Efficient search for statistically significant dependency rules in binary data

Analyzing statistical dependencies is a fundamental problem in all empirical science. Dependencies help us understand causes and effects, create new scientific theories, and invent cures to problems. Nowadays, large amounts of data is available, but efficient computational tools for analyzing the data are missing. In this research, we develop efficient algorithms for a commonly occurring search problem - searching for the statistically most significant dependency rules in binary data. We consider dependency rules of the form X->A or X->not A, where X is a set of positive-valued attributes and A is a single attribute. Such rules describe which factors either increase or decrease the probability of the consequent A. A classical example are genetic and environmental factors, which can either cause or prevent a disease. The emphasis in this research is that the discovered dependencies should be genuine - i.e. they should also hold in future data. This is an important distinction from the traditional association rules, which - in spite of their name and a similar appearance to dependency rules - do not necessarily represent statistical dependencies at all or represent only spurious connections, which occur by chance. Therefore, the principal objective is to search for the rules with statistical significance measures. Another important objective is to search for only non-redundant rules, which express the real causes of dependence, without any occasional extra factors. The extra factors do not add any new information on the dependence, but can only blur it and make it less accurate in future data. The problem is computationally very demanding, because the number of all possible rules increases exponentially with the number of attributes. In addition, neither the statistical dependency nor the statistical significance are monotonic properties, which means that the traditional pruning techniques do not work. As a solution, we first derive the mathematical basis for pruning the search space with any well-behaving statistical significance measures. The mathematical theory is complemented by a new algorithmic invention, which enables an efficient search without any heuristic restrictions. The resulting algorithm can be used to search for both positive and negative dependencies with any commonly used statistical measures, like Fisher's exact test, the chi-squared measure, mutual information, and z scores. According to our experiments, the algorithm is well-scalable, especially with Fisher's exact test. It can easily handle even the densest data sets with 10000-20000 attributes. Still, the results are globally optimal, which is a remarkable improvement over the existing solutions. In practice, this means that the user does not have to worry whether the dependencies hold in future data or if the data still contains better, but undiscovered dependencies.

Scottish Football Association or Sweet Fanny Adams

Tämä pro gradu -tutkielma käsittelee kielisidonnaisen huumorin kääntämistä. Ennen itse kääntämisen käsittelyä täytyy kuitenkin määritellä mitä tarkoitetaan käsitteellä kielisidonnainen huumori . Aluksi käsitellään huumoria ja sen ominaisuuksia sekä huumorin ja kulttuuristen, fysiologisten ja sosiaalisten tekijöiden suhdetta. Huumori syntyy kun tietyt odotukset rikotaan, eli toimitaan joidenkin normien vastaisesti. Huumorin eräitä perusperiaatteita ovat ristiriitaisuus ja yhteensopimattomuus. Kielisidonnaisessa huumorissa ristiriitaisuus ja yhteensopimattomuus on havaittavissa kielen tasolla: kieltä käytetään tuottamaan moniselitteinen tai -mielinen koominen ilmaus. Sanaleikki, jossa käytetään yhtä sanaa jolla on yksi tai useampi merkitys, on tyypillinen esimerkki kielisidonnaisesta huumorista. Mutta kielisidonnainen huumori ei rajoitu pelkästään tämänkaltaisiin sanaleikkeihin (engl. pun), vaan kattaa käsitteenä laajemman valikoiman erilaisia kielisidonnaisen huumorin muotoja, esimerkiksi monimerkityksiset nimet, idiomaattisilla ilmauksilla tuotettu huumori, akrostikonit, kirjoituksen konventioita rikkomalla tuotettu huumori jne. Kielisidonnainen huumori on tutkielmassa luokiteltu ja määritelty omaksi huumorin alalajikseen. Kielisidonnaisen huumorin kielellinen monimerkityksisyys tekee sen kääntämisestä vaikeampaa kuin sellaisen tekstin, jossa kielen tasolla ei ilmene monimerkityksisyyttä. Tästä syystä kielisidonnainen huumori tarvitsee erilaisen käännösstrategian kuin esimerkiksi tieteellinen teksti. Seuraavaksi käydään aluksi läpi joitakin käännösteorian keskeisiä käsitteitä ja niiden suhdetta ja vaikutuksia kielisidonnaisen huumorin kääntämiseen. Sitten kuvataan kielisidonnaisen huumorin käännösprosessi, joka jakautuu kolmeen osaan: tunnistaminen, analyysi ja kääntäminen. Näiden kolmen pohjalta laaditaan kuuden eri käännösstrategian ryhmä. Kuusi eri päästrategiaa ovat käännössidonnaisen huumorikategorian säilyttäminen, kirjaimellinen käännös, muun tyylikeinon käyttäminen, kompensaatio, poisjättö ja toimitukselliset keinot. Strategiat käydään läpi deskriptiivisesti ja niiden käyttöä valaistaan esimerkkien avulla. Osa päästrategioista jakautuu alastrategioihin, jotka kuvaavat tarkemmin, minkälaisin keinoin lähtökielen kielisidonnainen käännösongelma voidaan siirtää kohdekieleen. Strategiat pyritään kuvaamaan siten, että ne voisivat olla avuksi käännettäessä minkä tahansa kieliparin välillä. Vaikka kuvatut käännösstrategiat käydään läpi deskriptiivisesti, on pyrkii tutkielma myös olemaan avuksi käytännön tilanteissa kielisidonnaista huumoria käännettäessä. Tätä varten on tutkielman lopussa annettu kuvaus yhden kielisidonnaisen huumoriongelman kääntämisprosessista. Yhdistämällä teoria käytäntöön kuvataan käännösprosessiesimerkissä yhden kielisidonnaisen huumoriongelman analyysi-ja kääntämisvaiheet. Tuloksena on viisi erilaista versiota samasta lähtötekstin käännösongelmasta. Tutkielma siis ensinnäkin määrittelee, mitä ja minkälaista on kielisidonnainen huumori sekä luokittelee sen. Toisekseen tutkielma kuvaa sen käännösprosessin ja määrittelee eri käännösstrategiat. Lisäksi esimerkin avulla esitellään eri käännösvaihtoehtoja. Avainsanat: kääntäminen, huumori, sanaleikki, kielisidonnainen

