Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the impact of alternative splicing in thyroid cancer

Por todo o mundo ha milhoes de pessoas afetadas pelo cancro. Existem multiplas causas possiveis para esta doenca, algumas tem origem genica. Enquanto que ha muitas alteracoes em celulas cancerigenas que as distinguem das saudaveis, existe tambem uma abundância de registos de mRNA aberrantes em celulas cancerigenas. Estes registos aberrantes irao levar a alteracoes nas proteinas sintetizadas que, por sua vez, poderao conferir as celulas propriedades novas, e potencialmente devastadoras. Uma possivel origem deste mRNA defeituoso e o splicing anormal de genes.O advento das tecnicas de sequenciacao de nova geracao tem revolucionado o campo da biologia molecular nos ultimos anos e trouxe inumeras novas abordagens para investigacao do cancro. O objetivo desta tese e recorrer a estas novas tecnicas, nomeadamente a tecnica RNA-seq, de modo a criar uma ferramenta capaz de detetar eventos de splicing alternativo aberrante e avaliar o seu impacto no proteoma da celula ou do organismo.No entanto, ferramentas modernas deste tipo sao frequentemente complexas de utilizar, necessitam de recursos computacionais poderosos e tambem exigem conhecimentos de programacao e outros conceitos da area da informatica por parte do utilizador, o que frequentemente nao se verifica para geneticistas ou especialistas de biologia molecular. Como tal, este projeto tambem se foca em permitir a estes investigadores fazer uso das ferramentas mencionadas atraves da criacao de um sistema distribuido que fornece os recursos computacionais necessarios para uma pipeline de RNA-seq e tambem uma interface web para facilitar a configuracao e execucao de experiencias nesta pipeline.Finalmente, a proposta de tese e avaliada em dados reais do projeto ENCODE.
Requirement for the SnoN Oncoprotein in Transforming Growth Factor β-Induced Oncogenic Transformation of Fibroblast Cells

ABSTRACT Transforming growth factor β (TGF-β) was originally identified by virtue of its ability to induce transformation of the AKR-2B and NRK fibroblasts but was later found to be a potent inhibitor of the growth of epithelial, endothelial, and lymphoid cells. Although the growth-inhibitory pathway of TGF-β mediated by the Smad proteins is well studied, the signaling pathway leading to the transforming activity of TGF-β in fibroblasts is not well understood. Here we show that SnoN, a member of the Ski family of oncoproteins, is required for TGF-β-induced proliferation and transformation of AKR-2B and NRK fibroblasts. TGF-β induces upregulation of snoN expression in both epithelial cells and fibroblasts through a common Smad-dependent mechanism. However, a strong and prolonged activation of snoN transcription that lasts for 8 to 24 h is detected only in these two fibroblast lines. This prolonged induction is mediated by Smad2 and appears to play an important role in the transformation of both AKR-2B and NRK cells. Reduction of snoN expression by small interfering RNA or shortening of the duration of snoN induction by a pharmacological inhibitor impaired TGF-β-induced anchorage-independent growth of AKR-2B cells. Interestingly, Smad2 and Smad3 play opposite roles in regulating snoN expression in both fibroblasts and epithelial cells. The Smad2/Smad4 complex activates snoN transcription by direct binding to the TGF-β-responsive element in the snoN promoter, while the Smad3/Smad4 complex inhibits it through a novel Smad inhibitory site. Mutations of Smad4 that render it defective in heterodimerization with Smad3, which are found in many human cancers, convert the activity of Smad3 on the snoN promoter from inhibitory to stimulatory, resulting in increased snoN expression in cancer cells. Thus, we demonstrate a novel role of SnoN in the transforming activity of TGF-β in fibroblasts and also uncovered a mechanism for the elevated SnoN expression in some human cancer cells.
Méthodologie de validation des modèles numériques utilisés lors de la prédiction des contraintes sur les aubes de turbines hydroélectriques

