Biochemical and molecular characterisation of the dyslipidaemia in Portugal

Tese de doutoramento, Biologia (Biologia de Sistemas), Universidade de Lisboa, Faculdade de Ciências, 2018Dyslipidaemia is one of the major modifiable independent risk factors for cardiovascular disease (CVD), with both genetic and environmental determinants. Although genetic risk factors are considered as non modifiable, their CVD-associated risk can be prevented if early identified. The correct and early identification of dyslipidaemia is important for a better patient management and could definitely contribute to CVD prevention. This thesis intended the most complete characterisation of the dyslipidaemia in the Portuguese population, both biochemically and molecularly. Reference values based on population-specific percentiles for lipid and lipoprotein biomarkers were provided for the first time in the Portuguese population, namely total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), apolipoprotein A1 (apoA1), apolipoprotein B (apoB), small, dense LDL-C (sdLDL-C), lipoprotein(a) [Lp(a)], as well apoB/apoA1 and sdLDL-C/LDL-C ratios, and non-HDL-C and remnant cholesterol. To our knowledge, the sdLDL-C percentiles were the first to be established in an European population. The percentiles were estimated through a rigorous methodology and compared with other population percentiles by a very visual and feasible method, showing relevant differences. These newly determined reference values for lipid biomarkers were then used to characterise the dyslipidaemia in our population, and can now be used in the clinic for a better patient care and management. More than cholesterol per se, our study highlighted apoB and sdLDL-C as important biomarkers to be used in dyslipidaemia evaluation. Individuals presenting extreme phenotypes were further investigated to assess possible monogenic causes, and three individuals were found to have familial hypercholesterolemia (FH), the most common genetic dyslipidaemia and one of the most common disorders that confer an increased cardiovascular risk. Finally, in an attempt to explore the causes for the FH phenotype, a polygenic risk score was validated for the first time in the Portuguese population. A total of 289 index cases were identified with monogenic FH and other causes for their dyslipidaemia, and also 100 were identified with polygenic hypercholesterolaemia, representing 53.21% of the cohort. From the monogenic causes, 91.35% have a mutation in LDLR, 4.84% in APOB, 1.04% in PCSK9 and 2.08% had mutations in phenocopies genes (LIPA, APOE, ALB), suggesting that all those monogenic and polygenic causes should be always investigated for a better patient identification. This study provided the most complete characterisation of the dyslipidaemia in the Portuguese population, and important evidences for dyslipidaemia evaluation has been produced. The results obtained have application, not only for Portugal or a south European populations, but also might have an worldwide utility for the dyslipidaemia assessment. Together, the results obtained provide useful information on an important cardiovascular risk factor and should help to tackle and identify at risk situations that need urgent measures.Fundação para a Ciência e a Tecnologia (SFRH/BD/52494/2014

A Predictive Model for the Parallel Processing of Digital Libraries

The computing world is facing the problem of a seemingly exponential increase in the amount of raw digital data, and the speed at which it is being collected, is eclipsing our ability to manage it manually. Combine this with the increasing expectations of a growing number of experienced computer users—including real-time access and a demand for expensive-to-process file types such as multimedia—and it is not hard to understand why managing data of this scale and providing timely access to useful information requires specialized algorithms, techniques, and software. Digital libraries are being used to help address these challenges. Drawing upon knowledge learned through traditional library science, digital libraries excel in providing structured user access to a wide variety of documents. They increasingly include tools for managing, moderating, and marking up these documents. Furthermore, they often feature phases where documents are independently processed and so can benefit from the application of parallel processing techniques—the focus of this thesis. Whether a digital library collection can benefit from parallel processing depends on considerations such as document type, processing cost per document, number of documents, and file-system input/output. To aid in deciding when to apply parallel processing techniques to digital libraries, this thesis explores the creation a model for predicting key outcomes of leveraging such techniques. It does so by implementing parallel processing in three distinct open-source digital library tools, undertaking experiments designed to measure key processing features (such as processing time versus number of compute nodes), and applying machine learning techniques to these features in order to derive a predictive model. The model created predicts parallel processing performance at 96% accuracy (adjusted r-squared) for a number of exemplar collection types. The result is a generally applicable tool for estimating the benefits of applying parallel processing to a wide range of digital collections

