Chemical data mining of the NCI human tumor cell line database

The NCI Developmental Therapeutics Program Human Tumor cell line data set is a publicly available database that contains cellular assay screening data for over 40 000 compounds tested in 60 human tumor cell lines. The database also contains microarray assay gene expression data for the cell lines, and so it provides an excellent information resource particularly for testing data mining methods that bridge chemical, biological, and genomic information. In this paper we describe a formal knowledge discovery approach to characterizing and data mining this set and report the results of some of our initial experiments in mining the set from a chemoinformatics perspective.     

Web service infrastructure for chemoinformatics

The vast increase of pertinent information available to drug discovery scientists means that there is a strong demand for tools and techniques for organizing and intelligently mining this information for manageable human consumption. At Indiana University, we have developed an infrastructure of chemoinformatics Web services that simplifies the access to this information and the computational techniques that can be applied to it. In this paper, we describe this infrastructure, give some examples of its use, and then discuss our plans to use it as a platform for chemoinformatics application development in the future.     

Euler–Poincaré Flows on <Emphasis Type="Italic">sl</Emphasis><Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> Opers and Integrability

We consider the action of vector field Vect(S ¹) on the space of an sl _n - opers on S ¹, i.e., a space of nth order differential operator . This action takes the sections of Ω ^–(n–1)/2 to those of Ω ^(n+1)/2, where Ω is the cotangent bundle on S ¹. In this paper we study Euler–Poincaré (EP) flows on the space of sl _n opers, in particular, we demonstrate explicitly EP flows on the space of third and fourth order differential operators (or sl ₃ and sl ₄ opers) and its relation to Drienfeld–Sokolov, Hirota–Satsuma and other coupled KdV type systems. We also discuss the Boussinesq equation associated with the third order operator. The solutions of the sl _n oper defines an immersion in homogeneous coordinates. We derive the Schwarzian KdV equation as an evolution of the solution curve associated to Δ ⁽ⁿ⁾, we study the factorization of higher order operators and its compatibility with the action of Vect(S ¹). We obtain the generalized Miura transformation and its connection to the modified Boussinesq equation for sl ₃ oper. We also study the eigenvalue problem associated to sl ₄ oper. We discuss flows on the special higher order differential operators for all u _i = f(u,u _x ,u _xx ⋯) and its connection to KdV equation. Finally we explore a relation between projective vector field equation and generalized Riccati equations.      

Persistence of nematic liquid crystalline phase in a polyfluorene‐based organic semiconductor: A high pressure study

The role of high pressure on a low molecular weight nematic liquid crystalline organic semiconductor, ethyl‐hexyl substituted polyfluorene (PF2/6) is investigated using photoluminescence (PL), Raman scattering, and X‐ray scattering studies at pressures from 1 to 8 GPa. The PL and the Raman data under pressure are consistent with each other with no abrupt changes in the pressure coefficients of PL or Raman peaks. The PL energies redshift and broaden, consistent with both enhanced intra‐ and interchain interactions. The Raman peak positions yield pressure coefficients similar to other phenyl based π‐conjugated polymers. The broadening of a doublet peak in the 1135 cm^?1 region indicates a more planar backbone conformation with increasing pressure. X‐ray scattering indicates that the torsion angle between adjacent repeats reduces with increasing pressure and reverts back with decompression. The intermolecular structure is weakly ordered (frozen nematic) and essentially maintained with increasing pressure, in contrast to a high molecular weight PF2/6. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2014 , 52, 1014–1023     

Suppression of chaos through coupling to an external chaotic system

We explore the behaviour of an ensemble of chaotic oscillators diffusively coupled only to an external chaotic system, whose intrinsic dynamics may be similar or dissimilar to the group. Counter-intuitively, we find that a dissimilar external system manages to suppress the intrinsic chaos of the oscillators to fixed point dynamics, at sufficiently high coupling strengths. So, while synchronization is induced readily by coupling to an identical external system, control to fixed states is achieved only if the external system is dissimilar. We quantify the efficacy of control by estimating the fraction of random initial states that go to fixed points, a measure analogous to basin stability. Lastly, we indicate the generality of this phenomenon by demonstrating suppression of chaotic oscillations by coupling to a common hyper-chaotic system. These results then indicate the easy controllability of chaotic oscillators by an external chaotic system, thereby suggesting a potent method that may help design control strategies.     

On dynamics of velocity vector potential in incompressible fluids

An elegant quaternionic formulation is given for the Lagrangian advection equation for velocity vector potential in fluid dynamics. At first we study the topological significance of a restricted conserved quantity viz., stream-helicity and later more realistic configuration of open streamlines is figured out. Also, using Clebsch parameterisation of the velocity vector potential yet another physical significance for the stream-helicity is provided. Finally we give a Nambu-Poisson formalism of the Lagrangian advection equation for velocity vector potential.     

Ionic liquid-mediated sol–gel coatings for capillary microextraction

Ionic liquid (IL)-mediated sol–gel hybrid organic–inorganic materials present enormous potential for effective use in analytical microextraction. This opportunity, however, has not yet been explored. One obstacle to materializing this prospect arises from high viscosity of ILs significantly slowing down sol–gel reactions. In this work, we developed a method that overcomes this hurdle and provides IL-mediated advanced sol–gel materials for capillary microextraction (CME). We examined two different ILs: (a) a phosphonium-based IL, trihexyltetradecylphosphonium tetrafluoroborate, and (b) a pyridinium-based ionic liquid, N-butyl-4-methylpyridinium tetrafluoroborate. These ILs were evaluated in conjunction with two types of hydroxy-terminated polymers: (a) two Si–OH terminated polymers (PDMS and BMPO), and (b) two C–OH terminated polymers (PEG and polyTHF) that differ in their sol–gel reactivity. Scanning electron microscopy results demonstrate that ILs can serve as porogenic agents in sol–gel reactions. The IL-mediated sol–gel coatings prepared with silanol-terminated polymers provided up to 28 times higher extractions in off-line CME-GC compared to analogous sol–gel coatings prepared without any IL in the sol solution. Contrary to this, the IL-mediated sol–gel coatings prepared with C–OH terminated polymers provided lower extraction efficiencies compared to their IL-free counterparts. These observations were explained by (a) lower sol–gel reactivity of C–OH groups in PEG and polyTHF compared to Si–OH groups in PDMS and in hydrolyzed alkoxysilane precursors and (b) extremely high viscosity of ionic liquids. This study shows that IL-generated porous morphology alone is not enough to provide effective extraction media: careful choice of the organic polymer and the precursor with close sol–gel reactivity must be made to ensure effective chemical bonding of the organic polymer to the created sol–gel material to be able to provide the desired sorbent characteristics. Additionally, IL-mediated sol–gel PDMS coatings provided run-to-run RSD values of 4.2–5.0% and detection limits ranging from 3.2 ng/L to 17.4 ng/L. PDMS sol–gels prepared without ILs provided RSD values of 2.8–14.1%, and detection limits ranging from 4.9 ng/L to 487.0 ng/L.