Hui and Walter's latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data

Diagnostic test sensitivity and specificity are probabilistic estimates with far reaching implications for disease control, management and genetic studies. In the absence of 'gold standard' tests, traditional Bayesian latent class models may be used to assess diagnostic test accuracies through the comparison of two or more tests performed on the same groups of individuals. The aim of this study was to extend such models to estimate diagnostic test parameters and true cohort-specific prevalence, using disease surveillance data. The traditional Hui-Walter latent class methodology was extended to allow for features seen in such data, including (i) unrecorded data (i.e. data for a second test available only on a subset of the sampled population) and (ii) cohort-specific sensitivities and specificities. The model was applied with and without the modelling of conditional dependence between tests. The utility of the extended model was demonstrated through application to bovine tuberculosis surveillance data from Northern and the Republic of Ireland. Simulation coupled with re-sampling techniques, demonstrated that the extended model has good predictive power to estimate the diagnostic parameters and true herd-level prevalence from surveillance data. Our methodology can aid in the interpretation of disease surveillance data, and the results can potentially refine disease control strategies.

Knowledge Management Techniques to Augment Textual CBR (PhD Thesis)

The past decade had witnessed an unprecedented growth in the amount of available digital content, and its volume is expected to continue to grow the next few years. Unstructured text data generated from web and enterprise sources form a large fraction of such content. Many of these contain large volumes of reusable data such as solutions to frequently occurring problems, and general know-how that may be reused in appropriate contexts. In this work, we address issues around leveraging unstructured text data from sources as diverse as the web and the enterprise within the Case-based Reasoning framework. Case-based Reasoning (CBR) provides a framework and methodology for systematic reuse of historical knowledge that is available in the form of problemsolution
pairs, in solving new problems. Here, we consider possibilities of enhancing Textual CBR systems under three main themes: procurement, maintenance and retrieval. We adapt and build upon the stateof-the-art techniques from data mining and natural language processing in addressing various challenges therein. Under procurement, we investigate the problem of extracting cases (i.e., problem-solution pairs) from data sources such as incident/experience
reports. We develop case-base maintenance methods specifically tuned to text targeted towards retaining solutions such that the utility of the filtered case base in solving new problems is maximized. Further, we address the problem of query suggestions for textual case-bases and show that exploiting the problem-solution partition can enhance retrieval effectiveness by prioritizing more useful query suggestions. Additionally, we illustrate interpretable clustering as a tool to drill-down to domain specific text collections (since CBR systems are usually very domain specific) and develop techniques for improved similarity assessment in social media sources such as microblogs. Through extensive empirical evaluations, we illustrate the improvements that we are able to
achieve over the state-of-the-art methods for the respective tasks.

An interview with Manuel Salto-Tellez on diagnostic pathology: the future is morphomolecular

Professor Manuel Salto-Tellez of Queen’s University, Belfast, Northern Ireland is an expert histopathologist and molecular diagnostician. Professor Salto-Tellez is a lead investigator at the Northern Ireland Molecular Pathology Laboratory and also serves as a member of the Editorial Advisory Board for Expert Review of Molecular Diagnostics. In this interview, he proposes directions for the future of molecular pathology and molecular diagnostics, integrating all aspects of pathology toward a common goal.

Endoscopic tri-modal imaging improves detection of gastric intestinal metaplasia among a high-risk patient population in Singapore

BACKGROUND: Detection of pre-neoplastic gastric mucosal changes and early gastric cancer (EGC) by white-light endoscopy (WLE) is often difficult. In this study we investigated whether combined autofluorescence imaging (AFI) and narrow band imaging (NBI) can improve detection of pre-neoplastic lesions and early gastric cancer in high-risk patients.

PATIENTS AND METHODS: Chinese patients who were 50-years-old or above with dyspepsia were examined by both high-resolution WLE and combined AFI followed by NBI (AFI-NBI), consecutively in a prospective randomized cross-over setting, by two experienced endoscopists. The primary outcome was diagnostic ability of the two methods for patients with pre-neoplastic lesions such as intestinal metaplasia (IM) and mucosal atrophy.

