Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. (C) 2012 Elsevier Ltd. All rights reserved.

Review of Complete Crime and Punishment Series

Some examples of topics covered include undocumented immigrants, guns, and terrorism within Crime and Criminal Behavior, vigilantes, Miranda warnings, and zero-tolerance policing within Police and Law Enforcement; insanity laws, DNA evidence, and victims' rights within Courts, Law, and Justice; gangs and prison violence, capital punishment, and prison privatization within Corrections; and school violence, violent juvenile offenders, and age of responsibility within Juvenile Crime and Justice. Note that Sage offers numerous reference works that provide focused analysis of key topics in the field of criminal justice, such as the Encyclopedia of Crime and Punishment (2002), the Encyclopedia of Race and Crime (2009), the Encyclopedia of Victimology and Crime Prevention (2010), the Encyclopedia of White Collar & Corporate Crime (2004), and the Encyclopedia of Interpersonal Violence (2008), available in print or as e-books via Sage Reference online.

Violence, Crime, and Violent Crime

I propose a dual conceptualization of violent crime. Since violent crime is both violence and crime, theories of aggression and deviance are required to understand it. I argue that both harm-doing and rule breaking are instrumental behaviors and that a bounded rational choice approach can account for both behaviors. However, while some of the causes of harm-doing and deviance (and violent and nonviolent crime) are the same, some are different. Theories of crime and deviance cannot explain why one only observes individual and group differences in violent crime and theories of aggression and violence cannot explain why one observes differences in all types of crimes. Such theories are “barking up the wrong tree.”

Economic change, crime, and mortality crisis in Russia: regional analysis

Objective: To identify which aspects of socioeconomic change were associated with the steep decline in life expectancy in Russia between 1990 and 1994.

Comment on Rule 14a-8(i)(9), Securities and Exchange Commission, June 30, 2015

The Securities and Exchange Commission has been analyzing its interpretation under Subsection (i)(9) of Rule 14a-8. This provision allows for the exclusion of shareholder proposals that conflict with those submitted by management. The staff has been examining its interpretation since instructed to do so by the chair of the SEC following a no action appeal in a case involving Whole Foods. A number of letters and memos submitted in connection with the review have analyzed the issue. At least one asserted that any change in interpretation required the Commission to go through the process of notice and comment. This letter asserts that notice and comment is not required, relying extensively on Perez v. Mortgage Bankers Association.