HEP-Frame: A software engineered framework to aid the development and efficient multicore execution of scientific code

This work was supported by FCT (Fundação para a Ciência e Tecnologia) within Project Scope (UID/CEC/00319/2013), by LIP (Laboratório de Instrumentação e Física Experimental de Partículas) and by Project Search-ON2 (NORTE-07-0162- FEDER-000086), co-funded by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte), under the National Strategic Reference Framework, through the European Regional Development Fund.

Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Development of procedures for the design, optimization and manufacturing of customized orthopaedic and trauma implants: Geometrical/anatomical modelling from 3D medical imaging

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

EuroDia: a beta-cell gene expression resource.

Type 2 diabetes mellitus (T2DM) is a major disease affecting nearly 280 million people worldwide. Whilst the pathophysiological mechanisms leading to disease are poorly understood, dysfunction of the insulin-producing pancreatic beta-cells is key event for disease development. Monitoring the gene expression profiles of pancreatic beta-cells under several genetic or chemical perturbations has shed light on genes and pathways involved in T2DM. The EuroDia database has been established to build a unique collection of gene expression measurements performed on beta-cells of three organisms, namely human, mouse and rat. The Gene Expression Data Analysis Interface (GEDAI) has been developed to support this database. The quality of each dataset is assessed by a series of quality control procedures to detect putative hybridization outliers. The system integrates a web interface to several standard analysis functions from R/Bioconductor to identify differentially expressed genes and pathways. It also allows the combination of multiple experiments performed on different array platforms of the same technology. The design of this system enables each user to rapidly design a custom analysis pipeline and thus produce their own list of genes and pathways. Raw and normalized data can be downloaded for each experiment. The flexible engine of this database (GEDAI) is currently used to handle gene expression data from several laboratory-run projects dealing with different organisms and platforms. Database URL: http://eurodia.vital-it.ch.

Analysing the innovation process in the EU Integrated Programme, ISAFRUIT

ISAFRUIT is an integrated European Union Project focussed on increasing fruit consumption as a means to improve human health, through evaluating the fruit chain and addressing bottlenecks therein.The innovations which are being developed throughout the ISAFRUIT Project have been analysed to determine both the success factors and the obstacles in reaching the commercialisation stage. Only 9.58% of the deliverables planned within the Project were focussed on developing technological innovations.There is evidence, however, of successes in the development of new innovations arising from the ISAFRUIT Project, with several other potential innovations in the pipeline. Of the technologies identified, 67% are still at the “invention stage”; that is, the stage prior to bridging the so-called “valley of death”, the stage between an invention and an innovation. Those which are considered to have moved over the “valley of death” either had industry partners included in the Project, or had consulted with industry to ensure that the technology was relevant, or met a recognised industry need. Many of the technologies which made less progress did not have the same interactions with industry. A number of other issues were identified which prevented further progress towards innovation. The need for scientists to publish scientific papers, both for their career pathways and to increase their chances of future funding, was identified as one issue, although the filing of patents is now becoming more accepted and recognised. The patenting system is considered complex by many scientists and is not well-understood. Finally, agreements between partners on the sharing of intellectual property rights can cause a delay in the innovation process.

