Automatic Lameness Detection in a Milking Robot : Instrumentation, measurement software, algorithms for data analysis and a neural network model

The aim of this thesis is to develop a fully automatic lameness detection system that operates in a milking robot. The instrumentation, measurement software, algorithms for data analysis and a neural network model for lameness detection were developed. Automatic milking has become a common practice in dairy husbandry, and in the year 2006 about 4000 farms worldwide used over 6000 milking robots. There is a worldwide movement with the objective of fully automating every process from feeding to milking. Increase in automation is a consequence of increasing farm sizes, the demand for more efficient production and the growth of labour costs. As the level of automation increases, the time that the cattle keeper uses for monitoring animals often decreases. This has created a need for systems for automatically monitoring the health of farm animals. The popularity of milking robots also offers a new and unique possibility to monitor animals in a single confined space up to four times daily. Lameness is a crucial welfare issue in the modern dairy industry. Limb disorders cause serious welfare, health and economic problems especially in loose housing of cattle. Lameness causes losses in milk production and leads to early culling of animals. These costs could be reduced with early identification and treatment. At present, only a few methods for automatically detecting lameness have been developed, and the most common methods used for lameness detection and assessment are various visual locomotion scoring systems. The problem with locomotion scoring is that it needs experience to be conducted properly, it is labour intensive as an on-farm method and the results are subjective. A four balance system for measuring the leg load distribution of dairy cows during milking in order to detect lameness was developed and set up in the University of Helsinki Research farm Suitia. The leg weights of 73 cows were successfully recorded during almost 10,000 robotic milkings over a period of 5 months. The cows were locomotion scored weekly, and the lame cows were inspected clinically for hoof lesions. Unsuccessful measurements, caused by cows standing outside the balances, were removed from the data with a special algorithm, and the mean leg loads and the number of kicks during milking was calculated. In order to develop an expert system to automatically detect lameness cases, a model was needed. A probabilistic neural network (PNN) classifier model was chosen for the task. The data was divided in two parts and 5,074 measurements from 37 cows were used to train the model. The operation of the model was evaluated for its ability to detect lameness in the validating dataset, which had 4,868 measurements from 36 cows. The model was able to classify 96% of the measurements correctly as sound or lame cows, and 100% of the lameness cases in the validation data were identified. The number of measurements causing false alarms was 1.1%. The developed model has the potential to be used for on-farm decision support and can be used in a real-time lameness monitoring system.

Data fusion and matching by maximizing statistical dependencies

The core aim of machine learning is to make a computer program learn from the experience. Learning from data is usually defined as a task of learning regularities or patterns in data in order to extract useful information, or to learn the underlying concept. An important sub-field of machine learning is called multi-view learning where the task is to learn from multiple data sets or views describing the same underlying concept. A typical example of such scenario would be to study a biological concept using several biological measurements like gene expression, protein expression and metabolic profiles, or to classify web pages based on their content and the contents of their hyperlinks. In this thesis, novel problem formulations and methods for multi-view learning are presented. The contributions include a linear data fusion approach during exploratory data analysis, a new measure to evaluate different kinds of representations for textual data, and an extension of multi-view learning for novel scenarios where the correspondence of samples in the different views or data sets is not known in advance. In order to infer the one-to-one correspondence of samples between two views, a novel concept of multi-view matching is proposed. The matching algorithm is completely data-driven and is demonstrated in several applications such as matching of metabolites between humans and mice, and matching of sentences between documents in two languages.

Microbiological characterisation of soils : Evaluation of some critical steps in data collection and experimental design

