***TASK***
the task is to simplify the input abstract of a biomedical literature

***INPUT***
the input is the abstract of a biomedical literature

***OUTPUT***
the output is the simplified abstract for the input abstract of a biomedical literature
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Input: Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation.
Output:  When species evolve, their genes duplicate and diverge to allow for adaptation of their functional repertoires to the changing environment. In this scenario, unrelated genes can convergently evolve to produce proteins with the same molecular function, termed “functionally analogous.” A quantitative determination of the reaction similarities among functionally analogous enzymes could provide insight about the different structural solutions nature has used to evolve similar catalysts. Bond changes between substrates and products, and between successive reaction intermediates, were used to compare the reactions catalyzed and the mechanisms of catalysis for 95 pairs of functionally analogous enzymes. Less than half of the reactions catalyzed by unrelated enzymes, but defined as similar by the Enzyme Commission (EC) classification, are similar in terms of bond changes, suggesting that this classification often fails to capture quantitative differences between many enzyme reactions. Furthermore, we addressed for the first time whether the chemical mechanisms by which similar overall reactions are achieved in functional analogs are also similar. We conclude that convergence of reaction is often accompanied by convergence of chemical mechanism. These results will be useful for classifying enzymes, guiding functional annotation of newly determined enzyme sequences and structures and for informing the engineering of enzymes with new functions.

Input:  Although facial cleanliness is part of the SAFE strategy for trachoma there is controversy over the reliability of measuring a clean face. A child’s face with no ocular and nasal discharge is clean and the endpoint of interest, regardless of the number of times it must be washed to achieve that endpoint. The issue of reliability rests on the reproducibility of graders to assess a clean face. We report the reproducibility of assessing a clean face in a field trial in Kongwa, Tanzania.
Seven graders were trained to assess the presence and absence of nasal and ocular discharge on children’s faces. Sixty children ages 1–7 years were recruited from a community and evaluated independently by seven graders, once and again about 50 minutes later. Intra-and inter-observer variation was calculated using unweighted kappa statistics. The average intra-observer agreement was kappa = 0.72, and the average inter-observer agreement was kappa = 0.78.
Intra-observer and inter-observer agreement was substantial for the assessment of clean faces using trained Tanzania staff who represent a variety of educational backgrounds. As long as training is provided, the estimate of clean faces in children should be reliable, and reflect the effort of families to keep ocular and nasal discharge off the faces. These data suggest assessment of clean faces could be added to trachoma surveys, which already measure environmental improvements, in districts.


Output:

The repeated infection that causes trachoma is spread from person to person via infected ocular and nasal secretions. The World Health Organization (WHO) strategy for trachoma control includes keeping children’s faces clean of discharges, yet “clean faces” are not measured in most of the district surveys that evaluate the impact of programs. We studied the reliability of assessing “clean faces” in 60 children in a village in Tanzania, using trained Tanzania staff with a variety of educational backgrounds. When assessing the same child twice after 50 minutes, the staff showed substantial agreement with themselves. The agreement between a senior grader and each staff member was also excellent. The data suggest that clean faces in children can be reliably assessed, and should be added to district surveys that are measuring the impact of programs on control of trachoma.
