affinity enhancement of antibodies: how low-affinity antibodies produced early in immune responses are followed by high-affinity antibodies later and in memory B-cell responses.

    PubMed

    Eisen, Herman N

    2014-05-01

    The antibodies produced initially in response to most antigens are high molecular weight (MW) immunoglobulins (IgM) with low affinity for the antigen, while the antibodies produced later are lower MW classes (e.g., IgG and IgA) with, on average, orders of magnitude higher affinity for that antigen. These changes, often termed affinity maturation, take place largely in small B-cell clusters (germinal center; GC) in lymphoid tissues in which proliferating antigen-stimulated B cells express the highly mutagenic cytidine deaminase that mediates immunoglobulin class-switching and sequence diversification of the immunoglobulin variable domains of antigen-binding receptors on B cells (BCR). Of the large library of BCR-mutated B cells thus rapidly generated, a small minority with affinity-enhancing mutations are selected to survive and differentiate into long-lived antibody-secreting plasma cells and memory B cells. BCRs are also endocytic receptors; they internalize and cleave BCR-bound antigen, yielding peptide-MHC complexes that are recognized by follicular helper T cells. Imperfect correlation between BCR affinity for antigen and cognate T-cell engagement may account for the increasing affinity heterogeneity that accompanies the increasing average affinity of antibodies. Conservation of mechanisms underlying mutation and selection of high-affinity antibodies over the ≈200 million years of evolution separating bird and mammal lineages points to the crucial role of antibody affinity enhancement in adaptive immunity.

  7. 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.

  8. Cesium cation affinities and basicities

    NASA Astrophysics Data System (ADS)

    Gal, Jean-François; Maria, Pierre-Charles; Massi, Lionel; Mayeux, Charly; Burk, Peeter; Tammiku-Taul, Jaana

    2007-11-01

    This review focuses on the quantitative data related to cesium cation interaction with neutral or negatively charged ligands. The techniques used for measuring the cesium cation affinity (enthalpies, CCA), and cesium cation basicities (Gibbs free energies, CCB) are briefly described. The quantum chemical calculations methods that were specifically designed for the determination of cesium cation adduct structures and the energetic aspects of the interaction are discussed. The experimental results, obtained essentially from mass spectrometry techniques, and complemented by thermochemical data, are tabulated and commented. In particular, the correlations between cesium cation affinities and lithium cation affinities for the various kinds of ligands (rare gases, polyatomic neutral molecules, among them aromatic compounds and negative ions) serve as a basis for the interpretation of the diverse electrostatic modes of interaction. A brief account of some recent analytical applications of ion/molecule reactions with Cs+, as well as other cationization approaches by Cs+, is given.

  9. "Clickable" agarose for affinity chromatography.

    PubMed

    Punna, Sreenivas; Kaltgrad, Eiton; Finn, M G

    2005-01-01

    Successful purification of biological molecules by affinity chromatography requires the attachment of desired ligands to biocompatible chromatographic supports. The Cu(I)-catalyzed cycloaddition of azides and alkynes-the premier example of "click chemistry"-is an efficient way to make covalent connections among diverse molecules and materials. Both azide and alkyne units are highly selective in their reactivity, being inert to most chemical functionalities and stable to wide ranges of solvent, temperature, and pH. We show that agarose beads bearing alkyne and azide groups can be easily made and are practical precursors to functionalized agarose materials for affinity chromatography.

  10. Overview of affinity tags for protein purification.

    PubMed

    Kimple, Michelle E; Brill, Allison L; Pasker, Renee L

    2013-01-01

    Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein-protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. PMID:24510596

  11. Quantifying Affinity among Chinese Dialects.

    ERIC Educational Resources Information Center

    Cheng, Chin-Chuan

    A study of the relationships between Chinese dialects based on a quantitative measure of dialect affinity is summarized. First, tone values in all the dialect localities available in the early 1970s were used to calculate the dialectal differences in terms of tone height with respect to the "yin and yang" split. In the late 1970s, calculations of…

  12. 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.…

  13. Symbolic clustering

    SciTech Connect

    Reinke, R.E.

    1991-01-01

    Clustering is the problem of finding a good organization for data. Because there are many kinds of clustering problems, and because there are many possible clusterings for any data set, clustering programs use knowledge and assumptions about individual problems to make clustering tractable. Cluster-analysis techniques allow knowledge to be expressed in the choice of a pairwise distance measure and in the choice of clustering algorithm. Conceptual clustering adds knowledge and preferences about cluster descriptions. In this study the author describes symbolic clustering, which adds representation choice to the set of ways a data analyst can use problem-specific knowledge. He develops an informal model for symbolic clustering, and uses it to suggest where and how knowledge can be expressed in clustering. A language for creating symbolic clusters, based on the model, was developed and tested on three real clustering problems. The study concludes with a discussion of the implications of the model and the results for clustering in general.

  14. The universal propagator

    NASA Technical Reports Server (NTRS)

    Klauder, John R.

    1993-01-01

    For a general Hamiltonian appropriate to a single canonical degree of freedom, a universal propagator with the property that it correctly evolves the coherent-state Hilbert space representatives for an arbitrary fiducial vector is characterized and defined. The universal propagator is explicitly constructed for the harmonic oscillator, with a result that differs from the conventional propagators for this system.

  15. Automatic identification of the number of food items in a meal using clustering techniques based on the monitoring of swallowing and chewing

    PubMed Central

    Lopez-Meyer, Paulo; Schuckers, Stephanie; Makeyev, Oleksandr; Fontana, Juan M.; Sazonov, Edward

    2012-01-01

    The number of distinct foods consumed in a meal is of significant clinical concern in the study of obesity and other eating disorders. This paper proposes the use of information contained in chewing and swallowing sequences for meal segmentation by food types. Data collected from experiments of 17 volunteers were analyzed using two different clustering techniques. First, an unsupervised clustering technique, Affinity Propagation (AP), was used to automatically identify the number of segments within a meal. Second, performance of the unsupervised AP method was compared to a supervised learning approach based on Agglomerative Hierarchical Clustering (AHC). While the AP method was able to obtain 90% accuracy in predicting the number of food items, the AHC achieved an accuracy >95%. Experimental results suggest that the proposed models of automatic meal segmentation may be utilized as part of an integral application for objective Monitoring of Ingestive Behavior in free living conditions. PMID:23125872

  16. Lectin affinity chromatography of glycolipids

    SciTech Connect

    Torres, B.V.; Smith, D.F.

    1987-05-01

    Since glycolipids (GLs) are either insoluble or form mixed micelles in water, lectin affinity chromatography in aqueous systems has not been applied to their separation. They have overcome this problem by using tetrahydrofuran (THF) in the mobile phase during chromatography. Affinity columns prepared with the GalNAc-specific Helix pomatia agglutinin (HPA) and equilibrated in THF specifically bind the (/sup 3/H)oligosaccharide derived from Forssman GL indicating that the immobilized HPA retained its carbohydrate-binding specificity in this solvent. Intact Forssman GL was bound by the HPA-column equilibrated in THF and was specifically eluted with 0.1 mg/ml GalNAc in THF. Purification of the Forssman GL was achieved when a crude lipid extract of sheep erythrocyte membranes was applied to the HPA-column in THF. Non-specifically bound GLs were eluted from the column using a step gradient of aqueous buffer in THF, while the addition of GalNAc was required to elute the specifically bound GLs. Using this procedure the A-active GLs were purified from a crude lipid extract of type A human erythrocytes in a single chromatographic step. The use of solvents that maintain carbohydrate-binding specificity and lipid solubility will permit the application of affinity chromatography on immobilized carbohydrate-binding proteins to intact GLs.

  17. 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

  18. Two-parameter twisted quantum affine algebras

    NASA Astrophysics Data System (ADS)

    Jing, Naihuan; Zhang, Honglian

    2016-09-01

    We establish Drinfeld realization for the two-parameter twisted quantum affine algebras using a new method. The Hopf algebra structure for Drinfeld generators is given for both untwisted and twisted two-parameter quantum affine algebras, which include the quantum affine algebras as special cases.

  19. 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.

  20. NASA Propagation Studies Website

    NASA Technical Reports Server (NTRS)

    Angkasa, Krisjani S.

    1996-01-01

    The NASA propagation studies objective is to enable the development of new commercial satellite communication systems and services by providing timely data and models about propagation of satellite radio signals through the intervening environment and to support NASA missions. In partnership with industry and academia, the program leverages unique NASA assets (currently Advanced Communications Technology Satellite) to obtain propagation data. The findings of the study are disseminated through referred journals, NASA reference publications, workshops, electronic media, and direct interface with industry.

  1. Purification of phage display-modified bacteriophage T4 by affinity chromatography

    PubMed Central

    2011-01-01

    Background Affinity chromatography is one of the most efficient protein purification strategies. This technique comprises a one-step procedure with a purification level in the order of several thousand-fold, adaptable for various proteins, differentiated in their size, shape, charge, and other properties. The aim of this work was to verify the possibility of applying affinity chromatography in bacteriophage purification, with the perspective of therapeutic purposes. T4 is a large, icosahedral phage that may serve as an efficient display platform for foreign peptides or proteins. Here we propose a new method of T4 phage purification by affinity chromatography after its modification with affinity tags (GST and Histag) by in vivo phage display. As any permanent introduction of extraneous DNA into a phage genome is strongly unfavourable for medical purposes, integration of foreign motifs with the phage genome was not applied. The phage was propagated in bacteria expressing fusions of the phage protein Hoc with affinity tags from bacterial plasmids, independently from the phage expression system. Results Elution profiles of phages modified with the specific affinity motifs (compared to non-specific phages) document their binding to the affinity resins and effective elution with standard competitive agents. Non-specific binding was also observed, but was 102-105 times weaker than the specific one. GST-modified bacteriophages were also effectively released from glutathione Sepharose by proteolytic cleavage. The possibility of proteolytic release was designed at the stage of expression vector construction. Decrease in LPS content in phage preparations was dependent on the washing intensity; intensive washing resulted in preparations of 11-40 EU/ml. Conclusions Affinity tags can be successfully incorporated into the T4 phage capsid by the in vivo phage display technique and they strongly elevate bacteriophage affinity to a specific resin. Affinity chromatography can be

  2. Limitations in scatter propagation

    NASA Astrophysics Data System (ADS)

    Lampert, E. W.

    1982-04-01

    A short description of the main scatter propagation mechanisms is presented; troposcatter, meteor burst communication and chaff scatter. For these propagation modes, in particular for troposcatter, the important specific limitations discussed are: link budget and resulting hardware consequences, diversity, mobility, information transfer and intermodulation and intersymbol interference, frequency range and future extension in frequency range for troposcatter, and compatibility with other services (EMC).

  3. 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.

  4. NASA propagation information center

    NASA Astrophysics Data System (ADS)

    Smith, Ernest K.; Flock, Warren L.

    1990-07-01

    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.

  5. Propagation data bases

    NASA Astrophysics Data System (ADS)

    1981-12-01

    Existing data bases accumulated as the result of experiments to gather propagation data on millimeter wave Earth-space links are described. The satellites used are described and results of the significant experiments conducted in the United States are summarized. The data bases consist primarily of cumulative attenuation statistics, though some depolarization measurements are included. Additional summaries of propagation data are cited.

  6. 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.

  7. 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.

  8. Wave propagation phenomena

    NASA Astrophysics Data System (ADS)

    Groenenboom, P. H. L.

    The phenomenon of wave propagation is encountered frequently in a variety of engineering disciplines. It has been realized that for a growing number of problems the solution can only be obtained by discretization of the boundary. Advantages of the Boundary Element Method (BEM) over domain-type methods are related to the reduction of the number of space dimensions and of the modelling effort. It is demonstrated how the BEM can be applied to wave propagation phenomena by establishing the fundamental relationships. A numerical solution procedure is also suggested. In connection with a discussion of the retarded potential formulation, it is shown how the wave propagation problem can be cast into a Boundary Integral Formulation (BIF). The wave propagation problem in the BIF can be solved by time-successive evaluation of the boundary integrals. The example of pressure wave propagation following a sodium-water reaction in a Liquid Metal cooled Fast Breeder Reactor steam generator is discussed.

  9. 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.

  10. The maximal affinity of ligands

    PubMed Central

    Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A.

    1999-01-01

    We explore the question of what are the best ligands for macromolecular targets. A survey of experimental data on a large number of the strongest-binding ligands indicates that the free energy of binding increases with the number of nonhydrogen atoms with an initial slope of ≈−1.5 kcal/mol (1 cal = 4.18 J) per atom. For ligands that contain more than 15 nonhydrogen atoms, the free energy of binding increases very little with relative molecular mass. This nonlinearity is largely ascribed to nonthermodynamic factors. An analysis of the dominant interactions suggests that van der Waals interactions and hydrophobic effects provide a reasonable basis for understanding binding affinities across the entire set of ligands. Interesting outliers that bind unusually strongly on a per atom basis include metal ions, covalently attached ligands, and a few well known complexes such as biotin–avidin. PMID:10468550

  11. Engineering antibody affinity and specificity.

    PubMed

    Webster, D M; Roberts, S; Cheetham, J C; Griest, R; Rees, A R

    1988-01-01

    A combination of ab initio calculations, "knowledge-based prediction", molecular graphics and site-directed mutagenesis has enabled us to probe the molecular details of antibody:antigen recognition and binding and to alter the affinity and specificity of an antibody for its antigen. The significance of electrostatic hydrogen bonding, hydrophilic/hydrophobic patch matching and van der Waals interactions as well as CDR:CDR interactions are discussed in relation to the results of site-directed mutagenesis experiments on the anti-lysozyme antibody Gloop2. The ability to generate reconstructed antibodies, chimeric antibodies, catalytic antibodies and the use of modelled antibodies for the design of drugs is discussed. PMID:3209295

  12. Proton affinities of hydrated molecules

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes

    2016-09-01

    Proton affinities (PA) of non-hydrated, M, and hydrated forms, M(H2O)1,2,3, of 20 organic molecules including alcohols, ethers, aldehydes, ketones and amines were calculated by the B3LYP/6-311++G(d,p) method. For homogeneous families, linear correlations were observed between PAs of the M(H2O)1,2,3 and the PAs of the non-hydrated molecules. Also, the absolute values of the hydration enthalpies of the protonated molecules decreased linearly with the PAs. The correlation functions predicted that for an amine with PA < 1100 kJ/mol the PA(M(H2O)) is larger than the corresponding PA, while for an amine with PA > 1100 kJ/mol the PA(M(H2O)) is smaller than the PA.

  13. Conformal field theory on affine Lie groups

    SciTech Connect

    Clubok, K.S.

    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.

  14. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display.

    PubMed

    Hanes, J; Schaffitzel, C; Knappik, A; Plückthun, A

    2000-12-01

    Here we applied ribosome display to in vitro selection and evolution of single-chain antibody fragments (scFvs) from a large synthetic library (Human Combinatorial Antibody Library; HuCAL) against bovine insulin. In three independent ribosome display experiments different clusters of closely related scFvs were selected, all of which bound the antigen with high affinity and specificity. All selected scFvs had affinity-matured up to 40-fold compared to their HuCAL progenitors, by accumulating point mutations during the ribosome display cycles. The dissociation constants of the isolated scFvs were as low as 82 pM, which validates the design of the naïve library and the power of this evolutionary method. We have thus mimicked the process of antibody generation and affinity maturation with a synthetic library in a cell-free system in just a few days, obtaining molecules with higher affinities than most natural antibodies.

  15. Molecular editing of cellular responses by the high-affinity receptor for IgE.

    PubMed

    Suzuki, Ryo; Leach, Sarah; Liu, Wenhua; Ralston, Evelyn; Scheffel, Jörg; Zhang, Weiguo; Lowell, Clifford A; Rivera, Juan

    2014-02-28

    Cellular responses elicited by cell surface receptors differ according to stimulus strength. We investigated how the high-affinity receptor for immunoglobulin E (IgE) modulates the response of mast cells to a high- or low-affinity stimulus. Both high- and low-affinity stimuli elicited similar receptor phosphorylation; however, differences were observed in receptor cluster size, mobility, distribution, and the cells' effector responses. Low-affinity stimulation increased receptor association with the Src family kinase Fgr and shifted signals from the adapter LAT1 to the related adapter LAT2. LAT1-dependent calcium signals required for mast cell degranulation were dampened, but the role of LAT2 in chemokine production was enhanced, altering immune cell recruitment at the site of inflammation. These findings uncover how receptor discrimination of stimulus strength can be interpreted as distinct in vivo outcomes.

  16. 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.

  17. Non-affine deformations in polymer hydrogels

    PubMed Central

    Wen, Qi; Basu, Anindita; Janmey, Paul A.; Yodh, A. G.

    2012-01-01

    Most theories of soft matter elasticity assume that the local strain in a sample after deformation is identical everywhere and equal to the macroscopic strain, or equivalently that the deformation is affine. We discuss the elasticity of hydrogels of crosslinked polymers with special attention to affine and non-affine theories of elasticity. Experimental procedures to measure non-affine deformations are also described. Entropic theories, which account for gel elasticity based on stretching out individual polymer chains, predict affine deformations. In contrast, simulations of network deformation that result in bending of the stiff constituent filaments generally predict non-affine behavior. Results from experiments show significant non-affine deformation in hydrogels even when they are formed by flexible polymers for which bending would appear to be negligible compared to stretching. However, this finding is not necessarily an experimental proof of the non-affine model for elasticity. We emphasize the insights gained from experiments using confocal rheoscope and show that, in addition to filament bending, sample micro-inhomogeneity can be a significant alternative source of non-affine deformation. PMID:23002395

  18. 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)

  19. Star Clusters in the Magellanic Clouds-1: Parameterisation and Classification of 1072 Clusters in the LMC

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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 (OGLE) III survey data. This study brings out 308 newly parameterised 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 catalog with parameters, classification, and cleaned and isochrone fitted CMDs 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.

  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. Database for propagation models

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.

    1991-01-01

    A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

  2. NASA Propagation Studies Website

    NASA Technical Reports Server (NTRS)

    Angkasa, Krisjani S.

    1996-01-01

    This paper describes an Internet website which provides information to enable the development of new commerical satellite systems and services by providing timely data and models about the propagation of satellite radio signals. In partnership with industry and academia, the program leverages NASA assets, currently the Advanced Communications Technology Satellite (ACTS), to obtain propagation data. The findings of the study are disseminated through refereed journals, NASA reference publications, workshops, electronic media, and direct interface with industry.

  3. 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 ...

  4. 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.

  5. Abell Clusters

    NASA Astrophysics Data System (ADS)

    Katgert, P.; Murdin, P.

    2000-11-01

    Abell clusters are the most conspicuous groupings of galaxies identified by George Abell on the plates of the first photographic survey made with the SCHMIDT TELESCOPE at Mount Palomar in the 1950s. Sometimes, the term Abell clusters is used as a synonym of nearby, optically selected galaxy clusters....

  6. 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.

  7. DNA motif elucidation using belief propagation.

    PubMed

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM. PMID:23814189

  8. Methods for Improving Aptamer Binding Affinity.

    PubMed

    Hasegawa, Hijiri; Savory, Nasa; Abe, Koichi; Ikebukuro, Kazunori

    2016-01-01

    Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers. PMID:27043498

  9. 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.

  10. 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.

  11. Automatic crack propagation tracking

    NASA Technical Reports Server (NTRS)

    Shephard, M. S.; Weidner, T. J.; Yehia, N. A. B.; Burd, G. S.

    1985-01-01

    A finite element based approach to fully automatic crack propagation tracking is presented. The procedure presented combines fully automatic mesh generation with linear fracture mechanics techniques in a geometrically based finite element code capable of automatically tracking cracks in two-dimensional domains. The automatic mesh generator employs the modified-quadtree technique. Crack propagation increment and direction are predicted using a modified maximum dilatational strain energy density criterion employing the numerical results obtained by meshes of quadratic displacement and singular crack tip finite elements. Example problems are included to demonstrate the procedure.

  12. Cosmic axion background propagation in galaxies

    NASA Astrophysics Data System (ADS)

    Day, Francesca V.

    2016-02-01

    Many extensions of the Standard Model include axions or axion-like particles (ALPs). Here we study ALP to photon conversion in the magnetic field of the Milky Way and starburst galaxies. By modelling the effects of the coherent and random magnetic fields, the warm ionized medium and the warm neutral medium on the conversion process, we simulate maps of the conversion probability across the sky for a range of ALP energies. In particular, we consider a diffuse cosmic ALP background (CAB) analogous to the CMB, whose existence is suggested by string models of inflation. ALP-photon conversion of a CAB in the magnetic fields of galaxy clusters has been proposed as an explanation of the cluster soft X-ray excess. We therefore study the phenomenology and expected photon signal of CAB propagation in the Milky Way. We find that, for the CAB parameters required to explain the cluster soft X-ray excess, the photon flux from ALP-photon conversion in the Milky Way would be unobservably small. The ALP-photon conversion probability in galaxy clusters is 3 orders of magnitude higher than that in the Milky Way. Furthermore, the morphology of the unresolved cosmic X-ray background is incompatible with a significant component from ALP-photon conversion. We also consider ALP-photon conversion in starburst galaxies, which host much higher magnetic fields. By considering the clumpy structure of the galactic plasma, we find that conversion probabilities comparable to those in clusters may be possible in starburst galaxies.

  13. A new clustering of antibody CDR loop conformations

    PubMed Central

    North, Benjamin; Lehmann, Andreas; Dunbrack, Roland L.

    2010-01-01

    Previous analyses of the complementarity determining regions (CDRs) of antibodies have focused on a small number of “canonical” conformations for each loop. This is primarily the result of the work of Chothia and colleagues, most recently in 1997. Because of the widespread utility of antibodies, we have revisited the clustering of conformations of the six CDR loops with the much larger amount of structural information currently available. In this work, we were careful to use a high-quality data set by eliminating low-resolution structures and CDRs with high B-factors or high conformational energies. We used a distance function based on directional statistics and an effective clustering algorithm using affinity propagation. With this data set of over 300 non-redundant antibody structures, we were able to cover 28 CDR-length combinations (e.g., L1 length 11, or “L1-11” in our nomenclature) for L1, L2, L3, H1 and H2. The Chothia analysis covered only 20 CDR-lengths. Only four of these had more than one conformational cluster, of which two could easily be distinguished by gene source (mouse/human; κ/λ) and one purely by the presence and positions of Pro residues (L3-9). Thus using the Chothia analysis does not require the complicated set of “structure-determining residues” that is often assumed. Of our 28 CDR-lengths, 15 of them have multiple conformational clusters including ten for which Chothia had only one canonical class. We have a total of 72 clusters for the non-H3 CDRs; approximately 85% of the non-H3 sequences can be assigned to a conformational cluster based on gene source and/or sequence. We found that earlier predictions of “bulged” vs. “non-bulged” conformations based on the presence or absence of anchor residues Arg/Lys94 and Asp101 of H3 have not held up, since all four combinations lead to a majority of conformations that are bulged. Thus the earlier analyses have been significantly enhanced by the increased data. We believe the

  14. Affinity Proteomics in the mountains: Alpbach 2015.

    PubMed

    Taussig, Michael J

    2016-09-25

    The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167

  15. Aptamers in Affinity Separations: Stationary Separation

    NASA Astrophysics Data System (ADS)

    Ravelet, Corinne; Peyrin, Eric

    The use of DNA or RNA aptamers as tools in analytical chemistry is a very promising field of research because of their capabilities to bind specifically the target molecules with an affinity similar to that of antibodies. Notably, they appear to be of great interest as target-specific ligands for the separation and capture of various analytes in affinity chromatography and related affinity-based methods such as magnetic bead technology. In this chapter, the recent developments of these aptamer-based separation/capture approaches are addressed.

  16. 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.

  17. COBE nonspinning attitude propagation

    NASA Technical Reports Server (NTRS)

    Chu, D.

    1989-01-01

    The Cosmic Background Explorer (COBE) spacecraft will exhibit complex attitude motion consisting of a spin rate of approximately -0.8 revolution per minute (rpm) about the x-axis and simultaneous precession of the spin axis at a rate of one revolution per orbit (rpo) about the nearly perpendicular spacecraft-to-Sun vector. The effect of the combined spinning and precession is to make accurate attitude propagation difficult and the 1-degree (3 sigma) solution accuracy goal problematic. To improve this situation, an intermediate reference frame is introduced, and the angular velocity divided into two parts. The nonspinning part is that which would be observed if there were no rotation about the X-axis. The spinning part is simply the X-axis component of the angular velocity. The two are propagated independently and combined whenever the complete attitude is needed. This approach is better than the usual one-step method because each of the two angular velocities look nearly constant in their respective reference frames. Since the angular velocities are almost constant, the approximations made in discrete time propagation are more nearly true. To demonstrate the advantages of this nonspinning method, attitude is propagated as outlined above and is then compared with the results of the one-step method. Over the 100-minute COBE orbit, the one-step error grows to several degrees while the nonspinning error remains negligible.

  18. Au20: A Tetrahedral Cluster

    SciTech Connect

    Li, Jun; Li, Xi; Zhai, Hua Jin; Wang, Lai S.

    2003-02-07

    Photoelectron spectroscopy revealed that a 20 atom gold cluster has an extremely large energy gap, which is even greater than that of C60, and an electron affinity comparable with that of C60. This observation suggests that the Au20 cluster must be extremely stable and chemically inert. Using relativistic density functional calculations, we found that Au20 possesses a remarkable tetrahedral structure, which is a fragment of the bulk face-centered cubic lattice of gold with a small structural relaxation. Au20 is thus a true cluster molecule, while at the same time it is exactly part of the bulk, but with very different properties. The tetrahedral Au20 may possess interesting catalytic properties and may be synthesized in bulk quantity or assembled on non-interacting surfaces.

  19. 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...

  20. 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

  1. Protein purification using PDZ affinity chromatography.

    PubMed

    Walkup, Ward G; Kennedy, Mary B

    2015-01-01

    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. PMID:25829303

  2. Designing Chaotic Systems by Piecewise Affine Systems

    NASA Astrophysics Data System (ADS)

    Wu, Tiantian; Li, Qingdu; Yang, Xiao-Song

    Based on mathematical analysis, this paper provides a methodology to ensure the existence of homoclinic orbits in a class of three-dimensional piecewise affine systems. In addition, two chaotic generators are provided to illustrate the effectiveness of the method.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Filling the Bose sea: symmetric quantum Hall edge states and affine characters

    NASA Astrophysics Data System (ADS)

    Ardonne, Eddy; Kedem, Rinat; Stone, Michael

    2005-01-01

    We explore the structure of the bosonic analogues of the k-clustered 'parafermion' quantum Hall states. We show how the many-boson wavefunctions of k-clustered quantum Hall droplets appear naturally as matrix elements of ladder operators in integrable representations of the affine Lie algebra \\widehat{su}(2)_k . Using results of Feigin and Stoyanovsky, we count the dimensions of spaces of symmetric polynomials with given k-clustering properties and show that as the droplet size grows the partition function of its edge excitations evolves into the character of the representation. This confirms that the Hilbert space of edge states coincides with the representation space of the \\widehat{su}(2)_k edge-current algebra. We also show that a spin-singlet, two-component k-clustered boson fluid is similarly related to integrable representations of \\widehat{su}(3) . Parafermions are not necessary for these constructions.

