An Open Source BI Approach: Concept Proof Tracking Fleet

É possível assistir nos dias de hoje, a um processo tecnológico evolutivo acentuado por toda a parte do globo. No caso das empresas, quer as pequenas, médias ou de grandes dimensões, estão cada vez mais dependentes dos sistemas informatizados para realizar os seus processos de negócio, e consequentemente à geração de informação referente aos negócios e onde, muitas das vezes, os dados não têm qualquer relacionamento entre si. A maioria dos sistemas convencionais informáticos não são projetados para gerir e armazenar informações estratégicas, impossibilitando assim que esta sirva de apoio como recurso estratégico. Portanto, as decisões são tomadas com base na experiência dos administradores, quando poderiam serem baseadas em factos históricos armazenados pelos diversos sistemas. Genericamente, as organizações possuem muitos dados, mas na maioria dos casos extraem pouca informação, o que é um problema em termos de mercados competitivos. Como as organizações procuram evoluir e superar a concorrência nas tomadas de decisão, surge neste contexto o termo Business Intelligence(BI). A GisGeo Information Systems é uma empresa que desenvolve software baseado em SIG (sistemas de informação geográfica) recorrendo a uma filosofia de ferramentas open-source. O seu principal produto baseia-se na localização geográfica dos vários tipos de viaturas, na recolha de dados, e consequentemente a sua análise (quilómetros percorridos, duração de uma viagem entre dois pontos definidos, consumo de combustível, etc.). Neste âmbito surge o tema deste projeto que tem objetivo de dar uma perspetiva diferente aos dados existentes, cruzando os conceitos BI com o sistema implementado na empresa de acordo com a sua filosofia. Neste projeto são abordados alguns dos conceitos mais importantes adjacentes a BI como, por exemplo, modelo dimensional, data Warehouse, o processo ETL e OLAP, seguindo a metodologia de Ralph Kimball. São também estudadas algumas das principais ferramentas open-source existentes no mercado, assim como quais as suas vantagens/desvantagens relativamente entre elas. Em conclusão, é então apresentada a solução desenvolvida de acordo com os critérios enumerados pela empresa como prova de conceito da aplicabilidade da área Business Intelligence ao ramo de Sistemas de informação Geográfica (SIG), recorrendo a uma ferramenta open-source que suporte visualização dos dados através de dashboards.

Octopus Standard Automated Perimetry, Pulsar Perimetry, Moorfields Motion Displacement Test and Heidelberg Retinal Tomography in Glaucoma Detection - A Comparison of Diagnostic Accuracy

Purpose: To investigate the accuracy of 4 clinical instruments in the detection of glaucomatous damage. Methods: 102 eyes of 55 test subjects (Age mean = 66.5yrs, range = [39; 89]) underwent Heidelberg Retinal Tomography (HRTIII), (disc area<2.43); and standard automated perimetry (SAP) using Octopus (Dynamic); Pulsar (TOP); and Moorfields Motion Displacement Test (MDT) (ESTA strategy). Eyes were separated into three groups 1) Healthy (H): IOP<21mmHg and healthy discs (clinical examination), 39 subjects, 78 eyes; 2) Glaucoma suspect (GS): Suspicious discs (clinical examination), 12 subjects, 15 eyes; 3) Glaucoma (G): progressive structural or functional loss, 14 subjects, 20 eyes. Clinical diagnostic precision was examined using the cut-off associated with the p<5% normative limit of MD (Octopus/Pulsar), PTD (MDT) and MRA (HRT) analysis. The sensitivity, specificity and accuracy were calculated for each instrument. Results: See table Conclusions: Despite the advantage of defining glaucoma suspects using clinical optic disc examination, the HRT did not yield significantly higher accuracy than functional measures. HRT, MDT and Octopus SAP yielded higher accuracy than Pulsar perimetry, although results did not reach statistical significance. Further studies are required to investigate the structure-function correlations between these instruments.

Gastric supply manipulation to modulate ghrelin production and enhance vascularization to the cardia: proof of the concept in a porcine model.

