Phase transition temperatures of side chain liquid crystal polymer from molecular dynamics simulation

In this paper, phase transition temperatures of side chain liquid crystal polymer were predicted by molecular dynamics simulation. We analyzed the change of energy and the degree of similarity(S) with the temperature varying. The simulated phase transition temperatures agree with the experimental values in a proper deviation.

Onshore-offshore variations of copepod community in northern South China Sea

Copepod communities in onshore and offshore waters show a gradient from primarily near shore to primarily oceanic species. Understanding the transition between these communities is fundamental to determining the range of coastal influence. Copepod communities in the northern South China Sea (nSCS) were studied based on samples collected by vertically towing a net in 10 February-6 March (winter) and 26 August-6 September (summer) of 2004. Calanoida species richness, total copepod abundance, Shannon-Weaver diversity index, and onshore-offshore occurrence of dominant species showed obvious change from onshore to offshore waters. Although the offshore stations had lower abundance than the shelf stations, they had more species and larger diversity index. Abundance of some species (groups) with dominance index > 5% (Calanus sinicus, Euchaeta spp., Temora spp., Paracalanus parvus, and Subeucalanus subtenuis) declined from onshore to offshore waters. Warm water species (Pleuromamma abdominalis, P. gracilis, and P. robusta) occurred in offshore waters in both cruises. Station (q-type) cluster analysis in winter and summer separated copepod community into onshore and offshore communities at similar to 40% level of similarity. The two communities were divided at the position of similar to 100-m isobath. In summer, C. sinicus occurred in the upwelling area east of Hainan Island, indicating the presence of an oversummering stock of this species.

Community structure of macrobenthos in coastal water off Rushan, southern Shandong Peninsula, and the relationships with environmental factors

To understand the present actuality of the marine ecosystem in the southern coastal water region of the Shandong Peninsula and the impact of the global change and the human activities to the marine ecosystem of the region, the macrobenthic community structure was researched based on data from 26 sampling stations carried out on four seasonal cruises from December 2006 to November 2007. The data was analyzed using PRIMER 6.0 and SPSS 15.0 software packages. The results showed that 236 macrobenthic species in total were collected from the research region by the field works. Most of the species belong to Polychaeta (76 species), Mollusca (75) and Crustacea (60). Of which, 33 species were common species by the four cruises. The dominant species were different among the four seasons, however, the polychaete species Nephtys oligobranchia and Sternaspis scutata were always dominant in the four seasons. The abundances and biomasses of the macrobenthos from the research region were variable in tire four seasons. The results of CLUSTER and MDS analysis showed that the similarities of macrobenthic structures among the stations were low, most of the similarities were at about 40% of similarity values, only that of two stations were up to 60%. In accordance with the similarity values of the macrobenthic structures, the 26 stations were clustered as six groups at arbitrary similarity level of 30%. The ABC curve indicated that the marcofauna communities in the research region had riot been disturbed distinctly. The results of BIOENV and BVSTEP (Spearman) analysis implied that the concentrations of organic matter in bottom water and heavy metal copper in sediment, water depth and temperature of bottom were the most significant environmental factors to affect the macrobentic community.

Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Case-based retrieval of 3-dimensional shapes for the design of metal castings

This paper describes research into retrieval based on 3-dimensional shapes for use in the metal casting industry. The purpose of the system is to advise a casting engineer on the design aspects of a new casting by reference to similar castings which have been prototyped and tested in the past. The key aspects of the system are the orientation of the shape within the mould, the positions of feeders and chills, and particular advice concerning special problems and solutions, and possible redesign. The main focus of this research is the effectiveness of similarity measures based on 3-dimensional shapes. The approach adopted here is to construct similarity measures based on a graphical representation deriving from a shape decomposition used extensively by experienced casting design engineers. The paper explains the graphical representation and discusses similarity measures based on it. Performance measures for the CBR system are given, and the results for trials of the system are presented. The competence of the current case-base is discussed, with reference to a representation of cases as points in an n-dimensional feature space, and its principal components visualization. A refinement of the case base is performed as a result of the competence analysis and the performance of the case-base before and after refinement is compared.

Structure and diversity of intertidal benthic diatom assemblages in contrasting shores: a case study from the Tagus estuary1

The structure of intertidal benthic diatoms assemblages in the Tagus estuary was investigated during a 2-year survey, carried out in six stations with different sediment texture. Nonparametric multivariate analyses were used to characterize spatial and temporal patterns of the assemblages and to link them to the measured environmental variables. In addition, diversity and other features related to community physiognomy, such as size-class or life-form distributions, were used to describe the diatom assemblages. A total of 183 diatom taxa were identified during cell counts and their biovolume was determined. Differences between stations (analysis of similarity (ANOSIM), R=0.932) were more evident than temporal patterns (R=0.308) and mud content alone was the environmental variable most correlated to the biotic data (BEST, rho=0.863). Mudflat stations were typically colonized by low diversity diatom assemblages (H' similar to 1.9), mainly composed of medium-sized motile epipelic species (250-1,000 mu m(3)), that showed species-specific seasonal blooms (e.g., Navicula gregaria Donkin). Sandy stations had more complex and diverse diatom assemblages (H' similar to 3.2). They were mostly composed by a large set of minute epipsammic species (<250 mu m(3)) that, generally, did not show temporal patterns. The structure of intertidal diatom assemblages was largely defined by the interplay between epipelon and epipsammon, and its diversity was explained within the framework of the Intermediate Disturbance Hypothesis. However, the spatial distribution of epipelic and epipsammic life-forms showed that the definition of both functional groups should not be over-simplified.