Kirjan tie lukijalle : Kirjakauppojen vakiintuminen Suomessa 1740 - 1860

Books Paths to Readers describes the history of the origins and consolidation of modern and open book stores in Finland 1740 1860. The thesis approaches the book trade as a part of a print culture. Instead of literary studies choice to concentrate on texts and writers, book history seeks to describe the print culture of a society and how the literary activities and societies interconnect. For book historians, printed works are creations of various individuals and groups: writers, printers, editors, book sellers, censors, critics and finally, readers. They all take part in the creation, delivery and interpretation of printed works. The study reveals the ways selling and distributing books have influenced the printed works and the literary and print culture. The research period 1740 1860 covers the so-called second revolution of the book, or the modernisation of the print culture. The thesis describes the history of 60 book stores and their 96 owners. The study concentrates on three themes: firstly, how the particular book trade network became a central institution for printed works distribution, secondly what were the relations between cosmopolitan European book markets and the national cultural sphere, and thirdly how book stores functioned as cultural institutions and business enterprises. Book stores that have a varied assortment and are targeted to all readers became the main institution for book trade in Finland during 1740 1860. It happened because of three features. First, the book binders monopoly on selling bound copies in Sweden was abolished in 1740s. As a consequence entrepreneurs could concentrate solely to trade activities and offer copies from various publishers at their stores. Secondly the common business model of bartering was replaced by selling copies for cash, first in the German book trade centre Leipzig in 1770s. The change intensified book markets activities and Finnish book stores foreign connections. Thirdly, after Finland was annexed to the Russian empire in 1809, the Grand duchy s administration steered foreign book trade to book stores (because of censorship demands). Up to 1830 s book stores were available only in Helsinki and Turku. During next ten years book stores opened in six regional centres. The early entrepreneurs ran usually vertical businesses consisting of printing, publishing and distribution activities. This strategy lowered costs, eased the delivery of printed works and helped to create elaborated centres for all book activities. These book stores main clientele consisted of the Swedish speaking gentry. During late 1840s various opinion leaders called for the development of a national Finnish print culture, and also book stores. As a result, during the five years before the beginning of the Crimean war (1853 1856) book stores were opened in almost all Finnish towns: at the beginning of the war 36 book stores operated in 21 towns. The later book sellers, mainly functioning in small towns among Finnish speaking people, settled usually strictly for selling activities. Book stores received most of their revenues from selling foreign titles. Swedish, German, French and Belgian (pirate editions of popular French novels) books were widely available for the multilingual gentry. Foreign titles and copies brought in most of the revenues. Censorship inspections or unfavourable custom fees would not limit the imports. Even if the local Finnish print production steadily rose, many copies, even titles, were never delivered via book stores. Only during the 1840 s and 1850 s the most advanced publishers would concentrate on creating publishing programmes and delivering their titles via book stores. Book sellers regulated commissions were small. They got even smaller because of large amounts of unsold copies, various and usual misunderstandings of consignments and accounts or plain accidents that destroyed shipments and warehouses. Also, the cultural aim of a creating large and assortments and the tendency of short selling periods demanded professional entrepreneurship, which many small town book sellers however lacked. In the midst of troublesome business efforts, co-operation and mutual concern of the book market s entrepreneurs were the key elements of the trade, although on local level book sellers would compete, sometimes even ferociously. The difficult circumstances (new censorship decree of 1850, Crimean war) and lack of entrepreneurship, experience and customers meant that half of the book stores opened in 1845 1860 was shut in less than five years. In 1858 the few leading publishers established The Finnish Book Publishers Association. Its first task was to create new business rules and manners for the book trade. The association s activities began to professionalise the whole network, but at the same time the earlier independence of regional publishing and selling enterprises diminished greatly. The consolidation of modern and open book store network in Finland is a history of a slow and complex development without clear signs of a beginning or an end. The ideal book store model was rarely accomplished in its all features. Nevertheless, book stores became the norm of the book trade. They managed to offer larger selections, reached larger clienteles and maintained constant activity better than any other book distribution model. In essential, the book stores methods have not changed up to present times.