L’objectif des presents travaux de recherche est de proposer une methode coherente pour la validation des modeles numeriques employes pour estimer les contraintes mecaniques, particulierement adaptee au secteur des turbines hydroelectriques. En effet, les modeles de simulation numerique visent a refleter la realite physique de pieces ou de systemes complexes de la maniere la plus fidele possible. Des lors qu’un modele mecanique, ou fluidique, est propose, il est necessaire de quantifier l’incertitude de celui-ci par rapport aux donnees experimentales. Une fois ce travail realise, il est alors possible de comparer differents modeles entre eux et, par consequent de valider ou non leur utilisation dans un contexte donne connu a priori. Pour ce faire, differentes approches quantitatives sont possibles. Cependant, afin de produire un travail de qualite, donnant des resultats fiables, il est primordial d’adopter une demarche rigoureuse et robuste qui laisse le moins d’interpretation possible a l’analyste. Dans cette optique, l’utilisation de la metrique de surface (Area Metric) est proposee pour quantifier les differences entre les resultats de simulation et les mesures experimentales. Cette methode presente de nombreux avantages par rapport aux methodes de validation classiques issues des statistiques traditionnelles et qui ne satisfont pas pour la plupart les recommandations formulees par l’ASME V&V. Celle-ci se base sur les distributions des donnees de simulation et experimentales pour quantifier l’adequation du modele numerique par rapport a la realite physique telle que mesuree par un dispositif experimental ayant lui-meme sa part d’incertitude. A noter que l’aboutissement de l’application de cette methode ne formule pas de conclusion univoque quant a la validite du modele. La metrique de surface quantifie seulement et uniquement le niveau d’adequation. Le critere de validite est determine par l’analyste qui tire ensuite ses conclusions en fonction de ce niveau d’adequation. Cette methode est appliquee sur un modele complexe : une roue de turbine hydroelectrique pour laquelle des mesures in situ par jauges de deformation etaient disponibles. Deux modeles fluidiques differents sont ainsi compares. De plus, une amelioration de cette methode est proposee afin de pallier les limitations rencontrees pour valider un modele de facon globale et non uniquement locale. Cette methode peut etre appliquee pour tous types de problematiques ou il est necessaire de valider un modele quelconque. En effet, la polyvalence de la metrique de surface peut etre mise a profit pour des mesures experimentales tres abondantes (ex. repetitions) ou lorsque celles-ci sont peu nombreuses.
A novel smart prodder with sensor feedback for material recognition in Humanitarian Demining applications

In this work a smart prodder, capable to give information about the material of a touched unknown object, is presented. The recognition process is based on the analysis of the interaction between a sensing unit and the object. The surface of the object is excited by a piezoelectric actuator and its response measured with another piezoelectric sensor. A prototype has been designed and built and experimental trials have been performed.
Effects of acute treatment with statins on cerebral autoregulation in patients after aneurysmal subarachnoid hemorrhage.

OBJECT The authors previously have demonstrated that acute treatment with pravastatin after aneurysmal subarachnoid hemorrhage (SAH) can ameliorate vasospasm-related delayed ischemic neurological deficits (DINDs). In the current study, they test the hypothesis that these effects are associated with improvement in indices describing autoregulation of cerebral blood flow. METHODS In this double-blind study, 80 patients between the ages of 18 and 84 years who had aneurysmal SAH were randomized equally to receive either 40 mg of oral pravastatin or placebo once daily for up to 14 days (medication was started 1.8 x 1.3 days after ictus). Autoregulation was measured using a daily transient hyperemic response test (THRT) on transcranial Doppler ultrasonography (800 measurements in 80 patients), and data were compared between the pravastatin and placebo groups and between patients with or without vasospasm, DINDs, or unfavorable outcome. Measurement of autoregulation also was performed using the pressure-reactivity index, a moving correlation coefficient between mean arterial and intracranial pressures (Days 0-5, 132 measurements in 32 patients). There was no difference in baseline autoregulation indices between the trial groups. The members of the pravastatin group not only had a shorter duration of impaired autoregulation but also had stronger transient hyperemic response ratios (THRRs) bilaterally. A negative correlation existed between the mean flow velocity in the middle cerebral artery and THRRs. Onset of DINDs occurred when bilateral autoregulation failed. On Days 3, 4, and 5, the pressure-reactivity index correlated significantly with ipsilateral impaired autoregulation. CONCLUSIONS The neuroprotective effects of acute treatment with pravastatin following aneurysmal SAH are associated with enhancement of autoregulation. A routine and daily assessment of cerebral autoregulation by using the THRT may help identify patients at high risk of DINDs.
Human platelet concentrates: a source of solvent/detergent‐treated highly enriched brain‐derived neurotrophic factor