Deciding between theories of how reasoning develops is hard

Although Sloutsky agrees with our interpretation of our data, he argues that the totality of the evidence supports his claim that children make inductive generalisations on the basis of similarity. Here we take issue with his characterisation of the alternative hypotheses in his informal analysis of the data, and suggest that a thorough Bayesian analysis, although practically very difficult, is likely to result in a more finely balanced outcome than he suggests. (c) 2008 Elsevier B.V. All rights reserved.

Cryptic plasmid pKA22 isolated from the naphthalene degrading derivative of Rhodococcus rhodochrous NCIMB13064

Cryptic plasmids were found in Rhodococcus rhodochrous NCIMB13064 derivatives which had lost the ability to utilize short-chain 1-chloroalkanes (chain length C-3-C-10) and had acquired the ability to degrade naphthalene. The reversions of these derivatives to the original phenotype were accompanied by the loss of the cryptic plasmids. The 4969-bp pKA22 plasmid was cloned in Escherichia coli and sequenced. This plasmid encodes a putative 33,200-Da protein which contains motifs typical of theta replicase proteins and shows a high degree of similarity to a putative theta replicase from Brevibacterium linens plasmid pRBL1 and to a putative protein encoded by ORF1 of the plasmid pAL5000 from Mycobacterium fortuitum. Two sets of long direct repeats were found in pKA22 which may be involved in the replication of the plasmid and recombination processes. (C) 1997 Academic Press.

Income, deprivation, and economic strain. An analysis of the European community household panel

This paper is concerned with the relationship between household income and life-style deprivation, and their combined impact on households' perceptions of economic strain. It takes as a point of departure findings from a number of European countries showing that the relationship between income and deprivation is weaker than widely assumed and that relative income poverty lines may perform poorly in terms of identifying the most deprived households. It proceeds to examine how far these conclusions about income and deprivation can be generalized to the countries included in the first wave of the European Community Household Panel. Results show that five distinct dimensions of deprivation emerge from an overall European analysis and that these are consistent across individual countries. While a good deal of similarity is observed in the income-deprivation relationship, countries differ in the strength of relationship between income and what is termed 'current liferstyle deprivation' with the relationship being generally weakest in the richer countries. The implications of these findings for the use of relative income poverty lines are developed. Extending this analysis to an assessment of how income and deprivation combine to influence perceptions of economic strain, we show that within-nation reference group processes operating in a uniform manner across countries can account for the bulk of the variation in strain. Cross-national differences can be accounted for by corresponding variation in income and deprivation levels.

Operators for Similarity Search: Semantics, Techniques and Usage Scenarios

This book provides a comprehensive tutorial on similarity operators. The authors systematically survey the set of similarity operators, primarily focusing on their semantics, while also touching upon mechanisms for processing them effectively.

The book starts off by providing introductory material on similarity search systems, highlighting the central role of similarity operators in such systems. This is followed by a systematic categorized overview of the variety of similarity operators that have been proposed in literature over the last two decades, including advanced operators such as RkNN, Reverse k-Ranks, Skyline k-Groups and K-N-Match. Since indexing is a core technology in the practical implementation of similarity operators, various indexing mechanisms are summarized. Finally, current research challenges are outlined, so as to enable interested readers to identify potential directions for future investigations.

In summary, this book offers a comprehensive overview of the field of similarity search operators, allowing readers to understand the area of similarity operators as it stands today, and in addition providing them with the background needed to understand recent novel approaches.

Context-dependent Combination of Sensor Information in Dempster-Shafer Theory for BDI

There has been much interest in the belief–desire–intention (BDI) agent-based model for developing scalable intelligent systems, e.g. using the AgentSpeak framework. However, reasoning from sensor information in these large-scale systems remains a significant challenge. For example, agents may be faced with information from heterogeneous sources which is uncertain and incomplete, while the sources themselves may be unreliable or conflicting. In order to derive meaningful conclusions, it is important that such information be correctly modelled and combined. In this paper, we choose to model uncertain sensor information in Dempster–Shafer (DS) theory. Unfortunately, as in other uncertainty theories, simple combination strategies in DS theory are often too restrictive (losing valuable information) or too permissive (resulting in ignorance). For this reason, we investigate how a context-dependent strategy originally defined for possibility theory can be adapted to DS theory. In particular, we use the notion of largely partially maximal consistent subsets (LPMCSes) to characterise the context for when to use Dempster’s original rule of combination and for when to resort to an alternative. To guide this process, we identify existing measures of similarity and conflict for finding LPMCSes along with quality of information heuristics to ensure that LPMCSes are formed around high-quality information. We then propose an intelligent sensor model for integrating this information into the AgentSpeak framework which is responsible for applying evidence propagation to construct compatible information, for performing context-dependent combination and for deriving beliefs for revising an agent’s belief base. Finally, we present a power grid scenario inspired by a real-world case study to demonstrate our work.