  10. BC(50): a generalized, unifying affinity descriptor.

    PubMed

    Vacca, Alberto; Francesconi, Oscar; Roelens, Stefano

    2012-12-01

    Assessing binding affinities is an unavoidable step that we come across any time interactions between binding species are investigated. A quantitative evaluation of binding affinities relies on the determination of binding constants but, whilst the binding constant fully defines the affinity of a reagent for a ligand when only one complex species is formed, the same is not true when the interacting partners form more than one complex of different stoichiometry, because all complexes contribute to the overall binding affinity. Unfortunately, this situation is the rule rather than the exception in chemical systems, but a generally accepted solution for this issue has not yet been settled. In this Personal Account, we describe the evolution, from the initial idea to a fully developed stage, of a binding descriptor that has been developed with the aim of filling this gap, thereby providing scientists in all fields of chemistry with a unifying tool for the assessment of binding affinities based on the knowledge of the binding constants in systems that involve any number of complex species.

  11. Affinity purification of aprotinin from bovine lung.

    PubMed

    Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun

    2015-05-01

    An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462

  12. 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…

  13. 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.

  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 time,…

  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. Cluster plasma and its dispersion relation

    SciTech Connect

    Tajima, T.; Downer, M.C.; Kishimoto, Y.

    1998-02-13

    It is shown that unlike a gas plasma or an electron plasma in a metal, an ionized cluster material ({open_quotes}cluster plasma{close_quotes}) permits propagation below the plasma cut-off of electromagnetic (EM) waves whose phase velocity is close to but below the speed of light. Its unique properties allow a variety of applications, including direct acceleration of particles with its EM fields and the phase matching of waves of high harmonic generation (HHG).

  17. 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.

  18. PIV uncertainty propagation

    NASA Astrophysics Data System (ADS)

    Sciacchitano, Andrea; Wieneke, Bernhard

    2016-08-01

    This paper discusses the propagation of the instantaneous uncertainty of PIV measurements to statistical and instantaneous quantities of interest derived from the velocity field. The expression of the uncertainty of vorticity, velocity divergence, mean value and Reynolds stresses is derived. It is shown that the uncertainty of vorticity and velocity divergence requires the knowledge of the spatial correlation between the error of the x and y particle image displacement, which depends upon the measurement spatial resolution. The uncertainty of statistical quantities is often dominated by the random uncertainty due to the finite sample size and decreases with the square root of the effective number of independent samples. Monte Carlo simulations are conducted to assess the accuracy of the uncertainty propagation formulae. Furthermore, three experimental assessments are carried out. In the first experiment, a turntable is used to simulate a rigid rotation flow field. The estimated uncertainty of the vorticity is compared with the actual vorticity error root-mean-square, with differences between the two quantities within 5-10% for different interrogation window sizes and overlap factors. A turbulent jet flow is investigated in the second experimental assessment. The reference velocity, which is used to compute the reference value of the instantaneous flow properties of interest, is obtained with an auxiliary PIV system, which features a higher dynamic range than the measurement system. Finally, the uncertainty quantification of statistical quantities is assessed via PIV measurements in a cavity flow. The comparison between estimated uncertainty and actual error demonstrates the accuracy of the proposed uncertainty propagation methodology.

  19. Propagation of disturbances in degenerate quantum systems

    NASA Astrophysics Data System (ADS)

    Chancellor, Nicholas; Haas, Stephan

    2011-07-01

    Disturbances in gapless quantum many-body models are known to travel an unlimited distance throughout the system. Here, we explore this phenomenon in finite clusters with degenerate ground states. The specific model studied here is the one-dimensional J1-J2 Heisenberg Hamiltonian at and close to the Majumdar-Ghosh point. Both open and periodic boundary conditions are considered. Quenches are performed using a local magnetic field. The degenerate Majumdar-Ghosh ground state allows disturbances which carry quantum entanglement to propagate throughout the system and thus dephase the entire system within the degenerate subspace. These disturbances can also carry polarization, but not energy, as all energy is stored locally. The local evolution of the part of the system where energy is stored drives the rest of the system through long-range entanglement. We also examine approximations for the ground state of this Hamiltonian in the strong field limit and study how couplings away from the Majumdar-Ghosh point affect the propagation of disturbances. We find that even in the case of approximate degeneracy, a disturbance can be propagated throughout a finite system.

  20. Temporal scaling in information propagation.

    PubMed

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

    2014-01-01

    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. PMID:24939414

  1. 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.

  2. Affinity chromatography of bacterial lactate dehydrogenases.

    PubMed Central

    Kelly, N; Delaney, M; O'Carra, P

    1978-01-01

    The affinity system used was the immobilized oxamate derivative previously used to purify mammalian lactate dehydrogenases. The bacterial dehydrogenases specific for the L-stereoisomer of lactate behaved in the same way as the mammalian enzymes, binding strongly in the presence of NADH. The D-lactate-specific enzymes, however, did not show any biospecific affinity for this gel. The L-specific enzymes could be purified to homogeneity in one affinity-chromatographic step. The D-specific enzymes could be efficiently separated from the L-specific ones and could then be further purified on an immobilized NAD derivative. The mechanism of activation of the lactate dehydrogenase from Streptococcus faecalis by fructose 1,6-bisphosphate was investigated by using the immobilized oxamate gel. PMID:666726

  3. Affinity chromatography of bacterial lactate dehydrogenases.

    PubMed

    Kelly, N; Delaney, M; O'Carra, P

    1978-06-01

    The affinity system used was the immobilized oxamate derivative previously used to purify mammalian lactate dehydrogenases. The bacterial dehydrogenases specific for the L-stereoisomer of lactate behaved in the same way as the mammalian enzymes, binding strongly in the presence of NADH. The D-lactate-specific enzymes, however, did not show any biospecific affinity for this gel. The L-specific enzymes could be purified to homogeneity in one affinity-chromatographic step. The D-specific enzymes could be efficiently separated from the L-specific ones and could then be further purified on an immobilized NAD derivative. The mechanism of activation of the lactate dehydrogenase from Streptococcus faecalis by fructose 1,6-bisphosphate was investigated by using the immobilized oxamate gel. PMID:666726

  4. 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.

  5. European and international collaboration in affinity proteomics.

    PubMed

    Stoevesandt, Oda; Taussig, Michael J

    2012-06-15

    In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New

  6. Displacement phenomena in lectin affinity chromatography.

    PubMed

    Cho, Wonryeon

    2015-10-01

    The work described here examines displacement phenomena that play a role in lectin affinity chromatography and their potential to impact reproducibility. This was achieved using Lycopersicon esculentum lectin (LEL), a lectin widely used in monitoring cancer. Four small identical LEL columns were coupled in series to form a single affinity chromatography system with the last in the series connected to an absorbance detector. The serial affinity column set (SACS) was then loaded with human plasma proteins. At the completion of loading, the column set was disassembled, the four columns were eluted individually, the captured proteins were trypsin digested, the peptides were deglycosylated with PNGase F, and the parent proteins were identified through mass spectral analyses. Significantly different sets of glycoproteins were selected by each column, some proteins appearing to be exclusively bound to the first column while others were bound further along in the series. Clearly, sample displacement chromatography (SDC) occurs. Glycoproteins were bound at different places in the column train, identifying the presence of glycoforms with different affinity on a single glycoprotein. It is not possible to see these phenomena in the single column mode of chromatography. Moreover, low abundance proteins were enriched, which facilitates detection. The great advantage of this method is that it differentiates between glycoproteins on the basis of their binding affinity. Displacement phenomena are concluded to be a significant component of the separation mechanism in heavily loaded lectin affinity chromatography columns. This further suggests that care must be exercised in sample loading of lectin columns to prevent analyte displacement with nonretained proteins. PMID:26348026

  7. The dynamics of metric-affine gravity

    SciTech Connect

    Vitagliano, Vincenzo; Sotiriou, Thomas P.; Liberati, Stefano

    2011-05-15

    Highlights: > The role and the dynamics of the connection in metric-affine theories is explored. > The most general second order action does not lead to a dynamical connection. > Including higher order invariants excites new degrees of freedom in the connection. > f(R) actions are also discussed and shown to be a non- representative class. - Abstract: Metric-affine theories of gravity provide an interesting alternative to general relativity: in such an approach, the metric and the affine (not necessarily symmetric) connection are independent quantities. Furthermore, the action should include covariant derivatives of the matter fields, with the covariant derivative naturally defined using the independent connection. As a result, in metric-affine theories a direct coupling involving matter and connection is also present. The role and the dynamics of the connection in such theories is explored. We employ power counting in order to construct the action and search for the minimal requirements it should satisfy for the connection to be dynamical. We find that for the most general action containing lower order invariants of the curvature and the torsion the independent connection does not carry any dynamics. It actually reduces to the role of an auxiliary field and can be completely eliminated algebraically in favour of the metric and the matter field, introducing extra interactions with respect to general relativity. However, we also show that including higher order terms in the action radically changes this picture and excites new degrees of freedom in the connection, making it (or parts of it) dynamical. Constructing actions that constitute exceptions to this rule requires significant fine tuned and/or extra a priori constraints on the connection. We also consider f(R) actions as a particular example in order to show that they constitute a distinct class of metric-affine theories with special properties, and as such they cannot be used as representative toy theories to

  8. Affine Invariant Character Recognition by Progressive Removing

    NASA Astrophysics Data System (ADS)

    Iwamura, Masakazu; Horimatsu, Akira; Niwa, Ryo; Kise, Koichi; Uchida, Seiichi; Omachi, Shinichiro

    Recognizing characters in scene images suffering from perspective distortion is a challenge. Although there are some methods to overcome this difficulty, they are time-consuming. In this paper, we propose a set of affine invariant features and a new recognition scheme called “progressive removing” that can help reduce the processing time. Progressive removing gradually removes less feasible categories and skew angles by using multiple classifiers. We observed that progressive removing and the use of the affine invariant features reduced the processing time by about 60% in comparison to a trivial one without decreasing the recognition rate.

  9. 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.

  10. Adsorption affinity of anions on metal oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Pechenyuk, S. I.; Semushina, Yu. P.; Kuz'mich, L. F.

    2013-03-01

    The dependences of anion (phosphate, carbonate, sulfate, chromate, oxalate, tartrate, and citrate) adsorption affinity anions from geometric characteristics, acid-base properties, and complex forming ability are generalized. It is shown that adsorption depends on the nature of both the anions and the ionic medium and adsorbent. It is established that anions are generally grouped into the following series of adsorption affinity reduction: PO{4/3-}, CO{3/2-} > C2O{4/2-}, C(OH)(CH2)2(COO){3/3-}, (CHOH)2(COO){2/2-} > CrO{4/2-} ≫ SO{4/2-}.

  11. 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.

  12. Collective thermoregulation in bee clusters.

    PubMed

    Ocko, Samuel A; Mahadevan, L

    2014-02-01

    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. PMID:24335563

  13. Collective thermoregulation in bee clusters.

    PubMed

    Ocko, Samuel A; Mahadevan, L

    2014-02-01

    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. Electrodynamic properties of fractal clusters

    NASA Astrophysics Data System (ADS)

    Maksimenko, V. V.; Zagaynov, V. A.; Agranovski, I. E.

    2014-07-01

    An influence of interference on a character of light interaction both with individual fractal cluster (FC) consisting of nanoparticles and with agglomerates of such clusters is investigated. Using methods of the multiple scattering theory, effective dielectric permeability of a micron-size FC composed of non-absorbing nanoparticles is calculated. The cluster could be characterized by a set of effective dielectric permeabilities. Their number coincides with the number of particles, where space arrangement in the cluster is correlated. If the fractal dimension is less than some critical value and frequency corresponds to the frequency of the visible spectrum, then the absolute value of effective dielectric permeability becomes very large. This results in strong renormalization (decrease) of the incident radiation wavelength inside the cluster. The renormalized photons are cycled or trapped inside the system of multi-scaled cavities inside the cluster. A lifetime of a photon localized inside an agglomerate of FCs is a macroscopic value allowing to observe the stimulated emission of the localized light. The latter opens up a possibility for creation of lasers without inverse population of energy levels. Moreover, this allows to reconsider problems of optical cloaking of macroscopic objects. One more feature of fractal structures is a possibility of unimpeded propagation of light when any resistance associated with scattering disappears.

  15. Collective thermoregulation in bee clusters

    PubMed Central

    Ocko, Samuel A.; Mahadevan, L.

    2014-01-01

    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. PMID:24335563

  16. Shaping propagation invariant laser beams

    NASA Astrophysics Data System (ADS)

    Soskind, Michael; Soskind, Rose; Soskind, Yakov

    2015-11-01

    Propagation-invariant structured laser beams possess several unique properties and play an important role in various photonics applications. The majority of propagation invariant beams are produced in the form of laser modes emanating from stable laser cavities. Therefore, their spatial structure is limited by the intracavity mode formation. We show that several types of anamorphic optical systems (AOSs) can be effectively employed to shape laser beams into a variety of propagation invariant structured fields with different shapes and phase distributions. We present a propagation matrix approach for designing AOSs and defining mode-matching conditions required for preserving propagation invariance of the output shaped fields. The propagation matrix approach was selected, as it provides a more straightforward approach in designing AOSs for shaping propagation-invariant laser beams than the alternative technique based on the Gouy phase evolution, especially in the case of multielement AOSs. Several practical configurations of optical systems that are suitable for shaping input laser beams into a diverse variety of structured propagation invariant laser beams are also presented. The laser beam shaping approach was applied by modeling propagation characteristics of several input laser beam types, including Hermite-Gaussian, Laguerre-Gaussian, and Ince-Gaussian structured field distributions. The influence of the Ince-Gaussian beam semifocal separation parameter and the azimuthal orientation between the input laser beams and the AOSs onto the resulting shape of the propagation invariant laser beams is presented as well.

  17. An analysis of rumor propagation based on propagation force

    NASA Astrophysics Data System (ADS)

    Zhao, Zhen-jun; Liu, Yong-mei; Wang, Ke-xi

    2016-02-01

    A propagation force is introduced into the analysis of rumor propagation to address uncertainty in the process. The propagation force is portrayed as a fuzzy variable, and a category of new parameters with fuzzy variables is defined. The classic susceptible, infected, recovered (SIR) model is modified using these parameters, a fuzzy reproductive number is introduced into the modified model, and the rationality of the fuzzy reproductive number is illuminated through calculation and comparison. Rumor control strategies are also discussed.

  18. Manganese-induced integrin affinity maturation promotes recruitment of alpha V beta 3 integrin to focal adhesions in endothelial cells: evidence for a role of phosphatidylinositol 3-kinase and Src.

    PubMed

    Dormond, Olivier; Ponsonnet, Lionel; Hasmim, Meriem; Foletti, Alessandro; Rüegg, Curzio

    2004-07-01

    Integrin activity is controlled by changes in affinity (i.e. ligand binding) and avidity (i.e. receptor clustering). Little is known, however, about the effect of affinity maturation on integrin avidity and on the associated signaling pathways. To study the effect of affinity maturation on integrin avidity, we stimulated human umbilical vein endothelial cells (HUVEC) with MnCl(2) to increase integrin affinity and monitored clustering of beta 1 and beta 3 integrins. In unstimulated HUVEC, beta 1 integrins were present in fibrillar adhesions, while alpha V beta 3 was detected in peripheral focal adhesions. Clustered beta 1 and beta 3 integrins expressed high affinity/ligand-induced binding site (LIBS) epitopes. MnCl(2)-stimulation promoted focal adhesion and actin stress fiber formation at the basal surface of the cells, and strongly enhanced mAb LM609 staining and expression of beta 3 high affinity/LIBS epitopes at focal adhesions. MnCl(2)-induced alpha V beta 3 clustering was blocked by a soluble RGD peptide, by wortmannin and LY294002, two pharmacological inhibitors of phosphatidylinositol 3-kinase (PI 3-K), and by over-expressing a dominant negative PI 3-K mutant protein. Conversely, over-expression of active PI 3-K and pharmacological inhibiton of Src with PP2 and CGP77675, enhanced basal and manganese-induced alpha V beta 3 clustering. Transient increased phosphorylation of protein kinase B/Akt, a direct target of PI 3K, occurred upon manganese stimulation. MnCl(2) did not alter beta 1 integrin distribution or beta1 high-affinity/LIBS epitope expression. Based on these results, we conclude that MnCl(2)-induced alpha V beta 3 integrin affinity maturation stimulates focal adhesion and actin stress fiber formation, and promotes recruitment of high affinity alpha V beta 3 to focal adhesions. Affinity-modulated alpha V beta 3 clustering requires PI3-K signaling and is negatively regulate by Src.

  19. 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.

  20. 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…

  1. Two bradykinin binding sites with picomolar affinities

    SciTech Connect

    Manning, D.C.; Vavrek, R.; Stewart, J.M.; Snyder, S.H.

    1986-05-01

    Bradykinin (BK) and related peptides exert a wide range of effects on several organ systems. We have attempted to sort out these effects by studying the binding interaction of (/sup 3/H)BK at the membrane level with in vitro receptor binding techniques. High specific activity (/sup 3/H)BK and an enzyme inhibitor cocktail has enabled us to label two BK binding sites with different affinity and peptide specificity in several guinea-pig tissues. In the guinea-pig ileum the high-affinity site has an equilibrium dissociation constant (Kd) for (/sup 3/H)BK of 13 pM and a maximal number of binding sites of 8.3 pmol/g of tissue wet weight. The low-affinity guinea-pig ileum site displays a Kd of 910 pM, a maximum number of binding sites of 14 pmol/g of tissue wet weight and shows a greater selectivity for BK analogs over Lysyl-BK analogs. Two similar sites can also be discriminated in kidney and heart. The potencies of a series of BK analogs at the high-affinity guinea-pig ileum site correlate well with their potencies in contracting ileal smooth muscle. The binding of (/sup 3/H)BK in the guinea-pig ileum is inhibited by physiological concentrations of monovalent and divalent cations.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. The ACTS propagation program

    NASA Technical Reports Server (NTRS)

    Chakraborty, Dayamoy; Davarian, Faramaz

    1991-01-01

    The purpose of the Advanced Communications Technology Satellite (ACTS) is to demonstrate the feasibility of the Ka-band (20 and 30 GHz) spectrum for satellite communications, as well as to help maintain U.S. leadership in satellite communications. ACTS incorporates such innovative schemes as time division multiple access (TDMA), microwave and baseband switching, onboard regeneration, and adaptive application of coding during rain-fade conditions. The success or failure of the ACTS experiment will depend on how accurately the rain-fade statistics and fade dynamics can be predicted in order to derive an appropriate algorithm that will combat weather vagaries, specifically for links with small terminals, such as very small aperture terminals (VSAT's) where the power margin is a premium. This article describes the planning process and hardware development program that will comply with the recommendations of the ACTS propagation study groups.

  7. Testing for clonal propagation.

    PubMed

    Gregorius, H-R

    2005-02-01

    The conceptual basis for testing clonal propagation is reconsidered with the result that two steps need to be distinguished clearly: (1) specification of the characteristics of multilocus genotype frequencies that result from sexual reproduction together with the kinds of deviations from these characteristics that are produced by clonal propagation, and (2) a statistical method for detecting these deviations in random samples. It is pointed out that a meaningful characterization of sexual reproduction reflects the association of genes in (multilocus) genotypes within the bounds set by the underlying gene frequencies. An appropriate measure of relative gene association is developed which is equivalent to a multilocus generalization of the standardized gametic disequilibrium (linkage disequilibrium). Its application to the characterization of sexually produced multilocus genotypes is demonstrated. The resulting hypothesis on the frequency of a sexually produced genotype is tested with the help of the (significance) probability of obtaining at least two copies of the genotype in question in a random sample of a given size. If at least two copies of the genotype are observed in a sample, and if the probability is significant, then the hypothesis of sexual reproduction is rejected in favor of the assumption that all copies of the genotype belong to the same clone. Common testing approaches rest on the hypothesis of completely independent association of genes in genotypes and on the (significance) probability of obtaining at least as many copies of a genotype as observed in a sample. The validity of these approaches is discussed in relation to the above considerations and recommendations are set out for conducting appropriate tests.

  8. Propagation effects at millimeter wavelengths

    NASA Astrophysics Data System (ADS)

    Crane, R. K.

    The lower atmosphere can affect millimeter wave communication system performance by producing large variations in signal level. Several different propagation phenomena are responsible absorption by oxygen and water vapor, scattering by turbulent fluctuations in the index of refraction, and attenuation by clouds, fog, or rain. Models are available for the calculation of propagation effects on a path when the meteorological conditions are known. This paper reviews the available propagation models for the prediction of link reliability.

  9. 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.

  10. Biological cluster evaluation for gene function prediction.

    PubMed

    Klie, Sebastian; Nikoloski, Zoran; Selbig, Joachim

    2014-06-01

    Recent advances in high-throughput omics techniques render it possible to decode the function of genes by using the "guilt-by-association" principle on biologically meaningful clusters of gene expression data. However, the existing frameworks for biological evaluation of gene clusters are hindered by two bottleneck issues: (1) the choice for the number of clusters, and (2) the external measures which do not take in consideration the structure of the analyzed data and the ontology of the existing biological knowledge. Here, we address the identified bottlenecks by developing a novel framework that allows not only for biological evaluation of gene expression clusters based on existing structured knowledge, but also for prediction of putative gene functions. The proposed framework facilitates propagation of statistical significance at each of the following steps: (1) estimating the number of clusters, (2) evaluating the clusters in terms of novel external structural measures, (3) selecting an optimal clustering algorithm, and (4) predicting gene functions. The framework also includes a method for evaluation of gene clusters based on the structure of the employed ontology. Moreover, our method for obtaining a probabilistic range for the number of clusters is demonstrated valid on synthetic data and available gene expression profiles from Saccharomyces cerevisiae. Finally, we propose a network-based approach for gene function prediction which relies on the clustering of optimal score and the employed ontology. Our approach effectively predicts gene function on the Saccharomyces cerevisiae data set and is also employed to obtain putative gene functions for an Arabidopsis thaliana data set.

  11. Affinity purification of metalloprotease from marine bacterium using immobilized metal affinity chromatography.

    PubMed

    Li, Shangyong; Wang, Linna; Yang, Juan; Bao, Jing; Liu, Junzhong; Lin, Shengxiang; Hao, Jianhua; Sun, Mi

    2016-06-01

    In this study, an efficient affinity purification protocol for an alkaline metalloprotease from marine bacterium was developed using immobilized metal affinity chromatography. After screening and optimization of the affinity ligands and spacer arm lengths, Cu-iminmodiacetic acid was chosen as the optimal affinity ligand, which was coupled to Sepharose 6B via a 14-atom spacer arm. The absorption analysis of this medium revealed a desorption constant Kd of 21.5 μg/mL and a theoretical maximum absorption Qmax of 24.9 mg/g. Thanks to this affinity medium, the enzyme could be purified by only one affinity purification step with a purity of approximately 95% pure when analyzed by high-performance liquid chromatography and reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis. The recovery of the protease activity reached 74.6%, which is much higher than the value obtained by traditional protocols (8.9%). These results contribute to the industrial purifications and contribute a significant reference for the purification of other metalloproteases. PMID:27058973

  12. 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.

  13. Smooth big bounce from affine quantization

    NASA Astrophysics Data System (ADS)

    Bergeron, Hervé; Dapor, Andrea; Gazeau, Jean Pierre; Małkiewicz, Przemysław

    2014-04-01

    We examine the possibility of dealing with gravitational singularities on a quantum level through the use of coherent state or wavelet quantization instead of canonical quantization. We consider the Robertson-Walker metric coupled to a perfect fluid. It is the simplest model of a gravitational collapse, and the results obtained here may serve as a useful starting point for more complex investigations in the future. We follow a quantization procedure based on affine coherent states or wavelets built from the unitary irreducible representation of the affine group of the real line with positive dilation. The main issue of our approach is the appearance of a quantum centrifugal potential allowing for regularization of the singularity, essential self-adjointness of the Hamiltonian, and unambiguous quantum dynamical evolution.

  14. 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.

  15. Artificial Affinity Proteins as Ligands of Immunoglobulins

    PubMed Central

    Mouratou, Barbara; Béhar, Ghislaine; Pecorari, Frédéric

    2015-01-01

    A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized. PMID:25647098

  16. Permeability of self-affine rough fractures

    PubMed

    Drazer; Koplik

    2000-12-01

    The permeability of two-dimensional fractures with self-affine fractal roughness is studied via analytic arguments and numerical simulations. The limit where the roughness amplitude is small compared with average fracture aperture is analyzed by a perturbation method, while in the opposite case of narrow aperture, we use heuristic arguments based on lubrication theory. Numerical simulations, using the lattice Boltzmann method, are used to examine the complete range of aperture sizes, and confirm the analytic arguments. PMID:11138092

  17. 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.

  18. Seismic wave propagation modeling

    SciTech Connect

    Jones, E.M.; Olsen, K.B.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). A hybrid, finite-difference technique was developed for modeling nonlinear soil amplification from three-dimensional, finite-fault radiation patters for earthquakes in arbitrary earth models. The method was applied to the 17 January 1994 Northridge earthquake. Particle velocities were computed on a plane at 5-km depth, immediately above the causative fault. Time-series of the strike-perpendicular, lateral velocities then were propagated vertically in a soil column typical of the San Fernando Valley. Suitable material models were adapted from a suite used to model ground motions at the US Nevada Test Site. The effects of nonlinearity reduced relative spectral amplitudes by about 40% at frequencies above 1.5 Hz but only by 10% at lower frequencies. Runs made with source-depth amplitudes increased by a factor of two showed relative amplitudes above 1.5 Hz reduced by a total of 70% above 1.5 Hz and 20% at lower frequencies. Runs made with elastic-plastic material models showed similar behavior to runs made with Masing-Rule models.

  19. Overview of affinity biosensors in food analysis.

    PubMed

    Patel, Pradip D

    2006-01-01

    The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field.

