Utility of sarcoma-specific fusion gene analysis in paraffin-embedded material for routine diagnosis at a specialist centre.

AIMS: Diagnosis of soft tissue sarcomas can be difficult. It can be aided by detection of specific genetic aberrations in many cases. This study assessed the utility of a molecular genetics/cytogenetics service as part of the routine diagnostic service at the Royal Marsden Hospital. METHODS: A retrospective audit was performed over a 15-month period to evaluate the diagnostic usefulness for soft tissue sarcomas with translocations of fluorescence in situ hybridisation (FISH) and reverse-transcriptase PCR (RT-PCR) in paraffin-embedded (PE) material. Results were compared with histology, and evaluated. RESULTS: Molecular investigations were performed on PE material in 158 samples (total 194 RT-PCR and 174 FISH tests), of which 85 were referral cases. Synovial sarcoma, Ewing sarcoma and low-grade fibromyxoid sarcoma were the most commonly tested tumours. Myxoid liposarcoma showed the best histological and molecular concordance, and alveolar rhabdomyosarcoma showed the best agreement between methods. FISH had a higher sensitivity for detecting tumours (73%, compared with 59% for RT-PCR) with a better success rate than RT-PCR, although the latter was specific in identifying the partner gene for each fusion. In particular, referral blocks in which methods of tissue fixation and processing were not certain resulted in higher RT-PCR failure rates. CONCLUSIONS: FISH and RT-PCR on PE tissue are practical and effective ancillary tools in the diagnosis of soft tissue sarcomas. They are useful in confirming doubtful histological diagnoses and excluding malignant diagnoses. PCR is less sensitive than FISH, and the use of both techniques is optimal for maximising the detection rate of translocation-positive sarcomas.

IMPLEMENTING BACK PAIN TREATMENT PATHWAYS IN CLINICAL PRACTICE: QUALITATATIVE ANALYSIS OF STAKEHOLDER PERCEPTIONS

Background
Evidence-based practice advocates utilising best current research evidence, while reflecting patient preference and clinical expertise in decision making. Successfully incorporating this evidence into practice is a complex process. Based on recommendations of existing guidelines and systematic evidence reviews conducted using the GRADE approach, treatment pathways for common spinal pain disorders were developed.

Aims
The aim of this study was to identify important potential facilitators to the integration of these pathways into routine clinical practice.

Methods
A 22 person stakeholder group consisting of patient representatives, clinicians, researchers and members of relevant clinical interest groups took part in a series of moderated focus groups, followed up with individual, semi-structured interviews. Data were analysed using content analysis.

Results
Participants identified a number of issues which were categorized into broad themes. Common facilitators to implementation included continual education and synthesis of research evidence which is reflective of everyday practice; as well as the use of clear, unambiguous messages in recommendations. Meeting additional training needs in new or extended areas of practice was also recognized as an important factor. Different stakeholders identified specific areas which could be associated with successful uptake. Patients frequently defined early involvement in a shared decision making process as important. Clinicians identified case based examples and information on important prognostic indicators as useful tools to aiding decisions.

Conclusion
A number of potential implementation strategies were identified. Further work will examine the impact of these and other important factors on the integration of evidence-based treatment recommendations into clinical practice.

Dynalog: an automated dynamic analysis framework for characterizing android applications

Android is becoming ubiquitous and currently has the largest share of the mobile OS market with billions of application downloads from the official app market. It has also become the platform most targeted by mobile malware that are becoming more sophisticated to evade state-of-the-art detection approaches. Many Android malware families employ obfuscation techniques in order to avoid detection and this may defeat static analysis based approaches. Dynamic analysis on the other hand may be used to overcome this limitation. Hence in this paper we propose DynaLog, a dynamic analysis based framework for characterizing Android applications. The framework provides the capability to analyse the behaviour of applications based on an extensive number of dynamic features. It provides an automated platform for mass analysis and characterization of apps that is useful for quickly identifying and isolating malicious applications. The DynaLog framework leverages existing open source tools to extract and log high level behaviours, API calls, and critical events that can be used to explore the characteristics of an application, thus providing an extensible dynamic analysis platform for detecting Android malware. DynaLog is evaluated using real malware samples and clean applications demonstrating its capabilities for effective analysis and detection of malicious applications.