Introduction. Selective embolization of the left-gastric artery (LGA) reduces levels of ghrelin and achieves significant short-term weight loss. However, embolization of the LGA would prevent the performance of bariatric procedures because the high-risk leakage area (gastroesophageal junction [GEJ]) would be devascularized. Aim. To assess an alternative vascular approach to the modulation of ghrelin levels and generate a blood flow manipulation, consequently increasing the vascular supply to the GEJ. Materials and methods. A total of 6 pigs underwent a laparoscopic clipping of the left gastroepiploic artery. Preoperative and postoperative CT angiographies were performed. Ghrelin levels were assessed perioperatively and then once per week for 3 weeks. Reactive oxygen species (ROS; expressed as ROS/mg of dry weight [DW]), mitochondria respiratory rate, and capillary lactates were assessed before and 1 hour after clipping (T0 and T1) and after 3 weeks of survival (T2), on seromuscular biopsies. A celiac trunk angiography was performed at 3 weeks. Results. Mean (±standard deviation) ghrelin levels were significantly reduced 1 hour after clipping (1902 ± 307.8 pg/mL vs 1084 ± 680.0; P = .04) and at 3 weeks (954.5 ± 473.2 pg/mL; P = .01). Mean ROS levels were statistically significantly decreased at the cardia at T2 when compared with T0 (0.018 ± 0.006 mg/DW vs 0.02957 ± 0.0096 mg/DW; P = .01) and T1 (0.0376 ± 0.008mg/DW; P = .007). Capillary lactates were significantly decreased after 3 weeks, and the mitochondria respiratory rate remained constant over time at the cardia and pylorus, showing significant regional differences. Conclusions. Manipulation of the gastric flow targeting the gastroepiploic arcade induces ghrelin reduction. An endovascular approach is currently under evaluation.

Ultra-high-resolution 3D imaging of atherosclerosis in mice with synchrotron differential phase contrast: a proof of concept study.

The goal of this study was to investigate the performance of 3D synchrotron differential phase contrast (DPC) imaging for the visualization of both macroscopic and microscopic aspects of atherosclerosis in the mouse vasculature ex vivo. The hearts and aortas of 2 atherosclerotic and 2 wild-type control mice were scanned with DPC imaging with an isotropic resolution of 15 μm. The coronary artery vessel walls were segmented in the DPC datasets to assess their thickness, and histological staining was performed at the level of atherosclerotic plaques. The DPC imaging allowed for the visualization of complex structures such as the coronary arteries and their branches, the thin fibrous cap of atherosclerotic plaques as well as the chordae tendineae. The coronary vessel wall thickness ranged from 37.4 ± 5.6 μm in proximal coronary arteries to 13.6 ± 3.3 μm in distal branches. No consistent differences in coronary vessel wall thickness were detected between the wild-type and atherosclerotic hearts in this proof-of-concept study, although the standard deviation in the atherosclerotic mice was higher in most segments, consistent with the observation of occasional focal vessel wall thickening. Overall, DPC imaging of the cardiovascular system of the mice allowed for a simultaneous detailed 3D morphological assessment of both large structures and microscopic details.

Social sensing for psychology: Automated interpersonal behavior assessment

In this article, we show how the use of state-of-the-art methods in computer science based on machine perception and learning allows the unobtrusive capture and automated analysis of interpersonal behavior in real time (social sensing). Given the high ecological validity of the behavioral sensing, the ease of behavioral-cue extraction for large groups over long observation periods in the field, the possibility of investigating completely new research questions, and the ability to provide people with immediate feedback on behavior, social sensing will fundamentally impact psychology.