Psychological resources, their social antecedents, and association with well-being and health behaviour in early adulthood

The success of entering work life, young people s psychological resources and self-reported well-being were studied in a longitudinal setting from a life-span developmental-contextual perspective in early adulthood. The aim was to analyse how psychosocial characteristics in early childhood and adolescence predict successful entrance into work life, how this is associated with well-being, and to assess the level of psychological resources such as dispositional optimism, personal meaning of work and coping in early adulthood. The role of these and social support, in the relationship between regional factors (such as place of residence and migration), self-reported health and life satisfaction was studied. The association between a specific coping strategy, i.e. eating and drinking in a stressful situation and eating habits, was studied to demonstrate how coping is associated with health behaviour. Multivariate methods, including binary logistic regression analyses and ANOVA, were used for statistical analyses. The subjects were members of the Northern Finland 1966 Birth Cohort, which consists of all women and men born in 1966 in the two northernmost provinces of Finland (n= 12,058). The most recent follow-up, at the age of 31 years when 11,637 subjects were alive, took place in 1997-1998. The results show, first, that social resources in the childhood family and adolescence school achievement predict entrance into the labour market. Secondly, psychosocial resources were found to mediate the relationship between migration from rural to urban areas, and subjective well-being. Thirdly, psychological resources at entrance into the labour market were found to develop from early infancy on. They are, however, influenced later by work history. Fourthly, stress-related eating and drinking, as a way of coping, was found to be directly associated with unhealthy eating habits and alcohol use. Gender differences were found in psychosocial resources predicting, and being associated with success in entering the labour market. For men, the role of attitudinal and psychological factors seems to be especially important in entrance into work life and in the development of psychological resources. For women, academic attainment was more important for successfully entering work life, and lack of emotional social support was a risk factor for stress-related eating only among women. Stress-related eating and drinking habits were predicted by a long history of unemployment as well as a low level of education among both genders, but not excluding an academic degree among men. The results emphasize the role of childhood psychosocial factors in preventing long-term unemployment and in enhancing psychological well-being in early adulthood. Success in entering work life, in terms of continuous work history, plays a crucial role for well-being and the amount of psychological resources in early adulthood. The results emphasize the crucial role of enhancing psychological resources for promoting positive health behaviour and diminishing regional differences in subjective well-being.

Negotiating and Renegotiating Conversational Ground Rules : Formation of an Artifact Designed to Mediate Exploratory Collaboration

