Species identification and authentication of some of the most important seafood products in Iranian markets using biotechnological methods based on DNA

This study describes the molecular identification of sixteen fish species present in processed products imported into Iran for human consumption. DNA barcoding using direct sequencing of about 650 bp of the mitochondrial Cytochrome Oxidase subunit I gene revealed incorrect labeling (31.25%). Substitution of fish species constitutes serious economic fraud, and our results increase concern regarding the trading of processed fish products in Iran from both health and conservation points of view.

Phylogenetic positions of several amitochondriate protozoa - Evidence from phylogenetic analysis of DNA topoisomerase II

Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, Entamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group - Archezoa. The main evidence for this is their 'lacking mitochondria' and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase 11 in G lamblia, T vaginalis and E histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase 11 make it avoid the defect of 'long-branch attraction' appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented by Giardia) may occupy a very low evolutionary position, generally these organisms are not as extremely primitive as was thought before; they should be polyphyletic groups diverging after the endosymbiotic origin of mitochondrion to adapt themselves to anaerobic parasitic life.

TRANSIENT SCANNING ELECTRON BEAM ANNEALING METHODS USED TO STUDY DIFFUSION AND DEFECTS IN IMPLANTED SILICON.

Rapid thermal annealing of arsenic and boron difluoride implants, such as those used for source/drain regions in CMOS, has been carried out using a scanning electron beam annealer, as part of a study of transient diffusion effects. Three types of e-beam anneal have been performed, with peak temperatures in the range 900 -1200 degree C; the normal isothermal e-beam anneals, together with sub-second fast anneals and 'dual-pulse' anneals, in which the sample undergoes an isothermal pre-anneal followed by rapid heating to the required anneal temperature is less than 0. 5s. The diffusion occuring during these anneal cycles has been modelled using SPS-1D, an implant and diffusion modelling program developed by one of the authors. This has been modified to incorporate simulated temperature vs. time cycles for the anneals. Results are presented applying the usual equilibrium clustering model, a transient point-defect enhancement to the diffusivity proposed recently by Fair and a new dynamic clustering model for arsenic. Good agreement with SIMS measurements is obtained using the dynamic clustering model, without recourse to a transient defect model.

Screening of healthcare workers for tuberculosis: development and validation of a new health economic model to inform practice

Methods for determining cost-effectiveness of different treatments are well established, unlike appraisal of non-drug interventions, including novel diagnostics and biomarkers.

A new apparatus for modelling excavations

Underground space is commonly exploited both to maximise the utility of costly land in urban development and to reduce the vertical load acting on the ground. Deep excavations are carried out to construct various types of underground infrastructure such as deep basements, subways and service tunnels. Although the soil response to excavation is known in principle, designers lack practical calculation methods for predicting both short- and long-term ground movements. As the understanding of how soil behaves around an excavation in both the short and long term is insufficient and usually empirical, the judgements used in design are also empirical and serious accidents are common. To gain a better understanding of the mechanisms involved in soil excavation, a new apparatus for the centrifuge model testing of deep excavations in soft clay has been developed. This apparatus simulates the field construction sequence of a multi-propped retaining wall during centrifuge flight. A comparison is given between the new technique and the previously used method of draining heavy fluid to simulate excavation in a centrifuge model. The new system has the benefit of giving the correct initial ground conditions before excavation and the proper earth pressure distribution on the retaining structures during excavation, whereas heavy fluid only gives an earth pressure coefficient of unity and is unable to capture any changes in the earth pressure coefficient of soil inside the zone of excavation, for example owing to wall movements. Settlements of the ground surface, changes in pore water pressure, variations in earth pressure, prop forces and bending moments in the retaining wall are all monitored during excavation. Furthermore, digital images taken of a cross-section during the test are analysed using particle image velocimetry to illustrate ground deformation and soil-structure interaction mechanisms. The significance of these observations is discussed.

Methods of monitoring of metro lining in Prague

There are several reasons for monitoring of underground structures and they have already been discussed many times, e.g. from the view of ageing or state after accidental event like flooding of Prague metro in 2002. Monitoring of Prague metro is realized in the framework of international research project sponsored by ESF-S3T. The monitoring methods used in Prague are either classical one or new or developing one. The reason for different monitoring methods is the different precision of each method and also for cross-checking between them and their evaluation. Namely we use convergence, tiltmetres, crackmetres, geophysical methods, laser scanning, computer vision and finally installation of MEMS monitoring devices. In the paper more details of each method and obtained results will be presented. The monitoring methods are complemented by wireless data collection and transfer for real-time monitoring. © 2012 Taylor & Francis Group.

Alternative methods for surface texturing

Surface texturing has a great potential to improve tribological performance. First, possible texturing methods were identified and classified according to their physical principles. In sequence, some alternative texturing methods are presented. Some of them are already currently used either in industry or in laboratory, and innovations or simplifications are described for them. Others are innovative techniques. Some were explored only tentatively, where basic ideas and simple experimental investigations were developed to check their validity. Others were explored in more detail, so that their practical applicability could be identified. The first texturing method was photochemical texturing using a simple and cheap apparatus. Masking with inkjet printing before chemical etching was also successful to texture metallic samples. A new method involving electrochemical texturing, without the need to previously mask the samples to be textured have been studied in terms of voltage, current, mechanical configuration of the apparatus and electrolyte flushing. Another method aims to generate randomly distributed circular pockets on steel surfaces and involves dispersion of small acid droplets in oil. The final method involves the selective formation of hard areas on a steel surface by locallised diffusion, which should then develop into a texture during wear.

