Ontología de ALUS

En este trabajo se describe una base de conocimiento de las ALU humanas. La ontología incorpora términos SO y GO y está orientada a describir el contexto genómico del conjunto de ALU. Para cada elemento ALU se almacenan el gen y transcrito más cercanos, así como su anotación funcional de acuerdo a GO, el estado de la cromatina circundante y los factores de transcripción presentes en la ALU. Se han incorporado reglas semánticas para facilitar el almacenamiento, consulta e integración de la información. La ontología de ALU es plenamente analizable mediante razonadores como Pellet y está parcialmente transferida a una wiki semántica.

Modeling and Simulation ofReal-Time System as a Tool to Improve Capacity Management - Case Fenix

Tämän tutkimustyön kohteena on TietoEnator Oy:n kehittämän Fenix-tietojärjestelmän kapasiteettitarpeen ennustaminen. Työn tavoitteena on tutustua Fenix-järjestelmän eri osa-alueisiin, löytää tapa eritellä ja mallintaa eri osa-alueiden vaikutus järjestelmän kuormitukseen ja selvittää alustavasti mitkä parametrit vaikuttavat kyseisten osa-alueiden luomaan kuormitukseen. Osa tätä työtä on tutkia eri vaihtoehtoja simuloinnille ja selvittää eri vaihtoehtojen soveltuvuus monimutkaisten järjestelmien mallintamiseen. Kerätyn tiedon pohjaltaluodaan järjestelmäntietovaraston kuormitusta kuvaava simulaatiomalli. Hyödyntämällä mallista saatua tietoa ja tuotantojärjestelmästä mitattua tietoa mallia kehitetään vastaamaan yhä lähemmin todellisen järjestelmän toimintaa. Mallista tarkastellaan esimerkiksi simuloitua järjestelmäkuormaa ja jonojen käyttäytymistä. Tuotantojärjestelmästä mitataan eri kuormalähteiden käytösmuutoksia esimerkiksi käyttäjämäärän ja kellonajan suhteessa. Tämän työn tulosten on tarkoitus toimia pohjana myöhemmin tehtävälle jatkotutkimukselle, jossa osa-alueiden parametrisointia tarkennetaan lisää, mallin kykyä kuvata todellista järjestelmää tehostetaanja mallin laajuutta kasvatetaan.

Mielipidekyselyjärjestelmän suunnittelu ja toteutus

Tämän työn tavoitteena on suunnitella yksinkertainen Internet-pohjainen mielipidekyselyjärjestelmä sekä esitellä yksityiskohtaisesti järjestelmän toteutus ja siihen liittyvät menetelmät. Menetelmistäesitellään ainoastaan ennalta valitut menetelmät järjestelmän toteutukseen, tietojen esittämiseen, esitystavan muotoiluun sekä tietojen varastointiin. Järjestelmä toteutetaan HTML- ja PHP-kielillä sekä käyttämällä CSS-menetelmän tyylimuotoiluja ja XML-kielen muotoiluun perustuvia tiedostoja tietovarastoina. Järjestelmän suunnitteluun liittyen työssä pyritään kuvaamaan järjestelmään toteutettavat kaksi erillistä käyttöliittymää, pääkäyttäjän käyttöliittymä ja normaalin käyttäjän käyttöliittymä, sekä näihin toteutettavat toiminnot. Pääkäyttäjän tärkeimmät toiminnot ovat mielipidekyselyiden luominen, käyttäjien lisääminen kyselyihin sekä kyselyiden tulosten seuranta. Normaalin käyttäjän toiminnot taas rajoittuvat kirjautumiseen ja kyselyyn vastaamiseen. Järjestelmän toteutuksen kuvauksessa kuvataan tarkasti edellä mainittujen kahden käyttöliittymän toiminnot sekä näiden toimintojen toteutustavat. Lisäksi toteutuksen kuvauksen yhteydessä määritellään tarkasti järjestelmän tietovarastoina toimivien tiedostojen sisällön muoto. Työn lopputuloksena syntyi valituilla toteutustavoilla toteutettu toimiva mielipidekyselyjärjestelmä sekä tämä järjestelmän suunnitteluun ja toteutuksen selvittämiseen keskittynyt dokumentti. Toteutetusta järjestelmästä ei tullut täydellinen vaan jatkokehityksessä voidaan harkita esimerkiksi tietokannan käyttämistä järjestelmän tietovarastoina sekä joidenkin lisäominaisuuksien toteuttamista. Tavoitteeseen päästiin kuitenkin, sillä toteutettu järjestelmä on toimiva ja käyttötarkoitukseensa sopiva.

