Evolvix BEST Names for semantic reproducibility across code2brain interfaces.

Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general-purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality.

Evidence that natural selection on codon usage in Drosophila pseudoobscura varies across codons.

Like other species of Drosophila, Drosophila pseudoobscura has a distinct bias toward the usage of C- and G-ending codons. Previous studies have indicated that this bias is due, at least in part, to natural selection. Codon bias clearly differs among amino acids (and other codon classes) in Drosophila, which may reflect differences in the intensity of selection on codon usage.

National trends in patient safety for four common conditions, 2005-2011.

Background: Changes in adverse-event rates among Medicare patients with common medical conditions and conditions requiring surgery remain largely unknown.

Methods: We used Medicare Patient Safety Monitoring System data abstracted from medical records on 21 adverse events in patients hospitalized in the United States between 2005 and 2011 for acute myocardial infarction, congestive heart failure, pneumonia, or conditions requiring surgery. We estimated trends in the rate of occurrence of adverse events for which patients were at risk, the proportion of patients with one or more adverse events, and the number of adverse events per 1000 hospitalizations.

Chart-confirmed guillain-barre syndrome after 2009 H1N1 influenza vaccination among the Medicare population, 2009-2010.

Given the increased risk of Guillain-Barré Syndrome (GBS) found with the 1976 swine influenza vaccine, both active surveillance and end-of-season analyses on chart-confirmed cases were performed across multiple US vaccine safety monitoring systems, including the Medicare system, to evaluate the association of GBS after 2009 monovalent H1N1 influenza vaccination. Medically reviewed cases consisted of H1N1-vaccinated Medicare beneficiaries who were hospitalized for GBS. These cases were then classified by using Brighton Collaboration diagnostic criteria.

Hospital-acquired pressure ulcers: results from the national Medicare Patient Safety Monitoring System study.

Objectives: To determine the national and state incidence levels of newly hospital-acquired pressure ulcers (PUs) in Medicare beneficiaries and to describe the clinical and demographic characteristics and outcomes of these individuals.

Design: Retrospective secondary analysis of the national Medicare Patient Safety Monitoring System (MPSMS) database.

Setting: Medicare-eligible hospitals across the United States and select territories.

Racial disparities in the frequency of patient safety events: results from the National Medicare Patient Safety Monitoring System.

Background: Although there is extensive evidence of racial disparities in processes and outcomes of medical care, there has been limited investigation of disparities in patient safety.

Objective: To determine whether there are racial disparities in the frequency of adverse events studied in the Medicare Patient Safety Monitoring System.

Design And Subjects: Abstraction of 102,623 randomly selected charts from hospital discharges of non-Hispanic white and black Medicare patients between January 1, 2004 and December 31, 2007 to assess frequency of patient safety events in 4 domains: general (pressure ulcers and falls), selected nosocomial infections, selected procedure-related adverse events, and adverse drug events due to anticoagulants and hypoglycemic agents.

Evaluation of Guillain-Barré Syndrome among recipients of influenza vaccine in 2000 and 2001.

Background: The 1976-1977 swine influenza vaccine was associated with an elevated risk of Guillain-Barré Syndrome (GBS), especially within 6 weeks after vaccination. A 2004 IOM report concluded that evidence was inadequate to accept or reject a causal relationship between subsequent influenza vaccine formulations and GBS. Studies published after the IOM report have been limited by passively reported data or lack of validation of coded diagnoses.

Identification of hospital-acquired catheter-associated urinary tract infections from Medicare claims: sensitivity and positive predictive value.

Background And Objective: Hospital-acquired catheter-associated urinary tract infection (CAUTI) is one of the first 6 conditions Medicare is targeting to reduce payment associated with hospital-acquired conditions under Congressional mandate. This study was to determine the positive predictive value (PPV) and sensitivity in identifying patients in Medicare claims who had urinary catheterization and who had hospital-acquired CAUTIs.

Research Design: CAUTIs identified by ICD-9-CM codes in Medicare claims were compared with those revealed by medical record abstraction in random samples of Medicare discharges in 2005 to 2006.

Estimation of isolation times of the island species in the Drosophila simulans complex from multilocus DNA sequence data.

Background: The Drosophila simulans species complex continues to serve as an important model system for the study of new species formation. The complex is comprised of the cosmopolitan species, D. simulans, and two island endemics, D.

A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana.

In many organisms, synonymous codon usage is biased by a history of natural selection. However, codon bias, itself, does not indicate that selection is ongoing; it may be a vestige of past selection. Simple statistical tests have been devised to infer ongoing selection on codon usage by comparing the derived state frequency spectra at polymorphic sites segregating either derived preferred codons or derived unpreferred codons; if selection is effective, the frequency of derived states should be higher in the former.

The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations.