Annotating the human genome

2 Abstract2.1 En françaisLe séquençage du génome humain est un pré-requis fondamental à la compréhension de la biologie de l'être humain. Ce projet achevé, les scientifiques ont dû faire face à une tâche aussi importante, comprendre cette suite de 3 milliards de lettres qui compose notre génome. Le consortium ENCODE (ENCyclopedia Of Dna Elements) fût formé comme une suite logique au projet du génome humain. Son rôle est d'identifier tous les éléments fonctionnels de notre génome incluant les régions transcrites, les sites d'attachement des facteurs de transcription, les sites hypersensibles à la DNAse I ainsi que les marqueurs de modification des histones. Dans le cadre de ma thèse doctorale, j'ai participé à 2 sous-projets d'ENCODE. En premier lieu, j'ai eu la tâche de développer et d'optimiser une technique de validation expérimentale à haut rendement de modèles de gènes qui m'a permis d'estimer la qualité de la plus récente annotation manuelle. Ce nouveau processus de validation est bien plus efficace que la technique RNAseq qui est actuellement en train de devenir la norme. Cette technique basée sur la RT-PCR, m'a notamment permis de découvrir de nouveaux exons dans 10% des régions interrogées. En second lieu j'ai participé à une étude ayant pour but d'identifier les extrémités de tous les gènes des chromosomes humains 21 et 22. Cette étude à permis l'identification à large échelle de transcrits chimères comportant des séquences provenant de deux gènes distincts pouvant être à une grande distance l'un de autre.2.2 In EnglishThe completion of the human genome sequence js the prerequisite to fully understand the biology of human beings. This project achieved, scientists had to face another challenging task, understanding the meaning of the 3 billion letters composing this genome. As a logical continuation of the human genome project, the ENCODE (ENCyclopedia Of DNA Elements) consortium was formed with the aim of annotating all its functional elements. These elements include transcribed regions, transcription binding sites, DNAse I hypersensitive sites and histone modification marks. In the frame of my PhD thesis, I was involved in two sub-projects of ENCODE. Firstly I developed and optimized an high throughput method to validate gene models, which allowed me to assess the quality of the most recent manually-curated annotation. This novel experimental validation pipeline is extremely effective, far more so than transcriptome profiling through RNA sequencing, which is becoming the norm. This RT-PCR-seq targeted-approach is likewise particularly efficient in identifying novel exons, as we discovered about 10% of loci with unannotated exons. Secondly, I participated to a study aiming to identify the gene boundaries of all genes in the human chromosome 21 and 22. This study led to the identification of chimeric transcripts that are composed of sequences coming form two distinct genes that can be map far away from each other.

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort.

BACKGROUND: Superinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy. To investigate the importance of this potential route to drug resistance, we developed a bioinformatics pipeline to detect superinfection from routinely collected genotyping data, and assessed whether superinfection contributed to increased drug resistance in a large European cohort of viremic, drug treated patients. METHODS: We used sequence data from routine genotypic tests spanning the protease and partial reverse transcriptase regions in the Virolab and EuResist databases that collated data from five European countries. Superinfection was indicated when sequences of a patient failed to cluster together in phylogenetic trees constructed with selected sets of control sequences. A subset of the indicated cases was validated by re-sequencing pol and env regions from the original samples. RESULTS: 4425 patients had at least two sequences in the database, with a total of 13816 distinct sequence entries (of which 86% belonged to subtype B). We identified 107 patients with phylogenetic evidence for superinfection. In 14 of these cases, we analyzed newly amplified sequences from the original samples for validation purposes: only 2 cases were verified as superinfections in the repeated analyses, the other 12 cases turned out to involve sample or sequence misidentification. Resistance to drugs used at the time of strain replacement did not change in these two patients. A third case could not be validated by re-sequencing, but was supported as superinfection by an intermediate sequence with high degenerate base pair count within the time frame of strain switching. Drug resistance increased in this single patient. CONCLUSIONS: Routine genotyping data are informative for the detection of HIV superinfection; however, most cases of non-monophyletic clustering in patient phylogenies arise from sample or sequence mix-up rather than from superinfection, which emphasizes the importance of validation. Non-transient superinfection was rare in our mainly treatment experienced cohort, and we found a single case of possible transmitted drug resistance by this route. We therefore conclude that in our large cohort, superinfection with drug resistant HIV did not compromise the efficiency of antiretroviral treatment.

