The Iterative Signature Algorithm for the analysis of large scale gene expression data

We present a new approach for the analysis of genome-wide expression data. Our method is designed to overcome the limitations of traditional techniques, when applied to large-scale data. Rather than alloting each gene to a single cluster, we assign both genes and conditions to context-dependent and potentially overlapping transcription modules. We provide a rigorous definition of a transcription module as the object to be retrieved from the expression data. An efficient algorithm, that searches for the modules encoded in the data by iteratively refining sets of genes and conditions until they match this definition, is established. Each iteration involves a linear map, induced by the normalized expression matrix, followed by the application of a threshold function. We argue that our method is in fact a generalization of Singular Value Decomposition, which corresponds to the special case where no threshold is applied. We show analytically that for noisy expression data our approach leads to better classification due to the implementation of the threshold. This result is confirmed by numerical analyses based on in-silico expression data. We discuss briefly results obtained by applying our algorithm to expression data from the yeast S. cerevisiae.Comment: Latex, 36 pages, 8 figure

Subpicosecond exciton dynamics in polyfluorene films from experiment and microscopic theory

The authors acknowledge financial support from the UK EPSRC (Grants EP/E065066/1, EP/E062636/1, EP/J009318/1 and EP/J009019/1), from the EPSRC Scottish Centre for Doctoral training in Condensed Matter Physics and from the European Union Seventh Framework Programme under Grant Agreement 321305.Electronic energy transfer (EET) in organic materials is a key mechanism that controls the efficiency of many processes, including light harvesting antennas in natural and artificial photosynthesis, organic solar cells, and biological systems. In this paper we have examined EET in solid-state thin-films of polyfluorene, a prototypical conjugated polymer, with ultrafast photoluminescence experiments and theoretical modeling. We observe EET occurring on a 680 ± 300 fs time scale by looking at the depolarisation of photoluminescence. An independent, predictive microscopic theoretical model is built by defining 125 000 chromophores containing both spatial and energetic disorder appropriate for a spin-coated thin film. The model predicts time-dependent exciton dynamics, without any fitting parameters, using the incoherent Förster-type hopping model. Electronic coupling between the chromophores is calculated by an improved version of the usual line-dipole model for resonant energy transfer. Without the need for higher level interactions, we find that the model is in general agreement with the experimentally observed 680 ± 300 fs depolarisation caused by EET. This leads us to conclude that femtosecond EET in polyfluorene can be described well by conventional resonant energy transfer, as long as the relevant microscopic parameters are well captured. The implications of this finding are that dipole-dipole resonant energy transfer can in some circumstances be fully adequate to describe ultrafast EET without needing to invoke strong or intermediate coupling mechanisms.PostprintPeer reviewe

Side-chain influence on the mass density and refractive index of polyfluorenes and star-shaped oligofluorene truxenes

The density of organic semiconductor films is an important quantity because it is related to intermolecular spacing which in turn determines the electronic and photophysical properties. We report thin film density and refractive index measurements of polyfluorenes and star-shaped oligofluorene truxene molecules. An ellipsometer and a procedure using a spectrophotometer were used to determine film thickness and mass of spin-coated films, respectively. We present a study of the effect of alkyl side-chain length on the volumetric mass density and refractive index of the materials studied. The density measured for poly(9,9-di-n-octylfluorene) (PF8) was 0.88 ± 0.04 g/cm3 and decreased with longer alkyl side chains. For the truxene molecule with butyl side chains (T3 butyl), we measured a density of 0.90 ± 0.04 g/cm3, which also decreased with increasing side-chain length

X-ray Raman scattering study of aligned polyfluorene

We present a non-resonant inelastic x-ray scattering study at the carbon K-edge on aligned poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl] and show that the x-ray Raman scattering technique can be used as a practical alternative to x-ray absorption measurements. We demonstrate that this novel method can be applied to studies on aligned $\pi$-conjugated polymers complementing diffraction and optical studies. Combining the experimental data and a very recently proposed theoretical scheme we demonstrate a unique property of x-ray Raman scattering by performing the symmetry decomposition on the density of unoccupied electronic states into $s$- and $p$-type symmetry contributions.Comment: 19 pages, 8 figure

Charge Delocalization in Self-Assembled Mixed-Valence Aromatic Cation Radicals

The spontaneous assembly of aromatic cation radicals (D+•) with their neutral counterpart (D) affords dimer cation radicals (D2+•). The intermolecular dimeric cation radicals are readily characterized by the appearance of an intervalence charge-resonance transition in the NIR region of their electronic spectra and by ESR spectroscopy. The X-ray crystal structure analysis and DFT calculations of a representative dimer cation radical (i.e., the octamethylbiphenylene dimer cation radical) have established that a hole (or single positive charge) is completely delocalized over both aromatic moieties. The energetics and the geometrical considerations for the formation of dimer cation radicals is deliberated with the aid of a series of cyclophane-like bichromophoric donors with drastically varied interplanar angles between the cofacially arranged aryl moieties. X-ray crystallography of a number of mixed-valence cation radicals derived from monochromophoric benzenoid donors established that they generally assemble in 1D stacks in the solid state. However, the use of polychromophoric intervalence cation radicals, where a single charge is effectively delocalized among all of the chromophores, can lead to higher-order assemblies with potential applications in long-range charge transport. As a proof of concept, we show that a single charge in the cation radical of a triptycene derivative is evenly distributed on all three benzenoid rings and this triptycene cation radical forms a 2D electronically coupled assembly, as established by X-ray crystallography

Deterministic Classifiers Accuracy Optimization for Cancer Microarray Data

The objective of this study was to improve classification accuracy in cancer microarray gene expression data using a collection of machine learning algorithms available in WEKA. State of the art deterministic classification methods, such as: Kernel Logistic Regression, Support Vector Machine, Stochastic Gradient Descent and Logistic Model Trees were applied on publicly available cancer microarray datasets aiming to discover regularities that provide insights to help characterization and diagnosis correctness on each cancer typology. The implemented models, relying on 10-fold cross-validation, parameterized to enhance accuracy, reached accuracy above 90%. Moreover, although the variety of methodologies, no significant statistic differences were registered between them, at significance level 0.05, confirming that all the selected methods are effective for this type of analysis.info:eu-repo/semantics/publishedVersio

The Al-Rich Part of the Fe-Al Phase Diagram

The Al-rich part of the Fe-Al phase diagram between 50 and 80 at.% Al including the complex intermetallic phases Fe$_{5}$Al$_{8}$ (ε), FeAl$_{2}$, Fe$_{2}$Al$_{5}$, and Fe4Al$_{13}$ was re-investigated in detail. A series of 19 alloys was produced and heat-treated at temperatures in the range from 600 to 1100 °C for up to 5000 h. The obtained data were further complemented by results from a number of diffusion couples, which helped to determine the homogeneity ranges of the phases FeAl$_{2}$, Fe$_{2}$Al$_{5}$, and Fe$_{4}$Al$_{13}$. All microstructures were inspected by scanning electron microscopy (SEM), and chemical compositions of the equilibrium phases as well as of the alloys were obtained by electron probe microanalysis (EPMA). Crystal structures and the variation of the lattice parameters were studied by x-ray diffraction (XRD) and differential thermal analysis (DTA) was applied to measure all types of transition temperatures. From these results, a revised version of the Al-rich part of the phase diagram was constructed