Rapid, reliable and inexpensive quality assessment of biotinylated cRNA

The interpretation of oligonucleotide array experiments depends on the quality of the target cRNA used. cRNA target quality is assessed by quantitative analysis of the representation of 5' and 3' sequences of control genes using commercially available Test arrays. The Test array provides an economically priced means of determining the quality of labeled target prior to analysis on whole genome expression arrays. This manuscript validates the use of a duplex RT-PCR assay as a faster (6 h) and less expensive (6 were chosen and classified as degraded cRNAs, and 31 samples with a ß-actin 3'/5' ratio <6 were selected as good quality cRNAs. Blinded samples were then used for the RT-PCR assay. After gel electrophoresis, optical densities of the amplified 3' and 5' fragments of ß-actin were measured and the 3'/5' ratio was calculated. There was a strong correlation (r² = 0.6802) between the array and the RT-PCR ß-actin 3'/5' ratios. Moreover, the RT-PCR 3'/5' ratio was significantly different (P < 0.0001) between undegraded (mean ± SD, 0.34 ± 0.09) and degraded (1.71 ± 0.83) samples. None of the other parameters analyzed, such as i) the starting amount of RNA, ii) RNA quality assessed using the Bioanalyzer Chip technology, or iii) the concentration and OD260/OD280 ratio of the purified biotinylated cRNA, correlated with cRNA quality.

Local Binary Patterns in Focal-Plane Processing. Analysis and Applications

Feature extraction is the part of pattern recognition, where the sensor data is transformed into a more suitable form for the machine to interpret. The purpose of this step is also to reduce the amount of information passed to the next stages of the system, and to preserve the essential information in the view of discriminating the data into different classes. For instance, in the case of image analysis the actual image intensities are vulnerable to various environmental effects, such as lighting changes and the feature extraction can be used as means for detecting features, which are invariant to certain types of illumination changes. Finally, classification tries to make decisions based on the previously transformed data. The main focus of this thesis is on developing new methods for the embedded feature extraction based on local non-parametric image descriptors. Also, feature analysis is carried out for the selected image features. Low-level Local Binary Pattern (LBP) based features are in a main role in the analysis. In the embedded domain, the pattern recognition system must usually meet strict performance constraints, such as high speed, compact size and low power consumption. The characteristics of the final system can be seen as a trade-off between these metrics, which is largely affected by the decisions made during the implementation phase. The implementation alternatives of the LBP based feature extraction are explored in the embedded domain in the context of focal-plane vision processors. In particular, the thesis demonstrates the LBP extraction with MIPA4k massively parallel focal-plane processor IC. Also higher level processing is incorporated to this framework, by means of a framework for implementing a single chip face recognition system. Furthermore, a new method for determining optical flow based on LBPs, designed in particular to the embedded domain is presented. Inspired by some of the principles observed through the feature analysis of the Local Binary Patterns, an extension to the well known non-parametric rank transform is proposed, and its performance is evaluated in face recognition experiments with a standard dataset. Finally, an a priori model where the LBPs are seen as combinations of n-tuples is also presented

Rankapuun ja -hakkeen laadun vaihtelu terminaalivarastoinnissa

Työssä tutkittiin polttoaineterminaalissa varastoitavan puupolttoaineen laadunmuutoksia. Tutkimuksessa tarkasteltiin hakettamattomien rankapuiden ja rankapuuhakkeen kosteuden ja lämpöarvon muutosta. Myös kuiva-ainetappiota tutkittiin aikaisempien tutkimusten perusteella. Tutkimusaineisto kerättiin Etelä-Savon Energian polttoaineterminaaleista. Kosteus-pitoisuuksia mitattiin Hydromette M2050 -pikakosteusmittarilla ja uunikuivaus-menetelmällä standardin SFS-EN 14774 mukaisesti. Tutkimuksessa huomattiin pikakosteusmittarin toimivan riittävän luotettavalla tasolla rankapuiden mittauksissa, mutta hakkeen mittauksissa mittari osoittautui toimimattomaksi. Varastointiaika ei vaikuttanut polttoaineiden lämpöarvoihin, mutta kosteuspitoisuus vaihteli suuresti. Tutkimustuloksista pääteltiin rangan kuivuvan terminaalivarastossa ja hakkeen kosteuden pysyvän vakiona. Energiasisällön puolesta rankapuuta voidaan varastoida yli 2 vuotta, mutta hakkeen varastointiaika tulisi pitää mahdollisimman lyhyenä.