Resistance Switching in Transparent Magnetic MgO Films

We have studied the abrupt and hysteretic changes of resistance in MgO-based capacitor devices. The switching behavior is discussed in terms of the formation and rupture of conduction filaments due to the migration of structural defects in the electric field, together with the redox events which affects the mobile carriers. The results presented in this paper suggest that MgO transparent films combining ferromagnetism and multilevel switching characteristics might pave the way for a new method for spintronic multibit data storage.

Projektisapuolten vaatimukset kolmannen sukupolven matkaviestinverkon rakentamisprojektin knowledge management -järjestelmälle

Projektin johtaminen informaatioaikakaudella merkitsee, yhä useammassa tapauksessa, virtuaalisen verkoston tietämyksen hallitsemista ja johtamista. Kolmannen sukupolven matkaviestinverkon rakentaminen on virtuaaliverkostoa hyväkseen käyttävä projekti, joka koostuu lukuisista osapuolista.Matkaviestinverkkoprojektien laajentuminen ja kilpailun kiristyminen alalla ovat nostaneet knowledge management -järjestelmien kysyntää. Kysyntä kohdistuu voimakkaimmin järjestelmiin, joiden avulla matkaviestinverkkotoimitusprojektin kaikki toiminnot pystytään käsittelemään yhdessä järjestelmässä. Tämän tutkimuksen pääasiallisena tavoitteena on ollut selvittää keskeisimmät vaatimukset kolmannen sukupolven matkaviestinverkon rakentamisprojektin knowledge management ?järjestelmälle. Tutkimus toteutettiin kirjallisuuden ja avoimien teemahaastattelujen avulla, käyttäen kvalitatiivisiä tutkimusmenetelmiä.Haastattelut osoittivat, että tärkeimmät vaatimukset kolmannen sukupolven matkaviestinverkkoja rakentavan projektiorganisaation knowledge management -järjestelmälle ovat: 1. Knowledge management -järjestelmän tulee toimia keskitettynä tietovarastona.2. Projektissa käsiteltävään tietoon on pystyttävä porautumaan vähintään prosessi- ja paikkatietoon pohjautuvista näkökulmista. 3. Pääsyn knowledge management -järjestelmään tulee olla mahdollista kaikille projektin osapuolille.4. Pääsyn knowledge management -järjestelmään tulee olla mahdollista mistä tahansa ja mihin kellonaikaan tahansa.5. Knowledge management -järjestelmän käyttöliittymän tulee olla mahdollisimman yksinkertainen. Järjestelmän tulee olla yhteydessä organisaatioiden muihin järjestelmiin.

Clinical neurophysiology in disorders of consciousness: brain function monitoring in the ICU and beyond.

Over the past two decades, electrophysiology has undergone unprecedented changes thanks to technical improvements, which simplify measurement and analysis and allow more compact data storage. This book covers in detail the spectrum of electrophysiology applications in patients with disorders of consciousness. Its content spans from clinical aspects of the management of subjects in the intensive care unit, including EEG, evoked potentials and related implications in terms of prognosis and patient management to research applications in subjects with ongoing consciousness impairment. While the first section provides up-to-date information for the interested clinician, the second part highlights the latest developments in this exciting field. The book comprehensively combines clinical and research information related to neurophysiology in disorder-of- consciousness patients, making it an easily accessible reference for neuro-ICU specialists, epileptologists and clinical neurophysiologists as well as researchers utilizing EEG and event-related potentials.

Sistemes encastats en temps real

En l’actualitat, els sistemes electrònics de processament de dades són cada cop més significatius dins del sector industrial. Són moltes les necessitats que sorgeixen en el món dels sistemes d’autentificació, de l’electrònica aeronàutica, d’equips d’emmagatzemament de dades, de telecomunicacions, etc. Aquestes necessitats tecnològiques exigeixen ser controlades per un sistema fiable, robust, totalment dependent amb els esdeveniments externs i que compleixi correctament les restriccions temporals imposades per tal de que realitzi el seu propòsit d’una manera eficient. Aquí és on entren en joc els sistemes encastats en temps real, els quals ofereixen una gran fiabilitat, disponibilitat, una ràpida resposta als esdeveniments externs del sistema, una alta garantia de funcionament i una àmplia possibilitat d’aplicacions. Aquest projecte està pensat per a fer una introducció al món dels sistemes encastats, com també explicar el funcionament del sistema operatiu en temps real FreeRTOS; el qual utilitza com a mètode de programació l’ús de tasques independents entre elles. Donarem una visió de les seves característiques de funcionament, com organitza tasques mitjançant un scheduler i uns exemples per a poder dissenyar-hi aplicacions.