Underwater Gigamosaicing

El procés de fusió de dues o més imatges de la mateixa escena en una d'única i més gran és conegut com a Image Mosaicing. Un cop finalitzat el procés de construcció d'un mosaic, els límits entre les imatges són habitualment visibles, degut a imprecisions en els registres fotomètric i geomètric. L'Image Blending és l'etapa del procediment de mosaicing a la que aquests artefactes són minimitzats o suprimits. Existeixen diverses metodologies a la literatura que tracten aquests problemes, però la majoria es troben orientades a la creació de panorames terrestres, imatges artístiques d'alta resolució o altres aplicacions a les quals el posicionament de la càmera o l'adquisició de les imatges no són etapes rellevants. El treball amb imatges subaquàtiques presenta desafiaments importants, degut a la presència d'scattering (reflexions de partícules en suspensió) i atenuació de la llum i a condicions físiques extremes a milers de metres de profunditat, amb control limitat dels sistemes d'adquisició i la utilització de tecnologia d'alt cost. Imatges amb il·luminació artificial similar, sense llum global com la oferta pel sol, han de ser unides sense mostrar una unió perceptible. Les imatges adquirides a gran profunditat presenten una qualitat altament depenent de la profunditat, i la seva degradació amb aquest factor és molt rellevant. El principal objectiu del treball és presentar dels principals problemes de la imatge subaquàtica, seleccionar les estratègies més adequades i tractar tota la seqüència adquisició-procesament-visualització del procés. Els resultats obtinguts demostren que la solució desenvolupada, basada en una Estratègia de Selecció de Límit Òptim, Fusió en el Domini del Gradient a les regions comunes i Emfatització Adaptativa d'Imatges amb baix nivell de detall permet obtenir uns resultats amb una alta qualitat. També s'ha proposat una estratègia, amb possibilitat d'implementació paral·lela, que permet processar mosaics de kilòmetres d'extensió amb resolució de centímetres per píxel.

Isolation of genetic mutation leading to abnormal phenotype in human through ultra-high-throughput sequencing (UHTS)

The introduction of Next Generation Sequencing (NGS) facilitated the task of localizing DNA variation and identifying the genetic cause of yet unsolved Mendelian disorders. Using Whole Exome Capture method and NGS, we identified the causative genetic aberration responsible for a number of monogenic disorders previously undetermined. Due to the novelty of the NGS method we benchmarked different algorithms to assess their merits and defects. This allowed us to establish a pipeline that we successfully used to pinpoint genes responsible for a form of West's syndrome, a Complex Intellectual Disability syndrome associated with patellar dislocation and celiac disease, and correcting some erroneous molecular diagnosis of Alport's syndrome in a Saudi Arabian family.

