Analyzing the temporal regulation of translation efficiency in mouse liver.

Mammalian physiology and behavior follow daily rhythms that are orchestrated by endogenous timekeepers known as circadian clocks. Rhythms in transcription are considered the main mechanism to engender rhythmic gene expression, but important roles for posttranscriptional mechanisms have recently emerged as well (reviewed in Lim and Allada (2013) [1]). We have recently reported on the use of ribosome profiling (RPF-seq), a method based on the high-throughput sequencing of ribosome protected mRNA fragments, to explore the temporal regulation of translation efficiency (Janich et al., 2015 [2]). Through the comparison of around-the-clock RPF-seq and matching RNA-seq data we were able to identify 150 genes, involved in ribosome biogenesis, iron metabolism and other pathways, whose rhythmicity is generated entirely at the level of protein synthesis. The temporal transcriptome and translatome data sets from this study have been deposited in NCBI's Gene Expression Omnibus under the accession number GSE67305. Here we provide additional information on the experimental setup and on important optimization steps pertaining to the ribosome profiling technique in mouse liver and to data analysis.

Comparing multiple criteria for species identification in two recently diverged seabirds

Correct species identification is a crucial issue in systematics with key implications for prioritising conservation effort. However, it can be particularly challenging in recently diverged species due to their strong similarity and relatedness. In such cases, species identification requires multiple and integrative approaches. In this study we used multiple criteria, namely plumage colouration, biometric measurements, geometric morphometrics, stable isotopes analysis (SIA) and genetics (mtDNA), to identify the species of 107 bycatch birds from two closely related seabird species, the Balearic (Puffinus mauretanicus) and Yelkouan (P. yelkouan) shearwaters. Biometric measurements, stable isotopes and genetic data produced two stable clusters of bycatch birds matching the two study species, as indicated by reference birds of known origin. Geometric morphometrics was excluded as a species identification criterion since the two clusters were not stable. The combination of plumage colouration, linear biometrics, stable isotope and genetic criteria was crucial to infer the species of 103 of the bycatch specimens. In the present study, particularly SIA emerged as a powerful criterion for species identification, but temporal stability of the isotopic values is critical for this purpose. Indeed, we found some variability in stable isotope values over the years within each species, but species differences explained most of the variance in the isotopic data. Yet this result pinpoints the importance of examining sources of variability in the isotopic data in a case-by-case basis prior to the cross-application of the SIA approach to other species. Our findings illustrate how the integration of several methodological approaches can help to correctly identify individuals from recently diverged species, as each criterion measures different biological phenomena and species divergence is not expressed simultaneously in all biological traits.

La efectividad de las políticas activas de mercado de trabajo para luchar contra el paro. La experiencia de Cataluña

El objetivo de este trabajo es evaluar la efectividad de las políticas activas llevadas a cabo por el Servicio de Ocupación de Cataluña (SOC) durante el año 2005. Los resultados obtenidos a partir de la aplicación de técnicas de matching muestran que la probabilidad de encontrar trabajo para un individuo que participó en alguna de las acciones del SOC analizadas es 5 puntos porcentuales superior en relación a los que no participaron. El análisis individualizado de los diferentes programas ha mostrado la eficacia de la mayor parte de las acciones realizadas. Por último, los resultados obtenidos también han puesto de manifiesto la mejora adicional que supone la combinación de algunas de las acciones.

Classification of textures seen from different distances and under varying illumination direction

Changes in the angle of illumination incident upon a 3D surface texture can significantly alter its appearance, implying variations in the image texture. These texture variations produce displacements of class members in the feature space, increasing the failure rates of texture classifiers. To avoid this problem, a model-based texture recognition system which classifies textures seen from different distances and under different illumination directions is presented in this paper. The system works on the basis of a surface model obtained by means of 4-source colour photometric stereo, used to generate 2D image textures under different illumination directions. The recognition system combines coocurrence matrices for feature extraction with a Nearest Neighbour classifier. Moreover, the recognition allows one to guess the approximate direction of the illumination used to capture the test image

Visual SLAM for 3D large-scale seabed acquisition employing underwater vehicles

This paper presents a novel technique to align partial 3D reconstructions of the seabed acquired by a stereo camera mounted on an autonomous underwater vehicle. Vehicle localization and seabed mapping is performed simultaneously by means of an Extended Kalman Filter. Passive landmarks are detected on the images and characterized considering 2D and 3D features. Landmarks are re-observed while the robot is navigating and data association becomes easier but robust. Once the survey is completed, vehicle trajectory is smoothed by a Rauch-Tung-Striebel filter obtaining an even better alignment of the 3D views and yet a large-scale acquisition of the seabed

