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

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.

Nonlinear force propagation, anisotropic stiffening and non-affine relaxation in a model cytoskeleton

NASA Astrophysics Data System (ADS)

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

2013-03-01

Forces are generated heterogeneously in living cells and transmitted through cytoskeletal networks that respond highly non-linearly. Here, we carry out high-bandwidth passive microrheology on vimentin networks reconstituted in vitro, and observe the nonlinear mechanical response due to forces propagating from a local source applied by an optical tweezer. Since the applied force is constant, the gel becomes equilibrated and the fluctuation-dissipation theorem can be employed to deduce the viscoelasticity of the local environment from the thermal fluctuations of colloidal probes. Our experiments unequivocally demonstrate the anisotropic stiffening of the cytoskeletal network behind the applied force, with greater stiffening in the parallel direction. Quantitative agreement with an affine continuum model is obtained, but only for the response at certain frequency ~ 10-1000 Hz which separates the high-frequency power law and low-frequency elastic behavior of the network. We argue that the failure of the model at lower frequencies is due to the presence of non-affinity, and observe that zero-frequency changes in particle separation can be fitted when an independently-measured, empirical nonaffinity factor is applied.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Bo; Govind, Niranjan; Aprà, Edoardo

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

Front propagation and clustering in the stochastic nonlocal Fisher equation

NASA Astrophysics Data System (ADS)

Ganan, Yehuda A.; Kessler, David A.

2018-04-01

In this work, we study the problem of front propagation and pattern formation in the stochastic nonlocal Fisher equation. We find a crossover between two regimes: a steadily propagating regime for not too large interaction range and a stochastic punctuated spreading regime for larger ranges. We show that the former regime is well described by the heuristic approximation of the system by a deterministic system where the linear growth term is cut off below some critical density. This deterministic system is seen not only to give the right front velocity, but also predicts the onset of clustering for interaction kernels which give rise to stable uniform states, such as the Gaussian kernel, for sufficiently large cutoff. Above the critical cutoff, distinct clusters emerge behind the front. These same features are present in the stochastic model for sufficiently small carrying capacity. In the latter, punctuated spreading, regime, the population is concentrated on clusters, as in the infinite range case, which divide and separate as a result of the stochastic noise. Due to the finite interaction range, if a fragment at the edge of the population separates sufficiently far, it stabilizes as a new cluster, and the processes begins anew. The deterministic cutoff model does not have this spreading for large interaction ranges, attesting to its purely stochastic origins. We show that this mode of spreading has an exponentially small mean spreading velocity, decaying with the range of the interaction kernel.

Front propagation and clustering in the stochastic nonlocal Fisher equation.

PubMed

Ganan, Yehuda A; Kessler, David A

2018-04-01

In this work, we study the problem of front propagation and pattern formation in the stochastic nonlocal Fisher equation. We find a crossover between two regimes: a steadily propagating regime for not too large interaction range and a stochastic punctuated spreading regime for larger ranges. We show that the former regime is well described by the heuristic approximation of the system by a deterministic system where the linear growth term is cut off below some critical density. This deterministic system is seen not only to give the right front velocity, but also predicts the onset of clustering for interaction kernels which give rise to stable uniform states, such as the Gaussian kernel, for sufficiently large cutoff. Above the critical cutoff, distinct clusters emerge behind the front. These same features are present in the stochastic model for sufficiently small carrying capacity. In the latter, punctuated spreading, regime, the population is concentrated on clusters, as in the infinite range case, which divide and separate as a result of the stochastic noise. Due to the finite interaction range, if a fragment at the edge of the population separates sufficiently far, it stabilizes as a new cluster, and the processes begins anew. The deterministic cutoff model does not have this spreading for large interaction ranges, attesting to its purely stochastic origins. We show that this mode of spreading has an exponentially small mean spreading velocity, decaying with the range of the interaction kernel.

Track propagation methods for the correlation of charged tracks with clusters in the calorimeter of the bar PANDA experiment

NASA Astrophysics Data System (ADS)

Nasawasd, T.; Simantathammakul, T.; Herold, C.; Stockmanns, T.; Ritman, J.; Kobdaj, C.

2018-02-01

To classify clusters of hits in the electromagnetic calorimeter (EMC) of bar PANDA (antiProton ANnihilation at DArmstadt), one has to match these EMC clusters with tracks of charged particles reconstructed from hits in the tracking system. Therefore the tracks are propagated to the surface of the EMC and associated with EMC clusters which are nearby and below a cut parameter. In this work, we propose a helix propagator to extrapolate the track from the Straw Tube Tracker (STT) to the inner surface of the EMC instead of the GEANE propagator which is already embedded within the PandaRoot computational framework. The results for both propagation methods show a similar quality, with a 30% gain in CPU time when using the helix propagator. We use Monte-Carlo truth information to compare the particle ID of the EMC clusters with the ID of the extrapolated points, thus deciding upon the correctness of the matches. By varying the cut parameter as a function of transverse momentum and particle type, our simulations show that the purity can be increased by 3-5% compared to the default value which is a constant cut in the bar PANDA simulation framework PandaRoot.

The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the

Ground and excited states of NH4: Electron propagator and quantum defect analysis

NASA Astrophysics Data System (ADS)

Ortiz, J. V.; Martín, I.; Velasco, A. M.; Lavín, C.

2004-05-01

Vertical excitation energies of the Rydberg radical NH4 are inferred from ab initio electron propagator calculations on the electron affinities of NH4+. The adiabatic ionization energy of NH4 is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine Einstein emission coefficients and radiative lifetimes. Comparisons with spectroscopic data and previous calculations are discussed.

An ellipsoidal calculus based on propagation and fusion.

PubMed

Ros, L; Sabater, A; Thomas, F

2002-01-01

Presents an ellipsoidal calculus based solely on two basic operations: propagation and fusion. Propagation refers to the problem of obtaining an ellipsoid that must satisfy an affine relation with another ellipsoid, and fusion to that of computing the ellipsoid that tightly bounds the intersection of two given ellipsoids. These two operations supersede the Minkowski sum and difference, affine transformation and intersection tight bounding of ellipsoids on which other ellipsoidal calculi are based. Actually, a Minkowski operation can be seen as a fusion followed by a propagation and an affine transformation as a particular case of propagation. Moreover, the presented formulation is numerically stable in the sense that it is immune to degeneracies of the involved ellipsoids and/or affine relations. Examples arising when manipulating uncertain geometric information in the context of the spatial interpretation of line drawings are extensively used as a testbed for the presented calculus.

GDPC: Gravitation-based Density Peaks Clustering algorithm

NASA Astrophysics Data System (ADS)

Jiang, Jianhua; Hao, Dehao; Chen, Yujun; Parmar, Milan; Li, Keqin

2018-07-01

The Density Peaks Clustering algorithm, which we refer to as DPC, is a novel and efficient density-based clustering approach, and it is published in Science in 2014. The DPC has advantages of discovering clusters with varying sizes and varying densities, but has some limitations of detecting the number of clusters and identifying anomalies. We develop an enhanced algorithm with an alternative decision graph based on gravitation theory and nearby distance to identify centroids and anomalies accurately. We apply our method to some UCI and synthetic data sets. We report comparative clustering performances using F-Measure and 2-dimensional vision. We also compare our method to other clustering algorithms, such as K-Means, Affinity Propagation (AP) and DPC. We present F-Measure scores and clustering accuracies of our GDPC algorithm compared to K-Means, AP and DPC on different data sets. We show that the GDPC has the superior performance in its capability of: (1) detecting the number of clusters obviously; (2) aggregating clusters with varying sizes, varying densities efficiently; (3) identifying anomalies accurately.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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.

Al7CX (X=Li-Cs) clusters: Stability and the prospect for cluster materials

NASA Astrophysics Data System (ADS)

Ashman, C.; Khanna, S. N.; Pederson, M. R.; Kortus, J.

2000-12-01

Al7C clusters, recently found to have a high-electron affinity and exceptional stability, are shown to form ionic molecules when combined with alkali-metal atoms. Our studies, based on an ab initio gradient-corrected density-functional scheme, show that Al7CX (X=Li-Cs) clusters have a very low-electron affinity and a high-ionization potential. When combined, the two- and four-atom composite clusters of Al7CLi units leave the Al7C clusters almost intact. Preliminary studies indicate that Al7CLi may be suitable to form cluster-based materials.

Fe-S Clusters and MutY Base Excision Repair Glycosylases: Purification, Kinetics, and DNA Affinity Measurements.

PubMed

Nuñez, Nicole N; Majumdar, Chandrima; Lay, Kori T; David, Sheila S

2018-01-01

A growing number of iron-sulfur (Fe-S) cluster cofactors have been identified in DNA repair proteins. MutY and its homologs are base excision repair (BER) glycosylases that prevent mutations associated with the common oxidation product of guanine (G), 8-oxo-7,8-dihydroguanine (OG) by catalyzing adenine (A) base excision from inappropriately formed OG:A mispairs. The finding of an [4Fe-4S] 2+ cluster cofactor in MutY, Endonuclease III, and structurally similar BER enzymes was surprising and initially thought to represent an example of a purely structural role for the cofactor. However, in the two decades subsequent to the initial discovery, purification and in vitro analysis of bacterial MutYs and mammalian homologs, such as human MUTYH and mouse Mutyh, have demonstrated that proper Fe-S cluster coordination is required for OG:A substrate recognition and adenine excision. In addition, the Fe-S cluster in MutY has been shown to be capable of redox chemistry in the presence of DNA. The work in our laboratory aimed at addressing the importance of the MutY Fe-S cluster has involved a battery of approaches, with the overarching hypothesis that understanding the role(s) of the Fe-S cluster is intimately associated with understanding the biological and chemical properties of MutY and its unique damaged DNA substrate as a whole. In this chapter, we focus on methods of enzyme expression and purification, detailed enzyme kinetics, and DNA affinity assays. The methods described herein have not only been leveraged to provide insight into the roles of the MutY Fe-S cluster but have also been provided crucial information needed to delineate the impact of inherited variants of the human homolog MUTYH associated with a colorectal cancer syndrome known as MUTYH-associated polyposis or MAP. Notably, many MAP-associated variants have been found adjacent to the Fe-S cluster further underscoring the intimate relationship between the cofactor, MUTYH-mediated DNA repair, and disease. �

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

PubMed Central

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

2014-01-01

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

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.

Affinity+: Semi-Structured Brainstorming on Large Displays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burtner, Edwin R.; May, Richard A.; Scarberry, Randall E.

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.

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

NASA Astrophysics Data System (ADS)

Gbaguidi, Audrey J.-M.

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

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

DOE PAGES

Gao, Zhiwen; Gao, Yanfei

2016-05-14

We report that 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 formore » 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. Finally, 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.« less

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Zhiwen; Gao, Yanfei

We report that 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 formore » 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. Finally, 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.« less

Data depth based clustering analysis

DOE PAGES

Jeong, Myeong -Hun; Cai, Yaping; Sullivan, Clair J.; ...

2016-01-01

Here, this paper proposes a new algorithm for identifying patterns within data, based on data depth. Such a clustering analysis has an enormous potential to discover previously unknown insights from existing data sets. Many clustering algorithms already exist for this purpose. However, most algorithms are not affine invariant. Therefore, they must operate with different parameters after the data sets are rotated, scaled, or translated. Further, most clustering algorithms, based on Euclidean distance, can be sensitive to noises because they have no global perspective. Parameter selection also significantly affects the clustering results of each algorithm. Unlike many existing clustering algorithms, themore » proposed algorithm, called data depth based clustering analysis (DBCA), is able to detect coherent clusters after the data sets are affine transformed without changing a parameter. It is also robust to noises because using data depth can measure centrality and outlyingness of the underlying data. Further, it can generate relatively stable clusters by varying the parameter. The experimental comparison with the leading state-of-the-art alternatives demonstrates that the proposed algorithm outperforms DBSCAN and HDBSCAN in terms of affine invariance, and exceeds or matches the ro-bustness to noises of DBSCAN or HDBSCAN. The robust-ness to parameter selection is also demonstrated through the case study of clustering twitter data.« less

Ground and excited states of the Rydberg radical H3O: Electron propagator and quantum defect analysis

NASA Astrophysics Data System (ADS)

Melin, Junia; Ortiz, J. V.; Martín, I.; Velasco, A. M.; Lavín, C.

2005-06-01

Vertical excitation energies of the Rydberg radical H3O are inferred from ab initio electron propagator calculations on the electron affinities of H3O+. The adiabatic ionization energy of H3O is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine oscillator strengths. Given that the experimental spectrum of H3O does not seem to be available, comparisons with previous calculations are discussed. A simple model Hamiltonian, suitable for the study of bound states with arbitrarily high energies is generated by these means.

Influences of Histidine-1 and Azaphenylalanine-4 on the Affinity, Anti-inflammatory, and Antiangiogenic Activities of Azapeptide Cluster of Differentiation 36 Receptor Modulators.

PubMed

Chignen Possi, Kelvine; Mulumba, Mukandila; Omri, Samy; Garcia-Ramos, Yesica; Tahiri, Houda; Chemtob, Sylvain; Ong, Huy; Lubell, William D

2017-11-22

Azapeptide analogues of growth hormone releasing peptide-6 (GHRP-6) exhibit promising affinity, selectivity, and modulator activity on the cluster of differentiation 36 receptor (CD36). For example, [A 1 , azaF 4 ]- and [azaY 4 ]-GHRP-6 (1a and 2b) were previously shown to bind selectively to CD36 and exhibited respectively significant antiangiogenic and slight angiogenic activities in a microvascular sprouting assay using choroid explants. The influences of the 1- and 4-position residues on the affinity, anti-inflammatory, and antiangiogenic activity of these azapeptides have now been studied in detail by the synthesis and analysis of a set of 25 analogues featuring Ala 1 or His 1 and a variety of aromatic side chains at the aza-amino acid residue in the 4-position. Although their binding affinities differed only by a factor of 17, the analogues exhibited significant differences in ability to modulate production of nitric oxide (NO) in macrophages and choroidal neovascularization.

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

PubMed

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

2013-01-01

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

Quasi-monochromatic ULF foreshock waves as observed by the four-spacecraft Cluster mission: 2. Oblique propagation

NASA Astrophysics Data System (ADS)

Eastwood, J. P.; Balogh, A.; Lucek, E. A.; Mazelle, C.; Dandouras, I.

2005-11-01

This paper presents the results of a statistical investigation into the nature of oblique wave propagation in the foreshock. Observations have shown that foreshock ULF waves tend to propagate obliquely to the background magnetic field. This is in contrast to theoretical work, which predicts that the growth rate of the mechanism responsible for the waves is maximized for parallel propagation, at least in the linear regime in homogenous plasma. Here we use data from the Cluster mission to study in detail the oblique propagation of a particular class of foreshock ULF wave, the 30 s quasi-monochromatic wave. We find that these waves persistently propagate at oblique angles to the magnetic field. Over the whole data set, the average value of θkB was found to be 21 ± 14°. Oblique propagation is observed even when the interplanetary magnetic field (IMF) cone angle is small, such that the convective component of the solar wind velocity, vE×B, is comparable to the wave speed. In this subset of the data, the mean value of θkB was 12.9 ± 7.1°. In the subset of data for which the IMF cone angle exceeded 45°, the mean value of θkB was 19.5 ± 10.7°. When the angle between the IMF and the x geocentric solar ecliptic (GSE) direction (i.e., the solar wind vector) is large, the wave k vectors tend to be confined in the plane defined by the x GSE direction and the magnetic field and a systematic deflection is observed. The dependence of θkB on vE×B is also studied.

On The Propagation And Modulation Of Electrostatic Solitary Waves Observed Near The Magnetopause On Cluster

NASA Astrophysics Data System (ADS)

Pickett, J. S.; Christopher, I. W.; Grison, B.; Grimald, S.; Santolík, O.; Décréau, P. M. E.; Lefebvre, B.; Engebretson, M. J.; Kistler, L. M.; Constantinescu, D.; Chen, L.-J.; Omura, Y.; Lakhina, G. S.; Gurnett, D. A.; Cornilleau-Wehrlin, N.; Fazakerley, A. N.; Dandouras, I.; Lucek, E.

2011-01-01

We present the results of a study of Electrostatic Solitary Waves (ESWs) in which propagation of a series of noncyclical ESWs is observed from one Cluster spacecraft to another over distances as great as tens of km and time lags as great as a few tens of ms. This propagation study was conducted for locations near the magnetopause on the magnetosheath side. Propagation was found primarily toward the earth with speeds on the order of 1500 to 2400 km/s. The sizes of the ESWs obtained from these velocities were on the order of 1 km along the magnetic field direction and several tens of km perpendicular. These results are consistent with measurements on single spacecraft in which the ESW propagation is observed with time lags of only ˜0.1 ms. Our results thus show the stability of ESWs over time periods much greater than their own characteristic pulse durations of a few 100s of microseconds. We present also the results of a study of ESW modulation at the magnetopause on the earthward side. We found that ESWs were modulated at ˜1.3 Hz, consistent with a Pc1 wave which was observed concurrently. During this time, tens of eV electron beams are present. We propose a Buneman type instability in which the E″″ component of the Pc1 waves provides a mechanism for accelerating electrons, resulting in the generation of the ESWs modulated at the Pc1 frequency.

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

Einstein’s gravity from a polynomial affine model

NASA Astrophysics Data System (ADS)

Castillo-Felisola, Oscar; Skirzewski, Aureliano

2018-03-01

We show that the effective field equations for a recently formulated polynomial affine model of gravity, in the sector of a torsion-free connection, accept general Einstein manifolds—with or without cosmological constant—as solutions. Moreover, the effective field equations are partially those obtained from a gravitational Yang–Mills theory known as Stephenson–Kilmister–Yang theory. Additionally, we find a generalization of a minimally coupled massless scalar field in General Relativity within a ‘minimally’ coupled scalar field in this affine model. Finally, we present a brief (perturbative) analysis of the propagators of the gravitational theory, and count the degrees of freedom. For completeness, we prove that a Birkhoff-like theorem is valid for the analyzed sector.

Methods for quantifying T cell receptor binding affinities and thermodynamics

PubMed Central

Piepenbrink, Kurt H.; Gloor, Brian E.; Armstrong, Kathryn M.; Baker, Brian M.

2013-01-01

αβ T cell receptors (TCRs) recognize peptide antigens bound and presented by class I or class II major histocompatibility complex (MHC) proteins. Recognition of a peptide/MHC complex is required for initiation and propagation of a cellular immune response, as well as the development and maintenance of the T cell repertoire. Here we discuss methods to quantify the affinities and thermodynamics of interactions between soluble ectodomains of TCRs and their peptide/MHC ligands, focusing on titration calorimetry, surface plasmon resonance, and fluorescence anisotropy. As TCRs typically bind ligand with weak-to-moderate affinities, we focus the discussion on means to enhance the accuracy and precision of low affinity measurements. In addition to further elucidating the biology of the T cell mediated immune response, more reliable low affinity measurements will aid with more probing studies with mutants or altered peptides that can help illuminate the physical underpinnings of how TCRs achieve their remarkable recognition properties. PMID:21609868

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.

Enhancing Community Detection By Affinity-based Edge Weighting Scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, Andy; Sanders, Geoffrey; Henson, Van

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 idealmore » 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.« less

Network module detection: Affinity search technique with the multi-node topological overlap measure

PubMed Central

Li, Ai; Horvath, Steve

2009-01-01

Background Many clustering procedures only allow the user to input a pairwise dissimilarity or distance measure between objects. We propose a clustering method that can input a multi-point dissimilarity measure d(i1, i2, ..., iP) where the number of points P can be larger than 2. The work is motivated by gene network analysis where clusters correspond to modules of highly interconnected nodes. Here, we define modules as clusters of network nodes with high multi-node topological overlap. The topological overlap measure is a robust measure of interconnectedness which is based on shared network neighbors. In previous work, we have shown that the multi-node topological overlap measure yields biologically meaningful results when used as input of network neighborhood analysis. Findings We adapt network neighborhood analysis for the use of module detection. We propose the Module Affinity Search Technique (MAST), which is a generalized version of the Cluster Affinity Search Technique (CAST). MAST can accommodate a multi-node dissimilarity measure. Clusters grow around user-defined or automatically chosen seeds (e.g. hub nodes). We propose both local and global cluster growth stopping rules. We use several simulations and a gene co-expression network application to argue that the MAST approach leads to biologically meaningful results. We compare MAST with hierarchical clustering and partitioning around medoid clustering. Conclusion Our flexible module detection method is implemented in the MTOM software which can be downloaded from the following webpage: PMID:19619323

Network module detection: Affinity search technique with the multi-node topological overlap measure.

PubMed

Li, Ai; Horvath, Steve

2009-07-20

Many clustering procedures only allow the user to input a pairwise dissimilarity or distance measure between objects. We propose a clustering method that can input a multi-point dissimilarity measure d(i1, i2, ..., iP) where the number of points P can be larger than 2. The work is motivated by gene network analysis where clusters correspond to modules of highly interconnected nodes. Here, we define modules as clusters of network nodes with high multi-node topological overlap. The topological overlap measure is a robust measure of interconnectedness which is based on shared network neighbors. In previous work, we have shown that the multi-node topological overlap measure yields biologically meaningful results when used as input of network neighborhood analysis. We adapt network neighborhood analysis for the use of module detection. We propose the Module Affinity Search Technique (MAST), which is a generalized version of the Cluster Affinity Search Technique (CAST). MAST can accommodate a multi-node dissimilarity measure. Clusters grow around user-defined or automatically chosen seeds (e.g. hub nodes). We propose both local and global cluster growth stopping rules. We use several simulations and a gene co-expression network application to argue that the MAST approach leads to biologically meaningful results. We compare MAST with hierarchical clustering and partitioning around medoid clustering. Our flexible module detection method is implemented in the MTOM software which can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/MTOM/

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

Energetics of charged metal clusters containing vacancies

NASA Astrophysics Data System (ADS)

Pogosov, Valentin V.; Reva, Vitalii I.

2018-01-01

We study theoretically large metal clusters containing vacancies. We propose an approach, which combines the Kohn-Sham results for monovacancy in a bulk of metal and analytical expansions in small parameters cv (relative concentration of vacancies) and RN,v -1, RN ,v being cluster radii. We obtain expressions of the ionization potential and electron affinity in the form of corrections to electron work function, which require only the characteristics of 3D defect-free metal. The Kohn-Sham method is used to calculate the electron profiles, ionization potential, electron affinity, electrical capacitance; dissociation, cohesion, and monovacancy-formation energies of the small perfect clusters NaN, MgN, AlN (N ≤ 270) and the clusters containing a monovacancy (N ≥ 12) in the stabilized-jellium model. The quantum-sized dependences for monovacancy-formation energies are calculated for the Schottky scenario and the "bubble blowing" scenario, and their asymptotic behavior is also determined. It is shown that the asymptotical behaviors of size dependences for these two mechanisms differ from each other and weakly depend on the number of atoms in the cluster. The contribution of monovacancy to energetics of charged clusters and the size dependences of their characteristics and asymptotics are discussed. It is shown that the difference between the characteristics for the neutral and charged clusters is entirely determined by size dependences of ionization potential and electron affinity. Obtained analytical dependences may be useful for the analysis of the results of photoionization experiments and for the estimation of the size dependences of the vacancy concentration including the vicinity of the melting point.

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

PubMed

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

2012-09-01

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.

High-Affinity Methanotrophy Informed by Genome-Wide Analysis of Upland Soil Cluster Alpha (USCα) from Axel Heiberg Island, Canadian High Arctic

NASA Astrophysics Data System (ADS)

Rusley, C.; Onstott, T. C.; Lau, M.

2017-12-01

Methane (CH4) is a potent greenhouse gas whose proper budgeting is vital to climate predictions. Recent studies have identified upland Arctic mineral cryosols as consistent CH4 sinks, drawing CH4 from both the atmosphere and underlying anaerobic soil layers. Global atmospheric CH4 uptake is proposed to be mediated by high-affinity methanotrophs based on the detection of the marker gene pmoA (particulate methane monooxygenase beta subunit). However, a lack of pure cultures and scarcity of genomic information have hindered our understanding of their metabolic capabilities and versatility. Together with the missing genetic linkage between its pmoA and 16S ribosomal RNA (rRNA) gene, the factors that control the distribution and magnitude of high-affinity methanotrophy in the Arctic permafrost-affected region have remained elusive. Using 21 metagenomic datasets of surface soils obtained from long-term core incubation experiments,1 this bioinformatics study aimed to reconstruct the draft genome of the Upland Soil Cluster α-proteobacteria (USCα), the high-affinity methanotroph previously detected in the samples,2 and to determine its phylogeny and metabolic requirements. We obtained a genome bin containing the high-affinity form of the USCα-like pmoA gene. The 3.03 Mbp assembly is 91.6% complete with a unique set of single-copy marker genes. The 16S rRNA gene fragment of USCα belongs to the α-proteobacterial family Beijerinckiaceae. Genome annotation indicates possible formaldehyde oxidation via tetrahydromethanopterin-linked C1 transfer pathways, acetate utilization, carbon fixation via the Calvin-Benson-Bassham cycle, and glycogen production. Notably, the key enzymes for formaldehyde assimilation via the serine and ribulose monophosphate pathways are missing. The presence of genes encoding nitrate reductase and hemoglobin suggests adaptation to low O2 under water-logged conditions. Since USCα has versatile carbon metabolisms, it may not be an obligate methanotroph

Spectral-element simulation of two-dimensional elastic wave propagation in fully heterogeneous media on a GPU cluster

NASA Astrophysics Data System (ADS)

Rudianto, Indra; Sudarmaji

2018-04-01

We present an implementation of the spectral-element method for simulation of two-dimensional elastic wave propagation in fully heterogeneous media. We have incorporated most of realistic geological features in the model, including surface topography, curved layer interfaces, and 2-D wave-speed heterogeneity. To accommodate such complexity, we use an unstructured quadrilateral meshing technique. Simulation was performed on a GPU cluster, which consists of 24 core processors Intel Xeon CPU and 4 NVIDIA Quadro graphics cards using CUDA and MPI implementation. We speed up the computation by a factor of about 5 compared to MPI only, and by a factor of about 40 compared to Serial implementation.

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.

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

PubMed

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

2004-10-01

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

A Dimensionality Reduction-Based Multi-Step Clustering Method for Robust Vessel Trajectory Analysis

PubMed Central

Liu, Jingxian; Wu, Kefeng

2017-01-01

traditional spectral clustering and fast affinity propagation clustering. Experimental results have illustrated its superior performance in terms of quantitative and qualitative evaluations. PMID:28777353

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

NASA Astrophysics Data System (ADS)

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

2013-08-01

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

Mass propagation of shoots of Stevia rebaudiana using a large scale bioreactor.

PubMed

Akita, M; Shigeoka, T; Koizumi, Y; Kawamura, M

1994-01-01

A procedure for the mass propagation of multiple shoots of Stevia rebaudiana is described. Isolated shoot primordia were used as the inoculum to obtain clusters of shoot primordia. Such clusters were grown in a 500 liter bioreactor to obtain shoots. A total of 64.6 Kg of shoots were propagated from 460 g of the inoculated shoot primordia. These shoots were easily acclimatized in soil.

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

Metric-affine f (R ,T ) theories of gravity and their applications

NASA Astrophysics Data System (ADS)

Barrientos, E.; Lobo, Francisco S. N.; Mendoza, S.; Olmo, Gonzalo J.; Rubiera-Garcia, D.

2018-05-01

We study f (R ,T ) theories of gravity, where T is the trace of the energy-momentum tensor Tμ ν, with independent metric and affine connection (metric-affine theories). We find that the resulting field equations share a close resemblance with their metric-affine f (R ) relatives once an effective energy-momentum tensor is introduced. As a result, the metric field equations are second-order and no new propagating degrees of freedom arise as compared to GR, which contrasts with the metric formulation of these theories, where a dynamical scalar degree of freedom is present. Analogously to its metric counterpart, the field equations impose the nonconservation of the energy-momentum tensor, which implies nongeodesic motion and consequently leads to the appearance of an extra force. The weak field limit leads to a modified Poisson equation formally identical to that found in Eddington-inspired Born-Infeld gravity. Furthermore, the coupling of these gravity theories to perfect fluids, electromagnetic, and scalar fields, and their potential applications are discussed.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

PubMed

Emmons, Scott; Kobourov, Stephen; Gallant, Mike; Börner, Katy

2016-01-01

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. 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. 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 graphs with well-defined clusters.

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

Subspace Clustering via Learning an Adaptive Low-Rank Graph.

PubMed

Yin, Ming; Xie, Shengli; Wu, Zongze; Zhang, Yun; Gao, Junbin

2018-08-01

By using a sparse representation or low-rank representation of data, the graph-based subspace clustering has recently attracted considerable attention in computer vision, given its capability and efficiency in clustering data. However, the graph weights built using the representation coefficients are not the exact ones as the traditional definition is in a deterministic way. The two steps of representation and clustering are conducted in an independent manner, thus an overall optimal result cannot be guaranteed. Furthermore, it is unclear how the clustering performance will be affected by using this graph. For example, the graph parameters, i.e., the weights on edges, have to be artificially pre-specified while it is very difficult to choose the optimum. To this end, in this paper, a novel subspace clustering via learning an adaptive low-rank graph affinity matrix is proposed, where the affinity matrix and the representation coefficients are learned in a unified framework. As such, the pre-computed graph regularizer is effectively obviated and better performance can be achieved. Experimental results on several famous databases demonstrate that the proposed method performs better against the state-of-the-art approaches, in clustering.

Clustering T cell GM1 Lipid Rafts Increases Cellular Resistance to Shear on Fibronectin through Changes in Integrin Affinity and Cytoskeletal Dynamics

PubMed Central

Mitchell, Jason S.; Brown, Wells S.; Woodside, Darren G.; Vanderslice, Peter; McIntyre, Bradley W.

2008-01-01

Lipid rafts are small laterally mobile microdomains that are highly enriched in lymphocyte signaling molecules. GM1 gangliosides are a common lipid raft component and have been shown to be important in many T cell functions. The aggregation of specific GM1 lipid rafts can control many T cell activation events, including their novel association with T cell integrins. We found that clustering GM1 lipid rafts can regulate β1 integrin function. This was apparent through increased resistance to shear flow dependent detachment of T cells adherent to the α4β1 and α5β1 integrin ligand fibronectin (FN). Adhesion strengthening as a result of clustering GM1 enriched lipid rafts correlated with increased cellular rigidity and morphology through the localization of cortical F-actin, the resistance to shear induced cell stretching, and an increase in the surface area and symmetry of the contact area between the cell surface and adhesive substrate. Furthermore, clustering GM1 lipid rafts could initiate integrin “inside-out” signaling mechanisms. This was seen through increased integrin-cytoskeleton associations and enhanced soluble binding of FN and VCAM-1 suggesting the induction of high affinity integrin conformations. The activation of these adhesion strengthening characteristics appear to be specific for the aggregation of GM1 lipid rafts as the aggregation of the heterogeneous raft associated molecule CD59 failed to activate these functions. These findings indicate a novel mechanism to signal to β1 integrins and to activate adhesion strengthening processes. PMID:19139760

Evaluation of affinity and pseudo-affinity adsorption processes for penicillin acylase purification.

PubMed

Fonseca, L P; Cabral, J M

1996-01-01

Affinity ligand (6-Aminopenicillanic acid, Amoxycillin, Ampicillin, Benzylpenicillin and 4-Phenylbutylanzine) of penicillin acylase (EC 3.5.1.11) were attached to hydrophilic gels like Sepharose 4B-CNBr and Minileak 'medium'. Ampicillin and 4-Phenylbutylamine were the affinity ligands that presented the higher concentrations attached to both gels. Penicillin acylase adsorption on these affinity gels was mainly dependent on the activated group of the gel, the affinity ligand attached and the experimental conditions of enzyme adsorption. Under affinity conditions only the ligands Amoxycillin, Ampicillin and 4-Phenylbutylamine, immobilized on Minileak, adsorbed the enzyme from osmotic shock extracts at different pH values. These affinity ligand systems were characterized by low adsorption capacities of penicillin acylase activity (1.2-2.1 IU mL-1 gel) and specific activity (1.5-2.9 IU mg-1 prot). Under pseudo-affinity conditions all the ligands attached both activated to gels (Sepharose 4B-CNBr and Minileak) adsorbed the enzyme. The affinity gels were characterized by higher values of adsorption capacity (3.7 and 55.6 IU mL-1 gel) and adsorbed specific activity (2.0 and 6.1 IU mg-1 prot) than those observed under affinity conditions. The space arm of Minileak gel, shown to be fundamental to enzyme adsorption under affinity conditions, preferentially adsorbed proteins in relation to the enzyme under pseudo-affinity conditions. However, this effect was partially minimized when the gel was derivatized by the affinity ligands at concentrations higher than 6 mumol mL-1 gel. Ampicillin was the affinity ligand that presented the best results for specific adsorption of penicillin acylase under affinity and pseudo-affinity adsorption processes. The Sepharose 4B-CNBr derivatized gel also presented a good adsorption capacity of enzyme activity (26.8 IU mL-1 gel) under pseudo-affinity adsorption processes.

Studies of Copper, Silver, and Gold Cluster Anions: Evidence of Electronic Shell Structure.

NASA Astrophysics Data System (ADS)

Pettiette, Claire Lynn

A new Ultraviolet Magnetic Time-of-Flight Photoelectron Spectrometer (MTOFPES) has been developed for the study of the electronic structure of clusters produced in a pulsed supersonic molecular beam. This is the first technique which has been successful in probing the valence electronic states of metal clusters. The ultraviolet photoelectron spectra of negative cluster ions of the noble metals have been taken at several different photon energies. These are presented along with the electron affinity and HOMO-LUMO gap measurements for Cu_6^- to Cu_ {41}^-, using 4.66 eV and 6.42 eV detachment energies; Ag_3^- to Ag_{21}^-, using 6.42 eV detachment energy; and Au_3^ - to Au_{21}^-, using 6.42 eV and 7.89 eV detachment energies. The spectra provide the first detailed probes of the s valence electrons of the noble metal clusters. In addition, the 6.42 eV and 7.89 eV spectra probe the first one to two electron volts of the molecular orbitals of the d valence electrons of copper and gold clusters. The electron affinity and HOMO-LUMO gap measurements of the noble metal clusters agree with the predictions of the ellipsoidal shell model for mono-valent metal clusters. In particular, cluster numbers 8, 20, and 40--which correspond to the spherical shell closings of this model--have low electron affinities and large HOMO-LUMO gaps. The spectra of the gold cluster ions indicate that the molecular orbital energies of the cluster valence electrons are more widely spaced for gold than for copper or silver. This is to be expected for the heavy atom clusters when relativistic effects are taken into account.

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

Size-restricted proton transfer within toluene-methanol cluster ions.

PubMed

Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek; Furlani, Thomas; DeLeon, Robert L; Garvey, James F

2008-11-20

To understand the interaction between toluene and methanol, the chemical reactivity of [(C6H5CH3)(CH3OH) n=1-7](+) cluster ions has been investigated via tandem quadrupole mass spectrometry and through calculations. Collision Induced Dissociation (CID) experiments show that the dissociated intracluster proton transfer reaction from the toluene cation to methanol clusters, forming protonated methanol clusters, only occurs for n = 2-4. For n = 5-7, CID spectra reveal that these larger clusters have to sequentially lose methanol monomers until they reach n = 4 to initiate the deprotonation of the toluene cation. Metastable decay data indicate that for n = 3 and n = 4 (CH3OH)3H(+) is the preferred fragment ion. The calculational results reveal that both the gross proton affinity of the methanol subcluster and the structure of the cluster itself play an important role in driving this proton transfer reaction. When n = 3, the cooperative effect of the methanols in the subcluster provides the most important contribution to allow the intracluster proton transfer reaction to occur with little or no energy barrier. As n >or= 4, the methanol subcluster is able to form ring structures to stabilize the cluster structures so that direct proton transfer is not a favored process. The preferred reaction product, the (CH3OH)3H(+) cluster ion, indicates that this size-restricted reaction is driven by both the proton affinity and the enhanced stability of the resulting product.

Structure of Greyhound hemoglobin: origin of high oxygen affinity.

PubMed

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

2011-05-01

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

A Clustering Algorithm for Ecological Stream Segment Identification from Spatially Extensive Digital Databases

NASA Astrophysics Data System (ADS)

Brenden, T. O.; Clark, R. D.; Wiley, M. J.; Seelbach, P. W.; Wang, L.

2005-05-01

Remote sensing and geographic information systems have made it possible to attribute variables for streams at increasingly detailed resolutions (e.g., individual river reaches). Nevertheless, management decisions still must be made at large scales because land and stream managers typically lack sufficient resources to manage on an individual reach basis. Managers thus require a method for identifying stream management units that are ecologically similar and that can be expected to respond similarly to management decisions. We have developed a spatially-constrained clustering algorithm that can merge neighboring river reaches with similar ecological characteristics into larger management units. The clustering algorithm is based on the Cluster Affinity Search Technique (CAST), which was developed for clustering gene expression data. Inputs to the clustering algorithm are the neighbor relationships of the reaches that comprise the digital river network, the ecological attributes of the reaches, and an affinity value, which identifies the minimum similarity for merging river reaches. In this presentation, we describe the clustering algorithm in greater detail and contrast its use with other methods (expert opinion, classification approach, regular clustering) for identifying management units using several Michigan watersheds as a backdrop.

Nonthermal Particles and Radiation Produced by Cluster Merger Shocks

DTIC Science & Technology

2003-09-10

NONTHERMAL PARTICLES AND RADIATION PRODUCED BY CLUSTER MERGER SHOCKS Robert C. Berrington and Charles D. Dermer Naval Research Laboratory, Code 7653...of the merging cluster and is assumed to be constant as the shock propagates outward from the cluster center. In this paper , we model the cluster ...emission in the60–250 eV band for a number of clus- ters. These clusters include Virgo , Coma, Fornax, A2199, A1795, and A4059 (Lieu et al. 1996a, 1996b

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.

Possible world based consistency learning model for clustering and classifying uncertain data.

PubMed

Liu, Han; Zhang, Xianchao; Zhang, Xiaotong

2018-06-01

Possible world has shown to be effective for handling various types of data uncertainty in uncertain data management. However, few uncertain data clustering and classification algorithms are proposed based on possible world. Moreover, existing possible world based algorithms suffer from the following issues: (1) they deal with each possible world independently and ignore the consistency principle across different possible worlds; (2) they require the extra post-processing procedure to obtain the final result, which causes that the effectiveness highly relies on the post-processing method and the efficiency is also not very good. In this paper, we propose a novel possible world based consistency learning model for uncertain data, which can be extended both for clustering and classifying uncertain data. This model utilizes the consistency principle to learn a consensus affinity matrix for uncertain data, which can make full use of the information across different possible worlds and then improve the clustering and classification performance. Meanwhile, this model imposes a new rank constraint on the Laplacian matrix of the consensus affinity matrix, thereby ensuring that the number of connected components in the consensus affinity matrix is exactly equal to the number of classes. This also means that the clustering and classification results can be directly obtained without any post-processing procedure. Furthermore, for the clustering and classification tasks, we respectively derive the efficient optimization methods to solve the proposed model. Experimental results on real benchmark datasets and real world uncertain datasets show that the proposed model outperforms the state-of-the-art uncertain data clustering and classification algorithms in effectiveness and performs competitively in efficiency. Copyright © 2018 Elsevier Ltd. All rights reserved.

A dynamic T cell–limited checkpoint regulates affinity-dependent B cell entry into the germinal center

PubMed Central

Schwickert, Tanja A.; Victora, Gabriel D.; Fooksman, David R.; Kamphorst, Alice O.; Mugnier, Monica R.; Gitlin, Alexander D.; Dustin, Michael L.

2011-01-01

The germinal center (GC) reaction is essential for the generation of the somatically hypermutated, high-affinity antibodies that mediate adaptive immunity. Entry into the GC is limited to a small number of B cell clones; however, the process by which this limited number of clones is selected is unclear. In this study, we demonstrate that low-affinity B cells intrinsically capable of seeding a GC reaction fail to expand and become activated in the presence of higher-affinity B cells even before GC coalescence. Live multiphoton imaging shows that selection is based on the amount of peptide–major histocompatibility complex (pMHC) presented to cognate T cells within clusters of responding B and T cells at the T–B border. We propose a model in which T cell help is restricted to the B cells with the highest amounts of pMHC, thus allowing for a dynamic affinity threshold to be imposed on antigen-binding B cells. PMID:21576382

Propagation of human spermatogonial stem cells in vitro.

PubMed

Sadri-Ardekani, Hooman; Mizrak, Sefika C; van Daalen, Saskia K M; Korver, Cindy M; Roepers-Gajadien, Hermien L; Koruji, Morteza; Hovingh, Suzanne; de Reijke, Theo M; de la Rosette, Jean J M C H; van der Veen, Fulco; de Rooij, Dirk G; Repping, Sjoerd; van Pelt, Ans M M

2009-11-18

Young boys treated with high-dose chemotherapy are often confronted with infertility once they reach adulthood. Cryopreserving testicular tissue before chemotherapy and autotransplantation of spermatogonial stem cells at a later stage could theoretically allow for restoration of fertility. To establish in vitro propagation of human spermatogonial stem cells from small testicular biopsies to obtain an adequate number of cells for successful transplantation. Study performed from April 2007 to July 2009 using testis material donated by 6 adult men who underwent orchidectomy as part of prostate cancer treatment. Testicular cells were isolated and cultured in supplemented StemPro medium; germline stem cell clusters that arose were subcultured on human placental laminin-coated dishes in the same medium. Presence of spermatogonia was determined by reverse transcriptase polymerase chain reaction and immunofluorescence for spermatogonial markers. To test for the presence of functional spermatogonial stem cells in culture, xenotransplantation to testes of immunodeficient mice was performed, and migrated human spermatogonial stem cells after transplantation were detected by COT-1 fluorescence in situ hybridization. The number of colonized spermatogonial stem cells transplanted at early and later points during culture were counted to determine propagation. Propagation of spermatogonial stem cells over time. Testicular cells could be cultured and propagated up to 15 weeks. Germline stem cell clusters arose in the testicular cell cultures from all 6 men and could be subcultured and propagated up to 28 weeks. Expression of spermatogonial markers on both the RNA and protein level was maintained throughout the entire culture period. In 4 of 6 men, xenotransplantation to mice demonstrated the presence of functional spermatogonial stem cells, even after prolonged in vitro culture. Spermatogonial stem cell numbers increased 53-fold within 19 days in the testicular cell culture and

Lp-dual affine surface area

NASA Astrophysics Data System (ADS)

Wei, Wang; Binwu, He

2008-12-01

According to the notion of Lp-affine surface area by Lutwak, in this paper, we introduce the concept of Lp-dual affine surface area. Further, we establish the affine isoperimetric inequality and the Blaschke-Santaló inequality for Lp-dual affine surface area. Besides, the dual Brunn-Minkowski inequality for Lp-dual affine surface area is presented.

A K-means multivariate approach for clustering independent components from magnetoencephalographic data.

PubMed

Spadone, Sara; de Pasquale, Francesco; Mantini, Dante; Della Penna, Stefania

2012-09-01

Independent component analysis (ICA) is typically applied on functional magnetic resonance imaging, electroencephalographic and magnetoencephalographic (MEG) data due to its data-driven nature. In these applications, ICA needs to be extended from single to multi-session and multi-subject studies for interpreting and assigning a statistical significance at the group level. Here a novel strategy for analyzing MEG independent components (ICs) is presented, Multivariate Algorithm for Grouping MEG Independent Components K-means based (MAGMICK). The proposed approach is able to capture spatio-temporal dynamics of brain activity in MEG studies by running ICA at subject level and then clustering the ICs across sessions and subjects. Distinctive features of MAGMICK are: i) the implementation of an efficient set of "MEG fingerprints" designed to summarize properties of MEG ICs as they are built on spatial, temporal and spectral parameters; ii) the implementation of a modified version of the standard K-means procedure to improve its data-driven character. This algorithm groups the obtained ICs automatically estimating the number of clusters through an adaptive weighting of the parameters and a constraint on the ICs independence, i.e. components coming from the same session (at subject level) or subject (at group level) cannot be grouped together. The performances of MAGMICK are illustrated by analyzing two sets of MEG data obtained during a finger tapping task and median nerve stimulation. The results demonstrate that the method can extract consistent patterns of spatial topography and spectral properties across sessions and subjects that are in good agreement with the literature. In addition, these results are compared to those from a modified version of affinity propagation clustering method. The comparison, evaluated in terms of different clustering validity indices, shows that our methodology often outperforms the clustering algorithm. Eventually, these results are

RCLUS, a new program for clustering associated species: A demonstration using a Mojave Desert plant community dataset

Treesearch

Stewart C. Sanderson; Jeffrey E. Ott; E. Durant McArthur; Kimball T. Harper

2006-01-01

This paper presents a new clustering program named RCLUS that was developed for species (R-mode) analysis of plant community data. RCLUS identifies clusters of co-occurring species that meet a user-specified cutoff level of positive association with each other. The "strict affinity" clustering algorithm in RCLUS builds clusters of species whose pairwise...