BACKGROUND: Human blood platelets (PLTs) contain brain‐derived neurotrophic factor (BDNF), a neurotrophin that binds to neurotrophic tropomyosin‐related kinase B (TrkB) receptor on central nervous system cells. This binding promotes neural synaptic plasticity and memory and prevents neuronal degeneration. Alterations in BDNF homeostasis are associated with aging and are found in several neurodegenerative conditions such as Alzheimer's, Huntington's, and Parkinson's diseases and multiple sclerosis. We have developed PLT viral inactivation and chromatographic fractionation processes and decided here to identify fractions enriched in BDNF.
Modélisation bayésienne algorithmique de la reconnaissance visuelle de mots et de l’attention visuelle

Dans cette these, nous proposons un nouveau modele conceptuel de la reconnaissance visuelle de mots implemente sous forme mathematique de facon a evaluer sa capacite a reproduire les observations experimentales du domaine. Une revue critique des modeles computationnels existants nous conduit a definir un cahier des charges sous la forme de cinq hypotheses qui sont a la base du modele conceptuel propose : le modele est dote d'une architecture a trois niveaux (sensoriel, perceptif et lexical) ; le traitement est parallele sur l'ensemble des lettres du stimulus ; l'encodage positionnel est distribue ; enfin, le traitement sensoriel des lettres integre position du regard, acuite visuelle et distribution de l'attention visuelle. L'implementation repose sur la methodologie de la modelisation bayesienne algorithmique, conduisant au modele BRAID (pour "Bayesian word Recognition with Attention, Interference and Dynamics"). Nous verifions la capacite du modele a rendre compte des donnees obtenues en perceptibilite des lettres (par exemple, effets de superiorite des mots et des pseudo-mots, effets de contexte), en reconnaissance de mots et en decision lexicale (par exemple, effets de frequence et de voisinage). Au total, nous simulons avec succes 28 experiences comportementales, permettant de rendre compte d'effets subtils dans chacun des domaines cibles. Nous discutons les choix theoriques du modele a la lumiere de ces resultats experimentaux, et proposons des perspectives d'extension du modele, soulignant la flexibilite du formalisme choisi.
Web based Interactive Visualization of Weather Radar Data

We present a novel web browser based interactive visualization application for exploring 3D weather radar data sets delivered by next generation phased array radars. The purpose is to aid in rapid observation of localized weather phenomenon, short term weather forecasting and disaster prevention. Our application allows remote users to access multiple data sets via a web browser application, and the ability to view ray casted weather data volumes atop 3D maps from different viewpoints, animated in time. The interface allows updating intensity threshold and color scale range for comprehending 3D precipitation shape at different intensity levels, vertical cross-sectional views for viewing the internal structure and orthographic projection onto 3D map to clearly locate the affected areas. A demo collated using Osaka city torrential rain data set was presented to domain experts and received encouraging remarks on usability and performance.
Electrophysiology Studies in Patients Undergoing ICD Implantation: Findings from the NCDR®

Background: Electrophysiology studies (EPS) have historically played a role in sudden death risk stratification. More recent studies point to the left ventricular ejection fraction (EF) as a guide to implantable cardioverter defibrillators (ICD) implantation. The extent of EPS use in patients undergoing ICD implantation in the current era remains unknown.
Betaxanthins as Substrates for Tyrosinase. An Approach to the Role of Tyrosinase in the Biosynthetic Pathway of Betalains1

