Microscopia multimodal prática: registro automático de imagens de microscopia ótica e de microscopia eletrônica de varredura

A discriminação de fases que são praticamente indistinguíveis ao microscópio ótico de luz refletida ou ao microscópio eletrônico de varredura (MEV) é um dos problemas clássicos da microscopia de minérios. Com o objetivo de resolver este problema vem sendo recentemente empregada a técnica de microscopia colocalizada, que consiste na junção de duas modalidades de microscopia, microscopia ótica e microscopia eletrônica de varredura. O objetivo da técnica é fornecer uma imagem de microscopia multimodal, tornando possível a identificação, em amostras de minerais, de fases que não seriam distinguíveis com o uso de uma única modalidade, superando assim as limitações individuais dos dois sistemas. O método de registro até então disponível na literatura para a fusão das imagens de microscopia ótica e de microscopia eletrônica de varredura é um procedimento trabalhoso e extremamente dependente da interação do operador, uma vez que envolve a calibração do sistema com uma malha padrão a cada rotina de aquisição de imagens. Por esse motivo a técnica existente não é prática. Este trabalho propõe uma metodologia para automatizar o processo de registro de imagens de microscopia ótica e de microscopia eletrônica de varredura de maneira a aperfeiçoar e simplificar o uso da técnica de microscopia colocalizada. O método proposto pode ser subdividido em dois procedimentos: obtenção da transformação e registro das imagens com uso desta transformação. A obtenção da transformação envolve, primeiramente, o pré-processamento dos pares de forma a executar um registro grosseiro entre as imagens de cada par. Em seguida, são obtidos pontos homólogos, nas imagens óticas e de MEV. Para tal, foram utilizados dois métodos, o primeiro desenvolvido com base no algoritmo SIFT e o segundo definido a partir da varredura pelo máximo valor do coeficiente de correlação. Na etapa seguinte é calculada a transformação. Foram empregadas duas abordagens distintas: a média ponderada local (LWM) e os mínimos quadrados ponderados com polinômios ortogonais (MQPPO). O LWM recebe como entradas os chamados pseudo-homólogos, pontos que são forçadamente distribuídos de forma regular na imagem de referência, e que revelam, na imagem a ser registrada, os deslocamentos locais relativos entre as imagens. Tais pseudo-homólogos podem ser obtidos tanto pelo SIFT como pelo método do coeficiente de correlação. Por outro lado, o MQPPO recebe um conjunto de pontos com a distribuição natural. A análise dos registro de imagens obtidos empregou como métrica o valor da correlação entre as imagens obtidas. Observou-se que com o uso das variantes propostas SIFT-LWM e SIFT-Correlação foram obtidos resultados ligeiramente superiores aos do método com a malha padrão e LWM. Assim, a proposta, além de reduzir drasticamente a intervenção do operador, ainda possibilitou resultados mais precisos. Por outro lado, o método baseado na transformação fornecida pelos mínimos quadrados ponderados com polinômios ortogonais mostrou resultados inferiores aos produzidos pelo método que faz uso da malha padrão.

Negotiating the boundaries between home and work practices: The case of home-workers

When people work from home, the domains of home and work are co-located, often under one roof. Home-workers have to cope with the meeting of two practices that have traditionally been physically separated. In light of this, we need to understand: how do people who work from home negotiate the boundaries between their home and work practices? What kinds of boundaries do people construct? How do boundaries affect the relationship between home and work as domains? What kinds of boundaries are available to home-workers? Are home-workers in charge of their boundaries or do they co-create them with others? How does this position home-workers in their domains? In order to address these questions, I analysed a variety of data, including newspaper columns, online forum discussions, interviews, and personal diary entries, using a discourse analytic approach that lends itself to issues of positioning. Current literature clashes over whether home-workers are in control of their boundaries, and over the relationship between home and work that arises out of boundary negotiations, i.e. whether home and work are dichotomous or layered. I seek to contribute to boundary theory by adopting a practice theory stance (Wenger, 1998) to guide my analysis. By viewing home and work as practices, I show that boundary negotiations depend on how home-workers are positioned, e.g. if they are positioned as peripheral in a domain, they lack influence over boundaries. I demonstrate that home and work constitute a number of different practices, rather than a rigid dichotomy, and that the way home and work are related are not the same for all home-workers. The application of practice concepts further shows how relationships between practices are created. The contribution of this work is a reconceptualisation of current boundary theory away from individual and cognitive notions (Nippert-Eng, 1996) into the realm of positioning.

