Revision of a Liquid Fuel Airblast Atomizer and Installation of a Laser Extinction System for Measurement of Soot Produced During Liquid Fuel Combustion

Studying liquid fuel combustion is necessary to better design combustion systems. Through more efficient combustors and alternative fuels, it is possible to reduce greenhouse gases and harmful emissions. In particular, coal-derived and Fischer-Tropsch liquid fuels are of interest because, in addition to producing fewer emissions, they have the potential to drastically reduce the United States' dependence on foreign oil. Major academic research institutions like the Pennsylvania State University perform cutting-edge research in many areas of combustion. The Combustion Research Laboratory (CRL) at Bucknell University is striving to develop the necessary equipment to be capable of both independent and collaborative research efforts with Penn State and in the process, advance the CRL to the forefront of combustion studies. The focus of this thesis is to advance the capabilities of the Combustion Research Lab at Bucknell. Specifically, this was accomplished through a revision to a previously designed liquid fuel injector, and through the design and installation of a laser extinction system for the measurement of soot produced during combustion. The previous liquid fuel injector with a 0.005" hole did not behave as expected. Through spray testing the 0.005" injector with water, it was determined that experimental errors were made in the original pressure testing of the injector. Using data from the spray testing experiment, new theoretical hole sizes of the injector were calculated. New injectors with 0.007" and 0.0085" orifices were fabricated and subsequently tested to qualitatively validate their behavior. The injectors were installed in the combustion rig in the CRL and hot-fire tested with liquid heptane. The 0.0085" injector yielded a manageable fuel pressure and produced a broad flame. A laser extinction system was designed and installed in the CRL. This involved the fabrication of a number of custom-designed parts and the specification of laser extinction equipment for purchase. A standard operating procedure for the laser extinction system was developed to provide a consistent, safe method for measuring soot formation during combustion.

The precipitous decline of the ortolan bunting Emberiza hortulana: time to build on scientific evidence to inform conservation management

In recent decades there has been a marked decline in most ortolan bunting Emberiza hortulana populations in temperate Europe, with many regional populations now extinct or on the brink of extinction. In contrast, Mediterranean and, as far as we know, eastern European popula-tions seem to have remained relatively stable. The causes of decline remain unclear but include: habitat loss and degradation, and related reduction in prey availability; climate change on the breeding grounds; altered population dynamics; illegal captures during migration; and environmental change in wintering areas. We review the current knowledge of the biology of the ortolan bunting and discuss the proposed causes of decline in relation to the different population trends in temperate and Mediterranean Europe. We suggest new avenues of research to identify the factors limiting ortolan bunting populations. The main evidence-based conservation measure that is likely to enhance habitat quality is the creation of patches of bare ground to produce sparsely vegetated foraging grounds in invertebrate-rich grassy habitats close to breeding areas.

The use of light- and electron microscopy for studies on the cell- and molecular biology of parasites and parasitic diseases

Lightmicroscopical (LM) and electron microscopi cal (EM) techniques, have had a major influence on the development and direction of cell biology, and particularly also on the investigation of complex host-parasite relationships. Earlier, microscopy has been rather descriptive, but new technical and scientific advances have changed the situation. Microscopy has now become analytical, quantitative and three-dimensional, with greater emphasis on analysis of live cells with fluorescent markers. The new or improved techniques that have become available include immunocytochemistry using immunogold labeling techniques or fluorescent probes, cryopreservation and cryosectioning, in situ hybridization, fluorescent reporters for subcellular localization, micro-analytical methods for elemental distribution, confocal laser scanning microscopy, scanning tunneling microscopy and live-imaging. Taken together, these tools are providing both researchers and students with a novel and multidimensional view of the intricate biological processes during parasite development in the host.

Primate Craniofacial Function and Biology

Book review: Primate Craniofacial Function and Biology

Bioconductor: Open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. We detail some of the design decisions, software paradigms and operational strategies that have allowed a small number of researchers to provide a wide variety of innovative, extensible, software solutions in a relatively short time. The use of an object oriented programming paradigm, the adoption and development of a software package system, designing by contract, distributed development and collaboration with other projects are elements of this project's success. Individually, each of these concepts are useful and important but when combined they have provided a strong basis for rapid development and deployment of innovative and flexible research software for scientific computation. A primary objective of this initiative is achievement of total remote reproducibility of novel algorithmic research results.

The tragedy of the commons in evolutionary biology

Garrett Hardin's tragedy of the commons is an analogy that shows how individuals driven by self-interest can end up destroying the resource upon which they all depend. The proposed solutions for humans rely on highly advanced skills such as negotiation, which raises the question of how non-human organisms manage to resolve similar tragedies. In recent years, this question has promoted evolutionary biologists to apply the tragedy of the commons to a wide range of biological systems. Here, we provide tools to categorize different types of tragedy and review different mechanisms, including kinship, policing and diminishing returns that can resolve conflicts that could otherwise end in tragedy. A central open question, however, is how often biological systems are able to resolve these scenarios rather than drive themselves extinct through individual-level selection favouring self-interested behaviours.

Resolving the tragedy of the commons: the feedback between intraspecific conflict and population density

Competition and conflict among individuals can favour exploitative strategies that undermine the common good. Theory suggests that this can lead to a tragedy of the commons and ultimately population extinction, a phenomenon known as evolutionary suicide. Here, I present a model of the evolutionary tragedy of the commons that explicitly considers the population dynamics where individuals invest in individually costly competitive traits. In the simplest form, this supports the notion that selection for high levels of conflict can cause evolutionary suicide. However, as competition comes with survival and fecundity costs, a feedback between the investment in competition and population density can act to reduce the level of conflict and prevent the population from going extinct. This suggests that the interaction between population ecology and the evolution of competition and conflict among individuals may be an important mechanism in resolving the level of competition and conflict among individuals.

Species-level selection reduces selfishness through competitive exclusion

Adaptation does not necessarily lead to traits which are optimal for the population. This is because selection is often the strongest at the individual or gene level. The evolution of selfishness can lead to a 'tragedy of the commons', where traits such as aggression or social cheating reduce population size and may lead to extinction. This suggests that species-level selection will result whenever species differ in the incentive to be selfish. We explore this idea in a simple model that combines individual-level selection with ecology in two interacting species. Our model is not influenced by kin or trait-group selection. We find that individual selection in combination with competitive exclusion greatly increases the likelihood that selfish species go extinct. A simple example of this would be a vertebrate species that invests heavily into squabbles over breeding sites, which is then excluded by a species that invests more into direct reproduction. A multispecies simulation shows that these extinctions result in communities containing species that are much less selfish. Our results suggest that species-level selection and community dynamics play an important role in regulating the intensity of conflicts in natural populations.