Tyrosinase or polyphenol oxidase (EC 1.14.18.1) is the key enzyme in melanin biosynthesis and in the enzymatic browning of fruits and vegetables. The role of tyrosinase in the secondary metabolism of plants still remains unclear, but its implication in betalain biosynthesis has been proposed. Betalains are an important class of water-soluble pigments, characteristic of plants belonging to the order Caryophyllales. In this article, the betaxanthins, tyrosine-betaxanthin (portulacaxanthin II) and dopaxanthin, are reported to be physiological substrates for tyrosinase. The direct activity of tyrosinase on selected betaxanthins is characterized in depth, and conversion of tyrosine-betaxanthin to dopaxanthin and its further oxidation to a series of compounds are described. Identity of the reaction products was studied by high-performance liquid chromatography and electrospray ionization-mass spectrometry. Masses determined for the reaction products were the same in all cases, 389 m/z ([M + H]+) and equal to that determined for betanidin. Data indicate that dopaxanthin-quinone is obtained and evolves to more stable species by intramolecular cyclization. Kinetic parameters for tyrosinase acting on dopaxanthin were evaluated, showing a high affinity for this substrate (Km = 84.3 μm). The biosynthetic scheme of betalains is reviewed and a branch is proposed based on the description of physiological substrates for tyrosinase. Lampranthus productus, Glottiphylum oligocarpum, and Glottiphylum pigmaeum are described as sources of stereopure (2S/S)-dopaxanthin.
Speech perception in cochlear implant users with the HiRes 120 strategy: a systematic review

Despite technological advances employed in signal processing strategies, one of the remaining obstacles are spectral gap details on the information transmitted. Considering its importance in speech perception, researchers have investigated mechanisms to optimize spectral details through virtual spectral channels. The clinical application of this technique resulted in a new approach to signal processing - the HiRes 120. Objective To assess the auditory performance of cochlear implant users with the HiRes 120 strategy. Methodology The literature review was conducted in an electronic database, with standard bibliographic search in the year 2011, using specific keywords. In order to select and evaluate the scientific studies found in the search, we setup search containing the following aspects: type of study, subjects, intervention used and evaluation of the results. Conclusion Scientific evidence points to an improvement in hearing performance in noisy environments with the HiRes 120 strategy, but this does not occur in quiet situations. The optimization of speech perception with this strategy is closely related to the cochlear implant user's age, to the time of sensory deprivation and the acclimatization time required to use the strategy's spectral information.
Conversion of MDP problems into heuristics based planning problems using temporal decomposition

This paper presents an approach for recasting Markov Decision Process (MDP) problems into heuristics based planning problems. The basic idea is to use temporal decomposition of the state space based on a subset of state space referred to as termination sample space. Specifically, the recasting of MDP problems is done in three steps. First step is to define a state space adaptation criterion based on the termination sample space. Second step is to define an action selection heuristic from each state. Third and final step is to define a recursion or backtracking methodology to avoid dead ends and infinite loops. All three steps have been described and discussed. A case study involving fault detection and alarm generation for the reaction wheels of a satellite mission has been discussed. The proposed approach has been compared with existing approaches for recasting MDP problems using the case study. Computational reduction achieved by the proposed approach is evident from the results.
Agent-based control for power quality enhancement in highly distributed generation networks

Distributed generation (DG) connected to distribution networks introduces significant challenges in terms of power quality and reliability of supply because many types of these new technologies are interfaced to the network through power electronic converters. A multi-agent control strategy based on a hierarchical control structure with various levels is proposed in this paper to enhance the power quality of the network. Furthermore, a highly DG network is split into small zones identified as Local Controllable Zones (LCZs) based on specific characteristics, operation and control requirements of each zone. The concept and methodology of the proposed control system are explained, including the simulation studies that demonstrate the operation between control agents. The case study is based on a radial distribution network and the simulation results examine the power quality performance especially in terms of voltage profile and harmonic content.
An un-tethered ROV for routine access and intervention in the deep sea

