Towards combining interactive mobile TV and smart spaces : architectures, tools and application development

Technological developments in microprocessors and ICT landscape have made a shift to a new era where computing power is embedded in numerous small distributed objects and devices in our everyday lives. These small computing devices are ne-tuned to perform a particular task and are increasingly reaching our society at every level. For example, home appliances such as programmable washing machines, microwave ovens etc., employ several sensors to improve performance and convenience. Similarly, cars have on-board computers that use information from many di erent sensors to control things such as fuel injectors, spark plug etc., to perform their tasks e ciently. These individual devices make life easy by helping in taking decisions and removing the burden from their users. All these objects and devices obtain some piece of information about the physical environment. Each of these devices is an island with no proper connectivity and information sharing between each other. Sharing of information between these heterogeneous devices could enable a whole new universe of innovative and intelligent applications. The information sharing between the devices is a diffcult task due to the heterogeneity and interoperability of devices. Smart Space vision is to overcome these issues of heterogeneity and interoperability so that the devices can understand each other and utilize services of each other by information sharing. This enables innovative local mashup applications based on shared data between heterogeneous devices. Smart homes are one such example of Smart Spaces which facilitate to bring the health care system to the patient, by intelligent interconnection of resources and their collective behavior, as opposed to bringing the patient into the health system. In addition, the use of mobile handheld devices has risen at a tremendous rate during the last few years and they have become an essential part of everyday life. Mobile phones o er a wide range of different services to their users including text and multimedia messages, Internet, audio, video, email applications and most recently TV services. The interactive TV provides a variety of applications for the viewers. The combination of interactive TV and the Smart Spaces could give innovative applications that are personalized, context-aware, ubiquitous and intelligent by enabling heterogeneous systems to collaborate each other by sharing information between them. There are many challenges in designing the frameworks and application development tools for rapid and easy development of these applications. The research work presented in this thesis addresses these issues. The original publications presented in the second part of this thesis propose architectures and methodologies for interactive and context-aware applications, and tools for the development of these applications. We demonstrated the suitability of our ontology-driven application development tools and rule basedapproach for the development of dynamic, context-aware ubiquitous iTV applications.

Toxoplasma gondii in experimentally infected Bos taurus and Bos indicus semen and tissues

Eighteen young steers were inoculated with Toxoplasma gondii and randomly distributed into three groups of six animals each: GI, 2.5x10(5) "P" strain oocysts, GII, 5.0x10(6) "RH" strain tachyzoites, and GIII (Control). Clinical, serological and parasitemia exams were realized. Parasite investigation by bioassay and PCR was realized on semen and fragments of skeletal musculature, lymph nodes, brain, retina, spleen, liver, lung, testicle, epididymis and seminal vesicle. Blood and semen samples were collected on days -2, -1, 1, 3, 5, 7, 14 and weekly thereafter, up to postinfection day (PID) 84. The inoculated steers (GI and GII) presented hyperthermia from PID 3 to 16. Antibodies against T. gondii were detected through the indirect fluorescence antibody test (IFAT) on PID 5 (1:16) in both inoculated groups (oocysts and tachyzoites), reaching peaks of 1:4096 on PID 7. Parasitemia outbursts occurred in all infected bovines, principally from PID 7 to 28, independent of the strain and inoculate used. Bioassays revealed the presence of parasites in semen samples of animals infected with oocysts (GI) and tachyzoites (GII) on several experimental days between PID 7 and 84. Tissue parasitism by T. gondii was diagnosed by bioassay and the PCR technique in several organ and tissue fragments. These findings suggest the possibility of sexual transmission of T. gondii in the bovine species.

