An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression

The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate gene expression databases. The study design consisted of two independent evaluations with 70 arrays from two different manufactured lots and used three human tissue sources as samples: placenta, brain and heart. Overall signal response was linear over three orders of magnitude and the sensitivity for any element was estimated to be 2 pg mRNA. The calculated coefficient of variation for differential expression for all non-differentiated elements was 12–14% across the entire signal range and did not vary with array batch or tissue source. The minimum detectable fold change for differential expression was 1.4. Accuracy, in terms of bias (observed minus expected differential expression ratio), was less than 1 part in 10 000 for all non-differentiated elements. The results presented in this report demonstrate the reproducible performance of the cDNA microarray technology platform and the methods provide a useful framework for evaluating other technologies that monitor changes in global mRNA expression.

Global modulation of cellular transcription by human cytomegalovirus is initiated by viral glycoprotein B

Human cytomegalovirus (HCMV) infection alters the expression of many cellular genes, including IFN-stimulated genes (ISGs) [Zhu, H., Cong, J.-P., Mamtora, G., Gingeras, T. & Shenk, T. (1998) Proc. Natl. Acad. Sci. USA 95, 14470–14475]. By using high-density cDNA microarrays, we show that the HCMV-regulated gene expression profile in fibroblasts does not differ substantially from the response generated by IFN. Furthermore, we identified the specific viral component triggering this response as the envelope glycoprotein B (gB). Cells treated with gB, but not other herpesviral glycoproteins, exhibited the same transcriptional profile as HCMV-infected cells. Thus, the interaction of gB with its as yet unidentified cellular receptor is the principal mechanism by which HCMV alters cellular gene expression early during infection. These findings highlight a pioneering paradigm for the consequences of virus–receptor interactions.

Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme.

Sin4 and Rgr1 proteins, previously shown by genetic studies to play both positive and negative roles in the transcriptional regulation of many genes, are identified here as components of mediator and RNA polymerase II holoenzyme complexes. Results with Sin4 deletion and Rgr1 truncation strains indicate the association of these proteins in a subcomplex comprising Sin4, Rgr1, Gal11, and a 50-kDa polypeptide. Taken together with the previous genetic evidence, our findings point to a role of the mediator in repression as well as in transcriptional activation.

Prediction of protein folding class using global description of amino acid sequence.

We present a method for predicting protein folding class based on global protein chain description and a voting process. Selection of the best descriptors was achieved by a computer-simulated neural network trained on a data base consisting of 83 folding classes. Protein-chain descriptors include overall composition, transition, and distribution of amino acid attributes, such as relative hydrophobicity, predicted secondary structure, and predicted solvent exposure. Cross-validation testing was performed on 15 of the largest classes. The test shows that proteins were assigned to the correct class (correct positive prediction) with an average accuracy of 71.7%, whereas the inverse prediction of proteins as not belonging to a particular class (correct negative prediction) was 90-95% accurate. When tested on 254 structures used in this study, the top two predictions contained the correct class in 91% of the cases.

A Novel Prediction Method for Early Recognition of Global Human Behaviour in Image Sequences

Human behaviour recognition has been, and still remains, a challenging problem that involves different areas of computational intelligence. The automated understanding of people activities from video sequences is an open research topic in which the computer vision and pattern recognition areas have made big efforts. In this paper, the problem is studied from a prediction point of view. We propose a novel method able to early detect behaviour using a small portion of the input, in addition to the capabilities of it to predict behaviour from new inputs. Specifically, we propose a predictive method based on a simple representation of trajectories of a person in the scene which allows a high level understanding of the global human behaviour. The representation of the trajectory is used as a descriptor of the activity of the individual. The descriptors are used as a cue of a classification stage for pattern recognition purposes. Classifiers are trained using the trajectory representation of the complete sequence. However, partial sequences are processed to evaluate the early prediction capabilities having a specific observation time of the scene. The experiments have been carried out using the three different dataset of the CAVIAR database taken into account the behaviour of an individual. Additionally, different classic classifiers have been used for experimentation in order to evaluate the robustness of the proposal. Results confirm the high accuracy of the proposal on the early recognition of people behaviours.

