Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

Natural preference of zebrafish (Danio rerio) for a dark environment

The zebrafish (Danio rerio) has been used as a model in neuroscience but knowledge about its behavior is limited. The aim of this study was to determine the preference of this fish species for a dark or light environment. Initially we used a place preference test and in a second experiment we applied an exit latency test. A two-chamber aquarium was used for the preference test. The aquarium consisted of a black chamber and a white chamber. In the first experiment the animal was placed in the aquarium and the time spent in the two compartments was recorded for 10 min. More time was spent in the black compartment (Wilcoxon matched-pairs signed-rank test, T = 7, N1 = N2 = 18, P = 0.0001). In the second experiment the animal was placed in the black or white compartment and the time it took to go from the initial compartment to the opposite one was recorded. The test lasted a maximum of 10 min. The results showed that the animal spent more time to go from the black to the white compartment (Mann-Whitney rank sum test, T = 48, N1 = 9, N2 = 8, P<0.0230). These data suggest that this fish species has a natural preference for a dark environment and this characteristic can be very useful for the development of new behavioral paradigms for fish.

Ikkuna virtuaaliympäristöön

Tämän kandidaatintutkielman tavoitteena on rakentaa käyttäjien laitteiden sijaintia monitoroiva järjestelmä luokkahuonetilaan. Sijaintitiedot siirretään visualisointiohjelmistoon, joka näyttää laitteet virtuaaliympäristössä. Työssä käydään läpi jo olemassa olevat toteutukset ja käydään lävitse käytettyjen työkalujen valintaperusteet. Työn toteutus kuvataan suunnittelusta toteutukseen. Työssä tehdään 3 erillistä testiä, joista saaduilla tuloksia käytetään tutkimusongelmien ratkaisussa.

A Template for Cloud Technology Deployment in an Energy Trading Environment

Nykyaikaiset pilvipalvelut tarjoavat suurille yrityksille mahdollisuuden tehostaa laskennallista tietojenkäsittelyä. Pilvipalveluiden käyttöönotto tuo mukanaan kuitenkin esimerkiksi useita tietoturvakysymyksiä, joiden vuoksi käyttöönoton tulee olla tarkasti suunniteltua. Tämä tutkimus esittelee kirjallisuuskatsaukseen perustuvan, asteittaisen suunnitelman pilvipalveluiden käyttöönotolle energialiiketoimintaympäristössä. Kohdeyrityksen sisäiset haastattelut ja katsaus nykyisiin energiateollisuuden pilviratkaisuihin muodostavat kokonaiskuvan käyttöönoton haasteista ja mahdollisuuksista. Tutkimuksen päätavoitteena on esittää ratkaisut tyypillisiin pilvipalvelun käyttöönotossa esiintyviin ongelmiin käyttöönottomallin avulla. Tutkimuksessa rakennettu käyttöönottomalli testattiin esimerkkitapauksen avulla ja malli todettiin toimivaksi. Ulkoisten palveluiden herättämien tietoturvakysymysten takia käyttöönoton ensimmäiset osiot, kuten lopputuotteen määrittely ja huolellinen suunnittelu, ovat koko käyttöönottoprosessin ydin. Lisäksi pilvipalveluiden käyttöönotto vaatii nykyiseltä käyttöympäristöltä uusia teknisiä ja hallinnollisia taitoja. Tutkimuksen tulokset osoittavat pilvipalveluiden monipuolisen hyödyn erityisesti laskentatehon tarpeen vaihdellessa. Käyttöönottomallin rinnalle luotu kustannusvertailu tukee kirjallisuuskatsauksessa esille tuotuja hyötyjä ja tarjoaa kohdeyritykselle perusteen tutkimuksen eteenpäin viemiselle.

Utilization of AMI-Technology in a Multilayered Demand Response Service Environment

This thesis studied the performance of Advanced metering infrastructure systems in a challenging Demand Response environment. The aim was to find out what kind of challenges and bottlenecks could be met when utilizing AMI-systems in challenging Demand Response tasks. To find out the challenges and bottlenecks, a multilayered demand response service concept was formed. The service consists of seven different market layers which consist of Nordic electricity market and the reserve markets of Fingrid. In the simulations the AMI-systems were benchmarked against these seven market layers. It was found out, that the current generation AMI-systems were capable of delivering Demand Response on the most challenging market layers, when observed from time critical viewpoint. Additionally, it was found out, that to enable wide scale Demand Response there are three major challenges to be acknowledged. The challenges hindering the utilization of wide scale Demand Response were related to poor standardization of the systems in use, possible problems in data connectivity solutions and the current electricity market regulation model.

