GENCODE: producing a reference annotation for ENCODE.

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

Volcanic debris avalanche deposits of the upper Maronne valley (Cantal Volcano, France): evidence for contrasted formation and transport mechanisms

The deposits of two volcanic debris avalanches (VDA I and II) that occur in the upper Maronne valley, northwest sector of Cantal Volcano, France, were studied to establish their mechanisms of formation, transport and deposition. These two volcanic debris avalanches that clearly differ with regard to their structures, textures and extensions, exemplify the wide spectrum of events associated with large-scale sector collapse. VDA I is voluminous (similar to1 km(3) in the upper Maronne valley) and widespread. The deposits comprise two distinct facies: the block facies that forms the intermediate and upper part of the unit and the mixed facies that crops out essentially at the base of the unit. The block facies consists of more or less brecciated lava, block-and-ash-flow breccia and pumice-flow tuff megablocks set in breccias resulting from block disaggregation. Mixing and differential movements are almost absent in this part of the VDA. The mixed facies consists of breccias rich in fine particles that originate from block disagregation, as well as being picked up from the substratum during movement. Mixing and differential movements are predominant in this zone. Analysis of fractures on lava megablocks suggests that shear stress during the initial sliding is the principal cause of fracture. These data strongly indicate that VDA I is purely gravitational and argue for a model in which the initial sliding mass transforms into a flow due to differential in situ fragmentation caused by the shear stress. VDA II is restricted to low-topography areas. Its volume, in the studied area, is about 0.3 km(3). The deposits consist of brecciated, rounded blocks and megablocks set in a fine-grained matrix composed essentially of volcanic glass. This unit is stratified, with a massive layer that contains all the megablocks at the base and in the intermediate part, and in the upper part a normally graded layer that contains only blocks <1 m in size. The different lithologies present are totally mixed. These observations suggest that VDA II may be of the Bezymianny-type and that it underwent a flow transformation from a turbulent to a stratified flow consisting of a basal hyperconcentrated laminar body overlain by a dilute layer. (C) 2000 Elsevier Science B.V. All rights reserved.

Yhteisö-tv palvelukonseptina, case: Finnish Satellite Television Oy

Menestyäkseen nykymaailmassa ihmiset ovat turvautuneet toisiinsa muodostaen samallaerilaisia yhteisöjä ja verkostoja. Näille yhteisöille on tunnusomaista, että niissä vaikuttavien jäsenien ajatustavat yhtyvät keskenään. Yhteisöissä syntyy uusia ideoita ja keksintöjä. Niiden välittäminen maailmalle on usein kuitenkin ongelmallista. Digitaalisuus, Internet ja monet muut uudet teknologiat tuovat yhden ratkaisun ongelmaan. Eräs uuden teknologian mahdollistama kanava on yhteisötelevisio, jonka kautta yhteisön viestintää voidaan tehokkaasti välittää. Yhteisöilläei kuitenkaan ole teknistä taitoa toteuttaa tällaista palvelua. Yhteisöille, kuten pk-yrityksille, kouluille, seuroille, yhdistyksille ja jopa yksittäisille ihmisille, tuleekin pystyä tarjoamaan valmis konsepti, joka on helposti heidän käytettävissään. Tämä diplomityö toimii teknisenä pohjana Finnish Satellite Television Oy:n yhteisö-tv -palvelukonseptille, joka tullaan ottamaan laajamittaiseen käyttöön vuoden 2007 aikana. Työssä käydään läpi yhteisön ja yhteisöllisyyden tunnusmerkit ja peruspiirteet, luodaan katsaus yhteisötelevision alkutaipaleisiin, nykytilaan ja sen eri ratkaisuihin. Lisäksi tutustutaan yhteisö-tv:n kansainvälisiin ja kotimaisiin kokeiluihin ja pilottiprojekteihin. Työn teknisessä osassa tutkitaan yhteisötelevision mahdollistaviin teknologioihin, siirtoteihin sekä digitaalisiin tuotantojärjestelmiin. Lopuksi työssä kootaan yhteen käytettävyydeltään, liikutettavuudeltaan ja kustannustehokkuudeltaan sopivimmat tekniset toteutusvaihtoehdot konseptin käyttöönottoa varten.