Fast and sensitive aflatoxin B1 and total aflatoxins ELISAs for analysis of peanuts, maize and feed ingredients

Aflatoxins are a group of carcinogenic compounds produced by Aspergillus fungi that can grow on different agricultural crops. Both acute and chronic exposure to these mycotoxins can cause serious illness. Due to the high occurrence of aflatoxins in crops worldwide fast and cost-effective analytical methods are required for the identification of contaminated agricultural commodities before they are processed into final products and placed on the market. In order to provide new tools for aflatoxin screening two prototype fast ELISA methods: one for the detection of aflatoxin B₁ and the other for total aflatoxins were developed. Seven monoclonal antibodies with unique high sensitivity and at the same time good cross-reactivity profiles were produced. The monoclonal antibodies were characterized and two antibodies showing IC₅₀ of 0.037 ng/mL and 0.031 ng/mL for aflatoxin B₁ were applied in simple and fast direct competitive ELISA tests. The methods were validated for peanut matrix as this crop is one of the most affected by aflatoxin contamination. The detection capabilities of aflatoxin B₁ and total aflatoxins ELISAs were 0.4 μg/kg and 0.3 μg/kg for aflatoxin B₁, respectively, which are one of the lowest reported values. Total aflatoxins ELISA was also validated for the detection of aflatoxins B₂, G₁ and G₂. The application of the developed tests was demonstrated by screening 32 peanut samples collected from the UK retailers. Total aflatoxins ELISA was further applied to analyse naturally contaminated maize porridge and distiller's dried grain with solubles samples and the results were correlated with these obtained by UHPLC-MS/MS method.

An innovative electroforming process for oil heated rotational moulding tools

Rotational moulding is a method to produce hollow plastic articles. Heating is normally carried out by placing the mould into a hot air oven where the plastic material in the mould is heated. The most common cooling media are water and forced air. Due to the inefficient nature of conventional hot air ovens most of the energy supplied by the oven does not go to heat the plastic and as a consequence the procedure has very long cycle times. Direct oil heating is an effective alternative in order to achieve better energy efficiency and cycle times. This research work has combined this technology with new innovative design of mould, applying the advantages of electroforming and rapid prototyping. Complex cavity geometries are manufactured by electroforming from a rapid prototyping mandrel. The approach involves conformal heating and cooling channels , where the oil flows into a parallel channel to the electroformed cavity (nickel or copper). Because of this the mould enables high temperature uniformity with direct heating and cooling of the electroformed shell, Uniform heating and cooling is important not only for good quality parts but also for good uniform wall thickness distribution in the rotationally moulded part. The experimental work with the manufactured prototype mould has enabled analysis of the thermal uniformity in the cavity, under different temperatures. Copyright © 2008 by ASME.

Computational approaches and tools for modeling biomass pyrolysis

Thesis (Ph.D.)--University of Washington, 2016-08

Mapping Learning and Game Mechanics for Serious Games Analysis in Engineering Education

In a world where students are increasing digitally tethered to powerful, ‘always on’ mobile devices, new models of engagement and approaches to teaching and learning are required from educators. Serious Games (SG) have proved to have instructional potential but there is still a lack of methodologies and tools not only for their design but also to support game analysis and assessment. This paper explores the use of SG to increase student engagement and retention. The development phase of the Circuit Warz game is presented to demonstrate how electronic engineering education can be radically reimagined to create immersive, highly engaging learning experiences that are problem-centered and pedagogically sound. The Learning Mechanics–Game Mechanics (LM-GM) framework for SG game analysis is introduced and its practical use in an educational game design scenario is shown as a case study.

Experimental study of forces and energies during shearing of steel sheet with angled tools

Shearing is a fast and inexpensive method to cut sheet metal that has been used since the beginning of the industrialism. Consequently, published experimental studies of shearing can be found from over a century back in time. Recent studies, however, are due to the availability of low cost digital computation power, mostly based on finite element simulations that guarantees quick results. Still, for validation of models and simulations, accurate experimental data is a requisite. When applicable, 2D models are in general desirable over 3D models because of advantages like low computation time and easy model formulation. Shearing of sheet metal with parallel tools is successfully modelled in 2D with a plane strain approximation, but with angled tools the approximation is less obvious. Therefore, plane strain approximations for shearing with angled tools were evaluated by shear experiments of high accuracy. Tool angle, tool clearance, and clamping of the sheet were varied in the experiments. The results showed that the measured forces in shearing with angled tools can be approximately calculated using force measurements from shearing with parallel tools. Shearing energy was introduced as a quantifiable measure of suitable tool clearance range. The effects of the shearing parameters on forces were in agreement with previous studies. Based on the agreement between calculations and experiments, analysis based on a plane strain assumption is considered applicable for angled tools with a small (up to 2 degrees) rake angle.

