Discrete Conditional Phase-type Model Utilising a Multiclass Support Vector Machine for the Prediction of Retinopathy of Prematurity

Retinopathy of prematurity (ROP) is a rare disease in which retinal blood vessels of premature infants fail to develop normally, and is one of the major causes of childhood blindness throughout the world. The Discrete Conditional Phase-type (DC-Ph) model consists of two components, the conditional component measuring the inter-relationships between covariates and the survival component which models the survival distribution using a Coxian phase-type distribution. This paper expands the DC-Ph models by introducing a support vector machine (SVM), in the role of the conditional component. The SVM is capable of classifying multiple outcomes and is used to identify the infant's risk of developing ROP. Class imbalance makes predicting rare events difficult. A new class decomposition technique, which deals with the problem of multiclass imbalance, is introduced. Based on the SVM classification, the length of stay in the neonatal ward is modelled using a 5, 8 or 9 phase Coxian distribution.

Treatment of retinopathy of prematurity in Northern Ireland, 2000-2011: a population-based study

Purpose To evaluate the incidence of treatment-requiring retinopathy of prematurity (ROP) over a 12-year-period in Northern Ireland. Methods The medical records of all infants treated for ROP from January 2000 to December 2011were retrospectively reviewed and cross-referenced with the Neonatal Intensive Care Outcomes Research and Evaluation (NICORE) database. Results The Northern Ireland population data showed an increase in the number of live births from 2000 to 2011. The proportion of babies born with a birth weight <1501 g and/or <32 weeks’ gestational age remained constant (χ2 trend = 3.220, P = 0.0727), although the proportion of these babies who died prior to 42 weeks’ gestation decreased from 2000 to 2011 (P = 0.0196 using χ2 for trend = 5.445; P = 0.0354 using χ2 = 20.809). The prevalence of treatment-requiring ROP in these infants increased from 1.05% in 2000 to 5.78% in 2011 (P < 0.001 using χ2 trend = 16.309; P < 0.001 using χ2 = 31.378). Conclusions The present population-based study highlights that the incidence of treatment- requiring ROP is increasing in Northern Ireland. The increasing number of infants requiring treatment will need to be taken into consideration in the commissioning process for ROP services in Northern Ireland.

Mining Money: the generative capacities of scientific and legal knowledge practices in the making of resource economies

In 1997 a scandal associated with Bre-X, a junior mining firm, and its prospecting activities in Indonesia, exposed to public scrutiny the ways in which mineral exploration firms acquire, assess and report on scientific claims about the natural environment. At stake here was not just how investors understood the provisional nature of scientific knowledge, but also evidence of fraud. Contemporaneous mining scandals not only included the salting of cores, but also unreliable proprietary sample preparation and assay methods, mis-representations of visual field estimates as drilling results and ‘overly optimistic’ geological reports. This paper reports on initiatives taken in the wake of these scandals and prompted by the Mining Standards Task Force (TSE/OSC 1999). For regulators, mandated to increase investor confidence in Canada’s leading role within the global mining industry, efforts focused first and foremost upon identifying and removing sources of error and wilfulness within the production and circulation of scientific knowledge claims. A common goal cross-cutting these initiatives was ‘a faithful representation of nature’ (Daston and Galison 2010), however, as the paper argues, this was manifest in an assemblage of practices governed by distinct and rival regulative visions of science and the making of markets in claims about ‘nature’. These ‘practices of fidelity’, it is argued, can be consequential in shaping the spatial and temporal dynamics of the marketization of nature.

Retinopathy of prematurity: Causes, prevention and treatment

Advances in neonatal intensive care have improved survival rates in extremely premature an infant, which has led to an increase of Retinopathy of Prematurity (ROP) in the developed world. Left untreated, infants are at risk of developing strabismus, myopia, vitreous haemorrhage, vitreo-retinal fibrosis, retinal detachment, secondary angle closure glaucoma and ultimately complete loss of vision. The improvements in the understanding and treatment of ROP have been supported by seminal research, and its complexity is still being explored. However the importance of early screening and treatment is essential in the prevention and treatment of this disease. The following paper will examine the causes and treatments of ROP, as well as implications for future neonatal practice.