RESULTS: Sixty-five patients were recruited. One patient with large advanced gastric cancer was found and excluded from the analysis. Among the remaining 64 patients, 38 (59%) had IM; of these, 26 (68%) were correctly identified by AFI-NBI (sensitivity 68%, specificity 23%) and only 13 (34%) by WLE (sensitivity 34%, specificity 65%). AFI-NBI detected more patients with IM than did WLE (p=0.011). Thirty-one patients (48%) had mucosal atrophy. Ten patients (32%) were identified by AFI-NBI (sensitivity 32%, specificity 79%) and four patients (13%) by WLE (sensitivity 13%, specificity 88%) (p=0.100). No dysplasia or EGC was found.

CONCLUSION: AFI-NBI identified significantly more patients with IM than did WLE. Our result warrants further studies to define the role of combined AFI-NBI endoscopy for detection of precancerous conditions.

Passive Intermodulation of Analog and Digital Signals on Transmission Lines with Distributed Nonlinearities: Modelling and Characterization

Passive intermodulation (PIM) often limits the performance of communication systems with analog and digitally-modulated signals and especially of systems supporting multiple carriers. Since the origins of the apparently multiple physical sources of nonlinearity causing PIM are not fully understood, the behavioral models are frequently used to describe the process of PIM generation. In this paper a polynomial model of memoryless nonlinearity is deduced from PIM measurements of a microstrip line with distributed nonlinearity with two-tone CW signals. The analytical model of nonlinearity is incorporated in Keysight Technology’s ADS simulator to evaluate the metrics of signal fidelity in the receive band for analog and digitally-modulated signals. PIM-induced distortion and cross-band interference with modulated signals are compared to those with two-tone CW signals. It is shown that conventional metrics can be applied to quantify the effect of distributed nonlinearities on signal fidelity. It is found that the two-tone CW test provides a worst-case estimate of cross-band interference for two-carrier modulated signals whereas with a three-carrier signal PIM interference in the receive band is noticeably overestimated. The simulated constellation diagrams for QPSK signals demonstrate that PIM interference exhibits the distinctive signatures of correlated distortion and this indicates that there are opportunities for mitigating PIM interference and that PIM interference cannot be treated as noise. One of the interesting results is that PIM distortion on a transmission line results in asymmetrical regrowth of output PIM interference for modulated signals.

On the application of optimal control techniques in lossy fieldbuses

The performance of real-time networks is under continuous improvement as a result of several trends in the digital world. However, these tendencies not only cause improvements, but also exacerbates a series of unideal aspects of real-time networks such as communication latency, jitter of the latency and packet drop rate. This Thesis focuses on the communication errors that appear on such realtime networks, from the point-of-view of automatic control. Specifically, it investigates the effects of packet drops in automatic control over fieldbuses, as well as the architectures and optimal techniques for their compensation. Firstly, a new approach to address the problems that rise in virtue of such packet drops, is proposed. This novel approach is based on the simultaneous transmission of several values in a single message. Such messages can be from sensor to controller, in which case they are comprised of several past sensor readings, or from controller to actuator in which case they are comprised of estimates of several future control values. A series of tests reveal the advantages of this approach. The above-explained approach is then expanded as to accommodate the techniques of contemporary optimal control. However, unlike the aforementioned approach, that deliberately does not send certain messages in order to make a more efficient use of network resources; in the second case, the techniques are used to reduce the effects of packet losses. After these two approaches that are based on data aggregation, it is also studied the optimal control in packet dropping fieldbuses, using generalized actuator output functions. This study ends with the development of a new optimal controller, as well as the function, among the generalized functions that dictate the actuator’s behaviour in the absence of a new control message, that leads to the optimal performance. The Thesis also presents a different line of research, related with the output oscillations that take place as a consequence of the use of classic co-design techniques of networked control. The proposed algorithm has the goal of allowing the execution of such classical co-design algorithms without causing an output oscillation that increases the value of the cost function. Such increases may, under certain circumstances, negate the advantages of the application of the classical co-design techniques. A yet another line of research, investigated algorithms, more efficient than contemporary ones, to generate task execution sequences that guarantee that at least a given number of activated jobs will be executed out of every set composed by a predetermined number of contiguous activations. This algorithm may, in the future, be applied to the generation of message transmission patterns in the above-mentioned techniques for the efficient use of network resources. The proposed task generation algorithm is better than its predecessors in the sense that it is capable of scheduling systems that cannot be scheduled by its predecessor algorithms. The Thesis also presents a mechanism that allows to perform multi-path routing in wireless sensor networks, while ensuring that no value will be counted in duplicate. Thereby, this technique improves the performance of wireless sensor networks, rendering them more suitable for control applications. As mentioned before, this Thesis is centered around techniques for the improvement of performance of distributed control systems in which several elements are connected through a fieldbus that may be subject to packet drops. The first three approaches are directly related to this topic, with the first two approaching the problem from an architectural standpoint, whereas the third one does so from more theoretical grounds. The fourth approach ensures that the approaches to this and similar problems that can be found in the literature that try to achieve goals similar to objectives of this Thesis, can do so without causing other problems that may invalidate the solutions in question. Then, the thesis presents an approach to the problem dealt with in it, which is centered in the efficient generation of the transmission patterns that are used in the aforementioned approaches.

