Markov Random Fields in Cancer Mutation Dependencies

Even though a large amount of evidence would suggest that PP2A serine/threonine protein phosphatase acts as a tumour suppressor the genomics data to support this claim is limited. We fit a sparse binary Markov random field with individual sample's total mutational frequency as an additional covariate to model the dependencies between the mutations occurring in the PP2A encoding genes. We utilize the data from recent large scale cancer genomics studies, where the whole genome from a human tumour biopsy has been analysed. Our results show a complex network of interactions between the occurrence of mutations in our twenty examined genes. According to our analysis the mutations occurring in the genes PPP2R1A, PPP2R3A, and PPP2R2B are identified as the key mutations. These genes form the core of the network of conditional dependency between the mutations in the investigated twenty genes. Additionally, we note that the mutations occurring in PPP2R4 seem to be more influential in samples with higher number of total mutations. The mutations occurring in the set of genes suggested by our results has been shown to contribute to the transformation of human cells. We conclude that our evidence further supports the claim that PP2A acts as a tumour suppressor and restoring PP2A activity is an appealing therapeutic strategy.

Sentence Compression with Supervised Machine Learning

The subject of the thesis is automatic sentence compression with machine learning, so that the compressed sentences remain both grammatical and retain their essential meaning. There are multiple possible uses for the compression of natural language sentences. In this thesis the focus is generation of television program subtitles, which often are compressed version of the original script of the program. The main part of the thesis consists of machine learning experiments for automatic sentence compression using different approaches to the problem. The machine learning methods used for this work are linear-chain conditional random fields and support vector machines. Also we take a look which automatic text analysis methods provide useful features for the task. The data used for machine learning is supplied by Lingsoft Inc. and consists of subtitles in both compressed an uncompressed form. The models are compared to a baseline system and comparisons are made both automatically and also using human evaluation, because of the potentially subjective nature of the output. The best result is achieved using a CRF - sequence classification using a rich feature set. All text analysis methods help classification and most useful method is morphological analysis. Tutkielman aihe on suomenkielisten lauseiden automaattinen tiivistäminen koneellisesti, niin että lyhennetyt lauseet säilyttävät olennaisen informaationsa ja pysyvät kieliopillisina. Luonnollisen kielen lauseiden tiivistämiselle on monta käyttötarkoitusta, mutta tässä tutkielmassa aihetta lähestytään television ohjelmien tekstittämisen kautta, johon käytännössä kuuluu alkuperäisen tekstin lyhentäminen televisioruudulle paremmin sopivaksi. Tutkielmassa kokeillaan erilaisia koneoppimismenetelmiä tekstin automaatiseen lyhentämiseen ja tarkastellaan miten hyvin erilaiset luonnollisen kielen analyysimenetelmät tuottavat informaatiota, joka auttaa näitä menetelmiä lyhentämään lauseita. Lisäksi tarkastellaan minkälainen lähestymistapa tuottaa parhaan lopputuloksen. Käytetyt koneoppimismenetelmät ovat tukivektorikone ja lineaarisen sekvenssin mallinen CRF. Koneoppimisen tukena käytetään tekstityksiä niiden eri käsittelyvaiheissa, jotka on saatu Lingsoft OY:ltä. Luotuja malleja vertaillaan Lopulta mallien lopputuloksia evaluoidaan automaattisesti ja koska teksti lopputuksena on jossain määrin subjektiivinen myös ihmisarviointiin perustuen. Vertailukohtana toimii kirjallisuudesta poimittu menetelmä. Tutkielman tuloksena paras lopputulos saadaan aikaan käyttäen CRF sekvenssi-luokittelijaa laajalla piirrejoukolla. Kaikki kokeillut teksin analyysimenetelmät auttavat luokittelussa, joista tärkeimmän panoksen antaa morfologinen analyysi.

Developing of the Variable Speed Drive -control in simulated parallel pumping systems

This thesis presents briefly the basic operation and use of centrifugal pumps and parallel pumping applications. The characteristics of parallel pumping applications are compared to circuitry, in order to search analogy between these technical fields. The purpose of studying circuitry is to find out if common software tools for solving circuit performance could be used to observe parallel pumping applications. The empirical part of the thesis introduces a simulation environment for parallel pumping systems, which is based on circuit components of Matlab Simulink —software. The created simulation environment ensures the observation of variable speed controlled parallel pumping systems in case of different controlling methods. The introduced simulation environment was evaluated by building a simulation model for actual parallel pumping system at Lappeenranta University of Technology. The simulated performance of the parallel pumps was compared to measured values of the actual system. The gathered information shows, that if the initial data of the system and pump perfonnance is adequate, the circuitry based simulation environment can be exploited to observe parallel pumping systems. The introduced simulation environment can represent the actual operation of parallel pumps in reasonably accuracy. There by the circuitry based simulation can be used as a researching tool to develop new controlling ways for parallel pumps.