Visual SLAM for underwater vehicles using video velocity log and natural landmarks

A visual SLAM system has been implemented and optimised for real-time deployment on an AUV equipped with calibrated stereo cameras. The system incorporates a novel approach to landmark description in which landmarks are local sub maps that consist of a cloud of 3D points and their associated SIFT/SURF descriptors. Landmarks are also sparsely distributed which simplifies and accelerates data association and map updates. In addition to landmark-based localisation the system utilises visual odometry to estimate the pose of the vehicle in 6 degrees of freedom by identifying temporal matches between consecutive local sub maps and computing the motion. Both the extended Kalman filter and unscented Kalman filter have been considered for filtering the observations. The output of the filter is also smoothed using the Rauch-Tung-Striebel (RTS) method to obtain a better alignment of the sequence of local sub maps and to deliver a large-scale 3D acquisition of the surveyed area. Synthetic experiments have been performed using a simulation environment in which ray tracing is used to generate synthetic images for the stereo system

Kunnallisen palveluyksikön toimintojen kehittäminen ja kustannusten

Työn tavoitteena on sisäisen palveluyksikön prosessikuvauksien kautta kehittää nykyistä toimintaa, laskea tuotettujen palveluiden yksikkökustannuksia ja arvioida palkitsemisen vaikutusta sisäisten tukipalveluiden tuottamisen tehostamiseen Nurmijärven kunnassa. Toimintolaskennalla saadaan aikaiseksi tuotetuille palveluille kustannukset ja tuotehinnoittelu. Tällä saadaan aikaan lähes aiheuttamisperiaatteen mukainen kustannusten kohdistaminen. Lisäksi työssä arvioidaan kustannusten kautta saavutettavaa toiminnan tehokkuutta. Työssä haastateltiin yksikön henkilökuntaa, minkä tuloksena saatiin toiminnasta prosessikuvaukset. Toimintolaskennassa tiedot kerättiin eri järjestelmistä ja yksikössä mitattiin työtehtävien hoitoon käytettyä aikaa. Kannusteiden vaikutuksista järjestettiin kolmen organisaation tietotekniikkayksiköiden henkilökunnalle kysely sekä yksikön esimiehet haastateltiin. Haastattelun avulla selvitettiin palkitsemisen nykytilannetta ja tulevaisuuden kehittämismahdollisuuksia. Tuloksena saatiin tukipalveluhinnasto, jolla toteutettiin sisäisten kustannusten kohdistaminen organisaatiossa. Tukipalveluprosessien kuvaamisen tuloksena saatiin toimenpide-ehdotuksia toteutukseen ja lisäkehittämishankkeita. Työntekijöiden kannustekyselyn tuloksena rahapalkitsemisen lisäksi nousi esiin esimiehen antaman palautteen arvostus sekä oman osaamisen kehittäminen.

Tuotekustannusmallin kehittäminen talotekniikkaelementtitehtaassa

Työn tavoitteena on talotekniikkaelementtitehtaan tuotekustannusmallin kehittäminen. Yritys tarvitsee tuotekohtaista kustannustietoa erityisesti varaston arvon määrittämiseen ja kustannusperusteiseen hinnoitteluun. Tuotekustannusmallin kehittäminen edellyttää nykyisen tuotekustannusmallin sisältämien virheiden ja puutteiden korjaamista. Työssä käydään läpi kaikki tuotekustannusmalliin tehdyt muutokset tuotantovaihekohtaisesti. Uusi tuotekustannusmalli perustuu lähinnä lisäys- ja standardikustannuslaskentaan. Malli laskee tuote- ja tilauskohtaisen minimiomakustannusarvon. Uusi tuotekustannusmalli kohdistaa tuotteille aiheuttamisperiaatteen mukaisesti monia sellaisia kustannuksia, jotka aikaisemmin on jätetty kokonaan kohdistamatta. Eristettyjen ilmanvaihtokanavien sekä vesi- ja lämpöjohtojen kustannusten havaittiin olevan aiemmin luultua matalammat. Elementtien runkojen kustannukset puolestaan nousivat uudessa mallissa. Työn aikana laadittiin myös taulukkolaskentasovellus, jonka avulla voidaan laskea tilaukseen sisältyvien elementtien hankintameno ja kustannusperusteinen hinta.

