Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes

Biofilms are communities of microbial cells that underpin diverse processes including sewage bioremediation, plant growth promotion, chronic infections and industrial biofouling. The cells resident in the biofilm are encased within a self-produced exopolymeric matrix that commonly comprises lipids, proteins that frequently exhibit amyloid-like properties, eDNA and exopolysaccharides. This matrix fulfils a variety of functions for the community, from providing structural rigidity and protection from the external environment to controlling gene regulation and nutrient adsorption. Critical to the development of novel strategies to control biofilm infections, or the capability to capitalize on the power of biofilm formation for industrial and biotechnological uses, is an in-depth knowledge of the biofilm matrix. This is with respect to the structure of the individual components, the nature of the interactions between the molecules and the three-dimensional spatial organization. We highlight recent advances in the understanding of the structural and functional role that carbohydrates and proteins play within the biofilm matrix to provide three-dimensional architectural integrity and functionality to the biofilm community. We highlight, where relevant, experimental techniques that are allowing the boundaries of our understanding of the biofilm matrix to be extended using Escherichia coli, Staphylococcus aureus, Vibrio cholerae, and Bacillus subtilis as exemplars.

Double ionization in R-matrix theory using a two-electron outer region

We have developed a two-electron outer region for use within R-matrix theory to describe double ionisation processes. The capability of this method is demonstrated for single-photon double ionisation of He in the photon energy region between 80 eV to 180 eV. The cross sections are in agreement with established data. The extended RMT method also provides information on higher-order processes, as demonstrated by the identification of signatures for sequential double ionisation processes involving an intermediate He⁺ state with n=2.

'The Blazing Torch': New Light on English Balladry as a Multi-Media Matrix

This paper investigates the inter-twining histories of two highly successful broadside ballads during the seventeenth century. Neither has been systematically studied before. A set of cultural relationships is opened for consideration by these songs: first, between the two ballads, which are different in several ways but set to the same tune; second, between the selected songs and other ballads on comparable themes; and third, between different editions of the two featured songs. In discussing each of these relationships, attention is paid not only to the texts but to the pictures and the tunes that helped to bring balladry to life for early-modern consumers. It is argued that balladry should be studied as an interconnected web and that individual publications drew significance from the manner in which they associated themselves – through shared pictures, tunes and narratives – with other examples of the genre.

Photoionization cross sections for O-like S IX: a Breit-Pauli R-matrix calculation

In this paper we present photoionization cross sections for the lowest five states of O-like S IX (1s(2)2s(2)2p(4) P-3(0,1,2), D-1(2), S-1(0)). The relativistic Breit-Pauli R-matrix codes were utilized including all terms of the 2s(2)2p(3), 2s2p(4), 2p(5), 2s(2)2p(2)3s, 3p, 3d and 2s2p(3)3s, 3p, 3d configurations in the expansion of the collision wavefunction for S X. It was also found that to achieve convergence of the low-lying energy separations of the target levels, an additional 21 configuration functions needed to be included in the configuration interaction expansion, incorporating two-electron excitations from the 2s and 2p shells to the 3s, 3p and 3d shells. The present work thus constitutes the most sophisticated photoionization evaluation for ground and metastable levels of the S IX ion. Direct comparisons have been made with the only available data found on the OPEN-ADAS database between level resolved contributions of the spectrum. This comparison for the background cross section exhibits excellent agreement at all photon energies for each partial photoionization cross section contribution investigated. Finally, the autoionizing bound states arising from numerous open channels have also been investigated and identified using the QB approach, a procedure for analyzing resonances in atomic and molecular collision theory which exploits the analytic properties of R-matrix theory. Major Rydberg resonance series are also presented and tabulated for the dominant linewidths considered.

Regenerated cellulose matrix-encapsulated active substances and method therefor.

