The development of an integrated modelling system to support decisions on organic farms

This paper was presented at the UK Organic Research 2002 Conference of the Colloquium of Organic Researchers (COR). An Integrated Decision Support System (IDSS) is developed which synthesises current understanding of organic farming by means of a multiple objective framework incorporating GIS, biophysical models and socio-economic models of the farming goals. The IDSS uses a multitiered concept of a farming system as a collection of micro-enterprises at the field level, with individual resource endowments, objectives and activities. Farm-level decision drivers trickle down to affect the micro-level field enterprise selection. Biophysical models describe typical forage, cereal, root and legume output and a user-friendly interfaces permits easy access and output display via a GIS. A prototype of the IDSS framework, being developed as a part of the SAC organic research programme is presented

Simple and Multistate Survival Curves

Objective and Sample: This investigation assessed the comprehension of survival curves in a community sample of 88 young and middle-aged adults when several aspects of good practice for graphical communication were implemented, and it compared comprehension for alternative presentation formats. Design, Method, and Measurements: After reading worked examples of using survival curves that provided explanation and answers, participants answered questions on survival data for pairs of treatments. Study 1 compared presenting survival curves for both treatments on the same figure against presentation via 2 separate figures. Study 2 compared presenting data for 3 possible outcome states via a single “multistate” figure for each treatment against presenting each outcome on a separate figure (with both treatments on the same figure). Both studies compared alternative forms of questioning (e.g., “number alive” versus “number dead”). Numeracy levels (self-rated and objective measures) were also assessed. Results: Comprehension was generally good—exceeding 90% correct answers on half the questions—and was similar across alternative graphical formats. Lower accuracy was observed for questions requiring a calculation but was significantly lower only when the requirement for calculation was not explicit (13%–28% decrements in performance). In study 1, this effect was most acute for those with lower levels of numeracy. Subjective (self-rated) numeracy and objective (measured) numeracy were both moderate positive predictors of overall task accuracy (r ≈ 0.3). Conclusions: A high degree of accuracy in extracting information from survival curves is possible, as long as any calculations that are required are made explicit (e.g., finding differences between 2 survival rates). Therefore, practitioners need not avoid using survival curves in discussions with patients, although clear and explicit explanations are important </jats:p

Magnetic field effects in few-level quantum dots: theory, and application to experiment

We examine several effects of an applied magnetic field on Anderson-type models for both single- and two-level quantum dots, and make direct comparison between numerical renormalization group (NRG) calculations and recent conductance measurements. On the theoretical side the focus is on magnetization, single-particle dynamics and zero-bias conductance, with emphasis on the universality arising in strongly correlated regimes; including a method to obtain the scaling behavior of field-induced Kondo resonance shifts over a very wide field range. NRG is also used to interpret recent experiments on spin-1/2 and spin-1 quantum dots in a magnetic field, which we argue do not wholly probe universal regimes of behavior; and the calculations are shown to yield good qualitative agreement with essentially all features seen in experiment. The results capture in particular the observed field-dependence of the Kondo conductance peak in a spin-1/2 dot, with quantitative deviations from experiment occurring at fields in excess of $\sim$ 5 T, indicating the eventual inadequacy of using the equilibrium single-particle spectrum to calculate the conductance at finite bias.Comment: 15 pages, 12 figures. Version as published in PR

Correlated electron physics in multilevel quantum dots: phase transitions, transport, and experiment

We study correlated two-level quantum dots, coupled in effective 1-channel fashion to metallic leads; with electron interactions including on-level and inter-level Coulomb repulsions, as well as the inter-orbital Hund's rule exchange favoring the spin-1 state in the relevant sector of the free dot. For arbitrary dot occupancy, the underlying phases, quantum phase transitions (QPTs), thermodynamics, single-particle dynamics and electronic transport properties are considered; and direct comparison is made to conductance experiments on lateral quantum dots. Two distinct phases arise generically, one characterised by a normal Fermi liquid fixed point (FP), the other by an underscreened (USC) spin-1 FP. Associated QPTs, which occur in general in a mixed valent regime of non-integral dot charge, are found to consist of continuous lines of Kosterlitz-Thouless transitions, separated by first order level-crossing transitions at high symmetry points. A `Friedel-Luttinger sum rule' is derived and, together with a deduced generalization of Luttinger's theorem to the USC phase (a singular Fermi liquid), is used to obtain a general result for the T=0 zero-bias conductance, expressed solely in terms of the dot occupancy and applicable to both phases. Relatedly, dynamical signatures of the QPT show two broad classes of behavior, corresponding to the collapse of either a Kondo resonance, or antiresonance, as the transition is approached from the Fermi liquid phase; the latter behavior being apparent in experimental differential conductance maps. The problem is studied using the numerical renormalization group method, combined with analytical arguments.Comment: 22 pages, 18 figures, submitted for publicatio

Chapter 3 Behavioural biology, conservation genomics, and population viability (Open Access)

This is the first book on captive animal behaviour, applied to welfare. It enables all aspects of zoo husbandry and management (nutrition, enclosure design, handling & training, enrichment, population management) to be based on a sound knowledge of the species, its evolutionary and natural history

Evolutionary and conservation genetics of the Seychelles warbler (Acrocephalus sechellensis)

In this thesis, I investigated how evolutionary forces and conservation action interact to shape neutral and adaptive genetic variation within and among populations. To accomplish this, I studied an island species, the Seychelles warbler (Acrocephalus sechellensis), with microsatellite markers and major histocompatibility complex (MHC) genes as measures of neutral and adaptive variation respectively. First, I used museum DNA and historical records to reveal a recent bottleneck that provides context for the contemporary genetic variation observed in this species. I then determined the impact of four translocations on genetic diversity over two decades. I found that diversity does not differ significantly between islands but the use of smaller founder sizes in two translocations has caused population divergence. These results indicate that stochastic genetic capture is important in translocations and that future assisted gene flow between populations may be necessary. As a tool for conservation practitioners, I wrote a technical report of the most recent translocation - to Frégate Island - detailing practicalities and outcomes to help inform future translocation policy. Using two translocation events as experiments, I then tested whether MHC-based social mate choice acts to maintain MHC diversity in the Seychelles warbler, finding that male age and heterozygosity, but not MHC, predicted pairing success. Lastly, I investigated survival and reproductive consequences of Ase-ua4, an MHC class I allele previously shown to confer a survival advantage in the Seychelles warbler. I found widespread patterns of allele frequency increase within cohorts consistent with the survival effect, but no overall increase in population allele frequency over time. I investigated potential antagonistic reproductive mechanisms, but found no clear evidence for why this allele is not driven towards fixation. Collectively, my results provide an interesting case study of the evolutionary conservation approach, whilst providing insight into the importance of maintaining genetic variation in natural populations

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

There is a high prevalence of coronary artery disease (CAD) in patients with left bundle branch block (LBBB); however there are many other causes for this electrocardiographic abnormality. Non-invasive assessment of these patients remains difficult, and all commonly used modalities exhibit several drawbacks. This often leads to these patients undergoing invasive coronary angiography which may not have been necessary. In this review, we examine the uses and limitations of commonly performed non-invasive tests for diagnosis of CAD in patients with LBBB