First Principles Theory of the Lattice Thermal Conductivity of Semiconductors

Thesis advisor: David A. BroidoUsing density functional perturbation theory and a full solution of the linearized phonon Boltzmann transport equation (BTE), a parameter-free theory of semiconductor thermal properties is developed. The approximations and shortcomings of previous approaches to thermal conductivity calculations are investigated. The use of empirical interatomic potentials in the BTE approach is shown to give poor agreement with measured values of thermal conductivity. By using the adiabatic bond charge model, the importance of accurate descriptions of phonon dispersions is highlighted. The extremely limited capacity of previous theoretical techniques in the realm of thermal conductivity prediction is highlighted; this is due to a dependence on adjustable parameters. Density functional perturbation theory is coupled with an iterative solution to the full Boltzmann transport equation creating a theoretical construct where thermal conductivity prediction becomes possible. Validation of the approach is demonstrated through the calculation of a range of thermal properties for a set of polar and non-polar semiconductors which are compared with measured values. The agreement between theory and measurement is very good, confirming the promise of the theoretical approach. Due to the significant computational effort required by the parameter-free calculations, new forms for room temperature relaxation time approximations are derived. The resulting forms produce thermal conductivity values in very good agreement with the ab initio data across a wide temperature range. It is therefore shown that accurate relaxation time approximations can be developed, fixing the adjustable parameters to the ab initio theory avoiding any comparison with measured data. This approach improves the accuracy of phonon relaxation times compared with previous models.Thesis (PhD) — Boston College, 2009.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Physics

Creative Futures: Building the Creative Economy through Universities.

The creative industries are founded on innovation. They are responsive, multifaceted and evolving and have developed new models of business in order to adapt and contribute to a world in economic, social and cultural flux. Over the past two decades UK universities have positioned themselves to provide pre-entry professional training for the creative economy. In their capacity as mediators between students and industry, universities have the capability to provide industry-relevant courses and learning opportunities. By maintaining close links with the creative economy, universities demonstrateboth responsiveness to industry needs and reciprocity by acting as catalysts and centres for knowledge exchange in helping to support innovation and development. Section 2 provides an overview of the creative economy in theUK and of the contribution of universities to it. In section 3 we provide evidence and examples that indicate a strengthening of teaching practices that ensures graduates are fully prepared for the realities of employment. Thesection also stresses the benefits to be derived by regional industry from the expertise and facilities offered by universities.In section 4 we assess the availability and levels of funding for higher education institutions seeking to develop innovation and enhance the economic impact of the creative industries. We recognise the key role playedin funding the creative industries sector by the Arts and Humanities Research Council (AHRC). We also examine more recent streams of funding put in place by UK government for research and knowledge transfer in the creativeindustries, such as those of the Technology Strategy Board.The report draws on data collected from Million+ subscribing universities. This was supplemented with more general material from the Arts and Humanities Research Council, the Department of Culture, Media and Sport and theTechnology Strategy Board. Data from the Higher Education Statistics Agency was consulted through the Higher Education Information Database for Institutions but these did not provide the level of detail required. Case studieswere more rewarding in their specific illustration of the principles and practices underpinning the contribution of universities to the creative economy. This qualitative approach particularly strengthened the discussions within section 3. The whole report benefited from a number of previous studies of aspects of the creative industries and the creative economy; these studies are acknowledged at the appropriate point in the footnotes

Creative Futures: Building the Creative Economy through Universities.