The process involves encapsulation or immobilization of the active solid substance in a cellulose framework by regenerating cellulose dissolved in an ionic liq. solvent in a regenerating soln. The active substance can be initially present in the ionic liq. or in the regenerating solvent either as a soln. or dispersion. The invention is applicable to mol. encapsulation and to entrapping of larger particles including enzymes, nanoparticles and macroscopic components, and to the formation of bulk materials with a wide range of morphol. forms. Thus, carbamoylmethylphosphine oxide (I) encapsulated in a cellulose matrix was realized by adding I to a 10% soln. of cellulose in 1-butyl-3-methylimidazolium chloride (ionic liq.) under vigorous stirring and then removing the ionic liq. with water. [on SciFinder(R)]

Comprehensive profiling and localisation of the matrix metalloproteinases in urothelial carcinoma

The matrix metalloproteinases (MMPs) are endopeptidases which break down the extracellular matrix and regulate cytokine and growth factor activity. Several MMPs have been implicated in the promotion of invasion and metastasis in a broad range of tumours including urothelial carcinoma. In this study, RNA from 132 normal bladder and urothelial carcinoma specimens was profiled for each of the 24 human MMPs, the four endogenous tissue inhibitors of MMPs (TIMPs) and several key growth factors and their receptors using quantitative real time RT-PCR. Laser capture microdissection (LCM) of RNA from 22 tumour and 11 normal frozen sections was performed allowing accurate RNA extraction from either stromal or epithelial compartments. This study confirms the over expression in bladder tumour tissue of well-documented MMPs and highlights a range of MMPs which have not previously been implicated in the development of urothelial cancer. In summary, MMP-2, MT1-MMP and the previously unreported MMP-28 were very highly expressed in tumour samples while MMPs 1, 7, 9, 11, 15, 19 and 23 were highly expressed. There was a significant positive correlation between transcript expression and tumour grade for MMPs 1, 2, 8, 10, 11, 12, 13, 14, 15 and 28 (P < 0.001). At the same confidence interval, TIMP-1 and TIMP-3 also correlated with increasing tumour grade. LCM revealed that most highly expressed MMPs are located primarily within the stromal compartment except MMP-13 which localised to the epithelial compartment. This work forms the basis for further functional studies, which will help to confirm the MMPs as potential diagnostic and therapeutic targets in early bladder cancer.

Scoup-SMT: Scalable Coupled Sparse Matrix-Tensor Factorization

How can we correlate neural activity in the human brain as it responds to words, with behavioral data expressed as answers to questions about these same words? In short, we want to find latent variables, that explain both the brain activity, as well as the behavioral responses. We show that this is an instance of the Coupled Matrix-Tensor Factorization (CMTF) problem. We propose Scoup-SMT, a novel, fast, and parallel algorithm that solves the CMTF problem and produces a sparse latent low-rank subspace of the data. In our experiments, we find that Scoup-SMT is 50-100 times faster than a state-of-the-art algorithm for CMTF, along with a 5 fold increase in sparsity. Moreover, we extend Scoup-SMT to handle missing data without degradation of performance. We apply Scoup-SMT to BrainQ, a dataset consisting of a (nouns, brain voxels, human subjects) tensor and a (nouns, properties) matrix, with coupling along the nouns dimension. Scoup-SMT is able to find meaningful latent variables, as well as to predict brain activity with competitive accuracy. Finally, we demonstrate the generality of Scoup-SMT, by applying it on a Facebook dataset (users, friends, wall-postings); there, Scoup-SMT spots spammer-like anomalies.

Relativistic radiatively damped R -matrix calculations of the electron-impact excitation of helium-like iron and krypton

Electron-impact excitation data for He-like ions are of significant importance for diagnostic applications to both laboratory and astrophysical plasmas. Here we report on the first fully relativistic R -matrix calculations with radiation damping for the He-like ions Fe 24+ and Kr 34+ . Effective collision strengths for these two ions have been determined with and without damping over a wide temperature range for all transitions between the 49 levels through n = 5. We find that damping has a pronounced effect on the effective collision strengths for excitation to some of the low-lying levels, but its effect on excitation to the vast majority of levels is small. At the energy of a resonance peak, we also investigate the effect of radiation damping on the angular distribution of scattered electrons. Finally, we compare our results for Fe 24+ with an earlier intermediate coupling frame transformation R -matrix calculation with radiation damping by Whiteford et al ( J. Phys. B: At. Mol. Opt. Phys. 34 3179) and find good agreement, especially for excitation to the lower levels.