Personalized Search

As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS

The Influence of APOE Genotype on Lipid Droplet Dynamics

Excess lipid droplet (LD) accumulation is associated with several pathological states, including neurodegenerative disorders such as Alzheimer’s disease (AD). However, the mechanism(s) by which changes in LD composition and dynamics may contribute to the pathophysiology of AD remains unclear. Apolipoprotein E (ApoE) is a droplet-related protein with a common variant (ApoE4) that confers the largest increase in genetic risk for late-onset AD. Interestingly, ApoE4 is associated with both increased neuroinflammation and excess LD accumulation. This dissertation work seeks to quantitatively profile the lipid and protein composition of LDs between the ‘neutral’ ApoE3 and ‘risk’ ApoE4 isoforms, in order to gain insight into potential LD-driven contributions to AD pathogenesis. Targeted replacement mice expressing human ApoE3 or ApoE4 were injected with saline (control) or LPS (inflammatory stimulus) and after 24 hours, hepatic lipid droplets were isolated and droplet proteomes and lipidomes were analyzed. Quantitative proteomics showed that LD fractions from E4 mice are enriched for proteins involved in innate immunity, while E3 LDs are enriched for proteins involved in lipid ß-oxidation. Lipidomics revealed a shift in the distribution of glycerophospholipids in E4 LDs with an increase in multiple phosphatidylcholine (PC) species. There was also substantial overlap between LD proteins and AD-proteomes of human whole brain tissue. To translate these findings to the brain, primary microglia from the same strain of mice were exposed to exogenous lipid, inflammatory stimulation, necroptotic N2A cells (nN2A), or a combination of treatments to evaluate lipid droplet accumulation and impact on cell function. Microglia from ApoE4 mice accumulated more LDs at baseline, with exogenous OA, LPS stimulation, and nN2As as a percentage of E3 control across multiple experiments. E4 microglia also secreted significantly more cytokines (TNF, IL-1β, IL-10) than E3 microglia in the control, oleic acid, and nN2A treatment conditions. Interestingly, droplet inhibitors for ACAT and DGAT both decreased droplet accumulation in cells, but did not ameliorate the cytokine response. Finally, we have established a biobank of APOE genotyped peripheral blood mononuclear cells (PBMCs) from research participants. These easily accessible immune cells will serve as a highly translational model to understand LD dynamics as it relates to ApoE and AD risk. In summary, E4 cells accumulate more LDs compared to E3 under all conditions tested, while the proteomic profile of E4 LDs support the hypothesis that E4 expression increases inflammation under basal conditions. This increased LD formation in non-aged, non-diseased E4 cells may suggest preclinical dysfunction associated with the highest risk APOE genotype, and a better understanding of LD dynamics within these cells and their functional implications may provide novel targets to improve E4-related outcomes

Management of Scientific Images: An approach to the extraction, annotation and retrieval of figures in the field of High Energy Physics