SDN in an ISP Environment

As computer networks grow larger and more complex there is a need for a new, simpler kind of approach to configuring them. Software Defined Networking (SDN) takes the control plane away from individual nodes and centralizes the network control by utilizing a flow based traffic management. In this thesis the suitability of SDN in a small ISP (Internet Service Provider) network is considered for an alternative to the current traditional core network and access network OSSs (Operations Support System), mainly to simplify the network management but also to see what else would SDN offer for such an environment. Combining information learned from a theoretical study on the matter to a more practical experiment of SDN network simulation using Mininet simulation software and OpenDayLight SDN controller software does this. Although the simulation shows that SDN is able to provide the functionality needed for the network, the immaturity of the technology suggests that for a small ISP network there is no need to utilize SDN just yet. For when SDN becomes more commonplace a brief transition plan is introduced.

Novel virtual environment and real-time simulation based methods for improving life-cycle efficiency of non-road mobile machinery

Virtual environments and real-time simulators (VERS) are becoming more and more important tools in research and development (R&D) process of non-road mobile machinery (NRMM). The virtual prototyping techniques enable faster and more cost-efficient development of machines compared to use of real life prototypes. High energy efficiency has become an important topic in the world of NRMM because of environmental and economic demands. The objective of this thesis is to develop VERS based methods for research and development of NRMM. A process using VERS for assessing effects of human operators on the life-cycle efficiency of NRMM was developed. Human in the loop simulations are ran using an underground mining loader to study the developed process. The simulations were ran in the virtual environment of the Laboratory of Intelligent Machines of Lappeenranta University of Technology. A physically adequate real-time simulation model of NRMM was shown to be reliable and cost effective in testing of hardware components by the means of hardware-in-the-loop (HIL) simulations. A control interface connecting integrated electro-hydraulic energy converter (IEHEC) with virtual simulation model of log crane was developed. IEHEC consists of a hydraulic pump-motor and an integrated electrical permanent magnet synchronous motorgenerator. The results show that state of the art real-time NRMM simulators are capable to solve factors related to energy consumption and productivity of the NRMM. A significant variation between the test drivers is found. The results show that VERS can be used for assessing human effects on the life-cycle efficiency of NRMM. HIL simulation responses compared to that achieved with conventional simulation method demonstrate the advances and drawbacks of various possible interfaces between the simulator and hardware part of the system under study. Novel ideas for arranging the interface are successfully tested and compared with the more traditional one. The proposed process for assessing the effects of operators on the life-cycle efficiency will be applied for wider group of operators in the future. Driving styles of the operators can be analysed statistically from sufficient large result data. The statistical analysis can find the most life-cycle efficient driving style for the specific environment and machinery. The proposed control interface for HIL simulation need to be further studied. The robustness and the adaptation of the interface in different situations must be verified. The future work will also include studying the suitability of the IEHEC for different working machines using the proposed HIL simulation method.

Consumers' opinions on scent marketing usage in retail environment

Tutkielman tarkoituksena on tutkia suomalaisten kuluttajien mielipiteitä ja käsityksiä tuoksumarkkinoinnin käytöstä vähittäistavarakauppa olosuhteissa. Tutkielma keskittyy tuoksumarkkinoinnin kahteen pääasialliseen osa-alueeseen vähittäistavarakaupassa; tuoksumarkkinointiin osana brändäystä ja tuoksumarkkinoinnin alitajuntaiseen käyttöön. Tutkielma on laadullinen tutkimus. Aineisto kerättiin viideltä suomalaiselta kuluttajalta ja aineistonkeruumenetelmänä toimi haastattelu. Tutkimuksen tulokset osoittavat kuluttajien mielipiteiden olevan positiivisia tuoksumarkkinoinnin käyttöä kohtaan. Tuloksien mukaan kuluttajat suosivat tuoksumarkkinoinnin käyttöä ennemmin brändäyksessä kuin tuoksumarkkinoinnin alitajuista käyttöä. Tuoksumarkkinoinnin alitajuista käyttöä ei kuitenkaan todettu täysin negatiiviseksi, sillä kuluttajat uskovat, että ostopäätös tehdään perustuen tärkeämpiin asioihin kuin tuoksuun, kuten esimerkiksi tuotteen hintaan perustuen. Kuluttajat uskovat, että alitajuisella käytöllä ei ole suurta vaikutusta asiakkaan ostopäätökseen muulloin kuin joissakin yksittäisissä heräteostoksissa.