The study of soil microbiota and their activities is central to the understanding of many ecosystem processes such as decomposition and nutrient cycling. The collection of microbiological data from soils generally involves several sequential steps of sampling, pretreatment and laboratory measurements. The reliability of results is dependent on reliable methods in every step. The aim of this thesis was to critically evaluate some central methods and procedures used in soil microbiological studies in order to increase our understanding of the factors that affect the measurement results and to provide guidance and new approaches for the design of experiments. The thesis focuses on four major themes: 1) soil microbiological heterogeneity and sampling, 2) storage of soil samples, 3) DNA extraction from soil, and 4) quantification of specific microbial groups by the most-probable-number (MPN) procedure. Soil heterogeneity and sampling are discussed as a single theme because knowledge on spatial (horizontal and vertical) and temporal variation is crucial when designing sampling procedures. Comparison of adjacent forest, meadow and cropped field plots showed that land use has a strong impact on the degree of horizontal variation of soil enzyme activities and bacterial community structure. However, regardless of the land use, the variation of microbiological characteristics appeared not to have predictable spatial structure at 0.5-10 m. Temporal and soil depth-related patterns were studied in relation to plant growth in cropped soil. The results showed that most enzyme activities and microbial biomass have a clear decreasing trend in the top 40 cm soil profile and a temporal pattern during the growing season. A new procedure for sampling of soil microbiological characteristics based on stratified sampling and pre-characterisation of samples was developed. A practical example demonstrated the potential of the new procedure to reduce the analysis efforts involved in laborious microbiological measurements without loss of precision. The investigation of storage of soil samples revealed that freezing (-20 °C) of small sample aliquots retains the activity of hydrolytic enzymes and the structure of the bacterial community in different soil matrices relatively well whereas air-drying cannot be recommended as a storage method for soil microbiological properties due to large reductions in activity. Freezing below -70 °C was the preferred method of storage for samples with high organic matter content. Comparison of different direct DNA extraction methods showed that the cell lysis treatment has a strong impact on the molecular size of DNA obtained and on the bacterial community structure detected. An improved MPN method for the enumeration of soil naphthalene degraders was introduced as an alternative to more complex MPN protocols or the DNA-based quantification approach. The main advantage of the new method is the simple protocol and the possibility to analyse a large number of samples and replicates simultaneously.

Oral health behaviour, conditions and care among dentate elderly patients in Lithuania: preventive aspects

The present cross-sectional study aimed to assess oral health behaviour, dental and periodontal conditions, dental care, and their relationships among elderly dentate patients in Lithuania. The target population in the study were dentate patients aged 60 and older attending public dental services in Kedainiai, Lithuania. The data collection took place between the autumn of 1999 and the winter of 2001. Data were collected by means of a self-administered questionnaire for all (n=174) and a clinical examination targeting about half of the subjects (n=100). The questionnaire inquired about oral health behaviour, the life-first and also the most recent dental treatments, sources on and self-assessed knowledge of oral self-care, a self-reported number of teeth, and socio-demographic information. The clinical examination included basic dental and periodontal conditions. A total of 82 women and 92 men completed the questionnaire; their mean age was 69.2 and their average number of teeth was 16.2 (CI 95% 15.4-17.1). In all, 25% had 21 or more teeth and 32% indicated wearing removable dentures. The oral health behaviour, the participants reported, was poor: 30% reported twice daily toothbrushing, 57% responded that they always use fluoride toothpaste, 19% indicated daily interdental cleaning, nearly all said they take sugar in their coffee and tea, and 30% indicated going for check-ups. As the main source of information on oral self-care, the subjects indicated health professionals (82%), followed by social contacts (72%), broadcasted media (58%), and printed media (42%). A total of 34% assessed their knowledge of oral self-care as good, and their self-assessed knowledge correlated (r=0.52) with professional guidance they had received about oral self-care. In their most recent treatment, conservative (39%) and non-conservative (34%) treatments dominated, and preventive ones were the least reported (7%). Regarding guidance in oral self-care, 54% reported having received such about toothbrushing, 32% about interdental cleaning, and 33% had been given visual information. Clinical examinations revealed the presence of plaque, calculus, bleeding on probing and deepened pockets in all of the subjects; 70% of the subjects were diagnosed with pockets of 6mm and deeper, 94% with caries, and 73% with overhangs of restorations. Those subjects assessing their knowledge of oral self-care as good and reporting a higher intensity of guidance in oral self-care as received, indicated practicing the recommended oral self-care more frequently. Twice daily toothbrushing was associated with good self-assessed knowledge of oral self-care (OR 4.1, p<0.001) and a university education (OR 5.6, p<0.001). Those subjects with better oral health behaviour had a greater number of teeth. Having 21 or more teeth was associated with good self-assessed knowledge of oral self-care (OR 4.1, p=0.03). Better periodontal conditions were associated with a higher frequency of toothbrushing. The presence of periodontal pockets of 6mm and deeper was associated with the level of self-assessed knowledge of oral self-care being below good (OR=3.0, p=0.04) and the level of dental cleanliness being poor (OR=2.7, p=0.02). To conclude, oral health behaviour and conditions call for improvement in elderly subjects in Lithuania. To improve the oral health of their elderly dentate patients, dentists should apply all the available tools of chair-side prevention and active guidance. The latter would be an effective means of updating the knowledge of oral self-care and supporting recommended oral health behaviour. A preventive approach should be strongly emphasized in countries with limited resources for oral health care, such as Lithuania. Author’s address: Sonata Vyšniauskaite, Department of Oral Public Health, Institute of Dentistry, University of Helsinki, P.O.Box 41, FI-00014 Helsinki, Finland. E-mail: sonata.vysniauskaite@helsinki.fi

