Inferring gene regulatory networks from gene expression data by a dynamic Bayesian network-based model

Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the efficiency of DBN in inferring GRNs is often hampered by missing values in expression data, and excessive computation time due to the large search space whereby DBN treats all genes as potential regulators for a target gene. In this paper, we proposed a DBN-based model with missing values imputation to improve inference efficiency, and potential regulators detection which aims to lessen computation time by limiting potential regulators based on expression changes. The performance of the proposed model is assessed by using time-series expression data of yeast cell cycle. The experimental results showed reduced computation time and improved efficiency in detecting gene-gene relationships

Inferring gene regulatory networks from gene expression data by a dynamic Bayesian network-based model

Enabled by recent advances in bioinformatics, the inference of gene regulatory networks (GRNs) from gene expression data has garnered much interest from researchers. This is due to the need of researchers to understand the dynamic behavior and uncover the vast information lay hidden within the networks. In this regard, dynamic Bayesian network (DBN) is extensively used to infer GRNs due to its ability to handle time-series microarray data and modeling feedback loops. However, the efficiency of DBN in inferring GRNs is often hampered by missing values in expression data, and excessive computation time due to the large search space whereby DBN treats all genes as potential regulators for a target gene. In this paper, we proposed a DBN-based model with missing values imputation to improve inference efficiency, and potential regulators detection which aims to lessen computation time by limiting potential regulators based on expression changes. The performance of the proposed model is assessed by using time-series expression data of yeast cell cycle. The experimental results showed reduced computation time and improved efficiency in detecting gene-gene relationships

Determination of the rate of kill, mode of action, and the bioactive components from the ethyl acetate sub-fraction of methanol extract of Phyllanthus amarus.

The time-kill rate of methanol extract of Phyllanthus amarus was determined in this study which showed that the extract caused a reduction of the viable cells of all the test bacteria after a contact time of 30 mins and there were virtually no surviving cells of all the test bacteria after a contact time of 180 mins. The extract was also found to cause leakages of cellular materials such as potassium ions, sodium ions, protein and nucleic acids from the test bacteria which led to the loss of cell viability. The ethyl acetate sub-fraction of the extract was analyzed by GC-MS and FTIR analysis and the result revealed the presence of Phytochemicals such as 1, 2-Benzenedicarboxilic acid mono (2-Ethylhexyl) ester, Columbin, 2-(6-Methylpyridin-2-ylmethyl) cyclohexane, 2(1H) Naphthalenone,3,5,6,7,8,8a-hexahydro-4,8a-dimethyl-6-(1-methylethenyl) which have all been reported to possess antibacterial activity against both gram-positive and gram-negative bacteria. The result of this study will contribute to the baseline data on the pharmacodynamics of the extract if applied as herbal medicine for human treatment thereby reducing the dosage and period of treatment. The finding also revealed that the ethyl acetate sub-fraction of methanol extract of P. amarus contains antibacterial phytochemicals that may be used to develop more potent, safe and cheap antimicrobial agents using nanotechnology. &nbsp

CP-odd Phase Correlations and Electric Dipole Moments

We revisit the constraints imposed by electric dipole moments (EDMs) of nucleons and heavy atoms on new CP-violating sources within supersymmetric theories. We point out that certain two-loop renormalization group corrections induce significant mixing between the basis-invariant CP-odd phases. In the framework of the constrained minimal supersymmetric standard model (CMSSM), the CP-odd invariant related to the soft trilinear A-phase at the GUT scale, theta_A, induces non-trivial and distinct CP-odd phases for the three gaugino masses at the weak scale. The latter give one-loop contributions to EDMs enhanced by tan beta, and can provide the dominant contribution to the electron EDM induced by theta_A. We perform a detailed analysis of the EDM constraints within the CMSSM, exhibiting the reach, in terms of sparticle spectra, which may be obtained assuming generic phases, as well as the limits on the CP-odd phases for some specific parameter points where detailed phenomenological studies are available. We also illustrate how this reach will expand with results from the next generation of experiments which are currently in development.Comment: 31 pages, 21 eps figures; v2: additional remarks on 2-loop threshold corrections and references added; v3: typos corrected, to appear in Phys. Rev.

Effects of CP Violation on Event Rates in the Direct Detection of Dark Matter

A full analytic analysis of the effects of CP violating phases on the event rates in the direct detection of dark matter in the scattering of neutralinos from nuclear targets is given. The analysis includes CP violating phases in softly broken supersymmetry in the framework of the minimal supersymmetric standard model (MSSM) when generational mixings are ignored. A numerical analysis shows that large CP violating phases including the constraints from the experimental limits on the neutron and the electron electric dipole moment (EDM) can produce substantial effects on the event rates in dark matter detectors.Comment: 17 pages, LaTex, including 2 figures; revised version to appear in the Physical Review

On the EDM Cancellations in D-brane models

We analyze the possibility of simultaneous electron, neutron, and mercury electric dipole moment (EDM) cancellations in the mSUGRA and D--brane models. We find that the mercury EDM constraint practically rules out the cancellation scenario in D-brane models whereas in the context of mSUGRA it is still allowed with some fine-tuning.Comment: 10 pages, to appear in Phys. Rev. Let

Slepton Flavor Nonuniversality, the Muon EDM and its Proposed sensitive Search at Brookhaven

We analyze the electric dipole moment of the electron ($d_e$), of the neutron ($d_n$) and of the muon ($d_{\mu}$) using the cancellation mechanism in the presence of nonuniversalities of the soft breaking parameters. It is shown that the nonuniversalities in the slepton sector produce a strong violation of the scaling relation $d_{\mu}/d_e\simeq m_{\mu}/m_e$ in the cancellation region. An analysis of $d_e, d_n$ and $d_{\mu}$ under the constraints of the current experimental limits on $d_e$ and $d_n$ and under the constraints of the recent Brookhaven result on $g_{\mu}-2$ shows that in the non-scaling region $d_{\mu}$ can be as large as ($10^{-24}-10^{-23}$)ecm and thus within reach of the recently proposed Brookhaven experiment for a sensitive search for $d_{\mu}$ at the level of $10^{-24}$ ecm.Comment: 24 pages, Latex, including 5 figures with additional reference

Mixing of the CP Even and the CP Odd Higgs Bosons and the EDM Constraints

The mixing among the CP even and the CP odd neutral Higgs bosons of MSSM by one loop induced effects in the presence of CP phases is investigated using three different mechanisms to satisfy the EDM constraints, i.e., a fine tuning of phases, a heavy sparticle spectrum, and the cancellation mechanism. It is shown that if a mixing effect among the CP even and the CP odd Higgs bosons is observed experimentally, then it is only the cancellation mechanism that can survive under the naturalness constraint.Comment: 14 pages, Latex and 4figures. A new paragraph is added and few more references. One figure is modified. To appear in Phys. Rev.

Direct Observation of High-Temperature Polaronic Behavior In Colossal Magnetoresistive Manganites

The temperature dependence of the electronic and atomic structure of the colossal magnetoresistive oxides $La_{1-x}Sr_{x}MnO_{3}$ (x = 0.3, 0.4) has been studied using core and valence level photoemission, x-ray absorption and emission, and extended x-ray absorption fine structure spectroscopy. A dramatic and reversible change of the electronic structure is observed on crossing the Curie temperature, including charge localization and spin moment increase of Mn, together with Jahn-Teller distortions, both signatures of polaron formation. Our data are also consistent with a phase-separation scenario.Comment: 5 pages, 4 figures, revte