Agent-based management systems for many-core platforms : rigorous design and efficient implementation

Due to various advantages such as flexibility, scalability and updatability, software intensive systems are increasingly embedded in everyday life. The constantly growing number of functions executed by these systems requires a high level of performance from the underlying platform. The main approach to incrementing performance has been the increase of operating frequency of a chip. However, this has led to the problem of power dissipation, which has shifted the focus of research to parallel and distributed computing. Parallel many-core platforms can provide the required level of computational power along with low power consumption. On the one hand, this enables parallel execution of highly intensive applications. With their computational power, these platforms are likely to be used in various application domains: from home use electronics (e.g., video processing) to complex critical control systems. On the other hand, the utilization of the resources has to be efficient in terms of performance and power consumption. However, the high level of on-chip integration results in the increase of the probability of various faults and creation of hotspots leading to thermal problems. Additionally, radiation, which is frequent in space but becomes an issue also at the ground level, can cause transient faults. This can eventually induce a faulty execution of applications. Therefore, it is crucial to develop methods that enable efficient as well as resilient execution of applications. The main objective of the thesis is to propose an approach to design agentbased systems for many-core platforms in a rigorous manner. When designing such a system, we explore and integrate various dynamic reconfiguration mechanisms into agents functionality. The use of these mechanisms enhances resilience of the underlying platform whilst maintaining performance at an acceptable level. The design of the system proceeds according to a formal refinement approach which allows us to ensure correct behaviour of the system with respect to postulated properties. To enable analysis of the proposed system in terms of area overhead as well as performance, we explore an approach, where the developed rigorous models are transformed into a high-level implementation language. Specifically, we investigate methods for deriving fault-free implementations from these models into, e.g., a hardware description language, namely VHDL.

Readout architectures for hybrid pixel detector readout chips

The original contribution of this thesis to knowledge are novel digital readout architectures for hybrid pixel readout chips. The thesis presents asynchronous bus-based architecture, a data-node based column architecture and a network-based pixel matrix architecture for data transportation. It is shown that the data-node architecture achieves readout efficiency 99% with half the output rate as a bus-based system. The network-based solution avoids “broken” columns due to some manufacturing errors, and it distributes internal data traffic more evenly across the pixel matrix than column-based architectures. An improvement of > 10% to the efficiency is achieved with uniform and non-uniform hit occupancies. Architectural design has been done using transaction level modeling (TLM) and sequential high-level design techniques for reducing the design and simulation time. It has been possible to simulate tens of column and full chip architectures using the high-level techniques. A decrease of > 10 in run-time is observed using these techniques compared to register transfer level (RTL) design technique. Reduction of 50% for lines-of-code (LoC) for the high-level models compared to the RTL description has been achieved. Two architectures are then demonstrated in two hybrid pixel readout chips. The first chip, Timepix3 has been designed for the Medipix3 collaboration. According to the measurements, it consumes < 1 W/cm^2. It also delivers up to 40 Mhits/s/cm^2 with 10-bit time-over-threshold (ToT) and 18-bit time-of-arrival (ToA) of 1.5625 ns. The chip uses a token-arbitrated, asynchronous two-phase handshake column bus for internal data transfer. It has also been successfully used in a multi-chip particle tracking telescope. The second chip, VeloPix, is a readout chip being designed for the upgrade of Vertex Locator (VELO) of the LHCb experiment at CERN. Based on the simulations, it consumes < 1.5 W/cm^2 while delivering up to 320 Mpackets/s/cm^2, each packet containing up to 8 pixels. VeloPix uses a node-based data fabric for achieving throughput of 13.3 Mpackets/s from the column to the EoC. By combining Monte Carlo physics data with high-level simulations, it has been demonstrated that the architecture meets requirements of the VELO (260 Mpackets/s/cm^2 with efficiency of 99%).

