Automated tumour annotation and analysis for molecular pathology using TissueMark (R)

Objective: Molecular pathology relies on identifying anomalies using PCR or analysis of DNA/RNA. This is important in solid tumours where molecular stratification of patients define targeted treatment. These molecular biomarkers rely on examination of tumour, annotation for possible macro dissection/tumour cell enrichment and the estimation of % tumour. Manually marking up tumour is error prone. Method: We have developed a method for automated tumour mark-up and % cell calculations using image analysis called TissueMark® based on texture analysis for lung, colorectal and breast (cases=245, 100, 100 respectively). Pathologists marked slides for tumour and reviewed the automated analysis. A subset of slides was manually counted for tumour cells to provide a benchmark for automated image analysis. Results: There was a strong concordance between pathological and automated mark-up (100 % acceptance rate for macro-dissection). We also showed a strong concordance between manually/automatic drawn boundaries (median exclusion/inclusion error of 91.70 %/89 %). EGFR mutation analysis was precisely the same for manual and automated annotation-based macrodissection. The annotation accuracy rates in breast and colorectal cancer were 83 and 80 % respectively. Finally, region-based estimations of tumour percentage using image analysis showed significant correlation with actual cell counts. Conclusion: Image analysis can be used for macro-dissection to (i) annotate tissue for tumour and (ii) estimate the % tumour cells and represents an approach to standardising/improving molecular diagnostics.

Analysis of electric vehicle charging using the traditional generation expansion planning analysis tool WASP-IV

Electric vehicles (EV) are proposed as a measure to reduce greenhouse gas emissions in transport and support increased wind power penetration across modern power systems. Optimal benefits can only be achieved, if EVs are deployed effectively, so that the exhaust emissions are not substituted by additional emissions in the electricity sector, which can be implemented using Smart Grid controls. This research presents the results of an EV roll-out in the all island grid (AIG) in Ireland using the long term generation expansion planning model called the Wien Automatic System Planning IV (WASP-IV) tool to measure carbon dioxide emissions and changes in total energy. The model incorporates all generators and operational requirements while meeting environmental emissions, fuel availability and generator operational and maintenance constraints to optimize economic dispatch and unit commitment power dispatch. In the study three distinct scenarios are investigated base case, peak and off-peak charging to simulate the impacts of EV’s in the AIG up to 2025.

Musicologist-driven writer identification in early music manuscripts

Recent renewed interest in computational writer identification has resulted in an increased number of publications. In relation to historical musicology its application has so far been limited. One of the obstacles seems to be that the clarity of the images from the scans available for computational analysis is often not sufficient. In this paper, the use of the Hinge feature is proposed to avoid segmentation and staff-line removal for effective feature extraction from low quality scans. The use of an auto encoder in Hinge feature space is suggested as an alternative to staff-line removal by image processing, and their performance is compared. The result of the experiment shows an accuracy of 87 % for the dataset containing 84 writers’ samples, and superiority of our segmentation and staff-line removal free approach. Practical analysis on Bach’s autograph manuscript of the Well-Tempered Clavier II (Additional MS. 35021 in the British Library, London) is also presented and the extensive applicability of our approach is demonstrated.

Music for Mercer's: The Mercer's Hospital Music Collection and Charity Music in Eighteenth-Century Dublin

Account of benefit concerts in support of Mercer's Hospital, Dublin 1736-80 and an analysis of extant manuscript and printed music sources dating from c.1736-c.1771

The BRUTUS Automatic Cryptanalytic Framework: Testing CAESAR Authenticated Encryption Candidates for Weaknesses

This report summarizes our results from security analysis covering all 57 competitions for authenticated encryption: security, applicability, and robustness (CAESAR) first-round candidates and over 210 implementations. We have manually identified security issues with three candidates, two of which are more serious, and these ciphers have been withdrawn from the competition. We have developed a testing framework, BRUTUS, to facilitate automatic detection of simple security lapses and susceptible statistical structures across all ciphers. From this testing, we have security usage notes on four submissions and statistical notes on a further four. We highlight that some of the CAESAR algorithms pose an elevated risk if employed in real-life protocols due to a class of adaptive-chosen-plaintext attacks. Although authenticated encryption with associated data are often defined (and are best used) as discrete primitives that authenticate and transmit only complete messages, in practice, these algorithms are easily implemented in a fashion that outputs observable ciphertext data when the algorithm has not received all of the (attacker-controlled) plaintext. For an implementor, this strategy appears to offer seemingly harmless and compliant storage and latency advantages. If the algorithm uses the same state for secret keying information, encryption, and integrity protection, and the internal mixing permutation is not cryptographically strong, an attacker can exploit the ciphertext–plaintext feedback loop to reveal secret state information or even keying material. We conclude that the main advantages of exhaustive, automated cryptanalysis are that it acts as a very necessary sanity check for implementations and gives the cryptanalyst insights that can be used to focus more specific attack methods on given candidates.