Strategic knowledge serendipity and arbitrage & intellectual venture capitalists: An emerging breed of knowledge entrepreneurs; and Part II: Global and Local (GloCal) knowledge logistics for innovation and competitiveness. ACES Working Papers, August 2009

Strategic Knowledge: While entrepreneurship may occur as a natural result of personal drive, it occurs most often, most robustly and is most sustainable in an environment designed to encourage it. Potential entrepreneurs become active entrepreneurs when the conditions are most supportive of their commercial opportunities and their business thus helping channel the two key qualities they exhibit as individuals obsessed maniacs and clairvoyant oracles (Carayannis, GWU Lectures, 2000-2005) and (Carayannis et at, 2003a) towards the generation of sustainable wealth. So far, entrepreneurial scholars who turn into intellectual venture capitalists by founding knowledge-driven companies remain one of the least explored specie in the territory of entrepreneurship. GloCal: The increasing engagement of firms within global knowledge and production networks and their ability to source knowledge globally as well as locally (GloCally), for the development of innovation capacities will shape the future of UK's knowledge resources and its role in the global economy. Practices such as off-shoring R&D activities are widely adopted, creating challenging, and not very well understood, issues related to cross-country and inter-firm knowledge and technology flows. We seek to address the internationalisation and networking of research and innovation activities, including the roles and strategies of enterprises, universities, research centres, governments in a cross-country and inter-sectoral way, to assess the impact and the implications for sustaining and enhancing the competitiveness of UK firms and other British knowledge producers and users.

Global and local (GloCal) knowledge logistics for innovation and competitiveness. ACES Working Papers, August 2010

The increasing engagement of firms within global knowledge and production networks and their ability to source knowledge globally as well as locally (GloCally), for the development of innovation capacities will shape the future of UK's knowledge resources and its role in the global economy. Practices such as off-shoring R&D activities are widely adopted, creating challenging, and not very well understood, issues related to cross-country and inter-firm knowledge and technology flows. We seek to address the internationalisation and networking of research and innovation activities, including the roles and strategies of enterprises, universities, research centres, governments in a cross-country and inter-sectoral way, to assess the impact and the implications for sustaining and enhancing the competitiveness of UK firms and other British knowledge producers and users.

Implementação do sistema GSM-R na rede ferroviária nacional : projeto-piloto

O GSM -R-Global System for Mobile Communications Railway começou o seu desenvolvimento em 1992 pela UIC (União Internacional dos Caminhos de ferro) com a criação do EIRENE (European lntegrated Railway Radio Enhanced Network) e constitui a componente de telecomunicações do sistema ERTMS - European Railway Trajjic Management System em conjunto com o ETCS - European Train Contrai System e o ATP­ Automatic Train Protection. O GSM-R baseia-se assim no GSM público com algumas adaptações e um conjunto de funcionalidades adicionais necessárias à sua utilização especificamente ferroviária. Em termos de rádio as principais diferenças relativamente à norma GSM, residem no facto de o sistema GSM-R suportar velocidades até aos 500 km/h, suportando handovers e seleção/re-seleção de células mais rápidos do que na norma do GSM original. Por outro lado, ao nível funcional e aplicacional, novas funções específicas da ferrovia foram consideradas, tais como por exemplo o controlo automático dos comboios e as chamadas de emergência. O GSM-R encontra-se já instalado em diversos países europeus. Em Portugal encontra-se instalado na Linha de Cascais e entre a Estação do Oriente e a Ponte 25 Abril, atualmente ainda numa fase experimental. O Estágio decorreu na empresa Refer Telecom - Serviços de Telecomunicações S.A. (RT) que é uma empresa do grupo REFER E.P.E. Mais concretamente, o estágio integrou-se nas atividades da Direção de Comunicações Móveis, pertencente à Direção de Coordenação de Sistemas Ferroviários da REFER Telecom. Neste Relatório de Estágio pretende-se fazer uma apresentação das atividades com participação e acompanhamento do estagiário, integrada numa descrição de todas as fases em que se dividiu a implementação do Projeto-piloto GSM-R em Portugal, desde a elaboração dos elementos técnicos para o concurso até à sua implementação no terreno. Pretende-se ainda enquadrar os principais aspetos relacionados com a utilização de algumas ferramentas de suporte à operação e à manutenção ao sistema GSM-R. Neste contexto são apresentados os conhecimentos teóricos e práticos adquiridos com a realização do estágio, incluindo o estudo necessário para compreender a arquitetura complexa do sistema GSM-R e tecnologias associadas, sobre a sua implementação no terreno e a operação e manutenção dos equipamentos, assim como sobre as áreas da contratação e da gestão de projetos. O Projeto-piloto GSM-R é um dos mais importantes projetos de telecomunicações ferroviárias instalado em Portugal nos últimos anos, pois visa projetar a ferrovia nacional para o futuro, com melhores comunicações em termos de qualidade, segurança, fiabilidade, interoperabilidade e sustentabilidade. Trata-se assim de uma importante experiência profissional e pessoal, muito enriquecedora, e que no seu conjunto abre novas perspectivas para o futuro.