Modelling Cutting States in Rough Turning of 34CrNiMo6 Steel

Rough turning is an important form of manufacturing cylinder-symmetric parts. Thus far, increasing the level of automation in rough turning has included process monitoring methods or adaptive turning control methods that aim to keep the process conditions constant. However, in order to improve process safety, quality and efficiency, an adaptive turning control should be transformed into an intelligent machining system optimizing cutting values to match process conditions or to actively seek to improve process conditions. In this study, primary and secondary chatter and chip formation are studied to understand how to measure the effect of these phenomena to the process conditions and how to avoid undesired cutting conditions. The concept of cutting state is used to address the combination of these phenomena and the current use of the power capacity of the lathe. The measures to the phenomena are not developed based on physical measures, but instead, the severity of the measures is modelled against expert opinion. Based on the concept of cutting state, an expert system style fuzzy control system capable of optimizing the cutting process was created. Important aspects of the system include the capability to adapt to several cutting phenomena appearing at once, even if the said phenomena would potentially require conflicting control action.

Drying kinetics of potato pulp waste

Potato pulp waste (PPW) drying was investigated under different experimental conditions (temperatures from 50 to 70 °C and air flow from 0.06 to 0.092 m³ m- 2 s- 1) as a possible way to recover the waste generated by potato chip industries and to select the best-fit model to the experimental results of PPW drying. As a criterion to evaluate the fitting of mathematical models, a method based on the sum of the scores assigned to the four evaluated statistical parameters was used: regression coefficient (R²), relative mean error P (%), root mean square error (RMSE), and reduced chi-square (χ²). The results revealed that temperature and air velocity are important parameters to reduce PPW drying time. The models Midilli and Diffusion had the lowest sum values, i.e., with the best fit to the drying data, satisfactorily representing the drying kinetics of PPW.

Somen kielinen d. Martinus Lutherin Pienembi catechismus saxan kielen jälken ojettu, a Canuto Carelio Vijdeburgio. Ja hänen culutuxellans painettu Stockholman caupungis

Arkit: A-K4.

Hakeperävaunun aerodynamiikan parantaminen

Raskaankaluston ajoneuvojen aerodynaaminen kehitys on kulkenut väärään suuntaan jo vuosisadan verran ja niiden muodon määräävä tekijä on kuljetustilan maksimointi ja toi-minnallisuus. Lähiaikoina on astumassa EU:ssa uusi direktiivi voimaan, joka sallii lisämas-san käyttämisen aerodynaamisiin lisäosiin. Työn tarkoituksena on tutkia mahdollisuuksia parantaa hakeperävaunun aerodynamiikkaa yksinkertaisilla lisäosilla. Työ on rajattu koskemaan perävaununetuosaan, -sivuosaan ja -pohjaan. Lisäksi rajoitteita asettaa Suomenlainsäädäntö ja EU:n direktiivit. Työssä perehdytään ilmanvastusvoiman syntymekanismeihin raskaankaluston ajoneuvojen kannalta ja käydään läpi merkittävimmät vaikuttavat tekijät ilmanvastusvoimiin sekä kuorma-auton perävaunun eri muotojen ja osien vaikutus. Perävaunuun asetettavien il-manohjaimien vaikutukset ja toiminta selvitetään. Avainasemassa hakeperävaunun aerodynamiikan parantamisessa on ilmavirtauksen estä-minen perävaunun alle sekä etupuolelta. Lisäksi virtausten muuttamien perävaunun takana on hyödyllistä. Merkittävimmät hyödyt saadaan niistä ratkaisuista, jotka estävät ilman virtausta perävau-nun alle sekä renkaisiin. Näitä ratkaisuja olivat sivuhelmat ja pohjan sekä renkaiden kote-lointi. Lisäksi ilmavirtauksen estäminen perävaunun edestä tuotti merkittävää hyötyä. Levy perävaunun välissä tai koko välin peittämällä saadaan aikaan huomattavaa vähenemistä ilmanvastuksessa.