Efeitos da poluição atmosférica (litorânea e industrial) em isoladores da rede elétrica da região metropolitana de Salvador

The performances of eight kinds of insulators from electrical distribution lines in Salvador-BA, Brazil, were evaluated considering the chemical and physical local environmental pollution. The parameters that were chosen as characteristic for the insulators' properties were leakage current and partial electrical discharge. A data storage processing system and a communication link to the lab were built for data acquisition. The results show that the main contribution to the poor performance of the insulators is settleable magnetite particulate matter on the insulator in addition to the long term wetness time, t4.

ZigBee-verkot ja evaluointilaitteen suunnittelu

In this thesis a closer look at ZigBee wireless network protocol was made and a ZigBee evaluation device was designed and built for testing it. ZigBee is a digital wireless network technology published in 2004, which was developed for wireless control and automation systems. It is based on the IEEE 802.15.4-2003 standard, and its aim was to create a reliable wireless networking protocol with secure data transmissions, low power consumption and low manufacturing costs. The low power consumption requirement has also led to a slow data rate and a short range, but in a ZigBee network individual network devices can route messages to each other, so short range is not a problem. In automation and control systems a fast data rate is not usually an important requirement either. ZigBee network can form automatically and one ZigBee network can theoretically include thousands of devices, all of which can communicate with each other. ZigBee network is also self-healing, so an individual device dropping out of the network, like breaking down, does not affect functionality of the network. Evaluation device was designed and implemented in four different versions, which were tested with six different antenna designs. All antennas were tested at a range of 100 meters in an open terrain using two different frequencies and transmission powers. Also a range test was performed for selected antennas using transmission power of 4,5 dBm, which was maximum power of the ZigBee chip used in the evaluation device. Range test resulted in a measured range of several hundred meters, which can be considered as a good result for a short-range technology.

Adopting the Vaadin Java framework to rebuild VTT’s Web Interfaces and Database Applications

With the growth in new technologies, using online tools have become an everyday lifestyle. It has a greater impact on researchers as the data obtained from various experiments needs to be analyzed and knowledge of programming has become mandatory even for pure biologists. Hence, VTT came up with a new tool, R Executables (REX) which is a web application designed to provide a graphical interface for biological data functions like Image analysis, Gene expression data analysis, plotting, disease and control studies etc., which employs R functions to provide results. REX provides a user interactive application for the biologists to directly enter the values and run the required analysis with a single click. The program processes the given data in the background and prints results rapidly. Due to growth of data and load on server, the interface has gained problems concerning time consumption, poor GUI, data storage issues, security, minimal user interactive experience and crashes with large amount of data. This thesis handles the methods by which these problems were resolved and made REX a better application for the future. The old REX was developed using Python Django and now, a new programming language, Vaadin has been implemented. Vaadin is a Java framework for developing web applications and the programming language is extremely similar to Java with new rich components. Vaadin provides better security, better speed, good and interactive interface. In this thesis, subset functionalities of REX was selected which includes IST bulk plotting and image segmentation and implemented those using Vaadin. A code of 662 lines was programmed by me which included Vaadin as the front-end handler while R language was used for back-end data retrieval, computing and plotting. The application is optimized to allow further functionalities to be migrated with ease from old REX. Future development is focused on including Hight throughput screening functions along with gene expression database handling

Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.