A classification of data quality assessment methods

Data quality (DQ) assessment can be significantly enhanced with the use of the right DQ assessment methods, which provide automated solutions to assess DQ. The range of DQ assessment methods is very broad: from data profiling and semantic profiling to data matching and data validation. This paper gives an overview of current methods for DQ assessment and classifies the DQ assessment methods into an existing taxonomy of DQ problems. Specific examples of the placement of each DQ method in the taxonomy are provided and illustrate why the method is relevant to the particular taxonomy position. The gaps in the taxonomy, where no current DQ methods exist, show where new methods are required and can guide future research and DQ tool development.

Development of a new apparatus for modeling deep excavation related problems in geotechnical centrifuge

Underground space is commonly exploited both to maximise the utility of costly land in urban development and to reduce the vertical load acting on the ground. Deep excavations are carried out to construct various types of underground infrastructure such as deep basements, subways and service tunnels. Although the soil response to excavation is known in principle, designers lack practical calculation methods for predicting both short- and long-term ground movements. As the understanding of how soil behaves around an excavation in both the short and long term is insufficient and usually empirical, the judgements used in design are also empirical and serious accidents are common. To gain a better understanding of the mechanisms involved in soil excavation, a new apparatus for the centrifuge model testing of deep excavations in soft clay has been developed. This apparatus simulates the field construction sequence of a multi-propped retaining wall during centrifuge flight. A comparison is given between the new technique and the previously used method of draining heavy fluid to simulate excavation in a centrifuge model. The new system has the benefit of giving the correct initial ground conditions before excavation and the proper earth pressure distribution on the retaining structures during excavation, whereas heavy fluid only gives an earth pressure coefficient of unity and is unable to capture any changes in the earth pressure coefficient of soil inside the zone of excavation, for example owing to wall movements. Settlements of the ground surface, changes in pore water pressure, variations in earth pressure, prop forces and bending moments in the retaining wall are all monitored during excavation. Furthermore, digital images taken of a cross-section during the test are analysed using particle image velocimetry to illustrate ground deformation and soil–structure interaction mechanisms. The significance of these observations is discussed.

Leadership of healthcare commissioning networks in England: a mixed-methods study on clinical commissioning groups.

To explore the relational challenges for general practitioner (GP) leaders setting up new network-centric commissioning organisations in the recent health policy reform in England, we use innovation network theory to identify key network leadership practices that facilitate healthcare innovation.

Geometric optimization methods for independent component analysis applied on gene expression data

DNA microarrays provide a huge amount of data and require therefore dimensionality reduction methods to extract meaningful biological information. Independent Component Analysis (ICA) was proposed by several authors as an interesting means. Unfortunately, experimental data are usually of poor quality- because of noise, outliers and lack of samples. Robustness to these hurdles will thus be a key feature for an ICA algorithm. This paper identifies a robust contrast function and proposes a new ICA algorithm. © 2007 IEEE.

A new approach to the analytical and numerical form-finding of tensegrity structures

We develop a new formulation for the form-finding of tensegrity structures in which the primary variables are the Cartesian components of element lengths. Both an analytical and a numerical implementation of the formulation are described; each require a description of the connectivity of the tensegrity, with the iterative numerical method also requiring a random starting vector of member force densities. The analytical and numerical form-finding of tensegrity structures is demonstrated through six examples, and the results obtained are compared and contrasted with those available in the literature to verify the accuracy and viability of the suggested methods. © 2013 Elsevier Ltd. All rights reserved.

Reconsideration of Phylogenetic Relationships of the Subclass Peritrichia (Ciliophora, Oligohymenophorea) Based on Small Subunit Ribosomal RNA Gene Sequences, with the Establishment of a New Subclass Mobilia Kahl, 1933

Based on its characteristic oral apparatus, the ciliate subclass Peritrichia has long been recognized as a monophyletic assemblage composed of the orders Mobilida and Sessilida. Following the application of molecular methods, the monophyly of Peritrichia has recently been questioned. We investigated the phylogenetic relationships of the peritrichous ciliates based on four further complete small subunit ribosomal RNA sequences of mobilids, namely Urceolaria urechi, Trichodina meretricis, Trichodina sinonovaculae, and Trichodina ruditapicis. In all phylogenetic trees, the mobilids never clustered with the sessilids, but instead formed a monophyletic assemblage related to the peniculines. By contrast, the sessilids formed a sister clade with the hymenostomes at a terminal position within the Oligohymenophorea. We therefore formally separate the mobilids from the sessilids (Peritrichia sensu stricto) and establish a new subclass, Mobilia Kahl, 1933, which contains the order Mobilida Kahl, 1933. We argue that the oral apparatus in the mobilians and sessilid peritrichs is a homoplasy, probably due to convergent evolution driven by their similar life-styles and feeding strategies. Morphologically, the mobilians are distinguished from all other oligohymenophoreans by the presence of the adhesive disc, this character being a synapomorphy for the Mobilia.

A new fluorescent quantitative PCR-based in vitro neutralization assay for white spot syndrome virus

A fluorescent quantitative PCR (FQ-PCR) assay utilizing SYBR green I dye is described for quantitation of white spot syndrome virus (WSSV) particles isolated from infected crayfish, Cambarus clarkii. For this assay, a primer set was designed which amplifies, with high efficiency and specificity, a 129 bp target sequence within ORF167 of the WSSV genome. Conveniently, WSSV particles can be added into the FQ-PCR assay with a simple and convenient method to release its DNA. To establish the basis for an in vitro neutralization test, primary cultures of shrimp cells were challenged with WSSV that had been incubated with a polyclonal anti-WSSV serum or with control proteins. The number of WSSV particles released from the cells after these treatments were assayed by FQ-PCR. This test may serve as a method to screen monoclonal antibody pools or recombinant antibody pools for neutralizing activity prior to in vivo animal experiments. (c) 2007 Elsevier B.V. All rights reserved.