Prediction of protein-protein interaction types using association rule based classification

This article has been made available through the Brunel Open Access Publishing Fund - Copyright @ 2009 Park et alBackground: Protein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help in the functional annotation of new protein complexes and in the prediction of protein interaction partners by knowledge driven approaches. Results: This work addresses pattern discovery of the interaction sites for four different interaction types to characterize and uses them for the prediction of PPI types employing Association Rule Based Classification (ARBC) which includes association rule generation and posterior classification. We incorporated domain information from protein complexes in SCOP proteins and identified 354 domain-interaction sites. 14 interface properties were calculated from amino acid and secondary structure composition and then used to generate a set of association rules characterizing these domain-interaction sites employing the APRIORI algorithm. Our results regarding the classification of PPI types based on a set of discovered association rules shows that the discriminative ability of association rules can significantly impact on the prediction power of classification models. We also showed that the accuracy of the classification can be improved through the use of structural domain information and also the use of secondary structure content. Conclusion: The advantage of our approach is that we can extract biologically significant information from the interpretation of the discovered association rules in terms of understandability and interpretability of rules. A web application based on our method can be found at http://bioinfo.ssu.ac.kr/~shpark/picasso/SHP was supported by the Korea Research Foundation Grant funded by the Korean Government(KRF-2005-214-E00050). JAR has been supported by the Programme Alβan, the European Union Programme of High level Scholarships for Latin America, scholarship E04D034854CL. SK was supported by Soongsil University Research Fund

EuCo2P2: A Model Molecular-Field Helical Heisenberg Antiferromagnet

The metallic compound EuCo2P2 with the body-centered tetragonal ThCr2Si2 structure containing Eu spins 7/2 was previously shown from single-crystal neutron diffraction measurements to exhibit a helical antiferromagnetic (AFM) structure below TN = 66.5 K with the helix axis along the c axis and with the ordered moments aligned within the ab-plane. Here we report crystallography, electrical resistivity, heat capacity, magnetization and magnetic susceptibility measurements on single crystals of this compound. We demonstrate that EuCo2P2 is a model molecular-field helical Heisenberg antiferromagnet from comparisons of the anisotropic magnetic susceptibility chi, high-field magnetization and magnetic heat capacity of EuCo2P2 single crystals at temperature T < TN with the predictions of our recent formulation of molecular field theory. Values of the Heisenberg exchange interactions between the Eu spins are derived from the data. The low-T magnetic heat capacity ~ T^3 arising from spin-wave excitations with no anisotropy gap is calculated and found to be comparable to the lattice heat capacity. The density of states at the Fermi energy of EuCo2P2 and the related compound BaCo2P2 are found from the heat capacity data to be large, 10 and 16 states/eV per formula unit for EuCo2P2 and BaCo2P2, respectively. These values are enhanced by a factor of ~2.5 above those found from DFT electronic structure calculations for the two compounds. The calculations also find ferromagnetic Eu-Eu exchange interactions within the ab-plane and AFM interactions between nearest- and next-nearest planes, in agreement with the MFT analysis of chi{ab}(T < TN).Comment: 20 pages, 17 figures, 3 tables, 46 references. This is an extended replacement of arXiv:1512.02958 with an additional coautho

Bose-Einstein condensation in antiferromagnets close to the saturation field

At zero temperature and strong applied magnetic fields the ground sate of an anisotropic antiferromagnet is a saturated paramagnet with fully aligned spins. We study the quantum phase transition as the field is reduced below an upper critical $H_{c2}$ and the system enters a XY-antiferromagnetic phase. Using a bond operator representation we consider a model spin-1 Heisenberg antiferromagnetic with single-ion anisotropy in hyper-cubic lattices under strong magnetic fields. We show that the transition at $H_{c2}$ can be interpreted as a Bose-Einstein condensation (BEC) of magnons. The theoretical results are used to analyze our magnetization versus field data in the organic compound $NiCl_2$-$4SC(NH_2)_2$ (DTN) at very low temperatures. This is the ideal BEC system to study this transition since $H_{c2}$ is sufficiently low to be reached with static magnetic fields (as opposed to pulsed fields). The scaling of the magnetization as a function of field and temperature close to $H_{c2}$ shows excellent agreement with the theoretical predictions. It allows to obtain the quantum critical exponents and confirm the BEC nature of the transition at $H_{c2}$.Comment: 4 pages, 1 figure. Accepted for publication in PRB