Valuing maternity care: a comparison of stated preference methods with an application to cost-benefit analysis

This research investigates whether a reconfiguration of maternity services, which collocates consultant- and midwifery-led care, reflects demand and value for money in Ireland. Qualitative and quantitative research is undertaken to investigate demand and an economic evaluation is performed to evaluate the costs and benefits of the different models of care. Qualitative research is undertaken to identify women’s motivations when choosing place of delivery. These data are further used to inform two stated preference techniques: a discrete choice experiment (DCE) and contingent valuation method (CVM). These are employed to identify women’s strengths of preferences for different features of care (DCE) and estimate women’s willingness to pay for maternity care (CVM), which is used to inform a cost-benefit analysis (CBA) on consultant- and midwifery-led care. The qualitative research suggests women do not have a clear preference for consultant or midwifery-led care, but rather a hybrid model of care which closely resembles the Domiciliary Care In and Out of Hospital (DOMINO) scheme. Women’s primary concern during care is safety, meaning women would only utilise midwifery-led care when co-located with consultant-led care. The DCE also finds women’s preferred package of care closely mirrors the DOMINO scheme with 39% of women expected to utilise this service. Consultant- and midwifery-led care would then be utilised by 34% and 27% of women, respectively. The CVM supports this hierarchy of preferences where consultant-led care is consistently valued more than midwifery-led care – women are willing to pay €956.03 for consultant-led care and €808.33 for midwifery-led care. A package of care for a woman availing of consultant- and midwifery-led care is estimated to cost €1,102.72 and €682.49, respectively. The CBA suggests both models of care are cost-beneficial and should be pursued in Ireland. This reconfiguration of maternity services would maximise women’s utility, while fulfilling important objectives of key government policy.

A cross-site, comparative effectiveness study of an integrated HIV and substance use treatment program.

Co-occurrence of HIV and substance abuse is associated with poor outcomes for HIV-related health and substance use. Integration of substance use and medical care holds promise for HIV patients, yet few integrated treatment models have been reported. Most of the reported models lack data on treatment outcomes in diverse settings. This study examined the substance use outcomes of an integrated treatment model for patients with both HIV and substance use at three different clinics. Sites differed by type and degree of integration, with one integrated academic medical center, one co-located academic medical center, and one co-located community health center. Participants (n=286) received integrated substance use and HIV treatment for 12 months and were interviewed at 6-month intervals. We used linear generalized estimating equation regression analysis to examine changes in Addiction Severity Index (ASI) alcohol and drug severity scores. To test whether our treatment was differentially effective across sites, we compared a full model including site by time point interaction terms to a reduced model including only site fixed effects. Alcohol severity scores decreased significantly at 6 and 12 months. Drug severity scores decreased significantly at 12 months. Once baseline severity variation was incorporated into the model, there was no evidence of variation in alcohol or drug score changes by site. Substance use outcomes did not differ by age, gender, income, or race. This integrated treatment model offers an option for treating diverse patients with HIV and substance use in a variety of clinic settings. Studies with control groups are needed to confirm these findings.

Review of the technology and reliability issues arising as optical interconnects migrate onto the circuit board

