Technology educational affordance: Bridging the gap between patterns of interaction and technology usage

Peer-reviewed

Contamination of genomic databases by HIV-1 and its possible consequences. A study in Bioinformatics.

Peer-reviewed

FOSS issues in technology transfers from the University to the Industry

FOSS has always been particularly welcome in Universities. Its spirit corresponds generally with the academic state of mind, and royalty-free technologies are particularly appreciated where money is usually lacking.But at the opposite side of the spectrum, the universities¿ TTO¿s (Technology Transfer Officers) are supposed to ¿valorize¿ the production of research departments and to enable profit making cooperations with the industry. How should FOSS licensing be tackled in such context?

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

Assessing technology-based spin-offs from university support units

This paper takes a regional studies approach to assess spin-offs from a university-based technology transfer network. We first detect the regional objectives, inputs and outputs needed to assess spin-offs from support programmes. We then provide evidence on regional mechanisms for firm creation. We analyse spin-offs created at Catalan universities and find that many efficient spin-offs have formal technology transfer agreements, and emerge from technology-oriented universities. We also find that higher innovation levels and experience from the parent university are associated with higher efficiency, which is positively related to future fundamental profitability. Finally, we propose regional policy making and research directions.

Protein contamination on Klason lignin contents in tropical grasses and legumes

The objective of this work was to evaluate the extent of protein contamination on Klason lignin (KL) in tropical grasses and legumes, and to propose an equation to estimate the protein-free content of Klason lignin (KLp). Five grass (30 samples) and 12 legume species (31 samples) were evaluated. Legumes had higher KL contents. Protein contamination was significant in both grasses and legumes, but greater in legume samples. The model to predict KLp was based on KL and crude protein (CP) contents, as follows: KLp = 0.8807KL - 0.0938KL x D - 0.00338CP (R2=0.935), in which D=0, for grasses, and D=1 for legumes.

Methods of Telecommunication Technology Forecasting

This master's thesis coversthe concepts of knowledge discovery, data mining and technology forecasting methods in telecommunications. It covers the various aspects of knowledge discoveryin data bases and discusses in detail the methods of data mining and technologyforecasting methods that are used in telecommunications. Main concern in the overall process of this thesis is to emphasize the methods that are being used in technology forecasting for telecommunications and data mining. It tries to answer to some extent to the question of do forecasts create a future? It also describes few difficulties that arise in technology forecasting. This thesis was done as part of my master's studies in Lappeenranta University of Technology.

Benchmarking project of the Department of Electrical Engineering of Lappeenranta University of Technology

Lappeenrannan teknillisen korkeakoulun sähkötekniikan osasto muutti 1.8.2005 sähkötekniikan tutkinnon kaksiportaiseksi ja vastaamaan näin Bologna-prosessia ja Suomen yliopistolainsäädäntöä. Tutkinnonuudistuksen myötä osasto haluaa varmistaa sähkötekniikan tutkintojen laadun ja vertailtavuuden sekä parantaa opiskelijoidensekä henkilökunnan liikkuvuutta. Tutkintojen laatu ja vertailtavuus osoitetaan sähkötekniikan osaston benchmark-projektilla, jossa kerätään tietoja maisteri- ja tohtorintutkintoa tarjoavista eurooppalaisista yliopistoista. Diplomityö käsittää BM-projektin kolmannen vaiheen suunnittelun ja toteutuksen sisältäen teoriaa benchmark-projekteille tyypillisistä toimintatavoista. Hyväksi havaitut menetelmiä, kuten kyselyt ja matriisit, on tässä työssä otettu soveltuvin osin sähkötekniikan osaston BM-projektin työkaluiksi. Diplomityössä analysoidaan työkalujen avulla BM-kumppaneilta kerättyjä tietoja sekä esitetään ratkaisuja, miten sähkötekniikan osastolla voidaan jatkaa parhaiden toimintatapojen löytämistä.

Study of post-deposition contamination in low-temperature deposited polysilicon films

The presence of hydrogen in polysilicon films obtained at low temperatures by hot-wire CVD and the post-deposition oxidation by air-exposure of the films are studied in this paper. The experimental results from several characterization techniques (infrared spectroscopy, X-ray photoelectron spectroscopy, secondary ion mass spectrometry and wavelength dispersive spectroscopy) showed that hydrogen and oxygen are homogeneously distributed at grain boundaries throughout the depth of the films. Hydrogen is introduced during the growth process and its concentration is higher in samples deposited at lower temperatures. Oxygen diffuses along the grain boundaries and binds to silicon atoms, mainly in Si 2O groups.

Effect of water contamination on the shear bond strength of five orthodontic adhesives

Objectives: To evaluate the shear bond strength and site of failure of brackets bonded to dry and wet enamel. Study design: 50 teeth were divided into ten groups of 5 teeth each (10 surfaces). In half the groups enamel was kept dry before bonding, and in the other half distilled water was applied to wet the surface after etching. The following groups were established: 1)Acid/Transbond-XT (dry/wet) XT; 2) Transbond Plus Self Etching Primer (TSEP)/Transbond-XT paste (dry/wet); 3) Concise (dry), Transbond MIP/Concise (wet), 4) FujiOrtho-LC (dry/wet); 5) SmartBond (dry/wet). Brackets were bonded to both buccal and lingual surfaces. Specimens were stored in distilled water (24 hours at 37ºC) and thermocycled. Brackets were debonded using a Universal testing machine (cross-head speed 1 mm/min). Failure sites were classified using a stereomicroscope. Results: No significant differences in bond strength were detected between the adhesives under wet and dry conditions except for Smart- Bond, whose bond strength was significantly lower under dry conditions. For all the adhesives most bond failures were of mixed site location except for Smartbond, which failed at the adhesive-bracket interface. Conclusions: Under wet conditions the bonding capacity of the adhesives tested was similar than under dry conditions, with the exception of SmartBond which improved under wet conditions