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.

A Complex Between Biotin Synthase and The Iron-Sulfur Cluster Assembly Chaperone HscA That Enhances In Vivo Cluster Assembly†

PubMed Central

Reyda, Michael R.; Fugate, Corey J.; Jarrett, Joseph T.

2009-01-01

Biotin synthase (BioB) is an iron-sulfur enzyme that catalyzes the last step in biotin biosynthesis, the insertion of sulfur between the C6 and C9 carbons of dethiobiotin to complete the thiophane ring of biotin. Recent in vitro experiments suggest that the sulfur is derived from a [2Fe-2S]2+ cluster within BioB, and that the remnants of this cluster dissociate from the enzyme following each turnover. In order for BioB to catalyze multiple rounds of biotin synthesis, the [2Fe-2S]2+ cluster in BioB must be reassembled, a process that could be carried out in vivo by the ISC or SUF iron-sulfur cluster assembly systems. The bacterial ISC system includes HscA, an Hsp70-class molecular chaperone, whose yeast homolog has been shown to play an important but nonessential role in assembly of mitochondrial FeS clusters in S. cerevesiae. In the present work we show that in E. coli, HscA significantly improves the efficiency of the in vivo assembly of the [2Fe-2S]2+ cluster on BioB under conditions of low to moderate iron. In vitro, we show that HscA binds with increased affinity to BioB missing one or both FeS clusters, with a maximum of two HscA molecules per BioB dimer. BioB binds to HscA in an ATP/ADP-independent manner and a high affinity complex is also formed with a truncated form of HscA that lacks the nucleotide binding domain. Further, the BioB:HscA complex binds the FeS cluster scaffold protein IscU in a noncompetitive manner, generating a complex that contains all three proteins. We propose that HscA plays a role in facilitating the transfer of FeS clusters from IscU into the appropriate target apoproteins such as biotin synthase, perhaps by enhancing or prolonging the requisite protein:protein interaction. PMID:19821612

A Hybrid Algorithm for Clustering of Time Series Data Based on Affinity Search Technique

PubMed Central

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. PMID:24982966

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

PubMed

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

2015-01-01

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

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

DOE PAGES

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

2015-06-01

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

Magneto-nanosensor platform for probing low-affinity protein–protein interactions and identification of a low-affinity PD-L1/PD-L2 interaction

PubMed Central

Lee, Jung-Rok; Bechstein, Daniel J. B.; Ooi, Chin Chun; Patel, Ashka; Gaster, Richard S.; Ng, Elaine; Gonzalez, Lino C.; Wang, Shan X.

2016-01-01

Substantial efforts have been made to understand the interactions between immune checkpoint receptors and their ligands targeted in immunotherapies against cancer. To carefully characterize the complete network of interactions involved and the binding affinities between their extracellular domains, an improved kinetic assay is needed to overcome limitations with surface plasmon resonance (SPR). Here, we present a magneto-nanosensor platform integrated with a microfluidic chip that allows measurement of dissociation constants in the micromolar-range. High-density conjugation of magnetic nanoparticles with prey proteins allows multivalent receptor interactions with sensor-immobilized bait proteins, more closely mimicking natural-receptor clustering on cells. The platform has advantages over traditional SPR in terms of insensitivity of signal responses to pH and salinity, less consumption of proteins and better sensitivities. Using this platform, we characterized the binding affinities of the PD-1—PD-L1/PD-L2 co-inhibitory receptor system, and discovered an unexpected interaction between the two known PD-1 ligands, PD-L1 and PD-L2. PMID:27447090

Three-Dimensional Modeling of Fracture Clusters in Geothermal Reservoirs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghassemi, Ahmad

The objective of this is to develop a 3-D numerical model for simulating mode I, II, and III (tensile, shear, and out-of-plane) propagation of multiple fractures and fracture clusters to accurately predict geothermal reservoir stimulation using the virtual multi-dimensional internal bond (VMIB). Effective development of enhanced geothermal systems can significantly benefit from improved modeling of hydraulic fracturing. In geothermal reservoirs, where the temperature can reach or exceed 350oC, thermal and poro-mechanical processes play an important role in fracture initiation and propagation. In this project hydraulic fracturing of hot subsurface rock mass will be numerically modeled by extending the virtual multiplemore » internal bond theory and implementing it in a finite element code, WARP3D, a three-dimensional finite element code for solid mechanics. The new constitutive model along with the poro-thermoelastic computational algorithms will allow modeling the initiation and propagation of clusters of fractures, and extension of pre-existing fractures. The work will enable the industry to realistically model stimulation of geothermal reservoirs. The project addresses the Geothermal Technologies Office objective of accurately predicting geothermal reservoir stimulation (GTO technology priority item). The project goal will be attained by: (i) development of the VMIB method for application to 3D analysis of fracture clusters; (ii) development of poro- and thermoelastic material sub-routines for use in 3D finite element code WARP3D; (iii) implementation of VMIB and the new material routines in WARP3D to enable simulation of clusters of fractures while accounting for the effects of the pore pressure, thermal stress and inelastic deformation; (iv) simulation of 3D fracture propagation and coalescence and formation of clusters, and comparison with laboratory compression tests; and (v) application of the model to interpretation of injection experiments (planned by

Affinity in electrophoresis.

PubMed

Heegaard, Niels H H

2009-06-01

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

Observations of cloud cluster hierarchies over the tropical western Pacific

NASA Technical Reports Server (NTRS)

Lau, K. M.; Nakazawa, T.; Sui, C. H.

1991-01-01

The structure and propagation of tropical-cloud clusters are investigated during two contrasting periods over the tropical western Pacific in order to determine possible similarities or differences and to compare with previous studies. Three fundamental periodicities are found in tropical convection in the region: 1 day, 2-3 days, and 10-15 days. It is noted that the 10-15-day time scale is closely related to the intraseasonal oscillations propagating from the Indian Ocean to the western Pacific. Large convective complexes, supercloud clusters (SSC) are found to organize in this time scale. The SCC is made up from several cloud clusters generated at 2-3-day intervals. The diurnal variation is found to be most pronounced over the maritime continent, and the amplitude of the diurnal cycle is shown to be modulated by the 2-3-day and 10-15-day oscillations.

Structural, electronic, vibrational and optical properties of Bin clusters

NASA Astrophysics Data System (ADS)

Liang, Dan; Shen, Wanting; Zhang, Chunfang; Lu, Pengfei; Wang, Shumin

2017-10-01

The neutral, anionic and cationic bismuth clusters with the size n up to 14 are investigated by using B3LYP functional within the regime of density functional theory and the LAN2DZ basis set. By analysis of the geometries of the Bin (n = 2-14) clusters, where cationic and anionic bismuth clusters are largely similar to those of neutral ones, a periodic effect by adding units with one to four atoms into smaller cluster to form larger cluster is drawn for the stable structures of bismuth clusters. An even-odd alteration is shown for the properties of the clusters, such as the calculated binding energies and dissociation energies, as well as frontier orbital energies, electron affinities, ionization energies. All the properties indicate that the Bi4 cluster is the most possible existence in bismuth-containing materials, which supports the most recent experiment. The orbital compositions, infrared and Raman activities and the ultraviolet absorption of the most possible tetramer bismuth cluster are given in detail to reveal the periodic tendency of adding bismuth atoms and the stability of tetramer bismuth cluster.

Discriminative clustering on manifold for adaptive transductive classification.

PubMed

Zhang, Zhao; Jia, Lei; Zhang, Min; Li, Bing; Zhang, Li; Li, Fanzhang

2017-10-01

In this paper, we mainly propose a novel adaptive transductive label propagation approach by joint discriminative clustering on manifolds for representing and classifying high-dimensional data. Our framework seamlessly combines the unsupervised manifold learning, discriminative clustering and adaptive classification into a unified model. Also, our method incorporates the adaptive graph weight construction with label propagation. Specifically, our method is capable of propagating label information using adaptive weights over low-dimensional manifold features, which is different from most existing studies that usually predict the labels and construct the weights in the original Euclidean space. For transductive classification by our formulation, we first perform the joint discriminative K-means clustering and manifold learning to capture the low-dimensional nonlinear manifolds. Then, we construct the adaptive weights over the learnt manifold features, where the adaptive weights are calculated through performing the joint minimization of the reconstruction errors over features and soft labels so that the graph weights can be joint-optimal for data representation and classification. Using the adaptive weights, we can easily estimate the unknown labels of samples. After that, our method returns the updated weights for further updating the manifold features. Extensive simulations on image classification and segmentation show that our proposed algorithm can deliver the state-of-the-art performance on several public datasets. Copyright © 2017 Elsevier Ltd. All rights reserved.

Adjoint affine fusion and tadpoles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Urichuk, Andrew, E-mail: andrew.urichuk@uleth.ca; Walton, Mark A., E-mail: walton@uleth.ca; International School for Advanced Studies

2016-06-15

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 writtenmore » 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.« less

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

THE DYNAMICS OF MERGING CLUSTERS: A MONTE CARLO SOLUTION APPLIED TO THE BULLET AND MUSKET BALL CLUSTERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawson, William A., E-mail: wadawson@ucdavis.edu

2013-08-01

Merging galaxy clusters have become one of the most important probes of dark matter, providing evidence for dark matter over modified gravity and even constraints on the dark matter self-interaction cross-section. To properly constrain the dark matter cross-section it is necessary to understand the dynamics of the merger, as the inferred cross-section is a function of both the velocity of the collision and the observed time since collision. While the best understanding of merging system dynamics comes from N-body simulations, these are computationally intensive and often explore only a limited volume of the merger phase space allowed by observed parametermore » uncertainty. Simple analytic models exist but the assumptions of these methods invalidate their results near the collision time, plus error propagation of the highly correlated merger parameters is unfeasible. To address these weaknesses I develop a Monte Carlo method to discern the properties of dissociative mergers and propagate the uncertainty of the measured cluster parameters in an accurate and Bayesian manner. I introduce this method, verify it against an existing hydrodynamic N-body simulation, and apply it to two known dissociative mergers: 1ES 0657-558 (Bullet Cluster) and DLSCL J0916.2+2951 (Musket Ball Cluster). I find that this method surpasses existing analytic models-providing accurate (10% level) dynamic parameter and uncertainty estimates throughout the merger history. This, coupled with minimal required a priori information (subcluster mass, redshift, and projected separation) and relatively fast computation ({approx}6 CPU hours), makes this method ideal for large samples of dissociative merging clusters.« less

Weighted community detection and data clustering using message passing

NASA Astrophysics Data System (ADS)

Shi, Cheng; Liu, Yanchen; Zhang, Pan

2018-03-01

Grouping objects into clusters based on the similarities or weights between them is one of the most important problems in science and engineering. In this work, by extending message-passing algorithms and spectral algorithms proposed for an unweighted community detection problem, we develop a non-parametric method based on statistical physics, by mapping the problem to the Potts model at the critical temperature of spin-glass transition and applying belief propagation to solve the marginals corresponding to the Boltzmann distribution. Our algorithm is robust to over-fitting and gives a principled way to determine whether there are significant clusters in the data and how many clusters there are. We apply our method to different clustering tasks. In the community detection problem in weighted and directed networks, we show that our algorithm significantly outperforms existing algorithms. In the clustering problem, where the data were generated by mixture models in the sparse regime, we show that our method works all the way down to the theoretical limit of detectability and gives accuracy very close to that of the optimal Bayesian inference. In the semi-supervised clustering problem, our method only needs several labels to work perfectly in classic datasets. Finally, we further develop Thouless-Anderson-Palmer equations which heavily reduce the computation complexity in dense networks but give almost the same performance as belief propagation.

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.

From clusters to bulk: A relativistic density functional investigation on a series of gold clusters Aun, n=6,…,147

NASA Astrophysics Data System (ADS)

Häberlen, Oliver D.; Chung, Sai-Cheong; Stener, Mauro; Rösch, Notker

1997-03-01

A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold-gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold-gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold-gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge

Stochastic fire-diffuse-fire model with realistic cluster dynamics.

PubMed

Calabrese, Ana; Fraiman, Daniel; Zysman, Daniel; Ponce Dawson, Silvina

2010-09-01

Living organisms use waves that propagate through excitable media to transport information. Ca2+ waves are a paradigmatic example of this type of processes. A large hierarchy of Ca2+ signals that range from localized release events to global waves has been observed in Xenopus laevis oocytes. In these cells, Ca2+ release occurs trough inositol 1,4,5-trisphosphate receptors (IP3Rs) which are organized in clusters of channels located on the membrane of the endoplasmic reticulum. In this article we construct a stochastic model for a cluster of IP3R 's that replicates the experimental observations reported in [D. Fraiman, Biophys. J. 90, 3897 (2006)]. We then couple this phenomenological cluster model with a reaction-diffusion equation, so as to have a discrete stochastic model for calcium dynamics. The model we propose describes the transition regimes between isolated release and steadily propagating waves as the IP3 concentration is increased.

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

Lp-mixed affine surface area

NASA Astrophysics Data System (ADS)

Wang, Weidong; Leng, Gangsong

2007-11-01

According to the three notions of mixed affine surface area, Lp-affine surface area and Lp-mixed affine surface area proposed by Lutwak, in this article, we give the concept of ith Lp-mixed affine surface area such that the first and second notions of Lutwak are its special cases. Further, some Lutwak's results are extended associated with this concept. Besides, applying this concept, we establish an inequality for the volumes and dual quermassintegrals of a class of star bodies.

Propagation of coherent light pulses with PHASE

NASA Astrophysics Data System (ADS)

Bahrdt, J.; Flechsig, U.; Grizzoli, W.; Siewert, F.

2014-09-01

The current status of the software package PHASE for the propagation of coherent light pulses along a synchrotron radiation beamline is presented. PHASE is based on an asymptotic expansion of the Fresnel-Kirchhoff integral (stationary phase approximation) which is usually truncated at the 2nd order. The limits of this approximation as well as possible extensions to higher orders are discussed. The accuracy is benchmarked against a direct integration of the Fresnel-Kirchhoff integral. Long range slope errors of optical elements can be included by means of 8th order polynomials in the optical element coordinates w and l. Only recently, a method for the description of short range slope errors has been implemented. The accuracy of this method is evaluated and examples for realistic slope errors are given. PHASE can be run either from a built-in graphical user interface or from any script language. The latter method provides substantial flexibility. Optical elements including apertures can be combined. Complete wave packages can be propagated, as well. Fourier propagators are included in the package, thus, the user may choose between a variety of propagators. Several means to speed up the computation time were tested - among them are the parallelization in a multi core environment and the parallelization on a cluster.

Efficient similarity-based data clustering by optimal object to cluster reallocation.

PubMed

Rossignol, Mathias; Lagrange, Mathieu; Cont, Arshia

2018-01-01

We present an iterative flat hard clustering algorithm designed to operate on arbitrary similarity matrices, with the only constraint that these matrices be symmetrical. Although functionally very close to kernel k-means, our proposal performs a maximization of average intra-class similarity, instead of a squared distance minimization, in order to remain closer to the semantics of similarities. We show that this approach permits the relaxing of some conditions on usable affinity matrices like semi-positiveness, as well as opening possibilities for computational optimization required for large datasets. Systematic evaluation on a variety of data sets shows that compared with kernel k-means and the spectral clustering methods, the proposed approach gives equivalent or better performance, while running much faster. Most notably, it significantly reduces memory access, which makes it a good choice for large data collections. Material enabling the reproducibility of the results is made available online.

A Smartphone Indoor Localization Algorithm Based on WLAN Location Fingerprinting with Feature Extraction and Clustering.

PubMed

Luo, Junhai; Fu, Liang

2017-06-09

With the development of communication technology, the demand for location-based services is growing rapidly. This paper presents an algorithm for indoor localization based on Received Signal Strength (RSS), which is collected from Access Points (APs). The proposed localization algorithm contains the offline information acquisition phase and online positioning phase. Firstly, the AP selection algorithm is reviewed and improved based on the stability of signals to remove useless AP; secondly, Kernel Principal Component Analysis (KPCA) is analyzed and used to remove the data redundancy and maintain useful characteristics for nonlinear feature extraction; thirdly, the Affinity Propagation Clustering (APC) algorithm utilizes RSS values to classify data samples and narrow the positioning range. In the online positioning phase, the classified data will be matched with the testing data to determine the position area, and the Maximum Likelihood (ML) estimate will be employed for precise positioning. Eventually, the proposed algorithm is implemented in a real-world environment for performance evaluation. Experimental results demonstrate that the proposed algorithm improves the accuracy and computational complexity.

Energy Efficient and Stable Weight Based Clustering for Mobile Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Bouk, Safdar H.; Sasase, Iwao

Recently several weighted clustering algorithms have been proposed, however, to the best of our knowledge; there is none that propagates weights to other nodes without weight message for leader election, normalizes node parameters and considers neighboring node parameters to calculate node weights. In this paper, we propose an Energy Efficient and Stable Weight Based Clustering (EE-SWBC) algorithm that elects cluster heads without sending any additional weight message. It propagates node parameters to its neighbors through neighbor discovery message (HELLO Message) and stores these parameters in neighborhood list. Each node normalizes parameters and efficiently calculates its own weight and the weights of neighboring nodes from that neighborhood table using Grey Decision Method (GDM). GDM finds the ideal solution (best node parameters in neighborhood list) and calculates node weights in comparison to the ideal solution. The node(s) with maximum weight (parameters closer to the ideal solution) are elected as cluster heads. In result, EE-SWBC fairly selects potential nodes with parameters closer to ideal solution with less overhead. Different performance metrics of EE-SWBC and Distributed Weighted Clustering Algorithm (DWCA) are compared through simulations. The simulation results show that EE-SWBC maintains fewer average numbers of stable clusters with minimum overhead, less energy consumption and fewer changes in cluster structure within network compared to DWCA.

Fundamentals of affinity cell separations.

PubMed

Zhang, Ye; Lyons, Veronica; Pappas, Dimitri

2018-03-01

Cell separations using affinity methods continue to be an enabling science for a wide variety of applications. In this review, we discuss the fundamental aspects of affinity separation, including the competing forces for cell capture and elution, cell-surface interactions, and models for cell adhesion. Factors affecting separation performance such as bond affinity, contact area, and temperature are presented. We also discuss and demonstrate the effects of nonspecific binding on separation performance. Metrics for evaluating cell separations are presented, along with methods of comparing separation techniques for cell isolation using affinity capture. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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…

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

PubMed

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

2006-02-07

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

Clustering coefficients of protein-protein interaction networks

NASA Astrophysics Data System (ADS)

Miller, Gerald A.; Shi, Yi Y.; Qian, Hong; Bomsztyk, Karol

2007-05-01

The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k other vertices determines all measurable properties. We study hidden variable models and find an averaging approximation that enables us to obtain a general analytical result for the propagator. Analytic results showing the validity of the approximation are obtained. We apply hidden variable models to protein-protein interaction networks (PINs) in which the hidden variable is the association free energy, determined by distributions that depend on biochemistry and evolution. We compute degree distributions as well as clustering coefficients of several PINs of different species; good agreement with measured data is obtained. For the human interactome two different parameter sets give the same degree distributions, but the computed clustering coefficients differ by a factor of about 2. This shows that degree distributions are not sufficient to determine the properties of PINs.

Affinity of C-Reactive Protein toward FcγRI Is Strongly Enhanced by the γ-Chain

PubMed Central

Röcker, Carlheinz; Manolov, Dimitar E.; Kuzmenkina, Elza V.; Tron, Kyrylo; Slatosch, Holger; Torzewski, Jan; Nienhaus, G. Ulrich

2007-01-01

C-reactive protein (CRP), the prototype human acute phase protein, is widely regarded as a key player in cardiovascular disease, but the identity of its cellular receptor is still under debate. By using ultrasensitive confocal imaging analysis, we have studied CRP binding to transfected COS-7 cells expressing the high-affinity IgG receptor FcγRI. Here we show that CRP binds to FcγRI on intact cells, with a kd of 10 ± 3 μmol/L. Transfection of COS-7 cells with a plasmid coding for both FcγRI and its functional counterpart, the γ-chain, markedly increases CRP affinity to FcγRI, resulting in a kd of 0.35 ± 0.10 μmol/L. The affinity increase results from an ∼30-fold enhanced association rate coefficient. The pronounced enhancement of affinity by the γ-chain suggests its crucial involvement in the CRP receptor interaction, possibly by mediating interactions between the transmembrane moieties of the receptors. Dissociation of CRP from the cell surfaces cannot be detected throughout the time course of several hours and is thus extremely slow. Considering the pentameric structure of CRP, this result indicates that multivalent binding and receptor clustering are crucially involved in the interaction of CRP with nucleated cells. PMID:17255341

A k-space method for acoustic propagation using coupled first-order equations in three dimensions.

PubMed

Tillett, Jason C; Daoud, Mohammad I; Lacefield, James C; Waag, Robert C

2009-09-01

A previously described two-dimensional k-space method for large-scale calculation of acoustic wave propagation in tissues is extended to three dimensions. The three-dimensional method contains all of the two-dimensional method features that allow accurate and stable calculation of propagation. These features are spectral calculation of spatial derivatives, temporal correction that produces exact propagation in a homogeneous medium, staggered spatial and temporal grids, and a perfectly matched boundary layer. Spectral evaluation of spatial derivatives is accomplished using a fast Fourier transform in three dimensions. This computational bottleneck requires all-to-all communication; execution time in a parallel implementation is therefore sensitive to node interconnect latency and bandwidth. Accuracy of the three-dimensional method is evaluated through comparisons with exact solutions for media having spherical inhomogeneities. Large-scale calculations in three dimensions were performed by distributing the nearly 50 variables per voxel that are used to implement the method over a cluster of computers. Two computer clusters used to evaluate method accuracy are compared. Comparisons of k-space calculations with exact methods including absorption highlight the need to model accurately the medium dispersion relationships, especially in large-scale media. Accurately modeled media allow the k-space method to calculate acoustic propagation in tissues over hundreds of wavelengths.

puma: a Bioconductor package for propagating uncertainty in microarray analysis.

PubMed

Pearson, Richard D; Liu, Xuejun; Sanguinetti, Guido; Milo, Marta; Lawrence, Neil D; Rattray, Magnus

2009-07-09

Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By determining uncertainties from Affymetrix GeneChip data and propagating these uncertainties to downstream analyses it has been shown that we can improve results of differential expression detection, principal component analysis and clustering. Previously, implementations of these uncertainty propagation methods have only been available as separate packages, written in different languages. Previous implementations have also suffered from being very costly to compute, and in the case of differential expression detection, have been limited in the experimental designs to which they can be applied. puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data. puma extends the differential expression detection methods of previous work from the 2-class case to the multi-factorial case. puma can be used to automatically create design and contrast matrices for typical experimental designs, which can be used both within the package itself but also in other Bioconductor packages. The implementation of differential expression detection methods has been parallelised leading to significant decreases in processing time on a range of computer architectures. puma incorporates the first R implementation of an uncertainty propagation version of principal component analysis, and an implementation of a clustering method based on uncertainty propagation. All of these techniques are brought together in a single, easy-to-use package with clear, task-based documentation. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. These methods can be used to improve results from more traditional analyses of microarray data. puma also offers improvements in terms of scope and speed of execution over previously available methods. puma is recommended for

Dye-ligand affinity systems.

PubMed

Denizli, A; Pişkin, E

2001-10-30

Dye-ligands have been considered as one of the important alternatives to natural counterparts for specific affinity chromatography. Dye-ligands are able to bind most types of proteins, in some cases in a remarkably specific manner. They are commercially available, inexpensive, and can easily be immobilized, especially on matrices bearing hydroxyl groups. Although dyes are all synthetic in nature, they are still classified as affinity ligands because they interact with the active sites of many proteins mimicking the structure of the substrates, cofactors, or binding agents for those proteins. A number of textile dyes, known as reactive dyes, have been used for protein purification. Most of these reactive dyes consist of a chromophore (either azo dyes, anthraquinone, or phathalocyanine), linked to a reactive group (often a mono- or dichlorotriazine ring). The interaction between the dye ligand and proteins can be by complex combination of electrostatic, hydrophobic, hydrogen bonding. Selection of the supporting matrix is the first important consideration in dye-affinity systems. There are several methods for immobilization of dye molecules onto the support matrix, in which usually several intermediate steps are followed. Both the adsorption and elution steps should carefully be optimized/designed for a successful separation. Dye-affinity systems in the form of spherical sorbents or as affinity membranes have been used in protein separation.

Fractal Clustering and Knowledge-driven Validation Assessment for Gene Expression Profiling.

PubMed

Wang, Lu-Yong; Balasubramanian, Ammaiappan; Chakraborty, Amit; Comaniciu, Dorin

2005-01-01

DNA microarray experiments generate a substantial amount of information about the global gene expression. Gene expression profiles can be represented as points in multi-dimensional space. It is essential to identify relevant groups of genes in biomedical research. Clustering is helpful in pattern recognition in gene expression profiles. A number of clustering techniques have been introduced. However, these traditional methods mainly utilize shape-based assumption or some distance metric to cluster the points in multi-dimension linear Euclidean space. Their results shows poor consistence with the functional annotation of genes in previous validation study. From a novel different perspective, we propose fractal clustering method to cluster genes using intrinsic (fractal) dimension from modern geometry. This method clusters points in such a way that points in the same clusters are more self-affine among themselves than to the points in other clusters. We assess this method using annotation-based validation assessment for gene clusters. It shows that this method is superior in identifying functional related gene groups than other traditional methods.

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

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri L.

2006-01-01

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

Magnetic switching in Crx (x = 2-8) and its oxide cluster series

NASA Astrophysics Data System (ADS)

Shah, Esha V.; Roy, Debesh R.

2018-04-01

First principle studies on the magnetic ground state structure, noncollinearity, binding energy and various electronic properties of a series of Crx (x = 2-8) clusters are performed. In order to investigate the effect of ionization and oxidation on the clusters, the anionic (Crx-) and oxidized (CrxO2) analogues of those clusters are also studied in detail. To calculate adiabatic electron affinity of CrxO2 clusters, additionally CrxO2- analogues are also included in the present work. An interesting even (non-magnetic) - odd (magnetic) feature in the considered cluster series has been noticed. The similar behavior is also reflected from their electronic properties as even (less reactive) - odd (more reactive). The most of the neutral and ionized chromium clusters, viz., Crx and Crx- are found to be noncollinear in their ground states, whereas oxidation stabilized those clusters into the collinear spin alignments. The bond distances of Cr clusters are found to be close with available experimental studies.

Affinity-aware checkpoint restart

DOE PAGES

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

2014-12-08

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

Affinity-aware checkpoint restart

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saini, Ajay; Rezaei, Arash; Mueller, Frank

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

Numerical Modeling of 3D Seismic Wave Propagation around Yogyakarta, the Southern Part of Central Java, Indonesia, Using Spectral-Element Method on MPI-GPU Cluster

NASA Astrophysics Data System (ADS)

Sudarmaji; Rudianto, Indra; Eka Nurcahya, Budi

2018-04-01

A strong tectonic earthquake with a magnitude of 5.9 Richter scale has been occurred in Yogyakarta and Central Java on May 26, 2006. The earthquake has caused severe damage in Yogyakarta and the southern part of Central Java, Indonesia. The understanding of seismic response of earthquake among ground shaking and the level of building damage is important. We present numerical modeling of 3D seismic wave propagation around Yogyakarta and the southern part of Central Java using spectral-element method on MPI-GPU (Graphics Processing Unit) computer cluster to observe its seismic response due to the earthquake. The homogeneous 3D realistic model is generated with detailed topography surface. The influences of free surface topography and layer discontinuity of the 3D model among the seismic response are observed. The seismic wave field is discretized using spectral-element method. The spectral-element method is solved on a mesh of hexahedral elements that is adapted to the free surface topography and the internal discontinuity of the model. To increase the data processing capabilities, the simulation is performed on a GPU cluster with implementation of MPI (Message Passing Interface).

Polypyrrole-chitosan conductive biomaterial synchronizes cardiomyocyte contraction and improves myocardial electrical impulse propagation.

PubMed

Cui, Zhi; Ni, Nathan C; Wu, Jun; Du, Guo-Qing; He, Sheng; Yau, Terrence M; Weisel, Richard D; Sung, Hsing-Wen; Li, Ren-Ke

2018-01-01

Background: The post-myocardial infarction (MI) scar interrupts electrical impulse propagation and delays regional contraction, which contributes to ventricular dysfunction. We investigated the potential of an injectable conductive biomaterial to restore scar tissue conductivity and re-establish synchronous ventricular contraction. Methods: A conductive biomaterial was generated by conjugating conductive polypyrrole (PPY) onto chitosan (CHI) backbones. Trypan blue staining of neonatal rat cardiomyocytes (CMs) cultured on biomaterials was used to evaluate the biocompatibility of the conductive biomaterials. Ca 2+ imaging was used to visualize beating CMs. A cryoablation injury rat model was used to investigate the ability of PPY:CHI to improve cardiac electrical propagation in the injured heart in vivo . Electromyography was used to evaluate conductivity of scar tissue ex vivo . Results: Cell survival and morphology were similar between cells cultured on biomaterials-coated and uncoated-control dishes. PPY:CHI established synchronous contraction of two distinct clusters of spontaneously-beating CMs. Intramyocardial PPY:CHI injection into the cryoablation-induced injured region improved electrical impulse propagation across the scarred tissue and decreased the QRS interval, whereas saline- or CHI-injected hearts continued to have delayed propagation patterns and significantly reduced conduction velocity compared to healthy controls. Ex vivo evaluation found that scar tissue from PPY:CHI-treated rat hearts had higher signal amplitude compared to those from saline- or CHI-treated rat heart tissue. Conclusions: The PPY:CHI biomaterial is electrically conductive, biocompatible and injectable. It improved synchronous contraction between physically separated beating CM clusters in vitro . Intra-myocardial injection of PPY:CHI following cardiac injury improved electrical impulse propagation of scar tissue in vivo .

Biased selection of propagation-related TUPs from phage display peptide libraries.

PubMed

Zade, Hesam Motaleb; Keshavarz, Reihaneh; Shekarabi, Hosna Sadat Zahed; Bakhshinejad, Babak

2017-08-01

Phage display is rapidly advancing as a screening strategy in drug discovery and drug delivery. Phage-encoded combinatorial peptide libraries can be screened through the affinity selection procedure of biopanning to find pharmaceutically relevant cell-specific ligands. However, the unwanted enrichment of target-unrelated peptides (TUPs) with no true affinity for the target presents an important barrier to the successful screening of phage display libraries. Propagation-related TUPs (Pr-TUPs) are an emerging but less-studied category of phage display-derived false-positive hits that are displayed on the surface of clones with faster propagation rates. Despite long regarded as an unbiased selection system, accumulating evidence suggests that biopanning may create biological bias toward selection of phage clones with certain displayed peptides. This bias can be dependent on or independent of the displayed sequence and may act as a major driving force for the isolation of fast-growing clones. Sequence-dependent bias is reflected by censorship or over-representation of some amino acids in the displayed peptide and sequence-independent bias is derived from either point mutations or rare recombination events occurring in the phage genome. It is of utmost interest to clean biopanning data by identifying and removing Pr-TUPs. Experimental and bioinformatic approaches can be exploited for Pr-TUP discovery. With no doubt, obtaining deeper insight into how Pr-TUPs emerge during biopanning and how they could be detected provides a basis for using cell-targeting peptides isolated from phage display screening in the development of disease-specific diagnostic and therapeutic platforms.

2017 Guralp Affinity Digitizer Evaluation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merchant, Bion J.

Sandia National Laboratories has tested and evaluated two Guralp Affinity digitizers. The Affinity digitizers are intended to record sensor output for seismic and infrasound monitoring applications. The purpose of this digitizer evaluation is to measure the performance characteristics in such areas as power consumption, input impedance, sensitivity, full scale, self- noise, dynamic range, system noise, response, passband, and timing. The Affinity digitizers are being evaluated for potential use in the International Monitoring System (IMS) of the Comprehensive Nuclear Test-Ban-Treaty Organization (CTBTO).

HIGH-ENERGY NEUTRINOS FROM SOURCES IN CLUSTERS OF GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 themore » 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.« less

First principles study of structural, electronic and magnetic properties of SnGe n (0, ±1) ( n = 1–17) clusters

NASA Astrophysics Data System (ADS)

Djaadi, Soumaia; Eddine Aiadi, Kamal; Mahtout, Sofiane

2018-04-01

The structures, relative stability and magnetic properties of pure Ge n +1, neutral cationic and anionic SnGe n (n = 1–17) clusters have been investigated by using the first principles density functional theory implemented in SIESTA packages. We find that with the increasing of cluster size, the Ge n +1 and SnGe n (0, ±1) clusters tend to adopt compact structures. It has been also found that the Sn atom occupied a peripheral position for SnGe n clusters when n < 12 and occupied a core position for n > 12. The structural and electronic properties such as optimized geometries, fragmentation energy, binding energy per atom, HOMO–LUMO gaps and second-order differences in energy of the pure Ge n +1 and SnGe n clusters in their ground state are calculated and analyzed. All isomers of neutral SnGe n clusters are generally nonmagnetic except for n = 1 and 4, where the total spin magnetic moments is 2μ b. The total (DOS) and partial density of states of these clusters have been calculated to understand the origin of peculiar magnetic properties. The cluster size dependence of vertical ionization potentials, vertical electronic affinities, chemical hardness, adiabatic electron affinities and adiabatic ionization potentials have been calculated and discussed.

Genetic affinities of Helicobacter pylori isolates from ethnic Arabs in Kuwait

PubMed Central

2010-01-01

Helicobacter pylori is one of the most genetically diverse of bacterial species, and since the 5'-end of cagA gene and the middle allele of vacA gene of H. pylori from different populations exhibit considerable polymorphisms, these sequence diversities were used to gain insights into the genetic affinities of this gastric pathogen from different populations. Because the genetic affinity of Arab strains from the Arabian Gulf is not known, we carried out genetic analysis based on sequence diversities of the cagA and the vacA genes of H. pylori from 9 ethnic Arabs in Kuwait. The analysis showed that the Kuwaiti isolates are closely related to the Indo-European group of strains, although some strains have a tendency to form a separate cluster close to the Indo- European group, but clearly distinct from East Asian strains. However, these results need to be confirmed by analyses of neutral markers (house-keeping genes in a multi-locus sequence typing [MLST]) platform. The profiling of virulence-associated genes may have resulted from ecologically distinct populations due to human migration and geographical separation over long periods of time. PMID:20602767

Scalable Prediction of Energy Consumption using Incremental Time Series Clustering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simmhan, Yogesh; Noor, Muhammad Usman

2013-10-09

Time series datasets are a canonical form of high velocity Big Data, and often generated by pervasive sensors, such as found in smart infrastructure. Performing predictive analytics on time series data can be computationally complex, and requires approximation techniques. In this paper, we motivate this problem using a real application from the smart grid domain. We propose an incremental clustering technique, along with a novel affinity score for determining cluster similarity, which help reduce the prediction error for cumulative time series within a cluster. We evaluate this technique, along with optimizations, using real datasets from smart meters, totaling ~700,000 datamore » points, and show the efficacy of our techniques in improving the prediction error of time series data within polynomial time.« less

Antisymmetric tensor generalizations of affine vector fields.

PubMed

Houri, Tsuyoshi; Morisawa, Yoshiyuki; Tomoda, Kentaro

2016-02-01

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

Clustering impact regime with shocks in freely evolving granular gas

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

2017-06-01

A freely cooling granular gas without any external force evolves from the initial homogeneous state to the inhomogeneous clustering state, at which the energy decay deviates from the Haff's law. The asymptotic behavior of energy in the inelastic hard sphere model have been predicted by several theories, which are based on the mode coupling theory or extension of inelastic hard rods gas. In this study, we revisited the clustering regime of freely evolving granular gas via large-scale molecular dynamics simulation with up to 16.7 million inelastic hard disks. We found novel regime regarding on collisions between "clusters" spontaneously appearing after clustering regime, which can only be identified more than a few million particles system. The volumetric dilatation pattern of semicircular shape originated from density shock propagation are well characterized on the appearing of "cluster impact" during the aggregation process of clusters.

The effect of ligand affinity on integrins' lateral diffusion in cultured cells.

PubMed

Mainali, Dipak; Smith, Emily A

2013-04-01

The role of ligand affinity in altering αPS2CβPS integrins' lateral mobility was studied using single particle tracking (SPT) with ligand-functionalized quantum dots (QDs) and fluorescence recovery after photobleaching (FRAP) with fluorescent protein tagged integrins. Integrins are ubiquitous transmembrane proteins that are vital for numerous cellular functions, including bidirectional signaling and cell anchorage. Wild-type and high ligand affinity mutant (αPS2CβPS-V409D) integrins were studied in S2 cells. As measured by SPT, the integrin mobile fraction decreased by 22% and had a 4× slower diffusion coefficient for αPS2CβPS-V409D compared to wild-type integrins. These differences are partially the result of αPS2CβPS-V409D integrins' increased clustering. For the wild-type integrins, the average of all diffusion coefficients measured by SPT was statistically similar to the ensemble FRAP results. A 75% slower average diffusion coefficient was measured by SPT compared to FRAP for αPS2CβPS-V409D integrins, and this may be the result of SPT measuring only ligand-bound integrins, in contrast all ligand-bound and ligand-unbound integrins are averaged in FRAP measurements. Specific binding of the ligand-functionalized QDs was 99% for integrin expressing cells. The results prove that the ligand binding affinity affects the lateral dynamics of a subset of integrins based on the complementary SPT and FRAP data.

Personality Types and Affinity for Computers

DTIC Science & Technology

1991-03-01

differences on personality dimensions between the respondents, and to explore the relationship between these differences and computer affinity. The results...between the respondents, and to explore the relationship between these differences and computer affinity. The results revealed no significant differences...type to this measure of computer affinity. 2 II. LITERATURZ REVIEW The interest of this study was the relationship between a person’s psychological

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

NASA Astrophysics Data System (ADS)

Zekri, Nouredine; Clerc, Jean Pierre

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

Smooth affine shear tight frames: digitization and applications

NASA Astrophysics Data System (ADS)

Zhuang, Xiaosheng

2015-08-01

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

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

Proton affinity and enthalpy of formation of formaldehyde

NASA Astrophysics Data System (ADS)

Czakó, Gábor; Nagy, Balázs; Tasi, Gyula; Somogyi, Árpád; Šimunek, Ján; Noga, Jozef; Braams, Bastiaan J.; Bowman, Joel M.; Császár; , Attila G.

The proton affinity and the enthalpy of formation of the prototypical carbonyl, formaldehyde, have been determined by the first-principles composite focal-point analysis (FPA) approach. The electronic structure computations employed the all-electron coupled-cluster method with up to single, double, triple, quadruple, and even pentuple excitations. In these computations the aug-cc-p(C)VXZ [X = 2(D), 3(T), 4(Q), 5, and 6] correlation-consistent Gaussian basis sets for C and O were used in conjunction with the corresponding aug-cc-pVXZ (X = 2-6) sets for H. The basis set limit values have been confirmed via explicitly correlated computations. Our FPA study supersedes previous computational work for the proton affinity and to some extent the enthalpy of formation of formaldehyde by accounting for (a) electron correlation beyond the "gold standard" CCSD(T) level; (b) the non-additivity of core electron correlation effects; (c) scalar relativity; (d) diagonal Born-Oppenheimer corrections computed at a correlated level; (e) anharmonicity of zero-point vibrational energies, based on global potential energy surfaces and variational vibrational computations; and (f) thermal corrections to enthalpies by direct summation over rovibrational energy levels. Our final proton affinities at 298.15 (0.0) K are ΔpaHo (H2CO) = 711.02 (704.98) ± 0.39 kJ mol-1. Our final enthalpies of formation at 298.15 (0.0) K are ΔfHo (H2CO) = -109.23 (-105.42) ± 0.33 kJ mol-1. The latter values are based on the enthalpy of the H2 + CO → H2CO reaction but supported by two further reaction schemes, H2O + C → H2CO and 2H + C + O → H2CO. These values, especially ΔpaHo (H2CO), have better accuracy and considerably lower uncertainty than the best previous recommendations and thus should be employed in future studies.

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

PubMed Central

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

2014-01-01

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

A hot X-ray filament associated with A3017 galaxy cluster

NASA Astrophysics Data System (ADS)

Parekh, V.; Durret, F.; Padmanabh, P.; Pandge, M. B.

2017-09-01

Recent simulations and observations have shown large-scale filaments in the cosmic web connecting nodes, with accreting materials (baryonic and dark matter) flowing through them. Current high-sensitivity observations also show that the propagation of shocks through filaments can heat them up and make filaments visible between two or more galaxy clusters or around massive clusters, based on optical and/or X-ray observations. We are reporting here the special case of the cluster A3017 associated with a hot filament. The temperature of the filament is 3.4^{-0.77}_{+1.30} keV and its length is ∼1 Mpc. We have analysed its archival Chandra data and report various properties. We also analysed GMRT 235/610 MHz radio data. Radio observations have revealed symmetric two-sided lobes that fill cavities in the A3017 cluster core region, associated with central active galactic nucleus. In the radio map, we also noticed a peculiar linear vertical radio structure in the X-ray filament region which might be associated with a cosmic filament shock. This radio structure could be a radio phoenix or old plasma where an old relativistic population is re-accelerated by shock propagation. Finally, we put an upper limit on the radio luminosity of the filament region.

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.

Automated atlas-based clustering of white matter fiber tracts from DTMRI.

PubMed

Maddah, Mahnaz; Mewes, Andrea U J; Haker, Steven; Grimson, W Eric L; Warfield, Simon K

2005-01-01

A new framework is presented for clustering fiber tracts into anatomically known bundles. This work is motivated by medical applications in which variation analysis of known bundles of fiber tracts in the human brain is desired. To include the anatomical knowledge in the clustering, we invoke an atlas of fiber tracts, labeled by the number of bundles of interest. In this work, we construct such an atlas and use it to cluster all fiber tracts in the white matter. To build the atlas, we start with a set of labeled ROIs specified by an expert and extract the fiber tracts initiating from each ROI. Affine registration is used to project the extracted fiber tracts of each subject to the atlas, whereas their B-spline representation is used to efficiently compare them to the fiber tracts in the atlas and assign cluster labels. Expert visual inspection of the result confirms that the proposed method is very promising and efficient in clustering of the known bundles of fiber tracts.

Single-step affinity purification for fungal proteomics.

PubMed

Liu, Hui-Lin; Osmani, Aysha H; Ukil, Leena; Son, Sunghun; Markossian, Sarine; Shen, Kuo-Fang; Govindaraghavan, Meera; Varadaraj, Archana; Hashmi, Shahr B; De Souza, Colin P; Osmani, Stephen A

2010-05-01

A single-step protein affinity purification protocol using Aspergillus nidulans is described. Detailed protocols for cell breakage, affinity purification, and depending on the application, methods for protein release from affinity beads are provided. Examples defining the utility of the approaches, which should be widely applicable, are included.

Anion photoelectron spectroscopy of radicals and clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Travis, Taylor R.

1999-12-01

Anion photoelectron spectroscopy is used to study free radicals and clusters. The low-lying 2Σ and 2π states of C 2nH (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 2H and C 4H. Other radicals studied include NCN and I 3. The author was able to observe the low-lying singlet and triplet states of NCNmore » for the first time. Measurement of the electron affinity of I 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.« less

Mobile Technology Affinity in Renal Transplant Recipients.

