Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.

Raskaan kaluston tiedonkeruujärjestelmä sulautettuna Java-ohjelmistona

Tämä insinöörityö tehtiin Sesca Logistics IT Oy:lle osana Tekesin VAMOS-hanketta. Logistiikan alan yritysten resursseja on kuluttanut puutteellinen ja hidas tietojen kulku toimiston ja ajoneuvon välillä. Perinteisesti ajoneuvosta tarvittujen tietojen kerääminen on tapahtunut kynällä paperille, ja tiedonkulku on perustunut puhelinyhteyteen toimiston ja ajoneuvon kuljettajan välillä. Työn tavoitteena oli toteuttaa automaattinen tietojenkeruu ajoneuvosta sekä ajoneuvon sisältämistä laitteista. Reaaliaikainen raskaan kaluston tiedonkeruujärjestelmä mahdollistaa ajoneuvoista automaattisesti kerättyjen tietojen helpon seurannan Internetin välityksellä. Työssä suunniteltiin raskaan kaluston ajoneuvotietokoneen sulautettu ohjelmisto sekä palvelinpään ohjelmisto ajoneuvosta lähetettyjen tietojen vastaanottamiseen. Työ aloitettiin arkkitehtuurisuunnittelulla, jonka tuloksena hahmotettiin järjestelmän olellisimmat komponentit sekä valittiin sopivimmat protokollat komponenttien väliseen tiedonsiirtoon Internet-verkossa. Ajoneuvotietokoneen ohjelmisto toteutettiin sulautettuna ohjelmistona Java ME -teknologialla, jossa hyödynnettiin UML-mallinnusta sekä tunnettuja suunnittelumalleja (design patterns). Palvelinpään tietojen vastaanottoohjelmisto toteutettiin Java SE -teknologialla. Työn lopputuloksena syntyi reaaliaikanen ja hajautettu tietojärjestelmä logistiikan alan tarpeisiin. Tietojärjestelmä kykenee tuottamaan reaalaikaista tietoa ajoneuvon sijainnista sekä ajoneuvon CAN-väylän sisältämistä tiedoista. Lisäksi tietojärjestelmä mahdollistaa tienhoitoajoneuvojen aurojen ja suolasirottimen seurannan. Tietojärjestelmän avulla yritykset voivat seurata kustannustehokkuuttaan ja saada nopeammin yksityiskohtaisempia tietoja ajoneuvojen tilasta.

Prevalence and clinical outcomes for patients with MET protein expression in patients with non-small cell lung cancer in Europe: Results from the European Thoracic Oncology Platform Lungscape Project.

Aim The reported prevalence of MET overexpression varies from 25-55% in non-small cell lung cancer (NSCLC) and clinical correlations are emerging slowly. In a well-defined NSCLC cohort of the Lungscape program, we explore the epidemiology, the natural history of IHC MET positivity and its association to OS, RFS and TTR. Methods Resected stage I-III NSCLC identified based on the quality of clinical data and FFPE tissue availability were assessed for MET expression using immunohistochemistry (IHC) on TMAs (CONFIRM anti total c-MET assay, clone SP44, Ventana BenchMark platform). All cases were analysed at participating pathology laboratories using the same protocol, after passing an external quality assurance program. MET positive status is defined as ≥ 50% of tumor cells staining with 2+ or 3+ intensity. Results A total of 2709 cases are included in the iBiobank and will be analysed. IHC MET expression is currently available for 1552 patients, with positive MET IHC staining in 380 cases [24.5%; IHC 3+ in 157 cases (41.3%) and 2+ in 223 cases (58.7%)]. The cohort of 1552 patients includes 48.2%, 44.7% and 4.4% cases of adenocarcinoma, squamous and large cell histologies, respectively. IHC MET status was independent of stage, age and smoking history. Significant differences in MET positivity were associated with gender (32% vs. 21% for female vs. male, p < 0.001), with performance status (25% vs. 18% for 0 vs. 1-3, p = 0.006), and histology (34%, 14% and 24% for adenocarcinoma, squamous and large cell carcinoma, p < 0.001). IHC MET positivity was independent of the IHC ALK status (p = 0.08). At last FU, 52% of patients were still alive, with a median FU of 4.8 yrs. No association of IHC MET was found with OS, RFS or TTR. Conclusions The preliminary results for this large multicentre European cohort describe a prevalence of MET overexpression that seems lower than previous observations in NSCLC, such as reported for the OAM4971g trial, suggesting potential biological differences between surgically resected and metastatic disease. Analysis for the full cohort is ongoing and results will be presented. Disclosure L. Bubendorf: Disclosures: Stock ownership: Roche Advisory boards: Roche, Pfizer Research support: Roche; K. Schulze: Full time employee of Roche; A. Das-Gupta: I am a full time employee of Roche. All other authors have declared no conflicts of interest.

