AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.

BACKGROUND: Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. RESULTS: Here we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal http://www.bioportal.uio.no, University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. CONCLUSION: The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.

Stochastic model for outcome prediction in acute illness.

The aims were to apply a stochastic model to predict outcome early in acute emergencies and to evaluate the effectiveness of various therapies in a consecutively monitored series of severely injured patients with noninvasive hemodynamic monitoring. The survival probabilities were calculated beginning shortly after admission to the emergency department (ED) and at subsequent intervals during their hospitalization. Cardiac function was evaluated by cardiac output (CI), heart rate (HR), and mean arterial blood pressure (MAP), pulmonary function by pulse oximetry (SapO(2)), and tissue perfusion function by transcutaneous oxygen indexed to FiO(2),(PtcO(2)/FiO(2)), and carbon dioxide (PtcCO(2)) tension. The survival probability (SP) of survivors averaged 81.5+/-1.1% (SEM) and for nonsurvivors 57.7+/-2.3% (p<0.001) in the first 24-hour period of resuscitation and subsequent management. The CI, SapO(2),PtcO(2)/FiO(2) and MAP were significantly higher in survivors than in nonsurvivors during the initial resuscitation, while HR and PtcCO(2) tensions were higher in the nonsurvivors. Predictions made during the initial resuscitation period in the first 24-hours after admission were compared with the actual outcome at hospital discharge, which were usually several weeks later; misclassifications were 9.6% (16/167). The therapeutic decision support system objectively evaluated the responses of alternative therapies based on responses of patients with similar clinical-hemodynamic states.

Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids.

Serial transfer of plastids from one eukaryotic host to another is the key process involved in evolution of secondhand plastids. Such transfers drastically change the environment of the plastids and hence the selection regimes, presumably leading to changes over time in the characteristics of plastid gene evolution and to misleading phylogenetic inferences. About half of the dinoflagellate protists species are photosynthetic and unique in harboring a diversity of plastids acquired from a wide range of eukaryotic algae. They are therefore ideal for studying evolutionary processes of plastids gained through secondary and tertiary endosymbioses. In the light of these processes, we have evaluated the origin of 2 types of dinoflagellate plastids, containing the peridinin or 19'-hexanoyloxyfucoxanthin (19'-HNOF) pigments, by inferring the phylogeny using "covarion" evolutionary models allowing the pattern of among-site rate variation to change over time. Our investigations of genes from secondary and tertiary plastids derived from the rhodophyte plastid lineage clearly reveal "heterotachy" processes characterized as stationary covarion substitution patterns and changes in proportion of variable sites across sequences. Failure to accommodate covarion-like substitution patterns can have strong effects on the plastid tree topology. Importantly, multigene analyses performed with probabilistic methods using among-site rate and covarion models of evolution conflict with proposed single origin of the peridinin- and 19'-HNOF-containing plastids, suggesting that analysis of secondhand plastids can be hampered by convergence in the evolutionary signature of the plastid DNA sequences. Another type of sequence convergence was detected at protein level involving the psaA gene. Excluding the psaA sequence from a concatenated protein alignment grouped the peridinin plastid with haptophytes, congruent with all DNA trees. Altogether, taking account of complex processes involved in the evolution of dinoflagellate plastid sequences (both at the DNA and amino acid level), we demonstrate the difficulty of excluding independent, tertiary origin for both the peridinin and 19'-HNOF plastids involving engulfment of haptophyte-like algae. In addition, the refined topologies suggest the red algal order, Porphyridales, as the endosymbiont ancestor of the secondary plastids in cryptophytes, haptophytes, and heterokonts.

A stochastic control program to predict outcome and to support therapeutic decisions: a preliminary report.

BACKGROUND AND OBJECTIVES: Early noninvasive hemodynamic monitoring with an outcome predictor and a therapeutic decision support system may be useful to identify and correct hemodynamic deficiencies in emergency patients. The first aim was to apply a stochastic (probability) search and display model to predict outcome as early as possible. The second aim was to explore the usefulness of a therapeutic decision support system to evaluate the relative effectiveness of various therapies. METHODS: A stochastic control and display program based on noninvasive hemodynamic monitoring was applied in 100 consecutive critically ill patients admitted to the emergency department of an inner city public hospital. The program continuously displayed the noninvasive hemodynamic data and the patient's predicted survival probability (SP) that was based on the patient's diagnosis, covariates, and hemodynamic data. The accuracy of the SP at the initial resuscitation on admission to the emergency department (ED) was evaluated by the actual outcome at hospital discharge. The therapeutic decision support program evaluated the relative effectiveness of various therapies on based on their hemodynamic and SP responses and outcome of patients with similar clinical-hemodynamic states. RESULTS: The cardiac index, mean arterial pressure, arterial saturation, transcutaneous oxygen and carbon dioxide tensions were appreciably higher in survivors than in nonsurvivors in the initial resuscitation. Heart rate was higher in the nonsurvivors. The calculated Survival Probability (SP) of survivors averaged 81 +/- 1.4% in the first 24-hour observation period. It was 58 +/- 2.2% for nonsurvivors during this period. Misclassifications were 10/100 or 10%.

Mathematical program for outcome prediction and therapeutic support for trauma beginning within 1 hr of admission: a preliminary report.

OBJECTIVES: The aims were a) to noninvasively monitor acute emergency trauma patients beginning within 1 hr after admission to the emergency department; b) to prospectively predict outcome; and c) to evaluate the relative effectiveness of various modes of therapy. DESIGN: Prospective outcome prediction study using a mathematical search and display model based on noninvasive hemodynamic monitoring. SETTING: A level I trauma service in a large university-run inner-city public hospital. PATIENTS: We studied 185 consecutively noninvasively monitored emergency patients. INTERVENTIONS: We noninvasively monitored cardiac index, mean arterial blood pressure, heart rate, pulse oximetry, and transcutaneous oxygen and carbon dioxide tensions beginning within 1-hr after emergency admission. MEASUREMENTS AND MAIN RESULTS: The cardiac index, pulse oximetry, transcutaneous oxygen tension, transcutaneous carbon dioxide tension, and mean arterial blood pressure were higher in survivors than in nonsurvivors in the initial resuscitation period and at the hemodynamic nadir. Heart rate and transcutaneous carbon dioxide tension were higher in the nonsurvivors. The calculated survival probability in the first hour observation period of survivors averaged 85 +/- 14% vs. 69 +/- 16% for nonsurvivors (p = .0001). Misclassifications of the series as a whole were 11.3%; after excluding brain death from severe head injury, there were 6.4% misclassifications. A decision support system evaluated the effects of various therapies based on responses of patients with similar clinical-hemodynamic states. CONCLUSION: Noninvasive hemodynamic monitoring and an information system provided a feasible approach to predict outcome early and to evaluate prospectively the efficacy of various therapies.