PubMed

Reber, S; Scheel, J; Stoessel, L; Schieber, K; Jank, S; Lüker, C; Vitinius, F; Grundmann, F; Eckardt, K-U; Prokosch, H-U; Erim, Y

Medication nonadherence is a common problem in renal transplant recipients (RTRs). Mobile health approaches to improve medication adherence are a current trend, and several medication adherence apps are available. However, it is unknown whether RTRs use these technologies and to what extent. In the present study, the mobile technology affinity of RTRs was analyzed. We hypothesized significant age differences in mobile technology affinity and that mobile technology affinity is associated with better cognitive functioning as well as higher educational level. A total of 109 RTRs (63% male) participated in the cross-sectional study, with an overall mean age of 51.8 ± 14.2 years. The study included the Technology Experience Questionnaire (TEQ) for the assessment of mobile technology affinity, a cognitive test battery, and sociodemographic data. Overall, 57.4% of the patients used a smartphone or tablet and almost 45% used apps. The TEQ sum score was 20.9 in a possible range from 6 (no affinity to technology) to 30 (very high affinity). Younger patients had significantly higher scores in mobile technology affinity. The only significant gender difference was found in having fun with using electronic devices: Men enjoyed technology more than women did. Mobile technology affinity was positively associated with cognitive functioning and educational level. Young adult patients might profit most from mobile health approaches. Furthermore, high educational level and normal cognitive functioning promote mobile technology affinity. This should be kept in mind when designing mobile technology health (mHealth) interventions for RTRs. For beneficial mHealth interventions, further research on potential barriers and desired technologic features is necessary to adapt apps to patients' needs. Copyright © 2017 Elsevier Inc. All rights reserved.

Propagation of classical swine fever virus in vitro circumventing heparan sulfate-adaptation.

PubMed

Eymann-Häni, Rita; Leifer, Immanuel; McCullough, Kenneth C; Summerfield, Artur; Ruggli, Nicolas

2011-09-01

Amplification of natural virus isolates in permanent cell lines can result in adaptation, in particular enhanced binding to heparan sulfate (HS)-containing glycosaminoglycans present on most vertebrate cells. This has been reported for several viruses, including the pestivirus classical swine fever virus (CSFV), the causative agent of a highly contagious hemorrhagic disease in pigs. Propagation of CSFV in cell culture is essential in virus diagnostics and research. Adaptation of CSFV to HS-binding has been related to amino acid changes in the viral E(rns) glycoprotein, resulting in viruses with altered replication characteristics in vitro and in vivo. Consequently, a compound blocking the HS-containing structures on cell surfaces was employed to monitor conversion from HS-independency to HS-dependency. It was shown that the porcine PEDSV.15 cell line permitted propagation of CSFV within a limited number of passages without adaptation to HS-binding. The selection of HS-dependent CSFV mutants was also prevented by propagation of the virus in the presence of DSTP 27. The importance of these findings can be seen from the altered ratio of cell-associated to secreted virus upon acquisition of enhanced HS-binding affinity, a phenotype proposed previously to be related to virulence in the natural host. Copyright © 2011 Elsevier B.V. All rights reserved.

A New Physics-Based Modeling of Multiple Non-Planar Hydraulic Fractures Propagation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Jing; Huang, Hai; Deo, Milind

Because of the low permeability in shale plays, closely spaced hydraulic fractures and multilateral horizontal wells are generally required to improve production. Therefore, understanding the potential fracture interaction and stress evolution is critical in optimizing fracture/well design and completion strategy in multi-stage horizontal wells. In this paper, a novel fully coupled reservoir flow and geomechanics model based on the dual-lattice system is developed to simulate multiple non-planar fractures propagation. The numerical model from Discrete Element Method (DEM) is used to simulate the mechanics of fracture propagations and interactions, while a conjugate irregular lattice network is generated to represent fluid flowmore » in both fractures and formation. The fluid flow in the formation is controlled by Darcy’s law, but within fractures it is simulated by using cubic law for laminar flow through parallel plates. Initiation, growth and coalescence of the microcracks will lead to the generation of macroscopic fractures, which is explicitly mimicked by failure and removal of bonds between particles from the discrete element network. We investigate the fracture propagation path in both homogeneous and heterogeneous reservoirs using the simulator developed. Stress shadow caused by the transverse fracture will change the orientation of principal stress in the fracture neighborhood, which may inhibit or alter the growth direction of nearby fracture clusters. However, the initial in-situ stress anisotropy often helps overcome this phenomenon. Under large in-situ stress anisotropy, the hydraulic fractures are more likely to propagate in a direction that is perpendicular to the minimum horizontal stress. Under small in-situ stress anisotropy, there is a greater chance for fractures from nearby clusters to merge with each other. Then, we examine the differences in fracture geometry caused by fracturing in cemented or uncemented wellbore. Moreover, the impact of

The Cutting Edge of Affinity Electrophoresis Technology

PubMed Central

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

2015-01-01

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

Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes.

PubMed

Cannistraci, Carlo Vittorio; Ravasi, Timothy; Montevecchi, Franco Maria; Ideker, Trey; Alessio, Massimo

2010-09-15

Nonlinear small datasets, which are characterized by low numbers of samples and very high numbers of measures, occur frequently in computational biology, and pose problems in their investigation. Unsupervised hybrid-two-phase (H2P) procedures-specifically dimension reduction (DR), coupled with clustering-provide valuable assistance, not only for unsupervised data classification, but also for visualization of the patterns hidden in high-dimensional feature space. 'Minimum Curvilinearity' (MC) is a principle that-for small datasets-suggests the approximation of curvilinear sample distances in the feature space by pair-wise distances over their minimum spanning tree (MST), and thus avoids the introduction of any tuning parameter. MC is used to design two novel forms of nonlinear machine learning (NML): Minimum Curvilinear embedding (MCE) for DR, and Minimum Curvilinear affinity propagation (MCAP) for clustering. Compared with several other unsupervised and supervised algorithms, MCE and MCAP, whether individually or combined in H2P, overcome the limits of classical approaches. High performance was attained in the visualization and classification of: (i) pain patients (proteomic measurements) in peripheral neuropathy; (ii) human organ tissues (genomic transcription factor measurements) on the basis of their embryological origin. MC provides a valuable framework to estimate nonlinear distances in small datasets. Its extension to large datasets is prefigured for novel NMLs. Classification of neuropathic pain by proteomic profiles offers new insights for future molecular and systems biology characterization of pain. Improvements in tissue embryological classification refine results obtained in an earlier study, and suggest a possible reinterpretation of skin attribution as mesodermal. https://sites.google.com/site/carlovittoriocannistraci/home.

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.

Ionization energies and electron affinities from a random-phase-approximation many-body Green's-function method including exchange interactions

NASA Astrophysics Data System (ADS)

Heßelmann, Andreas

2017-06-01

A many-body Green's-function method employing an infinite order summation of ring and exchange-ring contributions to the self-energy is presented. The individual correlation and relaxation contributions to the quasiparticle energies are calculated using an iterative scheme which utilizes density fitting of the particle-hole, particle-particle and hole-hole densities. It is shown that the ionization energies and electron affinities of this approach agree better with highly accurate coupled-cluster singles and doubles with perturbative triples energy difference results than those obtained with second-order Green's-function approaches. An analysis of the correlation and relaxation terms of the self-energy for the direct- and exchange-random-phase-approximation (RPA) Green's-function methods shows that the inclusion of exchange interactions leads to a reduction of the two contributions in magnitude. These differences, however, strongly cancel each other when summing the individual terms to the quasiparticle energies. Due to this, the direct- and exchange-RPA methods perform similarly for the description of ionization energies (IPs) and electron affinities (EAs). The coupled-cluster reference IPs and EAs, if corrected to the adiabatic energy differences between the neutral and charged molecules, were shown to be in very good agreement with experimental measurements.

Affinity Spaces and 21st Century Learning

ERIC Educational Resources Information Center

Gee, James Paul

2017-01-01

This article discusses video games as "attractors" to "affinity spaces." It argues that affinity spaces are key sites today where people teach and learn 21st Century skills. While affinity spaces are proliferating on the Internet as interest-and-passion-driven sites devoted to a common set of endeavors, they are not new, just…

Distributed computing for membrane-based modeling of action potential propagation.

PubMed

Porras, D; Rogers, J M; Smith, W M; Pollard, A E

2000-08-01

Action potential propagation simulations with physiologic membrane currents and macroscopic tissue dimensions are computationally expensive. We, therefore, analyzed distributed computing schemes to reduce execution time in workstation clusters by parallelizing solutions with message passing. Four schemes were considered in two-dimensional monodomain simulations with the Beeler-Reuter membrane equations. Parallel speedups measured with each scheme were compared to theoretical speedups, recognizing the relationship between speedup and code portions that executed serially. A data decomposition scheme based on total ionic current provided the best performance. Analysis of communication latencies in that scheme led to a load-balancing algorithm in which measured speedups at 89 +/- 2% and 75 +/- 8% of theoretical speedups were achieved in homogeneous and heterogeneous clusters of workstations. Speedups in this scheme with the Luo-Rudy dynamic membrane equations exceeded 3.0 with eight distributed workstations. Cluster speedups were comparable to those measured during parallel execution on a shared memory machine.

Coevolutionary dynamics of opinion propagation and social balance: The key role of small-worldness

NASA Astrophysics Data System (ADS)

Chen, Yan; Chen, Lixue; Sun, Xian; Zhang, Kai; Zhang, Jie; Li, Ping

2014-03-01

The propagation of various opinions in social networks, which influences human inter-relationships and even social structure, and hence is a most important part of social life. We have incorporated social balance into opinion propagation in social networks are influenced by social balance. The edges in networks can represent both friendly or hostile relations, and change with the opinions of individual nodes. We introduce a model to characterize the coevolutionary dynamics of these two dynamical processes on Watts-Strogatz (WS) small-world network. We employ two distinct evolution rules (i) opinion renewal; and (ii) relation adjustment. By changing the rewiring probability, and thus the small-worldness of the WS network, we found that the time for the system to reach balanced states depends critically on both the average path length and clustering coefficient of the network, which is different than other networked process like epidemic spreading. In particular, the system equilibrates most quickly when the underlying network demonstrates strong small-worldness, i.e., small average path lengths and large clustering coefficient. We also find that opinion clusters emerge in the process of the network approaching the global equilibrium, and a measure of global contrariety is proposed to quantify the balanced state of a social network.

Stripped interstellar gas in cluster cooling flows

NASA Technical Reports Server (NTRS)

Soker, Noam; Bregman, Joel N.; Sarazin, Craig L.

1991-01-01

It is suggested that nonlinear perturbations which lead to thermal instabilities in cooling flows might start as blobs of interstellar gas which are stipped out of cluster galaxies. Assuming that most of the gas produced by stellar mass loss in cluster galaxies is stripped from the galaxies, the total rate of such stripping is roughly 100 solar masses/yr, which is similar to the rates of cooling in cluster cooling flows. It is possible that a substantial portion of the cooling gas originates as blobs of interstellar gas stripped from galaxies. The magnetic fields within and outside of the low-entropy perturbations may help to maintain their identities by suppressing both thermal conduction and Kelvin-Helmholtz instabilities. These density fluctuations may disrupt the propagation of radio jets through the intracluster gas, which may be one mechanism for producing wideangle-tail radio galaxies.

Numerical models of jet disruption in cluster cooling flows

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

On the structure of self-affine convex bodies

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Stable dissipative optical vortex clusters by inhomogeneous effective diffusion.

PubMed

Li, Huishan; Lai, Shiquan; Qui, Yunli; Zhu, Xing; Xie, Jianing; Mihalache, Dumitru; He, Yingji

2017-10-30

We numerically show the generation of robust vortex clusters embedded in a two-dimensional beam propagating in a dissipative medium described by the generic cubic-quintic complex Ginzburg-Landau equation with an inhomogeneous effective diffusion term, which is asymmetrical in the two transverse directions and periodically modulated in the longitudinal direction. We show the generation of stable optical vortex clusters for different values of the winding number (topological charge) of the input optical beam. We have found that the number of individual vortex solitons that form the robust vortex cluster is equal to the winding number of the input beam. We have obtained the relationships between the amplitudes and oscillation periods of the inhomogeneous effective diffusion and the cubic gain and diffusion (viscosity) parameters, which depict the regions of existence and stability of vortex clusters. The obtained results offer a method to form robust vortex clusters embedded in two-dimensional optical beams, and we envisage potential applications in the area of structured light.

Structure, electronic and magnetic properties of Mn{sub n} (n=2-8) clusters: A DFT investigation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Vipin; Roy, Debesh R., E-mail: drr@ashd.svnit.ac.in

2016-05-06

A detail studyon the stability, electronic and magnetic properties of Mn{sub n} (n=2-8) cluster series is performed under the utilization ofdensity functional theory (DFT). The binding energy (B.E.), HOMO-LUMO energy gap (HLG), chemical hardness (η), ionization potential (I.P.), electron affinity (E.A)and electronegativity (χ) of these clusters are predicted. We have also studied the magnetic moments associated with the stable cluster isomers. The lowest energy structures for each cluster sizes aredetermined with a systematic search imposing all possible initial magnetic configuration on the cluster. All the calculations are carried out using a popular GGA functional PBE as proposed by Pardew, Burkemore » and Ernzerhof and implemented in the VASP program.« less

Classical affine W-algebras associated to Lie superalgebras

NASA Astrophysics Data System (ADS)

Suh, Uhi Rinn

2016-02-01

In this paper, we prove classical affine W-algebras associated to Lie superalgebras (W-superalgebras), which can be constructed in two different ways: via affine classical Hamiltonian reductions and via taking quasi-classical limits of quantum affine W-superalgebras. Also, we show that a classical finite W-superalgebra can be obtained by a Zhu algebra of a classical affine W-superalgebra. Using the definition by Hamiltonian reductions, we find free generators of a classical W-superalgebra associated to a minimal nilpotent. Moreover, we compute generators of the classical W-algebra associated to spo(2|3) and its principal nilpotent. In the last part of this paper, we introduce a generalization of classical affine W-superalgebras called classical affine fractional W-superalgebras. We show these have Poisson vertex algebra structures and find generators of a fractional W-superalgebra associated to a minimal nilpotent.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 showmore » 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.« less

Two Gene Clusters Coordinate Galactose and Lactose Metabolism in Streptococcus gordonii

PubMed Central

Zeng, Lin; Martino, Nicole C.

2012-01-01

Streptococcus gordonii is an early colonizer of the human oral cavity and an abundant constituent of oral biofilms. Two tandemly arranged gene clusters, designated lac and gal, were identified in the S. gordonii DL1 genome, which encode genes of the tagatose pathway (lacABCD) and sugar phosphotransferase system (PTS) enzyme II permeases. Genes encoding a predicted phospho-β-galactosidase (LacG), a DeoR family transcriptional regulator (LacR), and a transcriptional antiterminator (LacT) were also present in the clusters. Growth and PTS assays supported that the permease designated EIILac transports lactose and galactose, whereas EIIGal transports galactose. The expression of the gene for EIIGal was markedly upregulated in cells growing on galactose. Using promoter-cat fusions, a role for LacR in the regulation of the expressions of both gene clusters was demonstrated, and the gal cluster was also shown to be sensitive to repression by CcpA. The deletion of lacT caused an inability to grow on lactose, apparently because of its role in the regulation of the expression of the genes for EIILac, but had little effect on galactose utilization. S. gordonii maintained a selective advantage over Streptococcus mutans in a mixed-species competition assay, associated with its possession of a high-affinity galactose PTS, although S. mutans could persist better at low pHs. Collectively, these results support the concept that the galactose and lactose systems of S. gordonii are subject to complex regulation and that a high-affinity galactose PTS may be advantageous when S. gordonii is competing against the caries pathogen S. mutans in oral biofilms. PMID:22660715

Range of plasma ions in cold cluster gases near the critical point

NASA Astrophysics Data System (ADS)

Zhang, G.; Quevedo, H. J.; Bonasera, A.; Donovan, M.; Dyer, G.; Gaul, E.; Guardo, G. L.; Gulino, M.; La Cognata, M.; Lattuada, D.; Palmerini, S.; Pizzone, R. G.; Romano, S.; Smith, H.; Trippella, O.; Anzalone, A.; Spitaleri, C.; Ditmire, T.

2017-05-01

We measure the range of plasma ions in cold cluster gases by using the Petawatt laser at the University of Texas-Austin. The produced plasma propagated in all directions some hitting the cold cluster gas not illuminated by the laser. From the ratio of the measured ion distributions at different angles we can estimate the range of the ions in the cold cluster gas. It is much smaller than estimated using popular models, which take only into account the slowing down of charged particles in uniform matter. We discuss the ion range in systems prepared near a liquid-gas phase transition.

Classical affine W-algebras associated to Lie superalgebras

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suh, Uhi Rinn, E-mail: uhrisu1@math.snu.ac.kr

2016-02-15

In this paper, we prove classical affine W-algebras associated to Lie superalgebras (W-superalgebras), which can be constructed in two different ways: via affine classical Hamiltonian reductions and via taking quasi-classical limits of quantum affine W-superalgebras. Also, we show that a classical finite W-superalgebra can be obtained by a Zhu algebra of a classical affine W-superalgebra. Using the definition by Hamiltonian reductions, we find free generators of a classical W-superalgebra associated to a minimal nilpotent. Moreover, we compute generators of the classical W-algebra associated to spo(2|3) and its principal nilpotent. In the last part of this paper, we introduce a generalizationmore » of classical affine W-superalgebras called classical affine fractional W-superalgebras. We show these have Poisson vertex algebra structures and find generators of a fractional W-superalgebra associated to a minimal nilpotent.« less

Alternative Affinity Ligands for Immunoglobulins.

PubMed

Kruljec, Nika; Bratkovič, Tomaž

2017-08-16

The demand for recombinant therapeutic antibodies and Fc-fusion proteins is expected to increase in the years to come. Hence, extensive efforts are concentrated on improving the downstream processing. In particular, the development of better-affinity chromatography matrices, supporting robust time- and cost-effective antibody purification, is warranted. With the advances in molecular design and high-throughput screening approaches from chemical and biological combinatorial libraries, novel affinity ligands representing alternatives to bacterial immunoglobulin (Ig)-binding proteins have entered the scene. Here, we review the design, development, and properties of diverse classes of alternative antibody-binding ligands, ranging from engineered versions of Ig-binding proteins, to artificial binding proteins, peptides, aptamers, and synthetic small-molecular-weight compounds. We also provide examples of applications for the novel affinity matrices in chromatography and beyond.

Selection of imprinted nanoparticles by affinity chromatography.

PubMed

Guerreiro, António R; Chianella, Iva; Piletska, Elena; Whitcombe, Michael J; Piletsky, Sergey A

2009-04-15

Soluble molecularly imprinted nanoparticles were synthesised via iniferter initiated polymerisation and separated by size via gel permeation chromatography. Subsequent fractionation of these particles by affinity chromatography allowed the separation of high affinity fractions from the mixture of nanoparticles. Fractions selected this way possess affinity similar to that of natural antibodies (K(d) 6.6x10(-8)) M and were also able to discriminate between related functional analogues of the template.

Vaccine Efficacy and Affinity Maturation

NASA Astrophysics Data System (ADS)

Lee, Hayoun; Deem, Michael W.

2002-03-01

We propose macroscopic equations to describe variable vaccine efficacy between repeated vaccinee and first time vaccinee. The main ingredients are antigenic distance between epidemic strain and vaccne strain, and affinity maturation dynamics which differs in primary and second response. Increase of affinity by repeated vaccine leads to localization in immune space. This localization decreases the ability of the immune system to response to distant, but related epidemic strains.

The measured and calculated affinity of methyl and methoxy substituted benzoquinones for the QA site of bacterial reaction centers

PubMed Central

Zheng, Zhong; Dutton, P. Leslie; Gunner, M. R.

2010-01-01

Quinones play important roles in mitochondrial and photosynthetic energy conversion acting as intramembrane, mobile electron and proton carriers between catalytic sites in various electron transfer proteins. They display different affinity, selectivity, functionality and exchange dynamics in different binding sites. The computational analysis of quinone binding sheds light on the requirements for quinone affinity and specificity. The affinities of ten oxidized, neutral benzoquinones (BQs) were measured for the high affinity QA site in the detergent solubilized Rhodobacter sphaeroides bacterial photosynthetic reaction center. Multi-Conformation Continuum Electrostatics (MCCE) was then used to calculate their relative binding free energies by Grand Canonical Monte Carlo sampling with a rigid protein backbone, flexible ligand and side chain positions and protonation states. Van der Waals and torsion energies, Poisson-Boltzmann continuum electrostatics and accessible surface area dependent ligand-solvent interactions are considered. An initial, single cycle of GROMACS backbone optimization improves the match with experiment as do coupled ligand and side chain motions. The calculations match experiment with an RMSD of 2.29 and a slope of 1.28. The affinities are dominated by favorable protein-ligand van der Waals rather than electrostatic interactions. Each quinone appears in a closely clustered set of positions. Methyl and methoxy groups move into the same positions as found for the native quinone. Difficulties putting methyls into methoxy sites are observed. Calculations using an SAS dependent implicit van der Waals interaction smoothed out small clashes, providing a better match to experiment with a RMSD of 0.77 and a slope of 0.97. PMID:20607696

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

Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

PubMed

Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

2011-11-14

The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

Wiggler magnetic field assisted third harmonic generation in expanding clusters

NASA Astrophysics Data System (ADS)

Vij, Shivani

2018-04-01

A simple theoretical model is constructed to study the wiggler magnetic field assisted third harmonic generation of intense short pulse laser in a cluster in its expanding phase. The ponderomotive force of laser causes density perturbations in cluster electron density which couples with wiggler magnetic field to produce a nonlinear current that generates transverse third harmonic. An intense short pulse laser propagating through a gas embedded with atomic clusters, converts it into hot plasma balls via tunnel ionization. Initially, the electron plasma frequency inside the clusters ω pe > \\sqrt{3}{ω }1 (with ω 1 being the frequency of the laser). As the cluster expands under Coulomb force and hydrodynamic pressure, ω pe decreases to \\sqrt{3}{ω }1. At this time, there is resonant enhancement in the efficiency of the third harmonic generation. The efficiency of third harmonic generation is enhanced due to cluster plasmon resonance and by phase matching due to wiggler magnetic field. The effect of cluster size on the expansion rate is studied to observe that the clusters of different radii would expand differently. The impact of laser intensity and wiggler magnetic field on the efficiency of third harmonic generation is also explored.

THE LOCATION, CLUSTERING, AND PROPAGATION OF MASSIVE STAR FORMATION IN GIANT MOLECULAR CLOUDS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ochsendorf, Bram B.; Meixner, Margaret; Chastenet, Jérémy

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

High-Affinity Vanadate Transport System in the Cyanobacterium Anabaena variabilis ATCC 29413

PubMed Central

Pratte, Brenda S.; Thiel, Teresa

2006-01-01

High-affinity vanadate transport systems have not heretofore been identified in any organism. Anabaena variabilis, which can fix nitrogen by using an alternative V-dependent nitrogenase, transported vanadate well. The concentration of vanadate giving half-maximum V-nitrogenase activity when added to V-starved cells was about 3 × 10−9 M. The genes for an ABC-type vanadate transport system, vupABC, were found in A. variabilis about 5 kb from the major cluster of genes encoding the V-nitrogenase, and like those genes, the vupABC genes were repressed by molybdate; however, unlike the V-nitrogenase genes the vanadate transport genes were expressed in vegetative cells. A vupB mutant failed to grow by using V-nitrogenase unless high levels of vanadate were provided, suggesting that there was also a low-affinity vanadate transport system that functioned in the vupB mutant. The vupABC genes belong to a family of putative metal transport genes that include only one other characterized transport system, the tungstate transport genes of Eubacterium acidaminophilum. Similar genes are not present in the complete genomes of other bacterial strains that have a V-nitrogenase, including Azotobacter vinelandii, Rhodopseudomonas palustris, and Methanosarcina barkeri. PMID:16385036

An Integrated Intrusion Detection Model of Cluster-Based Wireless Sensor Network.

PubMed

Sun, Xuemei; Yan, Bo; Zhang, Xinzhong; Rong, Chuitian

2015-01-01

Considering wireless sensor network characteristics, this paper combines anomaly and mis-use detection and proposes an integrated detection model of cluster-based wireless sensor network, aiming at enhancing detection rate and reducing false rate. Adaboost algorithm with hierarchical structures is used for anomaly detection of sensor nodes, cluster-head nodes and Sink nodes. Cultural-Algorithm and Artificial-Fish-Swarm-Algorithm optimized Back Propagation is applied to mis-use detection of Sink node. Plenty of simulation demonstrates that this integrated model has a strong performance of intrusion detection.

Demonstration of slow light propagation in an optical fiber under dual pump light with co-propagation and counter-propagation

NASA Astrophysics Data System (ADS)

Qiu, Wei; Liu, Jianjun; Wang, Yuda; Yang, Yujing; Gao, Yuan; Lv, Pin; Jiang, Qiuli

2018-04-01

In this paper, a general theory of coherent population oscillation effect in an Er3+ -doped fiber under the dual-frequency pumping laser with counter-propagation and co-propagation at room temperature is presented. Using the numerical simulation, in case of dual frequency light waves (1480 nm and 980 nm) with co-propagation and counter-propagation, we analyze the effect of the pump optical power ratio (M) on the group speed of light. The group velocity of light can be varied with the change of M. We research the time delay and fractional delay in an Er3+-doped fiber under the dual-frequency pumping laser with counter-propagation and co-propagation. Compared to the methods of the single pumping, the larger time delay can be got by using the technique of dual-frequency laser pumped fiber with co-propagation and counter-propagation.

Non-Thermal Hard X-Ray Emission in Galaxy Clusters Observed with the BeppoSAX PDS

NASA Technical Reports Server (NTRS)

Nevalainen, Jukka H.; Oosterbroeck, T.; Bonamente, Max; Six, N. Frank (Technical Monitor)

2002-01-01

We studied the X-ray emission in a sample of clusters using the BeppoSAX PDS instrument in the 20 -- 80 keV energy band. We estimated the non-thermal cluster emission (HXR) by modeling the thermal contribution from the cluster gas and the non-thermal contamination from the AGN in the field, and propagating the corresponding uncertainties. We also evaluated and propagated the systematic uncertainties due to the background fluctuations. The resulting non-thermal component is detected at a sigma level in approx. 50 % of the non-significantly AGN-contaminated clusters, i.e. in clusters A2142, A2256, A3376, Coma, Ophiuchus and Virgo. Furthermore, Virgo is detected at a 4 sigma level. All the clusters detected at a 2 sigma level exhibit some degree of merger signatures, i.e. deviations from the azimuthally symmetric brightness and temperature distributions, while the relaxed clusters are detected at a lower confidence. The data are consistent with a scenario whereby relaxed clusters have no non-thermal hard X-ray component, whereas merger clusters do, with a 20 -- 80 keV luminosity of approx. 10(exp 42-44)((h(sub 50))(exp -2))(erg/s). Consistent with merger boosting of cluster temperatures, the non-thermal luminosity increases by 2-3 orders of magnitude between the average cluster temperatures 2 and 10 keV, as L(sub NTE) is proportional to T(sup j) with j = 2.4+/-0.3. These results corroborate the assumption which is the essential element in most non-thermal hard X-ray emission models. The co-added spectrum of all non-significantly AGN-contaminated clusters indicates a power-law spectrum for the non-thermal component with a photon index of 1.5+/-0.25 at 1 sigma confidence level. Unless there is a high energy cut-off in the electron velocity distribution, the total spectrum implies that Inverse Compton scatter of Cosmic Microwave Background photons from electron population dominates over the non-thermal bremsstrahlung in producing hard X-rays in clusters on the merger

Amphiphilic Bio-molecules/ZnO Interface: Enhancement of Bio-affinity and Dispersibility

NASA Astrophysics Data System (ADS)

Meng, Xiu-Qing; Fang, Yun-Zhang; Wu, Feng-Min

2012-01-01

The dispersibility of bio-molecules such as lecithins on the surface of ZnO nanowires are investigated for biosensor applications. Lecithins can be absorbed on an as-synthesized ZnO nanowire surface in the form of sub-micro sized clusters, while scattering well on those annealed under oxygen atmosphere. Wettability analysis reveals that the as-synthesized ZnO nanowires bear a super-hydrophobic surface, which convents to superhydrophilic after oxygen annealing. First-principles calculations indicate that the adsorption energy of ZnO with water is about 0.2 eV at a distance of 2 Å when it is superhydrophilic, suggesting that lecithin can be absorbed on the hydrophilic surface stably at this distance and the bio-affinity can be enhanced under this condition.

Notch and affinity boundaries in Drosophila.

PubMed

Herranz, Héctor; Milán, Marco

2006-02-01

Cells in multicellular organisms often do not intermingle freely with each other. Differential cell affinities can contribute to organizing cells into different tissues. Drosophila limbs and the vertebrate central nervous system are subdivided into compartments. Cells in adjacent compartments do not mix. Cell interactions mediated by Notch-family receptors have been implicated in the specification of these compartment boundaries. Two recent reports analyze the role of the Notch signaling pathway in the generation of an affinity boundary in the Drosophila wing. The first report analyzes the connection between Notch and the actin cytoskeleton. The second report analyzes the differential requirements of Notch and the transcription factor Suppressor of Hairless in generating the affinity boundary.

Thermal-depth matching in dynamic scene based on affine projection and feature registration

NASA Astrophysics Data System (ADS)

Wang, Hongyu; Jia, Tong; Wu, Chengdong; Li, Yongqiang

2018-03-01

This paper aims to study the construction of 3D temperature distribution reconstruction system based on depth and thermal infrared information. Initially, a traditional calibration method cannot be directly used, because the depth and thermal infrared camera is not sensitive to the color calibration board. Therefore, this paper aims to design a depth and thermal infrared camera calibration board to complete the calibration of the depth and thermal infrared camera. Meanwhile a local feature descriptors in thermal and depth images is proposed. The belief propagation matching algorithm is also investigated based on the space affine transformation matching and local feature matching. The 3D temperature distribution model is built based on the matching of 3D point cloud and 2D thermal infrared information. Experimental results show that the method can accurately construct the 3D temperature distribution model, and has strong robustness.

Acoustic Disturbances in Galaxy Clusters

NASA Astrophysics Data System (ADS)

Zweibel, Ellen G.; Mirnov, Vladimir V.; Ruszkowski, Mateusz; Reynolds, Christopher S.; Yang, H.-Y. Karen; Fabian, Andrew C.

2018-05-01

Galaxy cluster cores are pervaded by hot gas which radiates at far too high a rate to maintain any semblance of a steady state; this is referred to as the cooling flow problem. Of the many heating mechanisms that have been proposed to balance radiative cooling, one of the most attractive is the dissipation of acoustic waves generated by active galactic nuclei. Fabian et al. showed that if the waves are nearly adiabatic, wave damping due to heat conduction and viscosity must be well below standard Coulomb rates in order to allow the waves to propagate throughout the core. Because of the importance of this result, we have revisited wave dissipation under galaxy cluster conditions in a way that accounts for the self-limiting nature of dissipation by electron thermal conduction, allows the electron and ion temperature perturbations in the waves to evolve separately, and estimates kinetic effects by comparing to a semicollisionless theory. While these effects considerably enlarge the toolkit for analyzing observations of wavelike structures and developing a quantitative theory for wave heating, the drastic reduction of transport coefficients proposed in Fabian et al. remains the most viable path to acoustic wave heating of galaxy cluster cores.

An Integrated Intrusion Detection Model of Cluster-Based Wireless Sensor Network

PubMed Central

Sun, Xuemei; Yan, Bo; Zhang, Xinzhong; Rong, Chuitian

2015-01-01

Considering wireless sensor network characteristics, this paper combines anomaly and mis-use detection and proposes an integrated detection model of cluster-based wireless sensor network, aiming at enhancing detection rate and reducing false rate. Adaboost algorithm with hierarchical structures is used for anomaly detection of sensor nodes, cluster-head nodes and Sink nodes. Cultural-Algorithm and Artificial-Fish–Swarm-Algorithm optimized Back Propagation is applied to mis-use detection of Sink node. Plenty of simulation demonstrates that this integrated model has a strong performance of intrusion detection. PMID:26447696

Ground and excited states of CaSH through electron propagator calculations

NASA Astrophysics Data System (ADS)

Ortiz, J. V.

1990-05-01

Electron propagator calculations of electron affinities of CaSH + produce ground and excited state energies at the optimized, C s minimum of the neutral ground state and at a C ∞v geometry. Feynman-Dyson amplitudes (FDAs) describe the distribution of the least bound electron in various states. The neutral ground state differs from the cation by the occupation of a one-electron state dominated by Ca s functions. Described by FDAs with Ca-S π pseudosymmetry, corresponding excited states have unpaired electrons in orbitals displaying interference between Ca p and d functions. Above these lies a σ pseudosymmetry FDA with principal contributions from Ca d functions. Two FDAs with σ pseudosymmetry follow. Higher excited states exhibit considerable delocalization onto S.

PHARMACEUTICAL AND BIOMEDICAL APPLICATIONS OF AFFINITY CHROMATOGRAPHY: RECENT TRENDS AND DEVELOPMENTS

PubMed Central

Hage, David S.; Anguizola, Jeanethe A.; Bi, Cong; Li, Rong; Matsuda, Ryan; Papastavros, Efthimia; Pfaunmiller, Erika; Vargas, John; Zheng, Xiwei

2012-01-01

Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically-related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered. PMID:22305083

High-affinity K+ uptake in pepper plants.

PubMed

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

2005-06-01

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

Slowing Translation between Protein Domains by Increasing Affinity between mRNAs and the Ribosomal Anti-Shine-Dalgarno Sequence Improves Solubility.

PubMed

Vasquez, Kevin A; Hatridge, Taylor A; Curtis, Nicholas C; Contreras, Lydia M

2016-02-19

Recent studies have demonstrated that effective protein production requires coordination of multiple cotranslational cellular processes, which are heavily affected by translation timing. Until recently, protein engineering has focused on codon optimization to maximize protein production rates, mostly considering the effect of tRNA abundance. However, as it relates to complex multidomain proteins, it has been hypothesized that strategic translational pauses between domains and between distinct individual structural motifs can prevent interactions between nascent chain fragments that generate kinetically trapped misfolded peptides and thereby enhance protein yields. In this study, we introduce synthetic transient pauses between structural domains in a heterologous model protein based on designed patterns of affinity between the mRNA and the anti-Shine-Dalgarno (aSD) sequence on the ribosome. We demonstrate that optimizing translation attenuation at domain boundaries can predictably affect solubility patterns in bacteria. Exploration of the affinity space showed that modifying less than 1% of the nucleotides (on a small 12 amino acid linker) can vary soluble protein yields up to ∼7-fold without altering the primary sequence of the protein. In the context of longer linkers, where a larger number of distinct structural motifs can fold outside the ribosome, optimal synonymous codon variations resulted in an additional 2.1-fold increase in solubility, relative to that of nonoptimized linkers of the same length. While rational construction of 54 linkers of various affinities showed a significant correlation between protein solubility and predicted affinity, only weaker correlations were observed between tRNA abundance and protein solubility. We also demonstrate that naturally occurring high-affinity clusters are present between structural domains of β-galactosidase, one of Escherichia coli's largest native proteins. Interdomain ribosomal affinity is an important factor

Electron affinity of liquid water

DOE PAGES

Gaiduk, Alex P.; Pham, Tuan Anh; Govoni, Marco; ...

2018-01-16

Understanding redox and photochemical reactions in aqueous environments requires a precise knowledge of the ionization potential and electron affinity of liquid water. The former has been measured, but not the latter. We predict the electron affinity of liquid water and of its surface from first principles, coupling path-integral molecular dynamics with ab initio potentials, and many-body perturbation theory. Our results for the surface (0.8 eV) agree well with recent pump-probe spectroscopy measurements on amorphous ice. Those for the bulk (0.1-0.3 eV) differ from several estimates adopted in the literature, which we critically revisit. We show that the ionization potential ofmore » the bulk and surface are almost identical; instead their electron affinities differ substantially, with the conduction band edge of the surface much deeper in energy than that of the bulk. We also discuss the significant impact of nuclear quantum effects on the fundamental gap and band edges of the liquid.« less

Electron affinity of liquid water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaiduk, Alex P.; Pham, Tuan Anh; Govoni, Marco

Understanding redox and photochemical reactions in aqueous environments requires a precise knowledge of the ionization potential and electron affinity of liquid water. The former has been measured, but not the latter. We predict the electron affinity of liquid water and of its surface from first principles, coupling path-integral molecular dynamics with ab initio potentials, and many-body perturbation theory. Our results for the surface (0.8 eV) agree well with recent pump-probe spectroscopy measurements on amorphous ice. Those for the bulk (0.1-0.3 eV) differ from several estimates adopted in the literature, which we critically revisit. We show that the ionization potential ofmore » the bulk and surface are almost identical; instead their electron affinities differ substantially, with the conduction band edge of the surface much deeper in energy than that of the bulk. We also discuss the significant impact of nuclear quantum effects on the fundamental gap and band edges of the liquid.« less

F+ and F⁻ affinities of simple N(x)F(y) and O(x)F(y) compounds.

PubMed

Grant, Daniel J; Wang, Tsang-Hsiu; Vasiliu, Monica; Dixon, David A; Christe, Karl O

2011-03-07

Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for the neutral and ionic N(x)F(y) and O(x)F(y) systems using coupled cluster theory with single and double excitations and including a perturbative triples correction (CCSD(T)) method with correlation consistent basis sets extrapolated to the complete basis set (CBS) limit. To achieve near chemical accuracy (±1 kcal/mol), three corrections to the electronic energy were added to the frozen core CCSD(T)/CBS binding energies: corrections for core-valence, scalar relativistic, and first order atomic spin-orbit effects. Vibrational zero point energies were computed at the CCSD(T) level of theory where possible. The calculated heats of formation are in good agreement with the available experimental values, except for FOOF because of the neglect of higher order correlation corrections. The F(+) affinity in the N(x)F(y) series increases from N(2) to N(2)F(4) by 63 kcal/mol, while that in the O(2)F(y) series decreases by 18 kcal/mol from O(2) to O(2)F(2). Neither N(2) nor N(2)F(4) is predicted to bind F(-), and N(2)F(2) is a very weak Lewis acid with an F(-) affinity of about 10 kcal/mol for either the cis or trans isomer. The low F(-) affinities of the nitrogen fluorides explain why, in spite of the fact that many stable nitrogen fluoride cations are known, no nitrogen fluoride anions have been isolated so far. For example, the F(-) affinity of NF is predicted to be only 12.5 kcal/mol which explains the numerous experimental failures to prepare NF(2)(-) salts from the well-known strong acid HNF(2). The F(-) affinity of O(2) is predicted to have a small positive value and increases for O(2)F(2) by 23 kcal/mol, indicating that the O(2)F(3)(-) anion might be marginally stable at subambient temperatures. The calculated adiabatic ionization potentials and electron affinities are in good agreement with experiment considering that many of the experimental values are for vertical processes. © 2011

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

Electro-Optic Propagation

DTIC Science & Technology

2003-09-30

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

Electro-Optic Propagation

DTIC Science & Technology

2002-09-30

Electro - Optic Propagation Stephen Doss-Hammel SPAWARSYSCEN San Diego code 2858 49170 Propagation Path San Diego, CA 92152-7385 phone: (619...OBJECTIVES The electro - optical propagation objectives are: 1) The acquisition and analysis of mid-wave and long-wave infrared transmission and...elements to the electro - optical propagation model development. The first element is the design and execution of field experiments to generate useful

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

Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime

NASA Astrophysics Data System (ADS)

Caré, Bertrand R.; Soula, Hédi A.

2013-01-01

Many types of membrane receptors are found to be organized as clusters on the cell surface. We investigate the potential effect of such receptor clustering on the intracellular signal transduction stage. We consider a canonical pathway with a membrane receptor (R) activating a membrane-bound intracellular relay protein (G). We use Monte Carlo simulations to recreate biochemical reactions using different receptor spatial distributions and explore the dynamics of the signal transduction. Results show that activation of G by R is severely impaired by R clustering, leading to an apparent blunted biological effect compared to control. Paradoxically, this clustering decreases the half maximal effective dose (ED50) of the transduction stage, increasing the apparent affinity. We study an example of inter-receptor interaction in order to account for possible compensatory effects of clustering and observe the parameter range in which such interactions slightly counterbalance the loss of activation of G. The membrane receptors’ spatial distribution affects the internal stages of signal amplification, suggesting a functional role for membrane domains and receptor clustering independently of proximity-induced receptor-receptor interactions.

Water transport and clustering behavior in homopolymer and graft copolymer polylactide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, An; Koo, Donghun; Theryo, Grayce

2015-02-19

Polylactide is a bio-based and biodegradable polymer well-known for its renewable origins. Water sorption and clustering behavior in both a homopolymer polylactide and a graft copolymer of polylactide was studied using the quartz crystal microbalance/heat conduction calorimetry (QCM/HCC) technique. The graft copolymer, poly(1,5-cyclooctadiene-co-5-norbornene-2-methanol-graft-D,L-lactide), contained polylactide chains (95 wt.%) grafted onto a hydrophobic rubbery backbone (5 wt.%). Clustering is an important phenomenon in the study of water transport properties in polymers since the presence of water clusters can affect the water diffusivity. The HCC method using the thermal power signals and Van't Hoff's law were both employed to estimate the watermore » sorption enthalpy. Sorption enthalpy of water in both polymers was determined to be approximately -40 kJ/mol for all water activity levels. Zimm-Lundberg analysis showed that water clusters start to form at a water activity of 0.4. The engaged species induced clustering (ENSIC) model was used to curve fit sorption isotherms and showed that the affinity among water molecules is higher than that between water molecules and polymer chains. All the methods used indicate that clustering of water molecules exists in both polymers.« less

Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters.

PubMed

Kryachko, E S; Remacle, F

2005-12-08

The nature of the DNA-gold interaction determines and differentiates the affinity of the nucleobases (adenine, thymine, guanine, and cytosine) to gold. Our preliminary computational study [Kryachko, E. S.; Remacle, F. Nano Lett. 2005, 5, 735] demonstrates that two major bonding factors govern this interaction: the anchoring, either of the Au-N or Au-O type, and the nonconventional N-H...Au hydrogen bonding. In this paper, we offer insight into the nature of nucleobase-gold interactions and provide a detailed characterization of their different facets, i.e., geometrical, energetic, and spectroscopic aspects; the gold cluster size and gold coordination effects; proton affinity; and deprotonation energy. We then investigate how the Watson-Crick DNA pairing patterns are modulated by the nucleobase-gold interaction. We do so in terms of the proton affinities and deprotonation energies of those proton acceptors and proton donors which are involved in the interbase hydrogen bondings. A variety of properties of the most stable Watson-Crick [A x T]-Au3 and [G x C]-Au3 hybridized complexes are described and compared with the isolated Watson-Crick A x T and G x C ones. It is shown that enlarging the gold cluster size to Au6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G x C]-Au6 complex that bridges the G x C pair and thus leads to a significant strengthening of G x C pairing.

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

Benchmarking the Fundamental Electronic Properties of small TiO 2 Nanoclusters by GW and Coupled Cluster Theory Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berardo, Enrico; Kaplan, Ferdinand; Bhaskaran-Nair, Kiran

We study the vertical ionisation potential, electron affinity, fundamental gap and exciton binding energy values of small bare and hydroxylated TiO 2 nanoclusters to understand how the excited state properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G 0 W 0, qs GW, EA/IP-EOM-CCSD and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that for bare (i.e. non-hydroxylated) clusters all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow themore » same trends as the electron affinity and ionisation potentials predicted by the many-body methods but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend on the functional used and do not necessarily follow trends based on the many-body methods. The effect of hydroxylation of the clusters is to open up both the optical and fundamental gap. In conclusion, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the Madelung onsite potential.« less

Benchmarking the Fundamental Electronic Properties of small TiO 2 Nanoclusters by GW and Coupled Cluster Theory Calculations

DOE PAGES

Berardo, Enrico; Kaplan, Ferdinand; Bhaskaran-Nair, Kiran; ...

