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One limitation of MEDUSA is that the assignment of rate shifts is limited to the level of phylogenetic resolution.
To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1) experimental measurement of participating molecules, (2) assignment of rate laws to each reaction, and (3) parameter calibration with respect to the measurements.
We used TREE-PUZZLE (version 5.2; [ 74]) to compute the most probable assignment of rate categories for each position (option w: mixed rate heterogeneity with one invariable and 8 gamma rates).
Our system has permitted a detailed kinetic dissection of the splicing mechanism of this intein with the assignment of rate constants for every step involved in the splicing reaction, a task unprecedented not only for noncanonical inteins such as the Mja KlbA intein but also for standard inteins.
From the kinetic analysis presented, it is apparent that LacY binds sugar with a rate constant of at least 400 see (see the model in Figure 5C, inset, and the assignment of rate constants at the beginning of the discussion) followed by a weakly electrogenic step (CoutH+Lac → CoccH+Lac).
Our stepwise procedure, based on the flexible rate model of Rabosky et al. [ 17], integrates both phylogenetic and taxonomic data [Fig. 4], and involves the assignment of rate shifts [both birth and death rates] to the optimal branches on the phylogeny with unresolved tips until additional rate changes do not substantially improve the AIC score.
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They warned of practical difficulties in the measure's plan to make random assignments of rating agencies.
In conference negotiations to reconcile the House and Senate versions of the legislation on Tuesday, Senate Democrats said they were willing to remove Mr. Franken's language and accept a proposal by Mr. Frank calling for the Securities and Exchange Commission to study the conflict-of-interest issue without immediately imposing the requirement of random assignments of rating agencies.
Utilizing an improved method for the assignment of the rate constants to the complicated network of reaction pathways in the hydrodesulfurization (HDS) of polyaromatic sulfur compounds (PASCs), new understanding has been obtained concerning the intrinsic limitations to achieving the new distillate fuels standards.
For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations.
Flows wiThehigher CFCAits have higher protocol in schedusesg and code allocathen.
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