***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:  Risk of cardiovascular associated death in dialysis patients is the highest among all other co-morbidities. Improving the identification of patients with the highest cardiovascular risk to design an adequate treatment is, therefore, of utmost importance. There are several non-invasive cardiovascular state biomarkers based on the pulse (pressure) wave propagation properties, but their major determinants are not fully understood. In the current study we aimed to provide a framework to precisely dissect the information available in non-invasively recorded pulse wave in hemodialysis patients. Radial pressure wave profiles were recorded before, during and after two independent hemodialysis sessions in 35 anuric prevalent hemodialysis patients and once in a group of 32 healthy volunteers. Each recording was used to estimate six subject-specific parameters of pulse wave propagation model. Pressure profiles were also analyzed using SphygmoCor software (AtCor Medical, Australia) to derive values of already established biomarkers, i.e. augmentation index and sub-endocardial viability ratio (SEVR). Data preprocessing using propensity score matching allowed to compare hemodialysis and healthy groups. Augmentation index remained on average stable at 142 ± 28% during dialysis and had similar values in both considered groups. SEVR, whose pre-dialytic value was on average lower by 12% compared to healthy participants, was improved by hemodialysis, with post-dialytic values indistinguishable from those in healthy population (p-value > 0.2). The model, however, identified that the patients on hemodialysis had significantly increased stiffness of both large and small arteries compared to healthy counterparts (> 60% before dialysis with p-value < 0.05 or borderline) and that it was only transiently decreased during hemodialysis session. Additionally, correlation-based clustering revealed that augmentation index reflects the shape of heart ejection profile and SEVR is associated with stiffness of larger arteries. Patient-specific pulse wave propagation modeling coupled with radial pressure profile recording correctly identified increased arterial stiffness in hemodialysis patients, while regular pulse wave analysis based biomarkers failed to show significant differences. Further model testing in larger populations and investigating other biomarkers are needed to confirm these findings.


Output:

There are more than 2 million people receiving hemodialysis (HD) treatment worldwide. Cardiovascular disease is the most common cause of death in those patients. There are several non-invasive methods to assess if a person from general population has a high risk for developing cardiovascular disease, but it is unclear whether they are useful in hemodialysis patients. Here we assessed the ability of patient-specific pulse wave propagation modeling to correctly identify high cardiovascular risk factors in hemodialysis patients. We performed pulse wave analysis (PWA) in patients on hemodialysis and in healthy subjects. Recorded peripheral pressure profiles were simultaneously used to inform subject-specific mathematical model of pulse wave propagation. We found that standard PWA-derived biomarkers failed to clearly show the differences between hemodialysis patients and healthy subjects. However, proposed mathematical model of pulse wave propagation identified significantly increased arterial stiffness in HD patients and provided also the major determinants of PWA-derived biomarkers. Our study suggests that current pulse wave analysis based biomarkers can be insufficient to accurately diagnose hemodialysis patients. Proposed patient-specific pulse wave propagation modeling framework may be a new tool to assess the cardiovascular risk in both general and hemodialysis populations.