2017-06-19

We study the vertical ionisation potential, electron affinity, fundamental gap and exciton binding energy values of small bare and hydroxylated TiO 2 nanoclusters to understand how the excited state properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G 0 W 0, qs GW, EA/IP-EOM-CCSD and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that for bare (i.e. non-hydroxylated) clusters all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow themore » same trends as the electron affinity and ionisation potentials predicted by the many-body methods but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend on the functional used and do not necessarily follow trends based on the many-body methods. The effect of hydroxylation of the clusters is to open up both the optical and fundamental gap. In conclusion, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the Madelung onsite potential.« less

Employees' Perceptions of Female Affinity Groups

ERIC Educational Resources Information Center

Gabriel, Peter J.

2017-01-01

Female affinity groups offered by corporations are formalized corporate initiatives focused on networking and professional development opportunities for women (Welbourne & McLaughlin, 2013). The scholarly literature focused on female affinity groups was limited. The purpose of this grounded theory Dissertation in Practice study was to…

Cluster observations of reflected EMIC-triggered emission

NASA Astrophysics Data System (ADS)

Grison, B.; Darrouzet, F.; Santolík, O.; Cornilleau-Wehrlin, N.; Masson, A.

2016-05-01

On 19 March 2001, the Cluster fleet recorded an electromagnetic rising tone on the nightside of the plasmasphere. The emission was found to propagate toward the Earth and toward the magnetic equator at a group velocity of about 200 km/s. The Poynting vector is mainly oblique to the background magnetic field and directed toward the Earth. The propagation angle θk,B0 becomes more oblique with increasing magnetic latitude. Inside each rising tone θk,B0 is more field aligned for higher frequencies. Comparing our results to previous ray tracing analysis we conclude that this emission is a triggered electromagnetic ion cyclotron (EMIC) wave generated at the nightside plasmapause. We detect the wave just after its reflection in the plasmasphere. The reflection makes the tone slope shallower. This process can contribute to the formation of pearl pulsations.

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.

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

PubMed Central

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

2016-01-01

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

Spectroscopic Study of Local Interactions of Platinum in Small [CexOy]Ptx' - Clusters

NASA Astrophysics Data System (ADS)

Ray, Manisha; Kafader, Jared O.; Chick Jarrold, Caroline

2016-06-01

Cerium oxide is a good ionic conductor, and the conductivity can be enhanced with oxygen vacancies and doping. This conductivity may play an important role in the enhancement of noble or coinage metal toward the water-gas shift reaction when supported by cerium oxide. The ceria-supported platinum catalyst in particular has received much attention because of higher activity at lower temperatures (LT) compared to the most common commercial LT-WGS catalyst. We have used a combination of anion photoelectron spectroscopy and density functional theory calculations to study the interesting molecular and electronic structures and properties of cluster models of ceria-supported platinum. [CexOy]Ptx' - (x,x'=1,2 ; y≤2x') clusters exhibit evidence of ionic bonding possible because of the high electron affinity of Pt and the low ionization potential of cerium oxide clusters. In addition, Pt- is a common daughter ion resulting from photodissociation of [CexOy]Ptx' - clusters. Finally, several of the anion and neutral clusters have profoundly different structures. These features may play a role in the enhancement of catalytic activity toward the water-gas shift reaction.

Alternative splicing modulates Kv channel clustering through a molecular ball and chain mechanism

NASA Astrophysics Data System (ADS)

Zandany, Nitzan; Marciano, Shir; Magidovich, Elhanan; Frimerman, Teddy; Yehezkel, Rinat; Shem-Ad, Tzilhav; Lewin, Limor; Abdu, Uri; Orr, Irit; Yifrach, Ofer

2015-03-01

Ion channel clustering at the post-synaptic density serves a fundamental role in action potential generation and transmission. Here, we show that interaction between the Shaker Kv channel and the PSD-95 scaffold protein underlying channel clustering is modulated by the length of the intrinsically disordered C terminal channel tail. We further show that this tail functions as an entropic clock that times PSD-95 binding. We thus propose a ‘ball and chain’ mechanism to explain Kv channel binding to scaffold proteins, analogous to the mechanism describing channel fast inactivation. The physiological relevance of this mechanism is demonstrated in that alternative splicing of the Shaker channel gene to produce variants of distinct tail lengths resulted in differential channel cell surface expression levels and clustering metrics that correlate with differences in affinity of the variants for PSD-95. We suggest that modulating channel clustering by specific spatial-temporal spliced variant targeting serves a fundamental role in nervous system development and tuning.

Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations.

PubMed

Interlandi, Gianluca; Thomas, Wendy E

2016-07-01

The bacterial adhesin FimH consists of an allosterically regulated mannose-binding lectin domain and a covalently linked inhibitory pilin domain. Under normal conditions, the two domains are bound to each other, and FimH interacts weakly with mannose. However, under tensile force, the domains separate and the lectin domain undergoes conformational changes that strengthen its bond with mannose. Comparison of the crystallographic structures of the low and the high affinity state of the lectin domain reveals conformational changes mainly in the regulatory inter-domain region, the mannose binding site and a large β sheet that connects the two distally located regions. Here, molecular dynamics simulations investigated how conformational changes are propagated within and between different regions of the lectin domain. It was found that the inter-domain region moves towards the high affinity conformation as it becomes more compact and buries exposed hydrophobic surface after separation of the pilin domain. The mannose binding site was more rigid in the high affinity state, which prevented water penetration into the pocket. The large central β sheet demonstrated a soft spring-like twisting. Its twisting motion was moderately correlated to fluctuations in both the regulatory and the binding region, whereas a weak correlation was seen in a direct comparison of these two distal sites. The results suggest a so called "population shift" model whereby binding of the lectin domain to either the pilin domain or mannose locks the β sheet in a rather twisted or flat conformation, stabilizing the low or the high affinity state, respectively. Proteins 2016; 84:990-1008. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Compound immobilization and drug-affinity chromatography.

PubMed

Rix, Uwe; Gridling, Manuela; Superti-Furga, Giulio

2012-01-01

Bioactive small molecules act through modulating a yet unpredictable number of targets. It is therefore of critical importance to define the cellular target proteins of a compound as an entry point to understanding its mechanism of action. Often, this can be achieved in a direct fashion by chemical proteomics. As with any affinity chromatography, immobilization of the bait to a solid support is one of the earliest and most crucial steps in the process. Interfering with structural features that are important for identification of a target protein will be detrimental to binding affinity. Also, many molecules are sensitive to heat or to certain chemicals, such as acid or base, and might be destroyed during the process of immobilization, which therefore needs to be not only efficient, but also mild. The subsequent affinity chromatography step needs to preserve molecular and conformational integrity of both bait compound and proteins in order to result in the desired specific enrichment while ensuring a high level of compatibility with downstream analysis by mass spectrometry. Thus, the right choice of detergent, buffer, and protease inhibitors is also essential. This chapter describes a widely applicable procedure for the immobilization of small molecule drugs and for drug-affinity chromatography with subsequent protein identification by mass spectrometry.

Surfactant-free Colloidal Particles with Specific Binding Affinity

PubMed Central

2017-01-01

Colloidal particles with specific binding affinity are essential for in vivo and in vitro biosensing, targeted drug delivery, and micrometer-scale self-assembly. Key to these techniques are surface functionalizations that provide high affinities to specific target molecules. For stabilization in physiological environments, current particle coating methods rely on adsorbed surfactants. However, spontaneous desorption of these surfactants typically has an undesirable influence on lipid membranes. To address this issue and create particles for targeting molecules in lipid membranes, we present here a surfactant-free coating method that combines high binding affinity with stability at physiological conditions. After activating charge-stabilized polystyrene microparticles with EDC/Sulfo-NHS, we first coat the particles with a specific protein and subsequently covalently attach a dense layer of poly(ethyelene) glycol. This polymer layer provides colloidal stability at physiological conditions as well as antiadhesive properties, while the protein coating provides the specific affinity to the targeted molecule. We show that NeutrAvidin-functionalized particles bind specifically to biotinylated membranes and that Concanavalin A-functionalized particles bind specifically to the glycocortex of Dictyostelium discoideum cells. The affinity of the particles changes with protein density, which can be tuned during the coating procedure. The generic and surfactant-free coating method reported here transfers the high affinity and specificity of a protein onto colloidal polystyrene microparticles. PMID:28847149

Floristic affinities of the lowland savannahs of Belize and southern Mexico.

PubMed

Canché-Estrada, Idalia Arely; Ortiz-Díaz, Juan Javier; Tun-Garrido, Juan

2018-01-01

Environmental heterogeneity of Belize and southern Mexico savannahs as well as their geographical location suggest that these plant communities share floristic elements, making them conducive to a phytogeographical analysis. The aim of this study was to analyse the floristic affinities of nine savannahs of Belize and southern Mexico and to explain the similarities and differences amongst them. A binary data matrix containing 915 species was built based on the authors' own collections and on nine floristic lists already published. A second data matrix, consisting of 113 species representing trees, was also used since most literature on neotropical savannahs has focused on this life form. In addition, the ten most species-rich families as well as the characteristic species present in more than five savannahs were analysed. Floristic similarities were calculated using the Jaccard index. Dendrograms obtained in both types of analysis showed clusters with low similarity values, corresponding to geographic locations formed by the savannahs of Belize-Tabasco and the Yucatan Peninsula. The floristic affinities of the savannahs may be explained in terms of heterogeneity in climate and physiography. The Yucatan Peninsula and Belize-Tabasco groups have differences in climate type and the amount of rainfall. In addition, the Yucatan Peninsula savannahs are established at the bottom of karstic valleys, while the Belize and Tabasco savannahs develop on extensive flatlands. The savannahs of Oaxaca have the same climate type and amount of rainfall as those of the Yucatan Peninsula but they are distributed along peaks and the slopes of shale hills. Fabaceae and Poaceae mainly dominated the local floras with 121 and 116 species each; remarkably, Melastomataceae was absent in the Yucatan Peninsula and Oaxaca. Nine species occurred in five to seven savannahs, confirming that they are widespread in both Belize and southern Mexico, and the Neotropics. Geographic location and floristic

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.

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.

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. Copyright © 2015 Elsevier Inc. All rights reserved.

Cluster-cluster clustering

NASA Technical Reports Server (NTRS)

Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C. S.

1985-01-01

The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales.

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. Copyright © 2016 Elsevier B.V. All rights reserved.

β-globin gene cluster haplotypes in ethnic minority populations of southwest China

PubMed Central

Sun, Hao; Liu, Hongxian; Huang, Kai; Lin, Keqin; Huang, Xiaoqin; Chu, Jiayou; Ma, Shaohui; Yang, Zhaoqing

2017-01-01

The genetic diversity and relationships among ethnic minority populations of southwest China were investigated using seven polymorphic restriction enzyme sites in the β-globin gene cluster. The haplotypes of 1392 chromosomes from ten ethnic populations living in southwest China were determined. Linkage equilibrium and recombination hotspot were found between the 5′ sites and 3′ sites of the β-globin gene cluster. 5′ haplotypes 2 (+−−−), 6 (−++−+), 9 (−++++) and 3′ haplotype FW3 (−+) were the predominant haplotypes. Notably, haplotype 9 frequency was significantly high in the southwest populations, indicating their difference with other Chinese. The interpopulation differentiation of southwest Chinese minority populations is less than those in populations of northern China and other continents. Phylogenetic analysis shows that populations sharing same ethnic origin or language clustered to each other, indicating current β-globin cluster diversity in the Chinese populations reflects their ethnic origin and linguistic affiliations to a great extent. This study characterizes β-globin gene cluster haplotypes in southwest Chinese minorities for the first time, and reveals the genetic variability and affinity of these populations using β-globin cluster haplotype frequencies. The results suggest that ethnic origin plays an important role in shaping variations of the β-globin gene cluster in the southwestern ethnic populations of China. PMID:28205625

Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites

PubMed Central

Diermeier, Sarah D.; Németh, Attila; Rehli, Michael; Grummt, Ingrid; Längst, Gernot

2013-01-01

Enhancers and promoters often contain multiple binding sites for the same transcription factor, suggesting that homotypic clustering of binding sites may serve a role in transcription regulation. Here we show that clustering of binding sites for the transcription termination factor TTF-I downstream of the pre-rRNA coding region specifies transcription termination, increases the efficiency of transcription initiation and affects the three-dimensional structure of rRNA genes. On chromatin templates, but not on free rDNA, clustered binding sites promote cooperative binding of TTF-I, loading TTF-I to the downstream terminators before it binds to the rDNA promoter. Interaction of TTF-I with target sites upstream and downstream of the rDNA transcription unit connects these distal DNA elements by forming a chromatin loop between the rDNA promoter and the terminators. The results imply that clustered binding sites increase the binding affinity of transcription factors in chromatin, thus influencing the timing and strength of DNA-dependent processes. PMID:24068958

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

Direct Measurement of Equilibrium Constants for High-Affinity Hemoglobins

PubMed Central

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

2003-01-01

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (KD ≪ 1 μM) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and ∼100 μM−1 respectively, indicate that they are not capable of facilitating oxygen transport. PMID:12770899

Affine.m—Mathematica package for computations in representation theory of finite-dimensional and affine Lie algebras

NASA Astrophysics Data System (ADS)

Nazarov, Anton

2012-11-01

In this paper we present Affine.m-a program for computations in representation theory of finite-dimensional and affine Lie algebras and describe implemented algorithms. The algorithms are based on the properties of weights and Weyl symmetry. Computation of weight multiplicities in irreducible and Verma modules, branching of representations and tensor product decomposition are the most important problems for us. These problems have numerous applications in physics and we provide some examples of these applications. The program is implemented in the popular computer algebra system Mathematica and works with finite-dimensional and affine Lie algebras. Catalogue identifier: AENA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENB_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 24 844 No. of bytes in distributed program, including test data, etc.: 1 045 908 Distribution format: tar.gz Programming language: Mathematica. Computer: i386-i686, x86_64. Operating system: Linux, Windows, Mac OS, Solaris. RAM: 5-500 Mb Classification: 4.2, 5. Nature of problem: Representation theory of finite-dimensional Lie algebras has many applications in different branches of physics, including elementary particle physics, molecular physics, nuclear physics. Representations of affine Lie algebras appear in string theories and two-dimensional conformal field theory used for the description of critical phenomena in two-dimensional systems. Also Lie symmetries play a major role in a study of quantum integrable systems. Solution method: We work with weights and roots of finite-dimensional and affine Lie algebras and use Weyl symmetry extensively. Central problems which are the computations of weight multiplicities, branching and fusion coefficients are solved using one general recurrent

Hydride affinity scale of various substituted arylcarbeniums in acetonitrile.

PubMed

Zhu, Xiao-Qing; Wang, Chun-Hua

2010-12-23

Combined with the integral equation formalism polarized continuum model (IEFPCM), the hydride affinities of 96 various acylcarbenium ions in the gas phase and CH(3)CN were estimated by using the B3LYP/6-31+G(d)//B3LYP/6-31+G(d), B3LYP/6-311++G(2df,2p)//B3LYP/6-31+G(d), and BLYP/6-311++G(2df,2p)//B3LYP/6-31+G(d) methods for the first time. The results show that the combination of the BLYP/6-311++G(2df,2p)//B3LYP/6-31+G(d) method and IEFPCM could successfully predict the hydride affinities of arylcarbeniums in MeCN with a precision of about 3 kcal/mol. On the basis of the calculated results from the BLYP method, it can be found that the hydride affinity scale of the 96 arylcarbeniums in MeCN ranges from -130.76 kcal/mol for NO(2)-PhCH(+)-CN to -63.02 kcal/mol for p-(Me)(2)N-PhCH(+)-N(Me)(2), suggesting most of the arylcarbeniums are good hydride acceptors. Examination of the effect of the number of phenyl rings attached to the carbeniums on the hydride affinities shows that the increase of the hydride affinities takes place linearly with increasing number of benzene rings in the arylcarbeniums. Analyzing the effect of the substituents on the hydride affinities of arylcarbeniums indicates that electron-donating groups decrease the hydride affinities and electron-withdrawing groups show the opposite effect. The hydride affinities of arylcarbeniums are linearly dependent on the sum of the Hammett substituent parameters σ(p)(+). Inspection of the correlation of the solution-phase hydride affinities with gas-phase hydride affinities and aqueous-phase pK(R)(+) values reveals a remarkably good correspondence of ΔG(H(-)A)(R(+)) with both the gas-phase relative hydride affinities only if the α substituents X have no large electron-donating or -withdrawing properties and the pK(R)(+) values even though the media are dramatically different. The solution-phase hydride affinities also have a linear relationship with the electrophilicity parameter E, and this dependence can

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.

Affine group formulation of the Standard Model coupled to gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chou, Ching-Yi, E-mail: l2897107@mail.ncku.edu.tw; Ita, Eyo, E-mail: ita@usna.edu; Soo, Chopin, E-mail: cpsoo@mail.ncku.edu.tw

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 themore » 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.« less

Oligolysine-based saccharide clusters: synthesis and specificity.

PubMed Central

Frison, Natacha; Marceau, Philippe; Roche, Annie-Claude; Monsigny, Michel; Mayer, Roger

2002-01-01

In search of specific and highly selective sugar clusters for cell receptors, such as membrane lectins, various disaccharides were coupled to small peptide cores through an amide bond. In a first step, the reducing disaccharides, i.e. lactose and three different dimannoses, were converted into glycosyl-pyroglutamyl-beta-alanine derivatives. The free carboxylic group of these conjugates was then coupled to the alpha and epsilon amino groups of the core peptide (Lys( n )-Ala-Cys-NH2) with n =1 to 5, with complete substitution leading to homogeneous glycoclusters. The thiol group of the cysteine residue was used to tag the glycosylated oligolysines upon reaction with fluorescein iodoacetamide. The affinity of these glycoclusters towards two plant lectins was assessed by surface plasmon resonance. The selectivity of their cell uptake was investigated by flow cytometry using two types of cells: a human hepatoma cell line (HepG2 cells) expressing the plasma membrane galactose-specific lectin, and monocyte-derived dendritic cells expressing the plasma membrane mannose-specific lectin. The glycoclusters containing four or five disaccharides were shown to bind plant lectins and cell surface membrane lectins with a narrow selectivity and with a high affinity. PMID:12119048

Vegetative propagation [Chapter 9

Treesearch

Tara Luna

2009-01-01

For the past 30 years, interest in the propagation of native plants has been growing. Many desirable and ecologically important species, however, are difficult or very time consuming to propagate by seeds. Thus, nursery growers may want to investigate how to propagate a species of interest by vegetative propagation. This can be done by combining classic horticultural...

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.

PubMed

Shimo, Hanae; Arjunan, Satya Nanda Vel; Machiyama, Hiroaki; Nishino, Taiko; Suematsu, Makoto; Fujita, Hideaki; Tomita, Masaru; Takahashi, Koichi

2015-06-01

Oxidative stress mediated clustering of membrane protein band 3 plays an essential role in the clearance of damaged and aged red blood cells (RBCs) from the circulation. While a number of previous experimental studies have observed changes in band 3 distribution after oxidative treatment, the details of how these clusters are formed and how their properties change under different conditions have remained poorly understood. To address these issues, a framework that enables the simultaneous monitoring of the temporal and spatial changes following oxidation is needed. In this study, we established a novel simulation strategy that incorporates deterministic and stochastic reactions with particle reaction-diffusion processes, to model band 3 cluster formation at single molecule resolution. By integrating a kinetic model of RBC antioxidant metabolism with a model of band 3 diffusion, we developed a model that reproduces the time-dependent changes of glutathione and clustered band 3 levels, as well as band 3 distribution during oxidative treatment, observed in prior studies. We predicted that cluster formation is largely dependent on fast reverse reaction rates, strong affinity between clustering molecules, and irreversible hemichrome binding. We further predicted that under repeated oxidative perturbations, clusters tended to progressively grow and shift towards an irreversible state. Application of our model to simulate oxidation in RBCs with cytoskeletal deficiency also suggested that oxidation leads to more enhanced clustering compared to healthy RBCs. Taken together, our model enables the prediction of band 3 spatio-temporal profiles under various situations, thus providing valuable insights to potentially aid understanding mechanisms for removing senescent and premature RBCs.

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes

PubMed Central

Shimo, Hanae; Arjunan, Satya Nanda Vel; Machiyama, Hiroaki; Nishino, Taiko; Suematsu, Makoto; Fujita, Hideaki; Tomita, Masaru; Takahashi, Koichi

2015-01-01

Oxidative stress mediated clustering of membrane protein band 3 plays an essential role in the clearance of damaged and aged red blood cells (RBCs) from the circulation. While a number of previous experimental studies have observed changes in band 3 distribution after oxidative treatment, the details of how these clusters are formed and how their properties change under different conditions have remained poorly understood. To address these issues, a framework that enables the simultaneous monitoring of the temporal and spatial changes following oxidation is needed. In this study, we established a novel simulation strategy that incorporates deterministic and stochastic reactions with particle reaction-diffusion processes, to model band 3 cluster formation at single molecule resolution. By integrating a kinetic model of RBC antioxidant metabolism with a model of band 3 diffusion, we developed a model that reproduces the time-dependent changes of glutathione and clustered band 3 levels, as well as band 3 distribution during oxidative treatment, observed in prior studies. We predicted that cluster formation is largely dependent on fast reverse reaction rates, strong affinity between clustering molecules, and irreversible hemichrome binding. We further predicted that under repeated oxidative perturbations, clusters tended to progressively grow and shift towards an irreversible state. Application of our model to simulate oxidation in RBCs with cytoskeletal deficiency also suggested that oxidation leads to more enhanced clustering compared to healthy RBCs. Taken together, our model enables the prediction of band 3 spatio-temporal profiles under various situations, thus providing valuable insights to potentially aid understanding mechanisms for removing senescent and premature RBCs. PMID:26046580

Calculation of protein-ligand binding affinities.

PubMed

Gilson, Michael K; Zhou, Huan-Xiang

2007-01-01

Accurate methods of computing the affinity of a small molecule with a protein are needed to speed the discovery of new medications and biological probes. This paper reviews physics-based models of binding, beginning with a summary of the changes in potential energy, solvation energy, and configurational entropy that influence affinity, and a theoretical overview to frame the discussion of specific computational approaches. Important advances are reported in modeling protein-ligand energetics, such as the incorporation of electronic polarization and the use of quantum mechanical methods. Recent calculations suggest that changes in configurational entropy strongly oppose binding and must be included if accurate affinities are to be obtained. The linear interaction energy (LIE) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods are analyzed, as are free energy pathway methods, which show promise and may be ready for more extensive testing. Ultimately, major improvements in modeling accuracy will likely require advances on multiple fronts, as well as continued validation against experiment.

[Role of hemoglobin affinity to oxygen in adaptation to hypoxemia].

PubMed

Kwasiborski, Przemysław Jerzy; Kowalczyk, Paweł; Zieliński, Jakub; Przybylski, Jacek; Cwetsch, Andrzej

2010-04-01

One of the basic mechanisms of adapting to hypoxemia is a decrease in the affinity of hemoglobin for oxygen. This process occurs mainly due to the increased synthesis of 2,3-diphosphoglycerate (2,3-DPG) in the erythrocytes, as well as through the Bohr effect. Hemoglobin with decreased affinity for oxygen increases the oxygenation of tissues, because it gives up oxygen more easily during microcirculation. In foetal circulation, however, at a partial oxygen pressure (pO2) of 25 mmHg in the umbilical vein, the oxygen carrier is type F hemoglobin which has a high oxygen affinity. The commonly accepted role for hemoglobin F is limited to facilitating diffusion through the placenta. Is fetal life the only moment when haemoglobin F is useful? THE AIM OF STUDY was to create a mathematical model, which would answer the question at what conditions an increase, rather than a decrease, in haemoglobin oxygen affinity is of benefit to the body. Using the kinetics of dissociation of oxygen from hemoglobin described by the Hill equation as the basis for further discussion, we created a mathematical model describing the pO2 value in the microcirculatory system and its dependence on arterial blood pO2. The calculations were performed for hemoglobin with low oxygen affinity (adult type) and high-affinity hemoglobin (fetal type). The modelling took into account both physiological and pathological ranges of acid-base equilibrium and tissue oxygen extraction parameters. It was shown that for the physiological range of acid-base equilibrium and the resting level of tissue oxygen extraction parameters, with an arterial blood pO2 of 26.8 mmHg, the higher-affinity hemoglobin becomes the more effective oxygen carrier. It was also demonstrated that the arterial blood pO2, below which the high-affinity hemoglobin becomes the more effective carrier, is dependent on blood pH and the difference between the arterial and venous oxygen saturation levels. Simulations performed for the pathological

[Progresses in screening active compounds from herbal medicine by affinity chromatography].

PubMed

Feng, Ying-shu; Tong, Shan-shan; Xu, Xi-ming; Yu, Jiang-nan

2015-03-01

Affinity chromatography is a chromatographic method for separating molecules using the binding characteristics of the stationary phase with potential drug molecules. This method can be performed as a high throughput screening method and a chromatographic separation method to screen a variety of active drugs. This paper summarizes the history of affinity chromatography, screening technology of affinity chromatography, and application of affinity chromatography in screening bio-active compounds in herbal medicines, and then discusses its application prospects, in order to broaden applications of the affinity chromatography in drug screening.

Energy spectra of vibron and cluster models in molecular and nuclear systems

NASA Astrophysics Data System (ADS)

Jalili Majarshin, A.; Sabri, H.; Jafarizadeh, M. A.

2018-03-01

The relation of the algebraic cluster model, i.e., of the vibron model and its extension, to the collective structure, is discussed. In the first section of the paper, we study the energy spectra of vibron model, for diatomic molecule then we derive the rotation-vibration spectrum of 2α, 3α and 4α configuration in the low-lying spectrum of 8Be, 12C and 16O nuclei. All vibrational and rotational states with ground and excited A, E and F states appear to have been observed, moreover the transitional descriptions of the vibron model and α-cluster model were considered by using an infinite-dimensional algebraic method based on the affine \\widehat{SU(1,1)} Lie algebra. The calculated energy spectra are compared with experimental data. Applications to the rotation-vibration spectrum for the diatomic molecule and many-body nuclear clusters indicate that there are solvable models and they can be approximated very well using the transitional theory.

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

Iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis

PubMed Central

Landry, Aaron P.; Cheng, Zishuo; Ding, Huangen

2013-01-01

Iron-sulphur cluster biogenesis requires coordinated delivery of iron and sulphur to scaffold proteins, followed by transfer of the assembled clusters from scaffold proteins to target proteins. This complex process is accomplished by a group of dedicated iron-sulphur cluster assembly proteins that are conserved from bacteria to humans. While sulphur in iron-sulphur clusters is provided by L-cysteine via cysteine desulfurase, the iron donor(s) for iron-sulphur cluster assembly remains largely elusive. Here we report that among the primary iron-sulphur cluster assembly proteins, IscA has a unique and strong binding activity for mononuclear iron in vitro and in vivo. Furthermore, the ferric iron centre tightly bound in IscA can be readily extruded by L-cysteine, followed by reduction to ferrous iron for iron-sulphur cluster biogenesis. Substitution of the highly conserved residue tyrosine 40 with phenylalanine (Y40F) in IscA results in a mutant protein that has a diminished iron binding affinity but retains the iron-sulphur cluster binding activity. Genetic complementation studies show that the IscA Y40F mutant is inactive in vivo, suggesting that the iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis. PMID:23258274

Geometrical, electronic, and magnetic properties of CunFe (n=1-12) clusters: A density functional study

NASA Astrophysics Data System (ADS)

Ling, Wang; Dong, Die; Shi-Jian, Wang; Zheng-Quan, Zhao

2015-01-01

The geometrical, electronic, and magnetic properties of small CunFe (n=1-12) clusters have been investigated by using density functional method B3LYP and LanL2DZ basis set. The structural search reveals that Fe atoms in low-energy CunFe isomers tend to occupy the position with the maximum coordination number. The ground state CunFe clusters possess planar structure for n=2-5 and three-dimensional (3D) structure for n=6-12. The electronic properties of CunFe clusters are analyzed through the averaged binding energy, the second-order energy difference and HOMO-LUMO energy gap. It is found that the magic numbers of stability are 1, 3, 7 and 9 for the ground state CunFe clusters. The energy gap of Fe-encapsulated cage clusters is smaller than that of other configurations. The Cu5Fe and Cu7Fe clusters have a very large energy gap (>2.4 eV). The vertical ionization potential (VIP), electron affinity (EA) and photoelectron spectra are also calculated and simulated theoretically for all the ground-state clusters. The magnetic moment analyses for the ground-state CunFe clusters show that Fe atom can enhance the magnetic moment of the host cluster and carries most of the total magnetic moment.

Iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis.

PubMed

Landry, Aaron P; Cheng, Zishuo; Ding, Huangen

2013-03-07

Iron-sulphur cluster biogenesis requires coordinated delivery of iron and sulphur to scaffold proteins, followed by transfer of the assembled clusters from scaffold proteins to target proteins. This complex process is accomplished by a group of dedicated iron-sulphur cluster assembly proteins that are conserved from bacteria to humans. While sulphur in iron-sulphur clusters is provided by L-cysteine via cysteine desulfurase, the iron donor(s) for iron-sulphur cluster assembly remains largely elusive. Here we report that among the primary iron-sulphur cluster assembly proteins, IscA has a unique and strong binding activity for mononuclear iron in vitro and in vivo. Furthermore, the ferric iron centre tightly bound in IscA can be readily extruded by l-cysteine, followed by reduction to ferrous iron for iron-sulphur cluster biogenesis. Substitution of the highly conserved residue tyrosine 40 with phenylalanine (Y40F) in IscA results in a mutant protein that has a diminished iron binding affinity but retains the iron-sulphur cluster binding activity. Genetic complementation studies show that the IscA Y40F mutant is inactive in vivo, suggesting that the iron binding activity is essential for the function of IscA in iron-sulphur cluster biogenesis.

Temporal scaling in information propagation.

PubMed

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

2014-06-18

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

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.

Reducing Earth Topography Resolution for SMAP Mission Ground Tracks Using K-Means Clustering

NASA Technical Reports Server (NTRS)

Rizvi, Farheen

2013-01-01

The K-means clustering algorithm is used to reduce Earth topography resolution for the SMAP mission ground tracks. As SMAP propagates in orbit, knowledge of the radar antenna footprints on Earth is required for the antenna misalignment calibration. Each antenna footprint contains a latitude and longitude location pair on the Earth surface. There are 400 pairs in one data set for the calibration model. It is computationally expensive to calculate corresponding Earth elevation for these data pairs. Thus, the antenna footprint resolution is reduced. Similar topographical data pairs are grouped together with the K-means clustering algorithm. The resolution is reduced to the mean of each topographical cluster called the cluster centroid. The corresponding Earth elevation for each cluster centroid is assigned to the entire group. Results show that 400 data points are reduced to 60 while still maintaining algorithm performance and computational efficiency. In this work, sensitivity analysis is also performed to show a trade-off between algorithm performance versus computational efficiency as the number of cluster centroids and algorithm iterations are increased.

Mathematical analysis of frontal affinity chromatography in particle and membrane configurations.

PubMed

Tejeda-Mansir, A; Montesinos, R M; Guzmán, R

2001-10-30

The scaleup and optimization of large-scale affinity-chromatographic operations in the recovery, separation and purification of biochemical components is of major industrial importance. The development of mathematical models to describe affinity-chromatographic processes, and the use of these models in computer programs to predict column performance is an engineering approach that can help to attain these bioprocess engineering tasks successfully. Most affinity-chromatographic separations are operated in the frontal mode, using fixed-bed columns. Purely diffusive and perfusion particles and membrane-based affinity chromatography are among the main commercially available technologies for these separations. For a particular application, a basic understanding of the main similarities and differences between particle and membrane frontal affinity chromatography and how these characteristics are reflected in the transport models is of fundamental relevance. This review presents the basic theoretical considerations used in the development of particle and membrane affinity chromatography models that can be applied in the design and operation of large-scale affinity separations in fixed-bed columns. A transport model for column affinity chromatography that considers column dispersion, particle internal convection, external film resistance, finite kinetic rate, plus macropore and micropore resistances is analyzed as a framework for exploring further the mathematical analysis. Such models provide a general realistic description of almost all practical systems. Specific mathematical models that take into account geometric considerations and transport effects have been developed for both particle and membrane affinity chromatography systems. Some of the most common simplified models, based on linear driving-force (LDF) and equilibrium assumptions, are emphasized. Analytical solutions of the corresponding simplified dimensionless affinity models are presented. Particular

Weak affinity chromatography for evaluation of stereoisomers in early drug discovery.

PubMed

Duong-Thi, Minh-Dao; Bergström, Maria; Fex, Tomas; Svensson, Susanne; Ohlson, Sten; Isaksson, Roland

2013-07-01

In early drug discovery (e.g., in fragment screening), recognition of stereoisomeric structures is valuable and guides medicinal chemists to focus only on useful configurations. In this work, we concurrently screened mixtures of stereoisomers and estimated their affinities to a protein target (thrombin) using weak affinity chromatography-mass spectrometry (WAC-MS). Affinity determinations by WAC showed that minor changes in stereoisomeric configuration could have a major impact on affinity. The ability of WAC-MS to provide instant information about stereoselectivity and binding affinities directly from analyte mixtures is a great advantage in fragment library screening and drug lead development.

Atlas-based segmentation of brainstem regions in neuromelanin-sensitive magnetic resonance images

NASA Astrophysics Data System (ADS)

Puigvert, Marc; Castellanos, Gabriel; Uranga, Javier; Abad, Ricardo; Fernández-Seara, María. A.; Pastor, Pau; Pastor, María. A.; Muñoz-Barrutia, Arrate; Ortiz de Solórzano, Carlos

2015-03-01

We present a method for the automatic delineation of two neuromelanin rich brainstem structures -substantia nigra pars compacta (SN) and locus coeruleus (LC)- in neuromelanin sensitive magnetic resonance images of the brain. The segmentation method uses a dynamic multi-image reference atlas and a pre-registration atlas selection strategy. To create the atlas, a pool of 35 images of healthy subjects was pair-wise pre-registered and clustered in groups using an affinity propagation approach. Each group of the atlas is represented by a single exemplar image. Each new target image to be segmented is registered to the exemplars of each cluster. Then all the images of the highest performing clusters are enrolled into the final atlas, and the results of the registration with the target image are propagated using a majority voting approach. All registration processes used combined one two-stage affine and one elastic B-spline algorithm, to account for global positioning, region selection and local anatomic differences. In this paper, we present the algorithm, with emphasis in the atlas selection method and the registration scheme. We evaluate the performance of the atlas selection strategy using 35 healthy subjects and 5 Parkinson's disease patients. Then, we quantified the volume and contrast ratio of neuromelanin signal of these structures in 47 normal subjects and 40 Parkinson's disease patients to confirm that this method can detect neuromelanin-containing neurons loss in Parkinson's disease patients and could eventually be used for the early detection of SN and LC damage.

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.

Bioengineering of Bacteria To Assemble Custom-Made Polyester Affinity Resins

PubMed Central

Hay, Iain D.; Du, Jinping; Burr, Natalie

2014-01-01

Proof of concept for the in vivo bacterial production of a polyester resin displaying various customizable affinity protein binding domains is provided. This was achieved by engineering various protein binding domains into a bacterial polyester-synthesizing enzyme. Affinity binding domains based on various structural folds and derived from molecular libraries were used to demonstrate the potential of this technique. Designed ankyrin repeat proteins (DARPins), engineered OB-fold domains (OBodies), and VHH domains from camelid antibodies (nanobodies) were employed. The respective resins were produced in a single bacterial fermentation step, and a simple purification protocol was developed. Purified resins were suitable for most lab-scale affinity chromatography purposes. All of the affinity domains tested produced polyester beads with specific affinity for the target protein. The binding capacity of these affinity resins ranged from 90 to 600 nmol of protein per wet gram of polyester affinity resin, enabling purification of a recombinant protein target from a complex bacterial cell lysate up to a purity level of 96% in one step. The polyester resin was efficiently produced by conventional lab-scale shake flask fermentation, resulting in bacteria accumulating up to 55% of their cellular dry weight as polyester. A further proof of concept demonstrating the practicality of this technique was obtained through the intracellular coproduction of a specific affinity resin and its target. This enables in vivo binding and purification of the coproduced “target protein.” Overall, this study provides evidence for the use of molecular engineering of polyester synthases toward the microbial production of specific bioseparation resins implementing previously selected binding domains. PMID:25344238

PDZ affinity chromatography: a general method for affinity purification of proteins based on PDZ domains and their ligands.

PubMed

Walkup, Ward G; Kennedy, Mary B

2014-06-01

PDZ (PSD-95, DiscsLarge, ZO1) domains function in nature as protein binding domains within scaffold and membrane-associated proteins. They comprise ∼90 residues and make specific, high affinity interactions with complementary C-terminal peptide sequences, with other PDZ domains, and with phospholipids. We hypothesized that the specific, strong interactions of PDZ domains with their ligands would make them well suited for use in affinity chromatography. Here we describe a novel affinity chromatography method applicable for the purification of proteins that contain PDZ domain-binding ligands, either naturally or introduced by genetic engineering. We created a series of affinity resins comprised of PDZ domains from the scaffold protein PSD-95, or from neuronal nitric oxide synthase (nNOS), coupled to solid supports. We used them to purify heterologously expressed neuronal proteins or protein domains containing endogenous PDZ domain ligands, eluting the proteins with free PDZ domain peptide ligands. We show that Proteins of Interest (POIs) lacking endogenous PDZ domain ligands can be engineered as fusion products containing C-terminal PDZ domain ligand peptides or internal, N- or C-terminal PDZ domains and then can be purified by the same method. Using this method, we recovered recombinant GFP fused to a PDZ domain ligand in active form as verified by fluorescence yield. Similarly, chloramphenicol acetyltransferase (CAT) and β-Galactosidase (LacZ) fused to a C-terminal PDZ domain ligand or an N-terminal PDZ domain were purified in active form as assessed by enzymatic assay. In general, PDZ domains and ligands derived from PSD-95 were superior to those from nNOS for this method. PDZ Domain Affinity Chromatography promises to be a versatile and effective method for purification of a wide variety of natural and recombinant proteins. Copyright © 2014 Elsevier Inc. All rights reserved.

Multi-Affinity for Growing Rough Interfaces of Bacterial Colonies

NASA Astrophysics Data System (ADS)

Kobayashi, N.; Ozawa, T.; Saito, K.; Yamazaki, Y.; Matsuyama, T.; Matsushita, M.

We have examined whether rough interfaces of bacterial colonies are multi-affine. We have used the bacterial species called textit{Bacillus subtilis}, which has been found to exhibit a variety of colony patterns when varying both the concentration of nutrient and solidity of agar medium. Consequently, we have found that the colony interface on a nutrient-rich, solid agar medium is multi-affine. On the other hand, the colony interface on a nutrient-rich, semi-solid agar medium is self-affine.

Characterization of self-affinity in the global regime

NASA Astrophysics Data System (ADS)

Neimark, Alexander V.

1994-11-01

Methods for characterization of self-affine surfaces and measurements of their roughness exponents H are developed. It is shown that for smoothed surfaces, which underwent particular coarse graining or averaging of the small-scale fluctuations, the excess surface area Sex and the mean square root radius of curvature ac are related by two distinct asymptotic power laws if ac is well below or well above a certain crossover scale acr. In the local regime of self-affinity, when ac<affinity, when ac>>acr, Sex~(ac/acr)-2(1-H)/(2-H). The former scaling relationship is consistent with the well known definition of local fractal dimensions dloc=dtop+1-H. The latter scaling relationship offers alternatives for characterization of self-affinity over large scales by means of excess dimensions defined as dex=dtop+2(1-H)/(2-H) and can be used for determination of roughness exponents from the measurements provided in the global regime. The thermodynamic method of fractal analysis, proposed earlier for self-similar surfaces (A.V. Neimark, Pis'ma Zh. Eksp. Teor. Fiz. 51, 535 (1990) [JETP Lett. 51, 607 (1990)]; Physica A 191, 258 (1992)), is extended for self-affine surfaces for determination of fractal dimensions and roughness exponents from adsorption and capillary experimental data.

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

PubMed

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

2008-11-07

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

Assessment of the hybrid propagation model, Volume 1: Analysis of noise propagation effects

DOT National Transportation Integrated Search

2012-08-31

This is the first of two volumes of a report on the Hybrid Propagation Model (HPM), an advanced prediction model for aviation noise propagation. This volume presents the noise level predictions for eleven different sets of propagation conditions, run...

Structural, electronic, and magnetic properties of Y(n)O (n=2-14) clusters: Density functional study.

PubMed

Yang, Zhi; Xiong, Shi-Jie

2008-09-28

The geometries stability, electronic properties, and magnetism of Y(n)O clusters up to n=14 are systematically studied with density functional theory. In the lowest-energy structures of Y(n)O clusters, the equilibrium site of the oxygen atom gradually moves from an outer site of the cluster, via a surface site, and finally, to an interior site as the number of the Y atoms increases from 2 to 14. Starting from n=12, the O atom falls into the center of the cluster with the Y atoms forming the outer frame. The results show that clusters with n=2, 4, 8, and 12 are more stable than their respective neighbors, and that the total magnetic moments of Y(n)O clusters are all quite small except Y(12)O cluster. The lowest-energy structure of Y(12)O cluster is a perfect icosahedron with a large magnetic moment 6mu(B). In addition, we find that the total magnetic moments are quenched for n=2, 6, and 8 due to the closed-shell electronic configuration. The calculated ionization potentials and electron affinities are in good agreement with the experimental results, which imply that the present theoretical treatments are satisfactory.

Propagation of EMIC triggered emissions toward the magnetic equatorial plane

NASA Astrophysics Data System (ADS)

Grison, B.; Santolik, O.; Pickett, J. S.; Omura, Y.; Engebretson, M. J.; Dandouras, I. S.; Masson, A.; Decreau, P.; Cornilleau-Wehrlin, N.

2011-12-01

EMIC triggered emissions are observed close to the equatorial plane of the magnetosphere at locations where EMIC waves are commonly observed: close to the plasmapause region and in the dayside magnetosphere close to the magnetopause. Their overall characteristics (frequency with time dispersion, generation mechanism) make those waves the EMIC analogue of rising frequency whistler-mode chorus emissions. In our observations the Poynting flux of these emissions is usually clearly arriving from the equatorial region direction, especially when observations take place at more than 5 degrees of magnetic latitude. Simulations have also confirmed that the conditions of generation by interaction with energetic ions are at a maximum at the magnetic equator (lowest value of the background magnetic field along the field line). However in the Cluster case study presented here the Poynting flux of EMIC triggered emissions is propagating toward the equatorial region. The large angle between the wave vector and the background magnetic field is also unusual for this kind of emission. The rising tone starts just above half of the He+ gyrofrequency (Fhe+) and it disappears close to Fhe+. At the time of detection, the spacecraft magnetic latitude is larger than 10 degrees and L shell is about 4. The propagation sense of the emissions has been established using two independent methods: 1) sense of the parallel component of the Poynting flux for a single spacecraft and 2) timing of the emission detections at each of the four Cluster spacecraft which were in a relatively close configuration. We propose here to discuss this unexpected result considering a reflection of this emission at higher latitude.

Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import

PubMed Central

Azimi, Mohammad; Mofrad, Mohammad R. K.