The generation and amplification of intergalactic magnetic fields in analogue laboratory experiments with high power lasers

The advent of high-power laser facilities has, in the past two decades, opened a new field of research where astrophysical environments can be scaled down to laboratory dimensions, while preserving the essential physics. This is due to the invariance of the equations of magneto-hydrodynamics to a class of similarity transformations. Here we review the relevant scaling relations and their application in laboratory astrophysics experiments with a focus on the generation and amplification of magnetic fields in cosmic environment. The standard model for the origin of magnetic fields is a multi stage process whereby a vanishing magnetic seed is first generated by a rotational electric field and is then amplified by turbulent dynamo action to the characteristic values observed in astronomical bodies. We thus discuss the relevant seed generation mechanisms in cosmic environment including resistive mechanism, collision-less and fluid instabilities, as well as novel laboratory experiments using high power laser systems aimed at investigating the amplification of magnetic energy by magneto-hydrodynamic (MHD) turbulence. Future directions, including efforts to model in the laboratory the process of diffusive shock acceleration are also discussed, with an emphasis on the potential of laboratory experiments to further our understanding of plasma physics on cosmic scales.

The design and implementation of a study to investigate the effectiveness of community vs hospital eye service follow-up for patients with neovascular age-related macular degeneration with quiescent disease

Introduction
Standard treatment for neovascular age-related macular degeneration (nAMD) is intravitreal injections of anti-VEGF drugs. Following multiple injections, nAMD lesions often become quiescent but there is a high risk of reactivation, and regular review by hospital ophthalmologists is the norm. The present trial examines the feasibility of community optometrists making lesion reactivation decisions.

Methods
The Effectiveness of Community vs Hospital Eye Service (ECHoES) trial is a virtual trial; lesion reactivation decisions were made about vignettes that comprised clinical data, colour fundus photographs, and optical coherence tomograms displayed on a web-based platform. Participants were either hospital ophthalmologists or community optometrists. All participants were provided with webinar training on the disease, its management, and assessment of the retinal imaging outputs. In a balanced design, 96 participants each assessed 42 vignettes; a total of 288 vignettes were assessed seven times by each professional group.The primary outcome is a participant's judgement of lesion reactivation compared with a reference standard. Secondary outcomes are the frequency of sight threatening errors; judgements about specific lesion components; participant-rated confidence in their decisions about the primary outcome; cost effectiveness of follow-up by optometrists rather than ophthalmologists.

Discussion
This trial addresses an important question for the NHS, namely whether, with appropriate training, community optometrists can make retreatment decisions for patients with nAMD to the same standard as hospital ophthalmologists. The trial employed a novel approach as participation was entirely through a web-based application; the trial required very few resources compared with those that would have been needed for a conventional randomised controlled clinical trial.

Replicability of data collected for empirical estimation of relative pollen productivity

The effects of repeated survey and fieldwork timing on data derived from a recently proposed standard field methodology for empirical estimation of Relative Pollen Productivity have been tested. Seasonal variations in vegetation and associated pollen assemblages were studied in three contrasting cultural habitat types; semi-natural ancient woodlands, lowland heaths, and unimproved, traditionally managed hay meadows. Results show that in woodlands and heathlands the standard method generates vegetation data with a reasonable degree of similarity throughout the field season, though in some instances additional recording of woodland canopy cover should be undertaken, and differences were greater for woodland understorey taxa than for arboreal taxa. Large differences in vegetation cover were observed over the field season in the grassland community, and matching the phenological timing of surveys within and between studies is clearly important if RPP estimates from these sites are to be comparable. Pollen assemblages from closely co-located moss polsters collected on different visits are shown to be variable in all communities, to a greater degree than can be explained by the sampling error associated with pollen counting, and further study of moss polsters as pollen traps is recommended.

Analysis and visualization of seismic data using mutual information

Seismic data is difficult to analyze and classical mathematical tools reveal strong limitations in exposing hidden relationships between earthquakes. In this paper, we study earthquake phenomena in the perspective of complex systems. Global seismic data, covering the period from 1962 up to 2011 is analyzed. The events, characterized by their magnitude, geographic location and time of occurrence, are divided into groups, either according to the Flinn-Engdahl (F-E) seismic regions of Earth or using a rectangular grid based in latitude and longitude coordinates. Two methods of analysis are considered and compared in this study. In a first method, the distributions of magnitudes are approximated by Gutenberg-Richter (G-R) distributions and the parameters used to reveal the relationships among regions. In the second method, the mutual information is calculated and adopted as a measure of similarity between regions. In both cases, using clustering analysis, visualization maps are generated, providing an intuitive and useful representation of the complex relationships that are present among seismic data. Such relationships might not be perceived on classical geographic maps. Therefore, the generated charts are a valid alternative to other visualization tools, for understanding the global behavior of earthquakes.