Hakeperävaunun rungon esikorotuksen määritys

Hakeperävaunun rungon esikorotuksen suuruutta laskennallisesti ei ollut aiemmin määritet-ty Konepaja Antti Ranta Oy:ssä. Hakeperävaunun runko on valmistettu teräksestä. Tutki-muksessa luoduilla laskentamalleilla selvitettiin viisiakselisen hakeperävaunun rungon pys-tysuuntainen taipuma kuormitettuna. Tutkimus suoritettiin laskemalla hakeperävaunun pystysuuntainen siirtymä 42 tonnin ja 36 tonnin kokonaismassojen kuormituksilla hakeperävaunun rungon pituuden suhteen. Käsin-laskentamenetelmä on tässä tutkimuksessa englannin kieliseltä nimeltään conjugate beam method, suoraan käännettynä konjugaattipalkkimenetelmä. FE-analyysia sovellettiin kah-della eri laskentamallilla; käsinlaskentaa vertailevalla ja todellista hakeperävaunun runkoa vertailevilla FE-analyyseilla. Tutkimuksessa käytettyjen eri laskentatapojen tulokset vastasivat toisiaan sekä 42 tonnin että 36 tonnin kokonaismassojen kuormituksilla. Esikorotus määritettiin 42 tonnin koko-naismassalla kuormitetun todellista hakeperävaunun runkoa vastaavan 3D-mallin pysty-suuntaisesta taipumasta, josta luotiin esikorotettu hakeperävaunun rungon 3D-malli. Tutkimuksessa kehitettyjä laskentamalleja voidaan tulevaisuudessa käyttää yrityksen tuo-tekehityksessä. Esikorotuksella voidaan kompensoida pystysuuntaista taipumaa, jos esiko-rotuksesta ei ole haittaa itse rakenteelle.

Hakkuutähteen arvoketjun analysointi ja kannattavuuden tehostaminen

Suomen tavoitteena on nostaa metsähakkeen käyttö 25 TWh:iin vuoteen 2020 mennessä. Tavoitteen saavuttaminen edellyttää, että metsähakkeen käyttö ja tuotanto on kannatta-vuudeltaan houkuttelevaa. Suuri osa Suomen energiapuusta saadaan ainespuun hakkuun yhteydessä kerättävistä hakkuutähteistä, josta valmistetaan haketta lämpölaitosten tarpee-seen. Tämän työn tavoitteena oli tarkastella suomalaisen metsäteollisuusyrityksen metsähak-keen tuottamiseen liittyvää arvoketjua ja löytää sieltä ne prosessin osat, joissa arvoa syn-tyy eniten sekä ne prosessin osat, joissa arvoa mahdollisesti menetetään. Arvoketjun tarkastelun lisäksi työn tavoitteena oli selvittää mahdollisuuksia latvusmassa-hakkeen kannattavuuden parantamiseen case yrityksessä. Arvoketju analyysiin perustuen tutkimuksessa voitiin todeta suurimman metsäenergian arvon syntyvän hakkuutähteen kuivumisen seurauksena. Liian pitkä varastointiaika sitä vastoin aiheuttaa kuiva-ainetappiosta johtuvaa arvon menetystä hankintaketjussa. Suurin vaikutus hakkuutähdehakkeen kannattavuuteen on hakkeen alhaisella kosteudella. Tutkimuksessa todettiin lisäksi kaukokuljetuskustannusten vaikuttavan erityisen suuresti haketuotannon kannattavuuteen.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Role of Phosphorylation of the Oxysterol Binding Protein (OSBP) in (PI(4)P) and Sterol-Containing Membrane Recognition and Binding