Effect of physico-chemical conditions and operating parameters on flux and retention of different components in ultrafiltration and nanofiltration fractionation of sweet whey

Tässä väitöstutkimuksessa tutkittiin fysikaaliskemiallisten olosuhteiden ja toimintaparametrien vaikutusta juustoheran fraktiointiin. Kirjallisuusosassa on käsitelty heran ympäristövaikutusta, heran hyödyntämistä ja heran käsittelyä kalvotekniikalla. Kokeellinen osa on jaettu kahteen osaan, joista ensimmäinen käsittelee ultrasuodatusta ja toinen nanosuodatusta juustoheran fraktioinnissa. Ultrasuodatuskalvon valinta tehtiin perustuen kalvon cut-off lukuun, joka oli määritetty polyetyleeniglykoliliuoksilla olosuhteissa, joissa konsentraatiopolariosaatioei häiritse mittausta. Kriittisen vuon konseptia käytettiin sopivan proteiinikonsentraation löytämiseksi ultrasuodatuskokeisiin, koska heraproteiinit ovat tunnetusti kalvoa likaavia aineita. Ultrasuodatuskokeissa tutkittiin heran eri komponenttien suodattumista kalvon läpi ja siihen vaikuttavia ominaisuuksia. Herapermeaattien peptidifraktiot analysoitiin kokoekskluusiokromatografialla ja MALDI-TOF massaspektrometrillä. Kokeissa käytettävien nanosuodatuskalvojen keskimääräinen huokoskoko analysoitiin neutraaleilla liukoisilla aineilla ja zeta-potentiaalit virtauspotentiaalimittauksilla. Aminohappoja käytettiin malliaineina tutkittaessa huokoskoon ja varauksen merkitystä erotuksessa. Aminohappojen retentioon vaikuttivat pH ja liuoksen ionivahvuus sekä molekyylien väliset vuorovaikutukset. Heran ultrasuodatuksessa tuotettu permeaatti, joka sisälsi pieniä peptidejä, laktoosia ja suoloja, nanosuodatettiin happamassa ja emäksisessä pH:ssa. Emäksisissä oloissa tehdyssä nanosuodatuksessa foulaantumista tapahtui vähemmän ja permeaattivuo oli parempi. Emäksisissä oloissa myös selektiivisyys laktoosin erotuksessa peptideistä oli parempi verrattuna selektiivisyyteen happamissa oloissa.

A Study on Fractionation and Ultrafiltration of Proteins with Characterized Modified and Unmodified Membranes

Membrane filtration has become increasingly attractive in the processing of both foodand biotechnological products. However, the poor selectivity of the membranes and fouling are the critical factors limiting the development of UF systems for the specific fractionation of protein mixtures. This thesis gives an overview on fractionation of proteins from model protein solutions or from biological solutions. An attempt was made to improve the selectivity of the available membranes by modifying the membranes and by exploiting the different electrostatic interactions between the proteins and the membrane pore surfaces. Fractionation and UF behavior of proteins in the model solutions and in the corresponding biological solutions were compared. Characterization of the membranes and protein adsorptionto the membrane were investigated with combined flux and streaming potential studies. It has been shown that fouling of the membranes can be reduced using "self-rejecting" membranes at pH values where electrostatic repulsion is achieved between the membrane and the proteins in solution. This effect is best shown in UF of dilute single protein solutions at low ionic strengths and low pressures. Fractionation of model proteins in single, binary, and ternary solutionshas been carried out. The results have been compared to the results obtained from fractination of biological solutions. It was generally observed that fractination of proteins from biological solutions are more difficult to carry out owingto the presence of non studied protein components with different properties. Itcan be generally concluded that it is easier to enrich the smaller protein in the permeate but it is also possible to enrich the larger protein in the permeateat pH values close to the isoelectric point of the protein. It should be possible to find an optimal flux and modification to effectively improve the fractination of proteins even with very similar molar masses.

Distance Transforms on Gray-Level Surfaces

This thesis studies gray-level distance transforms, particularly the Distance Transform on Curved Space (DTOCS). The transform is produced by calculating distances on a gray-level surface. The DTOCS is improved by definingmore accurate local distances, and developing a faster transformation algorithm. The Optimal DTOCS enhances the locally Euclidean Weighted DTOCS (WDTOCS) with local distance coefficients, which minimize the maximum error from the Euclideandistance in the image plane, and produce more accurate global distance values.Convergence properties of the traditional mask operation, or sequential localtransformation, and the ordered propagation approach are analyzed, and compared to the new efficient priority pixel queue algorithm. The Route DTOCS algorithmdeveloped in this work can be used to find and visualize shortest routes between two points, or two point sets, along a varying height surface. In a digital image, there can be several paths sharing the same minimal length, and the Route DTOCS visualizes them all. A single optimal path can be extracted from the route set using a simple backtracking algorithm. A new extension of the priority pixel queue algorithm produces the nearest neighbor transform, or Voronoi or Dirichlet tessellation, simultaneously with the distance map. The transformation divides the image into regions so that each pixel belongs to the region surrounding the reference point, which is nearest according to the distance definition used. Applications and application ideas for the DTOCS and its extensions are presented, including obstacle avoidance, image compression and surface roughness evaluation.