Evaluation of follicular lymphoid depletion in the Bursa of Fabricius: an alternative methodology using digital image analysis and artificial neural networks

Fifty Bursa of Fabricius (BF) were examined by conventional optical microscopy and digital images were acquired and processed using Matlab® 6.5 software. The Artificial Neuronal Network (ANN) was generated using Neuroshell® Classifier software and the optical and digital data were compared. The ANN was able to make a comparable classification of digital and optical scores. The use of ANN was able to classify correctly the majority of the follicles, reaching sensibility and specificity of 89% and 96%, respectively. When the follicles were scored and grouped in a binary fashion the sensibility increased to 90% and obtained the maximum value for the specificity of 92%. These results demonstrate that the use of digital image analysis and ANN is a useful tool for the pathological classification of the BF lymphoid depletion. In addition it provides objective results that allow measuring the dimension of the error in the diagnosis and classification therefore making comparison between databases feasible.

A recombinant bovine herpesvirus 5 defective in thymidine kinase and glycoprotein E is attenuated and immunogenic for calves

Bovine herpesvirus 5 (BoHV-5) is an important pathogen of cattle in South America and efforts have been made to produce safer and more effective vaccines. In addition to afford protection, herpesvirus vaccines should allow serological differentiation of vaccinated from naturally, latently infected animals. We previously reported the construction and characterization in vitro of a double mutant BoHV-5 (BoHV-5gE/TK Δ) lacking the genes encoding thymidine kinase (tk) for attenuation, and glycoprotein E (gE) as the antigenic marker, as a vaccine candidate strain (Brum et al. 2010a). The present article reports an investigation on the attenuation and immunogenicity of this recombinant in calves. In a first experiment, 80 to 90-day-old seronegative calves (n=6) inoculated intranasally with the recombinant (titer of 10(7.5)TCID50) shed virus in low to moderate titers in nasal secretions for up to 6 days, yet did not develop any respiratory, systemic or neurological signs of infection. At day 30 post-infection (pi) all calves had BoHV-5 specific neutralizing (VN) antibodies in titers of 4 to 8 and were negative for anti-gE antibodies in a commercial ELISA test. Administration of dexamethasone (0.1mg/kg/day during 5 days) to four of these calves at day 42 pi did not result in virus shedding or increase in VN titers, indicating lack of viral reactivation. Secondly, a group of 8-month-old calves (n=9) vaccinated intramuscularly (IM) with the recombinant virus (10(7.5)TCID50/animal) did not shed virus in nasal secretions, remained healthy and developed VN titers from 2 to 8 at day 42 post-vaccination (pv), remaining negative for gE antibodies. Lastly, 21 calves (around 10 months old) maintained under field conditions were vaccinated IM with the recombinant virus (titer of 10(7.3)TCID50). All vaccinated animals developed VN titers from 2 to 16 at day 30 pv. A boost vaccination performed at day 240 pv resulted in a rapid and strong anamnestic antibody response, with VN titers reaching from 16 to 256 at day 14 post-booster. Again, serum samples remained negative for gE antibodies. Selected serum samples from vaccinated animals showed a broad VN activity against nine BoHV-5 and eight BoHV-1 field isolates. These results show that the recombinant virus is attenuated, immunogenic for calves and induces an antibody response differentiable from that induced by natural infection. Thus, the recombinant BoHV-5gE/TKΔ is an adequate candidate strain for a modified live vaccine.

