Wavelets and the generalization of the variogram

The experimental variogram computed in the usual way by the method of moments and the Haar wavelet transform are similar in that they filter data and yield informative summaries that may be interpreted. The variogram filters out constant values; wavelets can filter variation at several spatial scales and thereby provide a richer repertoire for analysis and demand no assumptions other than that of finite variance. This paper compares the two functions, identifying that part of the Haar wavelet transform that gives it its advantages. It goes on to show that the generalized variogram of order k=1, 2, and 3 filters linear, quadratic, and cubic polynomials from the data, respectively, which correspond with more complex wavelets in Daubechies's family. The additional filter coefficients of the latter can reveal features of the data that are not evident in its usual form. Three examples in which data recorded at regular intervals on transects are analyzed illustrate the extended form of the variogram. The apparent periodicity of gilgais in Australia seems to be accentuated as filter coefficients are added, but otherwise the analysis provides no new insight. Analysis of hyerpsectral data with a strong linear trend showed that the wavelet-based variograms filtered it out. Adding filter coefficients in the analysis of the topsoil across the Jurassic scarplands of England changed the upper bound of the variogram; it then resembled the within-class variogram computed by the method of moments. To elucidate these results, we simulated several series of data to represent a random process with values fluctuating about a mean, data with long-range linear trend, data with local trend, and data with stepped transitions. The results suggest that the wavelet variogram can filter out the effects of long-range trend, but not local trend, and of transitions from one class to another, as across boundaries.

Industrial radioactive barite scale: suppression of radium uptake by introduction of competing ions

Incorporation of radioactive isotopes during the formation of barite mineral scale is a widespread phenomenon occurring within the oil, mining and process industries. In a series of experiments radioactive barite/celestite solid solutions (SSBarite-Celcstite) have been synthesized under controlled conditions by the counter diffusion of Ra-226, Ba2+, Sr24+ and SO42- ions through a porous medium (silica gel), to investigate inhibiting effects in Ra uptake associated with the introduction of a competing ion (Sr2+). From characterization studies, the particle size and the morphology of the crystals appear to be related to the initial [Sr]/[Ba] molar ratio of the starting solution. Typically, systems richer in Sr produce smaller sized crystals and clusters characterized by a lower degree of order. The activity introduced to the system is mainly incorporated in the crystals generated from the barite/celestite solid solution as suggested by the activity profiles of the hydrogel columns analysed by gamma-spectrometry. There is a relationship between the initial [Sr]/[Ba] molar ratio of the starting solution and the activity exhibited by the synthesized crystals. An effective inhibition of the Ra-226 uptake during formation of the crystals (SSBarite-Celestite) was obtained through the introduction of a competing ion (Sr2+): the higher the initial [Sr]/[Ba] molar ratio of the starting solution, the lower the intensity of the activity peak in the crystals. (C) 2003 Published by Elsevier Ltd.

Arthropod community structure in pastures of an island archipelago (Azores): looking for local-regional species richness patterns at fine-scales

The arthropod species richness of pastures in three Azorean islands was used to examine the relationship between local and regional species richness over two years. Two groups of arthropods, spiders and sucking insects, representing two functionally different but common groups of pasture invertebrates were investigated. The local-regional species richness relationship was assessed over relatively fine scales: quadrats (= local scale) and within pastures (= regional scale). Mean plot species richness was used as a measure of local species richness (= alpha diversity) and regional species richness was estimated at the pasture level (= gamma diversity) with the 'first-order-Jackknife' estimator. Three related issues were addressed: (i) the role of estimated regional species richness and variables operating at the local scale (vegetation structure and diversity) in determining local species richness; (ii) quantification of the relative contributions of alpha and beta diversity to regional diversity using additive partitioning; and (iii) the occurrence of consistent patterns in different years by analysing independently between-year data. Species assemblages of spiders were saturated at the local scale (similar local species richness and increasing beta-diversity in richer regions) and were more dependent on vegetational structure than regional species richness. Sucking insect herbivores, by contrast, exhibited a linear relationship between local and regional species richness, consistent with the proportional sampling model. The patterns were consistent between years. These results imply that for spiders local processes are important, with assemblages in a particular patch being constrained by habitat structure. In contrast, for sucking insects, local processes may be insignificant in structuring communities.