Critical flux and fouling in ultrafiltration of proteins

In this thesis different parameters influencing critical flux in protein ultrafiltration and membrane foul-ing were studied. Short reviews of proteins, cross-flow ultrafiltration, flux decline and criticalflux and the basic theory of Partial Least Square analysis (PLS) are given at the beginning. The experiments were mainly performed using dilute solutions of globular proteins, commercial polymeric membranes and laboratory scale apparatuses. Fouling was studied by flux, streaming potential and FTIR-ATR measurements. Critical flux was evaluated by different kinds of stepwise procedures and by both con-stant pressure and constant flux methods. The critical flux was affected by transmembrane pressure, flow velocity, protein concentration, mem-brane hydrophobicity and protein and membrane charges. Generally, the lowest critical fluxes were obtained at the isoelectric points of the protein and the highest in the presence of electrostatic repulsion between the membrane surface and the protein molecules. In the laminar flow regime the critical flux increased with flow velocity, but not any more above this region. An increase in concentration de-creased the critical flux. Hydrophobic membranes showed fouling in all charge conditionsand, furthermore, especially at the beginning of the experiment even at very low transmembrane pressures. Fouling of these membranes was thought to be due to protein adsorption by hydrophobic interactions. The hydrophilic membranes used suffered more from reversible fouling and concentration polarisation than from irreversible foul-ing. They became fouled at higher transmembrane pressures becauseof pore blocking. In this thesis some new aspects on critical flux are presented that are important for ultrafiltration and fractionation of proteins.

Multi-purpose infrastructure for delivering and supporting mobile context-aware applications

The use of contextual information in mobile devices is receiving increasing attention in mobile and ubiquitous computing research. An important requirement for mobile development today is that devices should be able to interact with the context. In this paper we present a series of contributions regarding previous work on context-awareness. In the first place, we describe a client-server architecture that provides a mechanism for preparing target non context-aware applications in order to be delivered as context-aware applications in a semi-automatic way. Secondly, the framework used in the server to instantiate specific components for context-awareness, the Implicit Plasticity Framework, provides independence from the underlying mobile technology used in client device, as it is shown in the case studies presented. Finally, proposed infrastructure deals with the interaction among different context constraints provided by diverse sensors. All of these contributions are extensions to the infrastructure based on the Dichotomic View of plasticity, which now offers multi-purpose support.

The existence of FGFR1-5-HT1A receptor heterocomplexes in midbrain 5-HT neurons of the rat: relevance for neuroplasticity

The ascending midbrain 5-HT neurons to the forebrain may be dysregulated in depression and have a reduced trophic support. With in situ proximity ligation assay (PLA) and supported by coimmunoprecipitation and colocation of the FGFR1 and 5-HT1A immunoreactivities in the midbrain raphe cells, evidence for the existence of FGFR1-5-HT1A receptor heterocomplexes in the dorsal and median raphe nuclei of the Sprague Dawley rat as well as in the rat medullary raphe RN33B cells has been obtained. Especially after combined FGF-2 and 8-OH-DPAT treatment, a marked and significant increase in PLA clusters was found in the RN33B cells. Similar results were reached with the FRET technique in HEK293T cells, where TM-V of the 5HT1A receptor was found to be part of the receptor interface. The combined treatment with FGF-2 and the 5-HT1A agonist also synergistically increased FGFR1 and ERK1/2 phosphorylation in the raphe midline area of the midbrain and the RN33B cells as well as their differentiation, as seen from development of the increased number and length of extensions per cell and their increased 5-HT immunoreactivity. These signaling and differentiation events were dependent on the receptor interface since they were blocked by incubation with TM-V but not by TM-II. Together, the results indicate that the 5-HT1A autoreceptors by being part of a FGFR1-5-HT1A receptor heterocomplex in the midbrain raphe 5-HT nerve cells appear to have a trophic role in the central 5-HT neuron systems in addition to playing a key role in reducing the firing of these neurons

