EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data.

The R package EasyStrata facilitates the evaluation and visualization of stratified genome-wide association meta-analyses (GWAMAs) results. It provides (i) statistical methods to test and account for between-strata difference as a means to tackle gene-strata interaction effects and (ii) extended graphical features tailored for stratified GWAMA results. The software provides further features also suitable for general GWAMAs including functions to annotate, exclude or highlight specific loci in plots or to extract independent subsets of loci from genome-wide datasets. It is freely available and includes a user-friendly scripting interface that simplifies data handling and allows for combining statistical and graphical functions in a flexible fashion. AVAILABILITY: EasyStrata is available for free (under the GNU General Public License v3) from our Web site www.genepi-regensburg.de/easystrata and from the CRAN R package repository cran.r-project.org/web/packages/EasyStrata/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

On the Condition Monitoring of Induction machines

The research of condition monitoring of electric motors has been wide for several decades. The research and development at universities and in industry has provided means for the predictive condition monitoring. Many different devices and systems are developed and are widely used in industry, transportation and in civil engineering. In addition, many methods are developed and reported in scientific arenas in order to improve existing methods for the automatic analysis of faults. The methods, however, are not widely used as a part of condition monitoring systems. The main reasons are, firstly, that many methods are presented in scientific papers but their performance in different conditions is not evaluated, secondly, the methods include parameters that are so case specific that the implementation of a systemusing such methods would be far from straightforward. In this thesis, some of these methods are evaluated theoretically and tested with simulations and with a drive in a laboratory. A new automatic analysis method for the bearing fault detection is introduced. In the first part of this work the generation of the bearing fault originating signal is explained and its influence into the stator current is concerned with qualitative and quantitative estimation. The verification of the feasibility of the stator current measurement as a bearing fault indicatoris experimentally tested with the running 15 kW induction motor. The second part of this work concentrates on the bearing fault analysis using the vibration measurement signal. The performance of the micromachined silicon accelerometer chip in conjunction with the envelope spectrum analysis of the cyclic bearing faultis experimentally tested. Furthermore, different methods for the creation of feature extractors for the bearing fault classification are researched and an automatic fault classifier using multivariate statistical discrimination and fuzzy logic is introduced. It is often important that the on-line condition monitoring system is integrated with the industrial communications infrastructure. Two types of a sensor solutions are tested in the thesis: the first one is a sensor withcalculation capacity for example for the production of the envelope spectra; the other one can collect the measurement data in memory and another device can read the data via field bus. The data communications requirements highly depend onthe type of the sensor solution selected. If the data is already analysed in the sensor the data communications are needed only for the results but in the other case, all measurement data need to be transferred. The complexity of the classification method can be great if the data is analysed at the management level computer, but if the analysis is made in sensor itself, the analyses must be simple due to the restricted calculation and memory capacity.

Computational and Experimental Analysis of Flow Field in the Diffusers of Centrifugal Compressors

Centrifugal compressors are widely used for example in process industry, oil and gas industry, in small gas turbines and turbochargers. In order to achieve lower consumption of energy and operation costs the efficiency of the compressor needs to be improve. In the present work different pinches and low solidity vaned diffusers were utilized in order to improve the efficiency of a medium size centrifugal compressor. In this study, pinch means the decrement of the diffuser flow passage height. First different geometries were analyzed using computational fluid dynamics. The flow solver Finflo was used to solve the flow field. Finflo is a Navier-Stokes solver. The solver is capable to solve compressible, incompressible, steady and unsteady flow fields. Chien's k-e turbulence model was used. One of the numerically investigated pinched diffuser and one low solidity vaned diffuser were studied experimentally. The overall performance of the compressor and the static pressure distribution before and after the diffuser were measured. The flow entering and leaving the diffuser was measured using a three-hole Cobra-probe and Kiel-probes. The pinch and the low solidity vaned diffuser increased the efficiency of the compressor. Highest isentropic efficiency increment obtained was 3\% of the design isentropic efficiency of the original geometry. It was noticed in the numerical results that the pinch made to the hub and the shroud wall was most beneficial to the operation of the compressor. Also the pinch made to the hub was better than the pinchmade to the shroud. The pinch did not affect the operation range of the compressor, but the low solidity vaned diffuser slightly decreased the operation range.The unsteady phenomena in the vaneless diffuser were studied experimentally andnumerically. The unsteady static pressure was measured at the diffuser inlet and outlet, and time-accurate numerical simulation was conducted. The unsteady static pressure showed that most of the pressure variations lay at the passing frequency of every second blade. The pressure variations did not vanish in the diffuser and were visible at the diffuser outlet. However, the amplitude of the pressure variations decreased in the diffuser. The time-accurate calculations showed quite a good agreement with the measured data. Agreement was very good at the design operation point, even though the computational grid was not dense enough inthe volute and in the exit cone. The time-accurate calculation over-predicted the amplitude of the pressure variations at high flow.