The development of automated methods for the determination of trace concentrations of carbomate pesticides in water using solid sorbent pre-concentration methods and high performance liquid chromatography /

Several automated reversed-phase HPLC methods have been developed to determine trace concentrations of carbamate pesticides (which are of concern in Ontario environmental samples) in water by utilizing two solid sorbent extraction techniques. One of the methods is known as on-line pre-concentration'. This technique involves passing 100 milliliters of sample water through a 3 cm pre-column, packed with 5 micron ODS sorbent, at flow rates varying from 5-10 mUmin. By the use of a valve apparatus, the HPLC system is then switched to a gradient mobile phase program consisting of acetonitrile and water. The analytes, Propoxur, Carbofuran, Carbaryl, Propham, Captan, Chloropropham, Barban, and Butylate, which are pre-concentrated on the pre-column, are eluted and separated on a 25 cm C-8 analytical column and determined by UV absorption at 220 nm. The total analytical time is 60 minutes, and the pre-column can be used repeatedly for the analysis of as many as thirty samples. The method is highly sensitive as 100 percent of the analytes present in the sample can be injected into the HPLC. No breakthrough of any of the analytes was observed and the minimum detectable concentrations range from 10 to 480 ng/L. The developed method is totally automated for the analysis of one sample. When the above mobile phase is modified with a buffer solution, Aminocarb, Benomyl, and its degradation product, MBC, can also be detected along with the above pesticides with baseline resolution for all of the analytes. The method can also be easily modified to determine Benomyl and MBC both as solute and as particulate matter. By using a commercially available solid phase extraction cartridge, in lieu of a pre-column, for the extraction and concentration of analytes, a completely automated method has been developed with the aid of the Waters Millilab Workstation. Sample water is loaded at 10 mL/min through a cartridge and the concentrated analytes are eluted from the sorbent with acetonitrile. The resulting eluate is blown-down under nitrogen, made up to volume with water, and injected into the HPLC. The total analytical time is 90 minutes. Fifty percent of the analytes present in the sample can be injected into the HPLC, and recoveries for the above eight pesticides ranged from 84 to 93 percent. The minimum detectable concentrations range from 20 to 960 ng/L. The developed method is totally automated for the analysis of up to thirty consecutive samples. The method has proven to be applicable to both purer water samples as well as untreated lake water samples.

Efficient Strategy-Proof Allocation Functions in Linear Production Economies

In a linear production model, we characterize the class of efficient and strategy-proof allocation functions, and the class of efficient and coalition strategy-proof allocation functions. In the former class, requiring equal treatment of equals allows us to identify a unique allocation function. This function is also the unique member of the latter class which satisfies uniform treatment of uniforms.

Strategy-proof tie-breaking

We study a general class of priority-based allocation problems with weak priority orders and identify conditions under which there exists a strategy-proof mechanism which always chooses an agent-optimal stable, or constrained efficient, matching. A priority structure for which these two requirements are compatible is called solvable. For the general class of priority-based allocation problems with weak priority orders,we introduce three simple necessary conditions on the priority structure. We show that these conditions completely characterize solvable environments within the class of indifferences at the bottom (IB) environments, where ties occur only at the bottom of the priority structure. This generalizes and unifies previously known results on solvable and unsolvable environments established in school choice, housing markets and house allocation with existing tenants. We show how the previously known solvable cases can be viewed as extreme cases of solvable environments. For sufficiency of our conditions we introduce a version of the agent-proposing deferred acceptance algorithm with exogenous and preference-based tie-breaking.

Développement et caractérisation d’une méthode photonique pour créer des distributions spatiales de protéines