Adapting prospective structural analysis to strengthen sustainable management and capacity building in community-based natural resource management contexts

Local communities collectively managing common pool resources can play an important role in sustainable management, but they often lack the skills and context-specific tools required for such management. The complex dynamics of social-ecological systems (SES), the need for management capacities, and communities’ limited empowerment and participation skills present challenges for community-based natural resource management (CBNRM) strategies. We analyzed the applicability of prospective structural analysis (PSA), a strategic foresight tool, to support decision making and to foster sustainable management and capacity building in CBNRM contexts and the modifications necessary to use the tool in such contexts. By testing PSA in three SES in Colombia, Mexico, and Argentina, we gathered information regarding the potential of this tool and its adaptation requirements. The results suggest that the tool can be adapted to these contexts and contribute to fostering sustainable management and capacity building. It helped identify the systems’ dynamics, thus increasing the communities’ knowledge about their SES and informing the decision-making process. Additionally, it drove a learning process that both fostered empowerment and built participation skills. The process demanded both time and effort, and required external monitoring and facilitation, but community members could be trained to master it. Thus, we suggest that the PSA technique has the potential to strengthen CBNRM and that other initiatives could use it, but they must be aware of these requirements.

School Mobility for Children in Out-of-Home Placement: Incidence, Educational Outcomes, and Tools for Mitigation

Thesis (Ph.D.)--University of Washington, 2016-08

An overview on how failure analysis contributes to flight safety in the Portuguese Air Force

Failure analysis has been, throughout the years, a fundamental tool used in the aerospace sector, supporting assessments performed by sustainment and design engineers mainly related to failure modes and material suitability. The predicted service life of aircrafts often exceeds 40 years, and the design assured life rarely accounts for all in service loads and in service environmental menaces that aging aircrafts must deal with throughout their service lives. From the most conservative safe-life conceptual design approaches to the most recent on-condition based design approaches, assessing the condition and predicting the failure modes of components and materials are essential for the development of adequate preventive and corrective maintenance actions as well as for the accomplishment and optimization of scheduled maintenance programs of aircrafts. Moreover, as the operational conditions of aircrafts may vary significantly from operator to operator (especially in military aircraft), it is necessary to access if the defined maintenance programs are adequate to guarantee the continuous reliability and safe usage of the aircrafts, preventing catastrophic failures which bear significant maintenance and repair costs, and that may lead to the loss of human lives. Thus being, failure analysis and material investigations performed as part of aircraft accidents and incidents investigations arise as powerful tools of the utmost importance for safety assurance and cost reduction within the aeronautical and aerospace sectors. The Portuguese Air Force (PRTAF) has operated different aircrafts throughout its long existence, and in some cases, has operated a particular type of aircraft for more than 30 years, gathering a great amount of expertise in: assessing failure modes of the aircrafts materials; conducting aircrafts accidents and incidents investigations (sometimes with the participation of the aircraft manufacturers and/or other operators); and in the development of design and repair solutions for in-service related problems. This paper addresses several studies to support the thesis that failure analysis plays a key role in flight safety improvement within the PRTAF. It presents a short summary of developed

Analysis of surfaces for characterization of fungal burden: does it matter?

Objectives: Mycological contamination of occupational environments can be a result of fungal spores’ dispersion in the air and on surfaces. Therefore, it is very important to assess it in both types of the samples. In the present study we assessed fungal contamination in the air and in the surface samples to show relevance of surfaces sampling in complementing the results obtained in the air samples. Material and Methods: In total, 42 settings were assessed by the analysis of air and surfaces samples. The settings were divided into settings with a high fungal load (7 poultry farms and 7 pig farms, 3 cork industries, 3 waste management plants, 2 wastewater treatment plants and 1 horse stable) and a low fungal load (10 hospital canteens, 8 college canteens and 1 maternity hospital). In addition to culture-based methods, molecular tools were also applied to detect fungal burden in the settings with a higher fungal load. Results: From the 218 sampling sites, 140 (64.2%) presented different species in the examined surfaces when compared with the species identified in the air. A positive association in the high fungal load settings was found between the presence of different species in the air and surfaces. Wastewater treatment plants constituted the setting with the highest number of different species between the air and surface. Conclusions: We observed that surfaces sampling and application of molecular tools showed the same efficacy of species detection in high fungal load settings, corroborating the fact that surface sampling is crucial for a correct and complete analysis of occupational scenarios.