Evidence-based perspective on CP rehabilitation : Reviews on physiotherapy, physiotherapy-related motor-based interventions and orthotic devices

This thesis utilises an evidence-based approach to critically evaluate and summarize effectiveness research on physiotherapy, physiotherapy-related motor-based interventions and orthotic devices in children and adolescents with cerebral palsy (CP). It aims to assess the methodological challenges of the systematic reviews and trials, to evaluate the effectiveness of interventions in current use, and to make suggestions for future trials Methods: Systematic reviews were searched from computerized bibliographic databases up to August 2007 for physiotherapy and physiotherapy-related interventions, and up to May 2003 for orthotic devices. Two reviewers independently identified, selected, and assessed the quality of the reviews using the Overview Quality Assessment Questionnaire complemented with decision rules. From a sample of 14 randomized controlled trials (RCT) published between January 1990 and June 2003 we analysed the methods of sampling, recruitment, and comparability of groups; defined the components of a complex intervention; identified outcome measures based on the International Classification of Functioning, Disability and Health (ICF); analysed the clinical interpretation of score changes; and analysed trial reporting using a modified 33-item CONSORT (Consolidated Standards of Reporting Trials) checklist. The effectiveness of physiotherapy and physiotherapy-related interventions in children with diagnosed CP was evaluated in a systematic review of randomised controlled trials that were searched from computerized databases from January 1990 up to February 2007. Two reviewers independently assessed the methodological quality, extracted the data, classified the outcomes using the ICF, and considered the level of evidence according to van Tulder et al. (2003). Results: We identified 21 reviews on physiotherapy and physiotherapy-related interventions and five on orthotic devices. These reviews summarized 23 or 5 randomised controlled trials and 104 or 27 observational studies, respectively. Only six reviews were of high quality. These found some evidence supporting strength training, constraint-induced movement therapy or hippotherapy, and insufficient evidence on comprehensive interventions. Based on the original studies included in the reviews on orthotic devices we found some short-term effects of lower limb casting on passive range of movement, and of ankle-foot orthoses on equinus walk. Long term effects of lower limb orthoses have not been studied. Evidence of upper limb casting or orthoses is conflicting. In the sample of 14 RCTs, most trials used simple randomisation, complemented with matching or stratification, but only three specified the concealed allocation. Numerous studies provided sufficient details on the components of a complex intervention, but the overlap of outcome measures across studies was poor and the clinical interpretation of observed score changes was mostly missing. Almost half (48%) of the applicable CONSORT-based items (range 28 32) were reported adequately. Most reporting inadequacies were in outcome measures, sample size determination, details of the sequence generation, allocation concealment and implementation of the randomization, success of assessor blinding, recruitment and follow-up dates, intention-to-treat analysis, precision of the effect size, co-interventions, and adverse events. The systematic review identified 22 trials on eight intervention categories. Four trials were of high quality. Moderate evidence of effectiveness was established for upper extremity treatments on attained goals, active supination and developmental status, and of constraint-induced therapy on the amount and quality of hand use and new emerging behaviours. Moderate evidence of ineffectiveness was found for strength training's effect on walking speed and stride length. Conflicting evidence was found for strength training's effect on gross motor function. For the other intervention categories the evidence was limited due to the low methodological quality and the statistically insignificant results of the studies. Conclusions: The high-quality reviews provide both supportive and insufficient evidence on some physiotherapy interventions. The poor quality of most reviews calls for caution, although most reviews drew no conclusions on effectiveness due to the poor quality of the primary studies. A considerable number of RCTs of good to fair methodological and reporting quality indicate that informative and well-reported RCTs on complex interventions in children and adolescents with CP are feasible. Nevertheless, methodological improvement is needed in certain areas of the trial design and performance, and the trial authors are encouraged to follow the CONSORT criteria. Based on RCTs we established moderate evidence for some effectiveness of upper extremity training. Due to limitations in methodological quality and variations in population, interventions and outcomes, mostly limited evidence on the effectiveness of most physiotherapy interventions is available to guide clinical practice. Well-designed trials are needed, especially for focused physiotherapy interventions.