Atmospheric histories and global emissions of halons H-1211 (CBrClF 2 ), H-1301 (CBrF 3 ), and H-2402 (CBrF 2 CBrF 2 )

We report ground-based atmospheric measurements and emission estimates for the halons H-1211 (CBrClF₂), H-1301 (CBrF₃), and H-2402 (CBrF₂CBrF₂) from the AGAGE (Advanced Global Atmospheric Gases Experiment) and the National Oceanic and Atmospheric Administration global networks. We also include results from archived air samples in canisters and from polar firn in both hemispheres, thereby deriving an atmospheric record of nearly nine decades (1930s to present). All three halons were absent from the atmosphere until ~1970, when their atmospheric burdens started to increase rapidly. In recent years H-1211 and H-2402 mole fractions have been declining, but H-1301 has continued to grow. High-frequency observations show continuing emissions of H-1211 and H-1301 near most AGAGE sites. For H-2402 the only emissions detected were derived from the region surrounding the Sea of Japan/East Sea. Based on our observations, we derive global emissions using two different inversion approaches. Emissions for H-1211 declined from a peak of 11 kt yr⁻¹ (late 1990s) to 3.9 kt yr⁻¹ at the end of our record (mean of 2013–2015), for H-1301 from 5.4 kt yr⁻¹ (late 1980s) to 1.6 kt yr⁻¹, and for H-2402 from 1.8 kt yr⁻¹ (late 1980s) to 0.38 kt yr⁻¹. Yearly summed halon emissions have decreased substantially; nevertheless, since 2000 they have accounted for ~30% of the emissions of all major anthropogenic ozone depletion substances, when weighted by ozone depletion potentials.

Global database of surface ocean particulate organic carbon export fluxes diagnosed from the 234Th technique

Through the processes of the biological pump, carbon is exported to the deep ocean in the form of dissolved and particulate organic matter. There are several ways by which downward export fluxes can be estimated. The great attraction of the 234Th technique is that its fundamental operation allows a downward flux rate to be determined from a single water column profile of thorium coupled to an estimate of POC/234Th ratio in sinking matter. We present a database of 723 estimates of organic carbon export from the surface ocean derived from the 234Th technique. Data were collected from tables in papers published between 1985 and 2013 only. We also present sampling dates, publication dates and sampling areas. Most of the open ocean Longhurst provinces are represented by several measurements. However, the Western Pacific, the Atlantic Arctic, South Pacific and the South Indian Ocean are not well represented. There is a variety of integration depths ranging from surface to 220m. Globally the fluxes ranged from -22 to 125 mmol of C/m**2/d. We believe that this database is important for providing new global estimate of the magnitude of the biological carbon pump.