IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer

Subnetwork analysis can explore complex patterns of entire molecular pathways for the purpose of drug target identification. In this article, the gene expression profiles of a cohort of patients with breast cancer are integrated with protein-protein interaction (PPI) networks using, simultaneously, both edge scoring and node scoring. A novel optimization algorithm, integrated optimization method to identify deregulated subnetwork (IODNE), is developed to search for the optimal dysregulated subnetwork of the merged gene and protein network. IODNE is applied to select subnetworks for Luminal-A breast cancer from The Cancer Genome Atlas (TCGA) data. A large fraction of cancer-related genes and the well-known clinical targets, ER1/PR and HER2, are found by IODNE. This validates the utility of IODNE. When applying IODNE to the triple-negative breast cancer (TNBC) subtype data, we identified subnetworks that contain genes such as ERBB2, HRAS, PGR, CAD, POLE, and SLC2A1

Fractal Theory Space: Spacetime of Noninteger Dimensionality

We construct matter field theories in ``theory space'' that are fractal, and invariant under geometrical renormalization group (RG) transformations. We treat in detail complex scalars, and discuss issues related to fermions, chirality, and Yang-Mills gauge fields. In the continuum limit these models describe physics in a noninteger spatial dimension which appears above a RG invariant ``compactification scale,'' M. The energy distribution of KK modes above M is controlled by an exponent in a scaling relation of the vacuum energy (Coleman-Weinberg potential), and corresponds to the dimensionality. For truncated-s-simplex lattices with coordination number s the spacetime dimensionality is 1+(3+2ln(s)/ln(s+2)). The computations in theory space involve subtleties, owing to the 1+3 kinetic terms, yet the resulting dimensionalites are equivalent to thermal spin systems. Physical implications are discussed.Comment: 28 pages, 6 figures; Paper has been amplified with a more detailed discussion of a number of technical issue

The effect of gamma irradiation on selected growth factors and receptors mRNA in glycerol cryopreserved human amniotic membrane

Human amniotic membrane (HAM), due to its high biocompatibility, low immunogenicity, anti-microbial, anti-viral properties as well as the presence of its growth factors, has been used in various clinical applications. These growth factors are key factors in regulating many cellular processes such as cellular growth, proliferation and cellular differentiation. The current study aimed to explore the effect of glycerol cryopreservation and gamma irradiation on the selected growth factors and receptors mRNA present in HAM. Eight growth factors, namely, EGF, HGF, KGF, TGF-α, TGF-β1, TGF-β2, TGF-β3 and bFGF and two growth factor receptors, HGFR and KGFR were evaluated in this study. The total RNA was extracted and converted to complimentary DNA using commercial kits. Subsequently, the mRNA expressions of these growth factors were evaluated using quantitative PCR and the results were statistically analyzed using REST-MCS software. This study indicated the presence of these growth factors and receptors mRNA in fresh, glycerol cryopreserved and irradiated glycerol cryopreserved HAM. In glycerol cryopreserved HAM, the mRNA expression showed up-regulation of HGF and bFGF and down-regulation of the rest of 8 genes which were EGF, HGFR, KGF, KGFR, TGF-α, TGF-β1, TGF-β2 and TGF-β3. Interestingly, the glycerol cryopreserved HAM radiated with 15 kGy showed up-regulation in the mRNA expression of 7 genes, namely, EGF, HGF, KGF, KGFR, TGF-β1, TGF-β2 and TGF-β3 and down-regulated mRNA expression of HGFR, TGF-α and bFGF. However, these mRNA expressions did not show a statistically significant difference compared to control groups. Thus, it can be concluded that the glycerol cryopreservation did not have an effect on the growth factors’ and receptors’ mRNA expression levels in HAM. Similarly, 15 kGy gamma irradiation did not have an effect on the growth factors’ and receptors’ mRNA expression in glycerol cryopreserved HAM. This finding provides a useful information to clinicians and surgeons to choose the best method for HAM preservation that could benefit patients in their treatment

RFID en el servicio bibliotecario de la UTM

The central library of the Technical University of Manabí (UTM), offers the service of electronic equipment loans (laptops and tablets), in which theft has been presented. In the present article the integration of identification technologies through a web application is exposed. To do this, the requirements were raised, systems analysis and identification technologies were analyzed. Based on the study of art, the development methodology, programming languages, tools and technologies applied in the solution were described, the system architecture was designed with visual / audible alarm, the integrating system was developed and implemented and finally functional tests were carried out. As a result, it was evidenced that using bar code and RFID technology in the library service, there is better control of the entry and exit of electronic equipment, preventing any attempt at theft, and the university and general community receive a quality and speedy service.La biblioteca central de la Universidad Técnica de Manabí (Ecuador)brinda el servicio de préstamos de equipos electrónicos (portátiles y tabletas), en el que se han presentado hurtos de los mismos. En este artículo se expone la integración de RFID a través de una aplicación web. Para ello, se realizó el levantamiento de requerimientos, análisis de sistemas y de tecnologías de identificación, tomando como base el estudio del arte se describió la metodología de desarrollo, lenguajes de programación, herramientas y tecnologías aplicadas en la solución, se diseñó la arquitectura del sistema con alarma visual/sonora, se desarrolló e implantó el sistema integrador y, finalmente, se ejecutaron pruebas de funcionamiento. Como resultado se evidenció que al utilizar tecnología de código de barras y RFID en el servicio bibliotecario existe un mejor control de entrada y salida de los equipos electrónicos, previniendo de cualquier intento de hurto; a su vez, la comunidad universitaria y general recibe un servicio de calidad y rapidez