Investment Determinants and Future Shape of Russia's Power Generation

The reformation of power sector is still in the process of development. The present day situation in Russian electricity power market ischaracterized as transitional period: competitive electricity market is forming, new companies are being created and the power of government regulation is decreasing. The main aim of the reformation is to attract much-needed private investments to the power sector. The electricity consumption increases very rapidly and power sector has to cope with high demand. The goal of this master's thesis is to analyze the nowadays situation in Russian power sector, such as generation structure, condition of electricity networks, electricity price formation for end-users, shape of fuel sector and investments risks and attraction.The final result of this work is creation of scenario of Russian power sector future shape and analysis of the present day situation.

Competitiveness Survey of a Biofuel Power Plant

Työn tarkoituksena on tarkastella Euroopan siirtymätalousalueelta kotimaisen biopoltto-ainevoimalaitoksen kilpailukykyä potentiaalisimmiksi markkinakohteiksi arvioitujen nykyisten Eu-valtioiden osalta. Työ tehdään osana kokoluokaltaan 3,5 MWth/1,0 MWe pienvoimalaitoksen tuotekehityshanketta, joka on käynnistynyt Varkaudessa tämän vuoden maaliskuussa. Potentiaalisimpien siirtymätalousmaiden valintakriteereinä on käytetty aiempia tutkimuksia ja raportteja. Huomio keskitetään kiinteän biopolttoaineen resursseihin ja biopolttoaineisiin pohjautuvalle energiantuotannolle asetettuihin tavoitteisiin. Edellä mainittujen kriteerien pohjalta tarkasteltaviksi valittujen valtioiden osalta tehtiin tarkemmat kilpailukykyanalyysit, otettiin yhteyttä markkina-alueeltaalan ammattilaisiin ja kartoitettiin potentiaalisimmat markkinakohteet. Tavoitteena on arvioida varteenotettavin kilpailija kiinteisiin biopolttoaineisiin pohjautuvalle sähkön ja lämmön yhteistuotannolle, jonka perusteella laaditaan mallivoimalaitoksen kilpailukykyisen hinnan määrittämiseksi tiettyyn takaisinmaksuaikaan ja korkotekijään perustuen. Lopulta tehdään maakohtaisesti yhteenveto merkittävimmistä markkinapotentiaaliin vaikuttavista kilpailutekijöistä, arvioidaan potentiaalisin kohdemaa sekä esitetään mahdollinen investoinnin rahoitusvaihtoehto ja keinoja markkinoida tuotetta potentiaalisille asiakkaille.

Early diagnosis of osteoporosis by means of orthopantomograms and oral x-rays: a systematic review

Osteoporosis is a systemic bone disease that is characterized by a generalized reduction of the bone mass. It is the main cause of fractures in elderly women. Bone densitometry is used in the lumbar spine and hip in order to detect osteoporosis in its early stages. Different studies have observed a correlation between the bone mineral density of the jaw (BMD) and that of the lumbar spine and/or hip. On the other hand, there are studies that evaluate the findings in the orthopantomograms and perapical X-rays, correlating them with the early diagnosis of osteoporosis and highlighting the role of the dentist in the early diagnosis of this disease. Materials and methods: A search was carried out in the Medline-Pubmed database in order to identify those articles that deal with the association between the X-ray findings observed in the orthopantomograms and the diagnosis of the osteoporosis, as well as those that deal with the bone mineral density of the jaw. Results: There were 406 articles, and with the limits established, this number was reduced to 21. Almost all of the articles indicate that when examining oral X-rays, it is possible to detect signs indicative of osteoporosis. Discussion: The radiomorphometric indices use measurements in orthopantomograms and evaluate possible loss of bone mineral density. They can be analyzed alone or along with the visual indices. In the periapical X-rays, the photodensimetric analyses and the trabecular pattern appear to be the most useful. There are seven studies that analyze the densitometry of the jaw, but only three do so independently of the photodensitometric analysis. Conclusions: The combination of mandibular indices, along with surveys on the risk of fracture, can be useful as indicators of early diagnosis of osteoporosis. Visual and morphometric indices appear to be especially important in the orthopantomograms. Photodensitometry indices and the trabecular pattern are used in periapical X-rays. Studies on mandibular dual-energy X-ray absorptiometry are inconclusive

Analysis of parapoxvirus genomes.

