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.

Synthesis and evaluation of a solid supported molecular tweezer type receptor for cholesterol

A new macroporous stationary phase bearing 'tweezer' receptors that exhibit specificity for cholesterol has been constructed from rigid multifunctional vinylic monomers derived from 3,5-dibromobenzoic acid, propargyl alcohol and cholesterol. The synthesis of the novel tweezer monomer that contains two cholesterol receptor arms using palladium mediated Sonogashira methodologies and carbonate couplings is reported. The subsequent co-polymerisation of this tweezer monomer with a range of cross-linking agents via a 'pseudo' molecular imprinting approach afforded a diverse set of macroporous materials. The selectivity and efficacy of these materials for cholesterol binding was assessed using a chromatographic screening process. The optimum macroporous stationary phase material composition was subsequently used to construct monolithic solid phase extraction columns for use in the selective extraction of cholesterol from multi-component mixtures of structurally related steroids.

Studies on the parallel synthesis and evaluation of new heterocyclic extractants for the partitioning of minor actinides

Multiple parallel synthesis and evaluation have been combined in order to identify new nitrogen heterocycles for the partitioning of minor actinides(III) such as americium(III) from lanthanides such as europium(Ill). An array of triazine-containing molecules was made using multiple parallel syntheses from diketones and amide hydrazides. An excess of each of the resulting purified reagents was dissolved in 1,1,2,2-tetrachloroethane containing 2-bromodecanoic acid, and equilibrated with an aqueous solution containing the radiotracers Eu-152 and Am-241 in nitric acid ([Eu] + [Am] < 400 nanomol dm(-3)). Gamma counting of the organic and aqueous phases led to the identification of several new reagents for the selective extraction of americium(III). In particular, 6-(2-pyridyl)-2-(5,6-dialkyl-1,2,4-triazaphenyl)pyridines were found to be effective reagents for the separation of americium(III) from europium(III), (SFAm/Eu was ca. 30 in [HNO3] = 0.013 mol/L).

Ubiquitous monitoring and behavioural change: a semiotic perspective

We are soon approaching the pervasive-era ofcomputing, where computers are embedded intoobjects and the environment in order to provide newservices to users. Significant levels of data arerequired in order for these services to function asintended, and it is this collection of data which werefer to as ubiquitous monitoring. Existing monitoringtechniques have often been known to cause undesirableeffects, and it is anticipated that ubiquitousmonitoring, with its increased coverage, will lead toincreases in their occurrence and impact. To date, theeffects of ubiquitous monitoring on human behaviourhave not been sufficiently investigated, furtherincreasing the risk of undesirable effects. We propose apreliminary model consisting of a series of factorsbelieved to influence human behavior and augmentedby the Theory of Planned Behaviour. This model mayallow us to understand, predict, and therefore preventany undesirable effects caused by ubiquitousmonitoring.

Isolation of culturable yeasts from market wines and evaluation of the 5 center dot 8S-ITS rDNA sequence analysis for identification purposes

Aims: To test the possibility that wines available in the marketplace may contain culturable yeasts and to evaluate the 5.8S-ITS rDNA sequence analysis as adequate means for the identification of isolates. Methods and Results: As a case study, typical Greek wines were surveyed. Sequence analysis of the 5.8S-ITS rDNA was tested for its robustness in species or strain identification. Sixteen isolates could be assigned into the species Brettanomyces bruxellensis, Saccharomyces cerevisiae and Rhodotorula pinicola, whereas four isolates could not be safely identified. B. bruxellensis was the dominant species present in house wines, while non-Saccharomyces sp. were viable in aged wines of high alcohol content. Conclusions: Yeast population depends on postfermentation procedures or storage conditions. Although 5.8S-ITS rDNA sequence analysis is generally a rapid method to identify wine yeast isolates at the species level, or even below that, it may not be sufficient for some genera. Significance and Impact of the Study: This is the first report to show that commercial wines may possess diverse and potentially harmful yeast populations. The knowledge of yeasts able to reside in this niche environment is essential towards integrated quality assurance programmes. For selected species, the 5.8S-ITS rDNA sequence analysis is a rapid and accurate means.