El entorno de la información en la primera década del siglo XXI no tiene precedentes. Las barreras físicas que han limitado el acceso al conocimiento están desapareciendo a medida que los métodos tradicionales de acceso a información se reemplazan o se mejoran gracias al uso de sistemas basados en computador. Los sistemas digitales son capaces de gestionar colecciones mucho más grandes de documentos, confrontando a los usuarios de información con la avalancha de documentos asociados a su tópico de interés. Esta nueva situación ha creado un incentivo para el desarrollo de técnicas de minería de datos y la creación de motores de búsqueda más eficientes y capaces de limitar los resultados de búsqueda a un subconjunto reducido de los más relevantes. Sin embargo, la mayoría de los motores de búsqueda en la actualidad trabajan con descripciones textuales. Estas descripciones se pueden extraer o bien del contenido o a través de fuentes externas. La recuperación basada en el contenido no textual de documentos es un tema de investigación continua. En particular, la recuperación de imágenes y el desentrañar la información contenida en ellas están suscitando un gran interés en la comunidad científica. Las bibliotecas digitales se sitúan en una posición especial dentro de los sistemas que facilitan el acceso al conocimiento. Actúan como repositorios de documentos que comparten algunas características comunes (por ejemplo, pertenecer a la misma área de conocimiento o ser publicados por la misma institución) y como tales contienen documentos considerados de interés para un grupo particular de usuarios. Además, facilitan funcionalidades de recuperación sobre las colecciones gestionadas. Normalmente, las publicaciones científicas son las unidades más pequeñas gestionadas por las bibliotecas digitales científicas. Sin embargo, en el proceso de creación científica hay diferentes tipos de artefactos, entre otros: figuras y conjuntos de datos. Las figuras juegan un papel particularmente importante en el proceso de publicación científica. Representan los datos en una forma gráfica que nos permite mostrar patrones sobre grandes conjuntos de datos y transmitir ideas complejas de un modo fácilmente entendible. Los sistemas existentes para bibliotecas digitales facilitan el acceso a figuras, pero solo como parte de los ficheros sobre los que se serializa la publicación entera. El objetivo de esta tesis es proponer un conjunto de métodos ytécnicas que permitan transformar las figuras en productos de primera clase dentro del proceso de publicación científica, permitiendo que los investigadores puedan obtener el máximo beneficio a la hora de realizar búsquedas y revisiones de bibliografía existente. Los métodos y técnicas propuestos están orientados a facilitar la adquisición, anotación semántica y búsqueda de figuras contenidas en publicaciones científicas. Para demostrar la completitud de la investigación se han ilustrado las teorías propuestas mediante ejemplos en el campo de la Física de Partículas (también conocido como Física de Altas Energías). Para aquellos casos en los que se han necesitadoo en las figuras que aparecen con más frecuencia en las publicaciones de Física de Partículas: los gráficos científicos denominados en inglés con el término plots. Los prototipos que propuestas más detalladas han desarrollado para esta tesis se han integrado parcialmente dentro del software Invenio (1) para bibliotecas digitales, así como dentro de INSPIRE, una de las mayores bibliotecas digitales en Física de Partículas mantenida gracias a la colaboración de grandes laboratorios y centros de investigación como son el CERN, SLAC, DESY y Fermilab. 1). http://invenio-software.org

Use of an interactive iTextbook in a college nutrition course: effects on student comprehension, knowledge, application, and engagement

Colleges and universities have started to recognize the benefits of shifting from a professor-centered instructional paradigm that focuses on the dissemination of information to the learner to a student-centered paradigm. This latter paradigm is designed to provide an environment that enables the student to personalize, analyze, synthesize, and apply the information learned both inside and outside the classroom. Few would argue that such a paradigm shift would be best supported with the provision of a cost-effective, digitally interactive textbook that supports this type of personalized student-centered learning anywhere, anytime. Additionally, an Internet-based textbook would give the student more control of when, what, and how much he/she learns allowing for a potentially deeper exploration of content. This quantitative study was conducted to ascertain if the use of an instructionally designed, interactive college nutrition textbook (iTextbook) with embedded links to digitally-rich supporting graphics, videos, figures, and self-assessments would significantly improve students’ knowledge acquisition and application of the information as compared to the use of an identical print textbook and a static electronic textbook (eTextbook) in a Portable Digital Format (PDF). This study also looked at the time-on-task for reading the textbook content in each of the three formats. Lastly, this study assessed if students would prefer this type of instructionally designed, digitally-rich iTextbook format rather than reading the same information in a print textbook or a PDF eTextbook. The results of the study alluded that while there was a trend for a higher mean exam score measuring knowledge acquisition and application of the information read in the iTextbook group and a lower mean exam score in the eTextbook group, the scores among the three formats were not significantly different. The time-on-task spent by each group reading the textbook content was also similar among the three formats. However, the students reading the eTextbook spent a significantly longer amount of time reading the eTextbook compared to the iTextbook yet obtained the lowest average exam score among the three groups. In response to a final questionnaire, students significantly preferred the iTextbook rather than the print or eTextbook formats. College students reading a textbook in an iTextbook format obtained similar exam scores as those reading the same content in a print or eTextbook format. Compared to the iTextbook, the time-on-task was not only longer for those reading the eTextbook format but this format also produced a lower exam score measuring knowledge acquisition and application. The iTextbook format was more favorably received by college students than the print or eTextbooks formats

The mechanisms underlying seasonal timing of breeding : a multi-level approach using bi-directional genomic selection on timing of egg-laying

