2,500 research outputs found

    Liberal Values in Legal Education

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    Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes

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    The rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating these parameters from cross-sectional population data using ordinary differential equations (ODE) ignore information about the genealogy of sampled HIV sequences, which has the potential to cause systematic bias and over-estimate certainty. Here, we describe an integrated approach, validated through extensive simulations, which combines genealogical inference and epidemiological modelling, to estimate rates of CTL escape and reversion in HIV epitopes. We show that there is substantial uncertainty about rates of viral escape and reversion from cross-sectional data, which arises from the inherent stochasticity in the evolutionary process. By application to empirical data, we find that point estimates of rates from a previously published ODE model and the integrated approach presented here are often similar, but can also differ several-fold depending on the structure of the genealogy. The model-based approach we apply provides a framework for the statistical analysis of escape and reversion in population data and highlights the need for longitudinal and denser cross-sectional sampling to enable accurate estimate of these key parameters

    Implementing LibGuides 2: An Academic Case Study

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    Pre-print articleSince 1997, the University of Saskatchewan Library has used “subject pages” to highlight key library resources. When Springshare announced it was launching LibGuides v2, a project team was assembled to transition a mixture of locally produced guides and guides created with the original LibGuides v1 software. This article synthesizes best practices for LibGuides found in the literature, outlines our best intentions in the migration process, and shares what actually transpired after considering factors such as technical challenges and institutional culture. We hope other academic libraries can learn from our experience and make decisions that suit their institution best

    Microsatellite genotyping in New Zealand's poplar and willow breeding program : fingerprinting, genetic diversity and rust resistance marker evaluation : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Breeding at Massey University, Palmerston North, New Zealand

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    Figure 2.4-2 (=Vialle et al., 2011 Fig 1) was removed for copyright reasons, but may be accessed via DOI: 10.1007/s13225-011-0129-6Poplars (Populus spp.) and willows (Salix spp.) are the most employed sustainable soil stabilisation tools by the pastoral sector in New Zealand. The poplar and willow breeding program at the New Zealand Institute for Plant & Food Research Limited (PFR) supports and improves the versatility of poplars and willows as soil stabilisation tools. Good germplasm management involves being able to accurately and objectively identify breeding material and characterise genetic diversity and relationships. Poplar rust is the primary pathogen of concern for the breeding program and evaluating candidate resistance markers could improve selection efficiency. We employed microsatellite markers to fingerprint and characterise the genetic diversity of the germplasm collection. In addition, we also evaluated SSR marker ‘ORPM277’s potential usefulness as a molecular marker to screen for rust resistance in New Zealand. We found that most microsatellite markers utilised in this study were moderately to highly polymorphic with Polymorphic Information Content values averaging 0.482 and 0.497 in the poplar and willow collections respectively. A DNA fingerprinting database was generated that differentiated between 95 poplar accessions and 197 willow accessions represented by 19 and 55 species groups respectively. Genetic variation was high and very similar in both poplar and willow groups, with the main source of variation coming from within genotypes. No correlation was found between phenotypic and genotypic rust resistance data using the ORPM277 microsatellite marker

    Comparative Assessment of Seaport Vulnerabilities to Climate Change: Pilot Study for North Atlantic Medium and High-Use Seaports

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    The Third U.S. National Climate Assessment indicates that seaport infrastructure is already being damaged by sea level rise, heavy downpours, and extreme heat, and that these damages are expected to continue with continued climate change. To facilitate far-sighted planning for a climate-resilient Marine Transportation System (MTS) the United States Army Corps of Engineers (USACE), in collaboration with University of Rhode Island researchers in the Department of Marine Affairs, are piloting a climate-vulnerability indexing method that is driven by data and informed by expert knowledge. This research will contribute to a better understanding of the regional distribution of climate-vulnerability across North Atlantic ports in order to inform transportation resilience and climate-adaptation planning. This pilot study will investigate the climate vulnerabilities of seaports by applying expert elicitation methods to develop indicators of climate vulnerability for the 22 medium and high use ports of the USACE North Atlantic Division. In addition to refining a set of high-level indicators of seaport climate vulnerability, this research will employ expert elicitation methods to weight and aggregate selected indicators to determine the suitability of available data to differentiate ports within a region in terms of relative climate vulnerabilities. Results will serve as an entry point to inform MTS decision-makers in the USACE and other agencies about the nature of seaport climate change vulnerability, its components and determinants, the mechanisms through which a port is vulnerable, and the suitability of available data to serve as high-level indicators of seaport climate vulnerability. Ultimately, this research will support climate resilient national and regional transportation policy. Two published reports are associated with this data set: - Report Number: ERDC/CHL CR-19-2 Title: Measuring Climate and Extreme Weather Vulnerability to Inform Resilience, Report 1: A Pilot Study for North Atlantic Medium- and High-Use Maritime Freight Nodes By R. Duncan McIntosh, Elizabeth L. Mclean, and Austin Becker Link: http://dx.doi.org/10.21079/11681/35196 - Report Number: ERDC/CHL CR-19-3 Title: Measuring Climate and Extreme Weather Vulnerability to Inform Resilience, Report 2: Port Decision-Makers\u27 Barriers to Climate and Extreme Weather Adaption By Elizabeth L. Mclean and Austin Becker Link: http://dx.doi.org/10.21079/11681/3519
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