3D Surface Modeling From Point Clouds

The goal of this thesis is to implement software for creating 3D models from point clouds. Point clouds are acquired with stereo cameras, monocular systems or laser scanners. The created 3D models are triangular models or NURBS (Non-Uniform Rational B-Splines) models. Triangular models are constructed from selected areas from the point clouds and resulted triangular models are translated into a set of quads. The quads are further translated into an estimated grid structure and used for NURBS surface approximation. Finally, we have a set of NURBS surfaces which represent the whole model. The problem wasn’t so easy to solve. The selected triangular surface reconstruction algorithm did not deal well with noise in point clouds. To handle this problem, a clustering method is introduced for simplificating the model and removing noise. As we had better results with the smaller point clouds produced by clustering, we used points in clusters to better estimate the grids for NURBS models. The overall results were good when the point cloud did not have much noise. The point clouds with small amount of error had good results as the triangular model was solid. NURBS surface reconstruction performed well on solid models.

Polyphenol intake and mortality risk: a re-analysis of the PREDIMED trial

Background: Polyphenols may lower the risk of cardiovascular disease (CVD) and other chronic diseases due to their antioxidant and anti-inflammatory properties, as well as their beneficial effects on blood pressure, lipids and insulin resistance. However, no previous epidemiological studies have evaluated the relationship between the intake of total polyphenols intake and polyphenol subclasses with overall mortality. Our aim was to evaluate whether polyphenol intake is associated with all-cause mortality in subjects at high cardiovascular risk. Methods: We used data from the PREDIMED study, a 7,447-participant, parallel-group, randomized, multicenter, controlled five-year feeding trial aimed at assessing the effects of the Mediterranean Diet in primary prevention of cardiovascular disease. Polyphenol intake was calculated by matching food consumption data from repeated food frequency questionnaires (FFQ) with the Phenol-Explorer database on the polyphenol content of each reported food. Hazard ratios (HR) and 95% confidence intervals (CI) between polyphenol intake and mortality were estimated using time-dependent Cox proportional hazard models. Results: Over an average of 4.8 years of follow-up, we observed 327 deaths. After multivariate adjustment, we found a 37% relative reduction in all-cause mortality comparing the highest versus the lowest quintiles of total polyphenol intake (hazard ratio (HR) = 0.63; 95% CI 0.41 to 0.97; P for trend = 0.12). Among the polyphenol subclasses, stilbenes and lignans were significantly associated with reduced all-cause mortality (HR =0.48; 95% CI 0.25 to 0.91; P for trend = 0.04 and HR = 0.60; 95% CI 0.37 to 0.97; P for trend = 0.03, respectively), with no significant associations apparent in the rest (flavonoids or phenolic acids). Conclusions: Among high-risk subjects, those who reported a high polyphenol intake, especially of stilbenes and lignans, showed a reduced risk of overall mortality compared to those with lower intakes. These results may be useful to determine optimal polyphenol intake or specific food sources of polyphenols that may reduce the risk of all-cause mortality.

Resurssien ja kyvykkyyksien vastaavuus alan muuttuviin vaatimuksiin

Tämän diplomityön tavoitteena on tutkia kohdeyrityksen strategista muutosta perinteisestä tuotetoimittajasta ratkaisujen toimittajaksi. Toimialan muutosta arvioidaan tarkemmin, jotta voidaan selvittää kuinka yrityksen tulisi mukauttaa resurssejaan ja kyvykkyyksiään sopeutuakseen muutoksen tuomiin uusiin haasteisiin. Tarkastelun alla on erityisesti yrityksen strateginen muutos ja kuinka löytää strategian kannalta ne dynaamiset kyvykkyydet joiden avulla yritys saa pysyvää kilpailuetua. Yritykset pyrkivät strategisessa suunnittelussaan pysyvään kilpailuetuun. Strategista johtamisen teorioita on esitetty useita ja niiden kautta on vaikea selittää nykyisin nopeasti muuttuvassa toimintaympäristössä toimivien yritysten menestystä. Dynaamisten kyvykkyyksistä on haettu selitystä menestyksen taakse. Yritysten tavoitellessa kokonaan uusia liiketoiminta-alueita niihin kohdistuu suuria muutoksia niin ulkoisesti kuin sisäisestikin. Tällöin on kriittistä tunnistaa ne ydinkyvykkyydet joiden avulla voidaan menestyä uusilla liiketoiminta-alueilla. Työn ensimmäisessä osassa esitetään strategiaan ja kyvykkyyksiin liittyviä teorioita. Teoriaosiossa tarkastellaan myös palveluyritykseksi muuntautumisen haasteita, jonka jälkeen esitellään kohdeyrityksen strategiset tavoitteet ja kuinka puuttuvia resursseja voidaan tunnistaa. Resurssipohjaisen lähestymistavan avulla päästiin hyvin käsiksi toimialan muutoksen aiheuttamiin puuttuviin resursseihin. Analyysin aikana tunnistettiin puutteita tavoitteisiin nähden ja tässä työssä nousi yhtenä keskeisimpänä esille ICT-osaaminen kohdeyrityksen siirtyessä laitevalmistajan roolista kohti ratkaisun toimittajaa. Tutkimuksen perusteella voidaan todeta, että resurssipohjaisen lähestymistavan avulla voidaan tunnistaa tämän tyyppisessä yrityksessä resurssipuutteita joita kehittämällä yritys voi saavuttaa pysyvää kilpailuetua.