  20. Overview of affinity biosensors in food analysis.

    PubMed

    Patel, Pradip D

    2006-01-01

    The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field. PMID:16792079

  1. A MEMS Dielectric Affinity Glucose Biosensor

    PubMed Central

    Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao

    2013-01-01

    Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215

  2. 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. PMID:26584922

  3. Trematode hemoglobins show exceptionally high oxygen affinity.

    PubMed

    Kiger, L; Rashid, A K; Griffon, N; Haque, M; Moens, L; Gibson, Q H; Poyart, C; Marden, M C

    1998-08-01

    Ligand binding studies were made with hemoglobin (Hb) isolated from trematode species Gastrothylax crumenifer (Gc), Paramphistomum epiclitum (Pe), Explanatum explanatum (Ee), parasitic worms of water buffalo Bubalus bubalis, and Isoparorchis hypselobagri (Ih) parasitic in the catfish Wallago attu. The kinetics of oxygen and carbon monoxide binding show very fast association rates. Whereas oxygen can be displaced on a millisecond time scale from human Hb at 25 degrees C, the dissociation of oxygen from trematode Hb may require a few seconds to over 20 s (for Hb Pe). Carbon monoxide dissociation is faster, however, than for other monomeric hemoglobins or myoglobins. Trematode hemoglobins also show a reduced rate of autoxidation; the oxy form is not readily oxidized by potassium ferricyanide, indicating that only the deoxy form reacts rapidly with this oxidizing agent. Unlike most vertebrate Hbs, the trematodes have a tyrosine residue at position E7 instead of the usual distal histidine. As for Hb Ascaris, which also displays a high oxygen affinity, the trematodes have a tyrosine in position B10; two H-bonds to the oxygen molecule are thought to be responsible for the very high oxygen affinity. The trematode hemoglobins display a combination of high association rates and very low dissociation rates, resulting in some of the highest oxygen affinities ever observed.

  4. Migration of adhesive glioma cells: Front propagation and fingering

    NASA Astrophysics Data System (ADS)

    Khain, Evgeniy; Katakowski, Mark; Charteris, Nicholas; Jiang, Feng; Chopp, Michael

    2012-07-01

    We investigate the migration of glioma cells as a front propagation phenomenon both theoretically (by using both discrete lattice modeling and a continuum approach) and experimentally. For small effective strength of cell-cell adhesion q, the front velocity does not depend on q. When q exceeds a critical threshold, a fingeringlike front propagation is observed due to cluster formation in the invasive zone. We show that the experiments correspond to the transient regime, before the regime of front propagation is established. We performed an additional experiment on cell migration. A detailed comparison with experimental observations showed that the theory correctly predicts the maximal migration distance but underestimates the migration of the main mass of cells.

  5. Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets

    PubMed Central

    Hazelett, Dennis J.; Lakeland, Daniel L.; Weiss, Joseph B.

    2009-01-01

    Methods: A new method was developed for identifying novel transcription factor regulatory targets based on calculating Local Affinity Density. Techniques from the signal-processing field were used, in particular the Hann digital filter, to calculate the relative binding affinity of different regions based on previously published in vitro binding data. To illustrate this approach, the complete genomes of Drosophila melanogaster and D.pseudoobscura were analyzed for binding sites of the homeodomain proteinc Tinman, an essential heart development gene in both Drosophila and Mouse. The significant binding regions were identified relative to genomic background and assigned to putative target genes. Valid candidates common to both species of Drosophila were selected as a test of conservation. Results: The new method was more sensitive than cluster searches for conserved binding motifs with respect to positive identification of known Tinman targets. Our Local Affinity Density method also identified a significantly greater proportion of Tinman-coexpressed genes than equivalent, optimized cluster searching. In addition, this new method predicted a significantly greater than expected number of genes with previously published RNAi phenotypes in the heart. Availability: Algorithms were implemented in Python, LISP, R and maxima, using MySQL to access locally mirrored sequence data from Ensembl (D.melanogaster release 4.3) and flybase (D.pseudoobscura). All code is licensed under GPL and freely available at http://www.ohsu.edu/cellbio/dev_biol_prog/affinitydensity/. Contact: hazelett@ohsu.edu PMID:19401399

  6. Effective propagation in a perturbed periodic structure

    NASA Astrophysics Data System (ADS)

    Maurel, Agnès; Pagneux, Vincent

    2008-08-01

    In a recent paper [D. Torrent, A. Hakansson, F. Cervera, and J. Sánchez-Dehesa, Phys. Rev. Lett. 96, 204302 (2006)] inspected the effective parameters of a cluster containing an ensemble of scatterers with a periodic or a weakly disordered arrangement. A small amount of disorder is shown to have a small influence on the characteristics of the acoustic wave propagation with respect to the periodic case. In this Brief Report, we inspect further the effect of a deviation in the scatterer distribution from the periodic distribution. The quasicrystalline approximation is shown to be an efficient tool to quantify this effect. An analytical formula for the effective wave number is obtained in one-dimensional acoustic medium and is compared with the Berryman result in the low-frequency limit. Direct numerical calculations show a good agreement with the analytical predictions.

  7. Effective propagation in a perturbed periodic structure

    SciTech Connect

    Maurel, Agnes; Pagneux, Vincent

    2008-08-01

    In a recent paper [D. Torrent, A. Hakansson, F. Cervera, and J. Sanchez-Dehesa, Phys. Rev. Lett. 96, 204302 (2006)] inspected the effective parameters of a cluster containing an ensemble of scatterers with a periodic or a weakly disordered arrangement. A small amount of disorder is shown to have a small influence on the characteristics of the acoustic wave propagation with respect to the periodic case. In this Brief Report, we inspect further the effect of a deviation in the scatterer distribution from the periodic distribution. The quasicrystalline approximation is shown to be an efficient tool to quantify this effect. An analytical formula for the effective wave number is obtained in one-dimensional acoustic medium and is compared with the Berryman result in the low-frequency limit. Direct numerical calculations show a good agreement with the analytical predictions.

  8. 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

  9. Light propagation and large-scale inhomogeneities

    SciTech Connect

    Brouzakis, Nikolaos; Tetradis, Nikolaos; Tzavara, Eleftheria E-mail: ntetrad@phys.uoa.gr

    2008-04-15

    We consider the effect on the propagation of light of inhomogeneities with sizes of order 10 Mpc or larger. The Universe is approximated through a variation of the Swiss-cheese model. The spherical inhomogeneities are void-like, with central underdensities surrounded by compensating overdense shells. We study the propagation of light in this background, assuming that the source and the observer occupy random positions, so that each beam travels through several inhomogeneities at random angles. The distribution of luminosity distances for sources with the same redshift is asymmetric, with a peak at a value larger than the average one. The width of the distribution and the location of the maximum increase with increasing redshift and length scale of the inhomogeneities. We compute the induced dispersion and bias of cosmological parameters derived from the supernova data. They are too small to explain the perceived acceleration without dark energy, even when the length scale of the inhomogeneities is comparable to the horizon distance. Moreover, the dispersion and bias induced by gravitational lensing at the scales of galaxies or clusters of galaxies are larger by at least an order of magnitude.

  10. 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.

  11. VLF Waveguide Propagation: The Basics

    NASA Astrophysics Data System (ADS)

    Lynn, Kenneth J. W.

    2010-10-01

    In recent times, research has moved towards using VLF radio transmissions propagating in the earth-ionosphere waveguide as a detector of a variety of transient geophysical phenomena. A correct interpretation of such results depends critically on understanding the propagation characteristics of the path being monitored. The observed effects will vary depending on time of day, path length, path orientation, magnetic latitude and VLF frequency. This paper provides a brief tutorial of the relevant propagation dependencies for medium to long VLF paths best understood in terms of waveguide mode theory together with results either not previously published, not published in the open scientific literature or whose significance has been little recognised.

  12. The RADLAC beam propagation experiment

    SciTech Connect

    Frost, C.A.; Shope, S.L.; Mazarakis, M.G.; Poukey, J.W.; Wagner, J.S.; Turman, B.N.; Crist, C.E. ); Welch, D.R.; Struve, K.W. )

    1992-01-01

    The most recent RADLAC experiments studied propagation and hose stability of a high current beam propagating in the atmosphere, and confirmed the convective nature of the hose instability. The unique combination of high beam current and extremely small initial perturbation, allowed saturation of the hose instability to be observed for the first time. Data on high current propagation was needed because the current scaling is more complex than energy scaling. It was important to collect data at atmospheric pressure to insure that subtle air chemistry effects such as avalanche did not distort the experiment. With this philosophy, the results should be directly scaleable to applications at higher energy.

  13. The RADLAC beam propagation experiment

    SciTech Connect

    Frost, C.A.; Shope, S.L.; Mazarakis, M.G.; Poukey, J.W.; Wagner, J.S.; Turman, B.N.; Crist, C.E.; Welch, D.R.; Struve, K.W.

    1992-06-01

    The most recent RADLAC experiments studied propagation and hose stability of a high current beam propagating in the atmosphere, and confirmed the convective nature of the hose instability. The unique combination of high beam current and extremely small initial perturbation, allowed saturation of the hose instability to be observed for the first time. Data on high current propagation was needed because the current scaling is more complex than energy scaling. It was important to collect data at atmospheric pressure to insure that subtle air chemistry effects such as avalanche did not distort the experiment. With this philosophy, the results should be directly scaleable to applications at higher energy.

  14. Cluster headache

    PubMed Central

    2010-01-01

    Introduction The revised International Headache Society (IHS) criteria for cluster headache are: attacks of severe or very severe, strictly unilateral pain, which is orbital, supraorbital, or temporal pain, lasting 15 to 180 minutes and occurring from once every other day to eight times daily. Methods and outcomes We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of interventions to abort cluster headache? What are the effects of interventions to prevent cluster headache? We searched: Medline, Embase, The Cochrane Library, and other important databases up to June 2009 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations, such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). Results We found 23 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. Conclusions In this systematic review, we present information relating to the effectiveness and safety of the following interventions: baclofen (oral); botulinum toxin (intramuscular); capsaicin (intranasal); chlorpromazine; civamide (intranasal); clonidine (transdermal); corticosteroids; ergotamine and dihydroergotamine (oral or intranasal); gabapentin (oral); greater occipital nerve injections (betamethasone plus xylocaine); high-dose and high-flow-rate oxygen; hyperbaric oxygen; leuprolide; lidocaine (intranasal); lithium (oral); melatonin; methysergide (oral); octreotide (subcutaneous); pizotifen (oral); sodium valproate (oral); sumatriptan (oral, subcutaneous, and intranasal); topiramate (oral); tricyclic antidepressants (TCAs); verapamil; and zolmitriptan (oral and intranasal). PMID:21718584

  15. 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.

  16. 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.

  17. Measuring an antibody affinity distribution molecule by molecule.

    PubMed

    Temirov, Jamshid P; Bradbury, Andrew R M; Werner, James H

    2008-11-15

    Single molecule fluorescence microscopy was used to observe the binding and unbinding of hapten decorated quantum dots to individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  18. Measuring an antibody affinity distribution molecule by molecule

    SciTech Connect

    Bradbury, Andrew M; Werner, James H; Temirov, Jamshid

    2008-01-01

    Single molecule fluorescence mIcroscopy was used to observe the binding and unbinding of hapten decorated quantum dots with individual surface immobilized antibodies. The fluorescence time history from an individual antibody site can be used to calculate its binding affinity. While quantum dot blinking occurs during these measurements, we describe a simple empirical method to correct the apparent/observed affinity to account for the blinking contribution. The combination of many single molecule affinity measurements from different antibodies yields not only the average affinity, it directly measures the full shape and character of the surface affinity distribution function.

  19. Metal-affinity separations: A new dimension in protein processing

    SciTech Connect

    Arnold, F.H. )

    1991-02-01

    Rapid growth in the preparative and high-resolution analytical applications of metal-affinity chromatography demonstrate the appeal of metal recognition as a basis for protein separations. Stable, inexpensive chelated metals effectively mimic biospecific interactions, providing selective ligands for protein binding. This article reviews recent progress in understanding the mechanisms of metal-protein recognition that underlie metal-affinity separations. Also discussed are schemes for integrating metal-affinity purifications into the expression and bioprocessing of recombinant proteins. Promising future developments include new metal-affinity processes for analytical and preparative-scale separations and a range of techniques for enhancing the selectivity of metal-affinity separations.

  20. Avoiding degenerate coframes in an affine gauge approach to quantum gravity

    SciTech Connect

    Mielke, E.W.; McCrea, J.D.; Ne`eman, Y.; Hehl, F.W.

    1993-04-01

    This report discusses the following concepts on quantum gravity: The affine gauge approach; affine gauge transformations versus active differomorphisms; affine gauge approach to quantum gravity with topology change.

  1. The NASA radiowave propagation program

    NASA Technical Reports Server (NTRS)

    Davarian, Faramaz

    1990-01-01

    The objectives of the NASA radiowave Propagation Program are to enable new satellite communication applications and to enhance existing satellite communication networks. These objectives are achieved by supporting radio wave propagation studies and disseminating the study results in a timely fashion. Studies initiated by this program in the 1980s enabled the infant concept of conducting mobile communications via satellite to reach a state of relative maturity in 1990. The program also supported the satellite communications community by publishing and revising two handbooks dealing with radio wave propagation effects for frequencies below and above 10 GHz, respectively. The program has served the international community through its support of the International Telecommunications Union. It supports state of the art work at universities. Currently, the program is focusing on the Advanced Communications Technology Satellite (ACTS) and its propagation needs. An overview of the program's involvement in the ACTS project is given.

  2. 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.

  3. The NASA radiowave propagation program

    NASA Astrophysics Data System (ADS)

    Davarian, Faramaz

    The objectives of the NASA radiowave Propagation Program are to enable new satellite communication applications and to enhance existing satellite communication networks. These objectives are achieved by supporting radio wave propagation studies and disseminating the study results in a timely fashion. Studies initiated by this program in the 1980s enabled the infant concept of conducting mobile communications via satellite to reach a state of relative maturity in 1990. The program also supported the satellite communications community by publishing and revising two handbooks dealing with radio wave propagation effects for frequencies below and above 10 GHz, respectively. The program has served the international community through its support of the International Telecommunications Union. It supports state of the art work at universities. Currently, the program is focusing on the Advanced Communications Technology Satellite (ACTS) and its propagation needs. An overview of the program's involvement in the ACTS project is given.

  4. Automated multi-subject fiber clustering of mouse brain using dominant sets.

    PubMed

    Dodero, Luca; Vascon, Sebastiano; Murino, Vittorio; Bifone, Angelo; Gozzi, Alessandro; Sona, Diego

    2014-01-01

    Mapping of structural and functional connectivity may provide deeper understanding of brain function and disfunction. Diffusion Magnetic Resonance Imaging (DMRI) is a powerful technique to non-invasively delineate white matter (WM) tracts and to obtain a three-dimensional description of the structural architecture of the brain. However, DMRI tractography methods produce highly multi-dimensional datasets whose interpretation requires advanced analytical tools. Indeed, manual identification of specific neuroanatomical tracts based on prior anatomical knowledge is time-consuming and prone to operator-induced bias. Here we propose an automatic multi-subject fiber clustering method that enables retrieval of group-wise WM fiber bundles. In order to account for variance across subjects, we developed a multi-subject approach based on a method known as Dominant Sets algorithm, via an intra- and cross-subject clustering. The intra-subject step allows us to reduce the complexity of the raw tractography data, thus obtaining homogeneous neuroanatomically-plausible bundles in each diffusion space. The cross-subject step, characterized by a proper space-invariant metric in the original diffusion space, enables the identification of the same WM bundles across multiple subjects without any prior neuroanatomical knowledge. Quantitative analysis was conducted comparing our algorithm with spectral clustering and affinity propagation methods on synthetic dataset. We also performed qualitative analysis on mouse brain tractography retrieving significant WM structures. The approach serves the final goal of detecting WM bundles at a population level, thus paving the way to the study of the WM organization across groups.

  5. Fundamentals of Seismic Wave Propagation

    NASA Astrophysics Data System (ADS)

    Chapman, Chris

    2004-08-01

    Presenting a comprehensive introduction to the propagation of high-frequency body-waves in elastodynamics, this volume develops the theory of seismic wave propagation in acoustic, elastic and anisotropic media to allow seismic waves to be modelled in complex, realistic three-dimensional Earth models. The book is a text for graduate courses in theoretical seismology, and a reference for all academic and industrial seismologists using numerical modelling methods. Exercises and suggestions for further reading are included in each chapter.

  6. High-affinity Cyclic Peptide Matriptase Inhibitors*

    PubMed Central

    Quimbar, Pedro; Malik, Uru; Sommerhoff, Christian P.; Kaas, Quentin; Chan, Lai Y.; Huang, Yen-Hua; Grundhuber, Maresa; Dunse, Kerry; Craik, David J.; Anderson, Marilyn A.; Daly, Norelle L.

    2013-01-01

    The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase. PMID:23548907

  7. Exploring Fluorous Affinity by Liquid Chromatography.

    PubMed

    Catani, Martina; Guzzinati, Roberta; Marchetti, Nicola; Pasti, Luisa; Cavazzini, Alberto

    2015-07-01

    Terms such as "fluorous affinity" and "fluorophilicity" have been used to describe the unique partition and sorption properties often exhibited by highly fluorinated organic compounds, that is molecules rich in sp(3) carbon-fluorine bonds. In this work, we made use of a highly fluorinated stationary phase and a series of benzene derivatives to study the effect of one single perfluorinated carbon on the chromatographic behavior and adsorption properties of molecules. For this purpose, the adsorption equilibria of α,α,α-trifluorotoluene, toluene, and other alkylbenzenes have been studied by means of nonlinear chromatography in a variety of acetonitrile/water eluents. Our results reveal that one single perfluorinated carbon is already enough to induce a drastic change in the adsorption properties of molecules on the perfluorinated stationary phase. In particular, it has been found that adsorption is monolayer if the perfluoroalkyl carbon is present but that, when this unit is missing, molecules arrange as multilayer stack structures. These findings can contribute to the understanding of molecular mechanisms of fluorous affinity. PMID:26047527

  8. 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.

  9. 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.

  10. 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.

  11. 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. PMID:27498895

  12. Negative homotropic cooperativity and affinity heterogeneity: preparation of yeast glyceraldehyde-3-phosphate dehydrogenase with maximal affinity homogeneity.

    PubMed Central

    Gennis, L S

    1976-01-01

    A three-step procedure including affinity chromatography on NAD+-azobenzamidopropyl-Sepharose has been designed for the purification of yeast glyceraldehyde-3-phosphate dehydrogenase [D-glyceraldehyde-3-phosphate: NAD+ oxidoreductase (phosphorylating), EC 1.2.1.12] with maximized specific activity and maximized homogeneity with respect to affinity for the coenzyme, NAD+.Binding isotherms allow the analysis of cooperativity patterns that disclose both the average ligand affinity in the system and the distribution of ligands among the sites, only for systems with complete affinity homogeneity. The presence of affinity heterogeneity, resulting from multiple oligomeric species differing only in their affinity for coenzyme, gives rise to isotherms which falsely manifest apparent negative cooperativity. A method for distinguishing negative homotropic cooperativity from affinity heterogeneity is suggested. PMID:186779

  13. High-energy Neutrinos from Sources in Clusters of Galaxies

    NASA Astrophysics Data System (ADS)

    Fang, Ke; Olinto, Angela V.

    2016-09-01

    High-energy cosmic rays can be accelerated in clusters of galaxies, by mega-parsec scale shocks induced by the accretion of gas during the formation of large-scale structures, or by powerful sources harbored in clusters. Once accelerated, the highest energy particles leave the cluster via almost rectilinear trajectories, while lower energy ones can be confined by the cluster magnetic field up to cosmological time and interact with the intracluster gas. Using a realistic model of the baryon distribution and the turbulent magnetic field in clusters, we studied the propagation and hadronic interaction of high-energy protons in the intracluster medium. We report the cumulative cosmic-ray and neutrino spectra generated by galaxy clusters, including embedded sources, and demonstrate that clusters can contribute a significant fraction of the observed IceCube neutrinos above 30 TeV while remaining undetected in high-energy cosmic rays and γ rays for reasonable choices of parameters and source scenarios.

  14. Large odd{endash}even effect in RbC{sup {minus}}{sub {ital n}} cluster size distributions

    SciTech Connect

    Vandenbosch, R.; Will, D.I.

    1996-04-01

    RbC{sub {ital n}} cluster anions have been produced by Rb sputtering of graphite. The intensity ratio of clusters with an even number of carbon atoms to those with an odd number of carbons is much larger for RbC{sup {minus}}{sub {ital n}} clusters than for C{sup {minus}}{sub {ital n}} clusters. {ital Ab} {ital initio} quantum mechanical calculations suggest that this arises from RbC{sub {ital n}} electron affinities that are close to zero or negative for odd {ital n}, rather than from an enhanced odd{endash}even alternation in the affinities. {copyright} {ital 1996 American Institute of Physics.}

  15. 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

  16. 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. PMID:27336405

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

    PubMed Central

    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. PMID:27336405

  18. Effectively nonlocal metric-affine gravity

    NASA Astrophysics Data System (ADS)

    Golovnev, Alexey; Koivisto, Tomi; Sandstad, Marit

    2016-03-01

    In metric-affine theories of gravity such as the C-theories, the spacetime connection is associated to a metric that is nontrivially related to the physical metric. In this article, such theories are rewritten in terms of a single metric, and it is shown that they can be recast as effectively nonlocal gravity. With some assumptions, known ghost-free theories with nonsingular and cosmologically interesting properties may be recovered. Relations between different formulations are analyzed at both perturbative and nonperturbative levels, taking carefully into account subtleties with boundary conditions in the presence of integral operators in the action, and equivalences between theories related by nonlocal redefinitions of the fields are verified at the level of equations of motion. This suggests a possible geometrical interpretation of nonlocal gravity as an emergent property of non-Riemannian spacetime structure.

  19. Affinity chromatography with an immobilized RNA enzyme.

    PubMed Central

    Vioque, A; Altman, S

    1986-01-01

    M1 RNA, the catalytic subunit of Escherichia coli RNase P, has been covalently linked at its 3' terminus to agarose beads. Unlike M1 RNA, which is active in solution in the absence of the protein component (C5) of RNase P, the RNA linked to the beads is active only in the presence of C5 protein. Affinity chromatography of crude extracts of E. coli on a column prepared from the beads to which the RNA has been crosslinked results in the purification of C5 protein in a single step. The protein has been purified in this manner from cells that contain a plasmid, pINIIIR20, which includes the gene that codes for C5 protein. A 6-fold amplification of the expression of C5 protein is found in these cells after induction as compared to cells that do not harbor the plasmid. Images PMID:3526344

  20. Wetting on rough self-affine surfaces

    NASA Astrophysics Data System (ADS)

    Palasantzas, George

    1995-05-01

    In this paper, we present a general investigation of the effective potential for complete wetting on self-affine rough surfaces. The roughness effect is investigated by means of the height-height correlation model in Fourier space ~(1+aξ2q2)-1-H. The parameters H and ξ are, respectively, the roughness exponent and the substrate in-plane correlation length. It is observed that the effect of H on the free interface profile is significant for ξ>ξ) regime is characterized by a power-law scaling ~Y-2.

  1. High-affinity neuropeptide Y receptor antagonists.

    PubMed Central

    Daniels, A J; Matthews, J E; Slepetis, R J; Jansen, M; Viveros, O H; Tadepalli, A; Harrington, W; Heyer, D; Landavazo, A; Leban, J J

    1995-01-01

    Neuropeptide Y (NPY) is one of the most abundant peptide transmitters in the mammalian brain. In the periphery it is costored and coreleased with norepinephrine from sympathetic nerve terminals. However, the physiological functions of this peptide remain unclear because of the absence of specific high-affinity receptor antagonists. Three potent NPY receptor antagonists were synthesized and tested for their biological activity in in vitro, ex vivo, and in vivo functional assays. We describe here the effects of these antagonists inhibiting specific radiolabeled NPY binding at Y1 and Y2 receptors and antagonizing the effects of NPY in human erythroleukemia cell intracellular calcium mobilization perfusion pressure in the isolated rat kidney, and mean arterial blood pressure in anesthetized rats. PMID:7568074

  2. 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. PMID:25570332

  3. Evaluation system of negative electron affinity photocathode

    NASA Astrophysics Data System (ADS)

    Fu, Rongguo; Chang, Benkang; Qian, Yunsheng; Wang, Guihua; Zong, Zhiyuan

    2001-10-01

    This article first describes the background of the research and manufacture of evaluation system of Negative Electron Affinity photocathode. This article designs a set of super high vacuum system for activating NEA photocathode on the base of activation theory, the process of design and debugging is given. The system is composed of three parts: super high vacuum system for GaAs material activation, multi-meter testing system, surface analysis system. The system is used for on-line evaluation of activating of NEA photocathode. The technical parameters and structure of the evaluation system of NEA photocathode are given in the paper. The system is finished and experiments are made. At last the picture of the system is given.

  4. The magic gold cluster Au20

    NASA Astrophysics Data System (ADS)

    Kryachko, E. S.; Remacle, F.

    The 20-nanogold cluster Au20 exhibits a large variety of two- and three-dimensional isomeric forms. Among them is the ground-state isomer Au20(Td) representing the stable cluster with a unique tetrahedral shape, with all atoms on the surface, and large HOMO-LUMO gap which even slightly exceeds that of the buckyball fullerene C60. The anionic cluster Au-20(Td) that holds its parent tetrahedral symmetry features a high catalytic activity. The list of the properties of the 20-nanogold clusters surveyed in the present work ranges from the energetic order of stability of its isomers to the optical absorption and excitation spectra of the Au20(Td) cluster. We also report the structures and properties of its doubly charged clusters Au2+20 and Au2-20 and computationally confirm that Au2-20 is indeed stable. The zero-point-energy-corrected adiabatic second electron affinity of Au20(Td) amounts to 0.43-0.53 eV that is consistent with the experimental data. In addition, we provide computational evidence of the existence of the novel, hollow cage isomer of Au20 and analyze its key properties.0

  5. Dye affinity cryogels for plasmid DNA purification.

    PubMed

    Çimen, Duygu; Yılmaz, Fatma; Perçin, Işık; Türkmen, Deniz; Denizli, Adil

    2015-11-01

    The aim of this study is to prepare megaporous dye-affinity cryogel discs for the purification of plasmid DNA (pDNA) from bacterial lysate. Poly(hydroxyethyl methacrylate) [PHEMA] cryogel discs were produced by free radical polymerization initiated by N,N,N',N'-tetramethylene diamine (TEMED) and ammonium persulfate (APS) redox pair in an ice bath. Cibacron Blue F3GA was used as an affinity ligand (loading amount: 68.9μmol/g polymer). The amount of pDNA adsorbed onto the PHEMA-Cibacron Blue F3GA cryogel discs first increased and then reached a plateau value (i.e., 32.5mg/g cryogel) at 3.0mg/mL pDNA concentration. Compared with the PHEMA cryogel (0.11mg/g cryogel), the pDNA adsorption capacity of the PHEMA-Cibacron Blue F3GA cryogel (32.4mg/g polymer) was improved significantly due to the Cibacron Blue 3GA immobilization onto the polymeric matrix. pDNA adsorption amount decreased from 11.7mg/g to 1.1mg/g with the increasing of NaCl concentration. The maximum pDNA adsorption was achieved at 4°C. The overall recovery of pDNA was calculated as 90%. The PHEMA-Cibacron Blue F3GA cryogel discs could be used five times without decreasing the pDNA adsorption capacity significantly. The results show that the PHEMA-Cibacron Blue F3GA cryogel discs promise high selectivity for pDNA. PMID:26249596

  6. Purification of glycolytic enzymes by using affinity-elution chromatography.

    PubMed Central

    Scopes, R K

    1977-01-01

    1. A systematic procedure for the purification of enzymes by affinity-elution chromatography is described. Enzymes are adsorbed on a cation-exchanger, and eluted with ligands specific for the enzyme concerned. 2. All of the glycolytic and some related enzymes present in rabbit muscle can be purified by the affinity-elution technique. The pH range for adsorption and elution of each enzyme was found, and the effects of minor variations of conditions are described. 3. A description of experimental conditions suitable for affinity elution of each enzyme is given, together with special features relevant to each individual enzyme. 4. Theoretical considerations of affinity elution chromatography are discussed, including its limitations, advantages and disadvantages compared with affinity-adsorption chromatography. Possible developments are suggested to cover enzymes which because of their adsorption characteristics are not at present amenable to affinity-elution procedures. PMID:192194

  7. Antibody-based affinity cryo-EM grid.

    PubMed

    Yu, Guimei; Li, Kunpeng; Jiang, Wen

    2016-05-01

    The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states.