Venäjän imperiumin paluu

Venäläiset ovat eurooppalainen sivistyskansa, joka on vaikuttanut merkittävällä tavalla maailman kohtaloihin. Kommunismin kukistuttua ja Neuvostoliiton hajottua venäläiset joutuivat hämmennyksen tilaan. Kansakunnan uusi nousu alkoi maantieteellisestä, sivistykselliseltä ja historialliselta pohjalta. Länsimaille oli yllätys, ettei Venäjä seurannut läntisiä demokraattisia esikuvia, vaan lähti luomaan uutta yhteiskuntaa omaa tietään kulkien. Valtion johtoon astuivat turvallisuusmiehet, jotka määrittelivät Venäjän kehitysstrategiat ja poliittiset tavoitteet. Heidän mukaansa Venäjän federaatio on imperiumi, eikä se alistu muiden johdettavaksi. Venäjä ei hyväksy Yhdysvaltojen johtamaa yksinapaista maailmaa. Venäjän pyrkimyksenä on kohota yhdeksi tärkeäksi maailmanpolitiikan keskukseksi ja haastaa muiden vaikuttajien kuten EU:n, Kiinan, Japanin ja Intian kanssa Yhdysvaltojen johtoasema. Tavoitteeseen pääseminen edellyttää yhteiskunnan voimavarojen keskittämistä. Vuodesta 1996 lähtien poliittinen valta on keskitetty tiukasti presidentille ja hänen johtamalleen hallintokoneistolle. Vladimir Putinin johdolla yhteiskunta vakautettiin autoritaariseen tyyliin. Vuosina 2008–2012 muodollisena, joskin vaaleilla valittuna, presidenttinä oli Putinin luottomies Dmitri Medvedev. Tuolloin todellisena Venäjän johtajana toimi pääministeri Putin. Medvedevin nelivuotiskauden päätyttyä Putin jatkaa valtion johdossa presidenttinä. Taloudelliset edellytykset harjoitetulle politiikalle ovat Venäjällä itsellään. Maa on maailman ainoa suurvalta, joka on riippumaton ulkomaisista energia- ja raaka-ainelähteistä, ja vuodesta 2002 vuoden 2008 lopulle jatkunut energian ja raaka-aineiden hintojen nousu on tukenut Venäjän talouskehitystä. Lisääntyneillä tuloilla on voitu monipuolisesti kehittää yhteiskuntaa, ja väestön enemmistö on tyytyväinen harjoitettuun politiikkaan. Venäjä selvisi nopeasti vuonna 2009 maailmaa kuristaneesta taloudellisesta kriisistä ja pääsi jälleen kasvu-uralla. Suurena ongelmana on vientiteollisuuden yksipuolinen painottuminen energia- ja raaka-ainesektoreille, jolloin talous on hyvin riippuvainen maailmantalouden kehityksestä. Suurten valtion omistamien yhtiöiden hallitsema elinkeinoelämä ei myöskään ole omiaan edistämään yrittäjyyttä, joka on kaiken innovatiivisuuden perusedellytys. Valtiojohtoinen autoritaarisuus ei ole tyydyttänyt kaikkia, mutta vanhaan venäläiseen tyyliin protestit on tukahdutettu, ja ulkomaisille arvostelijoille venäläiset ovat kertoneet kehittävänsä venäläistä, ”ohjattua” demokratiaa. Imperiumille erittäin tärkeän instrumentin muodostavat vahvat asevoimat, ja valtiojohtoinen autoritaarinen talouselämä antaa mahdollisuudet niiden kehittämiselle. Asevoimien kehityksen esteenä ei ole niinkään talous, vaan teknologinen ja innovatiivinen jälkeenjääneisyys. Vuonna 2003 käynnistetty asevoimien reformi on lähtenyt liikkeelle ja sen tuloksia oli havaittavissa elokuussa 2008 käydyssä Venäjän ja Georgian välisessä sodassa, joka päättyi Venäjän aseille voitokkaasti. Tuolloin kuitenkin todettiin asevoimien tekninen ja taktinen jälkeenjääneisyys, mikä johti asevoimien ja niitä tukevan teollisuuden uudistamiseen tähtäävien uudelleenjärjestelyiden kiirehtimiseen ja kehittämiseen.