With climate change being one of the major threats to current biodiversity, it is essential for species to adapt sufficiently in order to survive. Some species adapt their phenology faster, in reaction to increasing temperatures, compared to others, resulting in mismatched timing. For many seasonal breeding avian species in temperate zones, such as the great tit, the reproductive period is short and coincides with warmer temperatures and increased food supplies required for successful rearing of offspring. Therefore, seasonal breeders time their reproductive cycle to the changing seasons in order to maximize reproductive success and offspring survival. With springs getting warmer earlier in the year, it is of importance for great tit females to start laying earlier to be able to raise their offspring in an optimal period (i.e. sufficient food abundance). However, females show large variation in timing of breeding, which lies in the underlying physiology: different cues are used and translated by a cascade of neuro-endocrine processes along the hypothalamic-pituitary-gonadal-liver (HPGL) axis into a laying date. Natural selection could act on this variation between females, but it is still unclear on which of the compartments (brain, ovary, liver) of the HPGL axis cues act and thus where the variation in timing between females arises. It is of importance to understand how the components of the physiological mechanism contribute to genetic variation in timing before one is able to understand how natural selection can act on timing of reproduction. In this thesis, the main aim was to explore the molecular basis of the physiological mechanisms underlying avian seasonal timing of breeding. A promising way to do this is by comparing (extremely) early and (extremely) late laying females. In Chapter 2, I describe a large-scale selection experiment, where we created selection lines for early and late egg-laying using genomic selection. In this chapter we show that genomic selection on a complex trait such as timing of breeding is possible, because we find that the early and late selection line birds differ genomically and that this difference increases over the generations. In addition, we find that F3 generation birds differ also phenotypically, with a significant average difference in egg-laying dates of ~10 days between selection lines. By housing pairs of the selection lines in climate-controlled aviaries and in outdoor aviaries for two consecutive years and in contrasting environments (either artificial or semi-natural), I was able to determine that temperature has a direct effect on timing of breeding instead of via food phenology and that females laid on average earlier in the warm environment (Chapter 3). Further, because we obtained two laying dates per female, we evaluated whether our selection on laying date also changed the birds’ phenotypic plasticity and found early selection line females to initiated egg laying consistently ~9 days earlier compared to late selection line females in outdoor aviaries, but no difference in the degree of plasticity. This suggests that while natural selection may lead to a change in phenotype in the average environment it is unlikely to result in a correlated response on the degree of plasticity in timing of breeding. I also aimed to determine whether individual differences in timing of breeding in females are reflected in differences in their molecular biology and if so where. In Chapter 4 we generated comprehensive RNA expression data from a set of three tissues important in the neuro-endocrine cascade (HPGL axis) underlying avian seasonal timing of breeding, from three different time points and from two temperature treatments and two selection lines for breeding time. Time was the strongest driver in this study, but we found an interesting interaction between time and temperature in hypothalamus, with several genes involved in circadian rhythms differentially expressed. Even though the hypothalamus has been considered the final integration point of environmental cues and guide top down hormonal regulation and in this way direct ovarian function to time breeding, we find evidence for downstream regulation of timing of breeding in Chapter 5. Differences in key reproductive candidate gene expression between phenotypically early and late laying females were found exclusively in the ovary and liver. This also suggests that adaptation in the HPGL axis to changing environments might be downstream. The effects of the environment need to be translated into gene transcription (Chapter 4 and 5), for which DNA methylation is a likely key regulator. Therefore, in Chapter 6, we investigated in great tits whether methylation changes were tissue-specific or tissue-general and whether such methylation changes were associated with expression changes within and between tissues. Overall, we found a positive correlation between changes in DNA methylation in red blood cells and liver, both genome-wide as well as for the sites within the promoter region or transcription start site (TSS) separately. Within the TSS of genes, hyper-methylation over time in red blood cells was highly correlated with a decrease in the expression of the associated gene in the ovary. Tissue-general changes in DNA methylation could potentially be informative for changes in gene expression in inaccessible tissues. I explored the molecular basis of the physiological mechanism underlying seasonal timing of breeding in an avian model species; the great tit. I looked at the phenotype, investigated candidate gene and genome-wide gene expression. In addition, we looked at DNA methylation (in relation to gene expression). The main conclusions are that (1) genomic selection is possible in wild populations, (2) temperature directly influences timing of breeding and (3) that timing of breeding is regulated downstream in the HPLG axis. However, we are only scratching the surface of this complex trait and further studies (also considering other ‘endo-phenotypes’ and their interactions, see Chapter 7) are necessary in order to make predictions about whether birds in general, and great tits specifically, will adapt to rapidly changing environments. </p