Reflexive Space. A Constructionist Model of the Russian Reflexive Marker

This study examines the structure of the Russian Reflexive Marker ( ся/-сь) and offers a usage-based model building on Construction Grammar and a probabilistic view of linguistic structure. Traditionally, reflexive verbs are accounted for relative to non-reflexive verbs. These accounts assume that linguistic structures emerge as pairs. Furthermore, these accounts assume directionality where the semantics and structure of a reflexive verb can be derived from the non-reflexive verb. However, this directionality does not necessarily hold diachronically. Additionally, the semantics and the patterns associated with a particular reflexive verb are not always shared with the non-reflexive verb. Thus, a model is proposed that can accommodate the traditional pairs as well as for the possible deviations without postulating different systems. A random sample of 2000 instances marked with the Reflexive Marker was extracted from the Russian National Corpus and the sample used in this study contains 819 unique reflexive verbs. This study moves away from the traditional pair account and introduces the concept of Neighbor Verb. A neighbor verb exists for a reflexive verb if they share the same phonological form excluding the Reflexive Marker. It is claimed here that the Reflexive Marker constitutes a system in Russian and the relation between the reflexive and neighbor verbs constitutes a cross-paradigmatic relation. Furthermore, the relation between the reflexive and the neighbor verb is argued to be of symbolic connectivity rather than directionality. Effectively, the relation holding between particular instantiations can vary. The theoretical basis of the present study builds on this assumption. Several new variables are examined in order to systematically model variability of this symbolic connectivity, specifically the degree and strength of connectivity between items. In usage-based models, the lexicon does not constitute an unstructured list of items. Instead, items are assumed to be interconnected in a network. This interconnectedness is defined as Neighborhood in this study. Additionally, each verb carves its own niche within the Neighborhood and this interconnectedness is modeled through rhyme verbs constituting the degree of connectivity of a particular verb in the lexicon. The second component of the degree of connectivity concerns the status of a particular verb relative to its rhyme verbs. The connectivity within the neighborhood of a particular verb varies and this variability is quantified by using the Levenshtein distance. The second property of the lexical network is the strength of connectivity between items. Frequency of use has been one of the primary variables in functional linguistics used to probe this. In addition, a new variable called Constructional Entropy is introduced in this study building on information theory. It is a quantification of the amount of information carried by a particular reflexive verb in one or more argument constructions. The results of the lexical connectivity indicate that the reflexive verbs have statistically greater neighborhood distances than the neighbor verbs. This distributional property can be used to motivate the traditional observation that the reflexive verbs tend to have idiosyncratic properties. A set of argument constructions, generalizations over usage patterns, are proposed for the reflexive verbs in this study. In addition to the variables associated with the lexical connectivity, a number of variables proposed in the literature are explored and used as predictors in the model. The second part of this study introduces the use of a machine learning algorithm called Random Forests. The performance of the model indicates that it is capable, up to a degree, of disambiguating the proposed argument construction types of the Russian Reflexive Marker. Additionally, a global ranking of the predictors used in the model is offered. Finally, most construction grammars assume that argument construction form a network structure. A new method is proposed that establishes generalization over the argument constructions referred to as Linking Construction. In sum, this study explores the structural properties of the Russian Reflexive Marker and a new model is set forth that can accommodate both the traditional pairs and potential deviations from it in a principled manner.

A method for using random parameters in analyzing permanent sample plots

Summary

Nutritional status in commercial currant fields

Selostus: Herukkaviljelmien ravinnetila

Weeds in spring cereal fields in Finland - a third survey

Selostus: Kolmas kevätviljapeltojen rikkakasvikartoitus

Stress intensity factor of wood from crack-tip displacement fields obtained from digital image processing

Abstract

Constant and variable amplitude fatigue strength of high strength steel welds treated with ultrasonic impact treatment

Hitsattujen rakenteiden väsymiskestävyyttä pystytään parantamaan jälkikäsittelymenetelmillä, joistayksi, ultraäänikäsittely muokkaa hitsin geometriaa ja aiheuttaa puristusjäännösjännitystilan. Tässä tutkimuksessa verrataan kokeellisesti kuormaa kantamattoman hitsatun ja ui -käsitellyn rivan väsymislujuutta toisiinsa. Tutkimusohjelmaan kuuluu kahta teräslajia ja sekä vakio - että vaihtuva - amplitudista kuormitusta. Ultraäänikäsittelyllä saavutetaan väsymiskestoiän parantuminen vakio - ja vaihtuva - amplitudisella kuormituksella. Perusaineen lujuudella ei ole merkittää vaikutusta väsymislujuuteen kun liitos on hitsatussa tilassa. Tällöin väsymiskestävyyden määrää hitsin rajaviivan jännityskeskittymä. Ultraäänikäsitellyn hitsatunliitoksen väsymiskestävyys on suurempi korkeamman lujuuden omaavilla teräksillä. Tästä syystä korkealujuuksisten terästen käyttö ultraäänikäsiteltynä väsyttävästi kuormitetuissa kevytrakenteissa on perusteltua.