Synthesis and characterization of nanoperforated metal oxide thin films

For advanced devices in the application fields of data storage, solar cell and biosensing, one of the major challenges to achieve high efficiency is the fabrication of nanopatterned metal oxide surfaces. Such surfaces often require both precise structure at the nanometer scale and controllable patterned structure at the macro scale. Nowadays, the dominating candidates to fabricate nanopatterned surfaces are the lithographic technique and block-copolymer masks, most of which are unfortunately costly and inefficient. An alternative bottom-up approach, which involves organic/inorganic self-assembly and dip-coating deposition, has been studied intensively in recent years and has proven to be an effective technique for the fabrication of nanoperforated metal oxide thin films. The overall objective of this work was to optimize the synthesis conditions of nanoperforated TiO2 (NP-TiO2) thin films, especially to be compatible with mixed metal oxide systems. Another goal was to develop fabrication and processing of NP-TiO2 thin films towards largescale production and seek new applications for solar cells and biosensing. Besides the traditional dip-coating and drop-casting methods, inkjet printing was used to prepare thin films of metal oxides, with the advantage of depositing the ink onto target areas, further enabling cost-effective fabrication of micro-patterned nanoperforated metal oxide thin films. The films were characterized by water contact angle determination, Atomic Force Microscopy, Scanning Electron Microscopy, X-ray Photoelectron Spectroscopy and Grazing Incidence XRay Diffraction. In this study, well-ordered zinc titanate nanoperforated thin films with different Zn/Ti ratios were produced successfully with zinc precursor content up to 50 mol%, and the dominating phase was Zn2Ti3O8. NP-TiO2 structures were also obtained by a cost-efficient means, namely inkjet printing, at both ambient temperature and 60 °C. To further explore new biosensing applications of nanoperforated oxide thin films, inkjet printing was used for the fabrication of both continuous and patterned polymeric films onto NP-TiO2 and perfluorinated phosphate functionalized NP-TiO2 substrates, respectively. The NP-TiO2 films can be also functionalized with a fluoroalkylsilane, resulting in hydrophobic surfaces on both titania and silica. The surface energy contrast in the nanoperforations can be tuned by irradiating the films with UV light, which provides ideal model systems for wettability studies.

Development of a Blood Antigen Molecular Profiling Panel using Genotyping Technologies for Patients Requiring Frequent Transfusions

Contexte. Les phénotypes ABO et Rh(D) des donneurs de sang ainsi que des patients transfusés sont analysés de façon routinière pour assurer une complète compatibilité. Ces analyses sont accomplies par agglutination suite à une réaction anticorps-antigènes. Cependant, pour des questions de coûts et de temps d’analyses faramineux, les dons de sang ne sont pas testés sur une base routinière pour les antigènes mineurs du sang. Cette lacune peut résulter à une allo-immunisation des patients receveurs contre un ou plusieurs antigènes mineurs et ainsi amener des sévères complications pour de futures transfusions. Plan d’étude et Méthodes. Pour ainsi aborder le problème, nous avons produit un panel génétique basé sur la technologie « GenomeLab _SNPstream» de Beckman Coulter, dans l’optique d’analyser simultanément 22 antigènes mineurs du sang. La source d’ADN provient des globules blancs des patients préalablement isolés sur papiers FTA. Résultats. Les résultats démontrent que le taux de discordance des génotypes, mesuré par la corrélation des résultats de génotypage venant des deux directions de l’ADN, ainsi que le taux d’échec de génotypage sont très bas (0,1%). Également, la corrélation entre les résultats de phénotypes prédit par génotypage et les phénotypes réels obtenus par sérologie des globules rouges et plaquettes sanguines, varient entre 97% et 100%. Les erreurs expérimentales ou encore de traitement des bases de données ainsi que de rares polymorphismes influençant la conformation des antigènes, pourraient expliquer les différences de résultats. Cependant, compte tenu du fait que les résultats de phénotypages obtenus par génotypes seront toujours co-vérifiés avant toute transfusion sanguine par les technologies standards approuvés par les instances gouvernementales, les taux de corrélation obtenus sont de loin supérieurs aux critères de succès attendus pour le projet. Conclusion. Le profilage génétique des antigènes mineurs du sang permettra de créer une banque informatique centralisée des phénotypes des donneurs, permettant ainsi aux banques de sang de rapidement retrouver les profiles compatibles entre les donneurs et les receveurs.

Une politique concernant les données issues d’un programme de recherches interventionnelles en santé mondiale

Article

Plasma Polymerised Organic Thin Films-A Study on the Structural, Electrical and Nonlinear Optical Properties for Possible Applications