2013-01-01

Several in vitro studies have shown the presence of an affinity gradient in nuclear pore complex proteins for the import receptor Importinβ, at least partially contributing to nucleocytoplasmic transport, while others have historically argued against the presence of such a gradient. Nonetheless, the existence of an affinity gradient has remained an uncharacterized contributing factor. To shed light on the affinity gradient theory and better characterize how the existence of such an affinity gradient between the nuclear pore and the import receptor may influence the nucleocytoplasmic traffic, we have developed a general-purpose agent based modeling (ABM) framework that features a new method for relating rate constants to molecular binding and unbinding probabilities, and used our ABM approach to quantify the effects of a wide range of forward and reverse nucleoporin-Importinβ affinity gradients. Our results indicate that transport through the nuclear pore complex is maximized with an effective macroscopic affinity gradient of 2000 µM, 200 µM and 10 µM in the cytoplasmic, central channel and nuclear basket respectively. The transport rate at this gradient is approximately 10% higher than the transport rate for a comparable pore lacking any affinity gradient, which has a peak transport rate when all nucleoporins have an affinity of 200 µM for Importinβ. Furthermore, this optimal ratio of affinity gradients is representative of the ratio of affinities reported for the yeast nuclear pore complex – suggesting that the affinity gradient seen in vitro is highly optimized. PMID:24282617

Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data

DOE PAGES

Murugesan, Sugeerth; Bouchard, Kristofer; Chang, Edward; ...

2016-10-02

Here, we present ECoG ClusterFlow, a novel interactive visual analysis tool for the exploration of high-resolution Electrocorticography (ECoG) data. Our system detects and visualizes dynamic high-level structures, such as communities, using the time-varying spatial connectivity network derived from the high-resolution ECoG data. ECoG ClusterFlow provides a multi-scale visualization of the spatio-temporal patterns underlying the time-varying communities using two views: 1) an overview summarizing the evolution of clusters over time and 2) a hierarchical glyph-based technique that uses data aggregation and small multiples techniques to visualize the propagation of clusters in their spatial domain. ECoG ClusterFlow makes it possible 1) tomore » compare the spatio-temporal evolution patterns across various time intervals, 2) to compare the temporal information at varying levels of granularity, and 3) to investigate the evolution of spatial patterns without occluding the spatial context information. Lastly, we present case studies done in collaboration with neuroscientists on our team for both simulated and real epileptic seizure data aimed at evaluating the effectiveness of our approach.« less

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

PubMed

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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Methyl cation affinities of neutral and anionic maingroup-element hydrides: trends across the periodic table and correlation with proton affinities.

PubMed

Mulder, R Joshua; Guerra, Célia Fonseca; Bickelhaupt, F Matthias

2010-07-22

We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and corresponding entropies) at 298 K of all anionic (XH(n-1)(-)) and neutral bases (XH(n)) constituted by maingroup-element hydrides of groups 14-17 and the noble gases (i.e., group 18) along the periods 2-6. The cation affinity of the bases decreases from H(+) to CH(3)(+). To understand this trend, we have carried out quantitative bond energy decomposition analyses (EDA). Quantitative correlations are established between the MCA and PA values.

Carbon X-ray absorption spectra of fluoroethenes and acetone: A study at the coupled cluster, density functional, and static-exchange levels of theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fransson, Thomas; Norman, Patrick; Coriani, Sonia

2013-03-28

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as themore » state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger {pi}-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to {pi}*-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate {pi}*-peak separations due to spectral compressions, a characteristic which is inherent to

Carbon X-ray absorption spectra of fluoroethenes and acetone: a study at the coupled cluster, density functional, and static-exchange levels of theory.

PubMed

Fransson, Thomas; Coriani, Sonia; Christiansen, Ove; Norman, Patrick

2013-03-28

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π∗-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π∗-peak separations due to spectral compressions, a characteristic which is inherent to this

Asymptotic Representations of Quantum Affine Superalgebras

NASA Astrophysics Data System (ADS)

Zhang, Huafeng

2017-08-01

We study representations of the quantum affine superalgebra associated with a general linear Lie superalgebra. In the spirit of Hernandez-Jimbo, we construct inductive systems of Kirillov-Reshetikhin modules based on a cyclicity result that we established previously on tensor products of these modules, and realize their inductive limits as modules over its Borel subalgebra, the so-called q-Yangian. A new generic asymptotic limit of the same inductive systems is proposed, resulting in modules over the full quantum affine superalgebra. We derive generalized Baxter's relations in the sense of Frenkel-Hernandez for representations of the full quantum group.

The complex-scaled multiconfigurational spin-tensor electron propagator method for low-lying shape resonances in Be-, Mg- and Ca-

NASA Astrophysics Data System (ADS)

Tsogbayar, Tsednee; Yeager, Danny L.

2017-01-01

We further apply the complex scaled multiconfigurational spin-tensor electron propagator method (CMCSTEP) for the theoretical determination of resonance parameters with electron-atom systems including open-shell and highly correlated (non-dynamical correlation) atoms and molecules. The multiconfigurational spin-tensor electron propagator method (MCSTEP) developed and implemented by Yeager and his coworkers for real space gives very accurate and reliable ionization potentials and electron affinities. CMCSTEP uses a complex scaled multiconfigurational self-consistent field (CMCSCF) state as an initial state along with a dilated Hamiltonian where all of the electronic coordinates are scaled by a complex factor. CMCSTEP is designed for determining resonances. We apply CMCSTEP to get the lowest 2P (Be-, Mg-) and 2D (Mg-, Ca-) shape resonances using several different basis sets each with several complete active spaces. Many of these basis sets we employ have been used by others with different methods. Hence, we can directly compare results with different methods but using the same basis sets.

Relationships between chemical structure and affinity for acetylcholine receptors

PubMed Central

Abramson, F. B.; Barlow, R. B.; Mustafa, M. G.; Stephenson, R. P.

1969-01-01

1. Series of analogues of acetylcholine have been prepared in which the acetyl group was replaced by phenylacetyl, cyclohexylacetyl, diphenylacetyl, dicyclohexylacetyl, (±)-phenylcyclohexylacetyl, benziloyl and (±)-phenylcyclohexylhydroxyacetyl groups and the trimethylammonium group was replaced by Me2EtN+, MeEt2N+, Et3N+, [Formula: see text] Further series were prepared in which the acetoxyethyl group was replaced by ethoxyethyl, phenylethoxyethyl, cyclohexylethoxyethyl, diphenylethoxyethyl, and dicyclohexylethoxyethyl groups, and by n-pentyl, 5-phenylpentyl, 5-cyclohexylpentyl and 5:5-diphenylpentyl groups. 2. The ethoxyethyl and n-pentyl series contain some compounds which are agonists or partial agonists when tested on the isolated guinea-pig ileum, but all the other compounds are antagonists. 3. The affinity of the compounds for the postganglionic (“muscarinesensitive”) acetylcholine receptors has been measured in conditions in which the antagonists have been shown to be acting competitively. There were considerable differences between their affinities, the most active (log K, 9·8) having one million times the affinity of the least active (log K, 3·7). 4. The changes in affinity as the onium group was modified were not entirely independent of changes in the rest of the molecule. Increasing the size of the onium group, as judged from conductivity measurements on simpler onium salts, increased affinity in the series containing one large group (phenyl or cyclohexyl) but, in the series with two large groups, affinity declined when the size was increased beyond -+NMeEt2. 5. In general, the effects of changes in the rest of the molecule on affinity were bigger than the effects of changes in the onium group and there were bigger interactions. Affinity was increased to a greater extent by introducing one phenyl and one cyclohexyl group together than by introducing either two phenyl or two cyclohexyl groups; the increment was greater than the separate

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

Manipulation of visible-light polarization with dendritic cell-cluster metasurfaces.

PubMed

Fang, Zhen-Hua; Chen, Huan; An, Di; Luo, Chun-Rong; Zhao, Xiao-Peng

2018-06-26

Cross-polarization conversion plays an important role in visible light manipulation. Metasurface with asymmetric structure can be used to achieve polarization conversion of linearly polarized light. Based on this, we design a quasi-periodic dendritic metasurface model composed of asymmetric dendritic cells. The simulation indicates that the asymmetric dendritic structure can vertically rotate the polarization direction of the linear polarization wave in visible light. Silver dendritic cell-cluster metasurface samples were prepared by the bottom-up electrochemical deposition. It experimentally proved that they could realize the cross - polarization conversion in visible light. Cross-polarized propagating light is deflected into anomalous refraction channels. Dendritic cell-cluster metasurface with asymmetric quasi-periodic structure conveys significance in cross-polarization conversion research and features extensive practical application prospect and development potential.

Exploring the possibility to store the mixed oxygen-hydrogen cluster in clathrate hydrate in molar ratio 1:2 (O2+2H2).

PubMed

Qin, Yan; Du, Qi-Shi; Xie, Neng-Zhong; Li, Jian-Xiu; Huang, Ri-Bo

2017-05-01

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O 2 -2H 2 interaction structure is smaller than the dimension of CO 2 -2H 2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O 2 +2H 2 ) cluster in clathrate hydrate. Copyright © 2017 Elsevier Inc. All rights reserved.

Red cell 2,3-diphosphoglycerate and oxygen affinity.

PubMed

MacDonald, R

1977-06-01

The ease with which haemoglobin releases oxygen to the tissues is controlled by erythrocytic 2,3-diphosphoglycerate (2,3-DPG) such that an increase in the concentration of 2,3-DPG decreases oxygen affinity and vice versa. This review article describes the synthesis and breakdown of 2,3-DPG in the Embden-Meyerof pathway in red cells and briefly explains the molecular basis for its effect on oxygen affinity. Interaction of the effects of pH, Pco2, temperature and 2,3-DPG on the oxyhaemoglobin dissociation curve are discussed. The role of 2,3-DPG in the intraerythrocytic adaptation to various types of hypoxaemia is described. The increased oxygen affinity of blood stored in acid-citrate-dextrose (ACD) solution has been shown to be due to the decrease in the concentration of 2,3-DPG which occurs during storage. Methods of maintaining the concentration of 2,3-DPG in stored blood are described. The clinical implication of transfusion of elderly people, anaemic or pregnant patients with ACD stored blood to anaesthetically and surgically acceptable haemoglobin concentrations are discussed. Hypophosphataemia in association with parenteral feeding reduces 2,3-DPG concentration and so increases oxygen affinity. Since post-operative use of intravenous fluids such as dextrose or dextrose/saline also lead to hypophosphataemia, the addition of inorganic phosphorus to routine post-operative intravenous fluid may be advisable. Disorders of acid-base balance effect oxygen affinity not only by the direct effect of pH on the oxyhaemoglobin dissociation curve but by its control of 2,3-DPG metabolism. Management of acid-base disorders and pre-operative aklalinization of patients with sickle cell disease whould take account of this. It is known that anaesthesia alters the position of the oxyhaemoglobin dissociation curve, but it is thought that this is independent of any effects which anaesthetic agents may have on 2,3-DPG concentration. In vitro manipulation of 2,3-DPG concentration

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.

Camelid VHH affinity ligands enable separation of closely related biopharmaceuticals

PubMed Central

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

2016-01-01

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

Exploring Girls' Science Affinities Through an Informal Science Education Program

NASA Astrophysics Data System (ADS)

Todd, Brandy; Zvoch, Keith

2017-10-01

This study examines science interests, efficacy, attitudes, and identity—referred to as affinities, in the context of an informal science outreach program for girls. A mixed methods design was used to explore girls' science affinities before, during, and after participation in a cohort-based summer science camp. Multivariate analysis of survey data revealed that girls' science affinities varied as a function of the joint relationship between family background and number of years in the program, with girls from more affluent families predicted to increase affinities over time and girls from lower income families to experience initial gains in affinities that diminish over time. Qualitative examination of girls' perspectives on gender and science efficacy, attitudes toward science, and elements of science identities revealed a complex interplay of gendered stereotypes of science and girls' personal desires to prove themselves knowledgeable and competent scientists. Implications for the best practice in fostering science engagement and identities in middle school-aged girls are discussed.

Wave Propagation, Scattering and Imaging Using Dual-domain One-way and One-return Propagators

NASA Astrophysics Data System (ADS)

Wu, R.-S.

- Dual-domain one-way propagators implement wave propagation in heterogeneous media in mixed domains (space-wavenumber domains). One-way propagators neglect wave reverberations between heterogeneities but correctly handle the forward multiple-scattering including focusing/defocusing, diffraction, refraction and interference of waves. The algorithm shuttles between space-domain and wavenumber-domain using FFT, and the operations in the two domains are self-adaptive to the complexity of the media. The method makes the best use of the operations in each domain, resulting in efficient and accurate propagators. Due to recent progress, new versions of dual-domain methods overcame some limitations of the classical dual-domain methods (phase-screen or split-step Fourier methods) and can propagate large-angle waves quite accurately in media with strong velocity contrasts. These methods can deliver superior image quality (high resolution/high fidelity) for complex subsurface structures. One-way and one-return (De Wolf approximation) propagators can be also applied to wave-field modeling and simulations for some geophysical problems. In the article, a historical review and theoretical analysis of the Born, Rytov, and De Wolf approximations are given. A review on classical phase-screen or split-step Fourier methods is also given, followed by a summary and analysis of the new dual-domain propagators. The applications of the new propagators to seismic imaging and modeling are reviewed with several examples. For seismic imaging, the advantages and limitations of the traditional Kirchhoff migration and time-space domain finite-difference migration, when applied to 3-D complicated structures, are first analyzed. Then the special features, and applications of the new dual-domain methods are presented. Three versions of GSP (generalized screen propagators), the hybrid pseudo-screen, the wide-angle Padé-screen, and the higher-order generalized screen propagators are discussed. Recent

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.

Affinity Chart Analysis: A Method for Structured Collection, Aggregation, and Response to Customer Needs in Radiology.

PubMed

Boll, Daniel T; Rubin, Geoffrey D; Heye, Tobias; Pierce, Laura J

2017-04-01

The objective of this study is to analyze implementation of the voice-of-the-customer method to assess the current state of image postprocessing and reporting delivered by a radiology department and to plan improvements on the basis of referring physicians' preferences. The voice-of-the-customer method consisted of discovery, analysis, and optimization phases. Fifty referring physicians were invited to be interviewed. Interviews addressed the topics of structure, process, outcome, and support. Interviews were dissected into individual statements categorized as fact or feeling. Statements were grouped to find collective voices. Improvements were compiled from affinity charts and were processed by identifying insights. Ninety-four percent (47/50) of physicians participated, generating 352 statements (81 facts and 271 feelings) that subsequently underwent affinity chart clustering. The resultant affinity charts covered distinct themes: "we need you to know us better," "we need you to consider our workflow," "we need more from your services," "we want to review your data in certain ways," and "we want to do more with you." As a result of the insights gained, the following optimizations were implemented: a software application that improves study requesting, performance tracking, study prioritization, and longitudinal data archiving; six prototype reports containing tabulated data and annotated images; two prototype longitudinal reporting templates assessing aneurysm evolution and treatment-induced changes in organ size over time; and a teaching curriculum for trainees. This study has shown the clinical feasibility to assess the current state of image postprocessing and reporting and to implement improvements of and investments in image postprocessing and reporting infrastructure on the basis of referring physicians' preferences using the voice-of-the-customer method.

Slip accumulation and lateral propagation of active normal faults in Afar

NASA Astrophysics Data System (ADS)

Manighetti, I.; King, G. C. P.; Gaudemer, Y.; Scholz, C. H.; Doubre, C.

2001-01-01

We investigate fault growth in Afar, where normal fault systems are known to be currently growing fast and most are propagating to the northwest. Using digital elevation models, we have examined the cumulative slip distribution along 255 faults with lengths ranging from 0.3 to 60 km. Faults exhibiting the elliptical or "bell-shaped" slip profiles predicted by simple linear elastic fracture mechanics or elastic-plastic theories are rare. Most slip profiles are roughly linear for more than half of their length, with overall slopes always <0.035. For the dominant population of NW striking faults and fault systems longer than 2 km, the slip profiles are asymmetric, with slip being maximum near the eastern ends of the profiles where it drops abruptly to zero, whereas slip decreases roughly linearly and tapers in the direction of overall Aden rift propagation. At a more detailed level, most faults appear to be composed of distinct, shorter subfaults or segments, whose slip profiles, while different from one to the next, combine to produce the roughly linear overall slip decrease along the entire fault. On a larger scale, faults cluster into kinematically coupled systems, along which the slip on any scale individual fault or fault system complements that of its neighbors, so that the total slip of the whole system is roughly linearly related to its length, with an average slope again <0.035. We discuss the origin of these quasilinear, asymmetric profiles in terms of "initiation points" where slip starts, and "barriers" where fault propagation is arrested. In the absence of a barrier, slip apparently extends with a roughly linear profile, tapered in the direction of fault propagation.

WAVE2 Regulates High-Affinity Integrin Binding by Recruiting Vinculin and Talin to the Immunological Synapse▿

PubMed Central

Nolz, Jeffrey C.; Medeiros, Ricardo B.; Mitchell, Jason S.; Zhu, Peimin; Freedman, Bruce D.; Shimizu, Yoji; Billadeau, Daniel D.

2007-01-01

T-cell-receptor (TCR)-mediated integrin activation is required for T-cell-antigen-presenting cell conjugation and adhesion to extracellular matrix components. While it has been demonstrated that the actin cytoskeleton and its regulators play an essential role in this process, no mechanism has been established which directly links TCR-induced actin polymerization to the activation of integrins. Here, we demonstrate that TCR stimulation results in WAVE2-ARP2/3-dependent F-actin nucleation and the formation of a complex containing WAVE2, ARP2/3, vinculin, and talin. The verprolin-connecting-acidic (VCA) domain of WAVE2 mediates the formation of the ARP2/3-vinculin-talin signaling complex and talin recruitment to the immunological synapse (IS). Interestingly, although vinculin is not required for F-actin or integrin accumulation at the IS, it is required for the recruitment of talin. In addition, RNA interference of either WAVE2 or vinculin inhibits activation-dependent induction of high-affinity integrin binding to VCAM-1. Overall, these findings demonstrate a mechanism in which signals from the TCR produce WAVE2-ARP2/3-mediated de novo actin polymerization, leading to integrin clustering and high-affinity binding through the recruitment of vinculin and talin. PMID:17591693

WAVE2 regulates high-affinity integrin binding by recruiting vinculin and talin to the immunological synapse.

PubMed

Nolz, Jeffrey C; Medeiros, Ricardo B; Mitchell, Jason S; Zhu, Peimin; Freedman, Bruce D; Shimizu, Yoji; Billadeau, Daniel D

2007-09-01

T-cell-receptor (TCR)-mediated integrin activation is required for T-cell-antigen-presenting cell conjugation and adhesion to extracellular matrix components. While it has been demonstrated that the actin cytoskeleton and its regulators play an essential role in this process, no mechanism has been established which directly links TCR-induced actin polymerization to the activation of integrins. Here, we demonstrate that TCR stimulation results in WAVE2-ARP2/3-dependent F-actin nucleation and the formation of a complex containing WAVE2, ARP2/3, vinculin, and talin. The verprolin-connecting-acidic (VCA) domain of WAVE2 mediates the formation of the ARP2/3-vinculin-talin signaling complex and talin recruitment to the immunological synapse (IS). Interestingly, although vinculin is not required for F-actin or integrin accumulation at the IS, it is required for the recruitment of talin. In addition, RNA interference of either WAVE2 or vinculin inhibits activation-dependent induction of high-affinity integrin binding to VCAM-1. Overall, these findings demonstrate a mechanism in which signals from the TCR produce WAVE2-ARP2/3-mediated de novo actin polymerization, leading to integrin clustering and high-affinity binding through the recruitment of vinculin and talin.

Motion planning in velocity affine mechanical systems

NASA Astrophysics Data System (ADS)

Jakubiak, Janusz; Tchoń, Krzysztof; Magiera, Władysław

2010-09-01

We address the motion planning problem in specific mechanical systems whose linear and angular velocities depend affinely on control. The configuration space of these systems encompasses the rotation group, and the motion planning involves the system orientation. Derivation of the motion planning algorithm for velocity affine systems has been inspired by the continuation method. Performance of this algorithm is illustrated with examples of the kinematics of a serial nonholonomic manipulator, the plate-ball kinematics and the attitude control of a rigid body.

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

PubMed Central

Azad, Ariful; Ouzounis, Christos A; Kyrpides, Nikos C; Buluç, Aydin

2018-01-01

Abstract Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times and memory demands. Here, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ∼70 million nodes with ∼68 billion edges in ∼2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license. PMID:29315405

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

DOE PAGES

Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A.; ...

2018-01-05

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times andmore » memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.« less

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azad, Ariful; Pavlopoulos, Georgios A.; Ouzounis, Christos A.

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times andmore » memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.« less

Locating sources within a dense sensor array using graph clustering

NASA Astrophysics Data System (ADS)

Gerstoft, P.; Riahi, N.

2017-12-01

We develop a model-free technique to identify weak sources within dense sensor arrays using graph clustering. No knowledge about the propagation medium is needed except that signal strengths decay to insignificant levels within a scale that is shorter than the aperture. We then reinterpret the spatial coherence matrix of a wave field as a matrix whose support is a connectivity matrix of a graph with sensors as vertices. In a dense network, well-separated sources induce clusters in this graph. The geographic spread of these clusters can serve to localize the sources. The support of the covariance matrix is estimated from limited-time data using a hypothesis test with a robust phase-only coherence test statistic combined with a physical distance criterion. The latter criterion ensures graph sparsity and thus prevents clusters from forming by chance. We verify the approach and quantify its reliability on a simulated dataset. The method is then applied to data from a dense 5200 element geophone array that blanketed of the city of Long Beach (CA). The analysis exposes a helicopter traversing the array and oil production facilities.

Mainshock-Aftershocks Clustering Detection in Volcanic Regions

NASA Astrophysics Data System (ADS)

Garza Giron, R.; Brodsky, E. E.; Prejean, S. G.

2017-12-01

Crustal earthquakes tend to break their general Poissonean process behavior by gathering into two main kinds of seismic bursts: swarms and mainshock-aftershocks sequences. The former is commonly related to volcanic or geothermal processes whereas the latter is a characteristic feature of tectonically driven seismicity. We explore the mainshock-aftershock clustering behavior of different active volcanic regions in Japan and its comparison to non-volcanic regions. We find that aftershock production in volcanoes shows mainshock-aftershocks clustering similar to what is observed in non-volcanic areas. The ratio of volanic areas that cluster in mainshock-aftershocks sequences vs the areas that do not is comparable to the ratio of non-volcanic regions that show clustering vs the ones that do not. Furthermore, the level of production of aftershocks for most volcanic areas where clustering is present seems to be of the same order of magnitude, or slightly higher, as the median of the non-volcanic regions. An interesting example of highly aftershock-productive volcanoes emerges from the 2000 Miyakejima dike intrusion. A big seismic cluster started to build up rapidly in the south-west flank of Miyakejima to later propagate to the north-west towards the Kozushima and Niijima volcanoes. In Miyakejima the seismicity showed a swarm-like signature with a constant earthquake rate, whereas Kozushima and Niijima both had expressions of highly productive mainshock-aftershocks sequences. These findings are surprising given the alternative mechanisms available in volcanic systems for releasing deviatoric strain. We speculate that aftershock behavior might hold a relationship with the rheological properties of the rocks of each system and with the capacity of a system to accumulate or release the internal pressures caused by magmatic or hydrothermal systems.

Measurements of the talus in the assessment of population affinity.

PubMed

Bidmos, Mubarak A; Dayal, Manisha R; Adegboye, Oyelola A

2018-06-01

As part of their routine work, forensic anthropologists are expected to report population affinity as part of the biological profile of an individual. The skull is the most widely used bone for the estimation of population affinity but it is not always present in a forensic case. Thus, other bones that preserve well have been shown to give a good indication of either the sex or population affinity of an individual. In this study, the potential of measurements of the talus was investigated for the purpose of estimating population affinity in South Africans. Nine measurements from two hundred and twenty tali of South African Africans (SAA) and South African Whites (SAW) from the Raymond A. Dart Collection of Human Skeletons were used. Direct and step-wise discriminant function and logistic regression analyses were carried out using SPSS and SAS. Talar length was the best single variable for discriminating between these two groups for males while in females the head height was the best single predictor. Average accuracies for correct population affinity classification using logistic regression analysis were higher than those obtained from discriminant function analysis. This study was the first of its type to employ discriminant function analyses and logistic regression analyses to estimate the population affinity of an individual from the talus. Thus these equations can now be used by South African anthropologists when estimating the population affinity of dismembered or damaged or incomplete skeletal remains of SAA and SAW. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Excited state electron affinity calculations for aluminum

NASA Astrophysics Data System (ADS)

Hussein, Adnan Yousif

2017-08-01

Excited states of negative aluminum ion are reviewed, and calculations of electron affinities of the states (3s^23p^2)^1D and (3s3p^3){^5}{S}° relative to the (3s^23p)^2P° and (3s3p^2)^4P respectively of the neutral aluminum atom are reported in the framework of nonrelativistic configuration interaction (CI) method. A priori selected CI (SCI) with truncation energy error (Bunge in J Chem Phys 125:014107, 2006) and CI by parts (Bunge and Carbó-Dorca in J Chem Phys 125:014108, 2006) are used to approximate the valence nonrelativistic energy. Systematic studies of convergence of electron affinity with respect to the CI excitation level are reported. The calculated value of the electron affinity for ^1D state is 78.675(3) meV. Detailed Calculations on the ^5S°c state reveals that is 1216.8166(3) meV below the ^4P state.

Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics.

PubMed

Garnett, Graham A E; Starke, Melissa J; Shaurya, Alok; Li, Janessa; Hof, Fraser

2016-04-05

Proteome-wide studies of post-translationally methylated species using mass spectrometry are complicated by high sample diversity, competition for ionization among peptides, and mass redundancies. Antibody-based enrichment has powered methylation proteomics until now, but the reliability, pan-specificity, polyclonal nature, and stability of the available pan-specific antibodies are problematic and do not provide a standard, reliable platform for investigators. We have invented an anionic supramolecular host that can form host-guest complexes selectively with methyllysine-containing peptides and used it to create a methylysine-affinity column. The column resolves peptides on the basis of methylation-a feat impossible with a comparable commercial cation-exchange column. A proteolyzed nuclear extract was separated on the methyl-affinity column prior to standard proteomics analysis. This experiment demonstrates that such chemical methyl-affinity columns are capable of enriching and improving the analysis of methyllysine residues from complex protein mixtures. We discuss the importance of this advance in the context of biomolecule-driven enrichment methods.

The N-Terminal Domain of Human DNA Helicase Rtel1 Contains a Redox Active Iron-Sulfur Cluster

PubMed Central

Landry, Aaron P.

2014-01-01

Human telomere length regulator Rtel1 is a superfamily II DNA helicase and is essential for maintaining proper length of telomeres in chromosomes. Here we report that the N-terminal domain of human Rtel1 (RtelN) expressed in Escherichia coli cells produces a protein that contains a redox active iron-sulfur cluster with the redox midpoint potential of −248 ± 10 mV (pH 8.0). The iron-sulfur cluster in RtelN is sensitive to hydrogen peroxide and nitric oxide, indicating that reactive oxygen/nitrogen species may modulate the DNA helicase activity of Rtel1 via modification of its iron-sulfur cluster. Purified RtelN retains a weak binding affinity for the single-stranded (ss) and double-stranded (ds) DNA in vitro. However, modification of the iron-sulfur cluster by hydrogen peroxide or nitric oxide does not significantly affect the DNA binding activity of RtelN, suggesting that the iron-sulfur cluster is not directly involved in the DNA interaction in the N-terminal domain of Rtel1. PMID:25147792

The N-terminal domain of human DNA helicase Rtel1 contains a redox active iron-sulfur cluster.

PubMed

Landry, Aaron P; Ding, Huangen

2014-01-01

Human telomere length regulator Rtel1 is a superfamily II DNA helicase and is essential for maintaining proper length of telomeres in chromosomes. Here we report that the N-terminal domain of human Rtel1 (RtelN) expressed in Escherichia coli cells produces a protein that contains a redox active iron-sulfur cluster with the redox midpoint potential of -248 ± 10 mV (pH 8.0). The iron-sulfur cluster in RtelN is sensitive to hydrogen peroxide and nitric oxide, indicating that reactive oxygen/nitrogen species may modulate the DNA helicase activity of Rtel1 via modification of its iron-sulfur cluster. Purified RtelN retains a weak binding affinity for the single-stranded (ss) and double-stranded (ds) DNA in vitro. However, modification of the iron-sulfur cluster by hydrogen peroxide or nitric oxide does not significantly affect the DNA binding activity of RtelN, suggesting that the iron-sulfur cluster is not directly involved in the DNA interaction in the N-terminal domain of Rtel1.

Scalable properties of metal clusters: A comparative study of modern exchange-correlation functionals

NASA Astrophysics Data System (ADS)

Koitz, Ralph; Soini, Thomas M.; Genest, Alexander; Trickey, S. B.; Rösch, Notker

2012-07-01

The performance of eight generalized gradient approximation exchange-correlation (xc) functionals is assessed by a series of scalar relativistic all-electron calculations on octahedral palladium model clusters Pdn with n = 13, 19, 38, 55, 79, 147 and the analogous clusters Aun (for n up through 79). For these model systems, we determined the cohesive energies and average bond lengths of the optimized octahedral structures. We extrapolate these values to the bulk limits and compare with the corresponding experimental values. While the well-established functionals BP, PBE, and PW91 are the most accurate at predicting energies, the more recent forms PBEsol, VMTsol, and VT{84}sol significantly improve the accuracy of geometries. The observed trends are largely similar for both Pd and Au. In the same spirit, we also studied the scalability of the ionization potentials and electron affinities of the Pd clusters, and extrapolated those quantities to estimates of the work function. Overall, the xc functionals can be classified into four distinct groups according to the accuracy of the computed parameters. These results allow a judicious selection of xc approximations for treating transition metal clusters.

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

Thermodynamics of the Coma Cluster Outskirts

NASA Astrophysics Data System (ADS)

Simionescu, A.; Werner, N.; Urban, O.; Allen, S. W.; Fabian, A. C.; Mantz, A.; Matsushita, K.; Nulsen, P. E. J.; Sanders, J. S.; Sasaki, T.; Sato, T.; Takei, Y.; Walker, S. A.

2013-09-01

We present results from a large mosaic of Suzaku observations of the Coma Cluster, the nearest and X-ray brightest hot (~8 keV), dynamically active, non-cool core system, focusing on the thermodynamic properties of the intracluster medium on large scales. For azimuths not aligned with an infalling subcluster toward the southwest, our measured temperature and X-ray brightness profiles exhibit broadly consistent radial trends, with the temperature decreasing from about 8.5 keV at the cluster center to about 2 keV at a radius of 2 Mpc, which is the edge of our detection limit. The southwest merger significantly boosts the surface brightness, allowing us to detect X-ray emission out to ~2.2 Mpc along this direction. Apart from the southwestern infalling subcluster, the surface brightness profiles show multiple edges around radii of 30-40 arcmin. The azimuthally averaged temperature profile, as well as the deprojected density and pressure profiles, all show a sharp drop consistent with an outwardly-propagating shock front located at 40 arcmin, corresponding to the outermost edge of the giant radio halo observed at 352 MHz with the Westerbork Synthesis Radio Telescope. The shock front may be powering this radio emission. A clear entropy excess inside of r 500 reflects the violent merging events linked with these morphological features. Beyond r 500, the entropy profiles of the Coma Cluster along the relatively relaxed directions are consistent with the power-law behavior expected from simple models of gravitational large-scale structure formation. The pressure is also in agreement at these radii with the expected values measured from Sunyaev-Zel'dovich data from the Planck satellite. However, due to the large uncertainties associated with the Coma Cluster measurements, we cannot yet exclude an entropy flattening in this system consistent with that seen in more relaxed cool core clusters.

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...

Protein purification by aminosquarylium cyanine dye-affinity chromatography.

PubMed

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

2013-12-01

The most selective purification method for proteins and other biomolecules is affinity chromatography. This method is based on the unique biological-based specificity of the biomolecule-ligand interaction and commonly uses biological ligands. However, these ligands may present some drawbacks, mainly because of their cost and lability. Dye-affinity chromatography overcomes the limitations of biological ligands and is widely used owing to the low cost of synthetic dyes and to their resistance to biological and chemical degradation. In this work, immobilized aminosquarylium cyanine dyes are used in order to exploit affinity interactions with standard proteins such as lysozyme, α-chymotrypsin and trypsin. These studies evaluate the affinity interactions occurring between the immobilized ligand and the different proteins, as a reflection of the sum of several molecular interactions, namely ionic, hydrophobic and van der Waals, spread throughout the structure, in a defined spatial manner. The results show the possibility of using an aminosquarylium cyanine dye bearing a N-hexyl pendant chain, with a ligand density of 1.8 × 10(-2) mmol of dye/g of chromatographic support, to isolate lysozyme, α-chymotrypsin and trypsin from a mixture. The application of a decreasing ammonium sulfate gradient resulted in the recovery of lysozyme in the flowthrough. On the other hand, α-chymotrypsin and trypsin were retained, involving different interactions with the ligand. In conclusion, this study demonstrates the potential applicability of ligands such as aminosquarylium cyanine dyes for the separation and purification of proteins by affinity chromatography. Copyright © 2013 John Wiley & Sons, Ltd.

Shark Attack: high affinity binding proteins derived from shark vNAR domains by stepwise in vitro affinity maturation.

PubMed

Zielonka, Stefan; Weber, Niklas; Becker, Stefan; Doerner, Achim; Christmann, Andreas; Christmann, Christine; Uth, Christina; Fritz, Janine; Schäfer, Elena; Steinmann, Björn; Empting, Martin; Ockelmann, Pia; Lierz, Michael; Kolmar, Harald

2014-12-10

A novel method for stepwise in vitro affinity maturation of antigen-specific shark vNAR domains is described that exclusively relies on semi-synthetic repertoires derived from non-immunized sharks. Target-specific molecules were selected from a CDR3-randomized bamboo shark (Chiloscyllium plagiosum) vNAR library using yeast surface display as platform technology. Various antigen-binding vNAR domains were easily isolated by screening against several therapeutically relevant antigens, including the epithelial cell adhesion molecule (EpCAM), the Ephrin type-A receptor 2 (EphA2), and the human serine protease HTRA1. Affinity maturation was demonstrated for EpCAM and HTRA1 by diversifying CDR1 of target-enriched populations which allowed for the rapid selection of nanomolar binders. EpCAM-specific vNAR molecules were produced as soluble proteins and more extensively characterized via thermal shift assays and biolayer interferometry. Essentially, we demonstrate that high-affinity binders can be generated in vitro without largely compromising the desirable high thermostability of the vNAR scaffold. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Intra-cluster Globular Clusters in a Simulated Galaxy Cluster

NASA Astrophysics Data System (ADS)

Ramos-Almendares, Felipe; Abadi, Mario; Muriel, Hernán; Coenda, Valeria

2018-01-01

Using a cosmological dark matter simulation of a galaxy-cluster halo, we follow the temporal evolution of its globular cluster population. To mimic the red and blue globular cluster populations, we select at high redshift (z∼ 1) two sets of particles from individual galactic halos constrained by the fact that, at redshift z = 0, they have density profiles similar to observed ones. At redshift z = 0, approximately 60% of our selected globular clusters were removed from their original halos building up the intra-cluster globular cluster population, while the remaining 40% are still gravitationally bound to their original galactic halos. As the blue population is more extended than the red one, the intra-cluster globular cluster population is dominated by blue globular clusters, with a relative fraction that grows from 60% at redshift z = 0 up to 83% for redshift z∼ 2. In agreement with observational results for the Virgo galaxy cluster, the blue intra-cluster globular cluster population is more spatially extended than the red one, pointing to a tidally disrupted origin.

Increased hemoglobin O2 affinity protects during acute hypoxia

PubMed Central

Yalcin, Ozlem

2012-01-01

Acclimatization to hypoxia requires time to complete the adaptation mechanisms that influence oxygen (O2) transport and O2 utilization. Although decreasing hemoglobin (Hb) O2 affinity would favor the release of O2 to the tissues, increasing Hb O2 affinity would augment arterial O2 saturation during hypoxia. This study was designed to test the hypothesis that pharmacologically increasing the Hb O2 affinity will augment O2 transport during severe hypoxia (10 and 5% inspired O2) compared with normal Hb O2 affinity. RBC Hb O2 affinity was increased by infusion of 20 mg/kg of 5-hydroxymethyl-2-furfural (5HMF). Control animals received only the vehicle. The effects of increasing Hb O2 affinity were studied in the hamster window chamber model, in terms of systemic and microvascular hemodynamics and partial pressures of O2 (Po2). Pimonidazole binding to hypoxic areas of mice heart and brain was also studied. 5HMF decreased the Po2 at which the Hb is 50% saturated with O2 by 12.6 mmHg. During 10 and 5% O2 hypoxia, 5HMF increased arterial blood O2 saturation by 35 and 48% from the vehicle group, respectively. During 5% O2 hypoxia, blood pressure and heart rate were 58 and 30% higher for 5HMF compared with the vehicle. In addition, 5HMF preserved microvascular blood flow, whereas blood flow decreased to 40% of baseline in the vehicle group. Consequently, perivascular Po2 was three times higher in the 5HMF group compared with the control group at 5% O2 hypoxia. 5HMF also reduced heart and brain hypoxic areas in mice. Therefore, increased Hb O2 affinity resulted in hemodynamics and oxygenation benefits during severe hypoxia. This acute acclimatization process may have implications in survival during severe environmental hypoxia when logistic constraints prevent chronic acclimatization. PMID:22636677

Recent Impacts on Mars: Cluster Properties and Seismic Signal Predictions

NASA Astrophysics Data System (ADS)

Justine Daubar, Ingrid; Schmerr, Nicholas; Banks, Maria; Marusiak, Angela; Golombek, Matthew P.

2016-10-01

Impacts are a key source of seismic waves that are a primary constraint on the formation, evolution, and dynamics of planetary objects. Geophysical missions such as InSight (Banerdt et al., 2013) will monitor seismic signals from internal and external sources. New martian craters have been identified in orbital images (Malin et al., 2006; Daubar et al., 2013). Seismically detecting such impacts and subsequently imaging the resulting craters will provide extremely accurate epicenters and source crater sizes, enabling calibration of seismic velocities, the efficiency of impact-seismic coupling, and retrieval of detailed regional and local internal structure.To investigate recent impact-induced seismicity on Mars, we have assessed ~100 new, dated impact sites. In approximately half of new impacts, the bolide partially disintegrates in the atmosphere, forming multiple craters in a cluster. We incorporate the resulting, more complex, seismic effects in our model. To characterize the variation between sites, we focus on clustered impacts. We report statistics of craters within clusters: diameters, morphometry indicating subsurface layering, strewn-field azimuths indicating impact direction, and dispersion within clusters indicating combined effects of bolide strength and elevation of breakup.Measured parameters are converted to seismic predictions for impact sources using a scaling law relating crater diameter to the momentum and source duration, calibrated for impacts recorded by Apollo (Lognonne et al., 2009). We use plausible ranges for target properties, bolide densities, and impact velocities to bound the seismic moment. The expected seismic sources are modeled in the near field using a 3-D wave propagation code (Petersson et al., 2010) and in the far field using a 1-D wave propagation code (Friederich et al., 1995), for a martian seismic model. Thus we calculate the amplitudes of seismic phases at varying distances, which can be used to evaluate the detectability

Interplay between binding affinity and kinetics in protein-protein interactions.

PubMed

Cao, Huaiqing; Huang, Yongqi; Liu, Zhirong

2016-07-01

To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Database for propagation models

NASA Astrophysics Data System (ADS)

Kantak, Anil V.

1991-07-01

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.

Atomically precise organomimetic cluster nanomolecules assembled via perfluoroaryl-thiol SNAr chemistry

NASA Astrophysics Data System (ADS)

Qian, Elaine A.; Wixtrom, Alex I.; Axtell, Jonathan C.; Saebi, Azin; Jung, Dahee; Rehak, Pavel; Han, Yanxiao; Moully, Elamar Hakim; Mosallaei, Daniel; Chow, Sylvia; Messina, Marco S.; Wang, Jing Yang; Royappa, A. Timothy; Rheingold, Arnold L.; Maynard, Heather D.; Král, Petr; Spokoyny, Alexander M.

2017-04-01

The majority of biomolecules are intrinsically atomically precise, an important characteristic that enables rational engineering of their recognition and binding properties. However, imparting a similar precision to hybrid nanoparticles has been challenging because of the inherent limitations of existing chemical methods and building blocks. Here we report a new approach to form atomically precise and highly tunable hybrid nanomolecules with well-defined three-dimensionality. Perfunctionalization of atomically precise clusters with pentafluoroaryl-terminated linkers produces size-tunable rigid cluster nanomolecules. These species are amenable to facile modification with a variety of thiol-containing molecules and macromolecules. Assembly proceeds at room temperature within hours under mild conditions, and the resulting nanomolecules exhibit high stabilities because of their full covalency. We further demonstrate how these nanomolecules grafted with saccharides can exhibit dramatically improved binding affinity towards a protein. Ultimately, the developed strategy allows the rapid generation of precise molecular assemblies to investigate multivalent interactions.

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.

Binding of phosphoinositide-specific phospholipase C-zeta (PLC-zeta) to phospholipid membranes: potential role of an unstructured cluster of basic residues.

PubMed

Nomikos, Michail; Mulgrew-Nesbitt, Anna; Pallavi, Payal; Mihalyne, Gyongyi; Zaitseva, Irina; Swann, Karl; Lai, F Anthony; Murray, Diana; McLaughlin, Stuart

2007-06-01

Phospholipase C-zeta (PLC-zeta) is a sperm-specific enzyme that initiates the Ca2+ oscillations in mammalian eggs that activate embryo development. It shares considerable sequence homology with PLC-delta1, but lacks the PH domain that anchors PLC-delta1 to phosphatidylinositol 4,5-bisphosphate, PIP2. Thus it is unclear how PLC-zeta interacts with membranes. The linker region between the X and Y catalytic domains of PLC-zeta, however, contains a cluster of basic residues not present in PLC-delta1. Application of electrostatic theory to a homology model of PLC-zeta suggests this basic cluster could interact with acidic lipids. We measured the binding of catalytically competent mouse PLC-zeta to phospholipid vesicles: for 2:1 phosphatidylcholine/phosphatidylserine (PC/PS) vesicles, the molar partition coefficient, K, is too weak to be of physiological significance. Incorporating 1% PIP2 into the 2:1 PC/PS vesicles increases K about 10-fold, to 5x10(3) M-1, a biologically relevant value. Expressed fragments corresponding to the PLC-zeta X-Y linker region also bind with higher affinity to polyvalent than monovalent phosphoinositides on nitrocellulose filters. A peptide corresponding to the basic cluster (charge=+7) within the linker region, PLC-zeta-(374-385), binds to PC/PS vesicles with higher affinity than PLC-zeta, but its binding is less sensitive to incorporating PIP2. The acidic residues flanking this basic cluster in PLC-zeta may account for both these phenomena. FRET experiments suggest the basic cluster could not only anchor the protein to the membrane, but also enhance the local concentration of PIP2 adjacent to the catalytic domain.

Binding affinities of anti-acetylcholine receptor autoantibodies in myasthenia gravis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bray, J.J.; Drachman, D.B.

1982-01-01

Antibodies directed against acetylcholine (ACh) receptors are present in the sera of nearly 90% of patients with myasthenia gravis (MG), and are involved in the pathogenesis of this autoimmune disease. However, the antibody titers measured by the standard radioimmunoassay correspond poorly with the clinical severity of the disease. To determine whether this disparity could be accounted for by differences in the binding affinities of anti-ACh receptor antibodies in different patients, we have measured the binding affinities of these autoantibodies in 15 sera from MG patients. The affinity constants (K/sub o/), as determined by Scatchard analysis, were all in the rangemore » of 10/sup 10/ M/sup -1/, comparable to the highest values reported in immunized animals. The affinity constants were truly representative of the population of autoantibodies detected by the radioimmunoassay, as shown by the remarkable linearity of the Scatchard plots (r/sup 2/>0.90) and the close correlation between the antibody titers determined by extrapolation of the Scatchard plots and by saturation analysis (r = 0.99; p < 0.001). There was only a 6-fold variation in affinity constants measured in this series of patients despite widely differing antibody titers and severity of the disease. Factors other than the titer and affinity of anti-ACh receptor antibodies may correlate better with the clinical manifestations of MG.« less

Regulatory mechanisms of hemoglobin oxygen affinity in acidosis and alkalosis

PubMed Central

Bellingham, A. J.; Detter, J. C.; Lenfant, C.