Association between the increase in brain temperature and physical performance at different exercise intensities and protocols in a temperate environment

There is evidence that brain temperature (Tbrain) provides a more sensitive index than other core body temperatures in determining physical performance. However, no study has addressed whether the association between performance and increases in Tbrain in a temperate environment is dependent upon exercise intensity, and this was the primary aim of the present study. Adult male Wistar rats were subjected to constant exercise at three different speeds (18, 21, and 24 m/min) until the onset of volitional fatigue. Tbrain was continuously measured by a thermistor inserted through a brain guide cannula. Exercise induced a speed-dependent increase in Tbrain, with the fastest speed associated with a higher rate of Tbrain increase. Rats subjected to constant exercise had similar Tbrain values at the time of fatigue, although a pronounced individual variability was observed (38.7-41.7°C). There were negative correlations between the rate of Tbrain increase and performance for all speeds that were studied. These results indicate that performance during constant exercise is negatively associated with the increase in Tbrain, particularly with its rate of increase. We then investigated how an incremental-speed protocol affected the association between the increase in Tbrain and performance. At volitional fatigue, Tbrain was lower during incremental exercise compared with the Tbrain resulting from constant exercise (39.3±0.3 vs 40.3±0.1°C; P<0.05), and no association between the rate of Tbrain increase and performance was observed. These findings suggest that the influence of Tbrain on performance under temperate conditions is dependent on exercise protocol.

Hypertension is associated with greater heat exchange during exercise recovery in a hot environment

Individuals with systemic arterial hypertension have a higher risk of heat-related complications. Thus, the aim of this study was to examine the thermoregulatory responses of hypertensive subjects during recovery from moderate-intensity exercise performed in the heat. A total of eight essential hypertensive (H) and eight normotensive (N) male subjects (age=46.5±1.3 and 45.6±1.4 years, body mass index=25.8±0.8 and 25.6±0.6 kg/m2, mean arterial pressure=98.0±2.8 and 86.0±2.3 mmHg, respectively) rested for 30 min, performed 1 h of treadmill exercise at 50% of maximal oxygen consumption, and rested for 1 h after exercise in an environmental chamber at 38°C and 60% relative humidity. Skin and core temperatures were measured to calculate heat exchange parameters. Mean arterial pressure was higher in the hypertensive than in the normotensive subjects throughout the experiment (P<0.05, unpaired t-test). The hypertensive subjects stored less heat (H=-24.23±3.99 W·m−2vs N=-13.63±2.24 W·m−2, P=0.03, unpaired t-test), experienced greater variations in body temperature (H=-0.62±0.05°C vsN=-0.35±0.12°C, P=0.03, unpaired t-test), and had more evaporated sweat (H=-106.1±4.59 W·m−2vs N=-91.15±3.24 W·m−2, P=0.01, unpaired t-test) than the normotensive subjects during the period of recovery from exercise. In conclusion, essential hypertensive subjects showed greater sweat evaporation and increased heat dissipation and body cooling relative to normotensive subjects during recovery from moderate-intensity exercise performed in hot conditions.

The new era of customer experience in the omni-channel environment of a communication service provider

This study discusses the evolution of an omni-channel model in managing customer experience. The purpose of this thesis is to expand the current academic literature available on omni-channel and offer suggestions for omni-channel creation. This is done by studying the features of an omni-channel approach into engaging with customers and through the sub-objectives of describing the process behind its initiation as well as the special features communication service providers need to take in consideration. Theories used as a background for this study are related to customer experience, channel management, omni-channel and finally change management. The empirical study of this thesis consists of seven expert interviews conducted in a case company. The interviews were held between March and November 2014. One of the interviewees is the manager of an omni-channel development team, whilst the rest were in charge of the management of the various customer channels of the company. The organization and analysis of the interview data was conducted topically. The use of themes related to major theories on the subject was utilized to create linkages between theory and practice. The responses were also organized in two groups based on the viewpoint to map responses related to the company perspective as well as the customers´ perspective. The findings in this study are that omni-channel is among the best tools for companies to respond to the challenge induced by changing customer needs and preferences, as well as intensifying competitive environment. The omni-channel model was found to promote excellent customer experience and thus to be a source of competition advantage and increasing financial returns by creating an omni-experience for the customer. Through omniexperience customers see all of the transactions with a company presenting one brand and providing ease and effortlessness in every encounter. The processes behind omni-channel formulation were identified as customer experience proclaimed as the most important strategic goal, mapping and establishing a unified brand experience in all (service) channels and empowering the first line personnel as the gate keepers of omniexperience. Further the tools, measurement and supporting strategies were to be in accordance with the omni-channel strategy and the customer needs to become a partner in a two way transaction with the firm. Based on these findings a model for omni-channel creation is offered. Future research is needed to firstly, further test these findings and expand the theoretical framework on omni-channel, as it is quite scarce to date and secondly, to increase the generalizability of the model suggested.