Adaptive Routing Approaches for Networked Many-Core Systems

Through advances in technology, System-on-Chip design is moving towards integrating tens to hundreds of intellectual property blocks into a single chip. In such a many-core system, on-chip communication becomes a performance bottleneck for high performance designs. Network-on-Chip (NoC) has emerged as a viable solution for the communication challenges in highly complex chips. The NoC architecture paradigm, based on a modular packet-switched mechanism, can address many of the on-chip communication challenges such as wiring complexity, communication latency, and bandwidth. Furthermore, the combined benefits of 3D IC and NoC schemes provide the possibility of designing a high performance system in a limited chip area. The major advantages of 3D NoCs are the considerable reductions in average latency and power consumption. There are several factors degrading the performance of NoCs. In this thesis, we investigate three main performance-limiting factors: network congestion, faults, and the lack of efficient multicast support. We address these issues by the means of routing algorithms. Congestion of data packets may lead to increased network latency and power consumption. Thus, we propose three different approaches for alleviating such congestion in the network. The first approach is based on measuring the congestion information in different regions of the network, distributing the information over the network, and utilizing this information when making a routing decision. The second approach employs a learning method to dynamically find the less congested routes according to the underlying traffic. The third approach is based on a fuzzy-logic technique to perform better routing decisions when traffic information of different routes is available. Faults affect performance significantly, as then packets should take longer paths in order to be routed around the faults, which in turn increases congestion around the faulty regions. We propose four methods to tolerate faults at the link and switch level by using only the shortest paths as long as such path exists. The unique characteristic among these methods is the toleration of faults while also maintaining the performance of NoCs. To the best of our knowledge, these algorithms are the first approaches to bypassing faults prior to reaching them while avoiding unnecessary misrouting of packets. Current implementations of multicast communication result in a significant performance loss for unicast traffic. This is due to the fact that the routing rules of multicast packets limit the adaptivity of unicast packets. We present an approach in which both unicast and multicast packets can be efficiently routed within the network. While suggesting a more efficient multicast support, the proposed approach does not affect the performance of unicast routing at all. In addition, in order to reduce the overall path length of multicast packets, we present several partitioning methods along with their analytical models for latency measurement. This approach is discussed in the context of 3D mesh networks.

Freund's adjuvant-induced inflammation: clinical findings and its effect on hepcidin mRNA expression in horses

Hypoferremia observed during systemic inflammatory disorders is regulated by hepcidin. Hepcidin up-regulation is particularly important during acute inflammation, as it restricts the availability of iron, which is necessary for pathogenic microorganism growth before adaptive immunity occurs. The aim of this study was to evaluate the clinical findings and hepatic hepcidin mRNA expression in horses using a Freund's complete adjuvant (FCA) model of inflammation. The expression of hepcidin mRNA in the liver was determined in healthy horses following two intramuscular injections of FCA at 0 h and 12 h. Plasma iron and fibrinogen concentrations were measured at multiple time points between 0 h and 240 h post-FCA injection (PI). Hepcidin mRNA expression was determined by RT-qPCR using liver biopsy samples performed at 0 h (control), 6 h and 18 h PI. The mean plasma fibrinogen level was significantly different from the control values only between 120 and 216 h PI. The mean plasma iron level was significantly lower than the control between 16 and 72 h PI, reaching the lowest levels at 30 h PI (33 % of the initial value), and returned to the reference value from 96 h PI to the end of the experiment. Hepcidin mRNA expression increased at 6 h PI and remained high at 18 h PI. The iron plasma concentration was an earlier indicator of inflammatory processes in horses when compared with fibrinogen and might be useful for the early detection of inflammation in the horse. FCA administration caused the rapid onset of hypoferremia, and this effect was likely the result of up-regulated hepatic hepcidin gene expression. This study emphasizes the importance of hepcidin and iron metabolism during inflammation in horses.

Russia, China, India Foresight for Small and Medium size Enterprises in Uusimaa : Changes forecast in the Russian, Chinese and Indian operating environments from the viewpoint of small and middle-sized enterprises in Uusimaa

The report describes those factors of the future that are related to the growth and needs of Russia, China, and India and that may provide significant internationalisation potential for Uusimaa companies. The report examines the emerging trends and market-entry challenges for each country separately. Additionally, it evaluates the training needs of Uusimaa companies in terms of the current offerings available for education on topics related to Russia, China, and India. The report was created via the Delphi method: experts were interviewed, and both Trendwiki material and the latest literature were used to create a summary of experts’ views, statements, and reasons behind recent developments. This summary of views was sent back to the experts with the objective of reaching consensus synthesising the differing views or, at least, of providing argumentation for the various alternative lines of development. In addition to a number of outside experts and business leaders, all heads of Finpro’s Finland Trade Centers participated in the initial interviews. The summary was commented upon by all Finpro consultants and analysts for Russia, China, and India, with each focusing on his or her own area of expertise. The literature used consisted of reports, listed for each country, and an extensive selection of the most recent newspaper articles. The report was created in January-April 2010. On 22 April 2010 its results were reviewed at the final report presentation in cooperation with the Uusimaa ELY Centre.