  8. Prediction of Neutral Salt Elution Profiles for Affinity Chromatography

    NASA Astrophysics Data System (ADS)

    Robinson, Jack B.; Strottmann, James M.; Stellwagen, Earle

    1981-04-01

    Neutral salts exhibit very marked differences as eluants of proteins from affinity columns. We observe: (i) that the relative potencies of neutral salts as eluants are independent of the protein or the affinity ligand in the systems studied, (ii) that the absolute salt concentration necessary to elute any given protein bound to the affinity matrix is proportional to the algebraic sum of a set of elution coefficients defined herein for the separate ions present in the solution, and (iii) that the proportionality between elution potency and elution coefficient is a function of the affinity of the protein for the immobilized ligand. Given the concentration of one neutral salt required for elution of a protein of interest from an affinity column, the elution capability of any neutral salt at any temperature can be quantitatively predicted for that protein. Accordingly, application and elution protocols for affinity chromatography can be designed to optimize the yield and fold purification of proteins.

  9. Atmospheric millimeter wave propagation model

    NASA Astrophysics Data System (ADS)

    Liebe, H. J.

    1983-12-01

    The neutral atmosphere is characterized for the frequency range from 1 to 300 GHz as nonturbulent propagation medium. Attenuation and propagation delay effects are predicated from meteorological data sets: pressure, temperature, humidity, suspended particle concentration, and rain rate. The physical data base of the propagation model consists of four terms: (1) resonance information for 30 water vapor and 48 oxygen absorption lines in the form of intensity coefficients and center frequency for each line; (2) a composite (oxygen, water vapor, and nitrogen) continum spectrum; (3) a hydrosol attenuation term for haze, fog, and cloud conditions; and (4) a rain attenuation model. Oxygen lines extend into the mesosphere, where they behave in a complicated manner due to the Zeeman effect.

  10. 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

  11. Propagators in polymer quantum mechanics

    SciTech Connect

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

    2013-09-15

    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 μ{sub 0}, the length scale introduced in the polymer dynamics and which plays a role analog of that of Planck length in Quantum Gravity. -- Highlights: •Formulas for propagators of free and particle in a box in polymer quantum mechanics. •Initial conditions, composition and Green’s function character is checked. •Propagators reduce to corresponding Schrödinger ones in an appropriately defined limit. •Results show overall consistency of the polymer framework. •For the particle in a box results are also verified using formula from method of images.

  12. 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.

  13. NASA Propagation Program Status and Propagation Needs of Satcom Industry

    NASA Technical Reports Server (NTRS)

    Golshan, Nassar

    1996-01-01

    The program objective is to enable the development of new commercial satellite systems and services and to support NASA's programs by providing timely data and models about propagation of satellite radio signals though the intervening environment. Provisions include new services, higher frequencies, higher data rates, different environments (mobile, indoors, fixed), and different orbits (geostationary, low earth orbit).

  14. Nonstationary noise propagation with sources

    NASA Astrophysics Data System (ADS)

    Ben-Benjamin, J. S.; Cohen, L.

    2014-06-01

    We discuss a number of topics relevant to noise propagation in dispersive media. We formulate the problem of pulse propagation with a source term in phase space and show that a four dimensional Wigner distribution is required. The four dimensional Wigner distribution is that of space and time and also wavenumber and frequency. The four dimensional Wigner spectrum is equivalent to the space-time autocorrelation function. We also apply the quantum path method to improve the phase space approximation previously obtained. In addition we discuss motion in a Snell's law medium.

  15. Buckle propagation in tubular structures

    SciTech Connect

    Nogueira, A.C.; Tassoulas, J.L.

    1995-12-01

    A novel method for the analysis of buckle propagation in tubes such as tendons of tension leg platforms and pipelines for deep-water applications is presented. Results are reported for the propagation pressure and state deformation in tubes of various materials (SS-304, CS-1010 and X-52 steel tubes) with a wide range of values of the diameter-to-thickness ratio (D/t). Not only the method overcomes the prohibitive computational demands of earlier procedures, but also it is in excellent agreement with experimental data for all values of D/t investigated (from D/t = 78 to as low as D/t = 12.8).

  16. Affinity chromatography for purification of two urokinases from human urine.

    PubMed

    Takahashi, R; Akiba, K; Koike, M; Noguchi, T; Ezure, Y

    2000-05-26

    A new affinity chromatography (hydrophobic-mediated affinity chromatography), which was characterized by the matrix having both affinity site to urokinase and hydrophobic site, was established for the purification of urokinase from human urine. The hydrophobic affinity matrix (tentatively named PAS in the text) was prepared by immobilizing 6-aminocaproic acid on Sepharose CL-6B, followed by a coupling p-aminobenzamidine to a part of the hydrophobic site on the matrix. The PAS matrix was applied to the purification of urokinase from human urine, and high- and low-molecular weight pure urokinases were efficiently obtained in high yield by the present method. PMID:10892585

  17. Anion photoelectron spectroscopy of radicals and clusters

    SciTech Connect

    Travis, Taylor R.

    1999-12-16

    Anion photoelectron spectroscopy is used to study free radicals and clusters. The low-lying {sup 2}{Sigma} and {sup 2}{Pi} states of C{sub 2n}H (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 C{sub 2}H and C{sub 4}H. Other radicals studied include NCN and I{sub 3}. 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 I{sub 3} 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.

  18. 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

  19. AN AFFINE-INVARIANT SAMPLER FOR EXOPLANET FITTING AND DISCOVERY IN RADIAL VELOCITY DATA

    SciTech Connect

    Hou Fengji; Hogg, David W.; Goodman, Jonathan; Weare, Jonathan; Schwab, Christian

    2012-02-01

    Markov chain Monte Carlo (MCMC) proves to be powerful for Bayesian inference and in particular for exoplanet radial velocity fitting because MCMC provides more statistical information and makes better use of data than common approaches like chi-square fitting. However, the nonlinear density functions encountered in these problems can make MCMC time-consuming. In this paper, we apply an ensemble sampler respecting affine invariance to orbital parameter extraction from radial velocity data. This new sampler has only one free parameter, and does not require much tuning for good performance, which is important for automatization. The autocorrelation time of this sampler is approximately the same for all parameters and far smaller than Metropolis-Hastings, which means it requires many fewer function calls to produce the same number of independent samples. The affine-invariant sampler speeds up MCMC by hundreds of times compared with Metropolis-Hastings in the same computing situation. This novel sampler would be ideal for projects involving large data sets such as statistical investigations of planet distribution. The biggest obstacle to ensemble samplers is the existence of multiple local optima; we present a clustering technique to deal with local optima by clustering based on the likelihood of the walkers in the ensemble. We demonstrate the effectiveness of the sampler on real radial velocity data.

  20. An Affine-invariant Sampler for Exoplanet Fitting and Discovery in Radial Velocity Data

    NASA Astrophysics Data System (ADS)

    Hou, Fengji; Goodman, Jonathan; Hogg, David W.; Weare, Jonathan; Schwab, Christian

    2012-02-01

    Markov chain Monte Carlo (MCMC) proves to be powerful for Bayesian inference and in particular for exoplanet radial velocity fitting because MCMC provides more statistical information and makes better use of data than common approaches like chi-square fitting. However, the nonlinear density functions encountered in these problems can make MCMC time-consuming. In this paper, we apply an ensemble sampler respecting affine invariance to orbital parameter extraction from radial velocity data. This new sampler has only one free parameter, and does not require much tuning for good performance, which is important for automatization. The autocorrelation time of this sampler is approximately the same for all parameters and far smaller than Metropolis-Hastings, which means it requires many fewer function calls to produce the same number of independent samples. The affine-invariant sampler speeds up MCMC by hundreds of times compared with Metropolis-Hastings in the same computing situation. This novel sampler would be ideal for projects involving large data sets such as statistical investigations of planet distribution. The biggest obstacle to ensemble samplers is the existence of multiple local optima; we present a clustering technique to deal with local optima by clustering based on the likelihood of the walkers in the ensemble. We demonstrate the effectiveness of the sampler on real radial velocity data.

  1. Optical pulse propagation through clouds.

    PubMed

    Matter, J C; Bradley, R G

    1981-02-15

    The cloud impulse response (spatial and temporal) to optical pulse propagation has been measured. Experimental data are reported for the radiance function, pulse stretching, and (the first published) delay time. The results have been confirmed by Monte Carlo modeling. A geometric scattering model is presented explaining the temporal results for the test conditions.

  2. Optical pulse propagation through clouds.

    PubMed

    Matter, J C; Bradley, R G

    1981-07-01

    The cloud impulse response (spatial and temporal) to optical pulse propagation has been measured. Experimental data are reported for the radiance function, pulse stretching, and (the first published) delay time. The results have been confirmed by Monte Carlo modeling. A geometric scattering model is presented explaining the temporal results for the test conditions.

  3. 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)

  4. Wave equations for pulse propagation

    NASA Astrophysics Data System (ADS)

    Shore, B. W.

    1987-06-01

    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.

  5. Balloon atmospheric propagation experiment measurements

    NASA Technical Reports Server (NTRS)

    Minott, P. O.

    1973-01-01

    High altitude balloon measurements on laser beam fading during propagation through turbulent atmosphere show that a correlation between fading strength and stellar scintillation magnitudes exists. Graphs for stellar scintillation as a function of receiver aperture are used to predict fading bit error rates for neodymium-yag laser communication system.

  6. Complex Affine Toda Theories and Soliton Solutions

    NASA Astrophysics Data System (ADS)

    Zhu, Zhiqing

    1995-01-01

    Toda field theories (TFT's) constitute a large class of integrable (1 + 1)-dimensional field theories that are relativistically invariant: included are conformal field theories and integrable deformations away from conformality. Because they are soluble, for example, by the inverse scattering method, and because they are related to many other areas of field theory, they have been studied extensively in recent years. Hirota's method is a straightforward procedure to obtain soliton solutions to non-linear integrable equations. In Hirota's method, one first writes the nonlinear equations in Hirota's bilinear form, and then expands the so called tau-functions as a power series in an arbitrary parameter. The power series terminates at some finite order, thus the solutions obtained are exact. For an N-soliton solution, the number of terms in the expansion grows exponentially with N, making direct calculation of N-soliton solutions difficult. We extend Hirota's one -parameter expansion to an N-parameter expansion. In the new expansion series, many terms are identical to those in the (N - 1)-soliton solutions, and new terms grow only linearly with N. Furthermore, we note that the expansion must terminate at some finite order, thus the vanishing of higher order terms can be used as constraints on these new terms. It turns out that these constraints can be used to determine the new terms completely. We used this extended Hirota's method to find N-soliton solutions for complex affine TFT's based on a simply-laced Kac-Moody algebra. Soliton solutions for non-simply-laced complex ATFT's can be obtained for those of simply-laced complex ATFT's by folding or twisting. Even though some soliton solutions have already been obtained for complex ATFT's by various methods, the physical implications of these solutions have not yet been thoroughly discussed. There are infinitely many distinct topological solitons in any given complex affine Toda field theory and most of them have complex

  7. Genetic characteristics of vancomycin resistance gene cluster in Enterococcus spp.

    PubMed

    Chunhui, Chen; Xiaogang, Xu

    2015-05-01

    Vancomycin resistant enterococci has become an important nosocomial pathogen since it is discovered in late 1980s. The products, encoded by vancomycin resistant gene cluster in enterococci, catalyze the synthesis of peptidoglycan precursors with low affinity with glycopeptide antibiotics including vancomycin and teicoplanin and lead to resistance. These vancomycin resistant gene clusters are classified into nine types according to their gene sequences and organization, or D-Ala:D-Lac (VanA, VanB, VanD and VanM) and D-Ala:D-Ser (VanC, VanE, VanG, VanL and VanN) ligase gene clusters based on the differences of their encoded ligases. Moreover, these gene clusters are characterized by their different resistance levels and infection models. In this review, we summarize the classification, gene organization and infection model of vancomycin resistant gene cluster in Enterococcus spp.

  8. Nanostar Clustering Improves the Sensitivity of Plasmonic Assays.

    PubMed

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

    2015-08-19

    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

  9. Binding affinity prediction for protein-ligand complexes based on β contacts and B factor.

    PubMed

    Liu, Qian; Kwoh, Chee Keong; Li, Jinyan

    2013-11-25

    Accurate determination of protein-ligand binding affinity is a fundamental problem in biochemistry useful for many applications including drug design and protein-ligand docking. A number of scoring functions have been proposed for the prediction of protein-ligand binding affinity. However, accurate prediction is still a challenging problem because poor performance is often seen in the evaluation under the leave-one-cluster-out cross-validation (LCOCV). We introduce a new scoring function named B2BScore to improve the prediction performance. B2BScore integrates two physicochemical properties for protein-ligand binding affinity prediction. One is the property of β contacts. A β contact between two atoms requires no other atoms to interrupt the atomic contact and assumes that the two atoms should have enough direct contact area. The other is the property of B factor to capture the atomic mobility in the dynamic protein-ligand binding process. Tested on the PDBBind2009 data set, B2BScore shows superior prediction performance to existing methods on independent test data as well as under the LCOCV evaluation framework. In particular, B2BScore achieves a significant LCOCV improvement across 26 protein clusters-a big increase of the averaged Pearson's correlation coefficients from 0.418 to 0.518 and a significant decrease of standard deviation of the coefficients from 0.352 to 0.196. We also identified several important and intuitive contact descriptors of protein-ligand binding through the random forest learning in B2BScore. Some of these descriptors are closely related to contacts between carbon atoms without covalent-bond oxygen/nitrogen, preferred contacts of metal ions, interfacial backbone atoms from proteins, or π rings. Some others are negative descriptors relating to those contacts with nitrogen atoms without covalent-bond hydrogens or nonpreferred contacts of metal ions. These descriptors can be directly used to guide protein-ligand docking.

  10. Ligand Affinities Estimated by Quantum Chemical Calculations.

    PubMed

    Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

    2010-05-11

    We present quantum chemical estimates of ligand-binding affinities performed, for the first time, at a level of theory for which there is a hope that dispersion and polarization effects are properly accounted for (MP2/cc-pVTZ) and at the same time effects of solvation, entropy, and sampling are included. We have studied the binding of seven biotin analogues to the avidin tetramer. The calculations have been performed by the recently developed PMISP approach (polarizable multipole interactions with supermolecular pairs), which treats electrostatic interactions by multipoles up to quadrupoles, induction by anisotropic polarizabilities, and nonclassical interactions (dispersion, exchange repulsion, etc.) by explicit quantum chemical calculations, using a fragmentation approach, except for long-range interactions that are treated by standard molecular-mechanics Lennard-Jones terms. In order to include effects of sampling, 10 snapshots from a molecular dynamics simulation are studied for each biotin analogue. Solvation energies are estimated by the polarized continuum model (PCM), coupled to the multipole-polarizability model. Entropy effects are estimated from vibrational frequencies, calculated at the molecular mechanics level. We encounter several problems, not previously discussed, illustrating that we are first to apply such a method. For example, the PCM model is, in the present implementation, questionable for large molecules, owing to the use of a surface definition that gives numerous small cavities in a protein. PMID:26615702

  11. 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

  12. 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.

  13. 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

  14. Banach frames in the affine synthesis problem

    NASA Astrophysics Data System (ADS)

    Terekhin, Pavel A.

    2009-10-01

    We consider the problem of representing functions f\\in L^p(\\mathbb R^d) by a series in elements of the affine system \\displaystyle \\psi_{j,k}(x)=\\lvert\\det a_j\\rvert^{1/2}\\psi(a_jx-bk), \\qquad j\\in\\mathbb N, \\quad k\\in\\mathbb Z^d. The corresponding representation theorems are established on the basis of the frame inequalities \\displaystyle A\\Vert g\\Vert _q\\le\\Vert\\{(g,\\psi_{j,k})\\}\\Vert _Y\\le B\\Vert g\\Vert _q for the Fourier coefficients \\displaystyle(g,\\psi_{j,k})=\\int_{\\mathbb R^d}g(x)\\psi_{j,k}(x)\\,dx of functions g\\in L^q(\\mathbb R^d), 1/p+1/q=1, where {\\Vert\\cdot\\Vert}_Y is the norm in some Banach space of number families \\{y_{j,k}\\} and 0 are constants. In particular, it is proved that if the integral of a function \\psi\\in L^1\\cap L^p(\\mathbb R^d), 1, is nonzero, so \\displaystyle\\int_{\\mathbb R^d}\\psi(x)\\,dx\

  15. 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…

  16. 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.

  17. 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'…

  18. High affinity retinoic acid receptor antagonists: analogs of AGN 193109.

    PubMed

    Johnson, A T; Wang, L; Gillett, S J; Chandraratna, R A

    1999-02-22

    A series of high affinity retinoic acid receptor (RAR) antagonists were prepared based upon the known antagonist AGN 193109 (2). Introduction of various phenyl groups revealed a preference for substitution at the para-position relative to the meta-site. Antagonists with the highest affinities for the RARs possessed hydrophobic groups, however, the presence of polar functionality was also well tolerated.

  19. 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.

  20. Propagation studies of metastable intermolecular composites (MIC).

    SciTech Connect

    Son, S. F.; Busse, J. R.; Asay, B. W.; Peterson, P. D.; Mang, J. T.; Bockmon, B.; Pantoya, M.

    2002-01-01

    Thermite materials are attractive energetic materials because the reactions are highly exothermic, have high energy densities, and high temperatures of combustion. However, the application of thermite materials has been limited because of the relative slow release of energy compared to other energetic materials. Engineered nano-scale composite energetic materials, such as Al/MoO{sub 3}, show promise for additional energetic material applications because they can react very rapidly. The composite material studied in this work consists of tailored, ultra-fine grain (30-200 nm diameter) aluminum particles that dramatically increase energy release rates of these thermite materials. These reactant clusters of fuel and oxidizer particles are in nearly atomic scale proximity to each other but are constrained from reaction until triggered. Despite the growing importance of nano-scale energetic materials, even the most basic combustion characteristics of these materials have not been thoroughly studied. This paper reports initial studies of the ignition and combustion of metastable intermolecular composites (MIC) materials. The goals were lo obtain an improved understanding of flame propagation mechanisms and combustion behaviors associated with nano-structured energetic materials. Information on issues such as reaction rate and behavior as a function of composition (mixture ratio), initial static charge, and particle size are essential and will allow scientists to design applications incorporating the benefits of these compounds. The materials have been characterized, specifically focusing on particle size, shape, distribution and morphology.

  1. 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.

  2. 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.

  3. 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.

  4. 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. PMID:27473483

  5. Initiation process and propagation mechanism of positive streamer discharge in water

    NASA Astrophysics Data System (ADS)

    Fujita, Hidemasa; Kanazawa, Seiji; Ohtani, Kiyonobu; Komiya, Atsuki; Kaneko, Toshiro; Sato, Takehiko

    2014-12-01

    The aim of this study was to clarify the initiation process and the propagation mechanism of positive underwater streamers under the application of pulsed voltage with a duration of 10 μs, focusing on two different theories of electrical discharges in liquids: the bubble theory and the direct ionization theory. The initiation process, which is the time lag from the beginning of voltage application to streamer inception, was found to be related to the bubble theory. In this process, Joule heating resulted in the formation of a bubble cluster at the tip of a needle electrode. Streamer inception was observed from the tip of a protrusion on the surface of this bubble cluster, which acted as a virtual sharp electrode to enhance the local electric field to a level greater than 10 MV/cm. Streak imaging of secondary streamer propagation showed that luminescence preceded gas channel generation, suggesting a mechanism of direct ionization in water. Streak imaging of primary streamer propagation revealed intermittent propagation, synchronized with repetitive pulsed currents. Shadowgraph imaging of streamers synchronized with the light emission signal indicated the possibility of direct ionization in water for primary streamer propagation as well as for secondary streamer propagation.

  6. 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

  7. Clustering Home Activity Distributions for Automatic Detection of Mild Cognitive Impairment in Older Adults1

    PubMed Central

    Akl, Ahmad; Chikhaoui, Belkacem; Mattek, Nora; Kaye, Jeffrey; Austin, Daniel; Mihailidis, Alex

    2016-01-01

    The public health implications of growing numbers of older adults at risk for dementia places pressure on identifying dementia at its earliest stages so as to develop proactive management plans. The prodromal dementia phase commonly identified as mild cognitive impairment is an important target for this early detection of impending dementia amenable to treatment. In this paper, we propose a method for home-based automatic detection of mild cognitive impairment in older adults through continuous monitoring via unobtrusive sensing technologies. Our method is composed of two main stages: a training stage and a test stage. For training, room activity distributions are estimated for each subject using a time frame of ω weeks, and then affinity propagation is employed to cluster the activity distributions and to extract exemplars to represent the different emerging clusters. For testing, room activity distributions belonging to a test subject with unknown cognitive status are compared to the extracted exemplars and get assigned the labels of the exemplars that result in the smallest normalized Kullbak–Leibler divergence. The labels of the activity distributions are then used to determine the cognitive status of the test subject. Using the sensor and clinical data pertaining to 85 homes with single occupants, we were able to automatically detect mild cognitive impairment in older adults with an F0.5 score of 0.856. Also, we were able to detect the non-amnestic sub-type of mild cognitive impairment in older adults with an F0.5 score of 0.958. PMID:27617044

  8. Clustering Home Activity Distributions for Automatic Detection of Mild Cognitive Impairment in Older Adults1

    PubMed Central

    Akl, Ahmad; Chikhaoui, Belkacem; Mattek, Nora; Kaye, Jeffrey; Austin, Daniel; Mihailidis, Alex

    2016-01-01

    The public health implications of growing numbers of older adults at risk for dementia places pressure on identifying dementia at its earliest stages so as to develop proactive management plans. The prodromal dementia phase commonly identified as mild cognitive impairment is an important target for this early detection of impending dementia amenable to treatment. In this paper, we propose a method for home-based automatic detection of mild cognitive impairment in older adults through continuous monitoring via unobtrusive sensing technologies. Our method is composed of two main stages: a training stage and a test stage. For training, room activity distributions are estimated for each subject using a time frame of ω weeks, and then affinity propagation is employed to cluster the activity distributions and to extract exemplars to represent the different emerging clusters. For testing, room activity distributions belonging to a test subject with unknown cognitive status are compared to the extracted exemplars and get assigned the labels of the exemplars that result in the smallest normalized Kullbak–Leibler divergence. The labels of the activity distributions are then used to determine the cognitive status of the test subject. Using the sensor and clinical data pertaining to 85 homes with single occupants, we were able to automatically detect mild cognitive impairment in older adults with an F0.5 score of 0.856. Also, we were able to detect the non-amnestic sub-type of mild cognitive impairment in older adults with an F0.5 score of 0.958.

  9. Enzyme-gold affinity labelling of cellulose.

    PubMed

    Berg, R H; Erdos, G W; Gritzali, M; Brown, R D

    1988-04-01

    The enzyme-linked colloidal gold affinity labelling technique was tested as a method to localize cellulose on thin sections of plant cell walls and slime mold spores. Commercially available cellulase from cultures of Trichoderma reesei, the main components being cellobiohydrolase I and II (CBH I, CBH II) and endoglucanase (EG), was linked to colloidal gold by using standard techniques and applied as a dilute, buffered suspension to thin sections. After brief exposure, e.g., 15-30 minutes, cellulose exposed on the surface of sections was labelled with the enzyme-gold complex. Poststaining did not appear to have a deleterious effect on the labelled sections. The specificity of labelling was demonstrated by its complete inhibition when carboxymethylcellulose was incorporated in the labelling mixture, by lack of labelling of 1,4-beta-mannans or 1,3-beta-xylans in noncellulosic walls of marine algae, by lack of labelling of 1,4-beta-glucans in chitin, by much lower labelling density when done at 4 degrees C, and by lack of labelling when sections were predigested with cellulase. Labelling with the crude commercial cellulase was compared to labelling with purified CBH I-, CBH II-, and EG-linked colloidal gold, and the labelling pattern was similar. This method was found useful on conventionally fixed material and required no special preparation other than the use of inert (Ni or Au) grids and 0.5% gelatin to reduce nonspecific binding of the gold complex. Labelling was similar in the several embedding resins tested: LR White, Lowicryl K4M, Epon 812, and Spurr's.(ABSTRACT TRUNCATED AT 250 WORDS)

  10. Optimal affine-invariant matching: performance characterization

    NASA Astrophysics Data System (ADS)

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

    1992-04-01

    The geometric hashing scheme proposed by Lamdan and Wolfson can be 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. In a recent paper, we discussed errors that can occur with this method due to quantization, stability, symmetry, and noise problems. These errors make the original geometric hashing technique unsuitable for use on the factory floor. Beginning with an explicit noise model, which the original Lamdan and Wolfson technique lacks, we derived an optimal approach that overcomes these problems. We showed that the results obtained with the new algorithm are clearly better than the results from the original method. This paper addresses the performance characterization of the geometric hashing technique, more specifically the affine-invariant point matching, applied to the problem of recognizing and determining the pose of sheet metal parts. The experiments indicate that with a model having 10 to 14 points, with 2 points of the model undetected and 10 extraneous points detected, and with the model points perturbed by Gaussian noise of standard deviation 3 (0.58 of range), the average amount of computation required to obtain an answer is equivalent to trying 11 of the possible three-point bases. The misdetection rate, measured by the percentage of correct bases matches that fail to verify, is 0.9. The percentage of incorrect bases that successfully produced a match that did verify (false alarm rate) is 13. And, finally, 2 of the experiments failed to find a correct match and verify it. Results for experiments with real images are also presented.

  11. The Canadian Olympus propagation experiment

    NASA Astrophysics Data System (ADS)

    Olsen, R. L.; Makrakis, D.; Rogers, D. V.; Berube, R. C.; Lam, W. I.; Strickland, J. I.; Antar, Y. M. M.; Albert, J.; Tam, S. Y. K.; Foo, S. L.

    The planning of commercial and military satellite communications systems using the upper SHF and lower EHF bands has resulted in a need for more propagation data and models for these bands. This is especially true for VSAT systems using small attenuation margins for which accurate data are particularly scarce and existing models inaccurate. The Canadian Olympus propagation experiment, designed to obtain such data, is described. The experiment includes simultaneous attenuation and depolarization measurements using the 12-, 20-, and 30-GHz Olympus satellite beacons, radiometric measurements of attenuation at 14, 20, and 30 GHz, and polarimetric radar measurements at 9.6 GHz. One novel feature of the experiment is the attempt to use the radar data to help separate the statistics of melting layer attenuation from beacon-measured total attenuation.