Les cellules sont capables de détecter les distributions spatiales de protéines et ainsi de migrer ou s’étendre dans la direction appropriée. Une compréhension de la réponse cellulaire aux modifications de ces distributions spatiales de protéines est essentielle pour l’avancement des connaissances dans plusieurs domaines de recherches tels que le développement, l’immunologie ou l’oncologie. Un exemple particulièrement complexe est le guidage d’axones se déroulant pendant le développement du système nerveux. Ce dernier nécessite la présence de plusieurs distributions de molécules de guidages étant attractives ou répulsives pour connecter correctement ce réseau complexe qu’est le système nerveux. Puisque plusieurs indices de guidage collaborent, il est particulièrement difficile d’identifier la contribution individuelle ou la voie de signalisation qui est déclenchée in vivo, il est donc nécessaire d’utiliser des méthodes pour reproduire ces distributions de protéines in vitro. Plusieurs méthodes existent pour produire des gradients de protéines solubles ou liées aux substrats. Quelques méthodes pour produire des gradients solubles sont déjà couramment utilisées dans plusieurs laboratoires, mais elles limitent l’étude aux distributions de protéines qui sont normalement sécrétées in vivo. Les méthodes permettant de produire des distributions liées au substrat sont particulièrement complexes, ce qui restreint leur utilisation à quelques laboratoires. Premièrement, nous présentons une méthode simple qui exploite le photoblanchiment de molécules fluorescentes pour créer des motifs de protéines liées au substrat : Laser-assisted protein adsorption by photobleaching (LAPAP). Cette méthode permet de produire des motifs de protéines complexes d’une résolution micrométrique et d’une grande portée dynamique. Une caractérisation de la technique a été faite et en tant que preuve de fonctionnalité, des axones de neurones du ganglion spinal ont été guidés sur des gradients d’un peptide provenant de la laminine. Deuxièmement, LAPAP a été amélioré de manière à pouvoir fabriquer des motifs avec plusieurs composantes grâce à l’utilisation de lasers à différentes longueurs d’onde et d’anticorps conjugués à des fluorophores correspondants à ces longueurs d’onde. De plus, pour accélérer et simplifier le processus de fabrication, nous avons développé LAPAP à illumination à champ large qui utilise un modulateur spatial de lumière, une diode électroluminescente et un microscope standard pour imprimer directement un motif de protéines. Cette méthode est particulièrement simple comparativement à la version originale de LAPAP puisqu’elle n’implique pas le contrôle de la puissance laser et de platines motorisées, mais seulement d’envoyer l’image du motif désiré au modulateur spatial. Finalement, nous avons utilisé LAPAP pour démontrer que notre technique peut être utilisée dans des analyses de haut contenu pour quantifier les changements morphologiques résultant de la croissance neuronale sur des gradients de protéines de guidage. Nous avons produit des milliers de gradients de laminin-1 ayant différentes pentes et analysé les variations au niveau du guidage de neurites provenant d’une lignée cellulaire neuronale (RGC-5). Un algorithme pour analyser les images des cellules sur les gradients a été développé pour détecter chaque cellule et quantifier la position du centroïde du soma ainsi que les angles d’initiation, final et de braquage de chaque neurite. Ces données ont démontré que les gradients de laminine influencent l’angle d’initiation des neurites des RGC-5, mais n’influencent pas leur braquage. Nous croyons que les résultats présentés dans cette thèse faciliteront l’utilisation de motifs de protéines liées au substrat dans les laboratoires des sciences de la vie, puisque LAPAP peut être effectué à l’aide d’un microscope confocal ou d’un microscope standard légèrement modifié. Cela pourrait contribuer à l’augmentation du nombre de laboratoires travaillant sur le guidage avec des gradients liés au substrat afin d’atteindre la masse critique nécessaire à des percées majeures en neuroscience.

«Constrained-optimal strategy-proof assignment: beyond the groves mechanisms»

A single object must be allocated to at most one of n agents. Money transfers are possible and preferences are quasilinear. We offer an explicit description of the individually rational mechanisms which are Pareto-optimal in the class of feasible, strategy-proof, anonymous and envy-free mechanisms. These mechanisms form a one-parameter infinite family; the Vickrey mechanism is the only Groves mechanism in that family.

Strategy-proof preference aggregation

An aggregation rule maps each profile of individual strict preference orderings over a set of alternatives into a social ordering over that set. We call such a rule strategyproof if misreporting one’s preference never produces a social ordering that is strictly between the original ordering and one’s own preference. After describing a few examples of manipulable rules, we study in some detail three classes of strategy-proof rules: (i)rules based on a monotonic alteration of the majority relation generated by the preference profile; (ii)rules improving upon a fixed status-quo; and (iii) rules generalizing the Condorcet-Kemeny aggregation method.