1971-01-01

The recent reports of the effect of 2,3-diphosphoglycerate (2,3-DPG) on hemoglobin affinity for oxygen suggested that this substance may play a role in man's adaptation to acidosis and alkalosis. A study of the effect of induced acidosis and alkalosis on the oxyhemoglobin dissociation curve of normal man was therefore carried out, and the mechanisms involved in the physiological regulation of hemoglobin oxygen affinity examined. In acute changes of plasma pH there was no alteration in red cell 2,3-DPG content. However, there were changes in hemoglobin oxygen affinity and these correlated with changes in mean corpuscular hemoglobin concentration (MCHC). With maintained acidosis and alkalosis, red cell 2,3-DPG content was altered and correlated with the changes in hemoglobin oxygen affinity. Both of these mechanisms shift the hemoglobin oxygen dissociation curve opposite to the direct pH (Bohr) effect, and providing the rate of pH change is neither too rapid nor too large, they counteract the direct pH effect and the in vivo hemoglobin oxygen affinity remains unchanged. It is also shown that approximately 35% of the change in hemoglobin oxygen affinity resulting from an alteration in red cell 2,3-DPG, is explained by effect of 2,3-DPG on the red cell pH. PMID:5545127

Long-period seismicity reveals magma pathways above a laterally propagating dyke during the 2014-15 Bárðarbunga rifting event, Iceland

NASA Astrophysics Data System (ADS)

Woods, Jennifer; Donaldson, Clare; White, Robert S.; Caudron, Corentin; Brandsdóttir, Bryndís; Hudson, Thomas S.; Ágústsdóttir, Thorbjörg

2018-05-01

The 2014-15 Bárðarbunga-Holuhraun rifting event comprised the best-monitored dyke intrusion to date and the largest eruption in Iceland in 230 years. A huge variety of seismicity was produced, including over 30,000 volcano-tectonic earthquakes (VTs) associated with the dyke propagation at ∼6 km depth below sea level, and large-magnitude earthquakes accompanying the collapse of Bárðarbunga caldera. We here study the long-period seismicity associated with the rifting event. We systematically detect and locate both long-period events (LPs) and tremor during the dyke propagation phase and the first week of the eruption. We identify clusters of highly similar, repetitive LPs, which have a peak frequency of ∼1 Hz and clear P and S phases followed by a long-duration coda. The source mechanisms are remarkably consistent between clusters and also fundamentally different to those of the VTs. We accurately locate LP clusters near each of three ice cauldrons (depressions formed by basal melting) that were observed on the surface of Dyngjujökull glacier above the path of the dyke. Most events are in the vicinity of the northernmost cauldron, at shallower depth than the VTs associated with lateral dyke propagation. At the two northerly cauldrons, periods of shallow seismic tremor following the clusters of LPs are also observed. Given that the LPs occur at ∼4 km depth and in swarms during times of dyke-stalling, we infer that they result from excitation of magmatic fluid-filled cavities and indicate magma ascent. We suggest that the tremor is the climax of the vertical melt movement, arising from either rapid, repeated excitation of the same LP cavities, or sub-glacial eruption processes. This long-period seismicity therefore represents magma pathways between the depth of the dyke-VT earthquakes and the surface. Notably, we do not detect tremor associated with each cauldron, despite melt reaching the base of the overlying ice cap, a concern for hazard monitoring.

An improved affine projection algorithm for active noise cancellation

NASA Astrophysics Data System (ADS)

Zhang, Congyan; Wang, Mingjiang; Han, Yufei; Sun, Yunzhuo

2017-08-01

Affine projection algorithm is a signal reuse algorithm, and it has a good convergence rate compared to other traditional adaptive filtering algorithm. There are two factors that affect the performance of the algorithm, which are step factor and the projection length. In the paper, we propose a new variable step size affine projection algorithm (VSS-APA). It dynamically changes the step size according to certain rules, so that it can get smaller steady-state error and faster convergence speed. Simulation results can prove that its performance is superior to the traditional affine projection algorithm and in the active noise control (ANC) applications, the new algorithm can get very good results.

Insights into geometries, stabilities, electronic structures, reactivity descriptors, and magnetic properties of bimetallic Nim Cun-m (m = 1, 2; n = 3-13) clusters: Comparison with pure copper clusters.

PubMed

Singh, Raman K; Iwasa, Takeshi; Taketsugu, Tetsuya

2018-05-25

A long-range corrected density functional theory (LC-DFT) was applied to study the geometric structures, relative stabilities, electronic structures, reactivity descriptors and magnetic properties of the bimetallic NiCu n -1 and Ni 2 Cu n -2 (n = 3-13) clusters, obtained by doping one or two Ni atoms to the lowest energy structures of Cu n , followed by geometry optimizations. The optimized geometries revealed that the lowest energy structures of the NiCu n -1 and Ni 2 Cu n -2 clusters favor the Ni atom(s) situated at the most highly coordinated position of the host copper clusters. The averaged binding energy, the fragmentation energies and the second-order energy differences signified that the Ni doped clusters can continue to gain an energy during the growth process. The electronic structures revealed that the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies of the LC-DFT are reliable and can be used to predict the vertical ionization potential and the vertical electron affinity of the systems. The reactivity descriptors such as the chemical potential, chemical hardness and electrophilic power, and the reactivity principle such as the minimum polarizability principle are operative for characterizing and rationalizing the electronic structures of these clusters. Moreover, doping of Ni atoms into the copper clusters carry most of the total spin magnetic moment. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes.

PubMed

Srinivasulu, Yerukala Sathipati; Wang, Jyun-Rong; Hsu, Kai-Ti; Tsai, Ming-Ju; Charoenkwan, Phasit; Huang, Wen-Lin; Huang, Hui-Ling; Ho, Shinn-Ying

2015-01-01

Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been developed for predicting the binding affinity of protein-protein complexes based on structure and functional information. This work aims to predict the binding affinity of heterodimeric protein complexes from sequences only. This work proposes a support vector machine (SVM) based binding affinity classifier, called SVM-BAC, to classify heterodimeric protein complexes based on the prediction of their binding affinity. SVM-BAC identified 14 of 580 sequence descriptors (physicochemical, energetic and conformational properties of the 20 amino acids) to classify 216 heterodimeric protein complexes into low and high binding affinity. SVM-BAC yielded the training accuracy, sensitivity, specificity, AUC and test accuracy of 85.80%, 0.89, 0.83, 0.86 and 83.33%, respectively, better than existing machine learning algorithms. The 14 features and support vector regression were further used to estimate the binding affinities (Pkd) of 200 heterodimeric protein complexes. Prediction performance of a Jackknife test was the correlation coefficient of 0.34 and mean absolute error of 1.4. We further analyze three informative physicochemical properties according to their contribution to prediction performance. Results reveal that the following properties are effective in predicting the binding affinity of heterodimeric protein complexes: apparent partition energy based on buried molar fractions, relations between chemical structure and biological activity in principal component analysis IV, and normalized frequency of beta turn. The proposed sequence-based prediction method SVM-BAC uses an optimal feature selection method to identify 14 informative features to classify and predict binding affinity of heterodimeric protein complexes. The characterization

On propagation of axisymmetric waves in pressurized functionally graded elastomeric hollow cylinders

NASA Astrophysics Data System (ADS)

Wu, Bin; Su, Yipin; Liu, Dongying; Chen, Weiqiu; Zhang, Chuanzeng

2018-05-01

Soft materials can be designed with a functionally graded (FG) property for specific applications. Such material inhomogeneity can also be found in many soft biological tissues whose functionality is only partly understood to date. In this paper, we analyze the axisymmetric guided wave propagation in a pressurized FG elastomeric hollow cylinder. The cylinder is subjected to a combined action of axial pre-stretch and pressure difference applied to the inner and outer cylindrical surfaces. We consider both torsional waves and longitudinal waves propagating in the FG cylinder made of incompressible isotropic elastomer, which is characterized by the Mooney-Rivlin strain energy function but with the material parameters varying with the radial coordinate in an affine way. The pressure difference generates an inhomogeneous deformation field in the FG cylinder, which dramatically complicates the superimposed wave problem described by the small-on-large theory. A particularly efficient approach is hence employed which combines the state-space formalism for the incremental wave motion with the approximate laminate or multi-layer technique. Dispersion relations for the two types of axisymmetric guided waves are then derived analytically. The accuracy and convergence of the proposed approach is validated numerically. The effects of the pressure difference, material gradient, and axial pre-stretch on both the torsional and the longitudinal wave propagation characteristics are discussed in detail through numerical examples. It is found that the frequency of axisymmetric waves depends nonlinearly on the pressure difference and the material gradient, and an increase in the material gradient enhances the capability of the pressure difference to adjust the wave behavior in the FG cylinder. This work provides a theoretical guidance for characterizing FG soft materials by in-situ ultrasonic nondestructive evaluation and for designing tunable waveguides via material tailoring along

The glycocalyx promotes cooperative binding and clustering of adhesion receptors.

PubMed

Xu, Guang-Kui; Qian, Jin; Hu, Jinglei

2016-05-18

Cell adhesion plays a pivotal role in various biological processes, e.g., immune responses, cancer metastasis, and stem cell differentiation. The adhesion behaviors depend subtly on the binding kinetics of receptors and ligands restricted at the cell-substrate interfaces. Although much effort has been directed toward investigating the kinetics of adhesion molecules, the role of the glycocalyx, anchored on cell surfaces as an exterior layer, is still unclear. In this paper, we propose a theoretical approach to study the collective binding kinetics of a few and a large number of binders in the presence of the glycocalyx, representing the cases of initial and mature adhesions of cells, respectively. The analytical results are validated by finding good agreement with our Monte Carlo simulations. In the force loading case, the on-rate and affinity increase as more bonds form, whereas this cooperative effect is not observed in the displacement loading case. The increased thickness and stiffness of the glycocalyx tend to decrease the affinity for a few bonds, while they have less influence on the affinity for a large number of bonds. Moreover, for a flexible membrane with thermally-excited shape fluctuations, the glycocalyx is exhibited to promote the formation of bond clusters, mainly due to the cooperative binding of binders. This study helps to understand the cooperative kinetics of adhesion receptors under physiologically relevant loading conditions and sheds light on the novel role of the glycocalyx in cell adhesion.

Micron-size hydrogen cluster target for laser-driven proton acceleration

NASA Astrophysics Data System (ADS)

Jinno, S.; Kanasaki, M.; Uno, M.; Matsui, R.; Uesaka, M.; Kishimoto, Y.; Fukuda, Y.

2018-04-01

As a new laser-driven ion acceleration technique, we proposed a way to produce impurity-free, highly reproducible, and robust proton beams exceeding 100 MeV using a Coulomb explosion of micron-size hydrogen clusters. In this study, micron-size hydrogen clusters were generated by expanding the cooled high-pressure hydrogen gas into a vacuum via a conical nozzle connected to a solenoid valve cooled by a mechanical cryostat. The size distributions of the hydrogen clusters were evaluated by measuring the angular distribution of laser light scattered from the clusters. The data were analyzed mathematically based on the Mie scattering theory combined with the Tikhonov regularization method. The maximum size of the hydrogen cluster at 25 K and 6 MPa in the stagnation state was recognized to be 2.15 ± 0.10 μm. The mean cluster size decreased with increasing temperature, and was found to be much larger than that given by Hagena’s formula. This discrepancy suggests that the micron-size hydrogen clusters were formed by the atomization (spallation) of the liquid or supercritical fluid phase of hydrogen. In addition, the density profiles of the gas phase were evaluated for 25 to 80 K at 6 MPa using a Nomarski interferometer. Based on the measurement results and the equation of state for hydrogen, the cluster mass fraction was obtained. 3D particles-in-cell (PIC) simulations concerning the interaction processes of micron-size hydrogen clusters with high power laser pulses predicted the generation of protons exceeding 100 MeV and accelerating in a laser propagation direction via an anisotropic Coulomb explosion mechanism, thus demonstrating a future candidate in laser-driven proton sources for upcoming multi-petawatt lasers.

Second cluster integral from the spectrum of an infinite XXZ spin chain

NASA Astrophysics Data System (ADS)

Bibikov, P. N.

2015-03-01

First and second terms of the low-temperature cluster expansion for the free energy density of a magnetically polarized XXZ spin chain is obtained within the propagator approach suggested by E.W. Montroll and J.C. Ward. All the calculations employ only one- and two-magnon infinite-chain spectrums. In the XXX-point the result reproduces the well known S. Katsura's formula obtained 50 years ago by finite-chain calculations.

2DRMP: A suite of two-dimensional R-matrix propagation codes

NASA Astrophysics Data System (ADS)

Scott, N. S.; Scott, M. P.; Burke, P. G.; Stitt, T.; Faro-Maza, V.; Denis, C.; Maniopoulou, A.

2009-12-01

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionise the target. In this paper we describe 2DRMP, a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies. Program summaryProgram title: 2DRMP Catalogue identifier: AEEA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 196 717 No. of bytes in distributed program, including test data, etc.: 3 819 727 Distribution format: tar.gz Programming language: Fortran 95, MPI Computer: Tested on CRAY XT4 [1]; IBM eServer 575 [2]; Itanium II cluster [3] Operating system: Tested on UNICOS/lc [1]; IBM AIX [2]; Red Hat Linux Enterprise AS [3] Has the code been vectorised or parallelised?: Yes. 16 cores were used for small test run Classification: 2.4 External routines: BLAS, LAPACK, PBLAS, ScaLAPACK Subprograms used: ADAZ_v1_1 Nature of problem: 2DRMP is a suite of programs aimed at creating virtual experiments on high performance architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies. Solution method: Two-dimensional R-matrix propagation theory. The (r,r) space of the internal region is subdivided into a number of subregions. Local R-matrices are constructed

Superlinear variant of the dual affine scaling algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luz, C.; Cardosa, D.

1994-12-31

The affine scaling methods introduced by Dikin are generally considered the most efficient interior point algorithms from a computational point of view. However, it is actually an open question to know whether there is a polynomial affine scaling algorithm. This fact has motivated many investigations efforts and led to several convergence results. This is the case of the recently obtained results by Tsuchiya, Tseng and Luo and Tsuchiya and Muramatsu which, unlike the pioneering Dikin`s convergence result, do not require any non degeneracy assumption. This paper presents a new variant of the dual affine scaling algorithm for Linear Programming that,more » in a finite number of iterations, determines a primal-dual pair of optimal solutions. It is also shown the superlinear convergence of that variant without requiring any non degeneracy assumption.« less

Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis

PubMed Central

Tiller, Kathryn E.; Chowdhury, Ratul; Li, Tong; Ludwig, Seth D.; Sen, Sabyasachi; Maranas, Costas D.; Tessier, Peter M.

2017-01-01

The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs) that are permissive to mutagenesis while maintaining antigen binding. Next, we mutagenize the most permissive CDR positions using degenerate codons to encode wild-type residues and a small number of the most frequently occurring residues at each CDR position based on natural antibody diversity. This mutagenesis approach results in antibody libraries with variants that have a wide range of numbers of CDR mutations, including antibody domains with single mutations and others with tens of mutations. Finally, we sort the modest size libraries (~10 million variants) displayed on the surface of yeast to identify CDR mutations with the greatest increases in affinity. Importantly, we find that single-domain (VHH) antibodies specific for the α-synuclein protein (whose aggregation is associated with Parkinson’s disease) with the greatest gains in affinity (>5-fold) have several (four to six) CDR mutations. This finding highlights the importance of sampling combinations of CDR mutations during the first step of affinity maturation to maximize the efficiency of the process. Interestingly, we find that some natural diversity mutations simultaneously enhance all three key antibody properties (affinity, specificity, and stability) while other mutations enhance some of these properties (e.g., increased specificity) and display trade-offs in others (e.g., reduced affinity and/or stability). Computational modeling reveals that improvements in affinity are generally

2D Affine and Projective Shape Analysis.

PubMed

Bryner, Darshan; Klassen, Eric; Huiling Le; Srivastava, Anuj

2014-05-01

Current techniques for shape analysis tend to seek invariance to similarity transformations (rotation, translation, and scale), but certain imaging situations require invariance to larger groups, such as affine or projective groups. Here we present a general Riemannian framework for shape analysis of planar objects where metrics and related quantities are invariant to affine and projective groups. Highlighting two possibilities for representing object boundaries-ordered points (or landmarks) and parameterized curves-we study different combinations of these representations (points and curves) and transformations (affine and projective). Specifically, we provide solutions to three out of four situations and develop algorithms for computing geodesics and intrinsic sample statistics, leading up to Gaussian-type statistical models, and classifying test shapes using such models learned from training data. In the case of parameterized curves, we also achieve the desired goal of invariance to re-parameterizations. The geodesics are constructed by particularizing the path-straightening algorithm to geometries of current manifolds and are used, in turn, to compute shape statistics and Gaussian-type shape models. We demonstrate these ideas using a number of examples from shape and activity recognition.

Local uncontrollability for affine control systems with jumps

NASA Astrophysics Data System (ADS)

Treanţă, Savin

2017-09-01

This paper investigates affine control systems with jumps for which the ideal If(g1, …, gm) generated by the drift vector field f in the Lie algebra L(f, g1, …, gm) can be imbedded as a kernel of a linear first-order partial differential equation. It will lead us to uncontrollable affine control systems with jumps for which the corresponding reachable sets are included in explicitly described differentiable manifolds.

Mass spectrometric identification of intermediates in the O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion in FNR

PubMed Central

Crack, Jason C.; Thomson, Andrew J.

2017-01-01

The iron-sulfur cluster containing protein Fumarate and Nitrate Reduction (FNR) is the master regulator for the switch between anaerobic and aerobic respiration in Escherichia coli and many other bacteria. The [4Fe-4S] cluster functions as the sensory module, undergoing reaction with O2 that leads to conversion to a [2Fe-2S] form with loss of high-affinity DNA binding. Here, we report studies of the FNR cluster conversion reaction using time-resolved electrospray ionization mass spectrometry. The data provide insight into the reaction, permitting the detection of cluster conversion intermediates and products, including a [3Fe-3S] cluster and persulfide-coordinated [2Fe-2S] clusters [[2Fe-2S](S)n, where n = 1 or 2]. Analysis of kinetic data revealed a branched mechanism in which cluster sulfide oxidation occurs in parallel with cluster conversion and not as a subsequent, secondary reaction to generate [2Fe-2S](S)n species. This methodology shows great potential for broad application to studies of protein cofactor–small molecule interactions. PMID:28373574

A database for propagation models

NASA Technical Reports Server (NTRS)

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

1993-01-01

The NASA Propagation Program supports academic research that models various propagation phenomena in the space research frequency bands. NASA supports such research via school and institutions prominent in the field. The products of such efforts are particularly useful for researchers in the field of propagation phenomena and telecommunications systems engineers. The systems engineer usually needs a few propagation parameter values for a system design. Published literature on the subject, such as the Cunsultative Committee for International Radio (CCIR) publications, may help somewhat, but often times, the parameter values given in such publications use a particular set of conditions which may not quite include the requirements of the system design. The systems engineer must resort to programming the propagation phenomena model of interest and to obtain the parameter values to be used in the project. Furthermore, the researcher in the propagation field must then program the propagation models either to substantiate the model or to generate a new model. The researcher or the systems engineer must either be a skillful computer programmer or hire a programmer, which of course increases the cost of the effort. An increase in cost due to the inevitable programming effort may seem particularly inappropriate if the data generated by the experiment is to be used to substantiate the already well-established models, or a slight variation thereof. To help researchers and the systems engineers, it was recommended by the participants of NASA Propagation Experimenters (NAPEX) 15 held in London, Ontario, Canada on 28-29 June 1991, that propagation software should be constructed which will contain models and prediction methods of most propagation phenomenon. Moreover, the software should be flexible enough for the user to make slight changes to the models without expending a substantial effort in programming.

Robust fiber clustering of cerebral fiber bundles in white matter

NASA Astrophysics Data System (ADS)

Yao, Xufeng; Wang, Yongxiong; Zhuang, Songlin

2014-11-01

Diffusion tensor imaging fiber tracking (DTI-FT) has been widely accepted in the diagnosis and treatment of brain diseases. During the rendering pipeline of specific fiber tracts, the image noise and low resolution of DTI would lead to false propagations. In this paper, we propose a robust fiber clustering (FC) approach to diminish false fibers from one fiber tract. Our algorithm consists of three steps. Firstly, the optimized fiber assignment continuous tracking (FACT) is implemented to reconstruct one fiber tract; and then each curved fiber in the fiber tract is mapped to a point by kernel principal component analysis (KPCA); finally, the point clouds of fiber tract are clustered by hierarchical clustering which could distinguish false fibers from true fibers in one tract. In our experiment, the corticospinal tract (CST) in one case of human data in vivo was used to validate our method. Our method showed reliable capability in decreasing the false fibers in one tract. In conclusion, our method could effectively optimize the visualization of fiber bundles and would help a lot in the field of fiber evaluation.

Data-driven process decomposition and robust online distributed modelling for large-scale processes

NASA Astrophysics Data System (ADS)

Shu, Zhang; Lijuan, Li; Lijuan, Yao; Shipin, Yang; Tao, Zou

2018-02-01

With the increasing attention of networked control, system decomposition and distributed models show significant importance in the implementation of model-based control strategy. In this paper, a data-driven system decomposition and online distributed subsystem modelling algorithm was proposed for large-scale chemical processes. The key controlled variables are first partitioned by affinity propagation clustering algorithm into several clusters. Each cluster can be regarded as a subsystem. Then the inputs of each subsystem are selected by offline canonical correlation analysis between all process variables and its controlled variables. Process decomposition is then realised after the screening of input and output variables. When the system decomposition is finished, the online subsystem modelling can be carried out by recursively block-wise renewing the samples. The proposed algorithm was applied in the Tennessee Eastman process and the validity was verified.

Analytical Energy Gradients for Excited-State Coupled-Cluster Methods

NASA Astrophysics Data System (ADS)

Wladyslawski, Mark; Nooijen, Marcel

equations for the wavefunction amplitudes, the Lagrange multipliers, and the analytical gradient via the perturbation-independent generalized Hellmann-Feynman effective density matrix. This systematic automated derivation procedure is applied to obtain the detailed gradient equations for the excitation energy (EE-), double ionization potential (DIP-), and double electron affinity (DEA-) similarity transformed equation-of-motion coupled-cluster singles-and-doubles (STEOM-CCSD) methods. In addition, the derivatives of the closed-shell-reference excitation energy (EE-), ionization potential (IP-), and electron affinity (EA-) equation-of-motion coupled-cluster singles-and-doubles (EOM-CCSD) methods are derived. Furthermore, the perturbative EOM-PT and STEOM-PT gradients are obtained. The algebraic derivative expressions for these dozen methods are all derived here uniformly through the automated Lagrange multiplier process and are expressed compactly in a chain-rule/intermediate-density formulation, which facilitates a unified modular implementation of analytic energy gradients for CCSD/PT-based electronic methods. The working equations for these analytical gradients are presented in full detail, and their factorization and implementation into an efficient computer code are discussed.

Growth Behavior and Electronic Structure of Noble Metal-Doped Germanium Clusters.

PubMed

Mahtout, Sofiane; Siouani, Chaouki; Rabilloud, Franck

2018-01-18

Structures, energetics, and electronic properties of noble metal-doped germanium (MGe n with M = Cu, Ag, Au; n = 1-19) clusters are systematically investigated by using the density functional theory (DFT) approach. The endohedral structures in which the metal atom is encapsulated inside of a germanium cage appear at n = 10 when the dopant is Cu and n = 12 for M = Ag and Au. While Cu doping enhances the stability of the corresponding germanium frame, the binding energies of AgGe n and AuGe n are always lower than those of pure germanium clusters. Our results highlight the great stability of the CuGe 10 cluster in a D 4d structure and, to a lesser extent, that of AgGe 15 and AuGe 15 , which exhibits a hollow cage-like geometry. The sphere-type geometries obtained for n = 10-15 present a peculiar electronic structure in which the valence electrons of the noble metal and Ge atoms are delocalized and exhibit a shell structure associated with the quasi-spherical geometry. It is found that the coinage metal is able to give both s- and d-type electrons to be reorganized together with the valence electrons of Ge atoms through a pooling of electrons. The cluster size dependence of the stability, the frontier orbital energy gap, the vertical ionization potentials, and electron affinities are given.

Quantifying domain-ligand affinities and specificities by high-throughput holdup assay

PubMed Central

Vincentelli, Renaud; Luck, Katja; Poirson, Juline; Polanowska, Jolanta; Abdat, Julie; Blémont, Marilyne; Turchetto, Jeremy; Iv, François; Ricquier, Kevin; Straub, Marie-Laure; Forster, Anne; Cassonnet, Patricia; Borg, Jean-Paul; Jacob, Yves; Masson, Murielle; Nominé, Yves; Reboul, Jérôme; Wolff, Nicolas; Charbonnier, Sebastian; Travé, Gilles

2015-01-01

Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this aim, we developed the high-throughput holdup assay, a chromatographic approach that can measure up to a thousand domain-motif equilibrium binding affinities per day. Extracts of overexpressed domains are incubated with peptide-coated resins and subjected to filtration. Binding affinities are deduced from microfluidic capillary electrophoresis of flow-throughs. After benchmarking the approach on 210 PDZ-peptide pairs with known affinities, we determined the affinities of two viral PDZ-binding motifs derived from Human Papillomavirus E6 oncoproteins for 209 PDZ domains covering 79% of the human PDZome. We obtained exquisite sequence-dependent binding profiles, describing quantitatively the PDZome recognition specificity of each motif. This approach, applicable to many categories of domain-ligand interactions, has a wide potential for quantifying the specificities of interactomes. PMID:26053890

Affine theory of gravitation

NASA Astrophysics Data System (ADS)

Popławski, Nikodem

2014-01-01

We propose a theory of gravitation, in which the affine connection is the only dynamical variable describing the gravitational field. We construct a simple dynamical Lagrangian density that is entirely composed from the connection, via its curvature and torsion, and is a polynomial function of its derivatives. It is given by the contraction of the Ricci tensor with a tensor which is inverse to the symmetric, contracted square of the torsion tensor, . We vary the total action for the gravitational field and matter with respect to the affine connection, assuming that the matter fields couple to the connection only through . We derive the resulting field equations and show that they are identical with the Einstein equations of general relativity with a nonzero cosmological constant if the tensor is regarded as proportional to the metric tensor. The cosmological constant is simply a constant of proportionality between the two tensors, which together with and provides a natural system of units in gravitational physics. This theory therefore provides a physical construction of the metric as a polynomial function of the connection, and explains dark energy as an intrinsic property of spacetime.

FAST TRACK COMMUNICATION: Affine constellations without mutually unbiased counterparts

NASA Astrophysics Data System (ADS)

Weigert, Stefan; Durt, Thomas

2010-10-01

It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations. The observed discrepancies make a deeper relation between the two existence problems unlikely.

Star cluster formation in a turbulent molecular cloud self-regulated by photoionization feedback

NASA Astrophysics Data System (ADS)

Gavagnin, Elena; Bleuler, Andreas; Rosdahl, Joakim; Teyssier, Romain

2017-12-01

Most stars in the Galaxy are believed to be formed within star clusters from collapsing molecular clouds. However, the complete process of star formation, from the parent cloud to a gas-free star cluster, is still poorly understood. We perform radiation-hydrodynamical simulations of the collapse of a turbulent molecular cloud using the RAMSES-RT code. Stars are modelled using sink particles, from which we self-consistently follow the propagation of the ionizing radiation. We study how different feedback models affect the gas expulsion from the cloud and how they shape the final properties of the emerging star cluster. We find that the star formation efficiency is lower for stronger feedback models. Feedback also changes the high-mass end of the stellar mass function. Stronger feedback also allows the establishment of a lower density star cluster, which can maintain a virial or sub-virial state. In the absence of feedback, the star formation efficiency is very high, as well as the final stellar density. As a result, high-energy close encounters make the cluster evaporate quickly. Other indicators, such as mass segregation, statistics of multiple systems and escaping stars confirm this picture. Observations of young star clusters are in best agreement with our strong feedback simulation.

A statistical study of EMIC waves observed by Cluster: 1. Wave properties

NASA Astrophysics Data System (ADS)

Allen, R. C.; Zhang, J.-C.; Kistler, L. M.; Spence, H. E.; Lin, R.-L.; Klecker, B.; Dunlop, M. W.; André, M.; Jordanova, V. K.

2015-07-01

Electromagnetic ion cyclotron (EMIC) waves are an important mechanism for particle energization and losses inside the magnetosphere. In order to better understand the effects of these waves on particle dynamics, detailed information about the occurrence rate, wave power, ellipticity, normal angle, energy propagation angle distributions, and local plasma parameters are required. Previous statistical studies have used in situ observations to investigate the distribution of these parameters in the magnetic local time versus L-shell (MLT-L) frame within a limited magnetic latitude (MLAT) range. In this study, we present a statistical analysis of EMIC wave properties using 10 years (2001-2010) of data from Cluster, totaling 25,431 min of wave activity. Due to the polar orbit of Cluster, we are able to investigate EMIC waves at all MLATs and MLTs. This allows us to further investigate the MLAT dependence of various wave properties inside different MLT sectors and further explore the effects of Shabansky orbits on EMIC wave generation and propagation. The statistical analysis is presented in two papers. This paper focuses on the wave occurrence distribution as well as the distribution of wave properties. The companion paper focuses on local plasma parameters during wave observations as well as wave generation proxies.

Affinity proteomics to study endogenous protein complexes: Pointers, pitfalls, preferences and perspectives

PubMed Central

LaCava, John; Molloy, Kelly R.; Taylor, Martin S.; Domanski, Michal; Chait, Brian T.; Rout, Michael P.

2015-01-01

Dissecting and studying cellular systems requires the ability to specifically isolate distinct proteins along with the co-assembled constituents of their associated complexes. Affinity capture techniques leverage high affinity, high specificity reagents to target and capture proteins of interest along with specifically associated proteins from cell extracts. Affinity capture coupled to mass spectrometry (MS)-based proteomic analyses has enabled the isolation and characterization of a wide range of endogenous protein complexes. Here, we outline effective procedures for the affinity capture of protein complexes, highlighting best practices and common pitfalls. PMID:25757543

Approximate treatment of semicore states in GW calculations with application to Au clusters.

PubMed

Xian, Jiawei; Baroni, Stefano; Umari, P

2014-03-28

We address the treatment of transition metal atoms in GW electronic-structure calculations within the plane-wave pseudo-potential formalism. The contributions of s and p semi-core electrons to the self-energy, which are essential to grant an acceptable accuracy, are dealt with using a recently proposed scheme whereby the exchange components are treated exactly at the G0W0 level, whereas a suitable approximation to the correlation components is devised. This scheme is benchmarked for small gold nano-clusters, resulting in ionization potentials, electron affinities, and density of states in very good agreement with those obtained from calculations where s and p semicore states are treated as valence orbitals, and allowing us to apply this same scheme to clusters of intermediate size, Au20 and Au32, that would be otherwise very difficult to deal with.

Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes

PubMed Central

2015-01-01

Background Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been developed for predicting the binding affinity of protein-protein complexes based on structure and functional information. This work aims to predict the binding affinity of heterodimeric protein complexes from sequences only. Results This work proposes a support vector machine (SVM) based binding affinity classifier, called SVM-BAC, to classify heterodimeric protein complexes based on the prediction of their binding affinity. SVM-BAC identified 14 of 580 sequence descriptors (physicochemical, energetic and conformational properties of the 20 amino acids) to classify 216 heterodimeric protein complexes into low and high binding affinity. SVM-BAC yielded the training accuracy, sensitivity, specificity, AUC and test accuracy of 85.80%, 0.89, 0.83, 0.86 and 83.33%, respectively, better than existing machine learning algorithms. The 14 features and support vector regression were further used to estimate the binding affinities (Pkd) of 200 heterodimeric protein complexes. Prediction performance of a Jackknife test was the correlation coefficient of 0.34 and mean absolute error of 1.4. We further analyze three informative physicochemical properties according to their contribution to prediction performance. Results reveal that the following properties are effective in predicting the binding affinity of heterodimeric protein complexes: apparent partition energy based on buried molar fractions, relations between chemical structure and biological activity in principal component analysis IV, and normalized frequency of beta turn. Conclusions The proposed sequence-based prediction method SVM-BAC uses an optimal feature selection method to identify 14 informative features to classify and predict binding affinity of heterodimeric protein

Synthesis and binding affinity of neuropeptide Y at opiate receptors.

PubMed

Kiddle, James J; McCreery, Heather J; Soles, Sonia

2003-03-24

Neuropeptide Y and several metabolic fragments were synthesized and evaluated for binding affinity at non-selective opiate receptors. Neuropeptide Y and several C-terminal fragments were shown to bind to non-selective opiate receptors with an affinity similar to that of Leu-enkephalin.

Affinity resins as new tools for identifying target proteins of ascorbic acid.

PubMed

Iwaoka, Yuji; Nishino, Kohei; Ishikawa, Takahiro; Ito, Hideyuki; Sawa, Yoshihiro; Tai, Akihiro

2018-02-12

l-Ascorbic acid (AA) has diverse physiological functions, but little is known about the functional mechanisms of AA. In this study, we synthesized two types of affinity resin on which AA is immobilized in a stable form to identify new AA-targeted proteins, which can provide important clues for elucidating unknown functional mechanisms of AA. To our knowledge, an affinity resin on which AA as a ligand is immobilized has not been prepared, because AA is very unstable and rapidly degraded in an aqueous solution. By using the affinity resins, cytochrome c (cyt c) was identified as an AA-targeted protein, and we showed that oxidized cyt c exhibits specific affinity for AA. These results suggest that two kinds of AA-affinity resin can be powerful tools to identify new target proteins of AA.

Thermodynamic Bounds on the Ultra- and Infra-affinity of Hsp70 for Its Substrates

NASA Astrophysics Data System (ADS)

Nguyen, Basile; Hartich, David; Seifert, Udo; Rios, Paolo De Los

2017-07-01

The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting cells against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into organelles. These functions require high affinity for non-specific amino-acid sequences that are ubiquitous in proteins. It has been recently shown that this high affinity, called ultra-affinity, depends on a process driven out of equilibrium by ATP hydrolysis. Here we establish the thermodynamic bounds for ultra-affinity, and further show that the same reaction scheme can in principle be used both to strengthen and to weaken affinities (leading in this case to infra-affinity). We show that cofactors are essential to achieve affinity beyond the equilibrium range. Finally, biological implications are discussed.

Robust feature matching via support-line voting and affine-invariant ratios

NASA Astrophysics Data System (ADS)

Li, Jiayuan; Hu, Qingwu; Ai, Mingyao; Zhong, Ruofei

2017-10-01

Robust image matching is crucial for many applications of remote sensing and photogrammetry, such as image fusion, image registration, and change detection. In this paper, we propose a robust feature matching method based on support-line voting and affine-invariant ratios. We first use popular feature matching algorithms, such as SIFT, to obtain a set of initial matches. A support-line descriptor based on multiple adaptive binning gradient histograms is subsequently applied in the support-line voting stage to filter outliers. In addition, we use affine-invariant ratios computed by a two-line structure to refine the matching results and estimate the local affine transformation. The local affine model is more robust to distortions caused by elevation differences than the global affine transformation, especially for high-resolution remote sensing images and UAV images. Thus, the proposed method is suitable for both rigid and non-rigid image matching problems. Finally, we extract as many high-precision correspondences as possible based on the local affine extension and build a grid-wise affine model for remote sensing image registration. We compare the proposed method with six state-of-the-art algorithms on several data sets and show that our method significantly outperforms the other methods. The proposed method achieves 94.46% average precision on 15 challenging remote sensing image pairs, while the second-best method, RANSAC, only achieves 70.3%. In addition, the number of detected correct matches of the proposed method is approximately four times the number of initial SIFT matches.

Into the theory of the partial-filling affinity capillary electrophoresis and the determination of apparent stability constants of analyte-ligand complexes.

PubMed

Ansorge, Martin; Dubský, Pavel; Ušelová, Kateřina

2018-03-01

The partial-filling affinity capillary electrophoresis (pf-ACE) works with a ligand present in a background electrolyte that forms a weak complex with an analyte. In contrast to a more popular mobility-shift affinity capillary electrophoresis, only a short plug of the ligand is introduced into a capillary in the pf-ACE. Both methods can serve for determining apparent stability constants of the formed complexes but this task is hindered in the pf-ACE by the fact that the analyte spends only a part of its migration time in a contact with the ligand. In 1998, Amini and Westerlund published a linearization strategy that allows for extracting an effective mobility of an analyte in the presence of a neutral ligand out of the pf-ACE data. The main purpose of this paper is to show that the original formula is only approximate. We derive a new formula and demonstrate its applicability by means of computer simulations. We further inspect several strategies of data processing in the pf-ACE regarding a risk of an error propagation. This establishes a good practice of determining apparent stability constants of analyte-ligand complexes by means of the pf-ACE. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct optimization, affine gap costs, and node stability.

PubMed

Aagesen, Lone

2005-09-01

The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Robustness to changes in parameter costs is therefore a desired quality of a data set because the final conclusions will be less dependent on selecting a precise optimal cost set. Here, node stability is explored in relationship to separate versus combined analysis in three different data sets, all including several data partitions. Robustness to changes in cost sets is measured as number of successive changes that can be made in a given cost set before a specific clade is lost. The changes are in all cases base change cost, gap penalties, and adding/removing/changing affine gap costs. When combining data partitions, the number of clades that appear in the entire parameter space is not remarkably increased, in some cases this number even decreased. However, when combining data partitions the trees from cost sets including affine gap costs were always more similar than the trees were from cost sets without affine gap costs. This was not the case when the data partitions were analyzed independently. When data sets were combined approximately 80% of the clades found under cost sets including affine gap costs resisted at least one change to the cost set.

The signatures of the parental cluster on field planetary systems

NASA Astrophysics Data System (ADS)

Cai, Maxwell Xu; Portegies Zwart, Simon; van Elteren, Arjen

2018-03-01

Due to the high stellar densities in young clusters, planetary systems formed in these environments are likely to have experienced perturbations from encounters with other stars. We carry out direct N-body simulations of multiplanet systems in star clusters to study the combined effects of stellar encounters and internal planetary dynamics. These planetary systems eventually become part of the Galactic field population as the parental cluster dissolves, which is where most presently known exoplanets are observed. We show that perturbations induced by stellar encounters lead to distinct signatures in the field planetary systems, most prominently, the excited orbital inclinations and eccentricities. Planetary systems that form within the cluster's half-mass radius are more prone to such perturbations. The orbital elements are most strongly excited in the outermost orbit, but the effect propagates to the entire planetary system through secular evolution. Planet ejections may occur long after a stellar encounter. The surviving planets in these reduced systems tend to have, on average, higher inclinations and larger eccentricities compared to systems that were perturbed less strongly. As soon as the parental star cluster dissolves, external perturbations stop affecting the escaped planetary systems, and further evolution proceeds on a relaxation time-scale. The outer regions of these ejected planetary systems tend to relax so slowly that their state carries the memory of their last strong encounter in the star cluster. Regardless of the stellar density, we observe a robust anticorrelation between multiplicity and mean inclination/eccentricity. We speculate that the `Kepler dichotomy' observed in field planetary systems is a natural consequence of their early evolution in the parental cluster.

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

Proceedings of the Twentieth NASA Propagation Experimenters Meeting (NAPEX XX) and the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop

NASA Technical Reports Server (NTRS)

Golshan, Nassar (Editor)

1996-01-01

The NASA Propagation Experimenters (NAPEX) Meeting and associated Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop convene yearly to discuss studies supported by the NASA Propagation Program. Representatives from the satellite communications (satcom)industry, academia, and government with an interest in space-ground radio wave propagation have peer discussion of work in progress, disseminate propagation results, and interact with the satcom industry. NAPEX XX, in Fairbanks, Alaska, June 4-5, 1996, had three sessions: (1) "ACTS Propagation Study: Background, Objectives, and Outcomes," covered results from thirteen station-years of Ka-band experiments; (2) "Propagation Studies for Mobile and Personal Satellite Applications," provided the latest developments in measurement, modeling, and dissemination of propagation phenomena of interest to the mobile, personal, and aeronautical satcom industry; and (3)"Propagation Research Topics," covered a range of topics including space/ground optical propagation experiments, propagation databases, the NASA Propagation Web Site, and revision plans for the NASA propagation effects handbooks. The ACTS Miniworkshop, June 6, 1996, covered ACTS status, engineering support for ACTS propagation terminals, and the ACTS Propagation Data Center. A plenary session made specific recommendations for the future direction of the program.

Revision of the experimental electron affinity of BO

NASA Astrophysics Data System (ADS)

Rienstra, Jonathan C.; Schaefer, Henry F., III

1997-05-01

The experimental electron affinity of BO has proven questionable. We obtained the electron affinity of BO using the large aug-cc-pVQZ basis with SCF, CISD, CISD+Q, CCSD, and CCSD(T) methods and predict a value of 2.57 eV, or 0.55 eV smaller than the latest experimental value. The 2∑+ to 2Π excitation energy of BO has also been obtained with the CCSD(T) method and found to be 2.82 eV.

Multi-task learning with group information for human action recognition

NASA Astrophysics Data System (ADS)

Qian, Li; Wu, Song; Pu, Nan; Xu, Shulin; Xiao, Guoqiang

2018-04-01

Human action recognition is an important and challenging task in computer vision research, due to the variations in human motion performance, interpersonal differences and recording settings. In this paper, we propose a novel multi-task learning framework with group information (MTL-GI) for accurate and efficient human action recognition. Specifically, we firstly obtain group information through calculating the mutual information according to the latent relationship between Gaussian components and action categories, and clustering similar action categories into the same group by affinity propagation clustering. Additionally, in order to explore the relationships of related tasks, we incorporate group information into multi-task learning. Experimental results evaluated on two popular benchmarks (UCF50 and HMDB51 datasets) demonstrate the superiority of our proposed MTL-GI framework.

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.

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.

Vehicular sources in acoustic propagation experiments

NASA Astrophysics Data System (ADS)

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

1990-12-01

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.

PROPAGATOR: a synchronous stochastic wildfire propagation model with distributed computation engine

NASA Astrophysics Data System (ADS)

D´Andrea, M.; Fiorucci, P.; Biondi, G.; Negro, D.

2012-04-01

PROPAGATOR is a stochastic model of forest fire spread, useful as a rapid method for fire risk assessment. The model is based on a 2D stochastic cellular automaton. The domain of simulation is discretized using a square regular grid with cell size of 20x20 meters. The model uses high-resolution information such as elevation and type of vegetation on the ground. Input parameters are wind direction, speed and the ignition point of fire. The simulation of fire propagation is done via a stochastic mechanism of propagation between a burning cell and a non-burning cell belonging to its neighbourhood, i.e. the 8 adjacent cells in the rectangular grid. The fire spreads from one cell to its neighbours with a certain base probability, defined using vegetation types of two adjacent cells, and modified by taking into account the slope between them, wind direction and speed. The simulation is synchronous, and takes into account the time needed by the burning fire to cross each cell. Vegetation cover, slope, wind speed and direction affect the fire-propagation speed from cell to cell. The model simulates several mutually independent realizations of the same stochastic fire propagation process. Each of them provides a map of the area burned at each simulation time step. Propagator simulates self-extinction of the fire, and the propagation process continues until at least one cell of the domain is burning in each realization. The output of the model is a series of maps representing the probability of each cell of the domain to be affected by the fire at each time-step: these probabilities are obtained by evaluating the relative frequency of ignition of each cell with respect to the complete set of simulations. Propagator is available as a module in the OWIS (Opera Web Interfaces) system. The model simulation runs on a dedicated server and it is remote controlled from the client program, NAZCA. Ignition points of the simulation can be selected directly in a high-resolution, three

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.

Affinity interactions between natural pigments and human whole saliva.