  12. Long-range vertical propagation

    NASA Technical Reports Server (NTRS)

    Willshire, William L., Jr.; Garber, Donald P.

    1990-01-01

    Development of the advanced turboprop has led to concerns about en route noise. Advanced turboprops generate low-frequency, periodic noise signatures at relatively high levels. As demonstrated in a flight test of NASA Lewis Research Center's Propfan Test Assessment (PTA) airplane in Alabama in October 1987, the noise of an advanced turboprop operating at cruise altitudes can be audible on the ground. The assessment of the en route noise issue is difficult due to the variability in received noise levels caused by atmospheric propagation and the uncertainty in predicting community response to the relatively low-level en route noise, as compared to noise associated with airport operations. The En Route Noise Test was designed to address the atmospheric propagation of advanced turboprop noise from cruise altitudes and consisted of measuring the noise of an advance turboprop at cruise in close proximity to the turboprop and on the ground. Measured and predicted ground noise levels are presented.

  13. 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.

  14. Propagator for finite range potentials

    SciTech Connect

    Cacciari, Ilaria; Moretti, Paolo

    2006-12-15

    The Schroedinger equation in integral form is applied to the one-dimensional scattering problem in the case of a general finite range, nonsingular potential. A simple expression for the Laplace transform of the transmission propagator is obtained in terms of the associated Fredholm determinant, by means of matrix methods; the particular form of the kernel and the peculiar aspects of the transmission problem play an important role. The application to an array of delta potentials is shown.

  15. Calculating Sonic-Boom Propagation

    NASA Technical Reports Server (NTRS)

    Darden, C. M.; Ting, L.

    1987-01-01

    Nonlinear effects included, enabling more-realistic modeling. Modified Method of Characteristics Sonic Boom Extrapolation Program (MMOC) is computer program for sonic-boom propagation that includes shock coalescence and incorporates effects of asymmetries due to volume and lift. Numerically integrates nonlinear governing equations using data on initial data line approximately one body length from aircraft and yields sonic-boom pressure at ground as function of time or of position at given time. MMOC written in FORTRAN IV.

  16. 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.

  17. Light propagation through atomic vapours

    NASA Astrophysics Data System (ADS)

    Siddons, Paul

    2014-05-01

    This tutorial presents the theory necessary to model the propagation of light through an atomic vapour. The history of atom-light interaction theories is reviewed, and examples of resulting applications are provided. A numerical model is developed and results presented. Analytic solutions to the theory are found, based on approximations to the numerical work. These solutions are found to be in excellent agreement with experimental measurements.

  18. Selectively Promiscuous Opioid Ligands: Discovery of High Affinity/Low Efficacy Opioid Ligands with Substantial Nociceptin Opioid Peptide Receptor Affinity

    PubMed Central

    2015-01-01

    Emerging clinical and preclinical evidence suggests that a compound displaying high affinity for μ, κ, and δ opioid (MOP, KOP, and DOP) receptors and antagonist activity at each, coupled with moderate affinity and efficacy at nociceptin opioid peptide (NOP) receptors will have utility as a relapse prevention agent for multiple types of drug abuse. Members of the orvinol family of opioid ligands have the desired affinity profile but have typically displayed substantial efficacy at MOP and or KOP receptors. In this study it is shown that a phenyl ring analogue (1d) of buprenorphine displays the desired profile in vitro with high, nonselective affinity for the MOP, KOP, and DOP receptors coupled with moderate affinity for NOP receptors. In vivo, 1d lacked any opioid agonist activity and was an antagonist of both the MOP receptor agonist morphine and the KOP receptor agonist ethylketocyclazocine, confirming the desired opioid receptor profile in vivo. PMID:24761755

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. How Structure Defines Affinity in Protein-Protein Interactions

    PubMed Central

    Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

    2014-01-01

    Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

  4. The sodium ion affinities of asparagine, glutamine, histidine and arginine

    NASA Astrophysics Data System (ADS)

    Wang, Ping; Ohanessian, Gilles; Wesdemiotis, Chrys

    2008-01-01

    The sodium ion affinities of the amino acids Asn, Gln, His and Arg have been determined by experimental and computational approaches (for Asn, His and Arg). Na+-bound heterodimers with amino acid and peptide ligands (Pep1, Pep2) were produced by electrospray ionization. From the dissociation kinetics of these Pep1-Na+-Pep2 ions to Pep1-Na+ and Pep2-Na+, determined by collisionally activated dissociation, a ladder of relative affinities was constructed and subsequently converted to absolute affinities by anchoring the relative values to known Na+ affinities. The Na+ affinities of Asn, His and Arg, were calculated at the MP2(full)/6-311+G(2d,2p)//MP2/6-31G(d) level of ab initio theory. The resulting experimental and computed Na+ affinities are in excellent agreement with one another. These results, combined with those of our previous studies, yield the sodium ion affinities of 18 out of the 20 [alpha]-amino acids naturally occurring in peptides and proteins of living systems.

  5. Analysis of biomolecular interactions using affinity microcolumns: a review.

    PubMed

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

    2014-10-01

    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

  6. 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....

  7. 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....

  8. 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....

  9. 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....

  10. 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....

  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. Slow-Slip Propagation Speeds

    NASA Astrophysics Data System (ADS)

    Rubin, A. M.; Ampuero, J.

    2007-12-01

    Combined seismic and geodetic data from subduction zones and the Salton Trough have revealed slow slip events with reasonably well-defined propagation speeds. This in turn is suggestive of a more-or-less well- defined front separating nearly locked regions outside the slipping zone from interior regions that slide much more rapidly. Such crack-like nucleation fronts arise naturally in models of rate-and-state friction for lab-like values of a/b, where a and b are the coefficients of the velocity- and state-dependence of the frictional strength (with the surface being velocity-neutral for a/b=1). If the propagating front has a quasi-steady shape, the propagation and slip speeds are kinematically tied via the local slip gradient. Given a sufficiently sharp front, the slip gradient is given dimensionally by Δτp- r/μ', where Δτp-r is the peak-to-residual stress drop at the front and μ' the effective elastic shear modulus. Rate-and-state simulations indicate that Δτp-r is given reasonably accurately by bσ\\ln(Vmaxθi/Dc), where σ is the effective normal stress, Vmax is the maximum slip speed behind the propagating front, θi is the the value of "state" ahead of the propagating front, and Dc is the characteristic slip distance for state evolution. Except for a coefficient of order unity, Δτp-r is independent of the evolution law. This leads to Vprop/Vmax ~μ'/[bσ\\ln(Vmaxθi/Dc)]. For slip speeds a few orders of magnitude above background, \\ln(Vmaxθi/Dc) can with reasonable accuracy be assigned some representative value (~4-5, for example). Subduction zone transients propagate on the order of 10 km/day or 10-1 m/s. Geodetic data constrain the average slip speed to be a few times smaller than 1 cm/day or 10-7 m/s. However, numerical models indicate that the maximum slip speed at the front may be several times larger than the average, over a length scale that is probably too small to resolve geodetically, so a representative value of Vprop/Vmax may be ~106

  13. Tomography of high harmonic generation in a cluster jet.

    PubMed

    Pai, Chih-Hao; Kuo, Cheng-Cheng; Lin, Ming-Wei; Wang, Jyhpyng; Chen, Szu-yuan; Lin, Jiunn-Yuan

    2006-04-01

    Tomographic measurement of high harmonic generation in a cluster jet was demonstrated by programming the cluster density distribution with a laser machining technique. The growth of harmonic energy with the propagation of the pump pulse was resolved by scanning the end of the argon cluster distribution in the path of the pump pulse. A downstream shift of the position of rapid growth and a decrease of the slope with increasing backing pressure as results of changes in the phase-matching condition were observed, which explains the presence of an optimal backing pressure. PMID:16599232

  14. Probing the Determinants of Diacylglycerol Binding Affinity in C1B domain of Protein Kinase Cα

    PubMed Central

    Stewart, Mikaela D.; Morgan, Brittany; Massi, Francesca; Igumenova, Tatyana I.

    2012-01-01

    C1 domains are independently folded modules that are responsible for targeting their parent proteins to lipid membranes containing diacylglycerol (DAG), a ubiquitous second messenger. The DAG-binding affinities of C1 domains determine the threshold concentration of DAG required for the propagation of the signaling response and the selectivity of this response among the DAG receptors in the cell. The structural information currently available for C1 domains offers little insight into the molecular basis of their differential DAG-binding affinities. In this work, we characterized the C1B domain of Protein Kinase Cα (C1Bα) and its diagnostic mutant, Y123W, using solution NMR methods and molecular dynamics simulations. The mutation did not perturb the C1Bα structure or sub-nanosecond dynamics of the protein backbone, but resulted in a >100-fold increase of DAG binding affinity and substantial change in μs-timescale conformational dynamics, as quantified by NMR rotating-frame relaxation-dispersion methods. The differences in the conformational exchange behavior between the wild-type and Y123W C1Bα were localized to the hinge regions of ligand-binding loops. Molecular dynamics simulations provided insight into the identity of the exchanging conformers and revealed the significance of a particular residue, Gln128, in modulating the geometry of the ligand-binding site. Taken together with the results of binding studies, our findings suggest that the conformational dynamics and preferential partitioning of the tryptophan sidechain into the water-lipid interface are important factors that modulate the DAG-binding properties of C1 domains. PMID:21419781

  15. Survey on granularity clustering.

    PubMed

    Ding, Shifei; Du, Mingjing; Zhu, Hong

    2015-12-01

    With the rapid development of uncertain artificial intelligent and the arrival of big data era, conventional clustering analysis and granular computing fail to satisfy the requirements of intelligent information processing in this new case. There is the essential relationship between granular computing and clustering analysis, so some researchers try to combine granular computing with clustering analysis. In the idea of granularity, the researchers expand the researches in clustering analysis and look for the best clustering results with the help of the basic theories and methods of granular computing. Granularity clustering method which is proposed and studied has attracted more and more attention. This paper firstly summarizes the background of granularity clustering and the intrinsic connection between granular computing and clustering analysis, and then mainly reviews the research status and various methods of granularity clustering. Finally, we analyze existing problem and propose further research.

  16. Affine differential geometry analysis of human arm movements.

    PubMed

    Flash, Tamar; Handzel, Amir A

    2007-06-01

    Humans interact with their environment through sensory information and motor actions. These interactions may be understood via the underlying geometry of both perception and action. While the motor space is typically considered by default to be Euclidean, persistent behavioral observations point to a different underlying geometric structure. These observed regularities include the "two-thirds power law", which connects path curvature with velocity, and "local isochrony", which prescribes the relation between movement time and its extent. Starting with these empirical observations, we have developed a mathematical framework based on differential geometry, Lie group theory and Cartan's moving frame method for the analysis of human hand trajectories. We also use this method to identify possible motion primitives, i.e., elementary building blocks from which more complicated movements are constructed. We show that a natural geometric description of continuous repetitive hand trajectories is not Euclidean but equi-affine. Specifically, equi-affine velocity is piecewise constant along movement segments, and movement execution time for a given segment is proportional to its equi-affine arc-length. Using this mathematical framework, we then analyze experimentally recorded drawing movements. To examine movement segmentation and classification, the two fundamental equi-affine differential invariants-equi-affine arc-length and curvature are calculated for the recorded movements. We also discuss the possible role of conic sections, i.e., curves with constant equi-affine curvature, as motor primitives and focus in more detail on parabolas, the equi-affine geodesics. Finally, we explore possible schemes for the internal neural coding of motor commands by showing that the equi-affine framework is compatible with the common model of population coding of the hand velocity vector when combined with a simple assumption on its dynamics. We then discuss several alternative explanations

  17. Cluster automorphism groups of cluster algebras with coefficients

    NASA Astrophysics Data System (ADS)

    Chang, Wen; Zhu, Bin

    2016-10-01

    We study the cluster automorphism group of a skew-symmetric cluster algebra with geometric coefficients. For this, we introduce the notion of gluing free cluster algebra, and show that under a weak condition the cluster automorphism group of a gluing free cluster algebra is a subgroup of the cluster automorphism group of its principal part cluster algebra (i.e. the corresponding cluster algebra without coefficients). We show that several classes of cluster algebras with coefficients are gluing free, for example, cluster algebras with principal coefficients, cluster algebras with universal geometric coefficients, and cluster algebras from surfaces (except a 4-gon) with coefficients from boundaries. Moreover, except four kinds of surfaces, the cluster automorphism group of a cluster algebra from a surface with coefficients from boundaries is isomorphic to the cluster automorphism group of its principal part cluster algebra; for a cluster algebra with principal coefficients, its cluster automorphism group is isomorphic to the automorphism group of its initial quiver.

  18. Affinity- and topology-dependent bound on current fluctuations

    NASA Astrophysics Data System (ADS)

    Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

    2016-08-01

    We provide a proof of a recently conjectured universal bound on current fluctuations in Markovian processes. This bound establishes a link between the fluctuations of an individual observable current, the cycle affinities driving the system into a non-equilibrium steady state, and the topology of the network. The proof is based on a decomposition of the network into independent cycles with both positive affinity and positive stationary cycle current. This formalism allows for a refinement of the bound for systems in equilibrium or with locally vanishing affinities.

  19. 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.

  20. 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.

  1. 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. PMID:24681890

  2. 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.

  3. Modification Propagation in Complex Networks

    NASA Astrophysics Data System (ADS)

    Mouronte, Mary Luz; Vargas, María Luisa; Moyano, Luis Gregorio; Algarra, Francisco Javier García; Del Pozo, Luis Salvador

    To keep up with rapidly changing conditions, business systems and their associated networks are growing increasingly intricate as never before. By doing this, network management and operation costs not only rise, but are difficult even to measure. This fact must be regarded as a major constraint to system optimization initiatives, as well as a setback to derived economic benefits. In this work we introduce a simple model in order to estimate the relative cost associated to modification propagation in complex architectures. Our model can be used to anticipate costs caused by network evolution, as well as for planning and evaluating future architecture development while providing benefit optimization.

  4. Resource allocation using constraint propagation

    NASA Technical Reports Server (NTRS)

    Rogers, John S.

    1990-01-01

    The concept of constraint propagation was discussed. Performance increases are possible with careful application of these constraint mechanisms. The degree of performance increase is related to the interdependence of the different activities resource usage. Although this method of applying constraints to activities and resources is often beneficial, it is obvious that this is no panacea cure for the computational woes that are experienced by dynamic resource allocation and scheduling problems. A combined effort for execution optimization in all areas of the system during development and the selection of the appropriate development environment is still the best method of producing an efficient system.

  5. In vitro propagation of chrysanthemum.

    PubMed

    Nencheva, D

    2010-01-01

    Chrysanthemum flowers Chrysanthemum x grandiflorum (Ramat.) Kitam., are commercially significant worldwide as there are large number of cultivars for cut flowers, pot flowers, and garden flowers. Commercial in vitro multiplication of chrysanthemum is often based on stem nodal explants with lateral meristems. This chapter describes a protocol for in vitro propagation from stem nodal explants and by direct organogenesis from pedicel explants producing large number of true-to-type plantlets in 4-8 week on Murashige and Skoog (MS) based media. Also, true mutants with changed flower color are obtained without producing chimeras after gamma-irradiation in mutation breeding.

  6. Dense Stereo Matching Method Based on Local Affine Model.

    PubMed

    Li, Jie; Shi, Wenxuan; Deng, Dexiang; Jia, Wenyan; Sun, Mingui

    2013-07-01

    A new method for constructing an accurate disparity space image and performing an efficient cost aggregation in stereo matching based on local affine model is proposed in this paper. The key algorithm includes a new self-adapting dissimilarity measurement used for calculating the matching cost and a local affine model used in cost aggregation stage. Different from the traditional region-based methods, which try to change the matching window size or to calculate an adaptive weight to do the aggregation, the proposed method focuses on obtaining the efficient and accurate local affine model to aggregate the cost volume while preserving the disparity discontinuity. Moreover, the local affine model can be extended to the color space. Experimental results demonstrate that the proposed method is able to provide subpixel precision disparity maps compared with some state-of-the-art stereo matching methods. PMID:24163727

  7. On the thermodynamic basis of the affinity decay rate

    NASA Astrophysics Data System (ADS)

    Garcia-Colín, L. S.; Piña, E.; de la Selva, S. M. T.

    1990-03-01

    In the past five years exhaustive studies in chemical reactions have lead to an empirical equation describing how isothermal-isometric homogeneous reactions evolve towards equilibrium independently of their particular mechanism or rate law. Such an equation expresses the time rate of change of the chemical affinity as a linear function of the inverse of time. In this paper we show that by invoking the local equilibrium hypothesis one may provide, a time evolution equation for the chemical affinity that is uniquely given by the solution of the particular rate law of the reaction considered. Consequently such an equation is not of the same functional form for all reactions. On the other hand, integration of Dalton's law under specific initial conditions, together with the local equilibrium assumption and the ideality requirement for the reacting species, exhibits a unique inverse time decay for the chemical affinity. This explains the good fitting of the inverse in time dependence of the chemical affinity with experimental data.

  8. 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.

  9. Frontal affinity chromatography (FAC): theory and basic aspects.

    PubMed

    Kasai, Ken-ichi

    2014-01-01

    Frontal affinity chromatography (FAC) is a versatile analytical tool for determining specific interactions between biomolecules and is particularly useful in the field of glycobiology. This article presents its basic aspects, merits, and theory. PMID:25117240

  10. 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

  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. Cluster-based distributed face tracking in camera networks.

    PubMed

    Yoder, Josiah; Medeiros, Henry; Park, Johnny; Kak, Avinash C

    2010-10-01

    In this paper, we present a distributed multicamera face tracking system suitable for large wired camera networks. Unlike previous multicamera face tracking systems, our system does not require a central server to coordinate the entire tracking effort. Instead, an efficient camera clustering protocol is used to dynamically form groups of cameras for in-network tracking of individual faces. The clustering protocol includes cluster propagation mechanisms that allow the computational load of face tracking to be transferred to different cameras as the target objects move. Furthermore, the dynamic election of cluster leaders provides robustness against system failures. Our experimental results show that our cluster-based distributed face tracker is capable of accurately tracking multiple faces in real-time. The overall performance of the distributed system is comparable to that of a centralized face tracker, while presenting the advantages of scalability and robustness. PMID:20423804

  13. Hydride affinities of cumulated, isolated, and conjugated dienes in acetonitrile.

    PubMed

    Zhu, Xiao-Qing; Liang, Hao; Zhu, Yan; Cheng, Jin-Pei

    2008-11-01

    The hydride affinities (defined as the enthalpy changes in this work) of 15 polarized dienes [five phenyl sulfone substituted allenes (1a), the corresponding five isolated dienes (1b), and the corresponding five conjugated dienes (1c)] in acetonitrile solution were determined by titration calorimetry for the first time. The results display that the hydride affinity scales of the 15 dienes in acetonitrile range from -71.6 to -73.9 kcal/mol for 1a, from -46.2 to -49.7 kcal/mol for 1b, and from -45.0 to -46.5 kcal/mol for 1c, which indicates that the hydride-obtaining abilities of the cumulated dienes (1a) are not only much larger than those of the corresponding conjugated dienes (1c) but also much larger than those of the corresponding isolated dienes (1b). The hydrogen affinities of the 15 dienes as well as the hydrogen affinities and the proton affinities of the radical anions of the dienes (1(-*)) in acetonitrile were also evaluated by using relative thermodynamic cycles according to Hess's law. The results show that (i) the hydrogen affinities of the neutral dienes 1 cover a range from -44.5 to -45.6 kcal/mol for 1a, from -20.4 to -21.4 kcal/mol for 1b, and from -17.3 to -18.5 kcal/mol for 1c; (ii) the hydrogen affinities of the radical anions of the dienes (1(-*)) in acetonitrile cover a range from -40.6 to -47.2 kcal/mol for 1a(-*), from -21.6 to -29.6 kcal/mol for 1b(-*), and from -10.0 to -15.4 kcal/mol for 1c(-*); (iii) the proton affinities of the 15 1a(-*) in acetonitrile cover a range from -97.0 to -100.6 kcal/mol for 1a(-*), from -77.8 to -83.4 kcal/mol for 1b(-*), and from -66.2 to -68.9 kcal/mol for 1c(-*). The main reasons for the great difference between the cumulated dienes and the corresponding isolated and conjugated dienes in the hydride affinity, hydrogen affinity, and proton affinity have been examined. It is evident that these experimental results should be quite valuable to facilitate the elucidation of the origins of the especially high

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Flexible Linker Modulates Glycosaminoglycan Affinity of Decorin Binding Protein A.

    PubMed

    Morgan, Ashli; Sepuru, Krishna Mohan; Feng, Wei; Rajarathnam, Krishna; Wang, Xu

    2015-08-18

    Decorin binding protein A (DBPA) is a glycosaminoglycan (GAG)-binding adhesin found on the surface of the bacterium Borrelia burgdorferi (B. burgdorferi), the causative agent of Lyme disease. DBPA facilitates bacterial adherence to extracellular matrices of human tissues and is crucial during the early stage of the infection process. Interestingly, DBPA from different strains (B31, N40, and PBr) show significant differences in GAG affinities, but the structural basis for the differences is not clear. In this study, we show that GAG affinity of N40 DBPA is modulated in part by flexible segments that control access to the GAG binding site, such that shortening of the linker leads to higher GAG affinity when analyzed using ELISA, gel mobility shift assay, solution NMR, and isothermal titration calorimetry. Our observation that GAG affinity differences among different B. burgdorferi strains can be attributed to a flexible linker domain regulating access to the GAG-binding domain is novel. It also provides a rare example of how neutral amino acids and dynamic segments in GAG binding proteins can have a large influence on GAG affinity and provides insights into why the number of basic amino acids in the GAG-binding site may not be the only factor determining GAG affinity of proteins. PMID:26223367

  19. Burst propagation in Texas Helimak

    NASA Astrophysics Data System (ADS)

    Pereira, F. A. C.; Toufen, D. L.; Guimarães-Filho, Z. O.; Caldas, I. L.; Gentle, K. W.

    2016-05-01

    We present investigations of extreme events (bursts) propagating in the Texas Helimak, a toroidal plasma device in which the radial electric field can be changed by application of bias. In the experiments analyzed, a large grid of Langmuir probes measuring ion saturation current fluctuations is used to study the burst propagation and its dependence on the applied bias voltage. We confirm previous results reported on the turbulence intermittency in the Texas Helimak, extending them to a larger radial interval with a density ranging from a uniform decay to an almost uniform value. For our analysis, we introduce an improved procedure, based on a multiprobe bidimensional conditional averaging method, to assure precise determination of burst statistical properties and their spatial profiles. We verify that intermittent bursts have properties that vary in the radial direction. The number of bursts depends on the radial position and on the applied bias voltage. On the other hand, the burst characteristic time and size do not depend on the applied bias voltage. The bias voltage modifies the vertical and radial burst velocity profiles differently. The burst velocity is smaller than the turbulence phase velocity in almost all the analyzed region.

  20. 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.

  1. Orbit propagation in Minkowskian geometry

    NASA Astrophysics Data System (ADS)

    Roa, Javier; Peláez, Jesús

    2015-09-01

    The geometry of hyperbolic orbits suggests that Minkowskian geometry, and not Euclidean, may provide the most adequate description of the motion. This idea is explored in order to derive a new regularized formulation for propagating arbitrarily perturbed hyperbolic orbits. The mathematical foundations underlying Minkowski space-time are exploited to describe hyperbolic orbits. Hypercomplex numbers are introduced to define the rotations, vectors, and metrics in the problem: the evolution of the eccentricity vector is described on the Minkowski plane in terms of hyperbolic numbers, and the orbital plane is described on the inertial reference using quaternions. A set of eight orbital elements is introduced, namely a time-element, the components of the eccentricity vector in , the semimajor axis, and the components of the quaternion defining the orbital plane. The resulting formulation provides a deep insight into the geometry of hyperbolic orbits. The performance of the formulation in long-term propagations is studied. The orbits of four hyperbolic comets are integrated and the accuracy of the solution is compared to other regularized formulations. The resulting formulation improves the stability of the integration process and it is not affected by the perihelion passage. It provides a level of accuracy that may not be reached by the compared formulations, at the cost of increasing the computational time.

  2. 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.

  3. 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.

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

    PubMed

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

    2016-08-18

    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.

  5. 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.

  6. 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

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

    PubMed

    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

  8. Methylsorb: a simple method for quantifying DNA methylation using DNA-gold affinity interactions.

    PubMed

    Sina, Abu Ali Ibn; Carrascosa, Laura G; Palanisamy, Ramkumar; Rauf, Sakandar; Shiddiky, Muhammad J A; Trau, Matt

    2014-10-21

    The analysis of DNA methylation is becoming increasingly important both in the clinic and also as a research tool to unravel key epigenetic molecular mechanisms in biology. Current methodologies for the quantification of regional DNA methylation (i.e., the average methylation over a region of DNA in the genome) are largely affected by comprehensive DNA sequencing methodologies which tend to be expensive, tedious, and time-consuming for many applications. Herein, we report an alternative DNA methylation detection method referred to as "Methylsorb", which is based on the inherent affinity of DNA bases to the gold surface (i.e., the trend of the affinity interactions is adenine > cytosine ≥ guanine > thymine).1 Since the degree of gold-DNA affinity interaction is highly sequence dependent, it provides a new capability to detect DNA methylation by simply monitoring the relative adsorption of bisulfite treated DNA sequences onto a gold chip. Because the selective physical adsorption of DNA fragments to gold enable a direct read-out of regional DNA methylation, the current requirement for DNA sequencing is obviated. To demonstrate the utility of this method, we present data on the regional methylation status of two CpG clusters located in the EN1 and MIR200B genes in MCF7 and MDA-MB-231 cells. The methylation status of these regions was obtained from the change in relative mass on gold surface with respect to relative adsorption of an unmethylated DNA source and this was detected using surface plasmon resonance (SPR) in a label-free and real-time manner. We anticipate that the simplicity of this method, combined with the high level of accuracy for identifying the methylation status of cytosines in DNA, could find broad application in biology and diagnostics.

  9. Dike propagation in active volcanoes: importance, evidence, models and perspectives

    NASA Astrophysics Data System (ADS)

    Acocella, V.

