A comprehensive analysis of the phylogenetic signal in ramp sequences in 211 vertebrates.

Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework.

Codon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life.

Identical codon pairing and co-tRNA codon pairing increase translational efficiency within genes when two codons that encode the same amino acid are translated by the same tRNA before it diffuses from the ribosome. We examine the phylogenetic signal in both identical and co-tRNA codon pairing across 23 428 species using alignment-free and parsimony methods. We determined that conserved codon pairing typically has a smaller window size than the length of a ribosome, and codon pairing tracks phylogenies across various taxonomic groups.

Codon use and aversion is largely phylogenetically conserved across the tree of life.

Using parsimony, we analyzed codon usages across 12,337 species and 25,727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890,814 codons were parsimony informative.

CAM: an alignment-free method to recover phylogenies using codon aversion motifs.

Background: Common phylogenomic approaches for recovering phylogenies are often time-consuming and require annotations for orthologous gene relationships that are not always available. In contrast, alignment-free phylogenomic approaches typically use structure and oligomer frequencies to calculate pairwise distances between species. We have developed an approach to quickly calculate distances between species based on codon aversion.

A comparative study of adolescent risk assessment instruments: predictive and incremental validity.

Promising new adolescent risk assessment tools are being incorporated into clinical practice but currently possess limited evidence of predictive validity regarding their individual and/or combined use in risk assessments. The current study compares three structured adolescent risk instruments, Youth Level of Service/Case Management Inventory (YLS/CMI), Structured Assessment of Violence Risk in Youth (SAVRY), and Psychopathy Checklist: Youth Version (PCL:YV), for both predictive and incremental validity with respect to general and violent recidivism. Receiver operating characteristic and hierarchical logistic regression analyses revealed that the risk tools predicted general and violent recidivism to varying degrees of accuracy, but the SAVRY offered the most in incremental validity.

Concurrent and predictive validity of the psychopathy checklist: youth version across gender and ethnicity.

The concurrent and predictive validity of the Psychopathy Checklist: Youth Version (PCL:YV) were examined across gender and ethnicity using multiple outcome measures on a community-based sample of 130 adjudicated youths. The PCL:YV demonstrated concurrent validity with externalizing behavior problems but, it is important to note, was also associated with internalizing measures of negative affect. With a mean follow-up period of 3 years, the PCL:YV was found to predict general and violent recidivism in male, Native Canadian, and Caucasian youths.