This study highlights the formation of an artifact designed to mediate exploratory collaboration. The data for this study was collected during a Finnish adaptation of the thinking together approach. The aim of the approach is to teach pulps how to engage in educationally beneficial form of joint discussion, namely exploratory talk. At the heart of the approach lies a set of conversational ground rules aimed to promote the use of exploratory talk. The theoretical framework of the study is based on a sociocultural perspective on learning. A central argument in the framework is that physical and psychological tools play a crucial role in human action and learning. With the help of tools humans can escape the direct stimulus of the outside world and learn to control ourselves by using tools. During the implementation of the approach, the classroom community negotiates a set of six rules, which this study conceptualizes as an artifact that mediates exploratory collaboration. Prior research done about the thinking together approach has not extensively researched the formation of the rules, which give ample reason to conduct this study. The specific research questions asked were: What kind of negotiation trajectories did the ground rules form during the intervention? What meanings were negotiated for the ground rules during the intervention The methodological framework of the study is based on discourse analysis, which has been specified by adapting the social construction of intertextuality to analyze the meanings negotiated for the created rules. The study has town units of analysis: thematic episode and negotiation trajectory. A thematic episode is a stretch of talk-in-interaction where the participants talk about a certain ground rule or a theme relating to it. A negotiation trajectory is a chronological representation of the negotiation process of a certain ground rule during the intervention and is constructed of thematic episodes. Thematic episodes were analyzed with the adapted intertextuality analysis. A contrastive analysis was done on the trajectories. Lastly, the meanings negotiated for the created rules were compared to the guidelines provided by the approach. The main result of the study is the observation, that the meanings of the created rules were more aligned with the ground rules of cumulative talk, rather than exploratory talk. Although meanings relating also to exploratory talk were negotiated, they clearly were not the dominant form. In addition, the study observed that the trajectories of the rules were non identical. Despite connecting dimensions (symmetry, composition, continuity and explicitness) none of the trajectories shared exactly the same features as the others.

Anthropometric measures of obesity-their association with type 2 diabetes and hypertension across ethnic groups

Clinical trials have shown that weight reduction with lifestyles can delay or prevent diabetes and reduce blood pressure. An appropriate definition of obesity using anthropometric measures is useful in predicting diabetes and hypertension at the population level. However, there is debate on which of the measures of obesity is best or most strongly associated with diabetes and hypertension and on what are the optimal cut-off values for body mass index (BMI) and waist circumference (WC) in this regard. The aims of the study were 1) to compare the strength of the association for undiagnosed or newly diagnosed diabetes (or hypertension) with anthropometric measures of obesity in people of Asian origin, 2) to detect ethnic differences in the association of undiagnosed diabetes with obesity, 3) to identify ethnic- and sex-specific change point values of BMI and WC for changes in the prevalence of diabetes and 4) to evaluate the ethnic-specific WC cutoff values proposed by the International Diabetes Federation (IDF) in 2005 for central obesity. The study population comprised 28 435 men and 35 198 women, ≥ 25 years of age, from 39 cohorts participating in the DECODA and DECODE studies, including 5 Asian Indian (n = 13 537), 3 Mauritian Indian (n = 4505) and Mauritian Creole (n = 1075), 8 Chinese (n =10 801), 1 Filipino (n = 3841), 7 Japanese (n = 7934), 1 Mongolian (n = 1991), and 14 European (n = 20 979) studies. The prevalence of diabetes, hypertension and central obesity was estimated, using descriptive statistics, and the differences were determined with the χ2 test. The odds ratios (ORs) or  coefficients (from the logistic model) and hazard ratios (HRs, from the Cox model to interval censored data) for BMI, WC, waist-to-hip ratio (WHR), and waist-to-stature ratio (WSR) were estimated for diabetes and hypertension. The differences between BMI and WC, WHR or WSR were compared, applying paired homogeneity tests (Wald statistics with 1 df). Hierarchical three-level Bayesian change point analysis, adjusting for age, was applied to identify the most likely cut-off/change point values for BMI and WC in association with previously undiagnosed diabetes. The ORs for diabetes in men (women) with BMI, WC, WHR and WSR were 1.52 (1.59), 1.54 (1.70), 1.53 (1.50) and 1.62 (1.70), respectively and the corresponding ORs for hypertension were 1.68 (1.55), 1.66 (1.51), 1.45 (1.28) and 1.63 (1.50). For diabetes the OR for BMI did not differ from that for WC or WHR, but was lower than that for WSR (p = 0.001) in men while in women the ORs were higher for WC and WSR than for BMI (both p < 0.05). Hypertension was more strongly associated with BMI than with WHR in men (p < 0.001) and most strongly with BMI than with WHR (p < 0.001), WSR (p < 0.01) and WC (p < 0.05) in women. The HRs for incidence of diabetes and hypertension did not differ between BMI and the other three central obesity measures in Mauritian Indians and Mauritian Creoles during follow-ups of 5, 6 and 11 years. The prevalence of diabetes was highest in Asian Indians, lowest in Europeans and intermediate in others, given the same BMI or WC category. The  coefficients for diabetes in BMI (kg/m2) were (men/women): 0.34/0.28, 0.41/0.43, 0.42/0.61, 0.36/0.59 and 0.33/0.49 for Asian Indian, Chinese, Japanese, Mauritian Indian and European (overall homogeneity test: p > 0.05 in men and p < 0.001 in women). Similar results were obtained in WC (cm). Asian Indian women had lower  coefficients than women of other ethnicities. The change points for BMI were 29.5, 25.6, 24.0, 24.0 and 21.5 in men and 29.4, 25.2, 24.9, 25.3 and 22.5 (kg/m2) in women of European, Chinese, Mauritian Indian, Japanese, and Asian Indian descent. The change points for WC were 100, 85, 79 and 82 cm in men and 91, 82, 82 and 76 cm in women of European, Chinese, Mauritian Indian, and Asian Indian. The prevalence of central obesity using the 2005 IDF definition was higher in Japanese men but lower in Japanese women than in their Asian counterparts. The prevalence of central obesity was 52 times higher in Japanese men but 0.8 times lower in Japanese women compared to the National Cholesterol Education Programme definition. The findings suggest that both BMI and WC predicted diabetes and hypertension equally well in all ethnic groups. At the same BMI or WC level, the prevalence of diabetes was highest in Asian Indians, lowest in Europeans and intermediate in others. Ethnic- and sex-specific change points of BMI and WC should be considered in setting diagnostic criteria for obesity to detect undiagnosed or newly diagnosed diabetes.