Overvoltage Mitigation Techniques in Wind Power Generators

Advancements in power electronic semiconductor switching devices have lead to significantly faster switching times. In motor and generator applications, the fast switching times of pulse width modulated (PWM) inverters lead to overvoltages caused by voltage reflections with shorter and shorter cables. These excessive overvoltages may lead to a failure of the electrical machine in a matter of months. In this thesis, the causes behind the overvoltage phenomenon as well as its different mitigation techniques are studied. The most suitable techniques for mitigating the overvoltage phenomenon in wind power generator applications are chosen based on both simulations and actual measurements performed on a prototype. An RC filter at the terminals of the electrical machine and an inverter output filter designed to reduce the rise and fall times of voltage pulses are presented as a solution to the overvoltage problem. The performance and losses of both filter types are analysed.

Managing through measurement : A framework for successful operative level performance measurement

The research around performance measurement and management has focused mainly on the design, implementation and use of performance measurement systems. However, there is little evidence about the actual impacts of performance measurement on the different levels of business and operations of organisations, as well as the underlying factors that lead to a positive impact of performance measurement. The study thus focuses on this research gap, which can be considered both important and challenging to cover. The first objective of the study was to examine the impacts of performance measurement on different aspects of management, leadership and the quality of working life, after which the factors that facilitate and improve performance and performance measurement at the operative level of an organisation were examined. The second objective was to study how these factors operate in practice. The third objective focused on the construction of a framework for successful operative level performance measurement and the utilisation of the factors in the organisations. The research objectives have been studied through six research papers utilising empirical data from three separate studies, including two sets of interview data and one of quantitative data. The study applies mainly the hermeneutical research approach. As a contribution of the study, a framework for successful operative level performance measurement was formed by matching the findings of the current study and performance measurement theory. The study extents the prior research regarding the impacts of performance measurement and the factors that have a positive effect on operative level performance and performance measurement. The results indicate that under suitable circumstances, performance measurement has positive impacts on different aspects of management, leadership, and the quality of working life. The results reveal that for example the perception of the employees and the management of the impacts of performance measurement on leadership style differ considerably. Furthermore, the fragmented literature has been reorganised into six factors that facilitate and improve the performance of the operations and employees, and the use of performance measurement at the operative level of an organisation. Regarding the managerial implications of the study, managers who operate around performance measurement can utilise the framework for example by putting the different phases of the framework into practice.

Master data quality management in a global enterprise

In a networked business environment the visibility requirements towards the supply operations and customer interface has become tighter. In order to meet those requirements the master data of case company is seen as an enabler. However the current state of master data and its quality are not seen good enough to meet those requirements. In this thesis the target of research was to develop a process for managing master data quality as a continuous process and find solutions to cleanse the current customer and supplier data to meet the quality requirements defined in that process. Based on the theory of Master Data Management and data cleansing, small amount of master data was analyzed and cleansed using one commercial data cleansing solution available on the market. This was conducted in cooperation with the vendor as a proof of concept. In the proof of concept the cleansing solution’s applicability to improve the quality of current master data was proved. Based on those findings and the theory of data management the recommendations and proposals for improving the quality of data were given. In the results was also discovered that the biggest reasons for poor data quality is the lack of data governance in the company, and the current master data solutions and its restrictions.

Indirect likelihood inference (revised)

Standard indirect Inference (II) estimators take a given finite-dimensional statistic, Z_{n} , and then estimate the parameters by matching the sample statistic with the model-implied population moment. We here propose a novel estimation method that utilizes all available information contained in the distribution of Z_{n} , not just its first moment. This is done by computing the likelihood of Z_{n}, and then estimating the parameters by either maximizing the likelihood or computing the posterior mean for a given prior of the parameters. These are referred to as the maximum indirect likelihood (MIL) and Bayesian Indirect Likelihood (BIL) estimators, respectively. We show that the IL estimators are first-order equivalent to the corresponding moment-based II estimator that employs the optimal weighting matrix. However, due to higher-order features of Z_{n} , the IL estimators are higher order efficient relative to the standard II estimator. The likelihood of Z_{n} will in general be unknown and so simulated versions of IL estimators are developed. Monte Carlo results for a structural auction model and a DSGE model show that the proposed estimators indeed have attractive finite sample properties.