Squark Flavor Violation at the LHC

We consider the prospects for measuring squark flavor violation through the signal of single top production at the LHC. We study this signal in the context of R-symmetric supersymmetry, which allows for large flavor violation in the squark sector, however the results can also be generalized to the MSSM. The single top signal arises from squark pair production in which one squark decays to a top and gaugino, whereas the other squark decays to a non-top quark and gaugino. We study three decay patterns: (I) squark decay into a quark and neutralino LSP; (II) squark decay into a quark and neutralino NLSP, with subsequent decay of the NLSP to a photon and gravitino; (III) squark decay into a quark and chargino NLSP, with subsequent decay of the NLSP to a H^\pm/W^\pm and gravitino. Case II is the most promising, when the NLSP decay is prompt, since every event contains two hard photons that can be used to tag the events, reducing the background to a negligible level. Case I is promising if the neutralino LSP is bino-like. We carefully consider large SM backgrounds and identify a series of cuts to isolate the signal. Case III can occur in the MRSSM with Higgsino-like lightest gauginos. Due to the large Higgs coupling, squarks preferentially decay to top quarks, substantially reducing the potential flavor violating signal. Nevertheless, the flavor violating signal might still be identifiable if the chargino NLSP is long-lived.Comment: 9 figures and 4 table

High Energy Processes in Pulsar Wind Nebulae

Young pulsars produce relativistic winds which interact with matter ejected during the supernova explosion and the surrounding interstellar gas. Particles are accelerated to very high energies somewhere in the pulsar winds or at the shocks produced in collisions of the winds with the surrounding medium. As a result of interactions of relativistic leptons with the magnetic field and low energy radiation (of synchrotron origin, thermal, or microwave background), the non-thermal radiation is produced with the lowest possible energies up to $\sim$100 TeV. The high energy (TeV) gamma-ray emission has been originally observed from the Crab Nebula and recently from several other objects. Recent observations by the HESS Cherenkov telescopes allow to study for the first time morphology of the sources of high energy emission, showing unexpected spectral features. They might be also interpreted as due to acceleration of hadrons. However, theory of particle acceleration in the PWNe and models for production of radiation are still at their early stage of development since it becomes clear that realistic modeling of these objects should include their time evolution and three-dimensional geometry. In this paper we concentrate on the attempts to create a model for the high energy processes inside the PWNe which includes existence not only relativistic leptons but also hadrons inside the nebula. Such model should also take into account evolution of the nebula in time. Possible high energy expectations based on such a model are discussed in the context of new observations.Comment: 9 pages, 1 figure, Proc. Multimessenger approach to high energy gamma-ray source

Investigation on viscosity and non-isothermal crystallization behavior of P-bearing steelmaking slags with varying TiO2 content

The viscous flow and crystallization behavior of CaO-SiO2-MgO-Al2O3-FetO-P2O5-TiO2 steelmaking slags have been investigated over a wide range of temperatures under Ar (High purity, >99.999 pct) atmosphere, and the relationship between viscosity and structure was determined. The results indicated that the viscosity of the slags slightly decreased with increasing TiO2 content. The constructed nonisothermal continuous cooling transformation (CCT) diagrams revealed that the addition of TiO2 lowered the crystallization temperature. This can mainly be ascribed to that addition of TiO2 promotes the formation of [TiO6]-octahedra units and, consequently, the formation of MgFe2O4-Mg2TiO4 solid solution. Moreover, the decreasing viscosity has a significant effect on enhancing the diffusion of ion units, such as Ca2+ and [TiO4]-tetrahedra, from bulk melts to the crystal–melt interface. The crystallization of CaTiO3 and CaSiTiO5 was consequently accelerated, which can improve the phosphorus content in P-enriched phase (n2CaO·SiO2-3CaO·P2O5). Finally, the nonisothermal crystallization kinetics was characterized and the activation energy for the primary crystal growth was derived such that the activation energy increases from −265.93 to −185.41 KJ·mol−1 with the addition of TiO2 content, suggesting that TiO2 lowered the tendency for the slags to crystallize

B^0-\bar{B}^0 mixing and B \to X_s \gamma decay in the third type 2HDM: effects of NLO QCD contributions

In this paper, we calculated the next-to-leading order (NLO) new physics contributions to the mass splitting \dmd and the branching ratio \brbxsga induced by the charged Higgs loop diagrams in the third type of two-Higgs-doublet models (model III) and draw the constraints on the free parameters of model III. For the model III under consideration, we found that (a) an upper limit |\ltt|\leq 1.7 is obtained from the precision data of \dmd=0.502 \pm 0.007 ps^{-1}, while |\ltt| \approx 0.5 is favored phenomenologicaly; (b) for $B \to X_s \gamma$ decay, the NLO QCD contributions tend to cancel the LO new physics contributions; (c) a light charged Higgs boson with a mass around or even less than 200 GeV is still allowed at NLO level by the measured branching ratio \brbxsga: numerically, 188 \leq \mh \leq 215 GeV for (|\ltt|,|\lbb|)=(0.5,18); (d) the NLO QCD contributions tend to cancel the LO contributions effectively, the lower limit on \mh is consequently decreased by about 200 GeV; (e) the allowed region of \mh will be shifted toward heavy mass end for a non-zero relative phase $\theta$ between the Yukawa couplings \ltt and \lbb. The numerical results for the conventional model II are also presented for the sake of a comparison.Comment: 42 pages, 18 eps figures, Revtex, new references adde