The creative industries are founded on innovation. They are responsive, multifaceted and evolving and have developed new models of business in order to adapt and contribute to a world in economic, social and cultural flux. Over the past two decades UK universities have positioned themselves to provide pre-entry professional training for the creative economy. In their capacity as mediators between students and industry, universities have the capability to provide industry-relevant courses and learning opportunities. By maintaining close links with the creative economy, universities demonstrateboth responsiveness to industry needs and reciprocity by acting as catalysts and centres for knowledge exchange in helping to support innovation and development. Section 2 provides an overview of the creative economy in theUK and of the contribution of universities to it. In section 3 we provide evidence and examples that indicate a strengthening of teaching practices that ensures graduates are fully prepared for the realities of employment. Thesection also stresses the benefits to be derived by regional industry from the expertise and facilities offered by universities.In section 4 we assess the availability and levels of funding for higher education institutions seeking to develop innovation and enhance the economic impact of the creative industries. We recognise the key role playedin funding the creative industries sector by the Arts and Humanities Research Council (AHRC). We also examine more recent streams of funding put in place by UK government for research and knowledge transfer in the creativeindustries, such as those of the Technology Strategy Board.The report draws on data collected from Million+ subscribing universities. This was supplemented with more general material from the Arts and Humanities Research Council, the Department of Culture, Media and Sport and theTechnology Strategy Board. Data from the Higher Education Statistics Agency was consulted through the Higher Education Information Database for Institutions but these did not provide the level of detail required. Case studieswere more rewarding in their specific illustration of the principles and practices underpinning the contribution of universities to the creative economy. This qualitative approach particularly strengthened the discussions within section 3. The whole report benefited from a number of previous studies of aspects of the creative industries and the creative economy; these studies are acknowledged at the appropriate point in the footnotes

BioGateway: a semantic systems biology tool for the life sciences

Background: Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that address the properties of biological systems, independently from the origin of the knowledge. Semantic Web technologies prove to be well suited for knowledge integration, knowledge production (hypothesis formulation), knowledge querying and knowledge maintenance. Results: We implemented a semantically integrated resource named BioGateway, comprising the entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single entry point to query these resources through SPARQL. It constitutes a key component for a Semantic Systems Biology approach to generate new hypotheses concerning systems properties. In the course of developing BioGateway, we faced challenges that are common to other projects that involve large datasets in diverse representations. We present a detailed analysis of the obstacles that had to be overcome in creating BioGateway. We demonstrate the potential of a comprehensive application of Semantic Web technologies to global biomedical data. Conclusion: The time is ripe for launching a community effort aimed at a wider acceptance and application of Semantic Web technologies in the life sciences. We call for the creation of a forum that strives to implement a truly semantic life science foundation for Semantic Systems Biology

Tangram: A comprehensive toolbox for mobile element insertion detection

© 2014 Wu et al.; licensee BioMed Central Ltd. Background: Mobile elements (MEs) constitute greater than 50% of the human genome as a result of repeated insertion events during human genome evolution. Although most of these elements are now fixed in the population, some MEs, including ALU, L1, SVA and HERV-K elements, are still actively duplicating. Mobile element insertions (MEIs) have been associated with human genetic disorders, including Crohn\u27s disease, hemophilia, and various types of cancer, motivating the need for accurate MEI detection methods. To comprehensively identify and accurately characterize these variants in whole genome next-generation sequencing (NGS) data, a computationally efficient detection and genotyping method is required. Current computational tools are unable to call MEI polymorphisms with sufficiently high sensitivity and specificity, or call individual genotypes with sufficiently high accuracy.Results: Here we report Tangram, a computationally efficient MEI detection program that integrates read-pair (RP) and split-read (SR) mapping signals to detect MEI events. By utilizing SR mapping in its primary detection module, a feature unique to this software, Tangram is able to pinpoint MEI breakpoints with single-nucleotide precision. To understand the role of MEI events in disease, it is essential to produce accurate individual genotypes in clinical samples. Tangram is able to determine sample genotypes with very high accuracy. Using simulations and experimental datasets, we demonstrate that Tangram has superior sensitivity, specificity, breakpoint resolution and genotyping accuracy, when compared to other, recently developed MEI detection methods.Conclusions: Tangram serves as the primary MEI detection tool in the 1000 Genomes Project, and is implemented as a highly portable, memory-efficient, easy-to-use C++ computer program, built under an open-source development model

Clostridium difficile in Ready-to-Eat Salads, Scotland

Of 40 ready-to-eat salads, 3 (7.5%) were positive for Clostridium difficile by PCR. Two isolates were PCR ribotype 017 (toxin A–, B+), and 1 was PCR ribotype 001. Isolates were susceptible to vancomycin and metronidazole but variably resistant to other antimicrobial drugs. Ready-to-eat salads may be potential sources for virulent C. difficile