The automation and evaluation of nested clade phylogeographic analysis

Nested clade phylogeographic analysis (NCPA) is a popular method for reconstructing the demographic history of spatially distributed populations from genetic data. Although some parts of the analysis are automated, there is no unique and widely followed algorithm for doing this in its entirety, beginning with the data, and ending with the inferences drawn from the data. This article describes a method that automates NCPA, thereby providing a framework for replicating analyses in an objective way. To do so, a number of decisions need to be made so that the automated implementation is representative of previous analyses. We review how the NCPA procedure has evolved since its inception and conclude that there is scope for some variability in the manual application of NCPA. We apply the automated software to three published datasets previously analyzed manually and replicate many details of the manual analyses, suggesting that the current algorithm is representative of how a typical user will perform NCPA. We simulate a large number of replicate datasets for geographically distributed, but entirely random-mating, populations. These are then analyzed using the automated NCPA algorithm. Results indicate that NCPA tends to give a high frequency of false positives. In our simulations we observe that 14% of the clades give a conclusive inference that a demographic event has occurred, and that 75% of the datasets have at least one clade that gives such an inference. This is mainly due to the generation of multiple statistics per clade, of which only one is required to be significant to apply the inference key. We survey the inferences that have been made in recent publications and show that the most commonly inferred processes (restricted gene flow with isolation by distance and contiguous range expansion) are those that are commonly inferred in our simulations. However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy.

On the structural differences between markers and genomic AC microsatellites

AC microsatellites have proved particularly useful as genetic markers. For some purposes, such as in population biology, the inferences drawn depend on the quantitative values of their mutation rates. This, together with intrinsic biological interest, has led to widespread study of microsatellite mutational mechanisms. Now, however, inconsistencies are appearing in the results of marker-based versus non-marker-based studies of mutational mechanisms. The reasons for this have not been investigated, but one possibility, pursued here, is that the differences result from structural differences between markers and genomic microsatellites. Here we report a comparison between the CEPH AC marker microsatellites and the global population of AC microsatellites in the human genome. AC marker microsatellites are longer than the global average. Controlling for length, marker microsatellites contain on average fewer interruptions, and have longer segments, than their genomic counterparts. Related to this, marker microsatellites show a greater tendency to concentrate the majority of their repeats into one segment. These differences plausibly result from scientists selecting markers for their high polymorphism. In addition to the structural differences, there are differences in the base composition of flanking sequences, marker flanking regions being richer in C and G and poorer in A and T. Our results indicate that there are profound differences between marker and genomic microsatellites that almost certainly affect their mutation rates. There is a need for a unified model of mutational mechanisms that accounts for both marker-derived and genomic observations. A suggestion is made as to how this might be done.

Composition, color, and texture of Thai indigenous and broiler chicken muscles

Chemical compositions and physical properties of mixed-sex Thai indigenous (Gallus domesticus) and broiler (commercial breed, CP707) chicken biceps femoris and pectoralis muscles were determined. Indigenous chicken muscles contained higher protein contents but lower fat and ash contents compared to broiler muscles (P < 0.001). The amino acid profile of the indigenous chicken muscles was similar to that of the broiler muscles except they were slightly richer in glutamic acid (P < 0.05). The indigenous chicken muscles contained more saturated and less polyunsaturated fatty acids than the broiler muscles. There were no differences in the monounsaturated fatty acid contents between the breeds. The total collagen contents of indigenous pectoralis and biceps femoris muscles were 5.09 and 12.85 mg/g, respectively, which were higher than those found in broiler pectoralis (3.86 mg/g) and biceps femoris muscles (8.70 mg/g) (P < 0.001). Soluble collagen contents were lower for indigenous pectoralis and biceps femoris muscles, 22.16 vs. 31.38% and 26.06 vs. 33.87%, respectively. The CIE system values of lightness (L*), redness (a*), and yellowness (b*) of indigenous chicken muscles were higher than those of broiler muscles. The shear values of indigenous chicken muscles either raw or cooked were higher than those of broiler muscles (P < 0.05). After cooking, the shear values decreased for broiler biceps femoris and pectoralis muscles (P < 0.05), whereas no change was observed for indigenous chicken biceps femoris muscle (P > 0.05). Shear values increased for indigenous chicken pectoralis muscle (P < 0.05).

