***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:  Cellular differentiation entails reprogramming of the transcriptome from a
                    pluripotent to a unipotent fate. This process was suggested to coincide with a
                    global increase of repressive heterochromatin, which results in a reduction of
                    transcriptional plasticity and potential. Here we report the dynamics of the
                    transcriptome and an abundant heterochromatic histone modification,
                    dimethylation of histone H3 at lysine 9 (H3K9me2), during neuronal
                    differentiation of embryonic stem cells. In contrast to the prevailing model, we
                    find H3K9me2 to occupy over 50% of chromosomal regions already in stem
                    cells. Marked are most genomic regions that are devoid of transcription and a
                    subgroup of histone modifications. Importantly, no global increase occurs during
                    differentiation, but discrete local changes of H3K9me2 particularly at genic
                    regions can be detected. Mirroring the cell fate change, many genes show altered
                    expression upon differentiation. Quantitative sequencing of transcripts
                    demonstrates however that the total number of active genes is equal between stem
                    cells and several tested differentiated cell types. Together, these findings
                    reveal high prevalence of a heterochromatic mark in stem cells and challenge the
                    model of low abundance of epigenetic repression and resulting global basal level
                    transcription in stem cells. This suggests that cellular differentiation entails
                    local rather than global changes in epigenetic repression and transcriptional
                    activity.


Output:

Epigenetic modifications of DNA and bound histones are major determinants of cell
                    type–specific gene expression patterns. A prevalent model in stem cell
                    biology suggests that the loss of pluripotency entails global increase in
                    heterochromatin and coinciding shutdown of lineage unrelated genes. We performed
                    analysis of both H3K9 dimethylation pattern and the global transcriptome in an
                    advanced murine neuronal differentiation model. In this paradigm, we do not find
                    evidence for a global increase in heterochromatic H3K9 dimethylation or
                    reduction of transcriptome complexity as stem cells become terminally
                    differentiated post-mitotic neurons. This suggests that pluripotent embryonic
                    stem cells are not per se unique in regards to heterochromatin
                    abundance and transcriptional plasticity as compared to somatic cells. Instead,
                    focal changes in chromatin might help to stabilize cellular states at any
                    developmental stage.