Eight stomatitis papulosa (SP), four orf and two milker's nodes (MN) virus isolates were compared by restriction enzyme analysis. Considerable genetic heterogeneity was found not only between isolates belonging to the three different taxonomic groups but also between members of the same group. This heterogeneity precludes classification of parapoxviruses simply by comparison of their DNA cleavage patterns. Restriction maps were therefore prepared for 12 parapoxvirus DNAs. Fragments from defined regions of the genome were then selected and used as probes for cross-hybridizations to all other parapoxvirus DNAs. DNA fragments derived from an internal region of the genome hybridized strongly to all parapoxvirus isolates examined. In contrast, cross-hybridization of the end region of the DNA molecule was observed only between members of the same virus group. Molecular hybridization as a means of classifying parapoxvirus isolates is discussed.

Innovation Benchmark Study: Analysis of Innovation Processes in Finnish Companies

Liikevaihdon orgaaninen kasvu on ensisijainen tekijä ja haaste yritysjohdolle yrityksen omistaja-arvon kasvattamiseksi. Tutkimus tarkastelee suosivatko suomalaisyritykset pääasiallisesti olemassa olevaa liiketoimintaa palvelevia innovaatioita vai tukevatko nykyhetken toimintatavat myös uusia kasvua kiihdyttäviä radikaaleja innovaatioita. Lisäksi työ kartoitti suomalaisyritysten innovaatioprosessien kehitysalueita käyttäen itsearviointitutkimusta.Tulokset johtivat kolmeen johtopäätökseen. Tutkimus osoitti, että vastaajayritykset ovat keskittyneet innovaatiotoiminnassaan vahvasti ydinliiketoimintaansa, jättäen potentiaaliset kasvumahdollisuudet huomioimatta. Yritykset tavoittelevat maksimaalisia tuottoja keskittymällä tuotteidensa korkeaan suorituskykyyn. Lyhyen aikavälin epärealistiset tuotto-odotukset sekä projekteille suunnatut arviointikriteerit rajoittavat liiketoimintaa mullistavien radikaalien innovaatioiden kehittymistä organisaatiossa. Toiseksi, tutkimus osoitti, että suuri osa yrityksistä käyttää perinteisen projektien arviointi- ja kehitysprosessin lisäksi vaihtoehtoisia ja huonosti kontrolloitavissa olevia kehitysprosesseja, mikäli projektille annetaan kielteinen rahoituspäätös standardin prosessin sisällä. Kolmanneksi, suomalaisyritysten innovaatioprosesseissa paljastui merkittäviä puutteita mitattavien elementtien suhteen.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

Permanent magnet synchronous motor for industrial inverter applications - analysis and design

During the latest few years the need for new motor types has grown, since both high efficiency and an accurate dynamic performance are demanded in industrial applications. For this reason, new effective control systems such as direct torque control (DTC) have been developed. Permanent magnet synchronous motors (PMSM) are well suitable for new adjustable speed AC inverter drives, because their efficiency and power factor are not depending on the pole pair number and speed to the same extent as it is the case in induction motors. Therefore, an induction motor (IM) with a mechanical gearbox can often be replaced with a direct PM motor drive. Space as well as costs will be saved, because the efficiency increases and the cost of maintenance decreases as well. This thesis deals with design criterion, analytical calculation and analysis of the permanent magnet synchronous motor for both sinusoidal air-gap flux density and rectangular air-gapflux density. It is examined how the air-gap flux, flux densities, inductances and torque can be estimated analytically for salient pole and non-salient pole motors. It has been sought by means of analytical calculations for the ultimate construction for machines rotating at relative low 300 rpm to 600 rpm speeds, which are suitable speeds e.g. in Pulp&Paper industry. The calculations are verified by using Finite Element calculations and by measuring of prototype motor. The prototype motor is a 45 kW, 600 rpm PMSM with buried V-magnets, which is a very appropriate construction for high torque motors with a high performance. With the purposebuilt prototype machine it is possible not only to verify the analytical calculations but also to show whether the 600 rpm PMSM can replace the 1500 rpm IM with a gear. It can also be tested if the outer dimensions of the PMSM may be the same as for the IM and if the PMSM in this case can produce a 2.5 fold torque, in consequence of which it may be possible to achieve the same power. The thesis also considers the question how to design a permanent magnet synchronous motor for relatively low speed applications that require a high motor torqueand efficiency as well as bearable costs of permanent magnet materials. It is shown how a selection of different parameters affects the motor properties. Key words: Permanent magnet synchronous motor, PMSM, surface magnets, buried magnets

