***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:  The parasitic skin disease tungiasis (caused by the flea Tunga penetrans) affects resource-poor communities in Latin America, the Caribbean and sub-Saharan Africa. Prevalences in endemic areas are high, and severe pathology occurs commonly. However, risk factors for infestation have never been assessed in Africa.
A cross-sectional study was conducted in Erekiti, a rural community in Lagos State (Nigeria), where tungiasis is endemic. Individuals were examined clinically for the presence of tungiasis, and a questionnaire was applied. Data from 643 individuals (86.6% of the target population) were analyzed; 252 (42.5%) were infested with T. penetrans. In the multivariate logistic regression analysis, presence of pigs on the compounds (adjusted odds ratio = 17.98; 95% confidence interval: 5.55–58.23), sand or clay floor inside houses (9.33; 5.06–17.19), and having the common resting place outside the house (7.14; 4.0–14.29) were the most important risk factors identified. The regular use of closed footwear (0.34; 0.18–0.62) and the use of insecticides indoors (0.2; 0.05–0.83) were protective against infestation. The population attributable fractions associated with tungiasis were: sand or clay floor inside the house (73.7%), resting usually outside the house (65.5%), no regular use of closed footwear (51.1%), and pigs on the compound (37.9%).
The presence of tungiasis in Erekiti is determined to an important extent by a limited number of modifiable variables. Effective and sustainable intervention measures addressing these factors need to be implemented in this and other West African communities with high disease burden.


Output:

Tungiasis is a parasitic skin disease caused by the sand flea Tunga penetrans. After penetration into the skin, the flea grows and reaches the size of a pea. The disease is a neglected public health problem in endemic areas in Latin America, the Caribbean and Africa, and causes considerable morbidity in the affected communities. We performed a study in a rural community in Nigeria to detect factors associated with tungiasis. People were examined for the presence of sand flea lesions, and a questionnaire was applied. Of the 643 individuals examined, 252 (42.5%) had tungiasis. The most important factors independently associated with the disease were: presence of pigs on the compound (adjusted odds ratio [OR] = 17.98), sand or clay floor inside house (OR = 9.33), and having the common resting place outside the house (OR = 7.14). The regular use of closed footwear (OR = 0.34) and the use of insecticides indoors (OR = 0.2) were protective factors. Our data show that tungiasis in this community is determined to an important extent by some variables that may be a target for interventions.