Platform pricing and consumer foresight: The case of airports

Airports have become platforms that derive revenues from both aeronautical and commercial activities. The demand for these services is characterized by a one-way complementarity in that only air travelers can purchase retail goods at the airport terminals. We analyze a model of optimal airport behavior in which this one-way complementarity is subject to consumer foresight, i.e., consumers may not anticipate in full the ex post retail surplus when purchasing a flight ticket. An airport sets landing fees, and, in addition, also chooses the retail market structure by selecting the number of retail concessions to be awarded. We find that, with perfectly myopic consumers, the airport chooses to attract more passengers via low landing fees, and also sets the minimum possible number of retailers in order to increase the concessions’ revenues, from which it obtains the largest share of profits. However, even a very small amount of anticipation of the consumer surplus from retail activities changes significantly the airport’s choices: the optimal airport policy is dependent on the degree of differentiation in the retail market. When consumers instead have perfect foresight, the airport establishes a very competitive retail market, where consumers enjoy a large surplus. This attracts passengers and it is exploited by the airport by charging higher landing fees, which then constitute the largest share of its profits. Overall, the airport’s profits are maximal when consumers have perfect foresight. Keywords: two-sided markets, platform pricing, one-way demand complementarity, consumer foresight. JEL classification: L1, L2, L93.

Design and Validation of a Novel Generic Platform for the Production of Tetravalent IgG1-like Bispecific Antibodies.

We have designed and validated a novel generic platform for production of tetravalent IgG1-like chimeric bispecific Abs. The VH-CH1-hinge domains of mAb2 are fused through a peptidic linker to the N terminus of mAb1 H chain, and paired mutations at the CH1-CL interface mAb1 are introduced that force the correct pairing of the two different free L chains. Two different sets of these CH1-CL interface mutations, called CR3 and MUT4, were designed and tested, and prototypic bispecific Abs directed against CD5 and HLA-DR were produced (CD5xDR). Two different hinge sequences between mAb1 and mAb2 were also tested in the CD5xDR-CR3 or -MUT4 background, leading to bispecific Ab (BsAbs) with a more rigid or flexible structure. All four Abs produced bound with good specificity and affinity to CD5 and HLA-DR present either on the same target or on different cells. Indeed, the BsAbs were able to efficiently redirect killing of HLA-DR(+) leukemic cells by human CD5(+) cytokine-induced killer T cells. Finally, all BsAbs had a functional Fc, as shown by their capacity to activate human complement and NK cells and to mediate phagocytosis. CD5xDR-CR3 was chosen as the best format because it had overall the highest functional activity and was very stable in vitro in both neutral buffer and in serum. In vivo, CD5xDR-CR3 was shown to have significant therapeutic activity in a xenograft model of human leukemia.

