Phylotastic! Making Tree-of-Life Knowledge Accessible, Reusable and Convenient

Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user's needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a "phylotastic" system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.NESCent (the National Evolutionary Synthesis Center)NSF EF-0905606iPlant Collaborative (NSF) DBI-0735191Biodiversity Synthesis Center (BioSync) of the Encyclopedia of LifeComputer Science

Do Genetic Variants Modify the Effect of Smoking on Risk of Preeclampsia in Pregnancy?

Under embargo until: 2022-11-28Objective Maternal smoking is associated with as much as a 50% reduced risk of preeclampsia, despite increasing risk of other poor pregnancy outcomes that often co-occur with preeclampsia, such as preterm birth and fetal growth restriction. Researchers have long sought to understand whether this perplexing association is biologically based, or a result of noncausal mechanisms. We examined whether smoking-response genes modify the smoking-preeclampsia association to investigate potential biological explanations. Study Design We conducted a nested case–control study within the Norwegian Mother, Father and Child Birth Cohort (1999–2008) of 2,596 mother–child dyads. We used family-based log-linear Poisson regression to examine modification of the maternal smoking-preeclampsia relationship by maternal and fetal single nucleotide polymorphisms involved in cellular processes related to components of cigarette smoke (n = 1,915 with minor allele frequency ≥10%). We further investigated the influence of smoking cessation during pregnancy. Results Three polymorphisms showed overall (p < 0.001) multiplicative interaction between smoking and maternal genotype. For rs3765692 (TP73) and rs10770343 (PIK3C2G), protection associated with smoking was reduced with two maternal copies of the risk allele and was stronger in continuers than quitters (interaction p = 0.02 for both loci, based on testing 3-level smoking by 3-level genotype). For rs2278361 (APAF1) the inverse smoking-preeclampsia association was eliminated by the presence of a single risk allele, and again the trend was stronger in continuers than in quitters (interaction p = 0.01). Conclusion Evidence for gene–smoking interaction was limited, but differences by smoking cessation warrant further investigation. We demonstrate the potential utility of expanded dyad methods and gene–environment interaction analyses for outcomes with complex relationships between maternal and fetal genotypes and exposures.acceptedVersio

Ring test evaluation of the detection of influenza A virus in swine oral fluids by real-time reverse-transcription polymerase chain reaction and virus isolation

The probability of detecting influenza A virus (IAV) in oral fluid (OF) specimens was calculated for each of 13 assays based on real-time reverse-transcription polymerase chain reaction (rRT-PCR) and 7 assays based on virus isolation (VI). The OF specimens were inoculated with H1N1 or H3N2 IAV and serially diluted 10-fold (10(-1) to 10(-8)). Eight participating laboratories received 180 randomized OF samples (10 replicates × 8 dilutions × 2 IAV subtypes plus 20 IAV-negative samples) and performed the rRT-PCR and VI procedure(s) of their choice. Analysis of the results with a mixed-effect logistic-regression model identified dilution and assay as variables significant (P \u3c 0.0001) for IAV detection in OF by rRT-PCR or VI. Virus subtype was not significant for IAV detection by either rRT-PCR (P = 0.457) or VI (P = 0.101). For rRT-PCR the cycle threshold (Ct) values increased consistently with dilution but varied widely. Therefore, it was not possible to predict VI success on the basis of Ct values. The success of VI was inversely related to the dilution of the sample; the assay was generally unsuccessful at lower virus concentrations. Successful swine health monitoring and disease surveillance require assays with consistent performance, but significant differences in reproducibility were observed among the assays evaluated

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Abstract Background Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website ( http://www.phylotastic.org ), and a server image. Conclusions Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.http://deepblue.lib.umich.edu/bitstream/2027.42/112888/1/12859_2013_Article_5897.pd

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Background: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. Results: With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proofof- concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.Keywords: Web services, Taxonomy, Data reuse, Phylogeny, Tree of life, HackathonKeywords: Web services, Taxonomy, Data reuse, Phylogeny, Tree of life, Hackatho

In Search of Kinship: Within Group Deviation in Print Advertisements Identifying the Black Sheep From the Ordinary: Social Categorization and Within Group Deviation in Print Advertisements

The present study employs an extension of ingroup favoritism, using the black sheep hypothesis where subjects judge likable ingroup members more positively than similar outgroup members, while judging unlikable ingroup members more negatively than similar outgroup members. Positioned in an advertising context, this empirical study provides evidence of both ingroup favoritism and within group derogation of unlikable ingroup members. The evidence suggests that the recipient&apos;s overall evaluation of the advertisement is mediated by the spokesperson&apos;s similarity to the recipient and general likeability