PubMed

Yao, Jiang-Wu; Lin, Feng; Tao, Tao; Lin, Chang-Jian

2011-03-01

The aim of the present study was to assess the null hypothesis that there are no differences of affinity between pigments and human whole saliva (WS), and the affinity is not influenced by the functional groups of pigments, temperatures, pH values, and salt concentrations. The affinity constants of interactions between WS and theaflavin (TF)/curcumin (Cur)/cyanidin (Cy) were determined by surface plasmon resonance (SPR) and fluorescence quenching. Mass-uptake at various temperatures, pH values, and salt concentrations was also carried out. The order of affinity of the pigments binding to WS is TF>Cur>Cy. A large number of complexes and precipitations of pigments/proteins were formed through a quick, strong, and almost irreversible binding process. The mass-uptake of pigments was affected not only by the functional groups, but also by molecular weight of pigments, temperatures, pH values, and salt concentrations. The complex of pigments may easily and rapidly deposit onto the WS film, and are difficult to remove from the WS surface. However, the complex of pigments can be reduced by properly regulating the physicochemical conditions, such as temperatures, pH values, and salt concentrations. Copyright © 2010 Elsevier Ltd. All rights reserved.

Semiclassical propagation of Wigner functions.

PubMed

Dittrich, T; Gómez, E A; Pachón, L A

2010-06-07

We present a comprehensive study of semiclassical phase-space propagation in the Wigner representation, emphasizing numerical applications, in particular as an initial-value representation. Two semiclassical approximation schemes are discussed. The propagator of the Wigner function based on van Vleck's approximation replaces the Liouville propagator by a quantum spot with an oscillatory pattern reflecting the interference between pairs of classical trajectories. Employing phase-space path integration instead, caustics in the quantum spot are resolved in terms of Airy functions. We apply both to two benchmark models of nonlinear molecular potentials, the Morse oscillator and the quartic double well, to test them in standard tasks such as computing autocorrelation functions and propagating coherent states. The performance of semiclassical Wigner propagation is very good even in the presence of marked quantum effects, e.g., in coherent tunneling and in propagating Schrodinger cat states, and of classical chaos in four-dimensional phase space. We suggest options for an effective numerical implementation of our method and for integrating it in Monte-Carlo-Metropolis algorithms suitable for high-dimensional systems.

A Polymerase With Potential: The Fe-S Cluster in Human DNA Primase.

PubMed

Holt, Marilyn E; Salay, Lauren E; Chazin, Walter J

2017-01-01

Replication of DNA in eukaryotes is primarily executed by the combined action of processive DNA polymerases δ and ɛ. These enzymes cannot initiate synthesis of new DNA without the presence of a primer on the template ssDNA. The primers on both the leading and lagging strands are generated by DNA polymerase α-primase (pol-prim). DNA primase is a DNA-dependent RNA polymerase that synthesizes the first ~10 nucleotides and then transfers the substrate to polymerase α to complete primer synthesis. The mechanisms governing the coordination and handoff between primase and polymerase α are largely unknown. Isolated DNA primase contains a [4Fe-4S] 2+ cluster that has been shown to serve as a redox switch modulating DNA binding affinity. This discovery suggests a mechanism for modulating the priming activity of primase and handoff to polymerase α. In this chapter, we briefly discuss the current state of knowledge of primase structure and function, including the role of its iron-sulfur cluster. This is followed by providing the methods for expressing, purifying, and biophysically/structurally characterizing primase and its iron-sulfur cluster-containing domain, p58C. © 2017 Elsevier Inc. All rights reserved.

Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study.

PubMed

Han, Wen-Ge; Sandala, Gregory M; Giammona, Debra Ann; Bashford, Donald; Noodleman, Louis

2011-11-14

The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their Mössbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe Mössbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous Mössbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.

Affinity purification using recombinant PXR as a tool to characterize environmental ligands.

PubMed

Dagnino, Sonia; Bellet, Virginie; Grimaldi, Marina; Riu, Anne; Aït-Aïssa, Sélim; Cavaillès, Vincent; Fenet, Hélène; Balaguer, Patrick

2014-02-01

Many environmental endocrine disrupting compounds act as ligands for nuclear receptors. The human pregnane X receptor (hPXR), for instance, is activated by a variety of environmental ligands such as steroids, pharmaceutical drugs, pesticides, alkylphenols, polychlorinated biphenyls and polybromo diethylethers. Some of us have previously reported the occurrence of hPXR ligands in environmental samples but failed to identify them. The aim of this study was to test whether a PXR-affinity column, in which recombinant hPXR was immobilized on solid support, could help the purification of these chemicals. Using PXR ligands of different affinity (10 nM < EC50 < 10 μM), we demonstrated that the PXR-affinity preferentially column captured ligands with medium to high affinities (EC50 < 1 μM). Furthermore, by using the PXR-affinity column to analyze an environmental sample containing ERα, AhR, AR, and PXR activities, we show that (i) half of the PXR activity of the sample was due to compounds with medium to high affinity for PXR and (ii) PXR shared ligands with ERα, AR, and AhR. These findings demonstrate that the newly developed PXR-affinity column coupled to reporter cell lines represents a valuable tool for the characterization of the nature of PXR active compounds and should therefore guide and facilitate their further analysis. Copyright © 2012 Wiley Periodicals, Inc., a Wiley company.

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.

MgH Rydberg series: Transition energies from electron propagator theory and oscillator strengths from the molecular quantum defect orbital method

NASA Astrophysics Data System (ADS)

Corzo, H. H.; Velasco, A. M.; Lavín, C.; Ortiz, J. V.

2018-02-01

Vertical excitation energies belonging to several Rydberg series of MgH have been inferred from 3+ electron-propagator calculations of the electron affinities of MgH+ and are in close agreement with experiment. Many electronically excited states with n > 3 are reported for the first time and new insight is given on the assignment of several Rydberg series. Valence and Rydberg excited states of MgH are distinguished respectively by high and low pole strengths corresponding to Dyson orbitals of electron attachment to the cation. By applying the Molecular Quantum Defect Orbital method, oscillator strengths for electronic transitions involving Rydberg states also have been determined.

Let's get specific: the relationship between specificity and affinity.

PubMed

Eaton, B E; Gold, L; Zichi, D A

1995-10-01

The factors that lead to high-affinity binding are a good fit between the surfaces of the two molecules in their ground state and charge complementarity. Exactly the same factors give high specificity for a target. We argue that selection for high-affinity binding automatically leads to highly specific binding. This principle can be used to simplify screening approaches aimed at generating useful drugs.

Olympus propagation studies in the US: Propagation terminal hardware and experiments

NASA Technical Reports Server (NTRS)

Stutzmzn, Warren L.

1990-01-01

Virginia Tech is performing a comprehensive set of propagation measurements using the Olympus satellite beacons at 12.5, 20, and 30 GHz. These data will be used to characterize propagation conditions on small earth terminal (VSAT)-type networks for next generation small aperture Ka-band systems. The European Space Agency (ESA) satellite Olympus was launched July 12, 1989. The spacecraft contains a sophisticated package of propagation beacons operating at 12.5, 19.77, and 29.66 GHz (referred to as 12.5, 20, and 30 beacons). These beacons cover the east coast of the United States with sufficient power for attenuation measurements. The Virginia Satellite Communications Group is completing the hardware construction phase and will begin formal data collection in June.

Equation of motion coupled cluster methods for electron attachment and ionization potential in polyacenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaskaran-Nair, Kiran; Kowalski, Karol; Jarrell, Mark

2015-11-05

Polyacenes have attracted considerable attention due to their use in organic based optoelectronic materials. Polyacenes are polycyclic aromatic hydrocarbons composed of fused benzene rings. Key to understanding and design of new functional materials is an understanding of their excited state properties starting with their electron affinity (EA) and ionization potential (IP). We have developed a highly accurate and com- putationally e*fficient EA/IP equation of motion coupled cluster singles and doubles (EA/IP-EOMCCSD) method that is capable of treating large systems and large basis set. In this study we employ the EA/IP-EOMCCSD method to calculate the electron affinity and ionization potential ofmore » naphthalene, anthracene, tetracene, pentacene, hex- acene and heptacene. We have compared our results with other previous theoretical studies and experimental data. Our EA/IP results are in very good agreement with experiment and when compared with the other theoretical investigations our results represent the most accurate calculations as compared to experiment.« less

Immobilizing affinity proteins to nitrocellulose: a toolbox for paper-based assay developers.

PubMed

Holstein, Carly A; Chevalier, Aaron; Bennett, Steven; Anderson, Caitlin E; Keniston, Karen; Olsen, Cathryn; Li, Bing; Bales, Brian; Moore, David R; Fu, Elain; Baker, David; Yager, Paul

2016-02-01

To enable enhanced paper-based diagnostics with improved detection capabilities, new methods are needed to immobilize affinity reagents to porous substrates, especially for capture molecules other than IgG. To this end, we have developed and characterized three novel methods for immobilizing protein-based affinity reagents to nitrocellulose membranes. We have demonstrated these methods using recombinant affinity proteins for the influenza surface protein hemagglutinin, leveraging the customizability of these recombinant "flu binders" for the design of features for immobilization. The three approaches shown are: (1) covalent attachment of thiolated affinity protein to an epoxide-functionalized nitrocellulose membrane, (2) attachment of biotinylated affinity protein through a nitrocellulose-binding streptavidin anchor protein, and (3) fusion of affinity protein to a novel nitrocellulose-binding anchor protein for direct coupling and immobilization. We also characterized the use of direct adsorption for the flu binders, as a point of comparison and motivation for these novel methods. Finally, we demonstrated that these novel methods can provide improved performance to an influenza hemagglutinin assay, compared to a traditional antibody-based capture system. Taken together, this work advances the toolkit available for the development of next-generation paper-based diagnostics.

Host-Guest Complexes with Protein-Ligand-Like Affinities: Computational Analysis and Design

PubMed Central

Moghaddam, Sarvin; Inoue, Yoshihisa

2009-01-01

It has recently been discovered that guests combining a nonpolar core with cationic substituents bind cucurbit[7]uril (CB[7]) in water with ultra-high affinities. The present study uses the Mining Minima algorithm to study the physics of these extraordinary associations and to computationally test a new series of CB[7] ligands designed to bind with similarly high affinity. The calculations reproduce key experimental observations regarding the affinities of ferrocene-based guests with CB[7] and β-cyclodextrin and provide a coherent view of the roles of electrostatics and configurational entropy as determinants of affinity in these systems. The newly designed series of compounds is based on a bicyclo[2.2.2]octane core, which is similar in size and polarity to the ferrocene core of the existing series. Mining Minima predicts that these new compounds will, like the ferrocenes, bind CB[7] with extremely high affinities. PMID:19133781

THERMODYNAMICS OF THE COMA CLUSTER OUTSKIRTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simionescu, A.; Werner, N.; Urban, O.

2013-09-20

We present results from a large mosaic of Suzaku observations of the Coma Cluster, the nearest and X-ray brightest hot ({approx}8 keV), dynamically active, non-cool core system, focusing on the thermodynamic properties of the intracluster medium on large scales. For azimuths not aligned with an infalling subcluster toward the southwest, our measured temperature and X-ray brightness profiles exhibit broadly consistent radial trends, with the temperature decreasing from about 8.5 keV at the cluster center to about 2 keV at a radius of 2 Mpc, which is the edge of our detection limit. The southwest merger significantly boosts the surface brightness,more » allowing us to detect X-ray emission out to {approx}2.2 Mpc along this direction. Apart from the southwestern infalling subcluster, the surface brightness profiles show multiple edges around radii of 30-40 arcmin. The azimuthally averaged temperature profile, as well as the deprojected density and pressure profiles, all show a sharp drop consistent with an outwardly-propagating shock front located at 40 arcmin, corresponding to the outermost edge of the giant radio halo observed at 352 MHz with the Westerbork Synthesis Radio Telescope. The shock front may be powering this radio emission. A clear entropy excess inside of r{sub 500} reflects the violent merging events linked with these morphological features. Beyond r{sub 500}, the entropy profiles of the Coma Cluster along the relatively relaxed directions are consistent with the power-law behavior expected from simple models of gravitational large-scale structure formation. The pressure is also in agreement at these radii with the expected values measured from Sunyaev-Zel'dovich data from the Planck satellite. However, due to the large uncertainties associated with the Coma Cluster measurements, we cannot yet exclude an entropy flattening in this system consistent with that seen in more relaxed cool core clusters.« less

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'…

Effect of 2,3-diphosphoglycerate on oxygen affinity of blood in sickle cell anemia

PubMed Central

Charache, Samuel; Grisolia, Santiago; Fiedler, Adam J.; Hellegers, Andre E.

1970-01-01

Blood of patients with sickle cell anemia (SS) exhibits decreased affinity for oxygen, although the oxygen affinity of hemoglobin S is the same as that of hemoglobin A. SS red cells contain more 2,3-diphosphoglycerate (DPG) than normal erythrocytes. The oxygen affinity of hemolyzed red cells is decreased by added DPG, and hemolysates prepared from SS red cells do not differ from normal hemolysates in this regard. Reduction of oxygen affinity to the levels found in intact SS red cells required DPG concentrations in excess of those found in most SS patients. The same was true of oxygen affinity of patients with pyruvate kinase deficiency. Other organic phosphates, as well as inorganic ions, are known to alter the oxygen affinity of dilute solutions of hemoglobin. These substances, the state of aggregation of hemoglobin molecules, and cytoarchitectural factors probably play roles in determining oxygen affinity of both normal and SS red cells. PMID:5443181

Functional connectivity analysis in resting state fMRI with echo-state networks and non-metric clustering for network structure recovery

NASA Astrophysics Data System (ADS)

Wismüller, Axel; DSouza, Adora M.; Abidin, Anas Z.; Wang, Xixi; Hobbs, Susan K.; Nagarajan, Mahesh B.

2015-03-01

Echo state networks (ESN) are recurrent neural networks where the hidden layer is replaced with a fixed reservoir of neurons. Unlike feed-forward networks, neuron training in ESN is restricted to the output neurons alone thereby providing a computational advantage. We demonstrate the use of such ESNs in our mutual connectivity analysis (MCA) framework for recovering the primary motor cortex network associated with hand movement from resting state functional MRI (fMRI) data. Such a framework consists of two steps - (1) defining a pair-wise affinity matrix between different pixel time series within the brain to characterize network activity and (2) recovering network components from the affinity matrix with non-metric clustering. Here, ESNs are used to evaluate pair-wise cross-estimation performance between pixel time series to create the affinity matrix, which is subsequently subject to non-metric clustering with the Louvain method. For comparison, the ground truth of the motor cortex network structure is established with a task-based fMRI sequence. Overlap between the primary motor cortex network recovered with our model free MCA approach and the ground truth was measured with the Dice coefficient. Our results show that network recovery with our proposed MCA approach is in close agreement with the ground truth. Such network recovery is achieved without requiring low-pass filtering of the time series ensembles prior to analysis, an fMRI preprocessing step that has courted controversy in recent years. Thus, we conclude our MCA framework can allow recovery and visualization of the underlying functionally connected networks in the brain on resting state fMRI.

Genome Data Mining and Soil Survey for the Novel Group 5 [NiFe]-Hydrogenase To Explore the Diversity and Ecological Importance of Presumptive High-Affinity H2-Oxidizing Bacteria ▿†

PubMed Central

Constant, Philippe; Chowdhury, Soumitra Paul; Hesse, Laura; Pratscher, Jennifer; Conrad, Ralf

2011-01-01

Streptomyces soil isolates exhibiting the unique ability to oxidize atmospheric H2 possess genes specifying a putative high-affinity [NiFe]-hydrogenase. This study was undertaken to explore the taxonomic diversity and the ecological importance of this novel functional group. We propose to designate the genes encoding the small and large subunits of the putative high-affinity hydrogenase hhyS and hhyL, respectively. Genome data mining revealed that the hhyL gene is unevenly distributed in the phyla Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The hhyL gene sequences comprised a phylogenetically distinct group, namely, the group 5 [NiFe]-hydrogenase genes. The presumptive high-affinity H2-oxidizing bacteria constituting group 5 were shown to possess a hydrogenase gene cluster, including the genes encoding auxiliary and structural components of the enzyme and four additional open reading frames (ORFs) of unknown function. A soil survey confirmed that both high-affinity H2 oxidation activity and the hhyL gene are ubiquitous. A quantitative PCR assay revealed that soil contained 106 to 108 hhyL gene copies g (dry weight)−1. Assuming one hhyL gene copy per genome, the abundance of presumptive high-affinity H2-oxidizing bacteria was higher than the maximal population size for which maintenance energy requirements would be fully supplied through the H2 oxidation activity measured in soil. Our data indicate that the abundance of the hhyL gene should not be taken as a reliable proxy for the uptake of atmospheric H2 by soil, because high-affinity H2 oxidation is a facultatively mixotrophic metabolism, and microorganisms harboring a nonfunctional group 5 [NiFe]-hydrogenase may occur. PMID:21742924

Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography

PubMed Central

Chu, Xiakun; Wang, Jin

2014-01-01

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less) flexibility leads to weaker (stronger) coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition. PMID:25144525

Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

PubMed

Chu, Xiakun; Wang, Jin

2014-08-01

Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less) flexibility leads to weaker (stronger) coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.

A HIGH-LEVEL CALCULATION OF THE PROTON AFFINITY OF DIBORANE

EPA Science Inventory

The experimental proton affinity of diborane (B2H6) is based on an unstable species, B2H,+, 4 which has been observed only at low temperatures. The present work calculates the proton 5 affinity of diborane using the Gaussian-3 method and other high-level compound ab initio 6 met...

Approximate treatment of semicore states in GW calculations with application to Au clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xian, Jiawei; Baroni, Stefano; CNR-IOM Democritos, Theory-Elettra group, Trieste

We address the treatment of transition metal atoms in GW electronic-structure calculations within the plane-wave pseudo-potential formalism. The contributions of s and p semi-core electrons to the self-energy, which are essential to grant an acceptable accuracy, are dealt with using a recently proposed scheme whereby the exchange components are treated exactly at the G{sub 0}W{sub 0} level, whereas a suitable approximation to the correlation components is devised. This scheme is benchmarked for small gold nano-clusters, resulting in ionization potentials, electron affinities, and density of states in very good agreement with those obtained from calculations where s and p semicore statesmore » are treated as valence orbitals, and allowing us to apply this same scheme to clusters of intermediate size, Au{sub 20} and Au{sub 32}, that would be otherwise very difficult to deal with.« less

Propagation of Significant Figures.

ERIC Educational Resources Information Center

Schwartz, Lowell M.

1985-01-01

Shows that the rules of thumb for propagating significant figures through arithmetic calculations frequently yield misleading results. Also describes two procedures for performing this propagation more reliably than the rules of thumb. However, both require considerably more calculational effort than do the rules. (JN)

Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations.

PubMed

Okimoto, Noriaki; Suenaga, Atsushi; Taiji, Makoto

2017-11-01

In computational drug design, ranking a series of compound analogs in a manner that is consistent with experimental affinities remains a challenge. In this study, we evaluated the prediction of protein-ligand binding affinities using steered molecular dynamics simulations. First, we investigated the appropriate conditions for accurate predictions in these simulations. A conic harmonic restraint was applied to the system for efficient sampling of work values on the ligand unbinding pathway. We found that pulling velocity significantly influenced affinity predictions, but that the number of collectable trajectories was less influential. We identified the appropriate pulling velocity and collectable trajectories for binding affinity predictions as 1.25 Å/ns and 100, respectively, and these parameters were used to evaluate three target proteins (FK506 binding protein, trypsin, and cyclin-dependent kinase 2). For these proteins using our parameters, the accuracy of affinity prediction was higher and more stable when Jarzynski's equality was employed compared with the second-order cumulant expansion equation of Jarzynski's equality. Our results showed that steered molecular dynamics simulations are effective for predicting the rank order of ligands; thus, they are a potential tool for compound selection in hit-to-lead and lead optimization processes.

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

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

Aberrant antibody affinity selection in SHIP-deficient B cells.

PubMed

Leung, Wai-Hang; Tarasenko, Tatiana; Biesova, Zuzana; Kole, Hemanta; Walsh, Elizabeth R; Bolland, Silvia

2013-02-01

The strength of the Ag receptor signal influences development and negative selection of B cells, and it might also affect B-cell survival and selection in the GC. Here, we have used mice with B-cell-specific deletion of the 5'-inositol phosphatase SHIP as a model to study affinity selection in cells that are hyperresponsive to Ag and cytokine receptor stimulation. In the absence of SHIP, B cells have lower thresholds for Ag- and interferon (IFN)-induced activation, resulting in augmented negative selection in the BM and enhanced B-cell maturation in the periphery. Despite a tendency to spontaneously downregulate surface IgM expression, SHIP deficiency does not alter anergy induction in response to soluble hen-egg lysozyme Ag in the MDA4 transgenic model. SHIP-deficient B cells spontaneously produce isotype-switched antibodies; however, they are poor responders in immunization and infection models. While SHIP-deficient B cells form GCs and undergo mutation, they are not properly selected for high-affinity antibodies. These results illustrate the importance of negative regulation of B-cell responses, as lower thresholds for B-cell activation promote survival of low affinity and deleterious receptors to the detriment of optimal Ab affinity maturation. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modeling of slow crack propagation in heterogeneous rocks

NASA Astrophysics Data System (ADS)

Lengliné, Olivier; Stormo, Arne; Hansen, Alex; Schmittbuhl, Jean

2015-04-01

Crack propagation in heterogeneous media is a rich problem which involves the interplay of various physical processes. The problem has been intensively investigated theoretically, numerically, and experimentally, but a unifying model capturing all the experimental features has not been entirely achieved despite its broad range of implications in Earth sciences problems. The slow propagation of a crack front where long range elastic interactions are dominant, is of crucial importance to fill the gap between experiments and models. Several theoretical and numerical works have been devoted to quasi-static models. Such models give rise to an intermittent local activity characterized by a depinning transition and can be viewed as a critical phenomenon. However these models fail to reproduce all experimental conditions, notably the front morphology does not display any cross-over length with two different roughness exponents above and below the cross-over as observed experimentally. Here, we compare experimental observations of a slow interfacial crack propagation along an heterogeneous interface to numerical simulations from a cantilever fiber bundle model. The model consists of a planar set of brittle fibers between an elastic half-space and a rigid square root shaped plate which loads the system in a cantilever configuration. The latter is shown to provide an improved opening and stress field in the process zone around the crack tip. The model shares a similar scale invariant roughening of the crack front both at small and large scales and a similar power law distribution of the local velocity of the crack front to experiments. Implications for induced seismicity at the brittle-creep transition are discussed. We show that a creep route for induced seismicity is possible when heterogeneities exist along the fault. Indeed, seismic event occurrences in time and space are in strong relation with the development of the aseismic motion recorded during the experiment and the

Stable and solubilized active Au atom clusters for selective epoxidation of cis-cyclooctene with molecular oxygen

DOE PAGES

Qian, Linping; Wang, Zhen; Beletskiy, Evgeny V.; ...

2017-03-28

Here, the ability of Au catalysts to effect the challenging task of utilizing molecular oxygen for the selective epoxidation of cyclooctene is fascinating. Although supported nanometre-size Au particles are poorly active, here we show that solubilized atomic Au clusters, present in ng ml –1 concentrations and stabilized by ligands derived from the oxidized hydrocarbon products, are active. They can be formed from various Au sources. They generate initiators and propagators to trigger the onset of the auto-oxidation reaction with an apparent turnover frequency of 440 s –1, and continue to generate additional initiators throughout the auto-oxidation cycle without direct participationmore » in the cycle. Spectroscopic characterization suggests that 7–8 atom clusters are effective catalytically. Extension of work based on these understandings leads to the demonstration that these Au clusters are also effective in selective oxidation of cyclohexene, and that solubilized Pt clusters are also capable of generating initiators for cyclooctene epoxidation.« less

Stable and solubilized active Au atom clusters for selective epoxidation of cis-cyclooctene with molecular oxygen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qian, Linping; Wang, Zhen; Beletskiy, Evgeny V.

Here, the ability of Au catalysts to effect the challenging task of utilizing molecular oxygen for the selective epoxidation of cyclooctene is fascinating. Although supported nanometre-size Au particles are poorly active, here we show that solubilized atomic Au clusters, present in ng ml –1 concentrations and stabilized by ligands derived from the oxidized hydrocarbon products, are active. They can be formed from various Au sources. They generate initiators and propagators to trigger the onset of the auto-oxidation reaction with an apparent turnover frequency of 440 s –1, and continue to generate additional initiators throughout the auto-oxidation cycle without direct participationmore » in the cycle. Spectroscopic characterization suggests that 7–8 atom clusters are effective catalytically. Extension of work based on these understandings leads to the demonstration that these Au clusters are also effective in selective oxidation of cyclohexene, and that solubilized Pt clusters are also capable of generating initiators for cyclooctene epoxidation.« less

Electron affinity and excited states of methylglyoxal

NASA Astrophysics Data System (ADS)

Dauletyarov, Yerbolat; Dixon, Andrew R.; Wallace, Adam A.; Sanov, Andrei

2017-07-01

Using photoelectron imaging spectroscopy, we characterized the anion of methylglyoxal (X2A″ electronic state) and three lowest electronic states of the neutral methylglyoxal molecule: the closed-shell singlet ground state (X1A'), the lowest triplet state (a3A″), and the open-shell singlet state (A1A″). The adiabatic electron affinity (EA) of the ground state, EA(X1A') = 0.87(1) eV, spectroscopically determined for the first time, compares to 1.10(2) eV for unsubstituted glyoxal. The EAs (adiabatic attachment energies) of two excited states of methylglyoxal were also determined: EA(a3A″) = 3.27(2) eV and EA(A1A″) = 3.614(9) eV. The photodetachment of the anion to each of these two states produces the neutral species near the respective structural equilibria; hence, the a3A″ ← X2A″ and A1A″ ← X2A″ photodetachment transitions are dominated by intense peaks at their respective origins. The lowest-energy photodetachment transition, on the other hand, involves significant geometry relaxation in the X1A' state, which corresponds to a 60° internal rotation of the methyl group, compared to the anion structure. Accordingly, the X1A' ← X2A″ transition is characterized as a broad, congested band, whose vertical detachment energy, VDE = 1.20(4) eV, significantly exceeds the adiabatic EA. The experimental results are in excellent agreement with the ab initio predictions using several equation-of-motion methodologies, combined with coupled-cluster theory.

Semiclassical propagator of the Wigner function.

PubMed

Dittrich, Thomas; Viviescas, Carlos; Sandoval, Luis

2006-02-24

Propagation of the Wigner function is studied on two levels of semiclassical propagation: one based on the Van Vleck propagator, the other on phase-space path integration. Leading quantum corrections to the classical Liouville propagator take the form of a time-dependent quantum spot. Its oscillatory structure depends on whether the underlying classical flow is elliptic or hyperbolic. It can be interpreted as the result of interference of a pair of classical trajectories, indicating how quantum coherences are to be propagated semiclassically in phase space. The phase-space path-integral approach allows for a finer resolution of the quantum spot in terms of Airy functions.

Robust non-rigid registration algorithm based on local affine registration

NASA Astrophysics Data System (ADS)

Wu, Liyang; Xiong, Lei; Du, Shaoyi; Bi, Duyan; Fang, Ting; Liu, Kun; Wu, Dongpeng

2018-04-01

Aiming at the problem that the traditional point set non-rigid registration algorithm has low precision and slow convergence speed for complex local deformation data, this paper proposes a robust non-rigid registration algorithm based on local affine registration. The algorithm uses a hierarchical iterative method to complete the point set non-rigid registration from coarse to fine. In each iteration, the sub data point sets and sub model point sets are divided and the shape control points of each sub point set are updated. Then we use the control point guided affine ICP algorithm to solve the local affine transformation between the corresponding sub point sets. Next, the local affine transformation obtained by the previous step is used to update the sub data point sets and their shape control point sets. When the algorithm reaches the maximum iteration layer K, the loop ends and outputs the updated sub data point sets. Experimental results demonstrate that the accuracy and convergence of our algorithm are greatly improved compared with the traditional point set non-rigid registration algorithms.

Parallel Density-Based Clustering for Discovery of Ionospheric Phenomena

NASA Astrophysics Data System (ADS)

Pankratius, V.; Gowanlock, M.; Blair, D. M.

2015-12-01

Ionospheric total electron content maps derived from global networks of dual-frequency GPS receivers can reveal a plethora of ionospheric features in real-time and are key to space weather studies and natural hazard monitoring. However, growing data volumes from expanding sensor networks are making manual exploratory studies challenging. As the community is heading towards Big Data ionospheric science, automation and Computer-Aided Discovery become indispensable tools for scientists. One problem of machine learning methods is that they require domain-specific adaptations in order to be effective and useful for scientists. Addressing this problem, our Computer-Aided Discovery approach allows scientists to express various physical models as well as perturbation ranges for parameters. The search space is explored through an automated system and parallel processing of batched workloads, which finds corresponding matches and similarities in empirical data. We discuss density-based clustering as a particular method we employ in this process. Specifically, we adapt Density-Based Spatial Clustering of Applications with Noise (DBSCAN). This algorithm groups geospatial data points based on density. Clusters of points can be of arbitrary shape, and the number of clusters is not predetermined by the algorithm; only two input parameters need to be specified: (1) a distance threshold, (2) a minimum number of points within that threshold. We discuss an implementation of DBSCAN for batched workloads that is amenable to parallelization on manycore architectures such as Intel's Xeon Phi accelerator with 60+ general-purpose cores. This manycore parallelization can cluster large volumes of ionospheric total electronic content data quickly. Potential applications for cluster detection include the visualization, tracing, and examination of traveling ionospheric disturbances or other propagating phenomena. Acknowledgments. We acknowledge support from NSF ACI-1442997 (PI V. Pankratius).

Anisotropic thermal conduction with magnetic fields in galaxy clusters

NASA Astrophysics Data System (ADS)

Arth, Alexander; Dolag, Klaus; Beck, Alexander; Petkova, Margarita; Lesch, Harald

2015-08-01

Magnetic fields play an important role for the propagation and diffusion of charged particles, which are responsible for thermal conduction. In this poster, we present an implementation of thermal conduction including the anisotropic effects of magnetic fields for smoothed particle hydrodynamics (SPH). The anisotropic thermal conduction is mainly proceeding parallel to magnetic fields and suppressed perpendicular to the fields. We derive the SPH formalism for the anisotropic heat transport and solve the corresponding equation with an implicit conjugate gradient scheme. We discuss several issues of unphysical heat transport in the cases of extreme ansiotropies or unmagnetized regions and present possible numerical workarounds. We implement our algorithm into the cosmological simulation code GADGET and study its behaviour in several test cases. In general, we reproduce the analytical solutions of our idealised test problems, and obtain good results in cosmological simulations of galaxy cluster formations. Within galaxy clusters, the anisotropic conduction produces a net heat transport similar to an isotropic Spitzer conduction model with low efficiency. In contrast to isotropic conduction our new formalism allows small-scale structure in the temperature distribution to remain stable, because of their decoupling caused by magnetic field lines. Compared to observations, strong isotropic conduction leads to an oversmoothed temperature distribution within clusters, while the results obtained with anisotropic thermal conduction reproduce the observed temperature fluctuations well. A proper treatment of heat transport is crucial especially in the outskirts of clusters and also in high density regions. It's connection to the local dynamical state of the cluster also might contribute to the observed bimodal distribution of cool core and non cool core clusters. Our new scheme significantly advances the modelling of thermal conduction in numerical simulations and overall gives

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.…

On the vanishing couplings in ADE affine Toda field theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saitoh, Y.; Shimada, T.

In this paper, the authors show that certain vanishing couplins in the ADE affine Toda field theories remain vanishing even after higher-order corrections are included. This is a requisite property for the Lagrangian formulation of the theory. The authors develop a new perturbative formulation and treat affine Toda field theories as a massless theory with exponential interaction terms. The authors shown that the nonrenormalization comes from the Dynkin automorphism of the Lie algebra associated with these theories. A charge balance conditions plays an important role in our scheme. The all-order nonrenormalization of vanishing couplings in [bar A][sub n] affine Todamore » field theory is also proved in a standard massive scheme.« less

User needs for propagation data

NASA Technical Reports Server (NTRS)

Sullivan, Thomas M.

1993-01-01

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

Theoretical Analysis of Microwave Propagation.

DTIC Science & Technology

1984-04-01

effects of the turbulent atmosphere on wave propagation, US Department of Commerce, NTIS, Springfield, VA. * VanVleck, J.H. (1947), "The absorption of... turbulent atmosphere on wave propagation, US Department of Commerce, NTIS, Sprinifield, VA. -. A. Vigants (1975), "Space diversity engineering," BSTJ, Vol... Turbulence ., ...... 2-26 2.5 ATMOSPHERIC ABSORPTION. 2-26 2 .6 RAIN ATTENUATION ....... 2-29 3 TROPOSCATTER PROPAGATION .................... 3-1 3.1

[An examination of the determinants of social withdrawal and affinity for social withdrawal].

PubMed

Watanabe, Asami; Matsui, Yutaka; Takatsuka, Yusuke

2010-12-01

This study examined the determinants of social withdrawal using data from a survey by the Tokyo Metropolitan Government Office for Youth Affairs and Public Safety (2008). In addition, this study identified young people who showed an affinity for social withdrawal although they were not in a state of withdrawal, and examined the determinants of an affinity for social withdrawal. The results of stepwise discriminant analysis showed that factors such as social phobia, depression, violence, and emotional bonds with family differentiated between the general youth group and the social withdrawal group and the "affinity group". Social phobia, violence, and refusal to be interfered in self-decision making differentiated between the social withdrawal group and the "affinity group". This study shows that an "affinity group" should be cared as well as an actual withdrawal group.

[Serological affinity of some species of nonpathogenic corynebacteria].

PubMed

Furtat, I M; Nohina, T M; Mikhal's'kyĭ, L O; Vedenieieva, O A

2002-01-01

Serological peculiarities of the species strains Corynebacterium glutamicum, C. ammoniagenes, C. vitaeruminis, C. variabilis and strain of Corynebacterium sp. (Brevibacterium stationis) UCM Ac-719 have been investigated with the help of immunoenzyme analysis ELISA with the use of mice immune serum, specific to C. ammoniagenes UCM Ac-732T, C. vitaeruminis UCM Ac-718T, C. variabilis UCM Ac-717T, C. glutamicum UCM Ac-733 and Corynebacterium sp. UCM Ac-719. It has been established that the species of nonpathogenic corynebacteria differ between themselves as to the degree of serological affinity. C. variabilis, C. ammoniagenes and C. glutamicum are the least similar as to this indication. Weak antigenic relations have been revealed in C. vitaeruminis and C. ammoniagenes. The latter displayed the higher, as compared with other strains, affinity for Corynebacterium sp. UCM Ac-719. The highest degree of serological affinity within the species was registered in strains C. glutamicum and C. variabilis. Data obtained evidence that the ELISA method permits conducting the high-reliability species diagnosis of nonpathogenic corynebacteria on the basis of their antigenic characteristics.

Affinity chromatography: A versatile technique for antibody purification.

PubMed

Arora, Sushrut; Saxena, Vikas; Ayyar, B Vijayalakshmi

2017-03-01

Antibodies continue to be extremely utilized entities in myriad applications including basic research, imaging, targeted delivery, chromatography, diagnostics, and therapeutics. At production stage, antibodies are generally present in complex matrices and most of their intended applications necessitate purification. Antibody purification has always been a major bottleneck in downstream processing of antibodies, due to the need of high quality products and associated high costs. Over the years, extensive research has focused on finding better purification methodologies to overcome this holdup. Among a plethora of different techniques, affinity chromatography is one of the most selective, rapid and easy method for antibody purification. This review aims to provide a detailed overview on affinity chromatography and the components involved in purification. An array of support matrices along with various classes of affinity ligands detailing their underlying working principles, together with the advantages and limitations of each system in purifying different types of antibodies, accompanying recent developments and important practical methodological considerations to optimize purification procedure are discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Density functional study of the structural, electronic, and magnetic properties of Mo n and Mo n S ( n = 1 - 10) clusters

NASA Astrophysics Data System (ADS)

Ziane, M.; Amitouche, F.; Bouarab, S.; Vega, A.

2017-12-01

Structural and electronic properties of pure molybdenum Mo n and molybdenum-sulfide Mo n S ( n = 1 - 10) clusters were investigated in the framework of the density functional theory within the generalized gradient approximation to exchange and correlation with the aim of addressing how doping with a single S atom affects the geometries, magnetic properties, and reactivity of pure molybdenum clusters. These clusters exhibit a less marked tendency to dimerization than their isoelectronic Cr counterparts despite sharing their half-filled valence shell configuration. Doping with a single S impurity is enough to change the structure of the host molybdenum cluster to a large extent, as well as to modify the bonding pattern, the magnetic state and the magnetic moment distribution in the Mo host. Vertical ionization potentials and electron affinities are calculated to determine global reactivity indicators like the electronegativity and the chemical hardness. The results are discussed in terms of the thermodynamical and relative stabilities, charge transfer effects, and spin-polarized densities of electronic states.

Thermally stable solids based on endohedrally doped ZnS clusters.

PubMed

Matxain, Jon M; Piris, Mario; Lopez, Xabier; Ugalde, Jesus M

2009-01-01

The existence of inorganic, hollow, fullerene-like ZnS clusters has been theoretically predicted and then recently confirmed experimentally. These clusters were observed to trap alkali metals and halogens because the ionization energies (IE) of alkali metals are very similar to the electron affinities (EA) of halogens. This opens the possibility of forming molecular solids composed of these fullerene building blocks because the energy released due to the difference between the IE and EA would be very small. Herein we have focused on assembling bare Zn(12)S(12) and endohedral X@Zn(12)S(12)-Y@Zn(12)S(12) dimers (X = Na, K; Y = Cl, Br) by considering the square-faces-square orientation of every two adjacent clusters, which leads to a fcc cubic crystal structure in the solid. The structures were fully optimized in all cases, and their thermal stability was confirmed by ab initio thermal molecular dynamics calculations. The optimum lattice parameter of the solids was found to be around 13.8 A, which corresponds to distances of about 2.5 A between monomers, which is typical of covalent Zn-S bonds. The resulting solids are nanoporous materials similar to B(12)N(12). Due to their nanoporous structure, these zeolite-shaped solids could be used in heterogeneous catalysis and as storage materials and molecular sieves.

The evolution of slip surface roughness during earthquake propagation in carbonate faults

NASA Astrophysics Data System (ADS)

Zhu, B.; De Paola, N.; Llewellin, E. W.; Holdsworth, R.

2014-12-01

Slip surface roughness is understood to control the dynamics of earthquake propagation. Quantifying the micro- and nano-scale roughness of slip surfaces can give insight into the grain-scale processes controlling the strength of faults during earthquake propagation. Friction experiments were performed on fine-grained calcite gouges, at speed 1 ms-1, normal stress 18 MPa, displacements 0.009-1.46 m, and room temperature and humidity. Results show a two stage-evolution (S1-2) of the fault strength, with an initial increase up to peak value 0.82 (S1), followed by a sudden decrease to a low, steady-state value 0.18 (S2). Samples retrieved at the end of S1 show the development of a cohesive slip zone (SZ), made of micron-scale, angular clasts formed by brittle fracturing and cataclasis. The SZ of samples deformed up to S2, is composed of nanograin aggregates which exhibit polygonal grain boundaries indicating high temperature grain boundary sliding creep deformation. In both cases, the SZ is bounded by a sharply defined slip surface. The 3-D geometry of seven experimental slip surfaces (40μm×40μm) has been reconstructed by digital processing of sets of 1800 images of SZ cross sections acquired at 20 nm intervals perpendicular to the slip direction, using a slicing (Focussed Ion Beam) and viewing (Field Emission Scanning Electron Microscope) technique. Spectrum power density analyses show that nano- and micron-scale slip surface roughness is anisotropic for both S1 and S2 slip surfaces. At the nano- and micron-scale, root mean square values decrease with length for S1 slip surfaces, but only slightly for S2 surfaces, and are anisotropic in the slip-normal and slip-parallel directions. The anisotropy is reduced at the nano-scale, although S2 slip surfaces are still smoother parallel to slip than normal to slip. Hurst exponents vary through scales, and are anisotropic in the directions parallel and normal to slip. Variable Hurst exponents indicate that slip surface

MacA, a periplasmic membrane fusion protein of the macrolide transporter MacAB-TolC, binds lipopolysaccharide core specifically and with high affinity.

PubMed

Lu, Shuo; Zgurskaya, Helen I

2013-11-01

The Escherichia coli MacAB-TolC transporter has been implicated in efflux of macrolide antibiotics and secretion of enterotoxin STII. In this study, we found that purified MacA, a periplasmic membrane fusion protein, contains one tightly bound rough core lipopolysaccharide (R-LPS) molecule per MacA molecule. R-LPS was bound specifically to MacA protein with affinity exceeding that of polymyxin B. Sequence analyses showed that MacA contains two high-density clusters of positively charged amino acid residues located in the cytoplasmic N-terminal domain and the periplasmic C-terminal domain. Substitutions in the C-terminal cluster reducing the positive-charge density completely abolished binding of R-LPS. At the same time, these substitutions significantly reduced the functionality of MacA in the protection of E. coli against macrolides in vivo and in the in vitro MacB ATPase stimulation assays. Taken together, our results suggest that R-LPS or a similar glycolipid is a physiological substrate of MacAB-TolC.

Exploring high-affinity binding properties of octamer peptides by principal component analysis of tetramer peptides.

PubMed

Kume, Akiko; Kawai, Shun; Kato, Ryuji; Iwata, Shinmei; Shimizu, Kazunori; Honda, Hiroyuki

2017-02-01

To investigate the binding properties of a peptide sequence, we conducted principal component analysis (PCA) of the physicochemical features of a tetramer peptide library comprised of 512 peptides, and the variables were reduced to two principal components. We selected IL-2 and IgG as model proteins and the binding affinity to these proteins was assayed using the 512 peptides mentioned above. PCA of binding affinity data showed that 16 and 18 variables were suitable for localizing IL-2 and IgG high-affinity binding peptides, respectively, into a restricted region of the PCA plot. We then investigated whether the binding affinity of octamer peptide libraries could be predicted using the identified region in the tetramer PCA. The results show that octamer high-affinity binding peptides were also concentrated in the tetramer high-affinity binding region of both IL-2 and IgG. The average fluorescence intensity of high-affinity binding peptides was 3.3- and 2.1-fold higher than that of low-affinity binding peptides for IL-2 and IgG, respectively. We conclude that PCA may be used to identify octamer peptides with high- or low-affinity binding properties from data from a tetramer peptide library. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

How Much Binding Affinity Can be Gained by Filling a Cavity?

PubMed Central

Kawasaki, Yuko; Chufan, Eduardo E.; Lafont, Virginie; Hidaka, Koushi; Kiso, Yoshiaki; Amzel, L. Mario; Freire, Ernesto

2011-01-01

Binding affinity optimization is critical during drug development. Here we evaluate the thermodynamic consequences of filling a binding cavity with functionalities of increasing van der Waals radii (-H, -F, -Cl and CH3) that improve the geometric fit without participating in hydrogen bonding or other specific interactions. We observe a binding affinity increase of two orders of magnitude. There appears to be three phases in the process. The first phase is associated with the formation of stable van der Waals interactions. This phase is characterized by a gain in binding enthalpy and a loss in binding entropy, attributed to a loss of conformational degrees of freedom. For the specific case presented in this paper, the enthalpy gain amounts to −1.5 kcal/mol while the entropic losses amount to +0.9 kcal/mol resulting in a net 3.5-fold affinity gain. The second phase is characterized by simultaneous enthalpic and entropic gains. This phase improves the binding affinity 25-fold. The third phase represents the collapse of the trend and is triggered by the introduction of chemical functionalities larger than the binding cavity itself (CH(CH3)2). It is characterized by large enthalpy and affinity losses. The thermodynamic signatures associated with each phase provide guidelines for lead optimization. PMID:20028396

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.

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. Copyright © 2013 Elsevier B.V. All rights reserved.

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. [Amdt. 195-45, 56 FR 26926, June 12, 1991] ...

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. [Amdt. 195-45, 56 FR 26926, June 12, 1991] ...

49 CFR 195.111 - Fracture propagation.

Code of Federal Regulations, 2010 CFR

2010-10-01

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

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. [Amdt. 195-45, 56 FR 26926, June 12, 1991] ...

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. [Amdt. 195-45, 56 FR 26926, June 12, 1991] ...