Accuracy of absorbed dose in external photon beam radiotherapy : what level is sufficient and how to approach it?

Radiation therapy (RT) plays currently significant role in curative treatments of several cancers. External beam RT is carried out mostly by using megavoltage beams of linear accelerators. Tumor eradication and normal tissue complications correlate to dose absorbed in tissues. Normally this dependence is steep and it is crucial that actual dose within patient accurately correspond to the planned dose. All factors in a RT procedure contain uncertainties requiring strict quality assurance. From hospital physicist´s point of a view, technical quality control (QC), dose calculations and methods for verification of correct treatment location are the most important subjects. Most important factor in technical QC is the verification that radiation production of an accelerator, called output, is within narrow acceptable limits. The output measurements are carried out according to a locally chosen dosimetric QC program defining measurement time interval and action levels. Dose calculation algorithms need to be configured for the accelerators by using measured beam data. The uncertainty of such data sets limits for best achievable calculation accuracy. All these dosimetric measurements require good experience, are workful, take up resources needed for treatments and are prone to several random and systematic sources of errors. Appropriate verification of treatment location is more important in intensity modulated radiation therapy (IMRT) than in conventional RT. This is due to steep dose gradients produced within or close to healthy tissues locating only a few millimetres from the targeted volume. The thesis was concentrated in investigation of the quality of dosimetric measurements, the efficacy of dosimetric QC programs, the verification of measured beam data and the effect of positional errors on the dose received by the major salivary glands in head and neck IMRT. A method was developed for the estimation of the effect of the use of different dosimetric QC programs on the overall uncertainty of dose. Data were provided to facilitate the choice of a sufficient QC program. The method takes into account local output stability and reproducibility of the dosimetric QC measurements. A method based on the model fitting of the results of the QC measurements was proposed for the estimation of both of these factors. The reduction of random measurement errors and optimization of QC procedure were also investigated. A method and suggestions were presented for these purposes. The accuracy of beam data was evaluated in Finnish RT centres. Sufficient accuracy level was estimated for the beam data. A method based on the use of reference beam data was developed for the QC of beam data. Dosimetric and geometric accuracy requirements were evaluated for head and neck IMRT when function of the major salivary glands is intended to be spared. These criteria are based on the dose response obtained for the glands. Random measurement errors could be reduced enabling lowering of action levels and prolongation of measurement time interval from 1 month to even 6 months simultaneously maintaining dose accuracy. The combined effect of the proposed methods, suggestions and criteria was found to facilitate the avoidance of maximal dose errors of up to even about 8 %. In addition, their use may make the strictest recommended overall dose accuracy level of 3 % (1SD) achievable.

Local Politicizations : A Comparison of Finns and French Practicing Democracy

This study examines how do the processes of politicization differ in the Finnish and the French local contexts, and what kinds of consequences do these processes have on the local civic practices, the definitions and redefinitions of democracy and citizenship, the dynamics of power and resistance, and the ways of solving controversies in the public sphere. By means of comparative anthropology of the state , focusing on how democracy actually is practiced in different contexts, politicizations the processes of opening political arenas and recognizing controversy are analyzed. The focus of the study is on local activists engaged in different struggles on various levels of the local public spheres, and local politicians and civil servants participating in these struggles from their respective positions, in two middle-size European cities, Helsinki and Lyon. The empirical analyses of the book compare different political actors and levels of practicing democracy simultaneously. The study is empirically based on four different bodies of material: Ethnographic notes taken during a fieldwork among the activities of several local activist groups; 47 interviews of local activists and politicians; images representing different levels of public portrayals from activist websites (Helsinki N=274, Lyon N=232) and from city information magazines (Helsinki-info N=208, Lyon Citoyen N= 357); and finally, newspaper articles concerning local conflict issues, and reporting on the encounters between local citizens and representatives of the cities (January-June in 2005; Helsingin Sanomat N=96 and Le Progrès N= 102). The study makes three distinctive contributions to the study of current democratic societies: (1) a conceptual one by bringing politicization at the center of a comparison of political cultures, and by considering in parallel the ethnographic group styles theory by Nina Eliasoph and Paul Lichterman, the theory on counter-democracy by Pierre Rosanvallon and the pragmatist justification theory by Luc Boltanski and Laurent Thévenot; (2) an empirical one through the triangulation of ethnographic, thematic interview, visual, and newspaper data through which the different aspects of democratic practices are examined; and (3) a methodological one by developing new ways of analyzing comparative cases an application of Frame Analysis to visual material and the creation of Public Justification Analysis for analyzing morally loaded claims in newspaper reports thus building bridges between cultural, political, and pragmatic sociology. The results of the study indicate that the cultural tools the Finnish civic actors had at their disposal were prone to hinder more than support politicization, whereas the tools the French actors mainly relied on were frequently apt for making politicization possible. This crystallization is defined and detailed in many ways in the analyses of the book. Its consequences to the understanding and future research on the current developments of democracy are multiple, as politicization, while not assuring good results as such, is central to a functioning and vibrant democracy in which injustices can be fixed and new directions and solutions sought collectively.