Improving composite damage modelling through automatic placement of cohesive elements

Numerous experimental studies of damage in composite laminates have shown that intralaminar (in-plane) matrix cracks lead to interlaminar delamination (out-of-plane) at ply interfaces. The smearing of in-plane cracks over a volume, as a consequence of the use of continuum damage mechanics, does not always effectively capture the full extent of the interaction between the two failure mechanisms. A more accurate representation is obtained by adopting a discrete crack approach via the use of cohesive elements, for both in-plane and out-of-plane damage. The difficulty with cohesive elements is that their location must be determined a priori in order to generate the model; while ideally the position of the crack migration, and more generally the propagation path, should be obtained as part of the problem’s solution. With the aim of enhancing current modelling capabilities with truly predictive capabilities, a concept of automatic insertion of interface elements is utilized. The consideration of a simple traction criterion in relation to material strength, evaluated at each node of the model (or of the regions of the model where it is estimated cracks might form), allows for the determination of initial crack location and subsequent propagation by the insertion of cohesive elements during the course of the analysis. Several experimental results are modelled using the commercial package ABAQUS/Standard with an automatic insertion subroutine developed in this work, and the results are presented to demonstrate the capabilities of this technique.

Gesture interaction in music for instruments and electroacoustic sounds

Esta tese apresenta alguns aspectos em como o fenómeno do gesto musical pode ser compreendido na percepção da interação musical na música para instrumentos e sons electroacústicos. Através de exemplos de análise, classificação e categorização de diferentes relacões gestuais entre instrumentos e sons electroacústicos, pretende-se estabelecer modelos específicos de interacção que podem ser aplicados como método analítico assim como na composição musical. A pesquisa parte de uma variedade de definições sobre gesto musical na música em geral, na música contemporânea e na música electroacústica em particular, para subsequentemente incluir as relações entre dois eventos sonoros com características diferentes - o electroacústico e o instrumental. São essencialmente abordadas as relações entre gestos musicais através da análise de diversas características: altura, ritmo, timbre, dinâmica, características contrapontísticas, espectromorfológicas, semânticas e espaciais. O resultado da pesquisa teórica serviu de suporte à composição de diversas obras, onde estes aspectos são explorados sob o ponto de vista da criação musical.

Left ventricle functional analysis from coronary CT angiography

Coronary CT angiography is widely used in clinical practice for the assessment of coronary artery disease. Several studies have shown that the same exam can also be used to assess left ventricle (LV) function. LV function is usually evaluated using just the data from end-systolic and end-diastolic phases even though coronary CT angiography (CTA) provides data concerning multiple cardiac phases, along the cardiac cycle. This unused wealth of data, mostly due to its complexity and the lack of proper tools, has still to be explored in order to assess if further insight is possible regarding regional LV functional analysis. Furthermore, different parameters can be computed to characterize LV function and while some are well known by clinicians others still need to be evaluated concerning their value in clinical scenarios. The work presented in this thesis covers two steps towards extended use of CTA data: LV segmentation and functional analysis. A new semi-automatic segmentation method is presented to obtain LV data for all cardiac phases available in a CTA exam and a 3D editing tool was designed to allow users to fine tune the segmentations. Regarding segmentation evaluation, a methodology is proposed in order to help choose the similarity metrics to be used to compare segmentations. This methodology allows the detection of redundant measures that can be discarded. The evaluation was performed with the help of three experienced radiographers yielding low intraand inter-observer variability. In order to allow exploring the segmented data, several parameters characterizing global and regional LV function are computed for the available cardiac phases. The data thus obtained is shown using a set of visualizations allowing synchronized visual exploration. The main purpose is to provide means for clinicians to explore the data and gather insight over their meaning, as well as their correlation with each other and with diagnosis outcomes. Finally, an interactive method is proposed to help clinicians assess myocardial perfusion by providing automatic assignment of lesions, detected by clinicians, to a myocardial segment. This new approach has obtained positive feedback from clinicians and is not only an improvement over their current assessment method but also an important first step towards systematic validation of automatic myocardial perfusion assessment measures.