An O({radical}nL) primal-dual affine scaling algorithm for linear programming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Siming

1994-12-31

We present a new primal-dual affine scaling algorithm for linear programming. The search direction of the algorithm is a combination of classical affine scaling direction of Dikin and a recent new affine scaling direction of Jansen, Roos and Terlaky. The algorithm has an iteration complexity of O({radical}nL), comparing to O(nL) complexity of Jansen, Roos and Terlaky.

PREDICTING ER BINDING AFFINITY FOR EDC RANKING AND PRIORITIZATION: MODEL II

EPA Science Inventory

The training set used to derive a common reactivity pattern (COREPA) model for estrogen receptor (ER) binding affinity in Model I (see Abstract I in this series) was extended to include 47 rat estrogen receptor (rER) relative binding affinity (RBA) measurements in addition to the...

Affinity Purification of Proteins in Tag-Free Form: Split Intein-Mediated Ultrarapid Purification (SIRP).

PubMed

Guan, Dongli; Chen, Zhilei

2017-01-01

Proteins purified using affinity-based chromatography often exploit a recombinant affinity tag. Existing methods for the removal of the extraneous tag, needed for many applications, suffer from poor efficiency and/or high cost. Here we describe a simple, efficient, and potentially low-cost approach-split intein-mediated ultrarapid purification (SIRP)-for both the purification of the desired tagged protein from Escherichia coli lysate and removal of the tag in less than 1 h. The N- and C-fragment of a self-cleaving variant of a naturally split DnaE intein from Nostoc punctiforme are genetically fused to the N-terminus of an affinity tag and a protein of interest (POI), respectively. The N-intein/affinity tag is used to functionalize an affinity resin. The high affinity between the N- and C-fragment of DnaE intein enables the POI to be purified from the lysate via affinity to the resin, and the intein-mediated C-terminal cleavage reaction causes tagless POI to be released into the flow-through. The intein cleavage reaction is strongly inhibited by divalent ions (e.g., Zn 2+ ) under non-reducing conditions and is significantly enhanced by reducing conditions. The POI is cleaved efficiently regardless of the identity of the N-terminal amino acid except in the cases of threonine and proline, and the N-intein-functionalized affinity resin can be regenerated for multiple cycles of use.

Paper-based immune-affinity arrays for detection of multiple mycotoxins in cereals.

PubMed

Li, Li; Chen, Hongpu; Lv, Xiaolan; Wang, Min; Jiang, Xizhi; Jiang, Yifei; Wang, Heye; Zhao, Yongfu; Xia, Liru

2018-03-01

Mycotoxins produced by different species of fungi may coexist in cereals and feedstuffs, and could be highly toxic for humans and animals. For quantification of multiple mycotoxins in cereals, we developed a paper-based mycotoxin immune-affinity array. First, paper-based microzone arrays were fabricated by photolithography. Then, monoclonal mycotoxin antibodies were added in a copolymerization reaction with a cross-linker to form an immune-affinity monolith on the paper-based microzone array. With use of a competitive immune-response format, paper-based mycotoxin immune-affinity arrays were successfully applied to detect mycotoxins in samples. The detection limits for deoxynivalenol, zearalenone, T-2 toxin, and HT-2 toxin were 62.7, 10.8, 0.36, and 0.23 μg·kg -1 , respectively, which meet relevant requirements for these compounds in food. The recovery rates were 81-86% for deoxynivalenol, 89-117% for zearalenone, 79-86% for T-2 toxin, and 78-83% for HT-2 toxin, and showed the paper-based immune-affinity arrays had good reproducibility. In summary, the paper-based mycotoxin immune-affinity array provides a sensitive, rapid, accurate, stable, and convenient platform for detection of multiple mycotoxins in agro-foods. Graphical abstract Paper-based immune-affinity monolithic array. DON deoxynivalenol, HT-2 HT-2 toxin, T-2 T-2 toxin, PEGDA polyethylene glycol diacrylate, ZEN zearalenone.

Detachment of affinity-captured bioparticles by elastic deformation of a macroporous hydrogel

PubMed Central

Dainiak, Maria B.; Kumar, Ashok; Galaev, Igor Yu.; Mattiasson, Bo

2006-01-01

Adsorption of bioparticles to affinity surfaces involves polyvalent interactions, complicating greatly the recovery of the adsorbed material. A unique system for the efficient binding and release of different cells and particles is described. Affinity-bound bioparticles and synthetic particles are detached from the macroporous hydrogel matrix, a so-called cryogel, when the cryogel undergoes elastic deformation. The particle detachment upon elastic deformation is believed to be due to breaking of many of the multipoint attachments between the particles and the affinity matrix and the change in the distance between affinity ligands when the matrix is deformed. However, no release of affinity-bound protein occurred upon elastic deformation. The phenomenon of particle detachment upon elastic deformation is believed to be of a generic nature, because it was demonstrated for a variety of bioparticles of different sizes and for synthetic particles, for different ligand–receptor pairs (IgG–protein A, sugar–ConA, metal ion–chelating ligand), and when the deformation was caused by either external forces (mechanical deformation) or internal forces (the shrinkage of thermosensitive, macroporous hydrogel upon an increase in temperature). The elasticity of cryogel monoliths ensures high recovery of captured cells under mild conditions, with highly retained viability. This property, along with their continuous porous structure makes cryogel monoliths very attractive for applications in affinity cell separation. PMID:16418282

Structural correlates of affinity in fetal versus adult endplate nicotinic receptors

NASA Astrophysics Data System (ADS)

Nayak, Tapan Kumar; Chakraborty, Srirupa; Zheng, Wenjun; Auerbach, Anthony

2016-04-01

Adult-type nicotinic acetylcholine receptors (AChRs) mediate signalling at mature neuromuscular junctions and fetal-type AChRs are necessary for proper synapse development. Each AChR has two neurotransmitter binding sites located at the interface of a principal and a complementary subunit. Although all agonist binding sites have the same core of five aromatic amino acids, the fetal site has ~30-fold higher affinity for the neurotransmitter ACh. Here we use molecular dynamics simulations of adult versus fetal homology models to identify complementary-subunit residues near the core that influence affinity, and use single-channel electrophysiology to corroborate the results. Four residues in combination determine adult versus fetal affinity. Simulations suggest that at lower-affinity sites, one of these unsettles the core directly and the others (in loop E) increase backbone flexibility to unlock a key, complementary tryptophan from the core. Swapping only four amino acids is necessary and sufficient to exchange function between adult and fetal AChRs.

Selective retention of basic compounds by metal aquo-ion affinity chromatography.

PubMed

Asakawa, Yoshiki; Yamamoto, Eiichi; Asakawa, Naoki

2014-10-01

A novel metal aquo-ion affinity chromatography has been developed for the analysis of basic compounds using heat-treated silica gel containing hydrated metal cations (metal aquo-ions) as the packing material. The packing materials of the metal aquo-ion affinity chromatography were prepared by the immobilization of a single metal component such as Fe(III), Al(III), Ag(I), and Ni(II) on silica gel followed by extensive heat treatment. The immobilized metals form aquo-ions to present cation-exchange ability for basic analytes and the cation-exchange ability for basic analytes depends on pKa of the immobilized metal species. In the present study, to evaluate the retention characteristics of metal aquo-ion affinity chromatography, the on-line solid-phase extraction of drugs was investigated. Obtained data clearly evidence the selective retention capability of metal aquo-ion affinity chromatography for basic analytes with sufficient capacity. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions.

PubMed

Cohen, Ariel; Rosenthal, Eran; Shifman, Julia M

2017-11-10

Ubiquitin is a small protein that enables one of the most common post-translational modifications, where the whole ubiquitin molecule is attached to various target proteins, forming mono- or polyubiquitin conjugations. As a prototypical multispecific protein, ubiquitin interacts non-covalently with a variety of proteins in the cell, including ubiquitin-modifying enzymes and ubiquitin receptors that recognize signals from ubiquitin-conjugated substrates. To enable recognition of multiple targets and to support fast dissociation from the ubiquitin modifying enzymes, ubiquitin/protein interactions are characterized with low affinities, frequently in the higher μM and lower mM range. To determine how structure encodes low binding affinity of ubiquitin/protein complexes, we analyzed structures of more than a hundred such complexes compiled in the Ubiquitin Structural Relational Database. We calculated various structure-based features of ubiquitin/protein binding interfaces and compared them to the same features of general protein-protein interactions (PPIs) with various functions and generally higher affinities. Our analysis shows that ubiquitin/protein binding interfaces on average do not differ in size and shape complementarity from interfaces of higher-affinity PPIs. However, they contain fewer favorable hydrogen bonds and more unfavorable hydrophobic/charge interactions. We further analyzed how binding interfaces change upon affinity maturation of ubiquitin toward its target proteins. We demonstrate that while different features are improved in different experiments, the majority of the evolved complexes exhibit better shape complementarity and hydrogen bond pattern compared to wild-type complexes. Our analysis helps to understand how low-affinity PPIs have evolved and how they could be converted into high-affinity PPIs. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

A molecular determinant of phosphoinositide affinity in mammalian TRPV channels

NASA Astrophysics Data System (ADS)

Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A.; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor

2016-06-01

Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca2+-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6.

ISM stripping from cluster galaxies and inhomogeneities in cooling flows

NASA Technical Reports Server (NTRS)

Soker, Noam; Bregman, Joel N.; Sarazin, Craig L.

1990-01-01

Analyses of the x ray surface brightness profiles of cluster cooling flows suggest that the mass flow rate decreases towards the center of the cluster. It is often suggested that this decrease results from thermal instabilities, in which denser blobs of gas cool rapidly and drop below x ray emitting temperatures. If the seeds for the thermal instabilities are entropy perturbations, these perturbations must enter the flow already in the nonlinear regime. Otherwise, the blobs would take too long to cool. Here, researchers suggest that such nonlinear perturbations might start as blobs of interstellar gas which are stripped out of cluster galaxies. Assuming that most of the gas produced by stellar mass loss in cluster galaxies is stripped from the galaxies, the total rate of such stripping is roughly M sub Interstellar Matter (ISM) approx. 100 solar mass yr(-1). It is interesting that the typical rates of cooling in cluster cooling flows are M sub cool approx. 100 solar mass yr(-1). Thus, it is possible that a substantial portion of the cooling gas originates as blobs of interstellar gas stripped from galaxies. The magnetic fields within and outside of the low entropy perturbations can help to maintain their identities, both by suppressing thermal conduction and through the dynamical effects of magnetic tension. One significant question concerning this scenario is: Why are cooling flows seen only in a fraction of clusters, although one would expect gas stripping to be very common. It may be that the density perturbations only survive and cool efficiently in clusters with a very high intracluster gas density and with the focusing effect of a central dominant galaxy. Inhomogeneities in the intracluster medium caused by the stripping of interstellar gas from galaxies can have a number of other effects on clusters. For example, these density fluctuations may disrupt the propagation of radio jets through the intracluster gas, and this may be one mechanism for producing Wide

VHF electromagnetic wave propagation

NASA Astrophysics Data System (ADS)

Gole, P.

Theoretical and experimental study of large-scale VHF propagation characteristics is presented. Certain phenomena that are difficult to model, such as the effects of ground near the antenna, are examined from a purely experimental point of view. The characteristics of electromagnetic waves over a spherical surface and through a medium having a certain refractive index, such as is the case for waves propagated over the earth's surface, are analytically described. Two mathematical models are used, one for the case of the receiver being within the radioelectric horizon of the transmitter and the other for when it is not. Propagation phenomena likely to increase the false alarm probability of an air surveillance radar are briefly considered.

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.

NASA propagation information center

NASA Technical Reports Server (NTRS)

Smith, Ernest K.; Flock, Warren L.

1990-01-01

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.

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.

Parallel Splash Belief Propagation

DTIC Science & Technology

2010-08-01

s/ ROGER J. DZIEGIEL, Jr. MICHAEL J. WESSING, Deputy Chief Work Unit Manager For... Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC 20503. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. 1. REPORT DATE...Propagation algorithm outperforms synchronous, round-robin, wild-fire ( Ranganathan et al., 2007), and residual (Elidan et al., 2006) belief propagation

The accuracy of dynamic attitude propagation

NASA Technical Reports Server (NTRS)

Harvie, E.; Chu, D.; Woodard, M.

1990-01-01

Propagating attitude by integrating Euler's equation for rigid body motion has long been suggested for the Earth Radiation Budget Satellite (ERBS) but until now has not been implemented. Because of limited Sun visibility, propagation is necessary for yaw determination. With the deterioration of the gyros, dynamic propagation has become more attractive. Angular rates are derived from integrating Euler's equation with a stepsize of 1 second, using torques computed from telemetered control system data. The environmental torque model was quite basic. It included gravity gradient and unshadowed aerodynamic torques. Knowledge of control torques is critical to the accuracy of dynamic modeling. Due to their coarseness and sparsity, control actuator telemetry were smoothed before integration. The dynamic model was incorporated into existing ERBS attitude determination software. Modeled rates were then used for attitude propagation in the standard ERBS fine-attitude algorithm. In spite of the simplicity of the approach, the dynamically propagated attitude matched the attitude propagated with good gyros well for roll and yaw but diverged up to 3 degrees for pitch because of the very low resolution in pitch momentum wheel telemetry. When control anomalies significantly perturb the nominal attitude, the effect of telemetry granularity is reduced and the dynamically propagated attitudes are accurate on all three axes.

Accurate and sensitive quantification of protein-DNA binding affinity.

PubMed

Rastogi, Chaitanya; Rube, H Tomas; Kribelbauer, Judith F; Crocker, Justin; Loker, Ryan E; Martini, Gabriella D; Laptenko, Oleg; Freed-Pastor, William A; Prives, Carol; Stern, David L; Mann, Richard S; Bussemaker, Harmen J

2018-04-17

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes. Copyright © 2018 the Author(s). Published by PNAS.

Accurate and sensitive quantification of protein-DNA binding affinity

PubMed Central

Rastogi, Chaitanya; Rube, H. Tomas; Kribelbauer, Judith F.; Crocker, Justin; Loker, Ryan E.; Martini, Gabriella D.; Laptenko, Oleg; Freed-Pastor, William A.; Prives, Carol; Stern, David L.; Mann, Richard S.; Bussemaker, Harmen J.

2018-01-01

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes. PMID:29610332

Triggered emissions close to the proton gyrofrequency seen by Cluster

NASA Astrophysics Data System (ADS)

Grison, Benjamin; Pickett, Jolene; Omura, Yoshiharu; Santolik, Ondrej; Decreau, Pierrette; Masson, Arnaud; Engebretson, Mark; Cornilleau-Wehrlin, Nicole; Robert, Patrick; Dandouras, Iannis

Electromagnetic ion cyclotron (EMIC) triggered emissions have been recently observed onboard the Cluster spacecraft close to the plasmapause in the equatorial region of the magnetosphere. These waves appear as "risers": electromagnetic structures that have a positive frequency drift with time, i.e., the EMIC analogue of rising frequency whistler mode triggered emissions and chorus waves. In our first results concerning the emission process based on a single event, these risers have the following properties: they propagate away from the direction of the magnetic equator, they have elliptical left-handed polarization corresponding to the transverse Alfven mode, and frequency drifts of about 30 mHz/s. These risers are not common in the Cluster data set. Nevertheless a few other events were found with similar properties. Another interesting preliminary result is the existence of risers with a polarization opposite that of the EMIC triggered emissions and which correspond to the fast magnetosonic mode.

Proceedings of the Eighteenth NASA Propagation Experimenters Meeting (NAPEX 18) and the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop

NASA Technical Reports Server (NTRS)

Davarian, Faramaz (Editor)

1994-01-01

The NASA Propagation Experimenters Meeting (NAPEX), supported by the NASA Propagation Program, is convened annually to discuss studies made on radio wave propagation by investigators from domestic and international organizations. Participants included representatives from Canada, the Netherlands, England, and the United States, including researchers from universities, government agencies, and private industry. The meeting was organized into two technical sessions. The first session was dedicated to slant path propagation studies and experiments. The second session focused on propagation studies for mobile, personal, and sound broadcast systems. In total, 14 technical papers and some informal contributions were presented. Preceding NAPEX_17, the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop was held to review ACTS propagation activities.

Determinants of the Differential Antizyme-Binding Affinity of Ornithine Decarboxylase

PubMed Central

Liu, Yen-Chin; Hsu, Den-Hua; Huang, Chi-Liang; Liu, Yi-Liang; Liu, Guang-Yaw; Hung, Hui-Chih

2011-01-01

Ornithine decarboxylase (ODC) is a ubiquitous enzyme that is conserved in all species from bacteria to humans. Mammalian ODC is degraded by the proteasome in a ubiquitin-independent manner by direct binding to the antizyme (AZ). In contrast, Trypanosoma brucei ODC has a low binding affinity toward AZ. In this study, we identified key amino acid residues that govern the differential AZ binding affinity of human and Trypanosoma brucei ODC. Multiple sequence alignments of the ODC putative AZ-binding site highlights several key amino acid residues that are different between the human and Trypanosoma brucei ODC protein sequences, including residue 119, 124,125, 129, 136, 137 and 140 (the numbers is for human ODC). We generated a septuple human ODC mutant protein where these seven bases were mutated to match the Trypanosoma brucei ODC protein sequence. The septuple mutant protein was much less sensitive to AZ inhibition compared to the WT protein, suggesting that these amino acid residues play a role in human ODC-AZ binding. Additional experiments with sextuple mutants suggest that residue 137 plays a direct role in AZ binding, and residues 119 and 140 play secondary roles in AZ binding. The dissociation constants were also calculated to quantify the affinity of the ODC-AZ binding interaction. The K d value for the wild type ODC protein-AZ heterodimer ([ODC_WT]-AZ) is approximately 0.22 μM, while the K d value for the septuple mutant-AZ heterodimer ([ODC_7M]-AZ) is approximately 12.4 μM. The greater than 50-fold increase in [ODC_7M]-AZ binding affinity shows that the ODC-7M enzyme has a much lower binding affinity toward AZ. For the mutant proteins ODC_7M(-Q119H) and ODC_7M(-V137D), the K d was 1.4 and 1.2 μM, respectively. These affinities are 6-fold higher than the WT_ODC K d, which suggests that residues 119 and 137 play a role in AZ binding. PMID:22073206

Pressure wave propagation studies for oscillating cascades

NASA Technical Reports Server (NTRS)

Huff, Dennis L.

1992-01-01

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

Gelatin Nanoparticles with Enhanced Affinity for Calcium Phosphate.

PubMed

Farbod, Kambiz; Diba, Mani; Zinkevich, Tatiana; Schmidt, Stephan; Harrington, Matthew J; Kentgens, Arno P M; Leeuwenburgh, Sander C G

2016-05-01

Gelatin nanoparticles can be tuned with respect to their drug loading efficiency, degradation rate, and release kinetics, which renders these drug carriers highly suitable for a wide variety of biomedical applications. The ease of functionalization has rendered gelatin an interesting candidate material to introduce specific motifs for selective targeting to specific organs, but gelatin nanoparticles have not yet been modified to increase their affinity to mineralized tissue. By means of conjugating bone-targeting alendronate to biocompatible gelatin nanoparticles, a simple method is developed for the preparation of gelatin nanoparticles which exhibit strong affinity to mineralized surfaces. It has been shown that the degree of alendronate functionalization can be tuned by controlling the glutaraldehyde crosslinking density, the molar ratio between alendronate and glutaraldehyde, as well as the pH of the conjugation reaction. Moreover, it has been shown that the affinity of gelatin nanoparticles to calcium phosphate increases considerably upon functionalization with alendronate. In summary, gelatin nanoparticles have been developed, which exhibit great potential for use in bone-specific drug delivery and regenerative medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Relative binding affinities of monolignols to horseradish peroxidase

DOE PAGES

Sangha, Amandeep K.; Petridis, Loukas; Cheng, Xiaolin; ...

2016-07-22

Monolignol binding to the peroxidase active site is the first step in lignin polymerization in plant cell walls. Using molecular dynamics, docking, and free energy perturbation calculations, we investigate the binding of monolignols to horseradish peroxidase C. Our results suggest that p-coumaryl alcohol has the strongest binding affinity followed by sinapyl and coniferyl alcohol. Stacking interactions between the monolignol aromatic rings and nearby phenylalanine residues play an important role in determining the calculated relative binding affinities. p-Coumaryl and coniferyl alcohols bind in a pose productive for reaction in which a direct H-bond is formed between the phenolic –OH group andmore » a water molecule (W2) that may facilitate proton transfer during oxidation. In contrast, in the case of sinapyl alcohol there is no such direct interaction, the phenolic –OH group instead interacting with Pro139. Furthermore, since proton and electron transfer is the rate-limiting step in monolignol oxidation by peroxidase, the binding pose (and thus the formation of near attack conformation) appears to play a more important role than the overall binding affinity in determining the oxidation rate.« less

Proceedings of the Twenty-First NASA Propagation Experiments Meeting (NAPEX XXI) and the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop

NASA Technical Reports Server (NTRS)

Golshan, Nasser (Editor)

1997-01-01

The NASA Propagation Experimenters (NAPEX) meeting is convened each year to discuss studies supported by the NASA Propagation Program. Representatives from the satellite communications industry, academia and government who have an interest in space-ground radio wave propagation are invited to NAPEX meetings for discussions and exchange of information. The reports delivered at this meeting by program managers and investigators present recent activities and future plans. This forum provides an opportunity for peer discussion of work in progress, timely dissemination of propagation results, and close interaction with the satellite communications industry. NAPEX XXI took place in El Segundo, California on June 11-12, 1997 and consisted of three sessions. Session 1, entitled "ACTS Propagation Study Results & Outcome " covered the results of 20 station-years of Ka-band radio-wave propagation experiments. Session 11, 'Ka-band Propagation Studies and Models,' provided the latest developments in modeling, and analysis of experimental results about radio wave propagation phenomena for design of Ka-band satellite communications systems. Session 111, 'Propagation Research Topics,' covered a diverse range of propagation topics of interest to the space community, including overviews of handbooks and databases on radio wave propagation. The ACTS Propagation Studies miniworkshop was held on June 13, 1997 and consisted of a technical session in the morning and a plenary session in the afternoon. The morning session covered updates on the status of the ACTS Project & Propagation Program, engineering support for ACTS Propagation Terminals, and the Data Center. The plenary session made specific recommendations for the future direction of the program.

Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism

PubMed Central

Boughlala, Zakaria; Fonseca Guerra, Célia

2016-01-01

Abstract We have analyzed the structure and bonding of gas‐phase Cl−X and [HCl−X]+ complexes for X+= H+, CH3 +, Li+, and Na+, using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl− and HCl for the various cations. The Cl−X bond becomes longer and weaker along X+ = H+, CH3 +, Li+, and Na+. Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn–Sham molecular orbital (KS‐MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities. PMID:27551660

Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.

An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented.more » The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex.« less

Opposing intermolecular tuning of Ca2+ affinity for Calmodulin by its target peptides

NASA Astrophysics Data System (ADS)

Cheung, Margaret

We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with non-equilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+ signaling pathways in neurons. It was shown experimentally that Ca2+/CaM binds to the CaMKII peptide with higher affinity than the Ng peptide. The binding of CaMKII peptide to CaM in return increases the Ca2+ affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide, which binds to Ca2+-free CaM or Ca2+/CaM with similar binding affinity. Unlike CaM-CaMKII peptide that allowed structure determination by crystallography, the structural description of CaM-Ng peptide is unknown due to low binding affinity, therefore, we computationally generated an ensemble of CaM-Ng peptide structures by matching the changes in the chemical shifts of CaM upon Ng peptide binding from nuclear magnetic resonance experiments. We computed the changes in Ca2+ affinity for CaM with and without binding targets in atomistic models using Jarzynski's equality. We discovered the molecular underpinnings of lowered affinity of Ca2+ for CaM in the presence of Ng by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+ binding loops particularly at C-domain of CaM, enabling Ca2+release. In contrast, CaMKII increases Ca2+ affinity for the C-domain of CaM by stabilizing the two Ca2+ binding loops.

IA-2 autoantibody affinity in children at risk for type 1 diabetes.

PubMed

Krause, Stephanie; Chmiel, Ruth; Bonifacio, Ezio; Scholz, Marlon; Powell, Michael; Furmaniak, Jadwiga; Rees Smith, Bernard; Ziegler, Anette-G; Achenbach, Peter

2012-12-01

Autoantibodies to insulinoma-associated protein 2 (IA-2A) are associated with increased risk for type 1 diabetes. Here we examined IA-2A affinity and epitope specificity to assess heterogeneity in response intensity in relation to pathogenesis and diabetes risk in 50 children who were prospectively followed from birth. At first IA-2A appearance, affinity ranged from 10(7) to 10(11)L/mol and was high (>1.0×10(9)L/mol) in 41 (82%) children. IA-2A affinity was not associated with epitope specificity or HLA class II haplotype. On follow-up, affinity increased or remained high, and IA-2A were commonly against epitopes within the protein tyrosine phosphatase-like IA-2 domain and the homologue protein IA-2β. IA-2A were preceded or accompanied by other islet autoantibodies in 49 (98%) children, of which 34 progressed to diabetes. IA-2A affinity did not stratify diabetes risk. In conclusion, the IA-2A response in children is intense with rapid maturation against immunogenic epitopes and a strong association with diabetes development. Copyright © 2012 Elsevier Inc. All rights reserved.

An Investigation of State Educational Twitter Hashtags (SETHS) as Affinity Spaces

ERIC Educational Resources Information Center

Rosenberg, Joshua M.; Greenhalgh, Spencer P.; Koehler, Matthew J.; Hamilton, Erica R.; Akcaoglu, Mete

2016-01-01

Affinity spaces are digital or physical spaces in which participants interact with one another around content of shared interest and through a common portal (or platform). Among teachers, some of the largest affinity spaces may be those organized around hashtags on Twitter: These spaces are public, largely unmoderated, and thriving, yet very…

Elevated Temperature Crack Propagation

NASA Technical Reports Server (NTRS)

Orange, Thomas W.

1994-01-01

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

His86 from the N-terminus of frataxin coordinates iron and is required for Fe-S cluster synthesis.

PubMed

Gentry, Leslie E; Thacker, Matthew A; Doughty, Reece; Timkovich, Russell; Busenlehner, Laura S

2013-09-03

Human frataxin has a vital role in the biosynthesis of iron-sulfur (Fe-S) clusters in mitochondria, and its deficiency causes the neurodegenerative disease Friedreich's ataxia. Proposed functions for frataxin in the Fe-S pathway include iron donation to the Fe-S cluster machinery and regulation of cysteine desulfurase activity to control the rate of Fe-S production, although further molecular detail is required to distinguish these two possibilities. It is well established that frataxin can coordinate iron using glutamate and aspartate side chains on the protein surface; however, in this work we identify a new iron coordinating residue in the N-terminus of human frataxin using complementary spectroscopic and structural approaches. Further, we demonstrate that His86 in this N-terminal region is required for high affinity iron coordination and iron assembly of Fe-S clusters by ISCU as part of the Fe-S cluster biosynthetic complex. If a binding site that includes His86 is important for Fe-S cluster synthesis as part of its chaperone function, this raises the possibility that either iron binding at the acidic surface of frataxin may be spurious or that it is required for protein-protein interactions with the Fe-S biosynthetic quaternary complex. Our data suggest that iron coordination to frataxin may be significant to the Fe-S cluster biosynthesis pathway in mitochondria.

Proceedings of the Seventeenth NASA Propagation Experimenters Meeting (NAPEX 17) and the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop

NASA Technical Reports Server (NTRS)

Davarian, Faramaz (Editor)

1993-01-01

The NASA Propagation Experimenters Meeting (NAPEX) is convened annually to discuss studies made on radio wave propagation by investors from domestic and international organizations. NAPEX 17 was held on 15 June 1993. The meeting was organized into two technical sessions. The first session was dedicated to slant path propagation studies and experiments. The second session focused on propagation studies for mobile and personal communications. Preceding NAPEX 17, the Advanced Communications Technology Satellite (ACTS) Propagation Studies Miniworkshop was held on 14 June 1993 to review ACTS propagation activities with emphasis on ACTS experiments status and data collection, processing, and exchange.

ACTS Propagation Measurements in Maryland and Virginia

NASA Technical Reports Server (NTRS)

Dissanayake, Asoka; Lin, Kuan-Ting

1996-01-01

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

The geometry of propagating rifts

NASA Astrophysics Data System (ADS)

McKenzie, Dan

1986-03-01

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

Pushing antibody-based labeling systems to higher sensitivity by linker-assisted affinity enhancement.

PubMed

Gorris, Hans H; Bade, Steffen; Röckendorf, Niels; Fránek, Milan; Frey, Andreas

2011-08-17

The sensitivity of antibody/hapten-based labeling systems is limited by the natural affinity ceiling of immunoglobulins. Breaking this limit by antibody engineering is difficult. We thus attempted a different approach and investigated if the so-called bridge effect, a corecognition of the linker present between hapten and carrier protein during antibody generation, can be utilized to improve the affinity of such labeling systems. The well-known haptens 2,4-dinitrophenol (2,4-DNP) and 2,4-dichlorophenoxyacetic acid (2,4-D) were equipped with various linkers, and the resulting affinity change of their cognate antibodies was analyzed by ELISA. Anti-2,4-DNP antibodies exhibited the best affinity to their hapten when it was combined with aminobutanoic acid or aminohexanoic acid. The affinity of anti-2,4-D antibodies could be enhanced even further with longer aliphatic spacers connected to the hapten. The affinity toward aminoundecanoic acid-2,4-D derivatives, for instance, was improved about 100-fold compared to 2,4-D alone and yielded detection limits as low as 100 amoles of analyte. As the effect occurred for all antibodies and haptens tested, it may be sensible to implement the bridge effect in future antibody/hapten-labeling systems in order to achieve the highest sensitivity possible.

Influence of bone affinity on the skeletal distribution of fluorescently labeled bisphosphonates in vivo.

PubMed

Roelofs, Anke J; Stewart, Charlotte A; Sun, Shuting; Błażewska, Katarzyna M; Kashemirov, Boris A; McKenna, Charles E; Russell, R Graham G; Rogers, Michael J; Lundy, Mark W; Ebetino, Frank H; Coxon, Fraser P

2012-04-01

Bisphosphonates are widely used antiresorptive drugs that bind to calcium. It has become evident that these drugs have differing affinities for bone mineral; however, it is unclear whether such differences affect their distribution on mineral surfaces. In this study, fluorescent conjugates of risedronate, and its lower-affinity analogues deoxy-risedronate and 3-PEHPC, were used to compare the localization of compounds with differing mineral affinities in vivo. Binding to dentine in vitro confirmed differences in mineral binding between compounds, which was influenced predominantly by the characteristics of the parent compound but also by the choice of fluorescent tag. In growing rats, all compounds preferentially bound to forming endocortical as opposed to resorbing periosteal surfaces in cortical bone, 1 day after administration. At resorbing surfaces, lower-affinity compounds showed preferential binding to resorption lacunae, whereas the highest-affinity compound showed more uniform labeling. At forming surfaces, penetration into the mineralizing osteoid was found to inversely correlate with mineral affinity. These differences in distribution at resorbing and forming surfaces were not observed at quiescent surfaces. Lower-affinity compounds also showed a relatively higher degree of labeling of osteocyte lacunar walls and labeled lacunae deeper within cortical bone, indicating increased penetration of the osteocyte canalicular network. Similar differences in mineralizing surface and osteocyte network penetration between high- and low-affinity compounds were evident 7 days after administration, with fluorescent conjugates at forming surfaces buried under a new layer of bone. Fluorescent compounds were incorporated into these areas of newly formed bone, indicating that "recycling" had occurred, albeit at very low levels. Taken together, these findings indicate that the bone mineral affinity of bisphosphonates is likely to influence their distribution within the

Uncertainty Propagation in OMFIT

NASA Astrophysics Data System (ADS)

Smith, Sterling; Meneghini, Orso; Sung, Choongki

2017-10-01

A rigorous comparison of power balance fluxes and turbulent model fluxes requires the propagation of uncertainties in the kinetic profiles and their derivatives. Making extensive use of the python uncertainties package, the OMFIT framework has been used to propagate covariant uncertainties to provide an uncertainty in the power balance calculation from the ONETWO code, as well as through the turbulent fluxes calculated by the TGLF code. The covariant uncertainties arise from fitting 1D (constant on flux surface) density and temperature profiles and associated random errors with parameterized functions such as a modified tanh. The power balance and model fluxes can then be compared with quantification of the uncertainties. No effort is made at propagating systematic errors. A case study will be shown for the effects of resonant magnetic perturbations on the kinetic profiles and fluxes at the top of the pedestal. A separate attempt at modeling the random errors with Monte Carlo sampling will be compared to the method of propagating the fitting function parameter covariant uncertainties. Work supported by US DOE under DE-FC02-04ER54698, DE-FG2-95ER-54309, DE-SC 0012656.

Exploring Thermoresponsive Affinity Agents to Enhance Microdialysis Sampling Efficiency of Proteins

NASA Astrophysics Data System (ADS)

Vasicek, Thaddeus

Affinity agents increase microdialysis protein relative recovery, yet they have not seen widespread use within the microdialysis community due to their additional instrumentation requirements and prohibitive cost. This dissertation describes new affinity agents for microdialysis that require no additional instrumentation to use, have nearly 100% particle recovery, are 7 times more cost efficient than alternatives, and have low specificity enabling their use for a wide variety of proteins. Initially gold nanoparticles were chosen as an affinity ligand support due to their high surface area/volume ratio and colloidal stability. Poly (N-isopropylacrylamide) was immobilized to the gold nanoparticles, which served to sterically stabilize the particles and to act as a generic, reversible protein capture agent. A method was developed to reproducibly vary and quantify poly (N-isopropylacrylamide) graft density from 0.09 to 0.40 ligands/nm2 on gold nanoparticles. During characterization of the polymer coated gold nanoparticles, irreversible particle agglomeration was observed at low polymer graft density in ionic solutions, which prevented further development as a protein capture agent. Poly (N-isopropylacrylamide) nanogels, which have low nonspecific adsorption, low interparticle attractive forces owing to the low curvature of the particle, and a low Hamaker constant, were synthesized to overcome the agglomeration problem. A generic protein affinity ligand cibacron blue, was immobilized to the nanogels, which enabled rapid determination of particle recovery. The perfusion of the nanogels through a microdialysis probe was optimized yielding 100% particle recovery using a combination of a syringe and peristaltic pump. The microdialysis collection efficiency of CCL2, a physiologically relevant cytokine, was increased 3-fold with addition of the nanogel to the microdialysis perfusion fluid. The reduction in instrumentation requirements, low cost, and low specificity obtained

Affinity for Quantitative Tools: Undergraduate Marketing Students Moving beyond Quantitative Anxiety

ERIC Educational Resources Information Center

Tarasi, Crina O.; Wilson, J. Holton; Puri, Cheenu; Divine, Richard L.

2013-01-01

Marketing students are known as less likely to have an affinity for the quantitative aspects of the marketing discipline. In this article, we study the reasons why this might be true and develop a parsimonious 20-item scale for measuring quantitative affinity in undergraduate marketing students. The scale was administered to a sample of business…

Properties of Merger Shocks in Merging Galaxy Clusters

NASA Astrophysics Data System (ADS)

Ha, Ji-Hoon; Ryu, Dongsu; Kang, Hyesung

2018-04-01

X-ray shocks and radio relics detected in the cluster outskirts are commonly interpreted as shocks induced by mergers of subclumps. We study the properties of merger shocks in merging galaxy clusters, using a set of cosmological simulations for the large-scale structure formation of the universe. As a representative case, we focus on the simulated clusters that undergo almost head-on collisions with mass ratio ∼2. Due to the turbulent nature of the intracluster medium, shock surfaces are not smooth, but composed of shocks with different Mach numbers. As the merger shocks expand outward from the core to the outskirts, the average Mach number, < {M}s> , increases in time. We suggest that the shocks propagating along the merger axis could be manifested as X-ray shocks and/or radio relics. The kinetic energy through the shocks, F ϕ , peaks at ∼1 Gyr after their initial launching, or at ∼1–2 Mpc from the core. Because of the Mach number dependent model adopted here for the cosmic-ray (CR) acceleration efficiency, their CR-energy-weighted Mach number is higher with < {M}s{> }CR}∼ 3{--}4, compared to the kinetic-energy-weighted Mach number, < {M}s{> }φ ∼ 2{--}3. Most energetic shocks are to be found ahead of the lighter dark matter (DM) clump, while the heavier DM clump is located on the opposite side of clusters. Although our study is limited to the merger case considered, the results such as the means and variations of shock properties and their time evolution could be compared with the observed characteristics of merger shocks, constraining interpretations of relevant observations.

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.

Affinity Maturation of a Cyclic Peptide Handle for Therapeutic Antibodies Using Deep Mutational Scanning*

PubMed Central

van Rosmalen, Martijn; Janssen, Brian M. G.; Hendrikse, Natalie M.; van der Linden, Ardjan J.; Pieters, Pascal A.; Wanders, Dave; de Greef, Tom F. A.; Merkx, Maarten

2017-01-01

Meditopes are cyclic peptides that bind in a specific pocket in the antigen-binding fragment of a therapeutic antibody such as cetuximab. Provided their moderate affinity can be enhanced, meditope peptides could be used as specific non-covalent and paratope-independent handles in targeted drug delivery, molecular imaging, and therapeutic drug monitoring. Here we show that the affinity of a recently reported meditope for cetuximab can be substantially enhanced using a combination of yeast display and deep mutational scanning. Deep sequencing was used to construct a fitness landscape of this protein-peptide interaction, and four mutations were identified that together improved the affinity for cetuximab 10-fold to 15 nm. Importantly, the increased affinity translated into enhanced cetuximab-mediated recruitment to EGF receptor-overexpressing cancer cells. Although in silico Rosetta simulations correctly identified positions that were tolerant to mutation, modeling did not accurately predict the affinity-enhancing mutations. The experimental approach reported here should be generally applicable and could be used to develop meditope peptides with low nanomolar affinity for other therapeutic antibodies. PMID:27974464

A statistical study of EMIC waves observed by Cluster. 1. Wave properties. EMIC Wave Properties

DOE PAGES

Allen, R. C.; Zhang, J. -C.; Kistler, L. M.; ...

2015-07-23

Electromagnetic ion cyclotron (EMIC) waves are an important mechanism for particle energization and losses inside the magnetosphere. In order to better understand the effects of these waves on particle dynamics, detailed information about the occurrence rate, wave power, ellipticity, normal angle, energy propagation angle distributions, and local plasma parameters are required. Previous statistical studies have used in situ observations to investigate the distribution of these parameters in the magnetic local time versus L-shell (MLT-L) frame within a limited magnetic latitude (MLAT) range. In our study, we present a statistical analysis of EMIC wave properties using 10 years (2001–2010) of datamore » from Cluster, totaling 25,431 min of wave activity. Due to the polar orbit of Cluster, we are able to investigate EMIC waves at all MLATs and MLTs. This allows us to further investigate the MLAT dependence of various wave properties inside different MLT sectors and further explore the effects of Shabansky orbits on EMIC wave generation and propagation. Thus, the statistical analysis is presented in two papers. OUr paper focuses on the wave occurrence distribution as well as the distribution of wave properties. The companion paper focuses on local plasma parameters during wave observations as well as wave generation proxies.« less

Solitons and the energy-momentum tensor for affine Toda theory

NASA Astrophysics Data System (ADS)

Olive, D. I.; Turok, N.; Underwood, J. W. R.

1993-07-01

Following Leznov and Saveliev, we present the general solution to Toda field theories of conformal, affine or conformal affine type, associated with a simple Lie algebra g. These depend on a free massless field and on a group element. By putting the former to zero, soliton solutions to the affine Toda theories with imaginary coupling constant result with the soliton data encoded in the group element. As this requires a reformulation of the affine Kac-Moody algebra closely related to that already used to formulate the physical properties of the particle excitations, including their scattering matrices, a unified treatment of particles and solitons emerges. The physical energy—momentum tensor for a general solution is broken into a total derivative plus a part dependent only on the derivatives of the free field. Despite the non-linearity of the field equations and their complex nature the energy and momentum of the N-soliton solution is shown to be real, equalling the sum of contributions from the individual solitons. There are rank-g species of soliton, with masses given by a generalisation of a formula due to Hollowood, being proportional to the components of the left Perron-Frobenius eigenvector of the Cartan matrix of g.

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

Affine invariants of convex polygons.

PubMed

Flusser, Jan

2002-01-01

In this correspondence, we prove that the affine invariants, for image registration and object recognition, proposed recently by Yang and Cohen (see ibid., vol.8, no.7, p.934-46, July 1999) are algebraically dependent. We show how to select an independent and complete set of the invariants. The use of this new set leads to a significant reduction of the computing complexity without decreasing the discrimination power.

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

Structural Insights into the Affinity of Cel7A Carbohydrate-binding Module for Lignin*

PubMed Central

Strobel, Kathryn L.; Pfeiffer, Katherine A.; Blanch, Harvey W.; Clark, Douglas S.

2015-01-01

The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638

Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh.

PubMed

Khan, Faisal; Pandey, Atul Kumar; Tripathi, Manorma; Talwar, Sudha; Bisen, Prakash S; Borkar, Minal; Agrawal, Suraksha

2007-04-07

assessments revealed that north Indians are clustering with Caucasians. The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and both upper caste and Muslim populations are genetically closer to the Caucasians.

Multipoint propagators in cosmological gravitational instability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernardeau, Francis; Crocce, Martin; Scoccimarro, Roman

2008-11-15

We introduce the concept of multipoint propagators between linear cosmic fields and their nonlinear counterparts in the context of cosmological perturbation theory. Such functions express how a nonlinearly evolved Fourier mode depends on the full ensemble of modes in the initial density field. We identify and resum the dominant diagrams in the large-k limit, showing explicitly that multipoint propagators decay into the nonlinear regime at the same rate as the two-point propagator. These analytic results generalize the large-k limit behavior of the two-point propagator to arbitrary order. We measure the three-point propagator as a function of triangle shape in numericalmore » simulations and confirm the results of our high-k resummation. We show that any n-point spectrum can be reconstructed from multipoint propagators, which leads to a physical connection between nonlinear corrections to the power spectrum at small scales and higher-order correlations at large scales. As a first application of these results, we calculate the reduced bispectrum at one loop in renormalized perturbation theory and show that we can predict the decrease in its dependence on triangle shape at redshift zero, when standard perturbation theory is least successful.« less

Affinity approaches in RNAi-based therapeutics purification.

PubMed

Pereira, Patrícia; Queiroz, João A; Figueiras, Ana; Sousa, Fani

2016-05-15

The recent investigation on RNA interference (RNAi) related mechanisms and applications led to an increased awareness of the importance of RNA in biology. Nowadays, RNAi-based technology has emerged as a potentially powerful tool for silencing gene expression, being exploited to develop new therapeutics for treating a vast number of human disease conditions, as it is expected that this technology can be translated onto clinical applications in a near future. This approach makes use of a large number of small (namely short interfering RNAs, microRNAs and PIWI-interacting RNAs) and long non-coding RNAs (ncRNAs), which are likely to have a crucial role as the next generation therapeutics. The commercial and biomedical interest in these RNAi-based therapy applications have fostered the need to develop innovative procedures to easily and efficiently purify RNA, aiming to obtain the final product with high purity degree, good quality and biological activity. Recently, affinity chromatography has been applied to ncRNAs purification, in view of the high specificity. Therefore, this article intends to review the biogenesis pathways of regulatory ncRNAs and also to discuss the most significant and recent developments as well as applications of affinity chromatography in the challenging task of purifying ncRNAs. In addition, the importance of affinity chromatography in ncRNAs purification is addressed and prospects for what is forthcoming are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

Determination of hydride affinities of various aldehydes and ketones in acetonitrile.

PubMed

Zhu, Xiao-Qing; Chen, Xi; Mei, Lian-Rui

2011-05-06

The hydride affinities of 21 typical aldehydes and ketones in acetonitrile were determined by using an experimental method, which is valuable for chemists choosing suitable reducing agents to reduce them. The focus of this paper is to introduce a very facile experimental method, which can be used to determine the hydride affinities of various carbonyl compounds in solution.

Length-Two Representations of Quantum Affine Superalgebras and Baxter Operators