Searching for novel gene functions in yeast : identification of thousands of novel molecular interactions by protein-fragment complementation assay followed by automated gene function prediction and high-throughput lipidomics

La compréhension de processus biologiques complexes requiert des approches expérimentales et informatiques sophistiquées. Les récents progrès dans le domaine des stratégies génomiques fonctionnelles mettent dorénavant à notre disposition de puissants outils de collecte de données sur l’interconnectivité des gènes, des protéines et des petites molécules, dans le but d’étudier les principes organisationnels de leurs réseaux cellulaires. L’intégration de ces connaissances au sein d’un cadre de référence en biologie systémique permettrait la prédiction de nouvelles fonctions de gènes qui demeurent non caractérisées à ce jour. Afin de réaliser de telles prédictions à l’échelle génomique chez la levure Saccharomyces cerevisiae, nous avons développé une stratégie innovatrice qui combine le criblage interactomique à haut débit des interactions protéines-protéines, la prédiction de la fonction des gènes in silico ainsi que la validation de ces prédictions avec la lipidomique à haut débit. D’abord, nous avons exécuté un dépistage à grande échelle des interactions protéines-protéines à l’aide de la complémentation de fragments protéiques. Cette méthode a permis de déceler des interactions in vivo entre les protéines exprimées par leurs promoteurs naturels. De plus, aucun biais lié aux interactions des membranes n’a pu être mis en évidence avec cette méthode, comparativement aux autres techniques existantes qui décèlent les interactions protéines-protéines. Conséquemment, nous avons découvert plusieurs nouvelles interactions et nous avons augmenté la couverture d’un interactome d’homéostasie lipidique dont la compréhension demeure encore incomplète à ce jour. Par la suite, nous avons appliqué un algorithme d’apprentissage afin d’identifier huit gènes non caractérisés ayant un rôle potentiel dans le métabolisme des lipides. Finalement, nous avons étudié si ces gènes et un groupe de régulateurs transcriptionnels distincts, non préalablement impliqués avec les lipides, avaient un rôle dans l’homéostasie des lipides. Dans ce but, nous avons analysé les lipidomes des délétions mutantes de gènes sélectionnés. Afin d’examiner une grande quantité de souches, nous avons développé une plateforme à haut débit pour le criblage lipidomique à contenu élevé des bibliothèques de levures mutantes. Cette plateforme consiste en la spectrométrie de masse à haute resolution Orbitrap et en un cadre de traitement des données dédié et supportant le phénotypage des lipides de centaines de mutations de Saccharomyces cerevisiae. Les méthodes expérimentales en lipidomiques ont confirmé les prédictions fonctionnelles en démontrant certaines différences au sein des phénotypes métaboliques lipidiques des délétions mutantes ayant une absence des gènes YBR141C et YJR015W, connus pour leur implication dans le métabolisme des lipides. Une altération du phénotype lipidique a également été observé pour une délétion mutante du facteur de transcription KAR4 qui n’avait pas été auparavant lié au métabolisme lipidique. Tous ces résultats démontrent qu’un processus qui intègre l’acquisition de nouvelles interactions moléculaires, la prédiction informatique des fonctions des gènes et une plateforme lipidomique innovatrice à haut débit , constitue un ajout important aux méthodologies existantes en biologie systémique. Les développements en méthodologies génomiques fonctionnelles et en technologies lipidomiques fournissent donc de nouveaux moyens pour étudier les réseaux biologiques des eucaryotes supérieurs, incluant les mammifères. Par conséquent, le stratégie présenté ici détient un potentiel d’application au sein d’organismes plus complexes.

Automated synthesis of delay-reduced Reed-Muller universal logic module networks

This paper presents a new approach to implement Reed-Muller Universal Logic Module (RM-ULM) networks with reduced delay and hardware for synthesizing logic functions given in Reed-Muller (RM) form. Replication of single control line RM-ULM is used as the only design unit for defining any logic function. An algorithm is proposed that does exhaustive branching to reduce the number of levels and modules required to implement any logic function in RM form. This approach attains a reduction in delay, and power over other implementations of functions having large number of variables.

Development of a Fully Automated Image Analysis Method for High Density cDNA and array CGH Microarray Based Genomic Studies

In this thesis, different techniques for image analysis of high density microarrays have been investigated. Most of the existing image analysis techniques require prior knowledge of image specific parameters and direct user intervention for microarray image quantification. The objective of this research work was to develop of a fully automated image analysis method capable of accurately quantifying the intensity information from high density microarrays images. The method should be robust against noise and contaminations that commonly occur in different stages of microarray development.