Reality monitoring and visual hallucinations in Parkinson's disease

Between 8 and 40% of Parkinson disease (PD) patients will have visual hallucinations (VHs) during the course of their illness. Although cognitive impairment has been identified as a risk factor for hallucinations, more specific neuropsychological deficits underlying such phenomena have not been established. Research in psychopathology has converged to suggest that hallucinations are associated with confusion between internal representations of events and real events (i.e. impaired-source monitoring). We evaluated three groups: 17 Parkinson's patients with visual hallucinations, 20 Parkinson's patients without hallucinations and 20 age-matched controls, using tests of visual imagery, visual perception and memory, including tests of source monitoring and recollective experience. The study revealed that Parkinson's patients with hallucinations appear to have intact visual imagery processes and spatial perception. However, there were impairments in object perception and recognition memory, and poor recollection of the encoding episode in comparison to both non-hallucinating Parkinson's patients and healthy controls. Errors were especially likely to occur when encoding and retrieval cues were in different modalities. The findings raise the possibility that visual hallucinations in Parkinson's patients could stem from a combination of faulty perceptual processing of environmental stimuli, and less detailed recollection of experience combined with intact image generation. (C) 2002 Elsevier Science Ltd. All fights reserved.

A flexible monitoring and notification system for distributed resources

Resource monitoring in distributed systems is required to understand the 'health' of the overall system and to help identify particular problems, such as dysfunctional hardware, a faulty, system or application software. Desirable characteristics for monitoring systems are the ability to connect to any number of different types of monitoring agents and to provide different views of the system, based on a client's particular preferences. This paper outlines and discusses the ongoing activities within the GridRM wide-area resource-monitoring project.

Design and evaluation of intelligent classifier based intrusion detection system

We have discovered a novel approach of intrusion detection system using an intelligent data classifier based on a self organizing map (SOM). We have surveyed all other unsupervised intrusion detection methods, different alternative SOM based techniques and KDD winner IDS methods. This paper provides a robust designed and implemented intelligent data classifier technique based on a single large size (30x30) self organizing map (SOM) having the capability to detect all types of attacks given in the DARPA Archive 1999 the lowest false positive rate being 0.04 % and higher detection rate being 99.73% tested using full KDD data sets and 89.54% comparable detection rate and 0.18% lowest false positive rate tested using corrected data sets.

Design, implementation and evaluation of broadband low noise amplifier (LNA) for radiometer

The two major applications of microwave remote sensors are radiometer and radar. Because of its importance and the nature of the application, much research has been made on the various aspects of the radar. This paper will focus on the various aspects of the radiometer from a design point of view and the Low Noise Amplifier will be designed and implemented. The paper is based on a study in radio Frequency Communications engineering and understanding of electronic and RF circuits. Some research study about the radiometer and practical implementation of Low Noise Amplifier for Radiometer will be the main focus of this paper. Basically the paper is divided into two parts. In the first part some background study about the radiometer will be carried out and commonly used types of radiometer will be discussed. In the second part LNA for the radiometer will be designed.

Environmental evaluation of agri-environment schemes using participatory approaches: experiences of testing the Agri-Environmental Footprint Index

The Agri-Environment Footprint Index (AFI) has been developed as a generic methodology to assess changes in the overall environmental impacts from agriculture at the farm level and to assist in the evaluation of European agri-environmental schemes (AES). The methodology is based on multicriteria analysis (MCA) and involves stakeholder participation to provide a locally customised evaluation based on weighted environmental indicators. The methodology was subjected to a feasibility assessment in a series of case studies across the EU. The AFI approach was able to measure significant differences in environmental status between farms that participated in an AES and nonparticipants. Wider environmental concerns, beyond the scheme objectives, were also considered in some case studies and the benefits for identification of unintentional (and often beneficial) impacts of AESs are presented. The participatory approach to AES valuation proved efficient in different environments and administrative contexts. The approach proved to be appropriate for environmental evaluation of complex agri-environment systems and can complement any evaluation conducted under the Common Monitoring and Evaluation Framework. The applicability of the AFI in routine monitoring of AES impacts and in providing feedback to improve policy design is discussed.

Production and evaluation of dry alginate-chitosan microcapsules as an enteric delivery vehicle for probiotic bacteria

This study investigates the production of alginate microcapsules, which have been coated with the polysaccharide chitosan, and evaluates some of their properties with the intention of improving the gastrointestinal viability of a probiotic (Bifidobacterium breve) by encapsulation in this system. The microcapsules were dried by a variety of methods, and the most suitable was chosen. The work described in this Article is the first report detailing the effects of drying on the properties of these microcapsules and the viability of the bacteria within relative to wet microcapsules. The pH range over which chitosan and alginate form polyelectrolyte complexes was explored by spectrophotometry, and this extended into swelling studies on the microcapsules over a range of pHs associated with the gastrointestinal tract. It was shown that chitosan stabilizes the alginate microcapsules at pHs above 3, extending the stability of the capsules under these conditions. The effect of chitosan exposure time on the coating thickness was investigated for the first time by confocal laser scanning microscopy, and its penetration into the alginate matrix was shown to be particularly slow. Coating with chitosan was found to increase the survival of B. breve in simulated gastric fluid as well as prolong its release upon exposure to intestinal pH.