Mechanistic population Models in Biology: Model Derivation and Application

In general, models of ecological systems can be broadly categorized as ’top-down’ or ’bottom-up’ models, based on the hierarchical level that the model processes are formulated on. The structure of a top-down, also known as phenomenological, population model can be interpreted in terms of population characteristics, but it typically lacks an interpretation on a more basic level. In contrast, bottom-up, also known as mechanistic, population models are derived from assumptions and processes on a more basic level, which allows interpretation of the model parameters in terms of individual behavior. Both approaches, phenomenological and mechanistic modelling, can have their advantages and disadvantages in different situations. However, mechanistically derived models might be better at capturing the properties of the system at hand, and thus give more accurate predictions. In particular, when models are used for evolutionary studies, mechanistic models are more appropriate, since natural selection takes place on the individual level, and in mechanistic models the direct connection between model parameters and individual properties has already been established. The purpose of this thesis is twofold. Firstly, a systematical way to derive mechanistic discrete-time population models is presented. The derivation is based on combining explicitly modelled, continuous processes on the individual level within a reproductive period with a discrete-time maturation process between reproductive periods. Secondly, as an example of how evolutionary studies can be carried out in mechanistic models, the evolution of the timing of reproduction is investigated. Thus, these two lines of research, derivation of mechanistic population models and evolutionary studies, are complementary to each other.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Secondary Aural Symptoms in Relation to Cranio-Cervical and General Disorders

The present thesis comprises two study populations. The first study sample (SS1) consisted of 411 adults examined and interviewed at three annual visits. The second study sample (SS2) consisted of 1720 adults who filled in a mailed questionnaire about secondary otalgia, tinnitus and fullness of ears. In the second phase of the SS2, 100 subjects with otalgia were examined and interviewed by specialist in stomatognathic physiology and otorhinolaryngology. In the third phase, 36 subjects participated in a randomized, controlled and blinded trial of effectiveness of occlusal appliance on secondary otalgia, facial pain, headache and treatment need of temporomandibular disorders (TMD). The standardized prevalence of recurrent secondary otalgia was 6%, tinnitus 15% and fullness of ears 8%. Aural symptoms were more frequent among young than old subjects. They were associated with other, simultaneous aural symptoms, TMD pain, head and neck region pain, and visits to a physician. The subjects with aural symptoms more often had tenderness on palpation of masticatory muscles and clinical signs of temporomandibular joint than the subjects without. 85% of the subjects reporting secondary otalgia had cervical spine or temporomandibular disorder or both. In SS1, the final model of secondary otalgia included active need treatment for TMD, elevated level of stress symptoms, and bruxism. In SS2, the final models of aural symptoms included associated aural symptoms, young age, TMD pain, headache and shoulder ache. Stabilization splint more effectively alleviated secondary otalgia and active treatment need for TMD than a palatal control splint. In patients with aural pain, tinnitus or fullness of ears, it is important to first rule out otologic and nasopharyngeal diseases that may cause the symptoms. If no explanation for aural symptoms is found, temporomandibular and cervical spine disorders should be rouled out to minimize unnecessary visits to a physician.