Certain enabling technologies coupled with recent advances in robotic systems make it possible to consider supplementing many of the functions performed by vehicles with appropriately designed semi-autonomous systems. These systems are effectively a hybrid cross between ROV and AUV systems and poised to enable an important new class of undersea vehicle capable of intervention tasks under direct human control. It is now possible to radically redefine the meaning of the words “tethered vehicle” to include virtual tethering via acoustic and optical means or through the use of an extremely small optical fiber, providing not power but only high bandwidth communications. Battery-powered, hybrid-tethered vehicles will be able to perform a range of tasks that might otherwise require a conventional ROV. These functions will be performed at much lower cost by requiring less complex ships because of a greatly reduced dependence on complex, large, specialized tether and vehicle handling equipment, and a reduced need for dynamic positioning capability. Several key emerging technologies and capabilities make such a vehicle possible. Advances in both acoustic and optical “wireless” underwater communications and mico-tethers as pioneered by the HROV Nereus offer the potential to transform ROV type operations. By utilizing multiband acoustics and WHOI's newly developed through-water optical transceivers, variable bandwidth communications are possible. In late 2012, Nereus was interfaced to a specially configured acoustic and optical communications system and a series of field demonstrations conducted offshore, including highly interactive and complex manipulations, demonstrating what we term as the Nereid Technology.
Indoor Positioning with Virtual Fingerprint Mapping by Using Linear and Exponential Taper Functions

A 2D localization system is constructed by using Wireless Sensor Nodes (WSN) to create a Virtual Fingerprint map. Linear and exponential taper functions are utilized with the received signal strength distributions between the fingerprint nodes to generate virtual fingerprint maps. Thus, a real and virtual combined fingerprint map is generated across the test area. k-NN and k-NN weighted algorithms have been implemented on virtual fingerprint maps to find the coordinates of the unknown objects. The system Localization accuracies of less than a grid space are obtained in calculations.
A comparison of physical activity-related social-cognitive factors between those with type 1 diabetes, type 2 diabetes and diabetes free adults

Despite strong evidence supporting the benefits of physical activity in managing and preventing diabetes, the majority of Canadians living with or without diabetes are insufficiently active to achieve health benefits. The purpose of this study was to examine the difference in key physical activity-related, psychosocial constructs from major social-cognitive theories/models for individuals with type 1 diabetes (n = 695), type 2 diabetes (n = 1540) and those without diabetes (n = 829). The relatively similar scores reported for the social-cognitive constructs between the groups suggest that theoretically driven, generic population-based strategies operationalizing key socio-cognitive constructs for promoting physical activity may have utility for the general and diabetes specific populations. However, both diabetes groups reported significantly lower (p < 0.001) response efficacy (benefits of physical activity) scores, and higher scores for cons of performing physical activity than the non-diabetes group (p < 0.001). Further, the type 1 diabetes group had significantly higher (p < 0.05) physical activity cons scores than the other two study groups. The findings of this study may guide practitioners in designing population-based, physical activity programs that capitalize on generic strategies for the general and diabetes populations, and identify efforts as to where specific tailoring (e.g. emphasizing physical activity benefits) is needed for those living with diabetes.
Non-verbal communication interface using a data glove

Since the emergence of more sophisticated interaction devices, Human Computer Interaction (HCI) science has extended in all forms, where Non-Verbal Communication (NVC) is one of added issues. In this context, the use of gestures (actions expressed by body, face, and/or hands) as a natural solution for applications that require hands-free and no touch interaction with computers has been suggested, such as in virtual reality (VR) environments. This paper introduces an interaction system based on gestures, which implies a real-time hand gesture recognition and tracking method to identify different and dynamic hand postures as control tools of a virtual world. In order to improve the user experience, a set of different system functions into a virtual world had been implemented. Interaction can be performed by the user's execution of gestures through a data glove device. The ability to perform the implemented gestures by a participants' group is used as a critical evaluation of the system. The obtained results show that a high percentage of evaluated participants found the system as user-friendly.