Monitoring and all-optical signal processing techniques for transparent networks

Optical networks are under constant evolution. The growing demand for dynamism require devices that can accommodate different types of traffic. Thus the study of transparent optical networks arises. This approach makes optical networks more "elegant" , due to a more efficient use of network resources. In this thesis, the author proposes devices that intend to form alternative approaches both in the state of art of these same technologies both in the fitting of this technologies in transparent optical networks. Given that full transparency is difficult to achieve with current technology (perhaps with more developed optical computing this is possible), the author proposes techniques with different levels of transparency. On the topic of performance of optical networks, the author proposes two techniques for monitoring chromatic dispersion with different levels of transparency. In Chapter 3 the proposed technique seems to make more sense for long-haul optical transmission links and high transmission rates, not only due to its moderate complexity but also to its potential moderate/high cost. However it is proposed to several modulation formats, particularly those that have a protruding clock component. In Chapter 4 the transparency level was not tested for various modulation formats, however some transparency is achieved by not adding any electrical device after the receiver (other than an analog-digital converter). This allows that this technique can operate at high transmission rates in excess of 100 Gbit / s, if electro-optical asynchronous sampling is used before the optical receiver. Thus a low cost and low bandwidth photo-detector can be used. In chapter 5 is demonstrated a technique for simultaneously monitoring multiple impairments of the optical network by generating novel performance analysis diagrams and by use of artificial neural networks. In chapter 6 the author demonstrates an all-optical technique for controlling the optical state of polarization and an example of how all-optical signal processing can fully cooperate with optical performance monitoring.

Soft-computing techniques applied to artificial tissue temperature estimation

Tese dout., Engenharia electrónica e computação - Processamento de sinal, Universidade do Algarve, 2008

Diversifying medical imaging of breast lesions

Dissertação de mestrado, Engenharia Informática, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Machine learning techniques for music information retrieval

Tese de doutoramento, Informática (Engenharia Informática), Universidade de Lisboa, Faculdade de Ciências, 2015

Play it Again

Tese de doutoramento, Belas-Artes (Pintura), Universidade de Lisboa, Faculdade de Belas-Artes, 2016

A compositional scheduling framework for digital avionics systems

ARINC specification 653-2 describes the interface between application software and underlying middleware in a distributed real-time avionics system. The real-time workload in this system comprises of partitions, where each partition consists of one or more processes. Processes incur blocking and preemption overheads and can communicate with other processes in the system. In this work we develop compositional techniques for automated scheduling of such partitions and processes. At present, system designers manually schedule partitions based on interactions they have with the partition vendors. This approach is not only time consuming, but can also result in under utilization of resources. In contrast, the technique proposed in this paper is a principled approach for scheduling ARINC-653 partitions and therefore should facilitate system integration.