A ingerência do conhecimento explícito no conhecimento tácito: a técnica Alexander e a prática e ensino da flauta

O presente trabalho é o resultado duma investigação heurística sobre os efeitos do estudo da Técnica Alexander (TA) na prática e no ensino da flauta. Submeti-me a uma centena de aulas de Técnica Alexander e procedi a uma análise reflexiva da minha aprendizagem e prática individual e pedagógica, registando a sua evolução através da progressiva incorporação dos princípios e metodologias daquela técnica. A primeira parte descreve os princípios e procedimentos da TA enquadrando-a na problemática das relações entre conhecimento tácito e explícito, nos processos de controlo motor voluntário e involuntário, e na eficácia e eficiência dos automatismos neuromusculares. A segunda parte constitui a descrição e análise do processo transformador catalisado pelo estudo da TA: modificações na coordenação muscular; na técnica respiratória; no empunhar da flauta e na preparação para a emissão da primeira nota, e na relação entre o equilíbrio do instrumento e o movimento dos dedos. Vários procedimentos e exercícios desenvolvidos para a resolução de problemas pessoais são apresentados justificando a sua eficácia. A TA não proporciona apenas alterações na coordenação muscular mas pode modificar os processos mentais. Por isso alguns princípios para uma organização eficiente da prática são discutidos e concretizados nalguns exercícios que promovem maior variabilidade, alternância entre análise e integração e clareza na concepção do gesto técnico-musical. Por último, a evolução da minha abordagem pedagógica, incorporando procedimentos inspirados na TA e desenvolvidos ao longo da investigação são ilustrados com alguns alunos. A tese argumenta que a TA pode desempenhar um papel fundamental na melhoria do desempenho dum músico e revela-se uma ferramenta pedagógica que merece ser explorada mais sistematicamente num ensino mais baseado numa experimentação guiada que promova uma maior autoconsciência dos processos neuromusculares do que na instrução prescritiva e explícita.

Non-linear finite element analysis of thin composite structures

A non-conforming three-node triangular finite element with 18 degree of freedom, is used in conjugation with the Kirchhoff theory for the non-linear analysis of thin composite plate-shell structure. The formulation of the geometrically non-linear analysis is based on an updated Lagrangian formulation associated with the Newton-Raphson iterative technique, which incorporates an automatic arc-length control procedure.

Automatic processing of bidimensional images of ''omic'' expression blobs

In this work, a comprehensive review on automatic analysis of Proteomics and Genomics images is presented. Special emphasis is given to a particularly complex image produced by a technique called Two-Dimensional Gel Electrophoresis (2-DE), with thousands of spots (or blobs). Automatic methods for the detection, segmentation and matching of blob like features are discussed and proposed. In particular, a very robust procedure was achieved for processing 2-DE images, consisting mainly of two steps: a) A very trustworthy new approach for the automatic detection and segmentation of spots, based on the Watershed Transform, without any foreknowledge of spot shape or size, and without user intervention; b) A new method for spot matching, based on image registration, that performs well for either global or local distortions. The results of the proposed methods are compared to state-of-the-art academic and commercial products.

Analysis of underwater acoustic data via 3-D segmentation

The analysis of seabed structure is important in a wide variety of scientific and industrial applications. In this paper, underwater acoustic data produced by bottom-penetrating sonar (Topas) are analyzed using unsupervised volumetric segmentation, based on a three dimensional Gibbs-Markov model. The result is a concise and accurate description of the seabed, in which key structures are emphasized. This description is also very well suited to further operations, such as the enhancement and automatic recognition of important structures. Experimental results demonstrating the effectiveness of this approach are shown, using Topas data gathered in the North Sea off Horten, Norway.

Automatic recognition of seafloor features in sub-bottom profiles using eigenimages

Senior thesis written for Oceanography 445

On the development of an automatic voice pleasantness classification and intensity estimation system

In the last few years, the number of systems and devices that use voice based interaction has grown significantly. For a continued use of these systems, the interface must be reliable and pleasant in order to provide an optimal user experience. However there are currently very few studies that try to evaluate how pleasant is a voice from a perceptual point of view when the final application is a speech based interface. In this paper we present an objective definition for voice pleasantness based on the composition of a representative feature subset and a new automatic voice pleasantness classification and intensity estimation system. Our study is based on a database composed by European Portuguese female voices but the methodology can be extended to male voices or to other languages. In the objective performance evaluation the system achieved a 9.1% error rate for voice pleasantness classification and a 15.7% error rate for voice pleasantness intensity estimation.

Teacher placement report: investigation: action research project investigating methods for promoting creativity in double bass students attending a portuguese music school

The investigation which employed the action research method (qualitative analysis)was divided into four fases. In phases 1-3 the participants were six double bass students at Nossa Senhora do Cabo Music School. Pilot exercises in creativity were followed by broader and more ambitious projects. In phase 4 the techniques were tested and amplified during a summer course for twelve double bass students at Santa Cecilia College.