Podocyte molecules in the pancreas and lymphoid tissues and their association to autoimmunity of diabetes

Type 1 diabetes is a disease where the insulin-producing beta cells of the pancreas are destroyed by an autoimmune mechanism. The incidence of type 1 diabetes, as well as the incidence of the diabetic kidney complication, diabetic nephropathy, are increasing worldwide. Nephrin is a crucial molecule for the filtration function of the kidney. It localises in the podocyte foot processes partially forming the interpodocyte final sieve of the filtration barrier, the slit diaphragm. The expression of nephrin is altered in diabetic nephropathy. Recently, nephrin was found from the beta cells of the pancreas as well, which makes this molecule interesting in the context of type 1 diabetes and especially in diabetic nephropathy. In this thesis work, the expression of other podocyte molecules in the beta cells of the pancreas, in addition to nephrin, were deciphered. It was also hypothesised that patients with type 1 diabetes may develop autoantibodies against novel beta cell molecules comparably to the formation of autoantibodies to GAD, IA-2 and insulin. The possible association of such novel autoantibodies with the pathogenesis of diabetic nephropathy was also assessed. Furthermore, expression of nephrin in lymphoid tissues has been suggested, and this issue was more thoroughly deciphered here. The expression of nephrin in the human lymphoid tissues, and a set of podocyte molecules in the human, mouse and rat pancreas at the gene and protein level were studied by polymerase chain reaction (PCR) -based methods and immunochemical methods. To detect autoantibodies to novel beta cell molecules, specific radioimmunoprecipitation assays were developed. These assays were used to screen a follow-up material of 66 patients with type 1 diabetes and a patient material of 150 diabetic patients with signs of diabetic nephropathy. Nephrin expression was detected in the lymphoid follicle germinal centres, specifically in the follicular dendritic cells. In addition to the previously reported expression of nephrin in the pancreas, expression of the podocyte molecules, densin, filtrin, FAT and alpha-actinin-4 were detected in the beta cells. Circulating antibodies to nephrin, densin and filtrin were discovered in a subset of patients with type 1 diabetes. However, no association of these autoantibodies with the pathogenesis of diabetic nephropathy was detected. In conclusion, the expression of five podocyte molecules in the beta cells of the pancreas suggests some molecular similarities between the two cell types. The novel autoantibodies against shared molecules of the kidney podocytes and the pancreatic beta cells appear to be part of the common autoimmune mechanism in patients with type 1 diabetes. No data suggested that the autoantibodies would be active participants of the kidney injury detected in diabetic nephropathy.