    2011-12-01

    Most eruptions are fed by dikes; therefore, better knowledge of dike propagation is crucial to improve our understanding of how magma is transferred and extruded at volcanoes. Dike pattern data from a few tens of active volcanic edifices show how dike propagation in a volcano is not a random process; rather, it depends from the following factors (listed in order of importance): the presence of relief, the shape of the edifice, the proximity to the surface, and regional tectonic control. Relief enhances the development of radial dikes, which may also cluster following volcano elongation or regional patterns. Dikes approaching the surface of volcanic edifices, regardless of their initial orientation, reorient to become radial (parallel to the maximum gravitational stress); in presence of scarps, dikes reorient subparallel to the scarp (perpendicular to the minimum gravitational stress). These relationships have been also observed or inferred during eruptions at Etna, Stromboli, Vesuvio (Italy), Erta Ale (Afar) and Faial (Azores). While numerical modelling of dike propagation remains challenging, analogue models of dike emplacement have been performed over a few decades, also supporting part of the above-described evidence. Analogue models have been mostly conducted injecting air or water within gelatine and, recently, injecting vegetable oil within sand. More sophisticated analogue modelling is foreseen for the future, using a more appropriate scaling, a larger sensitivity and providing a more quantitative approach in capturing relationships. More in general, future research on dikes should be devoted towards identifying dike propagation paths, dike arrest mechanisms, and likely locations of vent formation at specific volcanoes, to better aid hazards assessment.

  10. 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.

  11. Genetic evidence supports linguistic affinity of Mlabri - a hunter-gatherer group in Thailand

    PubMed Central

    2010-01-01

    Background The Mlabri are a group of nomadic hunter-gatherers inhabiting the rural highlands of Thailand. Little is known about the origins of the Mlabri and linguistic evidence suggests that the present-day Mlabri language most likely arose from Tin, a Khmuic language in the Austro-Asiatic language family. This study aims to examine whether the genetic affinity of the Mlabri is consistent with this linguistic relationship, and to further explore the origins of this enigmatic population. Results We conducted a genome-wide analysis of genetic variation using more than fifty thousand single nucleotide polymorphisms (SNPs) typed in thirteen population samples from Thailand, including the Mlabri, Htin and neighboring populations of the Northern Highlands, speaking Austro-Asiatic, Tai-Kadai and Hmong-Mien languages. The Mlabri population showed higher LD and lower haplotype diversity when compared with its neighboring populations. Both model-free and Bayesian model-based clustering analyses indicated a close genetic relationship between the Mlabri and the Htin, a group speaking a Tin language. Conclusion Our results strongly suggested that the Mlabri share more recent common ancestry with the Htin. We thus provided, to our knowledge, the first genetic evidence that supports the linguistic affinity of Mlabri, and this association between linguistic and genetic classifications could reflect the same past population processes. PMID:20302622

  12. Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

    PubMed Central

    Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

  13. Stoichiometry and Affinity of Thioflavin T Binding to Sup35p Amyloid Fibrils.

    PubMed

    Sulatskaya, Anna I; Kuznetsova, Irina M; Belousov, Mikhail V; Bondarev, Stanislav A; Zhouravleva, Galina A; Turoverov, Konstantin K

    2016-01-01

    In this work two modes of binding of the fluorescent probe thioflavin T to yeast prion protein Sup35p amyloid fibrils were revealed by absorption spectrometry of solutions prepared by equilibrium microdialysis. These binding modes exhibited significant differences in binding affinity and stoichiometry. Moreover, the absorption spectrum and the molar extinction coefficient of the dye bound in each mode were determined. The fluorescence quantum yield of the dye bound in each mode was determined via a spectrofluorimetric study of the same solutions in which the recorded fluorescence intensity was corrected for the primary inner filter effect. As previously predicted, the existence of one of the detected binding modes may be due to the incorporation of the dye into the grooves along the fiber axis perpendicular to the β-sheets of the fibrils. It was assumed that the second type of binding with higher affinity may be due to the existence of ThT binding sites that are localized to areas where amyloid fibrils are clustered.

  14. 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.

  15. Chemometrics for the classification and calibration of seawater using the H+ affinity spectrum.

    PubMed

    Kortazar, L; Sáez, J; Astigarraga, E; Goienaga, N; Fernández, L

    2013-11-15

    In 1819 Alexander Marcet proposed that seawater contains small amounts of all soluble substances and that the relative abundances of some of them were constant. This hypothesis is nowadays known as Marcet's Principle or the principle of constancy of the composition of seawater. Based on this principle, the present research tried to prove that it is possible to detect polluted seawater samples using the seawater H(+) affinity spectrum by the application of the possibilities provided by chemometric tools. Seawater samples were classified using the principal component analysis (PCA) of the HBound spectra of the samples. It was concluded that the sampling points location does not have any influence in the cluster formation, while the season in which they were collected is significant. On the other hand, the seawater composition was calibrated using estuary water samples of different salinities. Once the major constituents were measured, the data analysis concluded that it is possible to make a calibration of the HBound spectrum vs. any of these constituents by means of partial least square (PLS) regression. Thus, the experimental evidence collected in this work confirms that it is possible to detect polluted sea or estuary water samples using these chemometric tools and the H(+) affinity spectrum because with polluted samples these multivariate methods lead to incoherent results. So, suspect polluted zones may be monitored in a simple way with a low cost method and spending much less time. PMID:24148380

  16. Stoichiometry and Affinity of Thioflavin T Binding to Sup35p Amyloid Fibrils

    PubMed Central

    Sulatskaya, Anna I.; Kuznetsova, Irina M.; Belousov, Mikhail V.; Bondarev, Stanislav A.; Zhouravleva, Galina A.; Turoverov, Konstantin K.

    2016-01-01

    In this work two modes of binding of the fluorescent probe thioflavin T to yeast prion protein Sup35p amyloid fibrils were revealed by absorption spectrometry of solutions prepared by equilibrium microdialysis. These binding modes exhibited significant differences in binding affinity and stoichiometry. Moreover, the absorption spectrum and the molar extinction coefficient of the dye bound in each mode were determined. The fluorescence quantum yield of the dye bound in each mode was determined via a spectrofluorimetric study of the same solutions in which the recorded fluorescence intensity was corrected for the primary inner filter effect. As previously predicted, the existence of one of the detected binding modes may be due to the incorporation of the dye into the grooves along the fiber axis perpendicular to the β-sheets of the fibrils. It was assumed that the second type of binding with higher affinity may be due to the existence of ThT binding sites that are localized to areas where amyloid fibrils are clustered. PMID:27228180

  17. Stoichiometry and Affinity of Thioflavin T Binding to Sup35p Amyloid Fibrils.

    PubMed

    Sulatskaya, Anna I; Kuznetsova, Irina M; Belousov, Mikhail V; Bondarev, Stanislav A; Zhouravleva, Galina A; Turoverov, Konstantin K

    2016-01-01

    In this work two modes of binding of the fluorescent probe thioflavin T to yeast prion protein Sup35p amyloid fibrils were revealed by absorption spectrometry of solutions prepared by equilibrium microdialysis. These binding modes exhibited significant differences in binding affinity and stoichiometry. Moreover, the absorption spectrum and the molar extinction coefficient of the dye bound in each mode were determined. The fluorescence quantum yield of the dye bound in each mode was determined via a spectrofluorimetric study of the same solutions in which the recorded fluorescence intensity was corrected for the primary inner filter effect. As previously predicted, the existence of one of the detected binding modes may be due to the incorporation of the dye into the grooves along the fiber axis perpendicular to the β-sheets of the fibrils. It was assumed that the second type of binding with higher affinity may be due to the existence of ThT binding sites that are localized to areas where amyloid fibrils are clustered. PMID:27228180

  18. 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.

  19. 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.

  20. The Quantum Nature of Drug-Receptor Interactions: Deuteration Changes Binding Affinities for Histamine Receptor Ligands

    PubMed Central

    Repič, Matej; Zakšek, Maja; Kotnik, Kristina; Fijan, Estera; Mavri, Janez

    2016-01-01

    In this article we report a combined experimental and computational study concerning the effects of deuteration on the binding of histamine and two other histaminergic agonists to 3H-tiotidine-labeled histamine H2 receptor in neonatal rat astrocytes. Binding affinities were measured by displacing radiolabeled tiotidine from H2 receptor binding sites present on cultured neonatal rat astrocytes. Quantum-chemical calculations were performed by employing the empirical quantization of nuclear motion within a cluster model of the receptor binding site extracted from the homology model of the entire H2 receptor. Structure of H2 receptor built by homology modelling is attached in the supporting information (S1 Table) Experiments clearly demonstrate that deuteration affects the binding by increasing the affinity for histamine and reducing it for 2-methylhistamine, while basically leaving it unchanged for 4-methylhistamine. Ab initio quantum-chemical calculations on the cluster system extracted from the homology H2 model along with the implicit quantization of the acidic N–H and O–H bonds demonstrate that these changes in the binding can be rationalized by the altered strength of the hydrogen bonding upon deuteration known as the Ubbelohde effect. Our computational analysis also reveals a new mechanism of histamine binding, which underlines an important role of Tyr250 residue. The present work is, to our best knowledge, the first study of nuclear quantum effects on ligand receptor binding. The ligand H/D substitution is relevant for therapy in the context of perdeuterated and thus more stable drugs that are expected to enter therapeutic practice in the near future. Moreover, presented approach may contribute towards understanding receptor activation, while a distant goal remains in silico discrimination between agonists and antagonists based on the receptor structure. PMID:27159606

  1. The Quantum Nature of Drug-Receptor Interactions: Deuteration Changes Binding Affinities for Histamine Receptor Ligands.

    PubMed

    Kržan, Mojca; Vianello, Robert; Maršavelski, Aleksandra; Repič, Matej; Zakšek, Maja; Kotnik, Kristina; Fijan, Estera; Mavri, Janez

    2016-01-01

    In this article we report a combined experimental and computational study concerning the effects of deuteration on the binding of histamine and two other histaminergic agonists to 3H-tiotidine-labeled histamine H2 receptor in neonatal rat astrocytes. Binding affinities were measured by displacing radiolabeled tiotidine from H2 receptor binding sites present on cultured neonatal rat astrocytes. Quantum-chemical calculations were performed by employing the empirical quantization of nuclear motion within a cluster model of the receptor binding site extracted from the homology model of the entire H2 receptor. Structure of H2 receptor built by homology modelling is attached in the supporting information (S1 Table) Experiments clearly demonstrate that deuteration affects the binding by increasing the affinity for histamine and reducing it for 2-methylhistamine, while basically leaving it unchanged for 4-methylhistamine. Ab initio quantum-chemical calculations on the cluster system extracted from the homology H2 model along with the implicit quantization of the acidic N-H and O-H bonds demonstrate that these changes in the binding can be rationalized by the altered strength of the hydrogen bonding upon deuteration known as the Ubbelohde effect. Our computational analysis also reveals a new mechanism of histamine binding, which underlines an important role of Tyr250 residue. The present work is, to our best knowledge, the first study of nuclear quantum effects on ligand receptor binding. The ligand H/D substitution is relevant for therapy in the context of perdeuterated and thus more stable drugs that are expected to enter therapeutic practice in the near future. Moreover, presented approach may contribute towards understanding receptor activation, while a distant goal remains in silico discrimination between agonists and antagonists based on the receptor structure. PMID:27159606

  2. 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.

  3. Density functional theory study on Ni-doped MgnNi (n = 1-7) clusters

    NASA Astrophysics Data System (ADS)

    Chen, Xue-Feng; Zhang, Yan; Qi, Kai-Tian; Li, Bing; Zhu, Zheng-He; Sheng, Yong

    2010-03-01

    The possible geometrical and the electronic structures of small MgnNi (n = 1-7) clusters are optimised by the density functional theory with a LANL2DZ basis set. The binding energy, the energy gap, the electron affinity, the dissociation energy and the second difference in energy are calculated and discussed. The properties of MgnNi clusters are also discussed when the number of Mg atom increases.

  4. 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.

  5. Progress in front propagation research

    NASA Astrophysics Data System (ADS)

    Fort, Joaquim; Pujol, Toni

    2008-08-01

    We review the progress in the field of front propagation in recent years. We survey many physical, biophysical and cross-disciplinary applications, including reduced-variable models of combustion flames, Reid's paradox of rapid forest range expansions, the European colonization of North America during the 19th century, the Neolithic transition in Europe from 13 000 to 5000 years ago, the description of subsistence boundaries, the formation of cultural boundaries, the spread of genetic mutations, theory and experiments on virus infections, models of cancer tumors, etc. Recent theoretical advances are unified in a single framework, encompassing very diverse systems such as those with biased random walks, distributed delays, sequential reaction and dispersion, cohabitation models, age structure and systems with several interacting species. Directions for future progress are outlined.

  6. Transhorizon propagation of decameter waves

    NASA Astrophysics Data System (ADS)

    Kalinin, Yu. K.; Shchelkalin, A. V.

    2013-04-01

    Solutions to the problem of the point source field in a spherically layered medium are analyzed. For a three-layer waveguide model, a solution in the form of the Watson integral was used. A consideration of the singularities in the plane of the integration variable made it possible to represent the integral as a superposition of three waves. Two of them are connected with the interaction of the primary spherical wave with the lower convex and upper concave interfaces. The third wave is connected with the alternate action with both interfaces. The fourth wave is caused by the interaction between the primary wave and random inhomogeneities of the external medium (the ionosphere). Here, simulation was carried out based on Green equations. The considered unique data of flight measurements of the point source field strength indicate the efficiency of simulating the transhorizon propagation of decameter waves based on the superposition of all four aforesaid wave packets.

  7. IBEX - annular beam propagation experiment

    SciTech Connect

    Mazarakis, M G; Miller, R B; Shope, S L; Poukey, J W; Ramirez, J J; Ekdahl, C A; Adler, R J

    1983-01-01

    IBEX is a 4-MV, 100-kA, 20-ns cylindrical isolated Blumlein accelerator. In the experiments reported here, the accelerator is fitted with a specially designed foilless diode which is completely immersed in a uniform magnetic field. Several diode geometries have been studied as a function of magnetic field strength. The beam propagates a distance of 50 cm (approx. 10 cyclotron wavelengths) in vacuum before either striking a beam stop or being extracted through a thin foil. The extracted beam was successfully transported 60 cm downstream into a drift pipe filled either with 80 or 640 torr air. The main objectives of this experiment were to establish the proper parameters for the most quiescent 4 MV, 20 to 40 kA annular beam, and to compare the results with available theory and numerical code simulations.

  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. Probabilistic modeling of propagating explosions

    SciTech Connect

    Luck, L.B.; Eisenhawer, S.W.; Bott, T.F.

    1996-03-01

    Weapons containing significant quantities of high explosives (HE) are sometimes located in close proximity to one another. If an explosion occurs in a weapon, the possibility of propagation to one or more additional weapons may exist, with severe consequences possibly resulting. In the general case, a system of concern consists of multiple weapons and various other objects in a complex, three-dimensional geometry. In each weapon, HE is enclosed by (casing) materials that function as protection in the event of a neighbor detonation but become a source of fragments if the HE is initiated. The protection afforded by the casing means that only high-momentum fragments, which occur rarely, are of concern. These fragments, generated in an initial donor weapon are transported to other weapons either directly or by ricochet. Interaction of a fragment with an acceptor weapon can produce a reaction in the acceptor HE and result in a second detonation. In this paper we describe a comprehensive methodology to estimate the probability of various consequences for fragment-induced propagating detonations in arrays of weapons containing HE. Analysis of this problem requires an approach that can both define the circumstances under which rare events can occur and calculate the probability of such occurrences. Our approach is based on combining process tree methodology with Monte Carlo transport simulation. Our Monte Carlo technique very effectively captures important features of these differences. Process tree methodology is described and its use is discussed for a simplified problem and to illustrate the power of Monte Carlo simulation in estimating fragment-induced detonation of an acceptor weapon.

  10. 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.

  11. 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.

  12. Wave propagation in solids and fluids

    SciTech Connect

    Davis, J. L.

    1988-01-01

    The fundamental principles of mathematical analysis for wave phenomena in gases, solids, and liquids are presented in an introduction for scientists and engineers. Chapters are devoted to oscillatory phenomena, the physics of wave propagation, partial differential equations for wave propagation, transverse vibration of strings, water waves, and sound waves. Consideration is given to the dynamics of viscous and inviscid fluids, wave propagation in elastic media, and variational methods in wave phenomena. 41 refs.

  13. 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.

  14. Proton affinities and photoelectron spectra of phenylalanine and N-methyl- and N,N-dimethylphenylalanine. Correlation of lone pair ionization energies with proton affinities and implications for N-methylation as a method to effect site specific protonation of peptides

    SciTech Connect

    Campbell, S.; Marzluff, E.M.; Rodgers, M.T.; Beauchamp, J.L. ); Rempe, M.E.; Schwinck, K.F.; Lichtenberger, D.L. )

    1994-06-15

    A Fourier transform ion cyclotron resonance (FT-ICR) technique for measuring gas-phase proton affinities is presented which utilizes collisional dissociation of proton-bound clusters by off-resonance translational excitation. A simplified RRKM analysis relates unimolecular dissociation rates to proton affinities. This technique is used to measure values for the proton affinities of phenylalanine and N-methyl- and N,N-dimethylphenylalanine of 220.3, 223.6, and 224.5 kcal/mol, respectively (relative to the proton affinity of NH[sub 3] = 204.0 kcal/mol). The proton affinity measured for phenylalanine is in excellent agreement with reported literature values. The photoelectron spectra of these three molecules are also presented and analyzed. Assignments of bands to specific ionization processes are aided by comparison with model compounds such as methyl-substituted amines and 2-phenylethylamines. These data are employed to examine the correlation of adiabatic nitrogen lone pair ionization energies with gas-phase proton affinities for phenylalanine, N-methylphenylalanine, and N,N-dimethylphenylalanine in comparison to correlations for other amino acids and selected aliphatic amines. 41 refs., 7 figs., 2 tabs.

  15. 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.

  16. Neural network construction via back-propagation

    SciTech Connect

    Burwick, T.T.

    1994-06-01

    A method is presented that combines back-propagation with multi-layer neural network construction. Back-propagation is used not only to adjust the weights but also the signal functions. Going from one network to an equivalent one that has additional linear units, the non-linearity of these units and thus their effective presence is then introduced via back-propagation (weight-splitting). The back-propagated error causes the network to include new units in order to minimize the error function. We also show how this formalism allows to escape local minima.

  17. 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

  18. Effectors of hemoglobin. Separation of allosteric and affinity factors.

    PubMed Central

    Marden, M C; Bohn, B; Kister, J; Poyart, C

    1990-01-01

    The relative contributions of the allosteric and affinity factors toward the change in p50 have been calculated for a series of effectors of hemoglobin (Hb). Shifts in the ligand affinity of deoxy Hb and the values for 50% ligand saturation (p50) were obtained from oxygen equilibrium data. Because the high-affinity parameters (liganded conformation) are poorly determined from the equilibrium curves, they were determined from kinetic measurements of the association and dissociation rates with CO as ligand. The CO on-rates were obtained by flash photolysis measurements. The off-rates were determined from the rate of oxidation of HbCO by ferricyanide, or by replacement of CO with NO. The partition function of fully liganded hemoglobin for oxygen and CO is only slightly changed by the effectors. Measurements were made in the presence of the effectors 2,3-diphosphoglycerate (DPG), inositol hexakisphosphate (IHP), bezafibrate (Bzf), and two recently synthesized derivatives of Bzf (LR16 and L35). Values of p50 change by over a factor of 60; the on-rates decrease by nearly a factor of 8, with little change in the off-rates for the liganded conformation. The data indicate that both allosteric and affinity parameters are changed by the effectors; the changes in ligand affinity represent the larger contribution toward shifts in p50. PMID:2306490

  19. Melanin affinity and its possible role in neurodegeneration.

    PubMed

    Karlsson, Oskar; Lindquist, Nils Gunnar

    2013-12-01

    Certain drugs with melanin affinity are known to have caused pigmentary lesions in the eye and skin. This was the basis for the hypothesis that compounds with melanin affinity may cause damage also in other melanin-bearing tissues such as the substantia nigra. The heterogeneity of compounds that binds to melanin is large. Toxins, drugs, and several other compounds have melanin affinity. Compounds showing the highest affinity are mainly organic amines and metal ions. The binding of toxicants to melanin probably protects the cells initially. However, the binding is normally, slowly reversible and melanin may accumulate the toxicant and gradually release it into the cytosol. Several studies indicate that neuromelanin may play a significant role both in the initiation and in the progression of neurodegeneration. MPTP/MPP(+) that has been causally linked with Parkinsonism has high affinity for neuromelanin, and the induced dopaminergic denervation correlates with the neuromelanin content in the cells. This shows that the toxicological implications of the accumulation of toxicants in pigmented neurons and its possible role in neurodegeneration should not be neglected. Extracellular neuromelanin has been reported to activate dendritic cells and microglia. An initial neuronal damage induced by a neurotoxicant that leaks neuromelanin from the cells may therefore lead to a vicious cycle of neuroinflammation and further neurodegeneration. Although there are many clues to the particular vulnerability of dopaminergic neurons of substantia nigra in Parkinson's disease, the critical factors are not known. Further studies to determine the importance of neuromelanin in neurodegeneration and Parkinson's disease are warranted.

  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%. PMID:26856529

  1. 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.

  2. Crystal Structure of A Plant Dual-Affinity Nitrate Transporter

    PubMed Central

    Sun, Ji; Bankston, John R.; Payandeh, Jian; Hinds, Thomas R.; Zagotta, William N.; Zheng, Ning

    2014-01-01

    Nitrate is a primary nutrient for plant growth, but its levels in soil can fluctuate by several orders of magnitude. Previous studies have identified Arabidopsis NRT1.1 as a dual-affinity nitrate transporter, which can take up nitrate over a wide range of concentrations. The mode of action of NRT1.1 is controlled by phosphorylation of a key residue, Thr101. Yet how this posttranslational modification switches the transporter between two affinity states remains unclear. Here we report the crystal structure of unphosphorylated NRT1.1, which reveals an unexpected homodimer in the inward-facing conformation. In this low-affinity state, the Thr101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, we show that functional NRT1.1 indeed dimerizes in the cell membrane and the phosphomimetic mutation of Thr101 converts the protein into a monophasic high affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, our results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes. PMID:24572362

  3. Fluorogen-Activating-Proteins as Universal Affinity Biosensors for Immunodetection

    PubMed Central

    Gallo, Eugenio; Vasilev, Kalin V.; Jarvik, Jonathan

    2014-01-01

    Fluorogen-activating-proteins (FAPs) are a novel platform of fluorescence biosensors utilized for protein discovery. The technology currently demands molecular manipulation methods that limit its application and adaptability. Here, we highlight an alternative approach based on universal affinity reagents for protein detection. The affinity reagents were engineered as bi-partite fusion proteins, where the specificity moiety is derived from IgG-binding proteins –Protein-A or Protein-G – and the signaling element is a FAP. In this manner, primary antibodies provide the antigenic selectivity against a desired protein in biological samples, while FAP affinity reagents target the constant region (Fc) of antibodies and provide the biosensor component of detection. Fluorescence results using various techniques indicate minimal background and high target specificity for exogenous and endogenous proteins in mammalian cells. Additionally, FAP-based affinity reagents provide enhanced properties of detection previously absent using conventional affinity systems. Distinct features explored in this report include: (1) unfixed signal wavelengths (excitation and emission) determined by the particular fluorogen chosen, (2) real-time user controlled fluorescence on-set and off-set, (3) signal wavelength substitution while performing live analysis, and (4) enhanced resistance to photobleaching. PMID:24122476

  4. Affinity Purification of Sequence-Specific DNA Binding Proteins

    NASA Astrophysics Data System (ADS)

    Kadonaga, James T.; Tjian, Robert

    1986-08-01

    We describe a method for affinity purification of sequence-specific DNA binding proteins that is fast and effective. Complementary chemically synthesized oligodeoxynucleotides that contain a recognition site for a sequence-specific DNA binding protein are annealed and ligated to give oligomers. This DNA is then covalently coupled to Sepharose CL-2B with cyanogen bromide to yield the affinity resin. A partially purified protein fraction is combined with competitor DNA and subsequently passed through the DNA-Sepharose resin. The desired sequence-specific DNA binding protein is purified because it preferentially binds to the recognition sites in the affinity resin rather than to the nonspecific competitor DNA in solution. For example, a protein fraction that is enriched for transcription factor Sp1 can be further purified 500- to 1000-fold by two sequential affinity chromatography steps to give Sp1 of an estimated 90% homogeneity with 30% yield. In addition, the use of tandem affinity columns containing different protein binding sites allows the simultaneous purification of multiple DNA binding proteins from the same extract. This method provides a means for the purification of rare sequence-specific DNA binding proteins, such as Sp1 and CAAT-binding transcription factor.

  5. 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.

  6. Emergence of coexisting percolating clusters in networks.

    PubMed

    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. PMID:27415281

  7. Theoretical Study of Chemisorption on Small Palladium Clusters

    NASA Astrophysics Data System (ADS)

    Hira, Ajit; Naranjo, Frank; Munoz, Felipe; Jaramillo, Danelle

    2015-03-01

    We continue our interest in the chemisorption of different atomic and molecular species on small clusters of metallic elements, by examining the interactions of H, H2, Li and O adsorbates with Pdn clusters (n = 2 thru 20). Transition-metal clusters are specially suited for the study of quantum size effects and for formation of metallic states, and are ideal candidates for catalytic processes. Hybrid ab initio methods of quantum chemistry (particularly the DFT-B3LYP model) are used to derive optimal geometries for the clusters of interest. We compare calculated binding energies, bond-lengths, ionization potentials, electron affinities and HOMO-LUMO gaps for the clusters. Of particular interest are the comparisons of binding strengths at the three important types of sites: edge (E), hollow (H), on-top (T), threefold sites and fourfold sites. Effects of crystal symmetries corresponding to the bulk structures are investigated. The capacity of Pd clusters to adsorb H atoms will be compared to Ni clusters. Research Supported by National Science Foundation.