Studies have demonstrated that the oxysterol binding protein (OSBP) acts as a phosphatidylinositol phosphate (PIP)-sterol exchanger at membrane contact sites (MCS) of the endoplasmic reticulum (ER) and Golgi. OSBP is known to pick up phosphatidylinositol-4-phosphate (PI(4)P) from the ER, transfer it to the trans-Golgi in exchange for a cholesterol molecule that is then transferred from the trans-Golgi to the ER. Upon further examination of this pathway by Ridgway et al. (1), it appeared that phosphorylation of OSBP played a role in the localization of OSBP. The dephosphorylation state of OSBP was linked to Golgi localization and the depletion of cholesterol at the ER. To mimic the phosphorylated state of OSBP, the mutant OSBP-S5E was designed by Ridgway et al. (1). The lipid and sterol recognition by wt-OSBP and its phosphomimic mutant OSBP-S5E were investigated using immobilized lipid bilayers and dual polarization interferometry (DPI). DPI is a technique in which the protein binding affinity to immobilized lipid bilayers is measured and the binding behavior is examined through real time. Lipid bilayers containing 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and varying concentrations of PI(4)Ps or sterols (cholesterol or 25-hydroxycholesterol) were immobilized on a silicon nitride chip. It was determined that wt-OSBP binds differently to PI(4)P-containing bilayers compared to OSBP-S5E. The binding behavior suggested that wt-OSBP extracts PI(4)P and the change in the binding behavior, in the case of OSBP-S5E, suggested that the phosphorylation of OSBP may prevent the recognition and/or extraction of PI(4)P. In the presence of sterols, the overall binding behavior of OSBP, regardless of phosphorylation state, was fairly similar. The maximum specific bound mass of OSBP to sterols did not differ as the concentration of sterols increased. However, comparing the maximum specific bound mass of OSBP to cholesterol with oxysterol (25-hydroxycholesterol), OSBP displayed nearly a 2-fold increase in bound mass. With the absence of the wt-OSBP-PI(4)P binding behavior, it can be speculated that the sterols were not extracted. In addition, the binding behavior of OSBP was further tested using a fluorescence based binding assay. Using 22-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-23,24-bisnor-5-cholen-3β-ol (22-NBD cholesterol), wt-OSBP a one site binding dissociation constant Kd, of 15 ± 1.4 nM was determined. OSBP-S5E did not bind to 22-NBD cholesterol and Kd value was not obtained.

L’influence du climat scolaire sur les résultats des élèves: effet-établissement ou perception individuelle?

La littérature montre que les résultats scolaires ne sont pas seulement imputables aux caractéristiques individuelles et familiales des élèves, mais qu’ils sont également influencés par l’établissement scolaire fréquenté. Utilisant une analyse multiniveaux comprenant deux niveaux hiérarchiques, soit l’élève et l’école, la présente recherche vise à démontrer l’impact du climat scolaire sur les résultats des élèves du secondaire. Dans ce contexte, le climat scolaire perçu est mesuré à partir de six indicateurs de perception mesurés à l’aide du Questionnaire sur l’Environnement Socioéducatif (QES) (Janosz, 2000). Les indicateurs utilisés pour rendre compte de l’effet-établissement sont ces indicateurs de climat scolaire agrégés par école. Les analyses ont été effectuées sur un échantillon transversal de 54 écoles publiques, parmi lesquelles 30 685 élèves âgés de 13 à 17 ans ont complété le questionnaire. Les résultats de l’analyse permettent de constater d’une part, que le climat scolaire influence bel et bien la réussite des élèves et d’autre part, qu’il est possible de différencier l’effet du climat perçu selon qu’il se situe au niveau de l’élève ou qu’il soit plutôt agrégé au niveau de l’école. À cet effet, seul le climat agrégé, plus particulièrement les climats éducatif et d’appartenance, permet d’expliquer les différences entre les écoles sur la base des résultats scolaires en français et en mathématiques.

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

Proteolytic processing of the CUX1 transcription factor generates an isoform, p110 that accelerates entry into S phase. To identify targets of p110 CUX1 that are involved in cell cycle progression, we performed genome-wide location analysis using a promoter microarray. Since there are no antibodies that specifically recognize p110, but not the full-length protein, we expressed physiological levels of a p110 isoform with two tags and purified chromatin by tandem affinity purification (ChAP). Conventional ChIP performed on synchronized populations of cells confirmed that p110 CUX1 is recruited to the promoter of cell cycle-related targets preferentially during S phase. Multiple approaches including silencing RNA (siRNA), transient infection with retroviral vectors, constitutive expression and reporter assays demonstrated that most cell cycle targets are activated whereas a few are repressed or not affected by p110 CUX1. Functional classes that were over-represented among targets included DNA replication initiation. Consistent with this finding, constitutive expression of p110 CUX1 led to a premature and more robust induction of replication genes during cell cycle progression, and stimulated the long-term replication of a plasmid bearing the oriP replicator of Epstein Barr virus (EBV).