Controlo de conversores de potência genéricos por FPGA

Dissertação para obtenção do grau de Mestre em Engenharia Eletrotécnica Ramo de Automação e Eletrónica Industrial

Consultoria e formação em marketing digital para PME’s

Trabalho de Projeto apresentado ao Instituto de Contabilidade e Administração do Porto para a obtenção do grau de Mestre em Marketing Digital, sob orientação de Doutor Freitas Santos

Embolização das artérias prostáticas no tratamento da hiperplasia benigna da próstata : estudo anátomo-clínico

Resumo: A hiperplasia benigna da próstata (HBP) tem elevada prevalência nos homens entre os 50 e 79 anos de idade, sendo ubiquitária com o envelhecimento. Devido à significativa morbi-mortalidade associada aos tratamentos médicos e cirúrgicos currentemente disponíveis, são necessárias novas tecnologias para melhorar os resultados e minimizar o desconforto dos doentes. Recentemente, estudos preliminares de experimentação animal e em 3 doentes tratados, sugeriram a embolização arterial prostática selectiva (EAPS) como hipótese terapêutica para a HBP. Decidimos investigar se a EAPS poderia ser um procedimento bem sucedido no tratamento da HBP gravemente sintomática. Para tal realizámos um estudo anátomo-radiológico e clínico em 63 doentes com recurso a uma terapêutica inovadora minimamente invasiva guiada pela imagem. Avaliámos 126 hemipélvis com recurso a Angio-RM, Angio-TC e Angiografia Digital de Subtracção, com o intuito de definir os padrões básicos de bifurcação das artérias ilíacas internas até agora apenas descritos em estudos cadavéricos. Estudámos ainda o suprimento vascular arterial prostático, identificando: 1 as artérias prostáticas; 2 origem e direcção; 3 os ramos intra-prostáticos; 4 anastomoses com outras artérias. Em relação aos resultados anatómicos, identificámos 181 artérias prostáticas, já que em 43.7% das hemipélvis existiam dois pedículos arteriais prostáticos com origens independentes. A origem mais frequente foi a artéria pudenda interna (39.7%), seguida do tronco comum glúteo-pudendo (21%) e da artéria vesical superior (18.2%). Origens menos frequentes foram a artéria obturadora (12.1%), as artérias glúteas inferior (3.9%)ou superior (1.7%), ramos rectais provenientes da artéria mesentérica inferior (1.7%) e a artéria pudenda acessória (1.7%). Identificaram-se anastomoses com as artérias adjacentes em 57.9% dos casos: com a terminação da artéria pudenda interna (41.6%),artérias prostáticas contra-laterais (18.2%) e homo-laterais (11.7%), com ramos rectais (15.6%) e com artérias vesicais (12.9%). Em relação ao estudo clínico tratámos 63 doentes (idades compreendidas entre 52 - 82 anos, média 69.5 anos) com HBP gravemente sintomática refractária à terapêutica médica há mais de 6 meses. Foi possível avaliação após o tratamento em 37 doentes: média de seguimento de 4.7 meses (variando entre 1 e 12 meses). A EAPS unilateral foi possível em todos os doentes, com embolização bilateral em 73% dos casos. A embolização bilateral não foi possível em 27% dos casos devido a tortuosidade, alterações ateroescleróticas e pequeno calibre das artérias ilíacas e/ou prostáticas. Em média houve uma melhoria do International Prostate Symptom Score (IPSS) de 10.8 pontos, da QoL de 1.5 pontos e do Internationl Index of Erectile Function (IIEF) de 2.1 pontos. Houve uma redução média do PSA de 30% (2.4 ng/mL), um aumento do pico de fluxo urinário (Qmax) de 3.1 - 3.85 mL/s e uma redução média do volume prostático de 21% (18.5 mL). Registou-se uma complicação major: pequena área de isquémia da parede vesical tratada cirurgicamente. Em 75% dos doentes tratados obteve-se sucesso clínico com franca melhoria dos sintomas, enquanto 25% dos doentes foram considerados insucesso clínico por se ter registado uma fraca ou ausente melhoria sintomática após a embolização. Os restantes doentes tratados estão sob controlo evolutivo, pararam toda a medicação