Features combination for art authentication studies: brushstroke and materials analysis of Amadeo de Souza-Cardoso

This work presents a tool to support authentication studies of paintings attributed to the modernist Portuguese artist Amadeo de Souza-Cardoso (1887-1918). The strategy adopted was to quantify and combine the information extracted from the analysis of the brushstroke with information on the pigments present in the paintings. The brushstroke analysis was performed combining Gabor filter and Scale Invariant Feature Transform. Hyperspectral imaging and elemental analysis were used to compare the materials in the painting with those present in a database of oil paint tubes used by the artist. The outputs of the tool are a quantitative indicator for authenticity, and a mapping image that indicates the areas where materials not coherent with Amadeo's palette were detected, if any. This output is a simple and effective way of assessing the results of the system. The method was tested in twelve paintings obtaining promising results.

Assisting digital forensic analysis via exploratory information visualisation

Background: Digital forensics is a rapidly expanding field, due to the continuing advances in computer technology and increases in data stage capabilities of devices. However, the tools supporting digital forensics investigations have not kept pace with this evolution, often leaving the investigator to analyse large volumes of textual data and rely heavily on their own intuition and experience. Aim: This research proposes that given the ability of information visualisation to provide an end user with an intuitive way to rapidly analyse large volumes of complex data, such approached could be applied to digital forensics datasets. Such methods will be investigated; supported by a review of literature regarding the use of such techniques in other fields. The hypothesis of this research body is that by utilising exploratory information visualisation techniques in the form of a tool to support digital forensic investigations, gains in investigative effectiveness can be realised. Method:To test the hypothesis, this research examines three different case studies which look at different forms of information visualisation and their implementation with a digital forensic dataset. Two of these case studies take the form of prototype tools developed by the researcher, and one case study utilises a tool created by a third party research group. A pilot study by the researcher is conducted on these cases, with the strengths and weaknesses of each being drawn into the next case study. The culmination of these case studies is a prototype tool which was developed to resemble a timeline visualisation of the user behaviour on a device. This tool was subjected to an experiment involving a class of university digital forensics students who were given a number of questions about a synthetic digital forensic dataset. Approximately half were given the prototype tool, named Insight, to use, and the others given a common open-source tool. The assessed metrics included: how long the participants took to complete all tasks, how accurate their answers to the tasks were, and how easy the participants found the tasks to complete. They were also asked for their feedback at multiple points throughout the task. Results:The results showed that there was a statistically significant increase in accuracy for one of the six tasks for the participants using the Insight prototype tool. Participants also found completing two of the six tasks significantly easier when using the prototype tool. There were no statistically significant different difference between the completion times of both participant groups. There were no statistically significant differences in the accuracy of participant answers for five of the six tasks. Conclusions: The results from this body of research show that there is evidence to suggest that there is the potential for gains in investigative effectiveness when information visualisation techniques are applied to a digital forensic dataset. Specifically, in some scenarios, the investigator can draw conclusions which are more accurate than those drawn when using primarily textual tools. There is also evidence so suggest that the investigators found these conclusions to be reached significantly more easily when using a tool with a visual format. None of the scenarios led to the investigators being at a significant disadvantage in terms of accuracy or usability when using the prototype visual tool over the textual tool. It is noted that this research did not show that the use of information visualisation techniques leads to any statistically significant difference in the time taken to complete a digital forensics investigation.

Performance of protective factors assessment in risk prediction for adults: systematic review and meta-analysis

Protective factors are neglected in risk assessment in adult psychiatric and criminal justice populations. This review investigated the predictive efficacy of selected tools that assess protective factors. Five databases were searched using comprehensive terms for records up to June 2014, resulting in 17 studies (n = 2,198). Results were combined in a multilevel meta-analysis using the R (R Core Team, R: A Language and Environment for Statistical Computing, Vienna, Austria: R Foundation for Statistical Computing, 2015) metafor package (Viechtbauer, Journal of Statistical Software, 2010, 36, 1). Prediction of outcomes was poor relative to a reference category of violent offending, with the exception of prediction of discharge from secure units. There were no significant differences between the predictive efficacy of risk scales, protective scales, and summary judgments. Protective factor assessment may be clinically useful, but more development is required. Claims that use of these tools is therapeutically beneficial require testing.