Mining biomedical information from scientific literature

The rapid evolution and proliferation of a world-wide computerized network, the Internet, resulted in an overwhelming and constantly growing amount of publicly available data and information, a fact that was also verified in biomedicine. However, the lack of structure of textual data inhibits its direct processing by computational solutions. Information extraction is the task of text mining that intends to automatically collect information from unstructured text data sources. The goal of the work described in this thesis was to build innovative solutions for biomedical information extraction from scientific literature, through the development of simple software artifacts for developers and biocurators, delivering more accurate, usable and faster results. We started by tackling named entity recognition - a crucial initial task - with the development of Gimli, a machine-learning-based solution that follows an incremental approach to optimize extracted linguistic characteristics for each concept type. Afterwards, Totum was built to harmonize concept names provided by heterogeneous systems, delivering a robust solution with improved performance results. Such approach takes advantage of heterogenous corpora to deliver cross-corpus harmonization that is not constrained to specific characteristics. Since previous solutions do not provide links to knowledge bases, Neji was built to streamline the development of complex and custom solutions for biomedical concept name recognition and normalization. This was achieved through a modular and flexible framework focused on speed and performance, integrating a large amount of processing modules optimized for the biomedical domain. To offer on-demand heterogenous biomedical concept identification, we developed BeCAS, a web application, service and widget. We also tackled relation mining by developing TrigNER, a machine-learning-based solution for biomedical event trigger recognition, which applies an automatic algorithm to obtain the best linguistic features and model parameters for each event type. Finally, in order to assist biocurators, Egas was developed to support rapid, interactive and real-time collaborative curation of biomedical documents, through manual and automatic in-line annotation of concepts and relations. Overall, the research work presented in this thesis contributed to a more accurate update of current biomedical knowledge bases, towards improved hypothesis generation and knowledge discovery.

Traditional algarvian distillats and liqueurs historic scientific aspects

All the evidence indicates that distillation and liqueurs preparation began in Monchique mountain because this place was pointed as a possible capital of the oldest population of Algarve and an important Arabic village (Barreto, 1972: 19). It was possible to find lots of vestiges like the alembic produced by Arabic population near the X century (Telo, 1988: 77). Traditionally the Algarvian people produce the Arbutus unedo L., fig, carob, grape distillates. At the same time they produce liqueur-using maceration of parts of plants or fruits in some kinds of distillates. Most of the work about Algarvian distillates started by studying the basic compounds of Arbutus unedo spirits by gas chromatography (GC) and mass spectrometry (MS) as well as other physical-chemical properties. In a second phase aged distillates were studied by their phenolic compounds evolution using high resolution liquid chromatography (HPLC). Volatile compounds of traditional liqueurs were identified by head space micro extraction solid phase (HE-SPME) and also analysed by gas chromatography mass spectrometry (GC-MS) and when possible confirmed with standards. Total phenols were determined by Folin-Ciocalteur method. Flavenoids were studied by high performance liquid chromatography (HPLC). Sensorial analysis was also done in every drink studies. The results showed that the arbutus distillate doesn’t present a high level of methanol according to the current legislation. The excesses of acidity or ethyl acetate present normal values when the fermentation is well done (Galego, et al. 1995: 341; Galego, et al. 1995: 685). During the aging process, the colour of spirits tend to become darker, the colour changes occurred more rapidly in the arbutus spirits located in cellars with higher temperatures (Galego, et al. 2001: 432). In the sensory evaluation of samples aged during 12 months into 50 L medium toasting level oak wood barrels, panellists considered that samples of arbutus spirit had too much wood flavour and they were not able to detect the characteristic aroma of arbutus fruit (Galego, et al., 2001: 183). Differences in liqueurs were observed using HS-SPME-GC, HS-SPME-GC-MS or HPLC analysis and this observation was confirmed by a sensorial panel (Galego, et al. 2003: 60).