Alzheimer's Disease Biomarkers, 2009

This report gives a comprehensive and up-to-date review of Alzheimer's disease biomarkers. Recent years have seen significant advances in this field. Whilst considerable effort has focused on A�_ and tau related markers, a substantial number of other molecules have been identified, that may offer new opportunities.This Report : Identifies 60 candidate Alzheimer's (AD) biomarkers and their associated studies. Of these, 49 are single species or single parameters, 7 are combinations or panels and 4 involve the measurement of two species or parameters or their ratios. These include proteins (n=34), genes (n=11), image-based parameters (n=7), small molecules (n=3), proteins + genes (n=2) and others (n=3). Of these, 30 (50%) relate to species identified in CSF and 19 (32%) were found in the blood. These candidate may be classified on the basis of their diagnostic utility, namely those which i) may allow AD to be detected when the disease has developed (48 of 75†= 64%), ii) may allow early detection of AD (18 of 75† = 24%) and iii) may allow AD to be predicted before the disease has begun to develop (9 of 75†= 12%). † Note: Of these, 11 were linked to two or more of these capabilities (e.g. allowed both early-stage detection as well as diagnosis after the disease has developed).Biomarkers: AD biomarkers identified in this report show significant diversity, however of the 60 described, 18 (30%) are associated with amyloid beta (A�_) and 9 (15%) relate to Tau. The remainder of the biomarkers (just over half) fall into a number of different groups. Of these, some are associated with other hypotheses on the pathogenesis of AD however the vast majority are individually unique and not obviously linked with other markers. Analysis and discussion presented in this report includes summaries of the studies and clinical trials that have lead to the identification of these markers. Where it has been calculated, diagnostic sensitivity, specificity and the capacity of these markers to differentiate patients with suspected AD from healthy controls and individuals believed to be suffering from other neurodegenerative conditions, have been indicated. These findings are discussed in relation to existing hypotheses on the pathogenesis of the AD and the current drug development pipeline. Many uncertainties remain in relation to the pathogenesis of AD, in diagnosing and treating the disease and many of the studies carried out to identify disease markers are at an early stage and will require confirmation through larger and longer investigations. Nevertheless, significant advances in the identification of AD biomarkers have now been made. Moreover, whilst much of the research on AD biomarkers has focused on amyloid and tau related species, it is evident that a substantial number of other species may provide important opportunities.Purpose of Report: To provide a comprehensive review of important and recently discovered candidate biomarkers of AD, in particular those with potential to reliably detect the disease or with utility in clinical development, drug repurposing, in studies of the pathogenesis and in monitoring drug response and the course of the disease. Other key goals were to identify markers that support current pipeline developments, indicate new potential drug targets or which advance understanding of the pathogenesis of this disease.Drug Repurposing: Studies of the pathogenesis of AD have identified aberrant changes in a number of other disease areas including inflammation, diabetes, oxidative stress, lipid metabolism and others. These findings have prompted studies to evaluate some existing approved drugs to treat AD. This report identifies studies of 9 established drug classes currently being investigated for potential repurposing.Alzheimer’s Disease: In 2005, the global prevalence of dementia was estimated at 25 million, with more than 4 million new cases occurring each year. It is also calculated that the number of people affected will double every 20 years, to 80 million by 2040, if a cure is not found. More than 50% of dementia cases are due to AD. Today, approximately 5 million individuals in the US suffer from AD, representing one in eight people over the age of 65. Direct and indirect costs of AD and other forms of dementia in the US are around $150 billion annually. Worldwide, costs for dementia care are estimated at $315 billion annually. Despite significant research into this debilitating and ultimately fatal disease, advances in the development of diagnostic tests for AD and moreover, effective treatments, remain elusive.Background: Alzheimer's disease is the most common cause of dementia, yet its clinical diagnosis remains uncertain until an eventual post-mortem histopathology examination is carried out. Currently, therapy for patients with Alzheimer disease only treats the symptoms; however, it is anticipated that new disease-modifying drugs will soon become available. The urgency for new and effective treatments for AD is matched by the need for new tests to detect and diagnose the condition. Uncertainties in the diagnosis of AD mean that the disease is often undiagnosed and under treated. Moreover, it is clear that clinical confirmation of AD, using cognitive tests, can only be made after substantial neuronal cell loss has occurred; a process that may have taken place over many years. Poor response to current therapies may therefore, in part, reflect the fact that such treatments are generally commenced only after neuronal damage has occurred. The absence of tests to detect or diagnose presymptomatic AD also means that there is no standard that can be applied to validate experimental findings (e.g. in drug discovery) without performing lengthy studies, and eventual confirmation by autopsy.These limitations are focusing considerable effort on the identification of biomarkers that advance understanding of the pathogenesis of AD and how the disease can be diagnosed in its early stages and treated. It is hoped that developments in these areas will help physicians to detect AD and guide therapy before the first signs of neuronal damage appears. The last 5-10 years have seen substantial research into the pathogenesis of AD and this has lead to the identification of a substantial number of AD biomarkers, which offer important insights into this disease. This report brings together the latest advances in the identification of AD biomarkers and analyses the opportunities they offer in drug R&D and diagnostics.��

Histology-driven data mining of lipid signatures from multiple imaging mass spectrometry analyses: application to human colorectal cancer liver metastasis biopsies.