Genotyping for genetic association studies: Methods and applications

In this thesis, two separate single nucleotide polymorphism (SNP) genotyping techniques were set up at the Finnish Genome Center, pooled genotyping was evaluated as a screening method for large-scale association studies, and finally, the former approaches were used to identify genetic factors predisposing to two distinct complex diseases by utilizing large epidemiological cohorts and also taking environmental factors into account. The first genotyping platform was based on traditional but improved restriction-fragment-length-polymorphism (RFLP) utilizing 384-microtiter well plates, multiplexing, small reaction volumes (5 µl), and automated genotype calling. We participated in the development of the second genotyping method, based on single nucleotide primer extension (SNuPeTM by Amersham Biosciences), by carrying out the alpha- and beta tests for the chemistry and the allele-calling software. Both techniques proved to be accurate, reliable, and suitable for projects with thousands of samples and tens of markers. Pooled genotyping (genotyping of pooled instead of individual DNA samples) was evaluated with Sequenom s MassArray MALDI-TOF, in addition to SNuPeTM and PCR-RFLP techniques. We used MassArray mainly as a point of comparison, because it is known to be well suited for pooled genotyping. All three methods were shown to be accurate, the standard deviations between measurements being 0.017 for the MassArray, 0.022 for the PCR-RFLP, and 0.026 for the SNuPeTM. The largest source of error in the process of pooled genotyping was shown to be the volumetric error, i.e., the preparation of pools. We also demonstrated that it would have been possible to narrow down the genetic locus underlying congenital chloride diarrhea (CLD), an autosomal recessive disorder, by using the pooling technique instead of genotyping individual samples. Although the approach seems to be well suited for traditional case-control studies, it is difficult to apply if any kind of stratification based on environmental factors is needed. Therefore we chose to continue with individual genotyping in the following association studies. Samples in the two separate large epidemiological cohorts were genotyped with the PCR-RFLP and SNuPeTM techniques. The first of these association studies concerned various pregnancy complications among 100,000 consecutive pregnancies in Finland, of which we genotyped 2292 patients and controls, in addition to a population sample of 644 blood donors, with 7 polymorphisms in the potentially thrombotic genes. In this thesis, the analysis of a sub-study of pregnancy-related venous thromboses was included. We showed that the impact of factor V Leiden polymorphism on pregnancy-related venous thrombosis, but not the other tested polymorphisms, was fairly large (odds ratio 11.6; 95% CI 3.6-33.6), and increased multiplicatively when combined with other risk factors such as obesity or advanced age. Owing to our study design, we were also able to estimate the risks at the population level. The second epidemiological cohort was the Helsinki Birth Cohort of men and women who were born during 1924-1933 in Helsinki. The aim was to identify genetic factors that might modify the well known link between small birth size and adult metabolic diseases, such as type 2 diabetes and impaired glucose tolerance. Among ~500 individuals with detailed birth measurements and current metabolic profile, we found that an insertion/deletion polymorphism of the angiotensin converting enzyme (ACE) gene was associated with the duration of gestation, and weight and length at birth. Interestingly, the ACE insertion allele was also associated with higher indices of insulin secretion (p=0.0004) in adult life, but only among individuals who were born small (those among the lowest third of birth weight). Likewise, low birth weight was associated with higher indices of insulin secretion (p=0.003), but only among carriers of the ACE insertion allele. The association with birth measurements was also found with a common haplotype of the glucocorticoid receptor (GR) gene. Furthermore, the association between short length at birth and adult impaired glucose tolerance was confined to carriers of this haplotype (p=0.007). These associations exemplify the interaction between environmental factors and genotype, which, possibly due to altered gene expression, predisposes to complex metabolic diseases. Indeed, we showed that the common GR gene haplotype associated with reduced mRNA expression in thymus of three individuals (p=0.0002).

Latent TGF-beta Binding Proteins : Adhesive functions and matrix association of LTBP-2 and potential functions of LTBP-1 and LTBP-3 in mesothelioma