  8. 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. PMID:22213663

  9. Specific capture of uranyl protein targets by metal affinity chromatography.

    PubMed

    Basset, Christian; Dedieu, Alain; Guérin, Philippe; Quéméneur, Eric; Meyer, Daniel; Vidaud, Claude

    2008-03-28

    To improve general understanding of biochemical mechanisms in the field of uranium toxicology, the identification of protein targets needs to be intensified. Immobilized metal affinity chromatography (IMAC) has been widely developed as a powerful tool for capturing metal binding proteins from biological extracts. However uranyl cations (UO2(2+)) have particular physico-chemical characteristics which prevent them from being immobilized on classical metal chelating supports. We report here on the first development of an immobilized uranyl affinity chromatography method, based on the cation-exchange properties of aminophosphonate groups for uranyl binding. The cation distribution coefficient and loading capacity on the support were determined. Then the stability of the uranyl-bonded phase under our chromatographic conditions was optimized to promote affinity mechanisms. The successful enrichment of uranyl binding proteins from human serum was then proven using proteomic and mass spectral analysis. PMID:18308325

  10. High affinity ligands from in vitro selection: Complex targets

    PubMed Central

    Morris, Kevin N.; Jensen, Kirk B.; Julin, Carol M.; Weil, Michael; Gold, Larry

    1998-01-01

    Human red blood cell membranes were used as a model system to determine if the systematic evolution of ligands by exponential enrichment (SELEX) methodology, an in vitro protocol for isolating high-affinity oligonucleotides that bind specifically to virtually any single protein, could be used with a complex mixture of potential targets. Ligands to multiple targets were generated simultaneously during the selection process, and the binding affinities of these ligands for their targets are comparable to those found in similar experiments against pure targets. A secondary selection scheme, deconvolution-SELEX, facilitates rapid isolation of the ligands to targets of special interest within the mixture. SELEX provides high-affinity compounds for multiple targets in a mixture and might allow a means for dissecting complex biological systems. PMID:9501188

  11. Recent advances in affinity capillary electrophoresis for binding studies.

    PubMed

    Albishri, Hassan M; El Deeb, Sami; AlGarabli, Noura; AlAstal, Raghda; Alhazmi, Hassan A; Nachbar, Markus; El-Hady, Deia Abd; Wätzig, Hermann

    2014-01-01

    The present review covers recent advances and important applications of affinity capillary electrophoresis (ACE). It provides an overview about various ACE types, including ACE-MS, the multiple injection mode, the use of microchips and field-amplified sample injection-ACE. The most common scenarios of the studied affinity interactions are protein-drug, protein-metal ion, protein-protein, protein-DNA, protein-carbohydrate, carbohydrate-drug, peptide-peptide, DNA-drug and antigen-antibody. Approaches for the improvements of ACE in term of precision, rinsing protocols and sensitivity are discussed. The combined use of computer simulation programs to support data evaluation is presented. In conclusion, the performance of ACE is compared with other techniques such as equilibrium dialysis, parallel artificial membrane permeability assay, high-performance affinity chromatography as well as surface plasmon resonance, ultraviolet, circular dichroism, nuclear magnetic resonance, Fourier transform infrared, fluorescence, MS and isothermal titration calorimetry. PMID:25534793

  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 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.

  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 (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.

  14. Latest technologies for the enhancement of antibody affinity.

    PubMed

    Wark, Kim L; Hudson, Peter J

    2006-08-01

    High affinity antibodies are crucial both for the discovery and validation of biomarkers for human health and disease and as clinical diagnostic and therapeutic reagents. This review describes some of the latest technologies for the design, mutation and selection of high affinity antibodies that provide a paradigm for molecular evolution of a far wider range of proteins including enzymes. Strategies include both in vivo and in vitro methods and embrace the latest concepts for antibody display and selection. Specifically, affinity enhancement can be tailored to the target-binding surface, typically the complementary determining region (CDR) loops in antibodies, whereas enhanced stability, expression or catalytic properties can be affected by selected changes to the core protein scaffold. Together, these technologies provide a rapid and powerful strategy to drive the next generation of protein-based reagents for numerous clinical, environmental and agribusiness applications.

  15. 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

  16. Convex Discriminative Multitask Clustering.

    PubMed

    Zhang, Xiao-Lei

    2015-01-01

    Multitask clustering tries to improve the clustering performance of multiple tasks simultaneously by taking their relationship into account. Most existing multitask clustering algorithms fall into the type of generative clustering, and none are formulated as convex optimization problems. In this paper, we propose two convex Discriminative Multitask Clustering (DMTC) objectives to address the problems. The first one aims to learn a shared feature representation, which can be seen as a technical combination of the convex multitask feature learning and the convex Multiclass Maximum Margin Clustering (M3C). The second one aims to learn the task relationship, which can be seen as a combination of the convex multitask relationship learning and M3C. The objectives of the two algorithms are solved in a uniform procedure by the efficient cutting-plane algorithm and further unified in the Bayesian framework. Experimental results on a toy problem and two benchmark data sets demonstrate the effectiveness of the proposed algorithms. PMID:26353206

  17. 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.

  18. 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

  19. Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment.

    PubMed

    Levay, Agata; Brenneman, Randall; Hoinka, Jan; Sant, David; Cardone, Marco; Trinchieri, Giorgio; Przytycka, Teresa M; Berezhnoy, Alexey

    2015-07-13

    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.

  20. Chondroitin sulfate cluster of epiphycan from salmon nasal cartilage defines binding specificity to collagens.

    PubMed

    Tatara, Yota; Kakizaki, Ikuko; Suto, Shinichiro; Ishioka, Haruna; Negishi, Mika; Endo, Masahiko

    2015-05-01

    Epiphycan (EPY) from salmon nasal cartilage has a glycosaminoglycan (GAG) domain that is heavily modified by chondroitin 4-sulfate and chondroitin 6-sulfate. The functional role of the GAG domain has not been investigated. The interaction of EPY with collagen was examined in vitro using surface plasmon resonance analysis. EPY was found to bind to type I collagen via clustered chondroitin sulfate (CS), while a single chain of CS was unable to bind. Types I, III, VII, VIII and X collagen showed high binding affinity with EPY, whereas types II, IV, V, VI and IX showed low binding affinities. Chemical modification of lysine residues in collagen decreased the affinity with the clustered CS. These results suggest that lysine residues of collagen are involved in the interaction with the clustered CS, and the difference in lysine modification defines the binding affinity to EPY. The clustered CS was also involved in an inter-saccharide interaction, and formed self-associated EPY. CS of EPY promoted fibril formation of type I collagen.

  1. Intense laser propagation in sapphire

    NASA Astrophysics Data System (ADS)

    Tate, Jennifer L.

    When a sufficiently energetic short laser pulse propagates through a medium it can generate an explosive increase in bandwidth leading to the creation of white light; this is known as supercontinuum generation (SCG). Although it is frequently referred to as a single process, SCG is actually the result of many different parallel and competing processes. In this work we investigate the contribution of the individual physical processes underlying the SCG effect, focusing specifically on Raman processes and plasma formation in sapphire. For our experiments we use an amplified Ti:sapphire laser system producing nearly transform limited 60 fs pulses at 800 nm. Typical pulse energies for the experiments are 1--3 muJ/pulse. Using a new experimental technique, the spectrally resolved interferometric double pump, we study the contribution of non-instantaneous Raman effects. We see two distinct Raman contributions in sapphire which are much stronger than indicated in previous work. One Raman process has a period of approximately 185 fs and is related to an available optical phonon; the second Raman process has a period of 20 fs and is related to defect states caused by an oxygen vacancy in the sapphire crystal. Data from the same experiment show that the SCG light is not phase stable at low excitation energies, but that the phase stability is restored and saturates with increasing laser intensity. In a separate experiment we investigate the dynamics of plasma formation using a pump-probe technique. We observe that in sapphire both the formation and the decay of the plasma occur over time scales much longer than predicted by current theory. The plasma rise time is ˜225 fs, while the decay time is ˜150 ps; we also observe that these values do not depend on input pulse energy. In addition to these experiments, we perform a numerical integration of the extended (3 + 1) dimensional nonlinear Schrodinger equation, which models the propagation of a short laser pulse through a

  2. 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

  3. Super-Alfvénic propagation of substorm reconnection signatures and Poynting flux.

    PubMed

    Shay, M A; Drake, J F; Eastwood, J P; Phan, T D

    2011-08-01

    The propagation of reconnection signatures and their associated energy are examined using kinetic particle-in-cell simulations and Cluster satellite observations. It is found that the quadrupolar out-of-plane magnetic field near the separatrices is associated with a kinetic Alfvén wave. For magnetotail parameters, the parallel propagation of this wave is super-Alfvénic (V(∥) ∼ 1500-5500 km/s) and generates substantial Poynting flux (S ∼ 10(-5)-10(-4) W/m(2)) consistent with Cluster observations of magnetic reconnection. This Poynting flux substantially exceeds that due to frozen-in ion bulk outflows and is sufficient to generate white light aurora in Earth's ionosphere. PMID:21902330

  4. 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.

  5. 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. PMID:25547607

  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. The metrizability problem for Lorentz-invariant affine connections

    NASA Astrophysics Data System (ADS)

    Urban, Zbyněk; Volná, Jana

    2016-07-01

    The invariant metrizability problem for affine connections on a manifold, formulated by Tanaka and Krupka for connected Lie groups actions, is considered in the particular cases of Lorentz and Poincaré (inhomogeneous Lorentz) groups. Conditions under which an affine connection on the open submanifold ℝ × (ℝ3\\{(0, 0, 0)}) of the Euclidean space ℝ4 coincides with the Levi-Civita connection of some SO(3, 1), respectively (ℝ4 × sSO(3, 1))-invariant metric field are studied. We give complete description of metrizable Lorentz-invariant connections. Explicit solutions (metric fields) of the invariant metrizability equations are found and their properties are discussed.

  8. Dynamic output feedback H ∞ control for affine fuzzy systems

    NASA Astrophysics Data System (ADS)

    Wang, Huimin; Yang, Guang-Hong

    2013-06-01

    This article investigates the problem of designing H ∞ dynamic output feedback controllers for nonlinear systems, which are described by affine fuzzy models. The system outputs have been chosen as premise variables, which can guarantee that the plant and the controller always switch to the same region. By using a piecewise Lyapunov function and adding slack matrix variables, a piecewise-affine dynamic output feedback controller design method is obtained in the formulation of linear matrix inequalities (LMIs), which can be efficiently solved numerically. In contrast to the existing work, the proposed approach needs less LMI constraints and leads to less conservatism. Finally, numerical examples illustrate the effectiveness of the new result.

  9. Affinity Chromatography Purification of Cytochrome c Binding Enzymes

    NASA Astrophysics Data System (ADS)

    Azzi, Angelo; Bill, Kurt; Broger, Clemens

    1982-04-01

    An efficient affinity chromatography procedure for the isolation of mitochondrial cytochrome c oxidase and reductase is described. Saccharomyces cerevisiae cytochrome c was used as a ligand, bound to a thiol-Sepharose 4B gel through cysteine-107. In this way, the site of interaction of cytochrome c with cytochrome oxidase and reductase remained unmodified and available for binding to a number of partner enzymes. The procedure is adequate for the purification of all those proteins having in common the property of binding with high affinity to cytochrome c--e.g., cytochrome c oxidase, reductase, and peroxidase, sulfite oxidase, and reaction centers of photosynthetic bacteria.

  10. Affinity Adsorbents Based on Carriers Activated by Epoxy-compounds

    NASA Astrophysics Data System (ADS)

    Klyashchitskii, B. A.; Kuznetsov, P. V.

    1984-10-01

    The review is devoted to the synthesis and applications of affinity adsorbents based on carriers activated by epoxy-compounds. The methods for the introduction of epoxy-groups into carriers of different chemical types are discussed and conditions for the immobilisation of three-dimensional spacers and low-molecular-weight and polymeric ligands on carriers containing epoxy-groups are considered. Data are presented on the properties and applications of adsorbents of this type in affinity chromatography. The bibliography includes 144 references.

  11. and as Vertex Operator Extensionsof Dual Affine Algebras

    NASA Astrophysics Data System (ADS)

    Bowcock, P.; Feigin, B. L.; Semikhatov, A. M.; Taormina, A.

    We discover a realisation of the affine Lie superalgebra and of the exceptional affine superalgebra as vertex operator extensions of two algebras with ``dual'' levels (and an auxiliary level-1 algebra). The duality relation between the levels is . We construct the representation of on a sum of tensor products of , , and modules and decompose it into a direct sum over the spectral flow orbit. This decomposition gives rise to character identities, which we also derive. The extension of the construction to is traced to the properties of embeddings into and their relation with the dual pairs. Conversely, we show how the representations are constructed from representations.

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

    DOE PAGES

    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, 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

  13. 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.

  14. 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...

  15. 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...

  16. 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.

  17. 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...

  18. 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.

  19. Diagnostics for the ATA beam propagation experiments

    SciTech Connect

    Fessenden, T.J.; Atchison, W.L.; Barletta, W.A.

    1981-11-01

    This report contains a discussion of the diagnostics required for the beam propagation experiment to be done with the ATA accelerator. Included are a list of the diagnostics needed; a description of the ATA experimental environment; the status of beam diagnostics available at Livermore including recent developments, and a prioritized list of accelerator and propagation diagnostics under consideration or in various stages of development.

  20. Propagation modeling for land mobile satellite systems

    NASA Technical Reports Server (NTRS)

    Barts, R. Michael; Stutzman, Warren L.

    1988-01-01

    A simplified empirical model for predicting primary fade statistics for a vegetatively shadowed mobile satellite signal is presented, and predictions based on the model are presented using propagation parameter values from experimental data. Results from the empirical model are used to drive a propagation simulator to produce the secondary fade statistics of average fade duration.

  1. Steps toward quantitative infrasound propagation modeling

    NASA Astrophysics Data System (ADS)

    Waxler, Roger; Assink, Jelle; Lalande, Jean-Marie; Velea, Doru

    2016-04-01

    Realistic propagation modeling requires propagation models capable of incorporating the relevant physical phenomena as well as sufficiently accurate atmospheric specifications. The wind speed and temperature gradients in the atmosphere provide multiple ducts in which low frequency sound, infrasound, can propagate efficiently. The winds in the atmosphere are quite variable, both temporally and spatially, causing the sound ducts to fluctuate. For ground to ground propagation the ducts can be borderline in that small perturbations can create or destroy a duct. In such cases the signal propagation is very sensitive to fluctuations in the wind, often producing highly dispersed signals. The accuracy of atmospheric specifications is constantly improving as sounding technology develops. There is, however, a disconnect between sound propagation and atmospheric specification in that atmospheric specifications are necessarily statistical in nature while sound propagates through a particular atmospheric state. In addition infrasonic signals can travel to great altitudes, on the order of 120 km, before refracting back to earth. At such altitudes the atmosphere becomes quite rare causing sound propagation to become highly non-linear and attenuating. Approaches to these problems will be presented.

  2. Propagation of a fluidization - combustion wave

    SciTech Connect

    Pron, G.P.; Gusachenko, L.K.; Zarko, V.E.

    1994-05-01

    A fluidization-combustion wave propagating through a fixed and initially cool bed was created by igniting coal at the top surface of the bed. The proposed physical interpretation of the phenomenon is in qualitative agreement with the experimental dependences of the characteristics of the process on determining parameters. A kindling regime with forced wave propagation is suggested.

  3. 3D Elastic Seismic Wave Propagation Code

    1998-09-23

    E3D is capable of simulating seismic wave propagation in a 3D heterogeneous earth. Seismic waves are initiated by earthquake, explosive, and/or other sources. These waves propagate through a 3D geologic model, and are simulated as synthetic seismograms or other graphical output.

  4. 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.

  5. 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.

  6. Reactions of intermetallic clusters

    NASA Astrophysics Data System (ADS)

    Farley, R. W.; Castleman, A. W., Jr.

    1990-02-01

    Reaction of bismuth-alkali clusters with closed-shell HX acids provides insight into the structures, formation, and stabilities of these intermetallic species. HC1 and HI are observed to quantitatively strip BixNay and BixKy, respectively, of their alkali component, leaving bare bismuth clusters as the only bismuth-containing species detected. Product bismuth clusters exhibit the same distribution observed when pure bismuth is evaporated in the source. Though evaporated simultaneously from the same crucible, this suggests alkali atoms condense onto existing bismuth clusters and have negligible effect on their formation and consequent distribution. The indistinguishibility of reacted and pure bismuth cluster distributions further argues against the simple replacement of alkali atoms with hydrogen in these reactions. This is considered further evidence that the alkali atoms are external to the stable bismuth Zintl anionic structures. Reactivities of BixNay clusters with HC1 are estimated to lie between 3×10-13 for Bi4Na, to greater than 4×10-11 for clusters possessing large numbers of alkali atoms. Bare bismuth clusters are observed in separate experiments to react significantly more slowly with rates of 1-9×10-14 and exhibit little variation of reactivity with size. The bismuth clusters may thus be considered a relatively inert substrate upon which the alkali overlayer reacts.

  7. Management of cluster headache.

    PubMed

    Tfelt-Hansen, Peer C; Jensen, Rigmor H

    2012-07-01

    The prevalence of cluster headache is 0.1% and cluster headache is often not diagnosed or misdiagnosed as migraine or sinusitis. In cluster headache there is often a considerable diagnostic delay - an average of 7 years in a population-based survey. Cluster headache is characterized by very severe or severe orbital or periorbital pain with a duration of 15-180 minutes. The cluster headache attacks are accompanied by characteristic associated unilateral symptoms such as tearing, nasal congestion and/or rhinorrhoea, eyelid oedema, miosis and/or ptosis. In addition, there is a sense of restlessness and agitation. Patients may have up to eight attacks per day. Episodic cluster headache (ECH) occurs in clusters of weeks to months duration, whereas chronic cluster headache (CCH) attacks occur for more than 1 year without remissions. Management of cluster headache is divided into acute attack treatment and prophylactic treatment. In ECH and CCH the attacks can be treated with oxygen (12 L/min) or subcutaneous sumatriptan 6 mg. For both oxygen and sumatriptan there are two randomized, placebo-controlled trials demonstrating efficacy. In both ECH and CCH, verapamil is the prophylactic drug of choice. Verapamil 360 mg/day was found to be superior to placebo in one clinical trial. In clinical practice, daily doses of 480-720 mg are mostly used. Thus, the dose of verapamil used in cluster headache treatment may be double the dose used in cardiology, and with the higher doses the PR interval should be checked with an ECG. At the start of a cluster, transitional preventive treatment such as corticosteroids or greater occipital nerve blockade can be given. In CCH and in long-standing clusters of ECH, lithium, methysergide, topiramate, valproic acid and ergotamine tartrate can be used as add-on prophylactic treatment. In drug-resistant CCH, neuromodulation with either occipital nerve stimulation or deep brain stimulation of the hypothalamus is an alternative treatment strategy

  8. The youngest globular clusters

    NASA Astrophysics Data System (ADS)

    Beck, Sara

    2015-11-01

    It is likely that all stars are born in clusters, but most clusters are not bound and disperse. None of the many protoclusters in our Galaxy are likely to develop into long-lived bound clusters. The super star clusters (SSCs) seen in starburst galaxies are more massive and compact and have better chances of survival. The birth and early development of SSCs takes place deep in molecular clouds, and during this crucial stage the embedded clusters are invisible to optical or UV observations but are studied via the radio-infrared supernebulae (RISN) they excite. We review observations of embedded clusters and identify RISN within 10 Mpc whose exciting clusters have ≈ 106 M⊙ or more in volumes of a few pc3 and which are likely to not only survive as bound clusters, but to evolve into objects as massive and compact as Galactic globulars. These clusters are distinguished by very high star formation efficiency η, at least a factor of 10 higher than the few percent seen in the Galaxy, probably due to the violent disturbances their host galaxies have undergone. We review recent observations of the kinematics of the ionized gas in RISN showing outflows through low-density channels in the ambient molecular cloud; this may protect the cloud from feedback by the embedded H II region.

  9. 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.

  10. Affinity chromatography and affinity labeling of rat liver succinyl-CoA synthetase.

    PubMed

    Ball, D J; Nishimura, J S

    1980-11-25

    Succinyl-CoA synthetase has been purified to apparent homogeneity from rat liver. The key step in the purification procedure involved adsorption on a GDP dialdehyde (dial-GDP)-adipic dihydrazide-Sepharose 4B column and elution by GDP-Mg2+. Like the pig heart enzyme (Brownie, E. R., and Bridger, W. A. (1972) Can. J. Biochem. 50, 719--724), the rat liver enzyme was an alpha beta heterodimer and only the alpha subunit was phosphorylated by [gamma-32P]GTP. The A 280(0.1%) of the enzyme was determined to be 0.5. Amino acid analyses revealed significant similarities in 50% of the amino acid residues of rat liver and Escherichia coli succinyl-CoA synthetases. However, immunodiffusion analysis failed to reveal any antigenic identity between the two enzymes. Incubation with the affinity label, dial-GDP, in the presence of Mg2+ resulted in a biphasic inactivation of the enzyme. The extent of the rapid phase of inactivation appeared to be related to the extent of dephosphorylation of the enzyme and was prevented by preincubation of the enzyme with GTP-Mg2+. The presence of GDP-Mg2+ in the incubation medium prevented the slow phase of the inactivation and retarded the rapid phase. Dephosphorylated enzyme was approximately 2 orders of magnitude more susceptible to inactivation by dial-GDP than phosphorylated enzyme. Labeling of succinyl-CoA synthetase with [3H]dial-GDP gave a linear relationship between inactivation and incorporation of radioactivity with an extrapolated value of less than 1.2 mol of analog/mol of enzyme at 100% inactivation. The distribution of the label in enzyme that was inactivated 40% was approximately 60% in the alpha subunit and 40% in the beta subunit. Thus, while phosphorylation of the enzyme occurs exclusively in the alpha subunit, the nucleotide binding site appears to include components from both alpha and beta subunits. PMID:7430155

  11. Wave propagation in magnetic fluids

    NASA Astrophysics Data System (ADS)

    Cissoko, Mahdy

    1987-08-01

    This paper deals within the relativistic framework with the wave propagation in magnetizable fluids, assumed to be perfect, magnetically soft, isotropic, and inhomogeneous with an arbitrary isotropic law χ=χ(T,r,||b||2) (χ,T,r,||b|| being the magnetic susceptibility, the proper temperature, the proper material density, and the strength of the magnetic field, respectively). The characteristic manifolds of the flow are determined in a very elegant and rigorous manner which avoids the extensive algebraic manipulations one usually encounters in the classical methods of characteristics. It is shown that in a magnetic medium there exists a hyperbolic region of nonsteady flows of magnetizable fluids. This implies the existence of magnetosonic waves of the same kind as in nonmagnetic fluids (χ or μ=const), that is, as in ordinary magnetohydrodynamics. However, in magnetic fluids there is the possibility of the development of instabilities similar to that which arise in nonmagnetic fluids with transverse and longitudinal pressure [M. Cissoko, Ann. Mat. Pura Appl. 111, 331 (1976)].

  12. 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.

  13. In vitro propagation of jojoba.

    PubMed

    Llorente, Berta E; Apóstolo, Nancy M

    2013-01-01

    Jojoba (Simmondsia chinensis (Link) Schn.) is a nontraditional crop in arid and semi-arid areas. Vegetative propagation can be achieved by layering, grafting, or rooting semi-hardwood cuttings, but the highest number of possible propagules is limited by the size of the plants and time of the year. Micropropagation is highly recommended strategy for obtaining jojoba elite clones. For culture initiation, single-node explants are cultivated on Murashige and Skoog medium (MS) supplemented with Gamborg's vitamins (B5), 11.1 μM BA (N(6)-benzyl-adenine), 0.5 μM IBA (indole-3-butyric acid), and 1.4 μM GA(3) (gibberellic acid). Internodal and apical cuttings proliferate on MS medium containing B5 vitamins and 4.4 μM BA. Rooting is achieved on MS medium (half strength mineral salt) amended with B5 vitamins and 14.7 μM IBA during 7 days and transferred to develop in auxin-free rooting medium. Plantlets are acclimatized using a graduated humidity regime on soil: peat: perlite (5:1:1) substrate. This micropagation protocol produces large numbers of uniform plants from selected genotypes of jojoba. PMID:23179687

  14. In vitro propagation of jojoba.

    PubMed

    Llorente, Berta E; Apóstolo, Nancy M

    2013-01-01

    Jojoba (Simmondsia chinensis (Link) Schn.) is a nontraditional crop in arid and semi-arid areas. Vegetative propagation can be achieved by layering, grafting, or rooting semi-hardwood cuttings, but the highest number of possible propagules is limited by the size of the plants and time of the year. Micropropagation is highly recommended strategy for obtaining jojoba elite clones. For culture initiation, single-node explants are cultivated on Murashige and Skoog medium (MS) supplemented with Gamborg's vitamins (B5), 11.1 μM BA (N(6)-benzyl-adenine), 0.5 μM IBA (indole-3-butyric acid), and 1.4 μM GA(3) (gibberellic acid). Internodal and apical cuttings proliferate on MS medium containing B5 vitamins and 4.4 μM BA. Rooting is achieved on MS medium (half strength mineral salt) amended with B5 vitamins and 14.7 μM IBA during 7 days and transferred to develop in auxin-free rooting medium. Plantlets are acclimatized using a graduated humidity regime on soil: peat: perlite (5:1:1) substrate. This micropagation protocol produces large numbers of uniform plants from selected genotypes of jojoba.

  15. S-Band propagation measurements

    NASA Astrophysics Data System (ADS)

    Briskman, Robert D.

    1994-08-01

    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.

  16. Topographic effects on infrasound propagation.

    PubMed

    McKenna, Mihan H; Gibson, Robert G; Walker, Bob E; McKenna, Jason; Winslow, Nathan W; Kofford, Aaron S

    2012-01-01

    Infrasound data were collected using portable arrays in a region of variable terrain elevation to quantify the effects of topography on observed signal amplitude and waveform features at distances less than 25 km from partially contained explosive sources during the Frozen Rock Experiment (FRE) in 2006. Observed infrasound signals varied in amplitude and waveform complexity, indicating propagation effects that are due in part to repeated local maxima and minima in the topography on the scale of the dominant wavelengths of the observed data. Numerical simulations using an empirically derived pressure source function combining published FRE accelerometer data and historical data from Project ESSEX, a time-domain parabolic equation model that accounted for local terrain elevation through terrain-masking, and local meteorological atmospheric profiles were able to explain some but not all of the observed signal features. Specifically, the simulations matched the timing of the observed infrasound signals but underestimated the waveform amplitude observed behind terrain features, suggesting complex scattering and absorption of energy associated with variable topography influences infrasonic energy more than previously observed.

  17. Topographic effects on infrasound propagation.

    PubMed

    McKenna, Mihan H; Gibson, Robert G; Walker, Bob E; McKenna, Jason; Winslow, Nathan W; Kofford, Aaron S

    2012-01-01

    Infrasound data were collected using portable arrays in a region of variable terrain elevation to quantify the effects of topography on observed signal amplitude and waveform features at distances less than 25 km from partially contained explosive sources during the Frozen Rock Experiment (FRE) in 2006. Observed infrasound signals varied in amplitude and waveform complexity, indicating propagation effects that are due in part to repeated local maxima and minima in the topography on the scale of the dominant wavelengths of the observed data. Numerical simulations using an empirically derived pressure source function combining published FRE accelerometer data and historical data from Project ESSEX, a time-domain parabolic equation model that accounted for local terrain elevation through terrain-masking, and local meteorological atmospheric profiles were able to explain some but not all of the observed signal features. Specifically, the simulations matched the timing of the observed infrasound signals but underestimated the waveform amplitude observed behind terrain features, suggesting complex scattering and absorption of energy associated with variable topography influences infrasonic energy more than previously observed. PMID:22280569

  18. 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.

  19. Propagation of an atmospheric pressure plasma plume

    SciTech Connect

    Lu, X.; Xiong, Q.; Xiong, Z.; Hu, J.; Zhou, F.; Gong, W.; Xian, Y.; Zou, C.; Tang, Z.; Jiang, Z.; Pan, Y.