Extension and evaluation of JXTA protocols for supporting reliable P2P distributed computing

Peer-reviewed

A Co-Processor Approach for Efficient Java Execution in Embedded Systems

This thesis deals with a hardware accelerated Java virtual machine, named REALJava. The REALJava virtual machine is targeted for resource constrained embedded systems. The goal is to attain increased computational performance with reduced power consumption. While these objectives are often seen as trade-offs, in this context both of them can be attained simultaneously by using dedicated hardware. The target level of the computational performance of the REALJava virtual machine is initially set to be as fast as the currently available full custom ASIC Java processors. As a secondary goal all of the components of the virtual machine are designed so that the resulting system can be scaled to support multiple co-processor cores. The virtual machine is designed using the hardware/software co-design paradigm. The partitioning between the two domains is flexible, allowing customizations to the resulting system, for instance the floating point support can be omitted from the hardware in order to decrease the size of the co-processor core. The communication between the hardware and the software domains is encapsulated into modules. This allows the REALJava virtual machine to be easily integrated into any system, simply by redesigning the communication modules. Besides the virtual machine and the related co-processor architecture, several performance enhancing techniques are presented. These include techniques related to instruction folding, stack handling, method invocation, constant loading and control in time domain. The REALJava virtual machine is prototyped using three different FPGA platforms. The original pipeline structure is modified to suit the FPGA environment. The performance of the resulting Java virtual machine is evaluated against existing Java solutions in the embedded systems field. The results show that the goals are attained, both in terms of computational performance and power consumption. Especially the computational performance is evaluated thoroughly, and the results show that the REALJava is more than twice as fast as the fastest full custom ASIC Java processor. In addition to standard Java virtual machine benchmarks, several new Java applications are designed to both verify the results and broaden the spectrum of the tests.

Java 3D

Tämä insinöörityö kertoo Java 3D -ohjelmointirajapinnan perusteista ja sen käytöstä kolmiulotteisen tietokonegrafiikan luomisessa Java ohjelmointikielellä. Java 3D on rajapinta Java-ohjelmointikielelle, jonka avulla voidaan luoda ja käsitellä kolmiulotteista tietokonegrafiikkaa. Java 3D -rajapinnan avulla käsitellään kolmiulotteista tietokonegrafiikka erityisen maisemagraafimallin avulla. Maisemagraafi on binääripuuta muistuttava malli, joka mahdollistaa kolmiulotteisten kohteiden ja niille tapahtuvien muunnoksien käsittelyn hierarkisessa järjestyksessä. Työssä käydään läpi Java 3D -maisemagraafien luominen ja kolmiulotteisessa avaruudessa sijaitseville kappaleille tehtäviä perusoperaatioita kuten siirtoa ja kiertoa. Lisäksi käydään läpi myös erilaisia animoinnissa ja interaktiossa käytettäviä luokkia, joiden avulla ohjelmoija saa automatisoitua muunnoksia sekä käyttäjä voi antaa syötteitä hiirellä ja näppäimistöllä. Näiden lisäksi käydään läpi myös mallin valaistusta, varjoja, teksturointia sekä omien kolmiulotteisten mallien tuontia Java 3D -maailmaan. Opinnäytetyön yhteydessä on tehty myös kirjo erilaisia esimerkkejä, jotka ovat saatavilla verkkosivustolta osoitteessa http://www.pahvilaatikko.org/j3d lisäksi kopio verkkosivustosta löytyy myös opinnäytetyön mukana tulevalta cd-levyltä.