Risk Assessment of Impacts of Climate Change for Key Marine Species in South Eastern Australia. Part 2: species profiles

[Extract] Blacklip and greenlip abalone form the basis of valuable fisheries in Tasmania, Victoria, South Australia and New South Wales (Figure 1.1). The Tasmanian abalone fishery is the largest wild abalone fishery in the world, producing more than 25% of the global catch (Miller et al. 2009). In 2008, the fishery had a gross landed value of $ 90 million. Blacklip abalone (BA), Haliotis rubra, is the predominant species harvested in Tasmania with 2461 t landed in 2008, compared to only 122 t of greenlip abalone (GA), H. laevigata (Tarbath and Gardner 2009). Since 2003, the BA fishery has been divided into five zones: Eastern, Western, Northern, Bass Strait, and Central West (Tarbath and Gardner 2009). The GA fishery is restricted to the north of the state and is managed by regions and separately from the BA fishery. In Victoria, approximately 1,200 t was landed in 2007/08, however, the current TAC is 774 t (2010/11). Catches are dominated by BA (96%) and the fishery is structured into three zones: Western, Central and Eastern. The South Australian fishery harvests approximately 880 t of abalone each year, about 60% of this is BA with the remainder comprising GA. Like Victoria, the South Australian fishery is divided into the Southern, Central and Western zones. Current annual catches in NSW were less than 75 t in 2009/10 and consist exclusively of BA. The commercial fisheries are assessed on a variable combination of commercial catch, effort and size-composition data, fishery-independent surveys and length-structured models. In Tasmania, 105,500 abalone were taken by recreational fishers in 2006/07, weighing an estimated 49 t. The number of recreational licenses has tripled since 1995, with 12,500 recreational diving licenses issued in 2007/08 (Lyle 2008). Recreational catches in SA are small, probably less than 1% of the TACC (Jones, 2009)

Risk Assessment of Impacts of Climate Change for Key Marine Species in South Eastern Australia. Part 2: species profiles

[Extract] Blacklip and greenlip abalone form the basis of valuable fisheries in Tasmania, Victoria, South Australia and New South Wales (Figure 1.1). The Tasmanian abalone fishery is the largest wild abalone fishery in the world, producing more than 25% of the global catch (Miller et al. 2009). In 2008, the fishery had a gross landed value of $ 90 million. Blacklip abalone (BA), Haliotis rubra, is the predominant species harvested in Tasmania with 2461 t landed in 2008, compared to only 122 t of greenlip abalone (GA), H. laevigata (Tarbath and Gardner 2009). Since 2003, the BA fishery has been divided into five zones: Eastern, Western, Northern, Bass Strait, and Central West (Tarbath and Gardner 2009). The GA fishery is restricted to the north of the state and is managed by regions and separately from the BA fishery. In Victoria, approximately 1,200 t was landed in 2007/08, however, the current TAC is 774 t (2010/11). Catches are dominated by BA (96%) and the fishery is structured into three zones: Western, Central and Eastern. The South Australian fishery harvests approximately 880 t of abalone each year, about 60% of this is BA with the remainder comprising GA. Like Victoria, the South Australian fishery is divided into the Southern, Central and Western zones. Current annual catches in NSW were less than 75 t in 2009/10 and consist exclusively of BA. The commercial fisheries are assessed on a variable combination of commercial catch, effort and size-composition data, fishery-independent surveys and length-structured models. In Tasmania, 105,500 abalone were taken by recreational fishers in 2006/07, weighing an estimated 49 t. The number of recreational licenses has tripled since 1995, with 12,500 recreational diving licenses issued in 2007/08 (Lyle 2008). Recreational catches in SA are small, probably less than 1% of the TACC (Jones, 2009)

Fungal iron availability during deep seated candidiasis is defined by a complex interplay involving systemic and local events

Peer reviewedPublisher PD