Endosseous dental implant fractures an analysis of 21 cases

Implant fracture is an infrequent cause of implant failure. The present study evaluates 21 fractured implants, with an analysis of patient age and sex, the type, length and diameter of the implant, positioning in the dental arch, the type of prosthetic rehabilitation involved, the number of abutments and pontics, the presence or absence of distal extensions or cantilevers, and loading time to fracture. Implant fracture was more common in males than in females (15:4), and the mean patient age was 56.9 years. Most cases (n = 19) corresponded to implant-supported fixed prostheses - 16 with cantilevers of different lengths- while only two fractured implants were supporting overdentures instead of fixed prostheses. The great majority of fractured implants (80.9%) were located in the molar and premolar regions, and most fractured within 3-4 years after loading. It is important to know and apply the measures required to prevent implant fracture, and to seek the best individualized solution for each case - though complete implant removal is usually the treatment of choice

Pinch-menetelmän soveltaminen sellutehtaassa

Työn tarkoituksena oli tutkia pinch-menetelmän soveltuvuutta toiminnassa olevassa UPM-Kymmene Oyj:n kaukaan sellutehtaassa ja kartoittaa pinch-analyysin avulla keittämön sekä haihduttamon lämpöenergiatarpeet sekä ylijäämät kesä ja talvitilanteissa vuodelle 1999. Kesätilanteeksi on katsottu riittävän elokuu ja talvitilanteeksi helmikuu. Työn alussa on lyhyesti käyty läpi pinch-tekniikkaan liittyvää teoriaa ja tutustutaan yleisesti työssä käytettyyn Pro_pi2 laskentaohjelmaan. Laskennan tulokset on muodostettu käsittelemällä tiedonkeruujärjestelmistä haettu virtaavien nesteiden tulo- ja kohdelämpötiloista sekä massavirroista muodostuva data Pro_pi2 laskentaohjelmalla. Tulokset on esitetty kappaleessa 5, jossa kesä ja talvitilanteista saatuja tuloksia on verrattu keskenään. Mielenkiinnon vuoksi mukaan vertailuun on otettu vuoden 1999 tietojen lisäksi myös tiedot vuoden 2000 talvelle. Pinch-menetelmään perustuvan Pro_pi2 laskentaohjelman todettiin soveltuvan ennemminkin lämmön talteenottojärjestelmän sekä tehtaan energiakäytön esisuunnitteluun kuin jo olemassa olevan tehtaan tutkimiseen.

Software methods for HTML files protection in local / corporate networks: review and implementation

Tässä luomistyössä on esitetty tutkimus informaation suojaamisen menetelmien osalta paikallisissa ja ryhmäkuntaisissa verkoissa. Tutkimukseen kuuluu nykyaikaisten kryptagraafisten järjestelmien, Internetin/Intranetin ohjelmointikeinojen ja pääsyoikeuksien jakelumenetelmien analyysi. Tutkimusten perusteella on laadittu ohjelmiston prototyyppi HTML-tiedostojen suojaamista varten. Ohjelmiston laatimisprosessi on sisältänyt vaatimusten, järjestelmän ja suojelukomponenttien suunnittelun ja protytyypin testauksen. Ohjelmiston realisoinnin jälkeen kirjoitettiin käyttöohjeet. Ohjelmiston prototyyppi suojaa informaatiota HTML-tiedoston koko käytön aikana ja eri yrityksissä voidaan käyttää sitä pienien laajennuksien jälkeen.

