Minimizing the average distance to a closest leaf in a phylogenetic tree

When performing an analysis on a collection of molecular sequences, it can be convenient to reduce the number of sequences under consideration while maintaining some characteristic of a larger collection of sequences. For example, one may wish to select a subset of high-quality sequences that represent the diversity of a larger collection of sequences. One may also wish to specialize a large database of characterized "reference sequences" to a smaller subset that is as close as possible on average to a collection of "query sequences" of interest. Such a representative subset can be useful whenever one wishes to find a set of reference sequences that is appropriate to use for comparative analysis of environmentally-derived sequences, such as for selecting "reference tree" sequences for phylogenetic placement of metagenomic reads. In this paper we formalize these problems in terms of the minimization of the Average Distance to the Closest Leaf (ADCL) and investigate algorithms to perform the relevant minimization. We show that the greedy algorithm is not effective, show that a variant of the Partitioning Among Medoids (PAM) heuristic gets stuck in local minima, and develop an exact dynamic programming approach. Using this exact program we note that the performance of PAM appears to be good for simulated trees, and is faster than the exact algorithm for small trees. On the other hand, the exact program gives solutions for all numbers of leaves less than or equal to the given desired number of leaves, while PAM only gives a solution for the pre-specified number of leaves. Via application to real data, we show that the ADCL criterion chooses chimeric sequences less often than random subsets, while the maximization of phylogenetic diversity chooses them more often than random. These algorithms have been implemented in publicly available software.Comment: Please contact us with any comments or questions

Whisper Dear That You Love Me

https://digitalcommons.library.umaine.edu/mmb-vp/2749/thumbnail.jp

Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation

Biosynthesis of retinoic acid from retinaldehyde (retinal) is catalysed by an aldehyde dehydrogenase (ALDH) and its oxidation by cytochrome P450 enzymes (CYPs). Herein we show by phylogenetic analysis that the ALDHs and CYPs in the retinoic acid pathway in animals are much closer in evolutionary terms to cyanobacterial orthologs than would be expected from the standard models of evolution

Production of Astaxanthin Using Modified E. coli Cells

There are several promising markets for naturally synthesized Astaxanthin, a carotenoid found in krill, shrimp, salmon, and other marine life that imparts to these creatures a pink coloring of the flesh and has demonstrated human health-promoting anti-inflammatory and antioxidant activity. Compared to Astaxanthin produced through chemical synthesis, Astaxanthin synthesized through natural fermentative processes (in yeast and algae) is esterified, imparting greater antioxidant activity as well as bioavailability and making it the preferred ingredient for nutraceutical formulations. Additionally, as consumer preferences trend toward natural production processes free from the use of petrochemical solvents which may pose hazards to health hazards, fermentative production coupled with an extraction process featuring more environment- and health-friendly solvents is desired. Recently, a strain of E.coli has been genetically optimized to produce Astaxanthin, offering a cheaper synthesis route compared with algal cultivation. Herein, the authors propose a process for the production of natural Astaxanthin through fermentation in genetically modified E.coli and recovery of the compound from biomass via supercritical CO2 extraction. The fermentation seed train is composed of three pre-seed, two seed, and three production fed-batch fermenters. Biomass from the production stage is collected in a harvest/surge tank for continuous downstream processing. The biomass is concentrated in broth, the cells are lysed, and the slurry of lysed cells are dried. The lysis product is loaded with fructose and diatomaceous earth in order to produce biomass pellets that are appropriate for the extraction phase. Supercritical CO2 with ethanol co-solvent is used to extract Astaxanthin from these pellets. Astaxanthin is heat-sensitive and has low accumulation in cells. Despite the expensive equipment necessary to preserve the structure and activity of the product and the low yearly production rate, the high selling price of Astaxanthin makes this process economically profitable, with an investor’s rate of return of 125%, net present value of $468 million, and return on investment of 171%

Detecting contaminated birthdates using generalized additive models.