    2009-02-15

    The ''plasma bullet'' behavior of atmospheric pressure plasma plumes has recently attracted significant interest. In this paper, a specially designed plasma jet device is used to study this phenomenon. It is found that a helium primary plasma can propagate through the wall of a dielectric tube and keep propagating inside the dielectric tube (secondary plasma). High-speed photographs show that the primary plasma disappears before the secondary plasma starts to propagate. Both plumes propagate at a hypersonic speed. Detailed studies on the dynamics of the plasma plumes show that the local electric field induced by the charges on the surface of the dielectric tube plays an important role in the ignition of the secondary plasma. This indicates that the propagation of the plasma plumes may be attributed to the local electric field induced by the charges in the bulletlike plasma volume.

  20. Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media

    NASA Astrophysics Data System (ADS)

    Fahrbach, Florian O.; Rohrbach, Alexander

    2012-01-01

    Laser beams that can self-reconstruct their initial beam profile even in the presence of massive phase perturbations are able to propagate deeper into inhomogeneous media. This ability has crucial advantages for light sheet-based microscopy in thick media, such as cell clusters, embryos, skin or brain tissue or plants, as well as scattering synthetic materials. A ring system around the central intensity maximum of a Bessel beam enables its self-reconstruction, but at the same time illuminates out-of-focus regions and deteriorates image contrast. Here we present a detection method that minimizes the negative effect of the ring system. The beam's propagation stability along one straight line enables the use of a confocal line principle, resulting in a significant increase in image contrast. The axial resolution could be improved by nearly 100% relative to the standard light-sheet techniques using scanned Gaussian beams, while demonstrating self-reconstruction also for high propagation depths.

  1. Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media.

    PubMed

    Fahrbach, Florian O; Rohrbach, Alexander

    2012-01-17

    Laser beams that can self-reconstruct their initial beam profile even in the presence of massive phase perturbations are able to propagate deeper into inhomogeneous media. This ability has crucial advantages for light sheet-based microscopy in thick media, such as cell clusters, embryos, skin or brain tissue or plants, as well as scattering synthetic materials. A ring system around the central intensity maximum of a Bessel beam enables its self-reconstruction, but at the same time illuminates out-of-focus regions and deteriorates image contrast. Here we present a detection method that minimizes the negative effect of the ring system. The beam's propagation stability along one straight line enables the use of a confocal line principle, resulting in a significant increase in image contrast. The axial resolution could be improved by nearly 100% relative to the standard light-sheet techniques using scanned Gaussian beams, while demonstrating self-reconstruction also for high propagation depths.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Cluster of DnaA Boxes Involved in Regulation of Streptomyces Chromosome Replication: from In Silico to In Vivo Studies†

    PubMed Central

    Smulczyk-Krawczyszyn, Aleksandra; Jakimowicz, Dagmara; Ruban-Ośmiałowska, Beata; Zawilak-Pawlik, Anna; Majka, Jerzy; Chater, Keith; Zakrzewska-Czerwińska, Jolanta

    2006-01-01

    In Streptomyces coelicolor, replication is initiated by the DnaA protein in the centrally located oriC region and proceeds bidirectionally until the replication forks reach the ends of the linear chromosome. We identified three clusters of DnaA boxes (H69, H24, and D78) which are in a relatively short segment of the chromosome centered on the oriC region. Of the clusters analyzed, D78 exhibited the highest affinity for the DnaA protein; the affinity of DnaA for the D78 cluster was about eightfold higher than the affinity for oriC. The high-affinity DnaA boxes appear to be involved in the control of chromosome replication. Deletion of D78 resulted in more frequent chromosome replication (an elevated ratio of origins to chromosome ends was observed) and activated aerial mycelium formation, leading to earlier colony maturation. In contrast, extra copies of D78 (delivered on a plasmid) caused slow colony growth, presumably because of a reduction in the frequency of initiation of chromosome replication. This suggests that the number of high-affinity DnaA boxes is relatively constant in hyphal compartments and that deletion of D78 therefore permits an increased copy number of either the chromosomal origin region or a plasmid harboring the D78 cluster. This system conceivably influences the timing of decisions to initiate aerial mycelial formation and sporulation. PMID:16923885

  8. Excitation wave propagation as a possible mechanism for signal transmission in pancreatic islets of Langerhans.

    PubMed Central

    Aslanidi, O V; Mornev, O A; Skyggebjerg, O; Arkhammar, P; Thastrup, O; Sørensen, M P; Christiansen, P L; Conradsen, K; Scott, A C

    2001-01-01

    In response to glucose application, beta-cells forming pancreatic islets of Langerhans start bursting oscillations of the membrane potential and intracellular calcium concentration, inducing insulin secretion by the cells. Until recently, it has been assumed that the bursting activity of beta-cells in a single islet of Langerhans is synchronized across the whole islet due to coupling between the cells. However, time delays of several seconds in the activity of distant cells are usually observed in the islets of Langerhans, indicating that electrical/calcium wave propagation through the islets can occur. This work presents both experimental and theoretical evidence for wave propagation in the islets of Langerhans. Experiments with Fura-2 fluorescence monitoring of spatiotemporal calcium dynamics in the islets have clearly shown such wave propagation. Furthermore, numerical simulations of the model describing a cluster of electrically coupled beta-cells have supported our view that the experimentally observed calcium waves are due to electric pulses propagating through the cluster. This point of view is also supported by independent experimental results. Based on the model equations, an approximate analytical expression for the wave velocity is introduced, indicating which parameters can alter the velocity. We point to the possible role of the observed waves as signals controlling the insulin secretion inside the islets of Langerhans, in particular, in the regions that cannot be reached by any external stimuli such as high glucose concentration outside the islets. PMID:11222284

  9. 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.

  10. N-Methyl-D-aspartate receptors are clustered and immobilized on dendrites of living cortical neurons.

    PubMed Central

    Benke, T A; Jones, O T; Collingridge, G L; Angelides, K J

    1993-01-01

    The response of nerve cells to synaptic inputs and the propagation of this activation is critically dependent on the cell-surface distribution of ion channels. In the hippocampus, Ca2+ influx through N-methyl-D-aspartate receptors (NMDAR) and/or voltage-dependent calcium channels on dendrites is thought to be critically involved in long-term potentiation, neurite outgrowth, epileptogenesis, synaptogenesis, and cell death. We report that conantokin-G (CntxG), a peptide from Conus geographus venom, competitively blocked with high affinity and specificity NMDAR-mediated currents in hippocampal neurons and is a reliable probe for exploring NMDAR distribution. Fluorescent derivatives of CntxG were prepared and used to directly determine NMDAR distribution on living hippocampal neurons by digital imaging and confocal fluorescence microscopy. In hippocampal slices, the CA1 dendritic subfield was strongly labeled by CntxG, whereas the CA3 mossy fiber region was not. On CA1 hippocampal neurons in culture, dendritic CntkG-sensitive NMDAR were clustered at sites of synaptic contacts, whereas somatic NMDAR were distributed diffusely and in patches. NMDAR distribution differed from the distribution of voltage-dependent calcium channels. A significant fraction of labeled NMDAR on somata and dendrites was found to be highly mobile: rates were consistent with the possible rapid recruitment of NMDAR to specific synaptic locations. The localization of NMDAR and modulation of this distribution demonstrated here may have important implications for the events that underlie neuronal processing and synaptic remodeling during associative synaptic modification. Images Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7689230

  11. Native Elution of Yeast Protein Complexes Obtained by Affinity Capture.

    PubMed

    LaCava, John; Fernandez-Martinez, Javier; Rout, Michael P

    2016-01-01

    This protocol describes two options for the native (nondenaturing) elution of protein complexes obtained by affinity capture. The first approach involves the elution of complexes purified through a tag that includes a human rhinovirus 3C protease (PreScission protease) cleavage site sequence between the protein of interest and the tag. Incubation with the protease cleaves immobilized complexes from the affinity medium. The second approach involves the release of protein A-tagged protein complexes using a competitive elution reagent called PEGylOx. The degree of purity of the native assemblies eluted is sample dependent and strongly influenced by the affinity capture. It should be noted that the efficiency of native elution is commonly lower than that of elution by a denaturing agent (e.g., SDS) and the release of the complex will be limited by the activity of the protease or the inhibition constant (Ki) of the competitive release agent. However, an advantage of native release is that some nonspecifically bound materials tend to stay adsorbed to the affinity medium, providing an eluted fraction of higher purity. Finally, keep in mind that the presence of the protease or elution peptide could potentially affect downstream applications; thus, their removal should be considered. PMID:27371597

  12. "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…

  13. 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.

  14. Background correction using dinucleotide affinities improves the performance of GCRMA

    PubMed Central

    Gharaibeh, Raad Z; Fodor, Anthony A; Gibas, Cynthia J

    2008-01-01

    Background High-density short oligonucleotide microarrays are a primary research tool for assessing global gene expression. Background noise on microarrays comprises a significant portion of the measured raw data, which can have serious implications for the interpretation of the generated data if not estimated correctly. Results We introduce an approach to calculate probe affinity based on sequence composition, incorporating nearest-neighbor (NN) information. Our model uses position-specific dinucleotide information, instead of the original single nucleotide approach, and adds up to 10% to the total variance explained (R2) when compared to the previously published model. We demonstrate that correcting for background noise using this approach enhances the performance of the GCRMA preprocessing algorithm when applied to control datasets, especially for detecting low intensity targets. Conclusion Modifying the previously published position-dependent affinity model to incorporate dinucleotide information significantly improves the performance of the model. The dinucleotide affinity model enhances the detection of differentially expressed genes when implemented as a background correction procedure in GeneChip preprocessing algorithms. This is conceptually consistent with physical models of binding affinity, which depend on the nearest-neighbor stacking interactions in addition to base-pairing. PMID:18947404

  15. 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"…

  16. 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…

  17. 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…

  18. Peptides@mica: from affinity to adhesion mechanism.

    PubMed

    Gladytz, A; John, T; Gladytz, T; Hassert, R; Pagel, M; Risselada, H J; Naumov, S; Beck-Sickinger, A G; Abel, B

    2016-09-14

    Investigating the adsorption of peptides on inorganic surfaces, on the molecular level, is fundamental for medicinal and analytical applications. Peptides can be potent as linkers between surfaces and living cells in biochips or in implantation medicine. Here, we studied the adsorption process of the positively charged pentapeptide RTHRK, a recently identified binding sequence for surface oxidized silicon, and novel analogues thereof to negatively charged mica surfaces. Homogeneous formation of monolayers in the nano- and low micromolar peptide concentration range was observed. We propose an alternative and efficient method to both quantify binding affinity and follow adhesion behavior. This method makes use of the thermodynamic relationship between surface coverage, measured by atomic force microscopy (AFM), and the concomitant free energy of adhesion. A knowledge-based fit to the autocorrelation of the AFM images was used to correct for a biased surface coverage introduced by the finite lateral resolution of the AFM. Binding affinities and mechanisms were further explored by large scale molecular dynamics (MD) simulations. The combination of well validated MD simulations with topological data from AFM revealed a better understanding of peptide adsorption processes on the atomistic scale. We demonstrate that binding affinity is strongly determined by a peptide's ability to form salt bridges and hydrogen bonds with the surface lattice. Consequently, differences in hydrogen bond formation lead to substantial differences in binding affinity despite conservation of the peptide's overall charge. Further, MD simulations give access to relative changes in binding energy of peptide variations in comparison to a lead compound. PMID:27491508

  19. Development of gadolinium based nanoparticles having an affinity towards melanin

    NASA Astrophysics Data System (ADS)

    Morlieras, Jessica; Chezal, Jean-Michel; Miot-Noirault, Elisabeth; Roux, Amandine; Heinrich-Balard, Laurence; Cohen, Richard; Tarrit, Sébastien; Truillet, Charles; Mignot, Anna; Hachani, Roxanne; Kryza, David; Antoine, Rodolphe; Dugourd, Philippe; Perriat, Pascal; Janier, Marc; Sancey, Lucie; Lux, François; Tillement, Olivier

    2013-01-01

    Small Rigid Platforms (SRPs) are sub-5 nanometre gadolinium based nanoparticles that have been developed for multimodal imaging and theranostic applications. They are composed of a polysiloxane network surrounded by gadolinium chelates. A covalent coupling with quinoxaline derivatives has been performed. Such derivatives have proven their affinity for melanin frequently expressed in primary melanoma cases. Three different quinoxaline derivatives have been synthesised and coupled to the nanoparticles. The affinity of the grafted nanoparticles for melanin has then been shown in vitro by surface plasmon resonance on a homemade melanin grafted gold chip.Small Rigid Platforms (SRPs) are sub-5 nanometre gadolinium based nanoparticles that have been developed for multimodal imaging and theranostic applications. They are composed of a polysiloxane network surrounded by gadolinium chelates. A covalent coupling with quinoxaline derivatives has been performed. Such derivatives have proven their affinity for melanin frequently expressed in primary melanoma cases. Three different quinoxaline derivatives have been synthesised and coupled to the nanoparticles. The affinity of the grafted nanoparticles for melanin has then been shown in vitro by surface plasmon resonance on a homemade melanin grafted gold chip. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr33457g

  20. Feature Matching with Affine-Function Transformation Models.

    PubMed

    Li, Hongsheng; Huang, Xiaolei; Huang, Junzhou; Zhang, Shaoting

    2014-12-01

    Feature matching is an important problem and has extensive uses in computer vision. However, existing feature matching methods support either a specific or a small set of transformation models. In this paper, we propose a unified feature matching framework which supports a large family of transformation models. We call the family of transformation models the affine-function family, in which all transformations can be expressed by affine functions with convex constraints. In this framework, the goal is to recover transformation parameters for every feature point in a template point set to calculate their optimal matching positions in an input image. Given pairwise feature dissimilarity values between all points in the template set and the input image, we create a convex dissimilarity function for each template point. Composition of such convex functions with any transformation model in the affine-function family is shown to have an equivalent convex optimization form that can be optimized efficiently. Four example transformation models in the affine-function family are introduced to show the flexibility of our proposed framework. Our framework achieves 0.0 percent matching errors for both CMU House and Hotel sequences following the experimental setup in [6]. PMID:26353148

  1. Smooth surfaces from bilinear patches: Discrete affine minimal surfaces.

    PubMed

    Käferböck, Florian; Pottmann, Helmut

    2013-06-01

    Motivated by applications in freeform architecture, we study surfaces which are composed of smoothly joined bilinear patches. These surfaces turn out to be discrete versions of negatively curved affine minimal surfaces and share many properties with their classical smooth counterparts. We present computational design approaches and study special cases which should be interesting for the architectural application.

  2. Properties of an affine transport equation and its holonomy

    NASA Astrophysics Data System (ADS)

    Vines, Justin; Nichols, David A.

    2016-10-01

    An affine transport equation was used recently to study properties of angular momentum and gravitational-wave memory effects in general relativity. In this paper, we investigate local properties of this transport equation in greater detail. Associated with this transport equation is a map between the tangent spaces at two points on a curve. This map consists of a homogeneous (linear) part given by the parallel transport map along the curve plus an inhomogeneous part, which is related to the development of a curve in a manifold into an affine tangent space. For closed curves, the affine transport equation defines a "generalized holonomy" that takes the form of an affine map on the tangent space. We explore the local properties of this generalized holonomy by using covariant bitensor methods to compute the generalized holonomy around geodesic polygon loops. We focus on triangles and "parallelogramoids" with sides formed from geodesic segments. For small loops, we recover the well-known result for the leading-order linear holonomy (˜ Riemann × area), and we derive the leading-order inhomogeneous part of the generalized holonomy (˜ Riemann × area^{3/2}). Our bitensor methods let us naturally compute higher-order corrections to these leading results. These corrections reveal the form of the finite-size effects that enter into the holonomy for larger loops; they could also provide quantitative errors on the leading-order results for finite loops.

  3. 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

  4. Bimolecular affinity purification: a variation of TAP with multiple applications.

    PubMed

    Starokadomskyy, Petro; Burstein, Ezra

    2014-01-01

    The identification of true interacting partners of any given bait can be plagued by the nonspecific purification of irrelevant proteins. To avoid this problem, Tandem Affinity Purification (TAP) is a widely used procedure in molecular biology as this reduces the chance of nonspecific proteins being present in the final preparation. In this approach, two different affinity tags are fused to the protein bait. Herein, we review in detail a variation on the TAP procedure that we have previously developed, where the affinity moieties are placed on two different proteins that form a complex in vivo. This variation, which we refer to as Bimolecular Affinity Purification (BAP), is suited for the identification of specific molecular complexes marked by the presence of two known proteins. We have utilized BAP for characterization of molecular complexes and evaluation of proteins interaction. Another application of BAP is the isolation of ubiquitin-like proteins (UBL)-modified fractions of a given protein and characterization of the lysine-acceptor site and structure of UBL-chains. PMID:24943324

  5. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    NASA Astrophysics Data System (ADS)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  6. 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…

  7. Calculation of antibody affinity in homogeneous and heterogeneous systems.

    PubMed

    Chalquest, R R

    1988-12-01

    Antibody affinity is an important determinant of all antibody-antigen reactions. A new computer program, AFCRV, was developed to calculate binding constants with data from a radioimmunoassay on most microcomputers in the laboratory by using constant-ratio dilution curves. Evaluation of a homogeneous or heterogeneous antibody in the presence of a single antigen can be accomplished.

  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. 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…

  10. Cluster Interest Inventory.

    ERIC Educational Resources Information Center

    Herzog, Douglas

    The Cluster Interest Inventory is designed to familiarize students with representative occupations in 13 career clusters: (1) agribusiness and natural resources, (2) business marketing, and office occupations, (3) communications and media, (4) consumer and homemaker, (5) fine arts and humanities, (6) health, (7) manufacturing and processing, (8)…

  11. Matlab Cluster Ensemble Toolbox

    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. Withmore » 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.« less

  12. [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.

  13. Blue emitting undecaplatinum clusters

    NASA Astrophysics Data System (ADS)

    Chakraborty, Indranath; Bhuin, Radha Gobinda; Bhat, Shridevi; Pradeep, T.

    2014-07-01

    A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents.A blue luminescent 11-atom platinum cluster showing step-like optical features and the absence of plasmon absorption was synthesized. The cluster was purified using high performance liquid chromatography (HPLC). Electrospray ionization (ESI) and matrix assisted laser desorption ionization (MALDI) mass spectrometry (MS) suggest a composition, Pt11(BBS)8, which was confirmed by a range of other experimental tools. The cluster is highly stable and compatible with many organic solvents. Electronic supplementary information (ESI) available: Details of experimental procedures, instrumentation, chromatogram of the crude cluster; SEM/EDAX, DLS, PXRD, TEM, FT-IR, and XPS of the isolated Pt11 cluster; UV/Vis, MALDI MS and SEM/EDAX of isolated 2 and 3; and 195Pt NMR of the K2PtCl6 standard. See DOI: 10.1039/c4nr02778g

  14. Muster: Massively Scalable Clustering

    2010-05-20

    Muster is a framework for scalable cluster analysis. It includes implementations of classic K-Medoids partitioning algorithms, as well as infrastructure for making these algorithms run scalably on very large systems. In particular, Muster contains algorithms such as CAPEK (described in reference 1) that are capable of clustering highly distributed data sets in-place on a hundred thousand or more processes.

  15. Illinois' Career Cluster Model

    ERIC Educational Resources Information Center

    Jankowski, Natasha A.; Kirby, Catherine L.; Bragg, Debra D.; Taylor, Jason L.; Oertle, Kathleen M.

    2009-01-01

    This booklet provides information to multiple stakeholders on the implementation of career clusters in Illinois. The booklet is an extension of the previous edition titled "An Introduction to Illinois CTE Programs of Study" (2008), and provides a resource for partners to understand Illinois' Career Cluster Model as its own adaptation of the…

  16. 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.

  17. 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…

  18. 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 probability…

  19. Spatial clustering method based on three-dimensional cloud model

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; Wang, Li; Deng, Yu; Liu, Jia

    2008-12-01

    Spatial clustering is one of those major methods applying to spatial data mining and knowledge discovery. The purpose of this paper is to set forth Spatial Clustering Method Based on Multidimensional Cloud Model, which can be widely applied to the research on classification and hierarchy in realm of spatial data mining and knowledge discovery. This paper summarizes all kinds of cloud model and analyzes the optimalizing form of spatial data-three-dimensional cloud model. The limitation which sets the weighing value subjectively in traditional way and propagation of error can be avoided. The implementation procedure of this method is advanced, and the feasibility of this method is proven through experiments effectively.

  20. Electron acceleration via high contrast laser interacting with submicron clusters

    SciTech Connect

    Zhang Lu; Chen Liming; Wang Weiming; Yan Wenchao; Yuan Dawei; Mao Jingyi; Wang Zhaohua; Liu Cheng; Shen Zhongwei; Li Yutong; Dong Quanli; Lu Xin; Ma Jinglong; Wei Zhiyi; Faenov, Anatoly; Pikuz, Tatiana; Li Dazhang; Sheng Zhengming; Zhang Jie

    2012-01-02

    We experimentally investigated electron acceleration from submicron size argon clusters-gas target irradiated by a 100 fs, 10 TW laser pulses having a high-contrast. Electron beams are observed in the longitudinal and transverse directions to the laser propagation. The measured energy of the longitudinal electron reaches 600 MeV and the charge of the electron beam in the transverse direction is more than 3 nC. A two-dimensional particle-in-cell simulation of the interaction has been performed and it shows an enhancement of electron charge by using the cluster-gas target.

  1. Cosmology with galaxy clusters

    NASA Astrophysics Data System (ADS)

    Sartoris, Barbara

    2015-08-01

    Clusters of galaxies are powerful probes to constrain parameters that describe the cosmological models and to distinguish among different models. Since, the evolution of the cluster mass function and large-scale clustering contain the informations about the linear growth rate of perturbations and the expansion history of the Universe, clusters have played an important role in establishing the current cosmological paradigm. It is crucial to know how to determine the cluster mass from observational quantities when using clusters as cosmological tools. For this, numerical simulations are helpful to define and study robust cluster mass proxies that have minimal and well understood scatter across the mass and redshift ranges of interest. Additionally, the bias in cluster mass determination can be constrained via observations of the strong and weak lensing effect, X-ray emission, the Sunyaev- Zel’dovic effect, and the dynamics of galaxies.A major advantage of X-ray surveys is that the observable-mass relation is tight. Moreover, clusters can be easily identified in X-ray as continuous, extended sources. As of today, interesting cosmological constraints have been obtained from relatively small cluster samples (~102), X-ray selected by the ROSAT satellite over a wide redshift range (0clusters, the ROSAT All-Sky Survey.The next generation of X-ray telescopes will enhance the statistics of detected clusters and enlarge their redshift coverage. In particular, eROSITA will produce a catalog of >105 clusters with photometric redshifts from multi-band optical surveys (e.g. PanSTARRS, DES, and LSST). This will vastly improve upon current cosmological constraints, especially by the synergy with other cluster surveys that

  2. 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

  3. 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.

  4. Myoglobin oxygen affinity in aquatic and terrestrial birds and mammals.

    PubMed

    Wright, Traver J; Davis, Randall W

    2015-07-01

    Myoglobin (Mb) is an oxygen binding protein found in vertebrate skeletal muscle, where it facilitates intracellular transport and storage of oxygen. This protein has evolved to suit unique physiological needs in the muscle of diving vertebrates that express Mb at much greater concentrations than their terrestrial counterparts. In this study, we characterized Mb oxygen affinity (P50) from 25 species of aquatic and terrestrial birds and mammals. Among diving species, we tested for correlations between Mb P50 and routine dive duration. Across all species examined, Mb P50 ranged from 2.40 to 4.85 mmHg. The mean P50 of Mb from terrestrial ungulates was 3.72±0.15 mmHg (range 3.70-3.74 mmHg). The P50 of cetaceans was similar to terrestrial ungulates ranging from 3.54 to 3.82 mmHg, with the exception of the melon-headed whale, which had a significantly higher P50 of 4.85 mmHg. Among pinnipeds, the P50 ranged from 3.23 to 3.81 mmHg and showed a trend for higher oxygen affinity in species with longer dive durations. Among diving birds, the P50 ranged from 2.40 to 3.36 mmHg and also showed a trend of higher affinities in species with longer dive durations. In pinnipeds and birds, low Mb P50 was associated with species whose muscles are metabolically active under hypoxic conditions associated with aerobic dives. Given the broad range of potential globin oxygen affinities, Mb P50 from diverse vertebrate species appears constrained within a relatively narrow range. High Mb oxygen affinity within this range may be adaptive for some vertebrates that make prolonged dives.

  5. 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

  6. 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. PMID:25053314

  7. Potential of ZrO clusters as replacement Pd catalyst

    NASA Astrophysics Data System (ADS)

    Behera, Swayamprabha; King, Nicholas; Samanta, Devleena; Jena, Puru

    2014-07-01

    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.

  8. 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.

  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. 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

    2011-03-01

    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.

  11. Propagation equations for deformable test bodies with microstructure in extended theories of gravity

    SciTech Connect

    Puetzfeld, Dirk; Obukhov, Yuri N.

    2007-10-15

    We derive the equations of motion in metric-affine gravity by making use of the conservation laws obtained from Noether's theorem. The results are given in the form of propagation equations for the multipole decomposition of the matter sources in metric-affine gravity, i.e., the canonical energy-momentum current and the hypermomentum current. In particular, the propagation equations allow for a derivation of the equations of motion of test particles in this generalized gravity theory, and allow for direct identification of the couplings between the matter currents and the gauge gravitational field strengths of the theory, namely, the curvature, the torsion, and the nonmetricity. We demonstrate that the possible non-Riemannian spacetime geometry can only be detected with the help of the test bodies that are formed of matter with microstructure. Ordinary gravitating matter, i.e., matter without microscopic internal degrees of freedom, can probe only the Riemannian spacetime geometry. Thereby, we generalize previous results of general relativity and Poincare gauge theory.

  12. 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

  13. 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. PMID:24611036

  14. Boosting domain wall propagation by notches

    NASA Astrophysics Data System (ADS)

    Yuan, H. Y.; Wang, X. R.

    2015-08-01

    We report a counterintuitive finding that notches in an otherwise homogeneous magnetic nanowire can boost current-induced domain wall (DW) propagation. DW motion in notch-modulated wires can be classified into three phases: (1) A DW is pinned around a notch when the current density is below the depinning current density. (2) DW propagation velocity is boosted by notches above the depinning current density and when nonadiabatic spin-transfer torque strength β is smaller than the Gilbert damping constant α . The boost can be multifold. (3) DW propagation velocity is hindered when β >α . The results are explained by using the Thiele equation.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Numerical wave propagation in ImageJ.

    PubMed

    Piedrahita-Quintero, Pablo; Castañeda, Raul; Garcia-Sucerquia, Jorge

    2015-07-20

    An ImageJ plugin for numerical wave propagation is presented. The plugin provides ImageJ, the well-known software for image processing, with the capability of computing numerical wave propagation by the use of angular spectrum, Fresnel, and Fresnel-Bluestein algorithms. The plugin enables numerical wave propagation within the robust environment provided by the complete set of built-in tools for image processing available in ImageJ. The plugin can be used for teaching and research purposes. We illustrate its use to numerically recreate Poisson's spot and Babinet's principle, and in the numerical reconstruction of digitally recorded holograms from millimeter-sized and pure phase microscopic objects.