Nongauge bright soliton of the nonlinear Schrodinger (NLS) equation and a family of generalized NLS equations

We present an approach to the bright soliton solution of the NLS equation from the standpoint of introducing a constant potential term in the equation. We discuss a `nongauge' bright soliton for which both the envelope and the phase depend only on the traveling variable. We also construct a family of generalized NLS equations with solitonic sech^p solutions in the traveling variable and find an exact equivalence with other nonlinear equations, such as the Korteveg-de Vries and Benjamin-Bona-Mahony equations when p=2Comment: ~4 pages, 3 figures, 16 references, published versio

The onset of solar cycle 24: What global acoustic modes are telling us

We study the response of the low-degree, solar p-mode frequencies to the unusually extended minimum of solar surface activity since 2007. A total of 4768 days of observations collected by the space-based, Sun-as-a-star helioseismic GOLF instrument are analyzed. A multi-step iterative maximum-likelihood fitting method is applied to subseries of 365 days and 91.25 days to extract the p-mode parameters. Temporal variations of the l=0, 1, and 2 p-mode frequencies are then obtained from April 1996 to May 2009. While the p-mode frequency shifts are closely correlated with solar surface activity proxies during the past solar cycles, the frequency shifts of the l=0 and l=2 modes show an increase from the second half of 2007, when no significant surface activity is observable. On the other hand, the l=1 modes follow the general decreasing trend of the solar surface activity. The different behaviours between the l=0 and l=2 modes and the l=1 modes can be interpreted as different geometrical responses to the spatial distribution of the solar magnetic field beneath the surface of the Sun. The analysis of the low-degree, solar p-mode frequency shifts indicates that the solar activity cycle 24 started late 2007, despite the absence of activity on the solar surface.Comment: To be accepted by A&A (with minor revisions), 4 pages, 3 figures, 1 tabl

Inferring Networks of Substitutable and Complementary Products

In a modern recommender system, it is important to understand how products relate to each other. For example, while a user is looking for mobile phones, it might make sense to recommend other phones, but once they buy a phone, we might instead want to recommend batteries, cases, or chargers. These two types of recommendations are referred to as substitutes and complements: substitutes are products that can be purchased instead of each other, while complements are products that can be purchased in addition to each other. Here we develop a method to infer networks of substitutable and complementary products. We formulate this as a supervised link prediction task, where we learn the semantics of substitutes and complements from data associated with products. The primary source of data we use is the text of product reviews, though our method also makes use of features such as ratings, specifications, prices, and brands. Methodologically, we build topic models that are trained to automatically discover topics from text that are successful at predicting and explaining such relationships. Experimentally, we evaluate our system on the Amazon product catalog, a large dataset consisting of 9 million products, 237 million links, and 144 million reviews.Comment: 12 pages, 6 figure

Renormalization Constants of Quark Operators for the Non-Perturbatively Improved Wilson Action

We present the results of an extensive lattice calculation of the renormalization constants of bilinear and four-quark operators for the non-perturbatively O(a)-improved Wilson action. The results are obtained in the quenched approximation at four values of the lattice coupling by using the non-perturbative RI/MOM renormalization method. Several sources of systematic uncertainties, including discretization errors and final volume effects, are examined. The contribution of the Goldstone pole, which in some cases may affect the extrapolation of the renormalization constants to the chiral limit, is non-perturbatively subtracted. The scale independent renormalization constants of bilinear quark operators have been also computed by using the lattice chiral Ward identities approach and compared with those obtained with the RI-MOM method. For those renormalization constants the non-perturbative estimates of which have been already presented in the literature we find an agreement which is typically at the level of 1%.Comment: 36 pages, 13 figures. Minor changes in the text and in one figure. Accepted for publication on JHE