***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
***DOCUMENTATION*** 
***EXAMPLES*** 
Input:
Output:

***EXAMPLES***
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:  Dengue is the most important arthropod borne viral disease worldwide in terms
                        of morbidity and mortality and is caused by any of the four serotypes of
                        dengue virus (DENV-1 to 4). Brazil is responsible for approximately
                        80% of dengue cases in the Americas, and since the introduction of
                        dengue in 1986, a total of 5,944,270 cases have been reported including
                        21,596 dengue hemorrhagic fever and 874 fatal cases. DENV can infect many
                        cell types and cause diverse clinical and pathological effects. The goal of
                        the study was to investigate the usefulness of NS1 capture tests as an
                        alternative tool to detect DENV in tissue specimens from previously
                        confirmed dengue fatal cases (n = 23)
                        that occurred in 2002 in Brazil.
A total of 74 tissue specimens were available: liver
                        (n = 23), lung
                        (n = 14), kidney
                        (n = 04), brain
                        (n = 10), heart
                        (n = 02), skin
                        (n = 01), spleen
                        (n = 15), thymus
                        (n = 03) and lymph nodes
                            (n = 02). We evaluated three tests
                        for NS1 antigen capture: first generation Dengue Early ELISA (PanBio
                        Diagnostics), Platelia NS1 (BioRad Laboratories) and the rapid test NS1 Ag
                        Strip (BioRad Laboratories). The overall dengue fatal case diagnosis based
                        on the tissues analyzed by Dengue Early ELISA, Platelia NS1 and the NS1 Ag
                        Strip was 34.7% (08/23), 60.8% (14/23) and 91.3%
                        (21/23), respectively. The Dengue Early ELISA detected NS1 in 22.9%
                        (17/74) of the specimens analyzed and the Platelia NS1 in 45.9%
                        (34/74). The highest sensitivity (78.3%; 58/74) was achieved by the
                        NS1 Ag Strip, and the differences in the sensitivities were statistically
                        significant (p<0.05). The NS1 Ag Strip was the most
                        sensitive in liver (91.3%; 21/23), lung (71.4%; 10/14), kidney
                        (100%; 4/4), brain (80%; 8/10), spleen (66.6%, 10/15)
                        and thymus (100%, 3/3) when compared to the other two ELISA
                        assays.
This study shows the DENV NS1 capture assay as a rapid and valuable approach
                        to postmortem dengue confirmation. With an increasing number of DHF and
                        fatal cases, the availability of new approaches useful for cases
                        confirmation plays an important tool for the disease surveillance.


Output:

Dengue manifestations may vary from asymptomatic to potentially fatal
                    complications. With an increasing number of Dengue Hemorrhagic fever (DHF) and
                    fatal cases, the availability of new approaches useful for cases confirmation
                    plays an important role for the disease surveillance. The diagnosis of fatal
                    cases in frozen and fixed tissues from autopsies can be determined by techniques
                    such as viral RT-PCR, in situ hybridization, viral proteins detection by
                    immunohistochemistry and NS3 specific immunostaining. We aimed to assess for the
                    first time the usefulness of NS1 capture tests as a diagnostic technique to
                    demonstrate DENV antigens in human tissue specimens. The highest sensitivity was
                    obtained by a rapid ICT which was also the most sensitive in liver, lung,
                    kidney, brain, spleen and thymus. Despite a number of studies demonstrating the
                    usefulness of DENV NS1 antigen detection by different ELISAs in plasma and/or
                    sera of dengue patients, no research has been done previously to demonstrate NS1
                    presence in tissues of fatal dengue cases. Moreover, the application of NS1 kits
                    to demonstrate the presence of DENV may provide a better understanding of viral
                    tropism in fatal cases and may be useful for studies of pathogenesis in vivo and
                    in experimental animals.
