RT-Bst: an integrated approach for reverse transcription and enrichment of cDNA from viral RNA

The synthesis of cDNA from RNA is challenging due to the inefficiency of reverse transcription (RT). In order to address this, a method was developed known as RT-Bst for sequential RT of RNA and Bst DNA polymerase amplification for enrichment of cDNA in a single tube reaction. Using genomic RNA from bacteriophage MS2, the yield of cDNA produced by RT alone and RT-Bst were compared by analysis of PCR-amplified products. Using random primers a superior performance was observed when amplifying MS2 RNA following RT-Bst compared to RT alone, indicating that greater quantities of cDNA were present after RT-Bst. RT-Bst was also compared with RT alone for their relative ability to produce sufficient cDNA to amplify 8 target regions spanning the respiratory syncytial virus (RSV) genome. Six out of 8 targets were amplified consistently by PCR subsequent to RT-Bst amplification whereas only 3 out of 8 targets could be amplified after RT alone. RSV sequences were selectively amplified using RSV specific primers from a mixed template containing an excess of MS2 RNA in a RT-Bst reaction without amplifying MS2 sequences. This suggests that RT-Bst can be used to amplify RNA sequences non-specifically using random primers and specifically using sequence specific primers and enhances the yield of cDNA when compared to RT alone.

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

The risk of viral dispersal and aerosolization by different hand-drying methods

Background World Health Organization hand hygiene guidelines state that if electric hand dryers are used, they should not aerosolize pathogens. Previous studies have investigated the dispersal by different hand-drying devices of chemical indicators, fungi and bacteria on the hands. This study assessed the aerosolization and dispersal of virus on the hands to determine any differences between hand-drying devices in their potential to contaminate other occupants of public washrooms and the washroom environment. Methods A suspension of MS2, an Escherichia coli bacteriophage virus, was used to artificially contaminate the hands of participants prior to using three different handdrying devices: jet air dryer, warm air dryer, paper towel dispenser. Virus was detected by plaque formation on agar plates layered with the host bacterium. Vertical dispersal of virus was assessed at a fixed distance (0.4 m) and over a range of different heights (0.0 – 1.8 m) from the floor. Horizontal dispersal was assessed at different distances of up to three metres from the hand-drying devices. Virus aerosolization and dispersal was also assessed at different times up to 15 minutes after use by means of air sampling at two distances (0.1 and 1.0 m) and at a distance behind and offset from each of the hand-drying devices. Results Over a range of heights, the jet air dryer was shown to produce over 60 times greater vertical dispersal of virus from the hands than a warm air dryer and over 1300 times greater than paper towels; the maximum being detected between 0.6 and 1.2 metres from the floor. Horizontal dispersal of virus by the jet air dryer was over 20 times greater than a warm air dryer and over 190 times greater than paper towels; virus being detected at distances of up to three metres. Air sampling at three different positions from the hand-drying devices 15 minutes after use showed that the jet air dryer produced over 50-times greater viral contamination of the air than a warm air dryer and over 110-times greater than paper towels. Conclusions Due to their high air speed, jet air dryers aerosolize and disperse more virus over a range of heights, greater distances, and for longer times than other hand drying devices. If hands are inadequately washed, they have a greater potential to contaminate other occupants of a public washroom and the washroom environment. Main messages: Jet air dryers with claimed air speeds of over 600 kph have a greater potential than warm air dryers or paper towels to aerosolize and disperse viruses on the hands of users. The choice of hand-drying device should be carefully considered. Jet air dryers may increase the risk of transmission of human viruses, such as norovirus, particularly if hand washing is inadequate.

Philosophies, traditional pedagogy, and new technologies: a report on a case study of EAP teachers' integration of technology into traditional practice

This chapter reports on a study of teachers in transition, developing their practice and their cognitions regarding the integration of learning technologies with traditional approaches to the teaching of English for Academic Purposes (EAP). Taking a case study approach, it examines developments in the practice of three teachers during and after a teacher education programme on the use of technology in the EAP classroom. This is a study of cognition, teaching philosophy, and the relationship between pedagogy, technology, and content, and how teachers situate these within their own practice. The setting is the rapidly changing UK higher education environment, where the speed of change is such that today's latest fashions and gadgets may well be yesterday's news tomorrow. Thus, this is not a tale of individual technologies or tools to make teachers' lives better. This is a story of people, of pedagogy's traditional values intersecting with technology, and the issues arising from this, alongside the evolution of strategies for dealing with these issues.

Dynamic Network Mechanisms of Relational Integration

A prominent hypothesis states that specialized neural modules within the human lateral frontopolar cortices (LFPCs) support “relational integration” (RI), the solving of complex problems using inter-related rules. However, it has been proposed that LFPC activity during RI could reflect the recruitment of additional “domain-general” resources when processing more difficult problems in general as opposed to RI specifi- cally. Moreover, theoretical research with computational models has demonstrated that RI may be supported by dynamic processes that occur throughout distributed networks of brain regions as opposed to within a discrete computational module. Here, we present fMRI findings from a novel deductive reasoning paradigm that controls for general difficulty while manipulating RI demands. In accordance with the domain- general perspective, we observe an increase in frontoparietal activation during challenging problems in general as opposed to RI specifically. Nonetheless, when examining frontoparietal activity using analyses of phase synchrony and psychophysiological interactions, we observe increased network connectivity during RI alone. Moreover, dynamic causal modeling with Bayesian model selection identifies the LFPC as the effective connectivity source. Based on these results, we propose that during RI an increase in network connectivity and a decrease in network metastability allows rules that are coded throughout working memory systems to be dynamically bound. This change in connectivity state is top-down propagated via a hierarchical system of domain-general networks with the LFPC at the apex. In this manner, the functional network perspective reconciles key propositions of the globalist, modular, and computational accounts of RI within a single unified framework.