Light has the greatest information carrying potential of all the perceivable interconnect mediums; consequently, optical fiber interconnects rapidly replaced copper in telecommunications networks, providing bandwidth capacity far in excess of its predecessors. As a result the modern telecommunications infrastructure has evolved into a global mesh of optical networks with VCSEL’s (Vertical Cavity Surface Emitting Lasers) dominating the short-link markets, predominately due to their low-cost. This cost benefit of VCSELs has allowed optical interconnects to again replace bandwidth limited copper as bottlenecks appear on VSR (Very Short Reach) interconnects between co-located equipment inside the CO (Central-Office). Spurred by the successful deployment in the VSR domain and in response to both intra-board backplane applications and inter-board requirements to extend the bandwidth between IC’s (Integrated Circuits), current research is migrating optical links toward board level USR (Ultra Short Reach) interconnects. Whilst reconfigurable Free Space Optical Interconnect (FSOI) are an option, they are complicated by precise line-of-sight alignment conditions hence benefits exist in developing guided wave technologies, which have been classified into three generations. First and second generation technologies are based upon optical fibers and are both capable of providing a suitable platform for intra-board applications. However, to allow component assembly, an integral requirement for inter-board applications, 3rd generation Opto-Electrical Circuit Boards (OECB’s) containing embedded waveguides are desirable. Currently, the greatest challenge preventing the deployment of OECB’s is achieving the out-of-plane coupling to SMT devices. With the most suitable low-cost platform being to integrate the optics into the OECB manufacturing process, several research avenues are being explored although none to date have demonstrated sufficient coupling performance. Once in place, the OECB assemblies will generate new reliability issues such as assembly configurations, manufacturing tolerances, and hermetic requirements that will also require development before total off-chip photonic interconnection can truly be achieved

Characterization of Inter-Body Interference in Context Aware Body Area Networking (CABAN)

The characterization and understanding of body to body communication channels is a pivotal step in the development of emerging wireless applications such as ad-hoc personnel localisation and context aware body area networks (CABAN). The latter is a recent innovation where the inherent mobility of body area networks can be used to improve the coexistence of multiple co-located BAN users. Rather than simply accepting reductions in communication performance, sensed changes in inter-network co-channel interference levels may facilitate intelligent inter-networking; for example merging or splitting with other BANs that remain in the same domain. This paper investigates the inter-body interference using controlled measurements of the full mesh interconnectivity between two ambulatory BANs operating in the same environment at 2.45 GHz. Each of the twelve network nodes reported received signal strength to allow for the creation of carrier to interference ratio time series with an overall entire mesh sampling period of 54 ms. The results indicate that even with two mobile networks, it is possible to identify the onset of co-channel interference as the BAN users move towards each other and, similarly, the transition to more favourable physical layer channel conditions as they move apart. © 2011 IEEE.

Multi-access communication system in a highly reverberant environment

We investigate by numerical EM simulation the potential communication channel capacity of a reverberant environment using the time reversal approach, excited at 2.4 GHz by ON-OFF keyed RF pulse excitation. It is shown that approximately 725 1.25MHz propagation channels can be allocated with the cavity contains a 4×4 ? or 1×1 ? LOS obstruction positioned between the transceiver antenna and the time reversal unit. Furthermore the results show that two co-located transceiver dipoles separated by a spacing of 3?/4 can successfully resolve a 10ns pulse. Our findings suggest that different independent channels with identical operating frequency can be realized in an enclosed environment such as ventilation duct or underground tunnel. This suggests that there is a possibility of implementing a parallel channel radio link with the minimum inter-antenna spacing of 3?/4 between the transceivers in a rich multipath environment. © 2012 IEEE.

Ambiguous Devices

Developed and performed in collaboration with Tom Davis (Bournemouth University), the work explores notions of presence and absence, technologically mediated communication and audience perception through the staging of ambiguous but repeatable performative interactions taking place on a co-located but distributed musical instrument. Public performances and installations include: CCRMA, Stanford University (2012); NIME conference, University of Michigan (2012); SARC, Queen's University Belfast (2013); INTIME symposium, Coventry University (2013); RE-NEW digital arts festival, Copenhagen (2013).

Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

BACKGROUND: Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis.

METHODS: In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer.

RESULTS: We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs.

CONCLUSION: To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors.

Signal Reliability Improvement Using Selection Combining Based Macro-Diversity for Off-Body Communications At 868 MHz

This paper investigates the potential improvement in signal reliability for outdoor short-range off-body communications channels at 868 MHz using the macro-diversity offered by multiple co-located base stations. In this study, ten identical hypothetical base stations were positioned equidistantly around the perimeter of a rectangle of length 6.67 m and width 3.3 m. A body worn node was placed on the central chest region of an adult male. Five scenarios, each considering different user trajectories, were then analyzed to test the efficacy of using macro-diversity when the desired link is subject to shadowing caused by the human body. A number of selection combining based macro-diversity configurations consisting of four and then ten base stations were considered. It was found that using a macro-diversity system consisting of four base stations (or equivalently signal branches), a maximum diversity gain of 22.5 dB could be obtained while implementing a 10-base station setup this figure could be improved to 25.2 dB.