Cardiovascular effects of short term exposure to electric and magnetic fields of electricity power transmission

In the electrical industry the 50 Hz electric and magnetic fields are often higher than in the average working environment. The electric and magnetic fields can be studied by measuring or by calculatingthe fields in the environment. For example, the electric field under a 400 kV power line is 1 to 10 kV/m, and the magnetic flux density is 1 to 15 µT. Electricand magnetic fields of a power line induce a weak electric field and electric currents in the exposed body. The average current density in a human being standing under a 400 kV line is 1 to 2 mA/m2. The aim of this study is to find out thepossible effects of short term exposure to electric and magnetic fields of electricity power transmission on workers' health, in particular the cardiovascular effects. The study consists of two parts; Experiment I: influence on extrasystoles, and Experiment II: influence on heart rate. In Experiment I two groups, 26 voluntary men (Group 1) and 27 transmission-line workers (Group 2), were measured. Their electrocardiogram (ECG) was recorded with an ambulatory recorder both in and outside the field. In Group 1 the fields were 1.7 to 4.9 kV/m and 1.1 to 7.1 pT; in Group 2 they were 0.1 to 10.2 kV/m and 1.0 to 15.4 pT. In the ECG analysis the only significant observation was a decrease in the heart rate after field exposure (Group 1). The drop cannot be explained with the first measuring method. Therefore Experiment II was carried out. In Experiment II two groups were used; Group 1 (26 male volunteers) were measured in real field exposure, Group 2 (15 male volunteers) in "sham" fields. The subjects of Group 1 spent 1 h outside the field, then 1 h in the field under a 400 kV transmission line, and then again 1 h outside the field. Under the 400 kV linethe field strength varied from 3.5 to 4.3 kV/m, and from 1.4 to 6.6 pT. Group 2spent the entire test period (3 h) in a 33 kV outdoor testing station in a "sham" field. ECG, blood pressure, and electroencephalogram (EEG) were measured by ambulatory methods. Before and after the field exposure, the subjects performed some cardiovascular autonomic function tests. The analysis of the results (Experiments I and II) showed that extrasystoles or arrythmias were as frequent in the field (below 4 kV/m and 4 pT) as outside it. In Experiment II there was no decrease detected in the heart rate, and the systolic and diastolic blood pressure stayed nearly the same. No health effects were found in this study.

A comparative performance study of four-pole induction motors and synchronous reluctance motors in variable speed drives

Design aspects of the Transversally Laminated Anisotropic (TLA) Synchronous Reluctance Motor (SynRM) are studied and the machine performance analysis compared to the Induction Motor (IM) is done. The SynRM rotor structure is designed and manufactured for a30 kW, four-pole, three-phase squirrel cage induction motor stator. Both the IMand SynRM were supplied by a sensorless Direct Torque Controlled (DTC) variablespeed drive. Attention is also paid to the estimation of the power range where the SynRM may compete successfully with a same size induction motor. A technicalloss reduction comparison between the IM and SynRM in variable speed drives is done. The Finite Element Method (FEM) is used to analyse the number, location and width of flux barriers used in a multiple segment rotor. It is sought for a high saliency ratio and a high torque of the motor. It is given a comparison between different FEM calculations to analyse SynRM performance. The possibility to take into account the effect of iron losses with FEM is studied. Comparison between the calculated and measured values shows that the design methods are reliable. A new application of the IEEE 112 measurement method is developed and used especially for determination of stray load losses in laboratory measurements. The study shows that, with some special measures, the efficiency of the TLA SynRM is equivalent to that of a high efficiency IM. The power factor of the SynRM at rated load is smaller than that of the IM. However, at lower partial load this difference decreases and this, probably, brings that the SynRM gets a better power factor in comparison with the IM. The big rotor inductance ratio of the SynRM allows a good estimating of the rotor position. This appears to be very advantageous for the designing of the rotor position sensor-less motor drive. In using the FEM designed multi-layer transversally laminated rotor with damper windings it is possible to design a directly network driven motor without degrading the motorefficiency or power factor compared to the performance of the IM.