FORM version 4.0

We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Groebner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Lastly, FORM 4.0 has become available as open source under the GNU General Public License version 3.Comment: 26 pages. Uses axodra

Corridors for LIFE; ecological network analysis Regione Emilia-Romagna - the plains of Provincia di Modena & Bologna

This report gives the result of an analysis of the ecological network, designed for the agricultural plains of the Provinces of Modena and and Bologna. Three ecosystem types were selected: woodland, wetland, and grassland. Species were selected which can be considered representative of these ecosystems. The LARCH model was used to assess whether these ecosystems still function as an ecological network. We found that the region has a serious fragmentation problem. After implementation of the ecological network the situation would improve much. Larger areas for nature rehabilitation would further improve the functioning of the ecological network

The protective layer of biofilm:A repellent function for a new class of amphiphilic proteins

Bacteria can survive harsh conditions when growing in complex communities of cells known as biofilms. The matrix of the biofilm presents a scaffold where cells are attached to each other and to the surface. The biofilm matrix is also a protective barrier that confers tolerance against various antimicrobial agents. In this issue of Molecular Microbiology, Kobayashi and Iwano (2012) show that the liquid permeability of Bacillus subtilis biofilms is determined by a small secreted protein, i.e. BslA (formerly called YuaB). BslA is important for the proper development of biofilms, but unlike exopolysaccharide and TasA, is not directly involved in cell cluster formation, and is synthesized following the production of exopolysaccharide and amyloid fibres. The amphiphilic BslA protein forms a polymer in vitro and localizes in vivo to the surface of the biofilm. The microstructures of the biofilm wrinkles are reduced in the bslA mutant strain and the liquid repellency of the biofilm surface is diminished. Exogenously added BslA42181 protein complements the bslA mutation and restores not only water repellency, but also the formation of aerial structures. This study demonstrates that amphiphilic proteins have an important role in liquid repellency of biofilms and it suggests that these polymers contribute to antimicrobial resistance

Plasmon scattering from single sub-wavelength holes

We map the complex electric fields associated with the scattering of surface plasmon polaritons by single sub-wavelength holes of different sizes in thick gold films. We identify and quantify the different modes associated with this event, including a radial surface wave with an angularly isotropic amplitude. This wave is shown to arise from the out-of-plane electric dipole induced in the hole, and we quantify the corresponding polarizability, which is in excellent agreement with electromagnetic theory. Time-resolved measurements reveal a time-delay of 38? +/- 18 fs between the surface plasmon polariton and the radial wave, which we attribute to the interaction with a broad hole resonance

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Distinguishing step relaxation mechanisms via pair correlation functions

Theoretical predictions of coupled step motion are tested by direct STM measurement of the fluctuations of near-neighbor pairs of steps on Si(111)-root3 x root3 R30 - Al at 970K. The average magnitude of the pair-correlation function is within one standard deviation of zero, consistent with uncorrelated near-neighbor step fluctuations. The time dependence of the pair-correlation function shows no statistically significant agreement with the predicted t^1/2 growth of pair correlations via rate-limiting atomic diffusion between adjacent steps. The physical considerations governing uncorrelated step fluctuations occurring via random attachment/detachment events at the step edge are discussed.Comment: 17 pages, 4 figure

Genetic Tool Development for a New Host for Biotechnology, the Thermotolerant Bacterium Bacillus coagulans

Bacillus coagulans has good potential as an industrial production organism for platform chemicals from renewable resources but has limited genetic tools available. Here, we present a targeted gene disruption system using the Cre-lox system, development of a LacZ reporter assay for monitoring gene transcription, and heterologous D-lactate dehydrogenase expression

Patients' preferences regarding shared decision-making in the treatment of inflammatory bowel disease: Results from a patient-empowerment study

Shared decision-making is gaining favor in clinical practice, although the extent to which patients want to be involved in choosing their treatment varies substantially. Because data are lacking on the preferences of patients with chronic diseases such as inflammatory bowel disease (IBD), we wanted to assess IBD patients' preferences about being involved in such decisions. Methods: Adult IBD patients were asked to anonymously complete an online survey on their preferences. Non-parametric tests (χ2) were used to determine the relationship between responses and respondents. Results: The questionnaire was completed by 1,067 patients, 617 with Crohn's disease and 450 with ulcerative colitis. Patients' mean age was 43 (SD 13.7) years; the majority were female (66%). In total, 866 patients (81%) reported it as 'very important' to be actively involved in the decision-making process, and another 177 (17%) rated it as 'quite important'. When asked how their treatment could be improved, 537 patients (50%) wanted close, equitable collaboration with their physician. This preference was significantly associated with a disease duration of ≤8 years (p = 0.03). Gender and type of IBD were not significantly associated with patients' preferences. Conclusions: This study demonstrates IBD patients' desire to be actively involved in the decision-making process. Further research is needed on physicians' perspectives on shared decision-making, and on finding predictive factors for developing a model for shared decision-making in IBD. Copyrigh