Logging residues from regeneration fellings for biofuel production - a GIS-based availability and supply cost analysis

Finland has large forest fuel resources. However, the use of forest fuels for energy production has been low, except for small-scale use in heating. According to national action plans and programs related to wood energy promotion, the utilization of such resources will be multiplied over the next few years. The most significant part of this growth will be based on the utilization of forest fuels, produced from logging residues of regeneration fellings, in industrial and municipal power and heating plants. Availability of logging residues was analyzed by means of resource and demand approaches in order to identify the most suitable regions with focus on increasing the forest fuel usage. The analysis included availability and supply cost comparisons between power plant sites and resource allocation in a least cost manner, and between a predefined power plant structure under demand and supply constraints. Spatial analysis of worksite factors and regional geographies were carried out using the GIS-model environment via geoprocessing and cartographic modeling tools. According to the results of analyses, the cost competitiveness of forest fuel supply should be improved in order to achieve the designed objectives in the near future. Availability and supply costs of forest fuels varied spatially and were very sensitive to worksite factors and transport distances. According to the site-specific analysis the supply potential between differentlocations can be multifold. However, due to technical and economical reasons ofthe fuel supply and dense power plant infrastructure, the supply potential is limited at plant level. Therefore, the potential and supply cost calculations aredepending on site-specific matters, where regional characteristics of resourcesand infrastructure should be taken into consideration, for example by using a GIS-modeling approach constructed in this study.

Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications

Background: The 22q11.2 deletion syndrome is the most frequent genomic disorder with an estimated frequency of 1/4000 live births. The majority of patients (90%) have the same deletion of 3 Mb (Typically Deleted Region, TDR) that results from aberrant recombination at meiosis between region specific low-copy repeats (LCRs). Methods: As a first step towards the characterization of recombination rates and breakpoints within the 22q11.2 region we have constructed a high resolution recombination breakpoint map based on pedigree analysis and a population-based historical recombination map based on LD analysis. Results: Our pedigree map allows the location of recombination breakpoints with a high resolution (potential recombination hotspots), and this approach has led to the identification of 5 breakpoint segments of 50 kb or less (8.6 kb the smallest), that coincide with historical hotspots. It has been suggested that aberrant recombination leading to deletion (and duplication) is caused by low rates of Allelic Homologous Recombination (AHR) within the affected region. However, recombination rate estimates for 22q11.2 region show that neither average recombination rates in the 22q11.2 region or within LCR22-2 (the LCR implicated in most deletions and duplications), are significantly below chromosome 22 averages. Furthermore, LCR22-2, the repeat most frequently implicated in rearrangements, is also the LCR22 with the highest levels of AHR. In addition, we find recombination events in the 22q11.2 region to cluster within families. Within this context, the same chromosome recombines twice in one family; first by AHR and in the next generation by NAHR resulting in an individual affected with the del22q11.2 syndrome. Conclusion: We show in the context of a first high resolution pedigree map of the 22q11.2 region that NAHR within LCR22 leading to duplications and deletions cannot be explained exclusively under a hypothesis of low AHR rates. In addition, we find that AHR recombination events cluster within families. If normal and aberrant recombination are mechanistically related, the fact that LCR22s undergo frequent AHR and that we find familial differences in recombination rates within the 22q11.2 region would have obvious health-related implications.

An expression of mixed animal model equations to account for different means and variances in the base population

This paper presents a general expression to predict breeding values using animal models when the base population is selected, i.e. the means and variances of breeding values in the base generation differ among individuals. Rules for forming the mixed model equations are also presented. A numerical example illustrates the procedure.