Latent transforming growth factor-beta (TGF-beta) binding proteins (LTBPs) -1, -3 and -4 are ECM components whose major function is to augment the secretion and matrix targeting of TGF-beta, a multipotent cytokine. LTBP-2 does not bind small latent TGF-beta but has suggested functions as a structural protein in ECM microfibrils. In the current work we focused on analyzing possible adhesive functions of LTBP-2 as well as on characterizing the kinetics and regulation of LTBP-2 secretion and ECM deposition. We also explored the role of TGF-beta binding LTBPs in endothelial cells activated to mimic angiogenesis as well as in malignant mesothelioma. We found that, unlike most adherent cells, several melanoma cell lines efficiently adhered to purified recombinant LTBP-2. Further characterization revealed that the adhesion was mediated by alpha3beta1 and alpha6beta1 integrins. Heparin also inhibited the melanoma cell adhesion suggesting a role for heparan sulphate proteoglycans. LTBP-2 was also identified as a haptotactic substrate for melanoma cell migration. We used cultured human embryonic lung fibroblasts to analyze the temporal and spatial association of LTBP-2 into ECM. By We found that LTBP-2 was efficiently assembled to the ECM only in confluent cultures following the deposition of fibronectin (FN) and fibrillin-1. In early, subconfluent cultures it remained primarily in soluble form after secretion. LTBP-2 colocalized transiently with FN and fibrillin-1. Silencing of fibrillin-1 expression by lentiviral shRNAs profoundly disrupted the deposition of LTBP-2 indicating that the ECM association of LTBP-2 depends on a pre-formed fibrillin-1 network. Considering the established role of TGF-beta as a regulator of angiogenesis we induced morphological activation of endothelial cells by phorbol 12-myristate 13-acetate (PMA) and followed the fate of LTBP-1 in the endothelial ECM. This resulted in profound proteolytic processing of LTBP-1 and release of latent TGF-beta complexes from the ECM. The processing was coupled with increased activation of MT-MMPs and specific upregulation of MT1-MMP. The major role of MT1-MMP in the proteolysis of LTBP-1 was confirmed by suppressing the expression with lentivirally induced short-hairpin RNAs as well as by various metalloproteinases inhibitors. TGF-beta can promote tumorigenesis of malignant mesothelioma (MM), which is an aggressive tumor of the pleura with poor prognosis. TGF-beta activity was analyzed in a panel of MM tumors by immunohistochemical staining of phosphorylated Smad-2 (P-Smad2). The tumor cells were strongly positive for P-Smad2 whereas LTBP-1 immunoreactivity was abundant in the stroma, and there was a negative correlation between LTBP-1 and P-Smad2 staining. In addition, the high P-Smad2 immunoreactivity correlated with shorter survival of patients. mRNA analysis revealed that TGF-beta1 was the most highly expressed isoform in both normal human pleura and MM tissue. LTBP-1 and LTBP-3 were both abundantly expressed. LTBP-1 was the predominant isoform in established MM cell lines whereas the expression of LTBP-3 was high in control cells. Suppression of LTBP-3 expression by siRNAs resulted in increased TGF-beta activity in MM cell lines accompanied by decreased proliferation. Our results suggest that decreased expression of LTBP-3 in MM could alter the targeting of TGF-beta to the ECM and lead to its increased activation. The current work emphasizes the coordinated process of the assembly and appropriate targeting of LTBPs with distinct adhesive or cytokine harboring properties into the ECM. The hierarchical assembly may have implications in the modulation of signaling events during morphogenesis and tissue remodeling.

Joint Regression and Association Models for Repeated Categorical Responses

The focus of this study is on statistical analysis of categorical responses, where the response values are dependent of each other. The most typical example of this kind of dependence is when repeated responses have been obtained from the same study unit. For example, in Paper I, the response of interest is the pneumococcal nasopharengyal carriage (yes/no) on 329 children. For each child, the carriage is measured nine times during the first 18 months of life, and thus repeated respones on each child cannot be assumed independent of each other. In the case of the above example, the interest typically lies in the carriage prevalence, and whether different risk factors affect the prevalence. Regression analysis is the established method for studying the effects of risk factors. In order to make correct inferences from the regression model, the associations between repeated responses need to be taken into account. The analysis of repeated categorical responses typically focus on regression modelling. However, further insights can also be gained by investigating the structure of the association. The central theme in this study is on the development of joint regression and association models. The analysis of repeated, or otherwise clustered, categorical responses is computationally difficult. Likelihood-based inference is often feasible only when the number of repeated responses for each study unit is small. In Paper IV, an algorithm is presented, which substantially facilitates maximum likelihood fitting, especially when the number of repeated responses increase. In addition, a notable result arising from this work is the freely available software for likelihood-based estimation of clustered categorical responses.

Puukaupan säännöt : Yksityismetsänomistajien ja metsäteollisuuden puukauppa Itä-Suomessa 1919 - 1939

