Behavioral Antecedents of Fuel Efficiency

The US Department of Defense is the largest institutional petroleum consumer in the world. In addition to the financial cost of petroleum-based fuels, the US DoD generates more CO2-equivalent greenhouse gases than the entirety of modern, industrialized nations like Sweden and Norway. Other dangers and externalities arise from the fuels supply chain, like toxin risks to fuel handlers, and human costs to transport fuel in-theater. Within the DoD, the USAF alone often rivals or exceeds the consumption of all other services combined. While the USAF prefers technical, hardware-based solutions to problems, and has given increasing attention to logistical solutions like route planning and aircraft mix optimization, very little research both in and out of the military looks into the impact of human decision making on fuel consumption. Industrial/organizational psychology, or “IO Psych,” is a growing field in the civilian world. This project applies IO psychometric measurements to investigate the variability within fuel consumption stemming from the choices that human operators make. Three studies are presented, revolving around this common theme. These studies are based on the Theory of Planned Behavior (TPB), a behavioral science model emphasizing the kind of deliberate, informed decision making. The first study using meta-analysis indicates the TPB model strongly predicts fuel-efficient behavior. The second study examines car drivers’ eco-friendly behavior. The results of the second study are congruent with the findings of the first study. The third study investigates the ecofriendly behaviors of military cargo pilots in the Air Force. Survey responses were collected from the population of 62 active duty, reserve, and Guard cargo airlift pilots flying the C-130, C-17, and C-5 platforms who flew a combined 477 cargo sorties within the measurement period. The pilots’ responses were compared against a measure of fuel consumption corrected for change to cargo weight. The results of this study indicate that the link between intention and behavior is weak

Antecedents of Fuel Efficiency

Reducing the United States Air Force (USAF)’s fuel use is a major budgetary concern, as the USAF consumes more fuel than the Army, Navy, Marine Corps and all other Department of Defense (DoD) agencies combined. This research focused on fuel efficiency of C-130 Hercules Aircraft Commanders (ACs) by proposing, constructing, and testing a survey measure of behavioral drivers of discretionary pro-environmental professional behaviors among USAF pilots

The shape of human gene family phylogenies

BACKGROUND: The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies. RESULTS: We find that gene duplication has produced gene family trees significantly less balanced than expected from a simple model of the process, and less balanced than species phylogenies: the opposite to what might be expected under the 2R hypothesis. CONCLUSION: While other explanations are plausible, we suggest that the greater imbalance of gene family trees than species trees is due to the prevalence of tandem duplications over regional duplications during the evolution of the human genome

The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods

<p>Abstract</p> <p>Background</p> <p>In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.</p> <p>Results</p> <p>We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.</p> <p>Conclusion</p> <p>We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.</p

Vertebrate phylogenomics and gene family evolution

This thesis is about 2 topics; the evolution of gene families by the birth-death process of gene duplication and gene loss, and phylogenetic inference. It is a central theme that these two processes are intimately associated - the phylogenies of gene families (of any gene) are shaped by the processes of gene duplication and gene loss, as much as by the processes of speciation and extinction occurring among the species the gene is evolving in. This has two results. Firstly, that we need to know, or assume, something about the processes of gene duplication and loss to correctly understand the pattern of speciation, or cladogenesis, in a group of organisms. Secondly, that we need to know, or assume, something about this pattern if we are to fully appreciate the effect of gene duplication and loss on a gene family phylogeny.The main part of this thesis investigates the use of reconciled tree methods in unravelling species phylogeny and the evolution of gene families. Part of this investigation involves placing reconciled tree methods (and the use of these methods to infer species phylogeny, known as gene tree parsimony), in the context of some related methods: supertree methods and "simultaneous analysis" of combined data. Two empirical studies complete this part of the thesis - one attempting to infer the higher-level phylogeny of vertebrates using gene tree parsimony, and another focusing on a lower taxonomic level, on primate phylogeny. This chapter attempts an integrated study of gene duplication and species phylogeny, which uses information about gene duplication to help date evolutionary events.Despite the close relationship between gene duplication and speciation on phylogenies, it is possible to study gene duplication independently. If we restrict ourselves to genes sampled from a single genome, gene family trees represent gene duplications and gene losses occurring during the history of a single species, so the complication of speciation and extinction is eliminated. By realising that the processes of gene duplication and loss in these trees are analogous to the processes of speciation and extinction in species phylogenies, we can harness a toolkit of methods developed for more traditional phylogenies to study these molecular processes. Two such methods are models of cladistic tree shape and birth-death models, which allow the first estimates of the rate of gene loss

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Reduced efficacy of praziquantel against Schistosoma mansoni associated with multiple-rounds of mass drug administration

The efficacy of praziquantel against Schistosoma mansoni was significantly lower in Ugandan schools that had received more prior rounds of mass drug administration, as determined by fitting a statistical model to parasite egg counts before and after treatment

Macrofaunal diversity of infralittoral cobble beds in the Maltese Islands

This research work was partially funded through the European Social Fund under a STEPS scheme grant awarded to JE.The Mediterranean “biocoenosis of infralittoral pebbles ” has been poorly studied, but is generally considered to be impoverished. Systematic sampling of cobble beds at 17 sites around the Maltese Islands yielded a total of 35,687 individuals belonging to 310 different taxa. Very shallow sites (<2 m depth) had a slightly poorer faunal assemblage than deeper ones (2 -12 m depth), but still included 152 taxa. These results suggest that infralittoral cobbles beds may not be as impoverished as previously thought, probably due to the high structural complexity of these habitats.peer-reviewe

New approaches for unravelling reassortment pathways

Background: Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment. Results: The current work describes the implementation of two approaches for robustly identifying reassortment events. The algorithms rest on the idea of significance of difference between phylogenetic trees or phylogenetic tree sets, and subtree pruning and regrafting operations, which mimic the effect of reassortment on tree topologies. The first method is based on a maximum likelihood (ML) framework (MLreassort) and the second implements a Bayesian approach (Breassort) for reassortment detection. We focus on reassortment events that are found by both methods. We test both methods on a simulated dataset and on a small collection of real viral data isolated in Hong Kong in 1999. Conclusions: The nature of segmented viral genomes present many challenges with respect to disease. The algorithms developed here can effectively identify reassortment events in small viral datasets and can be applied not only to influenza but also to other segmented viruses. Owing to computational demands of comparing tree topologies, further development in this area is necessary to allow their application to larger datasets