174 research outputs found
Managing contradictory evidence
The paper draws on the theory of mass assignment
to refine the underlying semantics of intuitionistic fuzzy sets.
Inconsistency can arise from several sources and it is dealt with
in different ways. All the representations of inconsistency and
contradiction in this paper arise from considering restricting
and positive evidence lattices. In particular this paper formally
addresses the operators, intersection and conjunction in detail.
Because union and disjunction are required to compute the
values for intersection and conjunction these are also covered
as part of the analysis
Semantic transfer and contradictory evidence in intuitionistic fuzzy sets
The relationship between object level intuitionistic
fuzzy sets and predicate based intuitionistic fuzzy sets is
explored. Mass assignment uses a process called semantic unification
to evaluate the degree to which one set supports another,
the inverse function is semantic separation. Intuitionistic fuzzy
sets are mapped onto a mass assignment framework and the
semantic unification operator is generalised to support both
mass assignment and intuitionistic fuzzy sets, as is semantic
separation. Transfer of inconsistent and contradictory evidence
are also dealt with
Reasoning consistently about inconsistency
Patching et al. and Hinde et al. in their work on
truth-space mass assignments, presented a semantic unification
function and a semantic separation function for mass assignment
logic that dealt with inconsistency. This paper takes these
two functions and while preserving the outside inconsistencies
shows how inconsistency can be reasoned about in a consistent
manner. This means that inconsistency that arises outside the
system need not enter the system, but needs to be represented
within the system, and can therefore be extracted appropriately
as output from the system to emerge as inconsistency on the
outside. The internal reasoning system need therefore only
concern itself with belief in truth, falsity and uncertainty
Managing contradictory evidence
The paper draws on the theory of mass assignment
to refine the underlying semantics of intuitionistic fuzzy sets.
Inconsistency can arise from several sources and it is dealt with
in different ways. All the representations of inconsistency and
contradiction in this paper arise from considering restricting
and positive evidence lattices. In particular this paper formally
addresses the operators, intersection and conjunction in detail.
Because union and disjunction are required to compute the
values for intersection and conjunction these are also covered
as part of the analysis
Reasoning Consistently about Inconsistency
Patching et al. and Hinde et al. in their work on
truth-space mass assignments, presented a semantic unification
function and a semantic separation function for mass assignment
logic that dealt with inconsistency. This paper takes these
two functions and while preserving the outside inconsistencies
shows how inconsistency can be reasoned about in a consistent
manner. This means that inconsistency that arises outside the
system need not enter the system, but needs to be represented
within the system, and can therefore be extracted appropriately
as output from the system to emerge as inconsistency on the
outside. The internal reasoning system need therefore only
concern itself with belief in truth, falsity and uncertainty
Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions
This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developedatLeedsalongsideProfessor SteveBaldwintowhomthisreviewisdedicated.Italsoreviewstwo biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins – synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs
Microbial transformations of selenite by methane-oxidizing bacteria
Abstract Methane oxidizing bacteria are well known for their role in the global methane cycle and their potential for microbial transformation of wide range of hydrocarbon and chlorinated hydrocarbon pollution. Recently, it has also emerged that methane-oxidizing bacteria interact with inorganic pollutants in the environment. Here we report what we believe to be the first study of the interaction of pure strains of methane-oxidizing bacteria with selenite. Results indicate that the commonly used laboratory model strains of methane oxidizing bacteria, Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b are both able to reduce the toxic selenite (SeO32-) but not selenate (SeO42-) to red spherical nanoparticulate elemental selenium (Se0), which was characterised via EDX and EXAFS. The cultures also produced volatile selenium-containing species, which suggests that both strains may have an additional activity that can either transform Se0 or selenite into volatile methylated forms of selenium. Transmission electron microscopy (TEM) measurements and experiments with the cell fractions: cytoplasm, cell wall and cell membrane show that the nanoparticles are formed mainly on the cell wall. Collectively these results are promising for the use of methane-oxidizing bacteria for bioremediation or suggest possible uses in the production of selenium nanoparticles for biotechnology
Efficiency of Purine Utilization by Helicobacter pylori: Roles for Adenosine Deaminase and a NupC Homolog
The ability to synthesize and salvage purines is crucial for colonization by a variety of human bacterial pathogens. Helicobacter pylori colonizes the gastric epithelium of humans, yet its specific purine requirements are poorly understood, and the transport mechanisms underlying purine uptake remain unknown. Using a fully defined synthetic growth medium, we determined that H. pylori 26695 possesses a complete salvage pathway that allows for growth on any biological purine nucleobase or nucleoside with the exception of xanthosine. Doubling times in this medium varied between 7 and 14 hours depending on the purine source, with hypoxanthine, inosine and adenosine representing the purines utilized most efficiently for growth. The ability to grow on adenine or adenosine was studied using enzyme assays, revealing deamination of adenosine but not adenine by H. pylori 26695 cell lysates. Using mutant analysis we show that a strain lacking the gene encoding a NupC homolog (HP1180) was growth-retarded in a defined medium supplemented with certain purines. This strain was attenuated for uptake of radiolabeled adenosine, guanosine, and inosine, showing a role for this transporter in uptake of purine nucleosides. Deletion of the GMP biosynthesis gene guaA had no discernible effect on mouse stomach colonization, in contrast to findings in numerous bacterial pathogens. In this study we define a more comprehensive model for purine acquisition and salvage in H. pylori that includes purine uptake by a NupC homolog and catabolism of adenosine via adenosine deaminase
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