The Dynamic Codon Biaser: calculating prokaryotic codon usage biases.

Bacterial genomes often reflect a bias in the usage of codons. These biases are often most notable within highly expressed genes. While deviations in codon usage can be attributed to selection or mutational biases, they can also be functional, for example controlling gene expression or guiding protein structure. Several different metrics have been developed to identify biases in codon usage. Previously we released a database, CBDB: The Codon Bias Database, in which users could retrieve precalculated codon bias data for bacterial RefSeq genomes. With the increase of bacterial genome sequence data since its release a new tool was needed. Here we present the Dynamic Codon Biaser (DCB) tool, a web application that dynamically calculates the codon usage bias statistics of prokaryotic genomes. DCB bases these calculations on 40 different highly expressed genes (HEGs) that are highly conserved across different prokaryotic species. A user can either specify an NCBI accession number or upload their own sequence. DCB returns both the bias statistics and the genome's HEG sequences. These calculations have several downstream applications, such as evolutionary studies and phage-host predictions. The source code is freely available, and the website is hosted at www.cbdb.info.

Adherence to AAP Healthy Newborn Discharge Criteria in a Tertiary Care Children's Hospital.

OBJECTIVES: In 2015, the American Academy of Pediatrics (AAP) published an updated consensus statement containing 17 discharge recommendations for healthy term newborn infants. In this study, we identify whether the AAP criteria were met before discharge at a tertiary care academic children's hospital. METHODS: A stratified random sample of charts from newborns who were discharged between June 1, 2015, and May 31, 2016, was reviewed. Of the 531 charts reviewed, 433 were included in the study. A review of each chart was performed, and data were collected. RESULTS: Descriptive statistics for our study population (N = 433) revealed that all 17 criteria were followed <5% of the time. The following criteria were met 100% of the time: clinical course and physical examination, postcircumcision bleeding, availability of family members or health care providers to address follow-up concerns, anticipatory guidance, first appointment with the physician scheduled or parents knowing how to do so, pulse oximetry screening, and hearing screening. These criteria were met at least 95% to 99% of the time: appropriate vital signs, regular void and stool frequency, appropriate jaundice and sepsis management, and metabolic screening. The following criteria were met 50% to 95% of the time: maternal serologies, hepatitis B vaccination, and social risk factor assessment. Four of the criteria were met <50% of the time: feeding assessment, maternal vaccination, follow-up timing for newborns discharged at <48 hours of life, and car safety-seat assessment. CONCLUSIONS: Our data reveal that the AAP healthy term newborn discharge recommendations are not consistently followed in our institution.