Intermediate-coupling R -matrix calculations of electron-impact excitation of Fe 5+

For applications to laboratory and astrophysical plasmas, there is a great need for accurate electron-impact excitation data between individual levels in the lower charge-state ions of iron. Recently, we have reported on the first intermediate-coupling R -matrix calculation of electron-impact excitation in Fe 4+ , in which the close-coupling expansion of the target included levels from both ground and excited configurations (Ballance et al 2007 J. Phys. B: At. Mol. Opt. Phys. [/0953-4075/40/23/f01] 40 F327 , 2008 Europhys. News 39 14). In this paper, we present the results of two large intermediate-coupling Dirac R -matrix calculations of electron-impact excitation of Fe 5+ . The results from the two calculations, which differ only in the configuration–interaction expansions of the target, are compared. These comparisons provide some indication of the accuracy of the calculations and the resulting data should be useful in modelling plasmas containing iron.

Electron-impact excitation of Fe2: a comparison of intermediate coupling frame transformation, Breit-Pauli and Dirac R-matrix calculations

Modeling the spectral emission of low-charge iron group ions enables the diagnostic determination of the local physical conditions of many cool plasma environments such as those found in H II regions, planetary nebulae, active galactic nuclei etc. Electron-impact excitation drives the population of the emitting levels and, hence, their emissivities. By carrying-out Breit-Pauli and intermediate coupling frame transformation (ICFT) R-matrix calculations for the electron-impact excitation of Fe$^{2+}$ which both use the exact same atomic structure and the same close-coupling expansion, we demonstrate the validity of the application of the powerful ICFT method to low-charge iron group ions. This is in contradiction to the finding of Bautista et al. [Ap.J.Lett, 718, L189, (2010)] who carried-out ICFT and Dirac R-matrix calculations for the same ion. We discuss possible reasons.

Relativistic radiatively damped R-matrix calculation of the electron-impact excitation of W46+

The current design plans for the International Thermonuclear\nExperimental Reactor ( ITER) call for tungsten to be employed for\ncertain plasma facing components in the divertor region. Thus, accurate\natomic collision data are needed for emission modelling of tungsten.\nElectron-impact excitation and radiative rates are of particular\nimportance for Ni-like W, since this ion emits some of the most intense\nspectral lines of all ionization stages. We report on a fully\nrelativistic 115-level R-matrix calculations of W46+, which includes the\neffects of radiation damping. Although radiation damping is very\nimportant in most highly ionized species, its effects are reduced in\nthis case because of the closed-shell Ni-like ground state. The rates\nfrom these relativistic atomic calculations will be employed for\ncollisional-radiative modelling of this ion.

Electron-impact excitation of Fe 4+ : an intermediate-coupling R -matrix calculation

For a number of years, there has been a major effort to calculate electron-impact excitation data for every ion stage of iron embodied by the ongoing efforts of the IRON project by Hummer et al (1993 Astron. Astrophys. 279 298). Due to the complexity of the targets, calculations for the lower stages of ionization have been limited to either intermediate-coupling calculations within the ground configurations or LS -coupling calculations of the ground and excited configurations. However, accurate excitation data between individual levels within both the ground and excited configurations of the low charge-state ions are urgently required for applications to both astrophysical and laboratory plasmas. Here we report on the results of the first intermediate-coupling R -matrix calculation of electron-impact excitation for Fe 4+ for which the close-coupling (CC) expansion includes not only those levels of the 3d 4 ground configuration, but also the levels of the 3d 3 4s, 3d 3 4p, 3d 3 4d and 3d 2 4s 2 excited configurations. With 359 levels in the CC expansion and over 2400 scattering channels for many of the J Π partial waves, this represents the largest electron–ion scattering calculation to date and it was performed on massively parallel computers using a recently developed set of relativistic parallel R -matrix programs.