Simultaneous Measurements of the Channel Response for Multiple Eavesdroppers Operating in the Vicinity of a Body Area Network at 2.45 GHz

Channel randomness can be exploited to generate secret keys. However, to ensure secrecy, it is necessary that the channel response of any eavesdropping party remain sufficiently de-correlated with that of the legitimate users'. In this paper, we investigate whether such de-correlation occurs for a body area network (BAN) operating in an indoor environment at 2.45 GHz. The hypothetical BAN configuration consisted of two legitimate transceivers, one situated on the user's left wrist and the other on the user's waist. The eavesdroppers were positioned in either a co-located or distributed manner in the area surrounding the BAN user. Using the simultaneous channel response measured at the legitimate BAN nodes and the eavesdropper positions for stationary and mobile scenarios, we analyze the localized correlation coefficient. This allows us to determine if it is possible to generate secret keys in the presence of multiple eavesdroppers in an indoor environment. Our experimental results show that although channel reciprocity was observed for both the stationary and the mobile scenarios, a higher de-correlation between the legitimate users' channels was observed for the stationary case. This indicates that mobile scenarios are better suited for secret key generation.

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.

Interference cancellation for distributed wireless systems

O tema principal desta tese é o problema de cancelamento de interferência para sistemas multi-utilizador, com antenas distribuídas. Como tal, ao iniciar, uma visão geral das principais propriedades de um sistema de antenas distribuídas é apresentada. Esta descrição inclui o estudo analítico do impacto da ligação, dos utilizadores do sistema, a mais antenas distribuídas. Durante essa análise é demonstrado que a propriedade mais importante do sistema para obtenção do ganho máximo, através da ligação de mais antenas de transmissão, é a simetria espacial e que os utilizadores nas fronteiras das células são os mais bene ciados. Tais resultados são comprovados através de simulação. O problema de cancelamento de interferência multi-utilizador é considerado tanto para o caso unidimensional (i.e. sem codi cação) como para o multidimensional (i.e. com codi cação). Para o caso unidimensional um algoritmo de pré-codi cação não-linear é proposto e avaliado, tendo como objectivo a minimização da taxa de erro de bit. Tanto o caso de portadora única como o de multipla-portadora são abordados, bem como o cenário de antenas colocadas e distribuidas. É demonstrado que o esquema proposto pode ser visto como uma extensão do bem conhecido esquema de zeros forçados, cuja desempenho é provado ser um limite inferior para o esquema generalizado. O algoritmo é avaliado, para diferentes cenários, através de simulação, a qual indica desempenho perto do óptimo, com baixa complexidade. Para o caso multi-dimensional um esquema para efectuar "dirty paper coding" binário, tendo como base códigos de dupla camada é proposto. No desenvolvimento deste esquema, a compressão com perdas de informação, é considerada como um subproblema. Resultados de simulação indicam transmissão dedigna proxima do limite de Shannon.

Comparisons of Fungal Spore Distributions Using Air Sampling at Worcester, England (2006-2010)

This study determined annual and monthly fluctuations in concentration of 20 fungal genera. The selection of taxa was made based upon their high frequency in the air as well as their well-known allergenic properties. Air samples were collected using a spore trap of Hirst design at an urban site where the trap continuously worked throughout a 5-year survey. Weather data were acquired from a meteorological station co-located with the air sampler. Influence of several meteorological parameters was then examined to reveal species–environment interactions and the potential location of fungal spore sources within the urban area. The maximum monthly sum of mean daily spore concentration varied between genera, and the earliest peaks were recorded for Pleospora sp. in April and Ustilago sp. in June. However, the majority of investigated spore types occurred in the greatest concentrations between August and September. Out of the 20 studied taxa, the most dominant genus was Cladosporium sp., which exceeded an allergenic threshold of 3000 s m-3 40 times during very rainy years and twice as much during dry years. A Spearman’s rank test showed that statistically significant (p B 0.05) relationships between spore concentration and weather parameters were mainly rs B 0.50. Potential sources of spores at Worcester were likely to be localised outside the city area.