Some functional properties of fractionated soy protein isolates obtained by microfiltration

Five soy proteins isolate (SPI) fractions were produced using two microfiltration membranes with different pore sizes. Fractionation was carried out on SPI produced by isoelectric precipitation of a crude protein extract. The five fractions were two retentates and two permeates from the two membranes, the fifth fraction was obtained as the retentate on the smaller-po re- sized membrane fed with the permeate from the larger-pore-sized membrane. Solubility, foaming and emulsifying properties of the collected fractionates were investigated. It was observed that in the pH range 3-8 the retentates featured superior solubility compared with permeates. There was no significant difference (p > 0.0 1) in solubility between the retentates and SPI at pH >= 6. Foaming characteristics of the fractions followed the same trend as solubility with regard to foam expansion. There was, however, no particular trend observed with regards to foam stability. Emulsions stabilised by the retentates exhibited higher values (p<0.01) of emulsion stability index (ESI) and emulsifying activity index (EAI) than those stabilised with permeates. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) profiles indicated that the fractions exhibiting high functionality in terms of solubility, foaming and emulsifying properties were also richer in 7S globulin soy protein subunits. Isoelectric focussing (IEF) profiles showed that retentates were richer in species with isoelectric points (pl) between 5.2 and 5.6 while permeates featured more prominently at pis between 4.5 and 4.8. (C) 2006 Elsevier Ltd. All rights reserved.

A study of the effects of adjunct cultures on the aroma compounds of Feta-type cheese

The influence of adjunct brine cultures on the volatile compounds in Feta-type cheeses made from bovine milk was studied. Four batches of brine were produced: one with no added adjuncts, a second containing Lactobacillus paracasei subsp. paracasei, a third containing Lb. paracasei subsp. paracasei plus Debaryomyces hansenii and a fourth with Lb. paracasei subsp. paracasei plus Yarrowia lipolytica. All the cultures were isolated from commercial Feta brines. Aroma compounds were analysed by dynamic headspace analysis, on-line coupled with GC/MS. The most important volatile compounds were quantified in the experimental cheeses; it was concluded that the use of Lb. paracasei subsp. paracasei and D. hansenii as adjuncts in the manufacture of Feta-type cheeses contribute to the formation of a richer pattern of aroma compounds, namely alcohols, aldehydes and esters. The inclusion of Y. lipolytica resulted in the production of undesirable aroma compounds that are not part of the usual volatile profile of high quality Feta cheeses. (C) 2004 Elsevier Ltd. All rights reserved.

A question of identity - wiring in the human

This paper discusses the RFID implants for identification via a sensor network. Brain-computer implants linked in to a wireless network. Biometric identification via body sensors is also discussed. The use of a network as a means for remote and distance monitoring of humans opens up a range of potential uses. Where implanted identification is concerned this immediately offers high security access to specific areas by means of only an RFID device. If a neural implant is employed then clearly the information exchanged with a network can take on a much richer form, allowing for identification and response to an individual's needs based on the signals apparent on their nervous system.

Letter processing and font information during reading: beyond distinctiveness, where vision meets design

Letter identification is a critical front end of the reading process. In general, conceptualizations of the identification process have emphasized arbitrary sets of distinctive features. However, a richer view of letter processing incorporates principles from the field of type design, including an emphasis on uniformities across letters within a font. The importance of uniformities is supported by a small body of research indicating that consistency of font increases letter identification efficiency. We review design concepts and the relevant literature, with the goal of stimulating further thinking about letter processing during reading.

Beyond the caves: the Palaeolithic rivers of south-west Britain

This paper introduces a new English Heritage (Aggregates Levy Sustainability Fund) project The Palaeolithic Rivers of South-West Britain (project no. 3847), and summarises the results of a first phase resource assessment. The goal of this ongoing project is to develop a new synthesis of the Lower and Middle Palaeolithic occupation of the south-west region, focusing upon river terrace-based archaeology and its implications for hominin landscape use. The resource assessment has reached two preliminary conclusions. Firstly that the region’s earliest Palaeolithic archaeological record is significantly richer than previously believed, and secondly that although find locations have been added in several areas which previously had very few or no finds (e.g.West Cornwall) the overall bias of finds to the south coast is maintained. The project has also revealed that the river terrace resource of South-West England offers potential for geochronological dating, landscape reconstruction, and improved contextualisation of the archaeological material. Some outreach components of the project are also summarised.