News Media, Crime and Fear of Violence

Finland witnessed a surge in crime news reporting during the 1990s. At the same time, there was a significant rise in the levels of fear of crime reported by surveys. This research examines whether and how the two phenomena: news media and fear of violence were associated with each other. The dissertation consists of five sub-studies and a summary article. The first sub-study is a review of crime reporting trends in Finland, in which I have reviewed prior research and used existing Finnish datasets on media contents and crime news media exposure. The second study examines the association between crime media consumption and fear of crime when personal and vicarious victimization experiences have been held constant. Apart from analyzing the impact of crime news consumption on fear, media effects on general social trust are analyzed in the third sub-study. In the fourth sub-study I have analyzed the contents of the Finnish Poliisi-TV programme and compared the consistency of the picture of violent crime between official data sources and the programme. In the fifth and final sub-study, the victim narratives of Poliisi-TV s violence news contents have been analyzed. The research provides a series of results which are unprecedented in Finland. First, it observes that as in many other countries, the quantity of crime news supply has increased quite markedly in Finland. Second, it verifies that exposure to crime news is related to being worried about violent victimization and avoidance behaviour. Third, it documents that exposure to TV crime reality-programming is associated with reduced social trust among Finnish adolescents. Fourth, the analysis of Poliisi-TV shows that it transmits a distorted view of crime when contrasted with primary data sources on crime, but that this distortion is not as big as could be expected from international research findings and epochal theories of sociology. Fifth, the portrayals of violence victims in Poliisi-TV do not fit the traditional ideal types of victims that are usually seen to dominate crime media. The fact that the victims of violence in Poliisi-TV are ordinary people represents a wider development of the changing significance of the crime victim in Finland. The research concludes that although the media most likely did have an effect on the rising public fears in the 1990s, the mechanism was not as straight forward as has often been claimed. It is likely that there are other factors in the fear-media equation that are affecting both fear levels and crime reporting and that these factors are interactive in nature. Finally, the research calls for a re-orientation of media criminology and suggests more emphasis on the positive implications of crime in the media. Keywords: crime, media, fear of crime, violence, victimization, news

Professional Driving : An Emphasis on Organizational Safety Climate

According to the literature and statistical figures, professional drivers constitute a high-risk group in traffic and should be investigated in connection with the factors related to safe driving. However, safety-related behaviours and outcomes among professional drivers have attracted very little attention from safety researchers. In addition, comparing different professional and non-professional driver groups in terms of critical on-the-road characteristics and outcomes has been indicated in the literature as being necessary for a more comprehensive understanding of driver groups and the nature of driving itself. The aim of the present study was to investigate professional driving from a safety climate stand point in relation to predominant driving-related factors and by considering the differences between driver groups. Hence, four Sub-studies were conducted according to a framework emphasizing the relationships between safety climate, driver groups, driver stress, human factors (i.e., driver behaviour and performance) and accidents. Demographic information, as well as data for driver behaviour, performance, and driver stress was collected by questionnaire. The data was analysed using factor analysis, analysis of covariance as well as hierarchical and logistic regression analysis. The results revealed multi-dimensional factor structures for the safety climate measures. Considering the relationships between variables, differences were evidenced regarding on-the-road stress reactions, risky driver behaviours and penalties, between the various professional and non-professional driver groups. Driver stress was found to be related to accidents. The results also indicated that the safety climate has positive relationships with both driver behaviour and performance, and as well as involvement in accidents. The present study has a number of critical implications resulting from the fact that the way in which the effects of safety climate on professional driving were investigated, as well as the differences between professional and non-professional driver groups, was unique. Additionally, for the first time, a safety climate scale was developed specifically for professional drivers. According to the results of the study and to previous literature, a tentative model was proposed representing a possible route for the relationships between safety climate, human factors, driver stress, driver groups and accidents, by emphasizing the effects of safety climate.