Automatic classification of scientific records using the German Subject Heading Authority File (SWD)

The following paper deals with an automatic text classification method which does not require training documents. For this method the German Subject Heading Authority File (SWD), provided by the linked data service of the German National Library is used. Recently the SWD was enriched with notations of the Dewey Decimal Classification (DDC). In consequence it became possible to utilize the subject headings as textual representations for the notations of the DDC. Basically, we we derive the classification of a text from the classification of the words in the text given by the thesaurus. The method was tested by classifying 3826 OAI-Records from 7 different repositories. Mean reciprocal rank and recall were chosen as evaluation measure. Direct comparison to a machine learning method has shown that this method is definitely competitive. Thus we can conclude that the enriched version of the SWD provides high quality information with a broad coverage for classification of German scientific articles.

Enabling Scientific Workflow Sharing through Coarse-Grained Interoperability

E-scientists want to run their scientific experiments on Distributed Computing Infrastructures (DCI) to be able to access large pools of resources and services. To run experiments on these infrastructures requires specific expertise that e-scientists may not have. Workflows can hide resources and services as a virtualization layer providing a user interface that e-scientists can use. There are many workflow systems used by research communities but they are not interoperable. To learn a workflow system and create workflows in this workflow system may require significant efforts from e-scientists. Considering these efforts it is not reasonable to expect that research communities will learn new workflow systems if they want to run workflows developed in other workflow systems. The solution is to create workflow interoperability solutions to allow workflow sharing. The FP7 Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs (SHIWA) project developed two interoperability solutions to support workflow sharing: Coarse-Grained Interoperability (CGI) and Fine-Grained Interoperability (FGI). The project created the SHIWA Simulation Platform (SSP) to implement the Coarse-Grained Interoperability approach as a production-level service for research communities. The paper describes the CGI approach and how it enables sharing and combining existing workflows into complex applications and run them on Distributed Computing Infrastructures. The paper also outlines the architecture, components and usage scenarios of the simulation platform.

Transforming scientific information with everyday thinking: A social representations perspective

Cette thèse examine la circulation et l'intégration des informations scientifiques dans la pensée quotidienne d'après la théorie des représentations sociales (TRS). En tant qu'alternative aux approches traditionnelles de la communication de la science, les transformations survenant entre le discours scientifique et le discours de sens commun sont considérées comme adaptatives. Deux études sur la circulation des informations dans les media (études 1 et 2) montrent des variations dans les thèmes de discours exposés aux profanes, et parmi les discours de ceux-ci, en fonction de différentes sources. Ensuite, le processus d'ancrage dans le positionnement préalable envers la science est étudié, pour l'explication qu'il fournit de la réception et de la transmission d'informations scientifiques dans le sens commun. Les effets d'ancrage dans les attitudes et croyances préexistants sont reportés dans différents contextes de circulation des informations scientifiques (études 3 à 7), incluant des études de type corrélationnel, experimental et de terrain. Globalement, cette thèse procure des arguments en faveur de la pertinence de la TRS pour la recherche sur la communication de la science, et suggère des développements théoriques et méthodologiques pour ces deux domaines de recherche. Drawing on the social representations theory (SRT), this thesis examines the circulation and integration of scientific information into everyday thinking. As an alternative to the traditional approaches of science communication, it considers transformations between scientific and common-sense discourses as adaptive. Two studies, focused on the spreading of information into the media (Studies 1 and 2), show variations in the themes of discourses introduced to laypersons and in the themes among laypersons' discourses, according to different sources. Anchoring in prior positioning toward science is then studied for the explanation it provides on the reception and transmission of scientific information into common sense. Anchoring effects in prior attitudes and beliefs are reported in different contexts of circulation of scientific information (Studies 3 to 7) by using results from correlational, field, and experimental studies. Overall, this thesis provides arguments for the relevance of SRT in science communication research and suggests theoretical and methodological developments for both domains of research.