Growth and mineral nutrition Of Ipomoea quamoclit

A greenhouse experiment was carried out from November 2006 to April 2007 at FCAV/UNESP, Brazil, aiming to study the dry mass production and the accumulation and distribution of macronutrients in Ipomoea quamoclit, an important weed for annual and perennial crops in Brazil. The plants were grown in seven liter pots with sand substrate, daily irrigated with Hoagland & Arnon nutrient solution. The experimental design was completely randomized with four replicates. The treatments corresponded to evaluation times at 14 day intervals, beginning 21 days after emergence (DAE). In each evaluation, the plants of four pots were analyzed in function of dry mass production and macronutrient content. I. quamoclit had a small dry mass and macronutrient accumulation at the beginning of the experimental stage, increasing after 77 DAE and reaching the maximum theoretical value at 146, 143, 140, 149, 142, 153, and 124 DAE, for dry mass, N, P, K, Ca, Mg, and S, respectively. K and N were the macronutrients most accumulated by I. quamoclit plants.

Growth and mineral nutrition of Solanum americanum

A greenhouse trial was carried out from November 1995 to April 1996 at FCAV/UNESP, Brazil, aiming to study the dry matter production and the accumulation and distribution of macronutrients in Solanum americanum, an important weed for annual and perennial crops in Brazil. The plants were grown in seven liter pots with sand substrate, irrigated daily with Hoagland & Arnon nutrient solution. The experimental design was completely randomized with four replicates. The treatments corresponded to evaluation times at 14 day intervals, beginning 21 days after emergence (DAE). In each evaluation, the plants of four pots were analyzed for dry matter production and macronutrient content. S. americanum had a small dry matter and macronutrient accumulation at the beginning of the experimental stage, increasing after 77 DAE and reaching the maximum theoretical value at 142, 142, 164, 149, 140, 149 and 152 DAE, for dry matter, N, P, K, Ca, Mg, and S, respectively. K and N were the most accumulated macronutrients for S. americanum plants.

Enabling Change in Universities: Enhancing Education for Sustainable Development with Tools for Quality Assurance