Erroneous patient birthdates are common in health databases. Detection of these errors usually involves manual verification, which can be resource intensive and impractical. By identifying a frequent manifestation of birthdate errors, this paper presents a principled and statistically driven procedure to identify erroneous patient birthdates

Annual baseline King-Devick oculomotor function testing is needed due to scores varying by age

Objective: To document baseline King-Devick (K-D) oculomotor function scores for male and female participants aged between 4 and 20 years old. Methods: Utilising a cross section of schools, rugby clubs and gymnastic clubs, 1936 participants (1300 male, 636 female) completed the spiral-bound K-D test for the identification of disturbed oculomotor function. Results: This study identified that overall, the baseline scores of the K-D test became faster by 1.4 (0.3 to 4.5) s per year, when compared with the previous age group in the same number of reading card groups. When comparing normative values of the original K-D validation study with the same age groups of the current cohort, participants aged 6 to 11 years recorded a faster baseline time (range 3.5 to 8.6 s), while those in the 12 to 14 years. age group recorded slower baseline times (range −3.9 to −7.9 s). Discussion: In general, there were age group differences, but not sex differences, for K-D test times in the current cohort. Analysis of single card times, across all age groups, showed changes likely due to improved reading time. Conclusion: The results support the need for individualised annual pre-injury baseline testing of the K-D test

Determinants of adults' intention to vaccinate against pandemic swine flu

This article has been made available through the Brunel Open Access Publishing Fund.This article has been made available through the Brunel Open Access Publishing Fund.Background: Vaccination is one of the cornerstones of controlling an influenza pandemic. To optimise vaccination rates in the general population, ways of identifying determinants that influence decisions to have or not to have a vaccination need to be understood. Therefore, this study aimed to predict intention to have a swine influenza vaccination in an adult population in the UK. An extension of the Theory of Planned Behaviour provided the theoretical framework for the study. Methods: Three hundred and sixty two adults from the UK, who were not in vaccination priority groups, completed either an online (n = 306) or pen and paper (n = 56) questionnaire. Data were collected from 30th October 2009, just after swine flu vaccination became available in the UK, and concluded on 31st December 2009. The main outcome of interest was future swine flu vaccination intentions. Results: The extended Theory of Planned Behaviour predicted 60% of adults’ intention to have a swine flu vaccination with attitude, subjective norm, perceived control, anticipating feelings of regret (the impact of missing a vaccination opportunity), intention to have a seasonal vaccine this year, one perceived barrier: “I cannot be bothered to get a swine flu vaccination” and two perceived benefits: “vaccination decreases my chance of getting swine flu or its complications” and “if I get vaccinated for swine flu, I will decrease the frequency of having to consult my doctor,” being significant predictors of intention. Black British were less likely to intend to have a vaccination compared to Asian or White respondents. Conclusions: Theoretical frameworks which identify determinants that influence decisions to have a pandemic influenza vaccination are useful. The implications of this research are discussed with a view to maximising any future pandemic influenza vaccination uptake using theoretically-driven applications.This article is available through the Brunel Open Access Publishing Fund

Dominant ethnicity: from minority to majority

This article argues that the world is in the midst of a long-term transition from dominant minority to dominant majority ethnicity. Whereas minority domination was common in premodern societies, modernity (with its accent on democracy and popular sovereignty) has engendered a shift to dominant majority ethnicity. The article begins with conceptual clarifications. The second section provides a broad overview of the general patterns of ethnic dominance that derive from the logic of modern nationalism and democratisation. The third section discusses remnants of dominant minorities in the modern era and suggests that their survival hinges on peculiar historical and social circumstances coupled with resistance to democratisation. The fourth section shifts the focus to dominant majorities in the modern era and their relationship to national identities. The article ends with a discussion of the fortunes of dominant ethnicity in the West

Vaccine innovation, translational research and the management of knowledge accumulation

What does it take to translate research into socially beneficial technologies like vaccines? Current policy that focuses on expanding research or strengthening incentives overlooks how the supply and demand of innovation is mediated by problem-solving processes that generate knowledge which is often fragmented and only locally valid. This paper details some of the conditions that allow fragmented, local knowledge to accumulate through a series of structured steps from the artificial simplicity of the laboratory to the complexity of real world application. Poliomyelitis is used as an illustrative case to highlight the importance of experimental animal models and the extent of co-ordination that can be required if they are missing. Implications for the governance and management of current attempts to produce vaccines for HIV, TB and Malaria are discussed. Article Outlin