Emotional agents at the square lattice

We introduce and investigate by numerical simulations a number of models of emotional agents at the square lattice. Our models describe the most general features of emotions such as the spontaneous emotional arousal, emotional relaxation, and transfers of emotions between different agents. Group emotions in the considered models are periodically fluctuating between two opposite valency levels and as result the mean value of such group emotions is zero. The oscillations amplitude depends strongly on probability ps of the individual spontaneous arousal. For small values of relaxation times tau we observed a stochastic resonance, i.e. the signal to noise ratio SNR is maximal for a non-zero ps parameter. The amplitude increases with the probability p of local affective interactions while the mean oscillations period increases with the relaxation time tau and is only weakly dependent on other system parameters. Presence of emotional antenna can enhance positive or negative emotions and for the optimal transition probability the antenna can change agents emotions at longer distances. The stochastic resonance was also observed for the influence of emotions on task execution efficiency.Comment: 28 pages, 19 figures, 3 table

A homology model of restriction endonuclease SfiI in complex with DNA

BACKGROUND: Restriction enzymes (REases) are commercial reagents commonly used in recombinant DNA technologies. They are attractive models for studying protein-DNA interactions and valuable targets for protein engineering. They are, however, extremely divergent: the amino acid sequence of a typical REase usually shows no detectable similarities to any other proteins, with rare exceptions of other REases that recognize identical or very similar sequences. From structural analyses and bioinformatics studies it has been learned that some REases belong to at least four unrelated and structurally distinct superfamilies of nucleases, PD-DxK, PLD, HNH, and GIY-YIG. Hence, they are extremely hard targets for structure prediction and homology-based inference of sequence-function relationships and the great majority of REases remain structurally and evolutionarily unclassified. RESULTS: SfiI is a REase which recognizes the interrupted palindromic sequence 5'GGCCNNNN^NGGCC3' and generates 3 nt long 3' overhangs upon cleavage. SfiI is an archetypal Type IIF enzyme, which functions as a tetramer and cleaves two copies of the recognition site in a concerted manner. Its sequence shows no similarity to other proteins and nothing is known about the localization of its active site or residues important for oligomerization. Using the threading approach for protein fold-recognition, we identified a remote relationship between SfiI and BglI, a dimeric Type IIP restriction enzyme from the PD-DxK superfamily of nucleases, which recognizes the 5'GCCNNNN^NGGC3' sequence and whose structure in complex with the substrate DNA is available. We constructed a homology model of SfiI in complex with its target sequence and used it to predict residues important for dimerization, tetramerization, DNA binding and catalysis. CONCLUSIONS: The bioinformatics analysis suggest that SfiI, a Type IIF enzyme, is more closely related to BglI, an "orthodox" Type IIP restriction enzyme, than to any other REase, including other Type IIF REases with known structures, such as NgoMIV. NgoMIV and BglI belong to two different, very remotely related branches of the PD-DxK superfamily: the α-class (EcoRI-like), and the β-class (EcoRV-like), respectively. Thus, our analysis provides evidence that the ability to tetramerize and cut the two DNA sequences in a concerted manner was developed independently at least two times in the evolution of the PD-DxK superfamily of REases. The model of SfiI will also serve as a convenient platform for further experimental analyses

Preoperative quantification of aortic valve stenosis: comparison of 64-slice computed tomography with transesophageal and transthoracic echocardiography and size of implanted prosthesis

Precise measurements of aortic complex diameters are essential for preoperative examinations of patients with aortic stenosis (AS) scheduled for aortic valve (AV) replacement. We aimed to prospectively compare the accuracy of transthoracic echocardiography (TTE), transoesophageal echocardiography (TEE) and multi-slice computed tomography (MSCT) measurements of the AV complex and to analyze the role of the multi-modality aortic annulus diameter (AAd) assessment in the selection of the optimal prosthesis to be implanted in patients surgically treated for degenerative AS. 20 patients (F/M: 3/17; age: 69 ± 6.5 years) with severe degenerative AS were enrolled into the study. TTE, TEE and MSCT including AV calcium score (AVCS) assessment were performed in all patients. The values of AAd obtained in the long AV complex axis (TTE, TEE, MSCT) and in multiplanar perpendicular imaging (MSCT) were compared to the size of implanted prosthesis. The mean AAd was 24 ± 3.6 mm using TTE, 26 ± 4.2 mm using TEE, and 26.9 ± 3.2 in MSCT (P = 0.04 vs. TTE). The mean diameter of the left ventricle out-flow tract in TTE (19.9 ± 2.7 mm) and TEE (19.5 ± 2.7 mm) were smaller than in MSCT (24.9 ± 3.3 mm, P < 0.001 for both). The mean size of implanted prosthesis (22.2 ± 2.3 mm) was significantly smaller than the mean AAd measured by TTE (P = 0.0039), TEE (P = 0.0004), and MSCT (P < 0.0001). The implanted prosthesis size correlated significantly to the AAd: r = 0.603, P = 0.005 for TTE, r = 0.592, P = 0.006 for TEE, and r = 0.791, P < 0.001 for MSCT. Obesity and extensive valve calcification (AV calcium score ≥ 3177Ag.U.) were identified as potent factors that caused a deterioration of both TTE and MSCT performance. The accuracy of AAd measurements in TEE was only limited by AV calcification. In multivariate regression analysis the mean value of the minimum and maximum AAd obtained in MSCT-multiplanar perpendicular imaging was an independent factor (r = 0.802, P < 0.0001) predicting the size of implanted prosthesis. In patients with AS echocardiography remains the main diagnostics tool in clinical practice. MSCT as a 3-dimentional modality allows for accurate measurement of entire AV complex and facilitates optimal matching of prosthesis size