Abstract:
In this study, Decision Trees (DT) based models were developed to discriminate compound bioactivities by using their chemical structure fingerprints provided in the PubChem system http://pubchem.ncbi.nlm.nih.gov webcite. The DT models were examined for filtering biological activity data contained in four assays deposited in the PubChem Bioassay Database including assays tested for 5HT1a agonists, antagonists, and HIV-1 RT-RNase H inhibitors. The 10-fold Cross Validation (CV) sensitivity, specificity and Matthews Correlation Coefficient (MCC) for the models are 57.2~80.5%, 97.3~99.0%, 0.4~0.5 respectively. A further evaluation was also performed for DT models built for two independent bioassays, where inhibitors for the same HIV RNase target were screened using different compound libraries, this experiment yields enrichment factor of 4.4 and 9.7.Our results suggest that the designed DT models can be used as a virtual screening technique as well as a complement to traditional approaches for hits selection.High-throughput screening (HTS) is an automated technique and has been effectively used for rapidly testing the activity of large numbers of compounds [1-3]. Advanced technologies and availability of large-scale chemical libraries allow for the examination of hundreds of thousands of compounds in a day via HTS. Although the extensive libraries containing several million compounds can be screened in a matter of days, only a small fraction of compounds can be selected for confirmatory screenings. Further examination of verified hits from the secondary dose-response assay can be eventually winnowed to a few to proceed to the medicinal chemistry phase for lead optimization [4,5]. The very low success rate from the hits-to-lead development presents a great challenge in the earlier screening phase to select promising hits from the HTS assay [4]. Thus, the study of HTS assay data and the development of a systematic knowledge-driven model is in demand and useful to facilitat

Abstract:
The neighboring analysis is achieved by evaluating the cosine scores of each bioassay pair and fraction of overlaps among the human-curated neighbors. Our results from the cosine score distribution analysis and assay neighbor clustering analysis on all PubChem bioassays suggest that strong correlations among the bioassays can be identified from their conceptual relevance. A comparison with other existing assay neighboring methods suggests that the text-mining based bioassay neighboring approach provides meaningful linkages among the PubChem bioassays, and complements the existing methods by identifying additional relationships among the bioassay entries.The text-mining based bioassay neighboring analysis is efficient for correlating bioassays and studying different aspects of a biological process, which are otherwise difficult to achieve by existing neighboring procedures due to the lack of specific annotations and structured information. It is suggested that the text-mining based bioassay neighboring analysis can be used as a standalone or as a complementary tool for the PubChem bioassay neighboring process to enable efficient integration of assay results and generate hypotheses for the discovery of bioactivities of the tested reagents.The number of High Throughput Screening (HTS) assays deposited in PubChem [1] has grown quickly in recent years. As of April 18th 2010, PubChem has over 2300 bioassay records that are publicly available, including primary HTS assays and confirmatory assays associated with hundreds of targets or cell lines. While a number of tools have been developed to utilize the chemical structure information and the bioactivity outcomes[2], the large volume of textual descriptions for assay protocols has made it a very challenging task to analyze and interpret such unstructured information toward the new and structured information.One systematic knowledge driven study of HTS assay data is to understand how they are inter-related. The PubChem datab

Abstract:
We investigate the interaction energy and the possibility of itinerant ferromagnetism in a strongly interacting Fermi gas at zero temperature in the absence of molecule formation. The interaction energy is obtained by summing the perturbative contributions of Galitskii-Feynman type to all orders in the gas parameter. It can be expressed by a simple phase space integral of an in-medium scattering phase shift. In both three and two dimensions (3D and 2D), the interaction energy shows a maximum before reaching the resonance from the Bose-Einstein condensate side, which provides a possible explanation of the experimental measurements of the interaction energy. This phenomenon can be theoretically explained by the qualitative change of the nature of the binary interaction in the medium. The appearance of an energy maximum has significant effects on the itinerant ferromagnetism. In 3D, the ferromagnetic transition is reentrant and itinerant ferromagnetism exists in a narrow window around the energy maximum. In 2D, the present theoretical approach suggests that itinerant ferromagnetism does not exist, which reflects the fact that the energy maximum becomes much lower than the energy of the fully polarized state.