This proposed thesis is entitled “Plasma Polymerised Organic Thin Films: A study on the Structural, Electrical, and Nonlinear Optical Properties for Possible Applications. Polymers and polymer based materials find enormous applications in the realm of electronics and optoelectronics. They are employed as both active and passive components in making various devices. Enormous research activities are going on in this area for the last three decades or so, and many useful contributions are made quite accidentally. Conducting polymers is such a discovery, and eversince the discovery of conducting polyacetylene, a new branch of science itself has emerged in the form of synthetic metals. Conducting polymers are useful materials for many applications like polymer displays, high density data storage, polymer FETs, polymer LEDs, photo voltaic devices and electrochemical cells. With the emergence of molecular electronics and its potential in finding useful applications, organic thin films are receiving an unusual attention by scientists and engineers alike. This is evident from the vast literature pertaining to this field appearing in various journals. Recently, computer aided design of organic molecules have added further impetus to the ongoing research activities in this area. Polymers, especially, conducting polymers can be prepared both in the bulk and in the thinfilm form. However, many applications necessitate that they are grown in the thin film form either as free standing or on appropriate substrates. As far as their bulk counterparts are concerned, they can be prepared by various polymerisation techniques such as chemical routes and electrochemical means. A survey of the literature reveals that polymers like polyaniline, polypyrrole, polythiophene, have been investigated with a view to studying their structural electrical and optical properties. Among the various alternate techniques employed for the preparation of polymer thin films, the method of plasma polymerisation needs special attention in this context. The technique of plasma polymerisation is an inexpensive method and often requires very less infra structure. This method includes the employment of ac, rf, dc, microwave and pulsed sources. They produce pinhole free homogeneous films on appropriate substrates under controlled conditions. In conventional plasma polymerisation set up, the monomer is fed into an evacuated chamber and an ac/rf/dc/ w/pulsed discharge is created which enables the monomer species to dissociate, leading to the formation of polymer thin films. However, it has been found that the structure and hence the properties exhibited by plasma polymerized thin films are quite different from that of their counterparts produced by other thin film preparation techniques such as electrochemical deposition or spin coating. The properties of these thin films can be tuned only if the interrelationship between the structure and other properties are understood from a fundamental point of view. So very often, a through evaluation of the various properties is a pre-requisite for tailoring the properties of the thin films for applications. It has been found that conjugation is a necessary condition for enhancing the conductivity of polymer thin films. RF technique of plasma polymerisation is an excellent tool to induce conjugation and this modifies the electrical properties too. Both oxidative and reductive doping can be employed to modify the electrical properties of the polymer thin films for various applications. This is where organic thin films based on polymers scored over inorganic thin films, where in large area devices can be fabricated with organic semiconductors which is difficult to achieve by inorganic materials. For such applications, a variety of polymers have been synthesized such as polyaniline, polythiophene, polypyrrole etc. There are newer polymers added to this family every now and then. There are many virgin areas where plasma polymers are yet to make a foray namely low-k dielectrics or as potential nonlinear optical materials such as optical limiters. There are also many materials which are not been prepared by the method of plasma polymerisation. Some of the materials which are not been dealt with are phenyl hydrazine and tea tree oil. The advantage of employing organic extracts like tea tree oil monomers as precursors for making plasma polymers is that there can be value addition to the already existing uses and possibility exists in converting them to electronic grade materials, especially semiconductors and optically active materials for photonic applications. One of the major motivations of this study is to synthesize plasma polymer thin films based on aniline, phenyl hydrazine, pyrrole, tea tree oil and eucalyptus oil by employing both rf and ac plasma polymerisation techniques. This will be carried out with the objective of growing thin films on various substrates such as glass, quartz and indium tin oxide (ITO) coated glass. There are various properties namely structural, electrical, dielectric permittivity, nonlinear optical properties which are to be evaluated to establish the relationship with the structure and the other properties. Special emphasis will be laid in evaluating the optical parameters like refractive index (n), extinction coefficient (k), the real and imaginary components of dielectric constant and the optical transition energies of the polymer thin films from the spectroscopic ellipsometric studies. Apart from evaluating these physical constants, it is also possible to predict whether a material exhibit nonlinear optical properties by ellipsometric investigations. So further studies using open aperture z-scan technique in order to evaluate the nonlinear optical properties of a few selected samples which are potential nonlinear optical materials is another objective of the present study. It will be another endeavour to offer an appropriate explanation for the nonlinear optical properties displayed by these films. Doping of plasma polymers is found to modify both the electrical conductivity and optical properties. Iodine is found to modify the properties of the polymer thin films. However insitu iodine doping is tricky and the film often looses its stability because of the escape of iodine. An appropriate insitu technique of doping will be developed to dope iodine in to the plasma polymerized thin films. Doping of polymer thin films with iodine results in improved and modified optical and electrical properties. However it requires tools like FTIR and UV-Vis-NIR spectroscopy to elucidate the structural and optical modifications imparted to the polymer films. This will be attempted here to establish the role of iodine in the modification of the properties exhibited by the films