The utility and limitations of chloroplast DNA analysis for identifying native British oak stands and for guiding replanting strategy

We report a method using variation in the chloroplast genome (cpDNA) to test whether oak stands of unknown provenance are of native and/or local origin. As an example, a sample of test oaks, of mostly unknown status in relation to nativeness and localness, were surveyed for cpDNA type. The sample comprised 126 selected trees, derived from 16 British seed stands, and 75 trees, selected for their superior phenotype (201 tree samples in total). To establish whether these two test groups are native and local, their cpDNA type was compared with that of material from known autochthonous origin (results of a previous study which examined variation in 1076 trees from 224 populations distributed across Great Britain). In the previous survey of autochthonous material, four cpDNA types were identified as native; thus if a test sample possessed a new haplotype then it could be classed as non-native. Every one of the 201 test samples possessed one of the four cpDNA types found within the autochthonous sample. Therefore none could be proven to be introduced and, on this basis, was considered likely to be native. The previous study of autochthonous material also found that cpDNA variation was highly structured geographically and, therefore, if the cpDNA type of the test sample did not match that of neighbouring autochthonous trees then it could be considered to be non-local. A high proportion of the seed stand group (44.2 per cent) and the phenotypically superior trees (58.7 per cent) possessed a cpDNA haplotype which matched that of the neighbouring autochthonous trees and, therefore, can be considered as local, or at least cannot be proven to be introduced. The remainder of the test sample could be divided into those which did not grow in an area of overall dominance (18.7 per cent of seed stand trees and 28 per cent of phenotypically superior) and those which failed to match the neighbouring autochthonous haplotype (37.1 per cent and 13.3 per cent, respectively). Most of the non-matching test samples were located within 50 km of an area dominated by a matching autochthonous haplotype (96.0 per cent and 93.5 per cent, respectively), and potentially indicates only local transfer. Whilst such genetic fingerprinting tests have proven useful for assessing the origin of stands of unknown provenance, there are potential limitations to using a marker from the chloroplast genome (mostly adaptively neutral) for classifying seed material into categories which have adaptive implications. These limitations are discussed, particularly within the context of selecting adaptively superior material for restocking native forests.

A matching pursuit-based signal complexity measure for the analysis of newborn EEG

This paper presents a new relative measure of signal complexity, referred to here as relative structural complexity, which is based on the matching pursuit (MP) decomposition. By relative, we refer to the fact that this new measure is highly dependent on the decomposition dictionary used by MP. The structural part of the definition points to the fact that this new measure is related to the structure, or composition, of the signal under analysis. After a formal definition, the proposed relative structural complexity measure is used in the analysis of newborn EEG. To do this, firstly, a time-frequency (TF) decomposition dictionary is specifically designed to compactly represent the newborn EEG seizure state using MP. We then show, through the analysis of synthetic and real newborn EEG data, that the relative structural complexity measure can indicate changes in EEG structure as it transitions between the two EEG states; namely seizure and background (non-seizure).

Non-cancer mortality among people diagnosed with cancer (Australia)

Objective To investigate whether people diagnosed with cancer have an increased risk of death from non-cancer causes compared to the general population. Methods The non-cancer mortality of people diagnosed with cancer in Queensland (Australia) between 1982 and 2002 who had not died before 1 January 1993 was compared to the mortality of the total Queensland population, matching by age group and sex, and reporting by standardised mortality ratios. Results Compared to the non-cancer mortality in the general population, cancer patients (all cancers combined) were nearly 50% more likely to die of non-cancer causes (SMR = 149.9, 95% CI = [147-153]). This varied by cancer site. Overall melanoma patients had significantly lower non-cancer mortality, female breast cancer patients had similar non-cancer mortality to the general population, while increased non-cancer mortality risks were observed for people diagnosed with cervical cancer, colorectal cancer, prostate cancer, non-Hodgkin lymphoma and lung cancer. Conclusions Although cancer-specific death rates underestimate the mortality directly associated with a diagnosis of cancer, quantifying the degree of underestimation is difficult due to various competing explanations. There remains an important role for future research in understanding the causes of morbidity among cancer survivors, particularly those looking at both co-morbid illnesses and reductions in quality of life.

Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators

SOX transcription factors perform a remarkable variety of important roles in vertebrate development, either activating or repressing specific target genes through interaction with different partner proteins. Surprisingly, these interactions are often mediated by the conserved, DNA-binding HMG domain, raising questions as to how each factor's specificity is generated. We propose a model whereby non-HMG domains may influence partner protein selection and/or binding stability.

Edge-to-edge matching model for predicting orientation relationships and habit planes-the improvements

The edge-to-edge matching model has been further developed along with the Cu/Cr system as an example. The conditions for zigzag atom rows to be matching directions are included and the critical value of interatomic spacing misfit along matching directions and the critical value of d-value mismatch between matching planes are proposed in the new version of the model. (c) 2005 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Comments on edge-to-edge matching and the equivalence of the invariant line, Delta g and Moire fringe approaches to the crystallographic features of precipitates

Three apparently distinct and different approaches have been proposed to account for the crystallographic features of diffusion-controlled precipitation. These three models are based on (a) an invariant line in the habit plane, (b) the parallelism of a pair of Deltags that are perpendicular to the habit plane and (c) the parallelism of a pair of Moire fringes that are in turn parallel to the habit plane. The purpose of the present paper is to show that these approaches are in fact absolutely equivalent and that when certain conditions are satisfied they are essentially the same as the recent edge-to-edge matching model put forward by the authors. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Edge-to-edge matching and its applications - Part I. Application to the simple HCP/BCC system

The edge-to-edge matching crystallographic model has been used to predict all the orientation relationships (OR) between crystals that have simple hexagonal close packed (HCP) and body-centered cubic (BCC) structures. Using the critical values for the interatomic spacing misfit along the matching directions and the cl-value mismatch between matching planes, the model predicted all the four common ORs, namely the Burgers OR, the Potter OR, the Pitsch-Schrader OR and the Rong Dunlop OR, together with the corresponding habit planes. Taking the c(H)/a(H) and a(H)/a(B) ratios as variables, where H and B denote the HCP and BCC structures respectively, the model also predicted the relationship between these variables and the four ORs. These predictions are perfectly consistent with the published experimental results. As was the case in the FCC/BCC system, the edge-to-edge matching model has been shown to be a powerful tool for predicting the crystallographic features of diffusion-controlled phase transformations. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Edge-to-edge matching and its applications - Part II. Application to Mg-Al, Mg-Y and Mg-Mn alloys

A model for the crystallography and morphology of diffusion-controlled phase transformations - edge-to-edge matching - has been used to predict the orientation relationships (OR) and habit planes of precipitates Mg17Al12 in Mg-Al alloy, Mg24Y5 in Mg-Y alloy and alpha-Mn in Mg-Mn alloy. Based on the crystal structures and lattice parameters only, the model predicts that the possible ORs between Mg17Al12 and Mg matrix are the near Burgers OR, the Potter OR, the Gjonnes-Ostmoe OR and the Crawley OR. In the Mg-Y alloy, the OR between Mg24Y5 precipitates and the Mg matrix is predicted to be the Burgers OR only. The model also predicts that there are no reproducible ORs between alpha-Mn and Mg in the Mg-Mn alloy. Combining the edge-to-edge matching model and W. Zhang's Deltag approach, the habit plane and side facets of the precipitate for each OR can be determined. All the predicted ORs and the corresponding habit planes in Mg-Al and Mg-Y alloys agree very well with the experimental results. (C) 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Application of edge-to-edge matching model to understand the in-plane texture of TiSi2 (C49) thin films on (001)(Si) surface

The edge-to-edge matching model, which was originally developed for predicting crystallographic features in diffusional phase transformations in solids, has been used to understand the formation of in-plane textures in TiSi2 (C49) thin films on Si single crystal (001)si surface. The model predicts all the four previously reported orientation relationships between C49 and Si substrate based on the actual atom matching across the interface and the basic crystallographic data only. The model has strong potential to be used to develop new thin film materials. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Understanding the crystallography of the eutectoid microstructure in a Zn-Al alloy using the edge-to-edge matching model