The 'Hill-Robertson (HR) effect' describes that linkage between sites under selection will reduce the overall effectiveness of selection in finite populations. Here we discuss the major concepts associated with the HR effect and present results of computer simulations focusing on the linkage effects generated by multiple sites under weak selection. Most models of linkage and selection forecast differences in effectiveness of selection between chromosomes or chromosomal regions involving a number of genes.

Fine-scale crossover rate heterogeneity in Drosophila pseudoobscura.

Broad-scale differences in crossover rate across the genome have been characterized in most genomes studied. Fine-scale differences, however, have only been examined in a few taxa, such as Arabidopsis, yeast, humans, and mice. No prior studies have directly looked for fine-scale recombination rate heterogeneity in Drosophila.

Unusual usage of AGG and TTG codons in humans and their viruses.

Prior analysis on human protein-coding DNA sequences has identified local base composition as the primary predictor of synonymous codon usage. However, in many organisms, codon usage is influenced by natural selection, particularly for efficient expression of functional gene products. Because viruses are expected to evolve codon usage in the context of their host's molecular machinery, their genomes provide another window into the forces that guide their host's molecular evolution.

Selection conflicts, gene expression, and codon usage trends in yeast.

Synonymous codon usage in yeast appears to be influenced by natural selection on gene expression, as well as regional variation in compositional bias. Because of the large number of potential targets of selection (i.e.

Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret.

The usage of preferred codons in Drosophila melanogaster is reduced in regions of lower recombination. This is consistent with population genetics theory, whereby the effectiveness of selection on multiple targets is limited by stochastic effects caused by linkage. However, because the selectively preferred codons in D.

Variability on the dot chromosome in the Drosophila simulans clade.

A recent study suggested that recent nuclear gene introgression between Drosophila simulans and D. mauritiana may have obscured efforts to estimate the phylogeny of the species of the D. simulans clade, which includes these two species and D.

Hidden evolution: progress and limitations in detecting multifarious natural selection.

From illustrative examples of research on the best-studied group of species to date, Drosophila melanogaster and its closest relatives, we argue that selection is multifarious, but often hidden. Selective fixation of new, highly advantageous alleles is the most parsimonious explanation for a typical pattern of molecular variation observed in genomic regions characterized by very low recombination: drastically reduced DNA sequence variation within species and typical levels of sequence divergence among species. At the same time, the identity of the gene (or genes) influenced by selection is not just difficult to discern; it may be impossible.

Single nucleotide polymorphism seeking long term association with complex disease.

Successful investigation of common diseases requires advances in our understanding of the organization of the genome. Linkage disequilibrium provides a theoretical basis for performing candidate gene or whole-genome association studies to analyze complex disease. However, to constructively interrogate SNPs for these studies, technologies with sufficient throughput and sensitivity are required.

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives.

The divergence of Drosophila pseudoobscura from its close relatives, D. persimilis and D. pseudoobscura bogotana, was examined using the pattern of DNA sequence variation in a common set of 50 inbred lines at 11 loci from diverse locations in the genome.

Interactions between natural selection, recombination and gene density in the genes of Drosophila.

In Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and strongly significant, association with recombination--as expected if recombination allows natural selection to act more efficiently when multiple linked sites segregate functional variation.

Differences in (G+C) content between species: a commentary on Forsdyke's "chromosomal viewpoint" of speciation.

Forsdyke (1999) has recently argued that differences in (G+C)%, or G+C content, may trigger new species formation. He further argues that the genic model has shortcomings that can be overcome by his "chromosomal" (hereafter, "G+C") model. We disagree on several counts.

Evolutionary history of microsatellites in the obscura group of Drosophila.

The evolutionary origins of microsatellites are not well understood. Some investigators have suggested that point mutations that expand repeat arrays beyond a threshold size trigger microsatellites to become variable. However, little empirical data has been brought forth on this and related issues.

The population genetics of the origin and divergence of the Drosophila simulans complex species.

The origins and divergence of Drosophila simulans and close relatives D. mauritiana and D. sechellia were examined using the patterns of DNA sequence variation found within and between species at 14 different genes.

Recent selection on synonymous codon usage in Drosophila.

Evidence from a variety of sources indicates that selection has influenced synonymous codon usage in Drosophila. It has generally been difficult, however, to distinguish selection that acted in the distant past from ongoing selection. However, under a neutral model, polymorphisms usually reflect more recent mutations than fixed differences between species and may, therefore, be useful for inferring recent selection.

Mutation pressure, natural selection, and the evolution of base composition in Drosophila.

Genome sequencing in a number of taxa has revealed variation in nucleotide composition both among regions of the genome and among functional classes of sites in DNA. Mutational biases, biased gene conversion, and natural selection have been proposed as causes of this variation. Here, we review patterns of base composition in Drosophila DNA.