A generic model for integration of Quality, Environment and Safety Management Systems

Purpose – The purpose of this paper is to propose a generic model of Integrated Management System of Quality, Environment and Safety (IMS-QES) that can be adapted and progressively to assimilate various Management Systems, of which highlights: ISO 9001 for Quality; ISO 14001 for Environment; OHSAS 18001 for Occupational Health and Safety. Design/methodology/approach – The model was designed in the real environment of a Portuguese Organization and 160 employees were surveyed. The rate response was equal to 86 percent. The conceived model was implemented in a first phase for the integration of Quality, Environment and Safety Management Systems. Findings – Among the main findings of the survey the paper highlights: the elimination of conflicts between individual systems with resources optimization; creation of added value to the business by eliminating several types of wastes; the integrated management of sustainability components in a global market; the improvement of partnerships with suppliers of goods and services; reducing the number of internal and external audits. Originality/value – This case study is one of the first Portuguese empirical researches about IMS-QES and the paper believes that it can be useful in the creation of a Portuguese guideline for integration, namely the Quality Management Systems; Environmental Management Systems and Occupational Health and Safety Management Systems among others.

Integration of Standardized Management Systems: A Dilemma?

Abstract: The growing proliferation of management systems standards (MSSs), and their individualized implementation, is a real problem faced by organizations. On the other hand, MSSs are aimed at improving efficiency and effectiveness of organizational responses in order to satisfy the requirements, needs and expectations of the stakeholders. Each organization has its own identity and this is an issue that cannot be neglected; hence, two possible approaches can be attended. First, continue with the implementation of individualized management systems (MSs); or, integrate the several MSSs versus related MSs into an integrated management system (IMS). Therefore, in this context, organizations are faced with a dilemma, as a result of the increasing proliferation and diversity of MSSs. This paper takes into account the knowledge gained through a case study conducted in the context of a Portuguese company and unveils some of the advantages and disadvantages of integration. A methodology is also proposed and presented to support organizations in developing and structuring the integration process of their individualized MSs, and consequently minimize problems that are generators of inefficiencies, value destruction and loss of competitiveness. The obtained results provide relevant information that can support Top Management decision in solving that dilemma and consequently promote a successful integration, including a better control of business risks associated to MSSs requirements and enhancing sustainable performance, considering the context in which organizations operate.

Virtual power producers integration into MASCEM

All over the world Distributed Generation is seen as a valuable help to get cleaner and more efficient electricity. Under this context distributed generators, owned by different decentralized players can provide a significant amount of the electricity generation. To get negotiation power and advantages of scale economy, these players can be aggregated giving place to a new concept: the Virtual Power Producer. Virtual Power Producers are multi-technology and multi-site heterogeneous entities. Virtual Power Producers should adopt organization and management methodologies so that they can make Distributed Generation a really profitable activity, able to participate in the market. In this paper we address the integration of Virtual Power Producers into an electricity market simulator –MASCEM – as a coalition of distributed producers.

Balancing market integration in MASCEM electricity market simulator

With the restructuring of the energy sector in industrialized countries there is an increased complexity in market players’ interactions along with emerging problems and new issues to be addressed. Decision support tools that facilitate the study and understanding of these markets are extremely useful to provide players with competitive advantage. In this context arises MASCEM, a multi-agent simulator for competitive electricity markets. It is essential to reinforce MASCEM with the ability to recreate electricity markets reality in the fullest possible extent, making it able to simulate as many types of markets models and players as possible. This paper presents the development of the Balancing Market in MASCEM. A key module to the study of competitive electricity markets, as it has well defined and distinct characteristics previously implemented.

Complex market integration in MASCEM electricity market simulator

The restructuring that the energy sector has suffered in industrialized countries originated a greater complexity in market players’ interactions, and thus new problems and issues to be addressed. Decision support tools that facilitate the study and understanding of these markets become extremely useful to provide players with competitive advantage. In this context arises MASCEM, a multi-agent system for simulating competitive electricity markets. To provide MASCEM with the capacity to recreate the electricity markets reality in the fullest possible extent, it is essential to make it able to simulate as many market models and player types as possible. This paper presents the development of the Complex Market in MASCEM. This module is fundamental to study competitive electricity markets, as it exhibits different characteristics from the already implemented market types.

The electric vehicle integration into the power system: an application to the portuguese case

Electric vehicles (EV) offer a great potential to address the integration of renewable energy sources (RES) in the power grid, and thus reduce the dependence on oil as well as the greenhouse gases (GHG) emissions. The high share of wind energy in the Portuguese energy mix expected for 2020 can led to eventual curtailment, especially during the winter when high levels of hydro generation occur. In this paper a methodology based on a unit commitment and economic dispatch is implemented, and a hydro-thermal dispatch is performed in order to evaluate the impact of the EVs integration into the grid. Results show that the considered 10 % penetration of EVs in the Portuguese fleet would increase load in 3 % and would not integrate a significant amount of wind energy because curtailment is already reduced in the absence of EVs. According to the results, the EV is charged mostly with thermal generation and the associated emissions are much higher than if they were calculated based on the generation mix.