Imaging mass spectrometry (IMS) represents an innovative tool in the cancer research pipeline, which is increasingly being used in clinical and pharmaceutical applications. The unique properties of the technique, especially the amount of data generated, make the handling of data from multiple IMS acquisitions challenging. This work presents a histology-driven IMS approach aiming to identify discriminant lipid signatures from the simultaneous mining of IMS data sets from multiple samples. The feasibility of the developed workflow is evaluated on a set of three human colorectal cancer liver metastasis (CRCLM) tissue sections. Lipid IMS on tissue sections was performed using MALDI-TOF/TOF MS in both negative and positive ionization modes after 1,5-diaminonaphthalene matrix deposition by sublimation. The combination of both positive and negative acquisition results was performed during data mining to simplify the process and interrogate a larger lipidome into a single analysis. To reduce the complexity of the IMS data sets, a sub data set was generated by randomly selecting a fixed number of spectra from a histologically defined region of interest, resulting in a 10-fold data reduction. Principal component analysis confirmed that the molecular selectivity of the regions of interest is maintained after data reduction. Partial least-squares and heat map analyses demonstrated a selective signature of the CRCLM, revealing lipids that are significantly up- and down-regulated in the tumor region. This comprehensive approach is thus of interest for defining disease signatures directly from IMS data sets by the use of combinatory data mining, opening novel routes of investigation for addressing the demands of the clinical setting.

Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples

Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline.

The microbiological signature of human cutaneous leishmaniasis lesions exhibits restricted bacterial diversity compared to healthy skin

Localised cutaneous leishmaniasis (LCL) is the most common form of cutaneous leishmaniasis characterised by single or multiple painless chronic ulcers, which commonly presents with secondary bacterial infection. Previous culture-based studies have found staphylococci, streptococci, and opportunistic pathogenic bacteria in LCL lesions, but there have been no comparisons to normal skin. In addition, this approach has strong bias for determining bacterial composition. The present study tested the hypothesis that bacterial communities in LCL lesions differ from those found on healthy skin (HS). Using a high throughput amplicon sequencing approach, which allows for better populational evaluation due to greater depth coverage and the Quantitative Insights Into Microbial Ecology pipeline, we compared the microbiological signature of LCL lesions with that of contralateral HS from the same individuals.Streptococcus, Staphylococcus,Fusobacterium and other strict or facultative anaerobic bacteria composed the LCL microbiome. Aerobic and facultative anaerobic bacteria found in HS, including environmental bacteria, were significantly decreased in LCL lesions (p < 0.01). This paper presents the first comprehensive microbiome identification from LCL lesions with next generation sequence methodology and shows a marked reduction of bacterial diversity in the lesions.

Probabilistic base calling of Solexa sequencing data.

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. RESULTS: We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. CONCLUSION: We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.

Mophological analysis of the human vasculature from medical imaging. Application to cerebral and coranary arteries

In this project, we have investigated new ways of modelling and analysis of human vasculature from Medical images. The research was divided in two main areas: cerebral vasculature analysis and coronary arteries modeling. Regarding cerebral vasculature analysis, we have studed cerebral aneurysms, internal carotid and the Circle of Willis (CoW). Aneurysms are abnormal vessel enlargements that can rupture causing important cerebral damages or death. The understanding of this pathology, together with its virtual treatment, and image diagnosis and prognosis, includes identification and detailed measurement of the aneurysms. In this context, we have proposed two automatic aneurysm isolation method, to separate the abnormal part of the vessel from the healthy part, to homogenize and speed-up the processing pipeline usually employed to study this pathology, [Cardenes2011TMI, arrabide2011MedPhys]. The results obtained from both methods have been also compared and validatied in [Cardenes2012MBEC]. A second important task here the analysis of the internal carotid [Bogunovic2011Media] and the automatic labelling of the CoW, Bogunovic2011MICCAI, Bogunovic2012TMI]. The second area of research covers the study of coronary arteries, specially coronary bifurcations because there is where the formation of atherosclerotic plaque is more common, and where the intervention is more challenging. Therefore, we proposed a novel modelling method from Computed Tomography Angiography (CTA) images, combined with Conventional Coronary Angiography (CCA), to obtain realistic vascular models of coronary bifurcations, presented in [Cardenes2011MICCAI], and fully validated including phantom experiments in [Cardene2013MedPhys]. The realistic models obtained from this method are being used to simulate stenting procedures, and to investigate the hemodynamic variables in coronary bifurcations in the works submitted in [Morlachi2012, Chiastra2012]. Additionally, another preliminary work has been done to reconstruct the coronary tree from rotational angiography, and published in [Cardenes2012ISBI].