Aligning Technology Innovation Processes for Possible Collaboration

Diplomityön tavoitteena on innovaatioprosessien selventäminen ja yhteensovittaminen radikaalien teknologia innovaatioiden osalta. Prosessien yhteensovittamisen edellytyksenä on teknologia innovaation radikaalisuuden ymmärtäminen. Kohteena on alkuvaiheen innovaatioprosessi jonka aikana virallinen yhteistyö ei vielä ole mandollista. Kehitetyn mallinavulla voidaan arvioida yrityksen kokemaa radikaalisuutta innovaatioprosessin alkuvaiheessa. On tärkeää ymmärtää miten vuorovaikutuksessa olevat yritykset kokevat innovaation radikaalisuuden prosessin alkuvaiheessa. Prosessien eroavaisuudet voidaan sanoa riippuvan yritysten näkökulmasta, koska niiden toiminnot määrittyvät koetun radikaalisuuden mukaan.Yhtäläisenä koettu radikaalisuus luo pohjan avoimelle vuorovaikutukselle ja antaa viitteitä syvemmästä yhteistyöstä tulevaisuudessa. Vertikaalisti sijoittuneiden yritysten prosessien esitetty yhteensovitus perustuu molemminpuoliseen radikaalisuuteen ja sisäisen hyväksynnän vastaavuuteen. Tällöin osapuolet ovat mukana samalla sitoumuksella prosessin jatkumisen ollessa epävarma.

Targeting Cytokines: Production and Characterization of Anti-TNF-α scFvs by Phage Display Technology.

The antibody display technology (ADT) such as phage display (PD) has substantially improved the production of monoclonal antibodies (mAbs) and Ab fragments through bypassing several limitations associated with the traditional approach of hybridoma technology. In the current study, we capitalized on the PD technology to produce high affinity single chain variable fragment (scFv) against tumor necrosis factor-alpha (TNF- α), which is a potent pro-inflammatory cytokine and plays important role in various inflammatory diseases and malignancies. To pursue production of scFv antibody fragments against human TNF- α, we performed five rounds of biopanning using stepwise decreased amount of TNF-α (1 to 0.1 μ g), a semi-synthetic phage antibody library (Tomlinson I + J) and TG1 cells. Antibody clones were isolated and selected through enzyme-linked immunosorbent assay (ELISA) screening. The selected scFv antibody fragments were further characterized by means of ELISA, PCR, restriction fragment length polymorphism (RFLP) and Western blot analyses as well as fluorescence microscopy and flow cytometry. Based upon binding affinity to TNF-α , 15 clones were selected out of 50 positive clones enriched from PD in vitro selection. The selected scFvs displayed high specificity and binding affinity with Kd values at nm range to human TNF-α . The immunofluorescence analysis revealed significant binding of the selected scFv antibody fragments to the Raji B lymphoblasts. The effectiveness of the selected scFv fragments was further validated by flow cytometry analysis in the lipopolysaccharide (LPS) treated mouse fibroblast L929 cells. Based upon these findings, we propose the selected fully human anti-TNF-α scFv antibody fragments as potential immunotherapy agents that may be translated into preclinical/clinical applications.

Organisaation innovatiivisuutta edistävät ja estävät tekijät. Case Technology Business Research Center

Tämän työn toimeksiantajaorganisaatio oli Lappeenrannan teknillisen yliopiston alainen, kauppatieteitä, teknologiaa ja tuotantotaloutta työssään yhdistävä tutkimusyksikkö, Technology Business Research Center, TBRC. Erään innovatiivisuustutkimusprojektin (InnoSpring) yhteydessä haluttiin selvittää myös oman tutkimusyksikön innovatiivisuuteen vaikuttavia, edistäviä ja estäviä tekijöitä. Tutkielman tavoitteena oli kartoittaa niitä seikkoja, jotka organisaation - tässä tapauksessa yliopiston tutkimusyksikön - henkilökunnan, projektityöntekijöiden, projektipäälliköiden sekä johdon mukaan vaikuttavat yksikön kykyyn luoda ja omaksua uutta, sen innovatiivisuuteen. Työ toteutettiin focus group-ryhmähaastattelumenetelmällä (kvalitatiivinen tutkimus), joihin osallistuivat omina ryhminään työntekijätaso, projektipäälliköt sekä johto.Haastattelut äänitettiin, litteroitiin ja koodattiin Atlas-Ti-ohjelmistolla. Loppuraportti verkostokuvineen luovutettiin tutkimuslaitokselle heinäkuussa 2005. Ryhmäkeskustelun teemoista ja kysymysten muodosta johtuen tulokset käsittelivät niin tutkimusyksikön nykyistä tilaa kuin eräänlaista "toivetilaa", millainen olisi ihanteellinen ja innovatiivinen työpaikka. Merkillepantavaa oli, että työssä tuli systemaattisesti esiin enemmän innovatiivisuutta edistäviä kuin ehkäiseviä seikkoja - vaikka osa edistävistä seikoista koskikin nimenomaan "toivetilaa". Keskustelluimpia teemoja olivat johtajuus,tavoitteellisuus ja strategian, yhteisen suunnan tarve. Samoin olemassa olevienprosessien kehittäminen, osaamisen (niin oman kuin koko organisaationkin) kokoaminen ja kehittäminen edelleen sekä tulosten jalkauttaminen.