Abstract:
We investigate the ferromagnetic transition in repulsive Fermi gases at zero temperature with upper branch and effective range effects. Based on a general effective Lagrangian that reproduces precisely the two-body $s$-wave scattering phase shift, we obtain a nonperturbative expression of the energy density as a function of the polarization by using the Bethe-Goldstone ladder resummation. For hard sphere potential, the predicted critical gas parameter $k_{\rm F}a=0.816$ and the spin susceptibility agree well with the results from fixed-node diffusion Monte Carlo calculations. In general, positive and negative effective ranges have opposite effects on the critical gas parameter $k_{\rm F}a$: While a positive effective range reduces the critical gas parameter, a negative effective range increases it. For attractive potential or Feshbach resonance model, the many-body upper branch exhibits an energy maximum at $k_{\rm F}a=\alpha$ with $\alpha=1.34$ from the Bethe-Goldstone ladder resummation, which is qualitatively consistent with experimental results. The many-body T-matrix has a positive-energy pole for $k_{\rm F}a>\alpha$ and it becomes impossible to distinguish the bound state and the scattering state. These positive-energy bound states become occupied and therefore the upper branch reaches an energy maximum at $k_{\rm F}a=\alpha$. In the zero range limit, there exists a narrow window ($0.86

Abstract:
QCD-like theories possess a positively definite fermion determinant at finite baryon chemical potential $\mu_{\text B}$ and the lattice simulation can be successfully performed. While the chiral perturbation theories are sufficient to describe the Bose condensate at low density, to describe the crossover from Bose-Einstein condensation (BEC) to BCS superfluidity at moderate density we should use some fermionic effective model of QCD, such as the Nambu-Jona-Lasinio model. In this paper, using two-color two-flavor QCD as an example, we examine how the Nambu-Jona-Lasinio model describes the weakly interacting Bose condensate at low density and the BEC-BCS crossover at moderate density. Near the quantum phase transition point $\mu_{\text B}=m_\pi$ ($m_\pi$ is the mass of pion/diquark multiplet), the Ginzburg-Landau free energy at the mean-field level can be reduced to the Gross-Pitaevskii free energy describing a weakly repulsive Bose condensate with a diquark-diquark scattering length identical to that predicted by the chiral perturbation theories. The Goldstone mode recovers the Bogoliubov excitation in weakly interacting Bose condensates. The results of in-medium chiral and diquark condensates predicted by chiral perturbation theories are analytically recovered. The BEC-BCS crossover and meson Mott transition at moderate baryon chemical potential as well as the beyond-mean-field corrections are studied. Part of our results can also be applied to real QCD at finite baryon or isospin chemical potential.

Abstract:
We investigate the BCS-BEC crossover at zero temperature in the frame of a relativistic model. The universality of the BCS-BEC crossover for non-relativistic systems breaks down in relativistic case and the crossover can be induced by changing the density. When the effective scattering length is much less than the fermion Compton wavelength, we recover the non-relativistic result if the gas is initially in non-relativistic state. At ultra-strong coupling where the scattering length is of the order of the Compton wavelength, a new BEC state appears. In this state the condensed bosons become nearly massless and anti-fermions are excited. The behavior of the Goldstone mode and the mixing between the amplitude and phase modes are significantly different in different condensed regions.

Abstract:
The non-relativistic $G_0 G$ formalism of BCS-BEC crossover at finite temperature is extended to relativistic fermion systems. The uncondensed pairs contribute a pseudogap to the fermion excitations. The theory recovers the BCS mean field approximation at zero temperature and the non-relativistic results in a proper limit. For massive fermions, when the coupling strength increases, there exist two crossovers from the weak coupling BCS superfluid to the non-relativistic BEC state and then to the relativistic BEC state. For color superconductivity at moderate baryon density, the matter is in the BCS-BEC crossover region, and the behavior of the pseudogap is quite similar to that found in high temperature superconductors.