The orientation relationship (OR) between the beta(Zn) phase and the alpha(Al) phase and the corresponding habit planes in a Zn-Al eutectoid alloy were accurately determined using convergent beam Kikuchi line diffraction patterns. In addition to the previously reported OR. [11 (2) over bar0](beta)parallel to[110](alpha), (0002)(beta)parallel to ((1) over bar 11)alpha, two new ORs were observed. They are: [11 (2) over bar0](beta)parallel to [110], ((1) over bar 101)(beta) 0.82 degrees from (002)(alpha) and [(1) over bar 100](beta)parallel to[112](alpha), (0002)(beta) 4.5 degrees from (111)(alpha). These ORs can be explained and understood using the recently developed edge-to-edge matching model. (c) 2006 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Edge-to-edge matching - The fundamentals

The basis of the present authors' edge-to-edge matching model for understanding the crystallography of partially coherent precipitates is the minimization of the energy of the interface between the two phases. For relatively simple crystal structures, this energy minimization occurs when close-packed, or relatively close-packed, rows of atoms match across the interface. Hence, the fundamental principle behind edge-to-edge matching is that the directions in each phase that correspond to the edges of the planes that meet in the interface should be close-packed, or relatively close-packed, rows of atoms. A few of the recently reported examples of what is termed edge-to-edge matching appear to ignore this fundamental principle. By comparing theoretical predictions with available experimental data, this article will explore the validity of this critical atom-row coincidence condition, in situations where the two phases have simple crystal Structures and in those where the precipitate has a more complex structure.

The Equilibrium Flux Method for the calculation of flows with non-equilbrium chemical reactions

The Equilibrium Flux Method [1] is a kinetic theory based finite volume method for calculating the flow of a compressible ideal gas. It is shown here that, in effect, the method solves the Euler equations with added pseudo-dissipative terms and that it is a natural upwinding scheme. The method can be easily modified so that the flow of a chemically reacting gas mixture can be calculated. Results from the method for a one-dimensional non-equilibrium reacting flow are shown to agree well with a conventional continuum solution. Results are also presented for the calculation of a plane two-dimensional flow, at hypersonic speed, of a dissociating gas around a blunt-nosed body.

The attentional demands of preferred and non-preferred gait patterns

The purpose of this study was to determine the attentional demands of natural and imposed gait, as well as the attentional costs of transitions between the walking and running co-ordination patterns. Seven healthy young men and four healthy young women undertook an auditory probe reaction time task concurrently with self-selected gait (Experiment 1) and imposed walking and running (Experiment 2) at different speeds on a motor-driven treadmill. In Experiment 1, where participants were free to choose their own movement pattern to match the speed of travel of the treadmill, normal gait control was shown to have a significant attentional cost, and hence not be automatic in the classical sense. However, this attentional cost did not differ between the two gait modes or at the transition point. In Experiment 2, where participants were required to maintain specific gait modes regardless of the treadmill speed, the maintenance of walking at speeds normally associated with running was found to have an attentional cost whereas this was not the case for running at normal walking speeds. Collectively the findings support a model of gait control in which the normal switching between gait modes is determined with minimal attention demand and in which it is possible to sustain non-preferred gait modes although, in the case of walking, only at a significant attentional/cognitive cost. © 2002 Elsevier Science B.V. All rights reserved.

Children’s respiratory health and daily particulate levels in ten non-urban communities

We conducted a study to assess the association between the acute respiratory health of children and the levels of particulates in communities near and away from active opencast coal mines. The study enrolled children aged 1–11 years from the general population of five socioeconomically matched pairs of nonurban communities in northern England. Diaries of respiratory events were collected for 1405 children, and information was collected on the consultations of 2442 children with family/general practitioners over the 6-week study periods during 1996–1997, with concurrent monitoring of particulate levels. The associations found between daily PM10 levels and respiratory symptoms were frequently small and positive and sometimes varied between communities. The magnitude of these associations were in line with those from previous studies, even though daily particulate levels were low, and the children were drawn from the general population, rather than from the population with respiratory problems. The associations among asthma reliever use, consultations with general practitioners, and daily particulate levels were of a similar strength but estimated less precisely. The strength of association between all respiratory health measures and particulate levels was similar in communities near and away from opencast coal mining sites.