***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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Output:

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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:  A community-based longitudinal study was performed in the Eastern Province of Zambia, in which repeated serological samplings were done to determine the incidence of human cysticercosis. Three sampling rounds were carried out at six months intervals. A total of 867 participants presented for all three samplings. All samples were tested for the presence of cysticercus antigens using a monoclonal antibody-based enzyme-linked immunosorbent assay (sero-Ag-ELISA), while a randomly selected sub-sample of 161 samples from each sampling round was tested for specific antibodies using a commercial enzyme-linked immunoelectrotransfer blot (EITB) assay. Stool samples (n = 226) were also collected during the final round of sampling for taeniosis diagnosis by coprology and coproantigen ELISA. Cysticercosis seroprevalence varied from 12.2% to 14.5% (sero-Ag) and from 33.5% to 38.5% (sero-Ab) during the study period. A taeniosis prevalence of 11.9% was determined. Incidence rates of 6300 (sero-Ag, per 100000 persons-year) and 23600 (sero-Ab, per 100000 persons-year) were determined. Seroreversion rates of 44% for sero-Ag and 38.7% for sero-Ab were recorded over the whole period. In conclusion, this study has shown the dynamic nature of T. solium infections; many of the people at risk become (re)infected due to the high environmental contamination, with a high number turning seronegative within a year after infection. An important number of infections probably never fully establish, leading to transient antibody responses and short-term antigen presence.


Output:

Human neurocysticercosis is an infection of the central nervous system caused by the larval stage of the pork tapeworm (Taenia solium). The infection occurs mainly in developing countries and is associated with poverty, poor sanitation and free-range pig management. It is estimated to be responsible for 30% of cases of acquired epilepsy in endemic areas. The limited number of human studies on this infection in Sub-Saharan Africa determined a high occurrence of cysticercosis. This study aimed to learn more about the transmission dynamics of this parasite in a rural endemic area in Eastern Zambia. A longitudinal study was carried out in which 867 participants were blood sampled three times, with a 6-month interval. Samples were analysed for the presence of cysticercal circulating antigens and specific antibodies. Results indicate that about 1 on 3 people get exposed to infection while only 1 on 10 people actually acquire infection. The study shows the dynamic nature of T. solium infections; many of the people at risk become (re)infected due to the high environmental contamination, with a high number turning seronegative within a year after infection. An important number of infections probably never fully establish, leading to short-term antibody and antigen presence.
