Identification of native American founder mtDNAs through the analysis of complete mtDNA sequences: Some caveats

In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian-and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.

A decoupled whole-building simulation engine for rapid exhaustive search of low-carbon and low-energy building refurbishment options

This paper presents the development of a new building physics and energy supply systems simulation platform. It has been adapted from both existing commercial models and empirical works, but designed to provide expedient exhaustive simulation of all salient types of energy- and carbon-reducing retrofit options. These options may include any combination of behavioural measures, building fabric and equipment upgrades, improved HVAC control strategies, or novel low-carbon energy supply technologies. We provide a methodological description of the proposed model, followed by two illustrative case studies of the tool when used to investigate retrofit options of a mixed-use office building and primary school in the UK. It is not the intention of this paper, nor would it be feasible, to provide a complete engineering decomposition of the proposed model, describing all calculation processes in detail. Instead, this paper concentrates on presenting the particular engineering aspects of the model which steer away from conventional practise. © 2011 Elsevier Ltd.

Opt-out options in new product co-development partnerships

We study three contractual arrangements—co-development, licensing, and co-development with opt-out options—for the joint development of new products between a small and financially constrained innovator firm and a large technology company, as in the case of a biotech innovator and a major pharma company. We formulate our arguments in the context of a two-stage model, characterized by technical risk and stochastically changing cost and revenue projections. The model captures the main disadvantages of traditional co-development and licensing arrangements: in co-development the small firm runs a risk of running out of capital as future costs rise, while licensing for milestone and royalty (M&R) payments, which eliminates the latter risk, introduces inefficiency, as profitable projects might be abandoned. Counter to intuition we show that the biotech's payoff in a licensing contract is not monotonically increasing in the M&R terms. We also show that an option clause in a co-development contract that gives the small firm the right but not the obligation to opt out of co-development and into a pre-agreed licensing arrangement avoids the problems associated with fully committed co-development or licensing: the probability that the small firm will run out of capital is greatly reduced or completely eliminated and profitable projects are never abandoned.

Model development & application for inland navigational canals

Several agencies in the United Kingdom have interest in the water quality of old navigational canals that have fallen into disuse after the decline of commercial canal transportation. The interested agencies desired a model to predict the water quantity and quality of inland navigational canals in order to evaluate management options to address the issues in the natural streams to which they discharge. Inland navigational canals have unique drivers of their hydrology and water quality compared to either natural streams, irrigation canals, or larger navigational canals connected to seas or oceans. Water in an inland canal is typically sourced from a reservoir and artificially pumped to a summit reach; its movement downhill is controlled by the activity of boats and overflow weirs. Stagnant impoundments between locks, which might normally be expected to result in a decrease in the concentration of sediment-associated pollutants, actually have surprisingly high levels of sediment due to boat traffic. Algal growth in the stagnant reach can be high. This paper describes a canal model developed to simulate hydrology and water quality in inland navigational canals. This model was successfully applied to the Kennet and Avon Canal to predict hydrology, sediment generation and transport, and algal growth and transport. The model is responsive to external influences such as sunlight, temperature, nutrient concentrations, boat traffic, and runoff from the contributing catchment area.

Tomorrow's cities - a framework for building resilience

Urbanisation is the great driving force of the twenty-first century. Cities are associated with both productivity and creativity, and the benefits offered by closely connected and high density living and working contribute to sustainability. At the same time, cities need extensive infrastructure – like water, power, sanitation and transportation systems – to operate effectively. Cities therefore comprise multiple components, forming both static and dynamic systems that are interconnected directly and indirectly on a number of levels, all forming the backdrop for the interaction of people and processes. Bringing together large numbers of people and complex products in rich interactions can lead to vulnerability from hazards, threats and even trends, whether natural hazards, epidemics, political upheaval, demographic changes, economic instability and/or mechanical failures; The key to countering vulnerability is the identification of critical systems and clear understanding of their interactions and dependencies. Critical systems can be assessed methodically to determine the implications of their failure and their interconnectivities with other systems to identify options. The overriding need is to support resilience – defined here as the degree to which a system or systems can continue to function effectively in a changing environment. Cities need to recognise the significance of devising adaptation strategies and processes to address a multitude of uncertainties relating to climate, economy, growth and demography. In this paper we put forward a framework to support cities in understanding the hazards, threats and trends that can make them vulnerable to unexpected changes and unpredictable shocks. The framework draws on an asset model of the city, in which components that contribute to resilience include social capital, economic assets, manufactured assets, and governance. The paper reviews the field, and draws together an overarching framework intended to help cities plan a robust trajectory towards increased resilience through flexibility, resourcefulness and responsiveness. It presents some brief case studies demonstrating the applicability of the proposed framework to a wide variety of circumstances.

Core design options for high conversion BWRs operating in Th- 233U fuel cycle

Several options of fuel assembly design are investigated for a BWR core operating in a closed self-sustainable Th-233U fuel cycle. The designs rely on an axially heterogeneous fuel assembly structure consisting of a single axial fissile zone "sandwiched" between two fertile blanket zones, in order to improve fertile to fissile conversion ratio. The main objective of the study was to identify the most promising assembly design parameters, dimensions of fissile and fertile zones, for achieving net breeding of 233U. The design challenge, in this respect, is that the fuel breeding potential is at odds with axial power peaking and the core minimum critical power ratio (CPR), hence limiting the maximum achievable core power rating. Calculations were performed with the BGCore system, which consists of the MCNP code coupled with fuel depletion and thermo-hydraulic feedback modules. A single 3-dimensional fuel assembly having reflective radial boundaries was modeled applying simplified restrictions on the maximum centerline fuel temperature and the CPR. It was found that axially heterogeneous fuel assembly design with a single fissile zone can potentially achieve net breeding, while matching conventional BWR core power rating under certain restrictions to the core loading pattern design. © 2013 Elsevier B.V. All rights reserved.

BWR fuel design options for self-sustainable Th-233U fuel cycle

In this work, we investigate a number of fuel assembly design options for a BWR core operating in a closed self-sustainable Th-233U fuel cycle. The designs rely on axially heterogeneous fuel assembly structure in order to improve fertile to fissile conversion ratio. One of the main assumptions of the current study was to restrict the fuel assembly geometry to a single axial fissile zone "sandwiched" between two fertile blanket zones. The main objective was to study the effect of the most important design parameters, such as dimensions of fissile and fertile zones and average void fraction, on the net breeding of 233U. The main design challenge in this respect is that the fuel breeding potential is at odds with axial power peaking and therefore limits the maximum achievable core power rating. The calculations were performed with BGCore system, which consists of MCNP code coupled with fuel depletion and thermo-hydraulic feedback modules. A single 3-dimensional fuel assembly with reflective radial boundaries was modeled applying simplified restrictions on maximum central line fuel temperature and Critical Power Ratio. It was found that axially heterogeneous fuel assembly design with single fissile zone can potentially achieve net breeding. In this case however, the achievable core power density is roughly one third of the reference BWR core.