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- Frisch, U., et al.
(author)
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"Locally homogeneous turbulence" : Is it an inconsistent framework?
- 2005
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In: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 17:8
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Journal article (peer-reviewed)abstract
- In his first 1941 paper Kolmogorov assumed that the velocity has increments that are homogeneous and independent of the velocity at a suitable reference point. This assumption of local homogeneity is consistent with the nonlinear dynamics only in an asymptotic sense when the reference point is far away. This inconsistency is illustrated numerically using the Burgers equation. Kolmogorov's derivation of the four-fifths law for the third-order structure function and its anisotropic generalization are actually valid only for homogeneous turbulence, but a local version due to Duchon and Robert still holds. A Kolmogorov-Landau approach is proposed to handle the effect of fluctuations in the large-scale velocity on small-scale statistical properties; it is only a mild extension of the 1941 theory and does not incorporate intermittency effects.
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| 3. |
- Kaplan, G.G., et al.
(author)
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The risk of developing Crohn's disease after an appendectomy : A meta-analysis
- 2008
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In: American Journal of Gastroenterology. - : Ovid Technologies (Wolters Kluwer Health). - 0002-9270 .- 1572-0241. ; 103:11, s. 2925-2931
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Journal article (peer-reviewed)abstract
- BACKGROUND: Studies exploring the association between appendectomy and Crohn's disease (CD) have reported conflicting findings. We conducted a systematic review of the literature and a meta-analysis to assess the risk of CD following an appendectomy and determine the effect of time between appendectomy and CD diagnosis. METHODS: MEDLINE was used to identify observational studies evaluating the association between appendectomy and CD. Authors were contacted when data were insufficient. Relative risks (RR) with 95% confidence intervals (CI) were calculated using a random effects model. Studies that analyzed their data by the interval between the appendectomy and the diagnosis of CD were assessed separately. The Woolf ?2 statistic was used to test for homogeneity. Egger's test was used to evaluate publication bias. RESULTS: The summary RR estimate for CD following an appendectomy was significantly elevated (RR 1.61, 95% CI 1.28-2.02), though heterogeneity was observed (P < 0.0001). The risk was elevated within the first year following the operation (RR 6.69, 95% CI 5.42-8.25). The risk of CD was also significantly increased 1-4 yr following an appendectomy (RR 1.99, 95% CI 1.66- 2.38), however, after 5 yr or more, the risk fell to baseline levels (RR 1.08, 95% CI 0.99-1.18). Publication bias was not detected (P = 0.2). CONCLUSION: The meta-analysis demonstrated a significant risk of CD following an appendectomy, though heterogeneity was observed between the studies. The elevated risk early after an appendectomy, which diminishes thereafter, likely reflects diagnostic problems in patients with incipient CD. © 2008 by Am. Coll. of Gastroenterology.
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| 4. |
- Kaplan, GG, et al.
(author)
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The risk of developing Crohn's disease after an appendectomy : A population-based cohort study in Sweden and Denmark
- 2007
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In: Gut. - : BMJ. - 0017-5749 .- 1468-3288. ; 56:10, s. 1387-1392
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Journal article (peer-reviewed)abstract
- Background: The relationship between appendectomy and Crohn's disease is controversial. A Swedish-Danish cohort study was conducted to assess the risk of developing Crohn's disease after an appendectomy. Methods: 709 353 appendectomy patients in Sweden (since 1964) and Denmark (since 1977) were followed for first hospitalisations for Crohn's disease to 2004. Standardised incidence ratios (SIR) served as relative risks. Results: Overall, 1655 Crohn's disease cases were observed during 11.1 million person-years of follow-up. Whereas appendectomy before the age of 10 years was not associated with the risk of Crohn's disease (SIR 1.00, 95% CI 0.80-1.25), the overall SIR of developing Crohn's disease was 1.52 (95% CI 1.45-1.59), being highest in the first 6 months (SIR 8.69, 95% CI 7.68-9.84). SIR diminished rapidly thereafter, with the risk of Crohn's disease reaching background levels after 5-10 years for Crohn's disease overall, as well as for Crohn's ileitis, ileocolonic Crohn's disease, Crohn's colitis and other/unspecified Crohn's disease. A long-term increased risk of Crohn's disease up to 20 years after the appendectomy was seen only in appendectomy patients without appendicitis or mesenteric lymphadenitis. Conclusion: The transient increased risk of Crohn's disease after an appendectomy is probably explained by diagnostic bias.
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| 5. |
- Lundberg, Marcus, 1974-, et al.
(author)
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Transition States in a Protein Environment : ONIOM QM:MM Modeling of Isopenicillin N Synthesis
- 2009
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In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 5:1, s. 222-234
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Journal article (peer-reviewed)abstract
- To highlight the role of the protein in metal enzyme catalysis, we optimize ONIOM QM:MM transition states and intermediates for the full reaction of the nonheme iron enzyme isopenicillin N synthase (IPNS). Optimizations of transition states in large protein systems are possible using our new geometry optimizer with quadratic coupling between the QM and MM regions [Vreven, T. et al. MoL Phys. 2006, 104, 701-704]. To highlight the effect of the metal center, results from the protein model are compared to results from an active site model containing only the metal center and coordinating residues [Lundberg, M. et al. Biochemistry 2008, 47, 1031-10421. The analysis suggests that the main catalytic effect comes from the metal center, while the protein controls the reactivity to achieve high product specificity. As an example, hydrophobic residues align the valine substrate radical in a favorable conformation for thiazolicline ring closure and contribute to product selectivity and high stereospecificity. A low-barrier pathway for P-lactam formation is found where the proton required for heterolytic O-O bond cleavage comes directly from the valine N-H group of the substrate. The alternative mechanism, where the proton in 0-0 bond cleavage initially comes from an iron water ligand, can be disfavored by the electrostatic interactions with the surrounding protein. Explicit protein effects on transition states are typically 1-6 kcal/mol in the present enzyme and can be understood by considering whether the transition state involves large movements of the substrate as well as whether it involves electron transfer.
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| 8. |
- Zheng, Guishan, et al.
(author)
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Implementation and Benchmark Tests of the DFTB Method and Its Application in the ONIOM Method
- 2009
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In: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608 .- 1097-461X. ; 109:9, s. 1841-1854
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Journal article (peer-reviewed)abstract
- We present the theoretical and implementation details of the DFTB method with analytical gradients into the Gaussian package. SCF optimization performance with DIIS method is compared with modified Broyden method and Anderson methods, from which DIIS method is to be preferred. The number of geometry optimization steps can be significantly decreased with the Berny algorithm compared to the conjugated gradient method. From the comparison of geometry parameters as well as trends in the change of HOMO and LUMO energies, the results show clearly that DFTB can reproduce values obtained at the B3LYP/6-31G(d) level well. We also investigated the DFTB method as the low level quantum mechanical (QM) method in an ONIOM (QM:QM') description for all amino acid model system and found DFTB promising as a method to describe polarization and charge-transfer effects in large systems.
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