Essays on multiple identities and motivated consumption: Exploring the role of identity centrality on self-brand connections

This dissertation consists of three essays on the role of identity centrality in the formation of consumer self-brand connections. It contributes to a better understanding of how consumers negotiate multiple identities in the marketplace when making brand choices. This is significant as much of the research on the self-concept and consumer behavior has focused on isolated self-dimensions or have examined single consumer identities in isolation. Theoretically grounded in identity process theory (Breakwell 1986), which suggests individuals construct their identity through multiple identity motives influencing identity centrality, enactment, and affect; this dissertation addresses these gaps by answering two specific questions: 1) What are the various identity motives that influence a consumer\u27s individual and group identity centrality leading to enhanced self-brand connections? 2) How does identity centrality influence reference group brand associations in the formation of self-brand connections? In Essay 1, a framework for conceptualizing the influence of multiple identity motives on self-brand connections is proposed driven by findings from consumer in-depth interviews. The framework suggests identity centrality mediates the relationship between the satisfaction of multiple identity motives on self-brand connections, and moderates self-brand connections when reference group brand associations are considered. Fourteen propositions are presented, and are empirically tested in Essays 2 and 3. In Essay 2, identity motives from identity process theory along with others identified in Essay 1 are empirically validated, using both hierarchical linear modeling and hierarchical multiple regression. The findings support the influence of two identity motives informing identity centrality, namely: recognition and continuity. This is significant, as prior research in consumer behavior has largely focused on the self-esteem and self-consistency motives (Grub and Grathwohl 1967; Sirgy 1982). Essay 3 investigates the moderating effect of identity centrality on the formation of self-brand connections as reference group brand associations are considered. It is found that the when the ingroup identity is highly central, stronger self-brand connections result. On the contrary, when the ingroup identity is low in centrality self-brand connections are mitigated. The differential effects of self-brand connections due to identity centrality provide insight into intra-group differences when the brand is consistent with the ingroup image. The results support a general importance of the role of identity centrality at both the individual and group levels, providing a catalyst for future studies examining the role of the self-concept in consumer behavior

Essays on multiple identities and motivated consumption: Exploring the role of identity centrality on self-brand connections

This dissertation consists of three essays on the role of identity centrality in the formation of consumer self-brand connections. It contributes to a better understanding of how consumers negotiate multiple identities in the marketplace when making brand choices. This is significant as much of the research on the self-concept and consumer behavior has focused on isolated self-dimensions or have examined single consumer identities in isolation. Theoretically grounded in identity process theory (Breakwell 1986), which suggests individuals construct their identity through multiple identity motives influencing identity centrality, enactment, and affect; this dissertation addresses these gaps by answering two specific questions: 1) What are the various identity motives that influence a consumer\u27s individual and group identity centrality leading to enhanced self-brand connections? 2) How does identity centrality influence reference group brand associations in the formation of self-brand connections? In Essay 1, a framework for conceptualizing the influence of multiple identity motives on self-brand connections is proposed driven by findings from consumer in-depth interviews. The framework suggests identity centrality mediates the relationship between the satisfaction of multiple identity motives on self-brand connections, and moderates self-brand connections when reference group brand associations are considered. Fourteen propositions are presented, and are empirically tested in Essays 2 and 3. In Essay 2, identity motives from identity process theory along with others identified in Essay 1 are empirically validated, using both hierarchical linear modeling and hierarchical multiple regression. The findings support the influence of two identity motives informing identity centrality, namely: recognition and continuity. This is significant, as prior research in consumer behavior has largely focused on the self-esteem and self-consistency motives (Grub and Grathwohl 1967; Sirgy 1982). Essay 3 investigates the moderating effect of identity centrality on the formation of self-brand connections as reference group brand associations are considered. It is found that the when the ingroup identity is highly central, stronger self-brand connections result. On the contrary, when the ingroup identity is low in centrality self-brand connections are mitigated. The differential effects of self-brand connections due to identity centrality provide insight into intra-group differences when the brand is consistent with the ingroup image. The results support a general importance of the role of identity centrality at both the individual and group levels, providing a catalyst for future studies examining the role of the self-concept in consumer behavior

The Rate of Oxidation of Hydriodic Acid by Sulphuric Acid

No Abstract