***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 threadworm, Strongyloides stercoralis, endemic in tropical and temperate climates, is a neglected tropical disease. Its diagnosis requires specific methods, and accurate information on its geographic distribution and global burden are lacking. We predicted prevalence, using Bayesian geostatistical modeling, and determined risk factors in northern Cambodia.
From February to June 2010, we performed a cross-sectional study among 2,396 participants from 60 villages in Preah Vihear Province, northern Cambodia. Two stool specimens per participant were examined using Koga agar plate culture and the Baermann method for detecting S. stercoralis infection. Environmental data was linked to parasitological and questionnaire data by location. Bayesian mixed logistic models were used to explore the spatial correlation of S. stercoralis infection risk. Bayesian Kriging was employed to predict risk at non-surveyed locations.
Of the 2,396 participants, 44.7% were infected with S. stercoralis. Of 1,071 strongyloidiasis cases, 339 (31.6%) were among schoolchildren and 425 (39.7%) were found in individuals under 16 years. The incidence of S. stercoralis infection statistically increased with age. Infection among male participants was significantly higher than among females (OR: 1.7; 95% CI: 1.4–2.0; P<0.001). Participants who defecated in latrines were infected significantly less than those who did not (OR: 0.6; 95% CI: 0.4–0.8; P = 0.001). Strongyloidiasis cases would be reduced by 39% if all participants defecated in latrines. Incidence of S. stercoralis infections did not show a strong tendency toward spatial clustering in this province. The risk of infection significantly decreased with increasing rainfall and soil organic carbon content, and increased in areas with rice fields.
Prevalence of S. stercoralis in rural Cambodia is very high and school-aged children and adults over 45 years were the most at risk for infection. Lack of access to adequate treatment for chronic uncomplicated strongyloidiasis is an urgent issue in Cambodia. We would expect to see similar prevalence rates elsewhere in Southeast Asia and other tropical resource poor countries.


Output:

Data on the prevalence and distribution of Strongyloides stercoralis (threadworm) is scarce in many resource-poor countries. We carried out a cross-sectional study during the dry season among 2,396 rural Cambodians of all ages. We used a rigorous diagnostic approach, involving two stool samples per person and two examination techniques, namely, Koga agar plate culture and the Baermann method. We predicted the spatial distribution of S. stercoralis using Bayesian Kriging analysis. Almost half of the participants (44.7%) were infected with S. stercoralis. Of the S. stercoralis cases, 39.7% involved participants under 16 years old. S. stercoralis infection prevalence was significantly higher in males than in females. Participants younger than 10 years old had a lower risk of infection than did older participants. Furthermore, our study showed that toilet use could prevent threadworm infections by 39%. Infection prevalence in the province was negatively associated with rainfall and soil organic content and positively associated with land covered by rice fields. We conclude that access to adequate treatment for S. stercoralis must be addressed in Cambodia. Infection prevalence is likely to be similar in other countries of the region and the developing world.