Understanding the early stages of the innovation diffusion process: awareness, influence and communication networks

The themes of awareness and influence within the innovation diffusion process are addressed. The innovation diffusion process is typically represented as stages, yet awareness and influence are somewhat under-represented in the literature. Awareness and influence are situated within the contextual setting of individual actors but also within the broader institutional forces. Understanding how actors become aware of an innovation and then how their opinion is influenced is important for creating a more innovation-active UK construction sector. Social network analysis is proposed as one technique for mapping how awareness and influence occur and what they look like as a network. Empirical data are gathered using two modes of enquiry. This is done through a pilot study consisting of chartered professionals and then through a case study organization as it attempted to diffuse an innovation. The analysis demonstrates significant variations across actors’ awareness and influence networks. It is argued that social network analysis can complement other research methods in order to present a richer picture of how actors become aware of innovations and where they draw their influences regarding adopting innovations. In summarizing the findings, a framework for understanding awareness and influence associated with innovation within the UK construction sector is presented. Finally, with the UK construction sector continually being encouraged to be innovative, understanding and managing an actor’s awareness and influence network will be beneficial. The overarching conclusion thus describes the need not only to build research capacity in this area but also to push the boundaries related to the research methods employed.

Phylogenies reveal predictive power of traditional medicine in bioprospecting

There is controversy about whether traditional medicine can guide drug discovery, and investment in ethnobotanically led research has fluctuated. One view is that traditionally used plants are not necessarily efficacious and there are no robust methods for distinguishing the ones that are most likely to be bioactive when selecting species for further testing. Here, we reconstruct a genus-level molecular phylogeny representing the 20,000 species found in the floras of three disparate biodiversity hotspots: Nepal, New Zealand and the Cape of South Africa. Borrowing phylogenetic methods from community ecology, we reveal significant clustering of the 1,500 traditionally used species, and provide a direct measure of the relatedness of the three medicinal floras. We demonstrate shared phylogenetic patterns across the floras: related plants from these regions are used to treat medical conditions in the same therapeutic areas. This strongly suggests independent discovery of plant efficacy, an interpretation corroborated by the presence of a significantly greater proportion of known bioactive species in these plant groups than in a random sample. Phylogenetic cross-cultural comparison can focus screening efforts on a subset of traditionally used plants that are richer in bioactive compounds, and could revitalise the use of traditional knowledge in bioprospecting.

Student teachers’ perceptions of reading and the teaching of reading: the implications for teacher education

This article reports on research which identified perceptions of reading and the teaching of reading held by trainee teachers and the impact on my provision as a teacher educator. It found that students’ past and present experiences of learning to read and being a reader influenced their perceptions of what reading is and of what it means to teach reading. As a teacher educator, I am not able to give students long experience of seeing children becoming readers, but I am able to give them richer experiences of reading in personally and culturally relevant contexts. This has implications for the nature of subject knowledge required by a student teacher of reading and the curriculum and practice of teacher education.

Precipitation scaling with temperature in warm and cold climates: an analysis of CMIP5 simulations

We investigate the scaling between precipitation and temperature changes in warm and cold climates using six models that have simulated the response to both increased CO2 and Last Glacial Maximum (LGM) boundary conditions. Globally, precipitation increases in warm climates and decreases in cold climates by between 1.5%/°C and 3%/°C. Precipitation sensitivity to temperature changes is lower over the land than over the ocean and lower over the tropical land than over the extratropical land, reflecting the constraint of water availability. The wet tropics get wetter in warm climates and drier in cold climates, but the changes in dry areas differ among models. Seasonal changes of tropical precipitation in a warmer world also reflect this “rich get richer” syndrome. Precipitation seasonality is decreased in the cold-climate state. The simulated changes in precipitation per degree temperature change are comparable to the observed changes in both the historical period and the LGM.