Developing a Service-Oriented Software Platform

Tehokkaasti toimiva sähköinen tiedonvälitys yrityksen omien sovellusten välillä sekä sen liikekumppaneiden kanssa on kasvanut merkittäväksi yrityksen kilpailukykyä lisääväksi tekijäksi. Yritysten erilaiset tietojärjestelmät asettavat haasteita tehokkaalle tiedonvälitykselle näiden järjestelmien välillä. Perinteiset EDI teknologioihin perustuvat sähköisen tiedonvälityksen ratkaisut eivät pysty mukautumaan nykyisin nopeasti muuttuviin markkinatilanteisiin. Palvelukeskeiseen arkkitehtuuriin ja Web-palveluihin perustuvat teknologiat mahdollistavat mukautumisen erilaisiin muutoksiin liiketoiminnassa nopeammin ja helpommin. Lisäksi ne nopeuttavat tiedon integrointia erilaisten tietojärjestelmien välillä, koska tiedonvälityksessä käytetään yleisesti hyväksyttyihin standardeihin perustuvia tiedonsiirtoprotokollia sekä tietoformaatteja. Diplomityössä esitellään keskeiset teknologiat ja menetelmät sähköisen tiedonvälityksen toteuttamiseen. Lisäksi työssä vertaillaan erilaisia vaihtoehtoja, joilla sähköinen tiedonvälitys voidaan toteuttaa. Vaihtoehtoina työssä ovat tiedonvälityspalveluiden ostaminen toiselta yritykseltä, olemassa olevan valmiin ohjelmiston hyödyntäminen, tai kokonaan uuden sovellusalustan kehittäminen. Työssä kuvaillaan palvelukeskeisen sovellusalustan toteutus, joka mahdollistaa tehokkaan sekä joustavan tiedonvälityksen sovellusten välillä. Alustan tarjoamien palveluiden päälle voidaan rakentaa erilaisia liiketoimintaa tukevia palveluita, jotka voivat hyödyntää sovellusalustan tarjoamia toiminnallisuuksia. Alustan toteutusta arvioidaan kolmen liiketoimintaskenaarion toteutuksesta saatujen kokemusten perusteella.

eLab, a Personal Learning Environment for the Green Open Innovation Platform

Open Innovation is a relatively new concept which involves a change of paradigm in the R+D+i processes of companies whose aim is to create new technologies or new processes. If to this change, we add the need for innovation in the new green and sustainability economy, and we set out to create a collaborative platform with a learning space where this can happen, we will be facing an overwhelming challenge which requires the application of intelligent programming technologies and languages at the service of education.The aim of the Green IDI (Green Open Innovation) ¿ Economic development and job creation vector in SMEs, based on the environment and sustainability project is to create a platform where companies and individual researchers can perform open innovation processes in the field of sustainability and the environment.The Green IDI (Green Open Innovation) project is funded under the program INNPACTO by the Ministry of Science and Innovation of Spain and is being developed through a consortium formed by the following institutions: GRUPO ICA; COMPARTIA; GRUPO INTERCOM; CETAQUA and the Instituto de Investigación en Inteligencia Artificial (IIIA) from Consejo Superior de Investigaciones Científicas (CSIC). Also the consortium include FUNDACIÓ PRIVADA BARCELONA DIGITAL; PIMEC and UNIVERSITAT OBERTA DE CATALUNYA (UOC).Sustainability and positive action for the environment are considered the principle vector of economic development for companies. As Nicolás Scoli says (2007) ¿in short, preventing unnecessary consumption and the efficient consumption of resources means producing greater wealth with less. Both effects lead to reduced pollution linked to production and consumption¿.The Spanish Sustainable Development Strategy (EEDS) plan defends consumption and sustainable production linked to social and economic development by adhering to the commitment not to endanger ecosystems and abolishing the idea that economic growth is directly proportional to the deterioration of the environment.Uniting the Open Innovation and New Green Economy concepts leads to the "Green Open Innovation¿ Platform creation project.This article analyses the concept of open innovation and defines the importance of the new green and sustainable economy. Lastly, it proposes the creation of eLab. The eLab is defined as an Open Green Innovation Platform personal and collaborative education space which is fed by the interactions of users and which enables innovation processes based on new green economy concepts to be carried out.The creation of a personal learning environment such as eLab on the Green Open Innovation Platform meets the need to offer a collaborative space where platform users can improve their skills regarding the environment and sustainability based on collaborative synergies through Information and Communication Technologies.

Where's my pet : Desarrollo de una aplicación con Java EE

Trabajo fin de grado acerca de la creación de una aplicación en Java EE para la localización de mascotas mediante el uso de reconocimiento facial en dispositivos móviles.

Integration of Real-Time Simulator, Motion Platform and Haptics

This thesis describes the process of the integration of a real-time simulator environment with a motion platform and a haptic device as a part of the Kvalive project. Several programs running on two computers were made to control the different devices of the environment. User tests were made to obtain information of needed improvements to make the simulator more realistic. Also new ideas for improving the simulator and directions of further research were obtained with the help of this research.