MyChemise: A 2D drawing program that uses morphing for visualisation purposes

MyChemise (My Chemical Structure Editor) is a new 2D structure editor. It is designed as a Java applet that enables the direct creation of structures in the Internet using a web browser. MyChemise saves files in a digital format (.cse) and the import and export of .mol files using the appropriate connection tables is also possible

Global Genotype-Phenotype Correlations in Pseudomonas aeruginosa

Once the genome sequence of an organism is obtained, attention turns from identifying genes to understanding their function, their organization and control of metabolic pathways and networks that determine its physiology. Recent technical advances in acquiring genome-wide data have led to substantial progress in identifying gene functions. However, we still do not know the function of a large number of genes and, even when a gene product has been assigned to a functional class, we cannot normally predict its contribution to the phenotypic behaviour of the cell or organism - the phenome. In this study, we assessed bacterial growth parameters of 4030 non-redundant PA14 transposon mutants in the pathogenic bacterium Pseudomonas aeruginosa. The genome-wide simultaneous analysis of 119 distinct growth-related phenotypes uncovered a comprehensive phenome and provided evidence that most genotypes are not phenotypically isolated but rather define specific complex phenotypic clusters of genotypes. Since phenotypic overlap was demonstrated to reflect the relatedness of genotypes on a global scale, knowledge of an organism's phenome might significantly contribute to the advancement of functional genomics

A General Framework for Ordering Fuzzy Sets

Abstract. Orderings and rankings of fuzzy sets have turned out to play a funda-mental role in various disciplines. Throughout the previous 25 years, a lot a different approaches to this issue have been introduced, ranging from rather simple ones to quite exotic ones. The aim of this paper is to present a new framework for com-paring fuzzy sets with respect to a general class of fuzzy orderings. This approach includes several known techniques based on generalizing the crisp linear ordering of real numbers by means of the extension principle, however, in its general form, it is applicable to any fuzzy subsets of any kind of universe for which a fuzzy ordering is known – no matter whether linear or partial.

An objective method for the production of isopach maps and implications for the estimation of tephra deposit volumes and their uncertainties

Characterization of explosive volcanic eruptive processes from interpretation of deposits is a key for assessing volcanic hazard and risk, particularly for infrequent large explosive eruptions and those whose deposits are transient in the geological record. While eruption size—determined by measurement and interpretation of tephra fall deposits—is of particular importance, uncertainties for such measurements and volume estimates are rarely presented. Here, tephra volume estimates are derived from isopach maps produced by modeling raw thickness data as cubic B-spline curves under tension. Isopachs are objectively determined in relation to original data and enable limitations in volume estimates from published maps to be investigated. The eruption volumes derived using spline isopachs differ from selected published estimates by 15–40 %, reflecting uncertainties in the volume estimation process. The formalized analysis enables identification of sources of uncertainty; eruptive volume uncertainties (>30 %) are much greater than thickness measurement uncertainties (~10 %). The number of measurements is a key factor in volume estimate uncertainty, regardless of method utilized for isopach production. Deposits processed using the cubic B-spline method are well described by 60 measurements distributed across each deposit; however, this figure is deposit and distribution dependent, increasing for geometrically complex deposits, such as those exhibiting bilobate dispersion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00445-015-0942-y) contains supplementary material, which is available to authorized users

Accomodating irregular subdomains in domain decomposition theory

Summary. In the theory for domain decomposition methods, it has previously often been assumed that each subdomain is the union of a small set of coarse shaperegular triangles or tetrahedra. Recent progress is reported, which makes it possible to analyze cases with irregular subdomains such as those produced by mesh partitioners. The goal is to extend the analytic tools so that they work for problems on subdomains that might not even be Lipschitz and to characterize the rates of convergence of domain decomposition methods in terms of a few, easy to understand, geometric parameters of the subregions. For two dimensions, some best possible results have already been obtained for scalar elliptic and compressible and almost incompressible linear elasticity problems; the subdomains should be John or Jones domains and the rates of convergence are determined by parameters that characterize such domains and that of an isoperimetric inequality. Technical issues for three dimensional problems will also be discussed.

Simple approach for the preparation of 15− 15N2-enriched water for nitrogen fixation assessments: evaluation, application and recommendations

Recent findings revealed that the commonly used 15N2 tracer assay for the determination of dinitrogen (N2) fixation can underestimate the activity of aquatic N2-fixing organisms. Therefore, a modification to the method using pre-prepared 15−15N2-enriched water was proposed. Here, we present a rigorous assessment and outline a simple procedure for the preparation of 15−15N2-enriched water. We recommend to fill sterile-filtered water into serum bottles and to add 15−15N2 gas to the water in amounts exceeding the standard N2 solubility, followed by vigorous agitation (vortex mixing ≥ 5 min). Optionally, water can be degassed at low-pressure (≥950 mbar) for 10 min prior to the 15−15N2 gas addition to indirectly enhance the 15−15N2 concentration. This preparation of 15−15N2-enriched water can be done within 1 h using standard laboratory equipment. The final 15N-atom% excess was 5% after replacing 2–5% of the incubation volume with 15−15N2-enriched water. Notably, the addition of 15−15N2-enriched water can alter levels of trace elements in the incubation water due to the contact of 15−15N2-enriched water with glass, plastic and rubber ware. In our tests, levels of trace elements (Fe, P, Mn, Mo, Cu, Zn) increased by up to 0.1 nmol L−1 in the final incubation volume, which may bias rate measurements in regions where N2 fixation is limited by trace elements. For these regions, we tested an alternative way to enrich water with 15−15N2. The 15−15N2 was injected as a bubble directly to the incubation water, followed by gentle shaking. Immediately thereafter, the bubble was replaced with water to stop the 15−15N2 equilibration. This approach achieved a 15N-atom% excess of 6.6 ± 1.7% when adding 2 mL 15−15N2 per liter of incubation water. The herein presented methodological tests offer guidelines for the 15N2 tracer assay and thus, are crucial to circumvent methodological draw-backs for future N2 fixation assessments