Enabling Change in Universities: Enhancing Education for Sustainable Development with Tools for Quality Assurance This thesis deals with enabling change in universities, more explicitly enhancing education for sustainable development with tools for quality assurance. Change management is a discipline within management that was developed in the 1980s because business changed from being predictable to unpredictable. The PEST mnemonic is a method to categorize factors enabling change; such as political, economic, socio-cultural and technological factors, which all affect higher education. A classification of a change, in either hard or soft, can help understanding the type of change that an organization is facing. Hard changes are more applied to problems that have clear objectives and indicators, with a known cause of the problem. Soft changes are applied to larger problems that affect the entire organization or beyond it. The basic definition for sustainable development is: the future generations should have similar opportunities as the previous. The UN has set as a global goal an integration of education for sustainable development (ESD) at all levels of education during 2005- 2014. The goal is set also in universities, the graduates of which are future leaders for all labor markets. The objective for ESD in higher education is that graduates obtain the competence to take economic, social and environmental costs and benefits into account when making decisions. Knowledge outcomes should aim for systematic and holistic thinking, which requires cross disciplinary education. So far, the development of ESD has not achieved its goals. The UN has identified a need for more transdisclipnary research in ESD. A joint global requirement for universities is quality assurance, the aim of which is to secure and improve teaching and learning. Quality, environmental and integrated management systems are used by some universities for filling the quality assurance requirements. The goal of this thesis is to open up new ways for enhancing ESD in universities, beyond the forerunners; by exploring how management systems could be used as tools for promoting ESD. The thesis is based on five studies. In the first study, I focus on if and how tools for quality assurance could be benefitted for promoting ESD. It is written from a new perspective, the memetic, for reaching a diversity of faculty. A meme is an idea that diffuses from brain to brain. It can be applied for cultural evolution. It is a theory that is based on the evolutionary theory by Darwin, applied for social sciences. In the second Paper, I present the results from the development of the pilot process model for enhancing ESD with management systems. The development of the model is based on a study that includes earlier studies, a survey in academia and an analysis of the practice in 11 universities in the Nordic countries. In the third study, I explore if the change depends on national culture or if it is global. It is a comparative study on both policy and implementation level, between the Nordic countries and China. The fourth study is a single case study based on change management. In this study, I identify what to consider in order to enable the change: enhancing ESD with tools for quality assurance in universities. In the fifth Paper, I present the results of the process model for enhancing ESD with management systems. The model was compared with identified drivers and barriers for enhancing ESD and for implementing management systems. Finally, the process model was piloted and applied for identifying sustainability aspects in curricula. Action research was chosen as methodology because there are not already implemented approaches using quality management for promoting ESD, why the only way to study this is to make it happen. Another reason for choosing action research is since it is essential to involve students and faculty for enhancing ESD. Action based research consists of the following phases: a) diagnosing, b) planning action, c) taking action and d) evaluating action. This research was made possible by a project called Education for Sustainable Development in Academia in the Nordic countries, ESDAN, in which activities were divided into these four phases. Each phase ended with an open seminar, where the results of the study were presented. The objective for the research project was to develop a process for including knowledge in sustainable development in curricula, which could be used in the quality assurance work. Eleven universities from the Nordic countries cooperated in the project. The aim was, by applying the process, to identify and publish examples of relevant sustainability aspects in different degree programs in universities in the Nordic countries. The project was partly financed by the Nordic Council of Ministers and partly by the participating pilot universities. Based on the results of my studies, I consider that quality, environmental and integrated management systems can be used for promoting ESD in universities. Relevant sustainability aspects have been identified in different fields of studies by applying the final process model. The final process model was compared with drivers and barriers for enhancing ESD and for implementing management systems in universities and with succeeding with management systems in industry. It corresponds with these, meaning that drivers are taken into account and barriers tackled. Both ESD and management systems in universities could be considered successful memes, which can reflect an effective way of communication among individuals. I have identified that management systems could be used as tools for hard changes and to support the soft change of enhancing ESD in universities with management system. Based on the change management study I have summarized recommendations on what to consider in order to enable the studied change. The main practical implications of the results are that the process model could be applied for assessment, benchmarking and communication of ESD, connected to quality assurance, when applied. This is possible because the information can be assembled in one picture, which facilitates comparison. The memetic approach can be applied for structuring. It is viable to make comparative studies between cultures, for getting insight in special characteristics of the own culture. Action based research is suitable for involving faculty. Change management can be applied for planning a change, which both enhancing ESD and developing management systems are identified to be.