Real-time Linux in electric drive systems

Reaaliaikaisten käyttöjärjestelmien käyttö sulautetuissa järjestelmissä on kasvamassa koko ajan. Sulautettuja tietokoneita käytetään yhä useammassa kohteessa kuten sähkökäyttöjen ohjauksessa. Sähkökäyttöjen ohjaus hoidetaan nykyisin yleensä nopealla digitaalisella signaaliprosessorilla (DSP), jolloin ohjelmointi ja päivittäminen on hidasta ja vaikeaa johtuen käytettävästä matalan tason Assembler-kielestä. Ratkaisuna yleiskäyttöisten prosessorien ja reaaliaikakäyttöjärjestelmien käyttö. Kaupalliset reaaliaikakäyttöjärjestelmät ovat kalliita ja lähdekoodin saaminen omaan käyttöön jopa mahdotonta. Linux on ei-kaupallinen avoimen lähdekoodin käyttöjärjestelmä, joten sen käyttö on ilmaista ja sitä voi muokata vapaasti. Linux:iin on saatavana useita laajennuksia, jotka tekevät siitä reaaliaikaisen käyttöjärjestelmän. Vaihtoehtoina joko kova (hard) tai pehmeä (soft) reaaliaikaisuus. Linux:iin on olemassa valmiita kehitysympäristöjä mutta ne kaipaavat parannusta ennen kuin niitä voidaan käyttää suuressa mittakaavassa teollisuudessa. Reaaliaika Linux ei sovellus nopeisiin ohjauslooppeihin (<100 ms) koska nopeus ei riitä vielä mutta nopeus kasvaa samalla kun prosessorit kehittyvät. Linux soveltuu hyvin rajapinnaksi nopean ohjauksen ja käyttäjän välille ja hitaampaan ohjaukseen.

Digitalización del sistema de control de nivel en calentadores y tanques de drenaje de una Central Nuclear

Contexto Una central nuclear, al igual que cualquier otro tipo de central generadora de energía eléctrica, mediante turbinas de vapor, está basada en un proceso termodinámico. El rendimiento de las mismas es función del salto entálpico del vapor, para mejorarlo las centrales están constituidas por un ciclo compound formado por turbina de alta presión y turbinas de baja presión, y un ciclo regenerativo consistente en calentar el agua de alimentación antes de su introducción a los generadores de vapor. Un ciclo regenerativo está basado en etapas de calentadores o cambiadores de calor para aprovechar al máximo la energía térmica del vapor, este proyecto está basado en la mejora y optimización del proceso de control de estos para contribuir a mejorar el rendimiento de la central. Objetivo Implementar un sistema de control que nos permita modernizar los clásicos sistemas basados en controles locales y comunicaciones analógicas. Mejorar el rendimiento del ciclo regenerativo de la central, aprovechando las mejoras tecnológicas que ofrece el mercado, tanto en el hardware como en el software de los sistemas de instrumentación y control. Optimizar el rendimiento de los lazos de control de cada uno de los elementos del ciclo regenerativo mediante estrategias de control. Procedimiento Desarrollo de un sistema de control actualizado considerando, como premisa principal, la fiabilidad del sistema, el análisis de fallos y la jerarquización del riesgo. Análisis y cálculo de los lazos de control considerando las premisas establecidas. Configuración de los lazos mediante estrategias de control que nos permitan optimizar y minimizar los efectos del fallo. Para ello se han utilizado parámetros y datos extraídos de la Central Nuclear de Ascó. Conclusiones Se ha modernizado y optimizado el sistema de control mejorando el rendimiento del ciclo regenerativo. Se ha conseguido un sistema más fiable, reduciendo el riesgo del fallo y disminuyendo los efectos de los mismos. El coste de un proyecto de estas características es inferior al de un sistema convencional y ofrece más posibilidades. Es un sistema abierto que permite utilizar e interconectar equipos de diferentes fabricantes, lo que favorece tanto el mantenimiento como las posibles ampliaciones futuras del sistema.

Security in multicast communication

Multicast is one method to transfer information in IPv4 based communication. Other methods are unicast and broadcast. Multicast is based on the group concept where data is sent from one point to a group of receivers and this remarkably saves bandwidth. Group members express an interest to receive data by using Internet Group Management Protocol and traffic is received by only those receivers who want it. The most common multicast applications are media streaming applications, surveillance applications and data collection applications. There are many data security methods to protect unicast communication that is the most common transfer method in Internet. Popular data security methods are encryption, authentication, access control and firewalls. The characteristics of multicast such as dynamic membership cause that all these data security mechanisms can not be used to protect multicast traffic. Nowadays the protection of multicast traffic is possible via traffic restrictions where traffic is allowed to propagate only to certain areas. One way to implement this is packet filters. Methods tested in this thesis are MVR, IGMP Filtering and access control lists which worked as supposed. These methods restrict the propagation of multicast but are laborious to configure in a large scale. There are also a few manufacturerspecific products that make possible to encrypt multicast traffic. These separate products are expensive and mainly intended to protect video transmissions via satellite. Investigation of multicast security has taken place for several years and the security methods that will be the results of the investigation are getting ready. An IETF working group called MSEC is standardizing these security methods. The target of this working group is to standardize data security protocols for multicast during 2004.