prostática, sem qualquer caso de disfunção sexual associada com o tratamento. Este trabalho constitui o primeiro estudo anatómico descritivo in vivo das artérias prostáticas, conseguido devido à utilização de técnicas de imagem nunca usadas para este fim. O uso clínico dos dados anatómicos acima referidos permitiu a implementação de técnicas de Radiologia de Intervenção no tratatamento de uma doença de elevada prevalência. ------------------------------- ABSTRACT: Benign prostatic hyperplasia (BPH) has high prevalence in men aged 50–79 years being ubiquitous with aging. Due to significant morbi-mortality associated with currently available medical and surgical treatments, there is the need for innovative technologies to continue to improve outcomes and minimize patient discomfort and morbidity. Recently, prostatic arterial embolization (PAE) was suggested as a treatmentoption for BPH based on preliminary results from animal studies and 3 treated patients. We decided to investigate if PAE might be a successful treatment option for severely symptomatic BPH patients. We performed a clinical and anatomical-radiological study in 63 patients with the use of an inovative image-guided minimally invasive technique. We evaluated 126 pelvic sides using Angio-MR or Angio-CT and Catheter Angiography before embolisation to treat symptomatic BPH. We aimed to define the main branching patterns of the male internal iliac arteries, so far only studied in the cadaver. We also evaluated the prostatic arterial supply, identifying: 1 the prostatic arteries; 2 origin and direction; 3 intra-prostatic branches; 4 anastomoses with surrounding arteries. Regarding the anatomical study we identified 181 prostatic arteries, because in 43.7% of pelvic sides 2 separate prostatic vascular pedicles were found. The most frequent origin was the internal pudendal artery (39.7%) with the common glutealpudendal trunk (21%) and superior vesical arteries (18.2%) the next commonest. Less frequent origins were the obturator artery (12.1%), the inferior (3.9%) or superior (1.7%) gluteal arteries, rectal branches from the inferior mesenteric artery (1.7%) and the accessory pudendal artery (1.7%). There were anastomoses with the surrounding arteries in 57.9% of cases: termination of the internal pudendal artery (41.6%), contralateral prostatic arteries (18.2%), same-side prostatic arteries (11.7%), rectal branches (15.6%), and vesical arteries (12.9%).Regarding the clinical study, we treated 63 patients aged 52–82 years (mean 69.5 years) who presented with symptomatic BPH refractory to medical treatment for at least 6 months. Follow-up evaluation (mean 4.7 months, range 1-12 months) was possible in 37 patients. PAE was achieved in all patients with bilateral embolization in 73%. In 27% PAE was performed unilaterally due to tortuosity, atherosclerotic changes and small size of iliac and prostatic arteries. There was a mean decrease in the IPSS of 10.8 points, a mean improvement in QoL of 1.5 points, and a mean increase in the sexual function score of 2.1 points. There was a mean PSA reduction of 30% (2.4 ng/mL), a Qmax increase of 3.1 to 3.85 mL/sec, and a mean prostate volume decrease of 21% (18.5 mL). There was one major complication: a small area of bladder wall ischemia treated by surgery. Overall, 75% of patients were considered clinical success with major improvement after PAE, while 25% of patients were considered clinical failure with little or no improvement after PAE. All remaining patients are under follow-up, stopped all prostatic medication, and reported no sexual dysfunction. This study is the first one to describe the radiological anatomy of the prostatic arteries, with the use of imaging techniques never used for this purpose before. The clinical use of the anatomical findings allowed the implementation of Interventional Radiology tehniques in the treatment of a disease with a high prevalence.