Jätehuollon tilannekuva puolustushallinnossa

Diplomityön tavoitteena oli tuottaa jätehuollon tilannekuva Suomen puolustushallinnolle. Diplomityön ensisijaiseksi tutkimustavoitteeksi määriteltiin jätehuollon nykytilan kartoitus vuonna 2013. Lisäksi diplomityössä tarkasteltiin jätehuollon suunnittelutyön merkitystä puolustushallinnolle sekä kartoitettiin lähitulevaisuuden painopistealueita puolustushallinnon jätehuollossa. Sisätilojen jätehuoltojärjestelyt eivät noudata samaa linjaa ulkojätepisteiden jäte-huoltojärjestelyjen kanssa. Tämä asettaa haasteita syntypaikkalajittelun toteuttamiselle ja edelleen jätehuoltotavoitteiden saavuttamiselle. Tähän jätehuollon epäkohtaan on mahdollista vaikuttaa jätehuollon prosessien selkeyttämisellä ja sopimusten tarkastelemisella yhdessä vuonna 2015 käynnistyvän puolustusvoimien Logistiikkalaitoksen kanssa. Laskennallisen vaikuttavuusanalyysin perusteella jätehuollon tehostamistoimilla on mahdollista saavuttaa myös kustannussäästöjä. Ulkojätepisteiden tehostamisella olisi mahdollista saavuttaa noin 25 % säästöt jätehuollon kustannuksissa. Tehokkaammalla syntypaikkalajittelulla olisi mahdollista saavuttaa noin 27–31 % säästöt jätteen käsittelymaksuissa. Jätehuoltotavoitteiden saavuttamisessa keskeinen rooli on myös jätehuollon tiedonhallinnalla ja raportoinnilla sekä jätehuollon käyttäjät tavoittavalla tiedotuksella. Jätehuollon suunnittelu- ja kehittämistyössä tulee pyrkiä käyttäjäläheisempään toteutukseen. Diplomityön pohjalta aloitetaan puolustushallinnon jätehuollon pitkän aikavälin toiminnallisen strategian suunnittelu. Pitkän aikavälin toiminnalliseen strategiaan sisällytetään uudet jätehuollon tavoitteet, joissa huomioidaan puolustushallinnon sisäisten tavoitteiden lisäksi myös valtakunnallinen jätesuunnittelu.

Accumulation of dry mass and macronutrients by sourgrass plants

The experiment was carried out aiming to analyze the dry mass production and distribution and the content and accumulation of macronutrients in sourgrass (Digitaria insularis) plants cultivated under mineral nutrition standard conditions. Plants grew in 7-liter pots filled with sand substrate and daily irrigated with nutrient solution, being maintained under greenhouse conditions. Treatments consisted of times of evaluation (21, 35, 49, 63, 77, 91, 105, 119, and 133 days after emergence - DAE) and were arranged in a completely randomized design with four replicates. Sourgrass showed small accumulation of dry mass (0.3 g per plant) and macronutrients (3.7 mg of N per plant, 0.4 mg of P per plant, 5.6 mg of K per plant, 0.9 mg of Ca per plant, 0.7 mg of Mg per plant, and 0.3 mg of S per plant) at vegetative growth stage (< 49 DAE). Those accumulations increased mainly after 77 DAE, reaching the maximum theoretical value at 143, 135, 141, 129, 125, 120, and 128 DAE, for dry mass (12.4 g per plant), N (163.2 mg per plant), P (27.1 mg per plant), K (260.5 mg per plant), Ca (47.6 mg per plant), Mg (30.9 mg per plant), and S (13.7 mg per plant), respectively. K and N were found with higher rates and, as a consequence, they were required and accumulated in greater amounts in plant tissues of sourgrass.

Carryover of Imazethapyr + Imazapic on Ryegrass and Non-tolerant Rice as Affected by Thickness of Soil Profile

Herbicides used in Clearfield(r) rice system may persist in the environment, damaging non-tolerant crops sown in succession and/or rotation. These damages vary according to soil characteristics, climate and soil management. The thickness of the soil profile may affect carryover effect; deeper soils may allow these molecules to leach, reaching areas below the roots absorption zone. The aim of this study was to evaluate the effect of the thickness of soil profile in the carryover of imazethapyr + imazapic on ryegrass and non-tolerant rice, sown in succession and rotation to rice, respectively. Lysimeters of different thicknesses (15, 20, 30, 40, 50 and 65 cm) were constructed, where 1 L ha-1 of the imazethapyr + imazapic formulated mixture was applied in tolerant rice. Firstly, imidazolinone-tolerant rice was planted, followed by ryegrass and non-tolerant rice in succession and rotation, respectively. Herbicide injury, height reduction and dry weight of non-tolerant species were assessed. There was no visual symptoms of herbicide injury on ryegrass sown 128 days after the herbicide application; however it causes dry weight mass reduction of plants. The herbicides persist in the soil and cause injury in non-tolerant rice, sown 280 days after application, and the deeper the soil profile, the lower the herbicides injury on irrigated rice.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.