The Finnish forest industry bought more than half of the timber used in factories and sawmills in the 1930s from non-industrial private forests (NIPF). This research investigates the rules conformed to this timber trade. The main research questions are: what were the rules that influenced the timber trade; and by whom they were set up? Attention is also paid to the factors which advanced the forest owners’ negotiation possibilities. A variety of sources were used: legal and company statutes, timber trade contracts, archives of the forest companies and organisations. Moreover, the written reminiscences collected by the Finnish Literature Society in the early 1970s were used to analyse the views of individual sellers and buyers. An institutional economics approach was applied as the theoretical framework of this study. In the timber trade the seller (forest owner) and the buyer (the employee of the forest company) agreed to the rules of the timber trade. They agreed about the amount and the price of the timber on sale, but also rules concerning, e.g., timber marking and harvesting. The forest companies had a strong control over the written contracts. Neither the private forest owners nor the forest organisations had much influence over these contracts. However, they managed to influence the rules which could not be found in the contracts. These written and unwritten rules regulated, for instance, the timber marking and measurement. The forest organisations such as Central Forestry Board Tapio (Keskusmetsäseura Tapio) and associations of forest owners (metsänhoitoyhdistykset) helped private forest owners in gaining more control over the timber marking. In timber marking, the forest owner selected trees to be included in the timber trade and gained more information, which he could use in the negotiations. The other rule, which was changed despite forest companies’ resistance, was the timber measurement. The Central Union of Agricultural Producers (MTK) negotiated with the Central Association of Finnish Woodworking Industries (SPKL) about changing the rules of the measurement practices. Even though SPKL did not support any changes, the new timber measurement law was accepted in the year 1938. The new law also created a supervisory authority to solve possible disagreements. Despite this the forest companies were still in charge of the measurement process in most cases. The private forest owners attained changes in the rules of the timber trade mainly during the 1930s. Earlier the relative weakness of the private forest organisations had diminished their negotiation positions. This changed in the 1930s as the private forest owners and their organisations became more active. At the same time the forest industry experienced a shortage of timber, especially pulp wood, and this provided the private forest owners with more leverage. Full-text (in Finnish) available at http://helda.helsinki.fi/handle/10224/4081

Essays on macroeconomic effects of fiscal policy rules

Economic and Monetary Union can be characterised as a complicated set of legislation and institutions governing monetary and fiscal responsibilities. The measures of fiscal responsibility are to be guided by the Stability and Growth Pact, which sets rules for fiscal policy and makes a discretionary fiscal policy virtually impossible. To analyse the effects of the fiscal and monetary policy mix, we modified the New Keynesian framework to allow for supply effects of fiscal policy. We show that defining a supply-side channel for fiscal policy using an endogenous output gap changes the stabilising properties of monetary policy rules. The stability conditions are affected by fiscal policy, so that the dichotomy between active (passive) monetary policy and passive (active) fiscal policy as stabilising regimes does not hold, and it is possible to have an active monetary - active fiscal policy regime consistent with dynamical stability of the economy. We show that, if we take supply-side effects into ac-count, we get more persistent inflation and output reactions. We also show that the dichotomy does not hold for a variety of different fiscal policy rules based on government debt and budget deficit, using the tax smoothing hypothesis and formulating the tax rules as difference equations. The debt rule with active monetary policy results in indeterminacy, while the deficit rule produces a determinate solution with active monetary policy, even with active fiscal policy. The combination of fiscal requirements in a rule results in cyclical responses to shocks. The amplitude of the cycle is larger with more weight on debt than on deficit. Combining optimised monetary policy with fiscal policy rules means that, under a discretionary monetary policy, the fiscal policy regime affects the size of the inflation bias. We also show that commitment to an optimal monetary policy not only corrects the inflation bias but also increases the persistence of output reactions. With fiscal policy rules based on the deficit we can retain the tax smoothing hypothesis also in a sticky price model.

Bending the Rules of Cell Protrusions : Molecular Mechanisms and Biological Roles of Inverse-BAR Proteins in Cell Morphogenesis

Plasma membrane adopts myriad of different shapes to carry out essential cellular processes such as nutrient uptake, immunological defence mechanisms and cell migration. Therefore, the details how different plasma membrane structures are made and remodelled are of the upmost importance. Bending of plasma membrane into different shapes requires substantial amount of force, which can be provided by the actin cytoskeleton, however, the molecules that regulate the interplay between the actin cytoskeleton and plasma membrane have remained elusive. Recent findings have placed new types of effectors at sites of plasma membrane remodelling, including BAR proteins, which can directly bind and deform plasma membrane into different shapes. In addition to their membrane-bending abilities, BAR proteins also harbor protein domains that intimately link them to the actin cytoskeleton. The ancient BAR domain fold has evolved into at least three structurally and functionally different sub-groups: the BAR, F-BAR and I-BAR domains. This thesis work describes the discovery and functional characterization of the Inverse-BAR domains (I-BARs). Using synthetic model membranes, we have shown that I-BAR domains bind and deform membranes into tubular structures through a binding-surface composed of positively charged amino acids. Importantly, the membrane-binding surface of I-BAR domains displays an inverse geometry to that of the BAR and F-BAR domains, and these structural differences explain why I-BAR domains induce cell protrusions whereas BAR and most F-BAR domains induce cell invaginations. In addition, our results indicate that the binding of I-BAR domains to membranes can alter the spatial organization of phosphoinositides within membranes. Intriguingly, we also found that some I-BAR domains can insert helical motifs into the membrane bilayer, which has important consequences for their membrane binding/bending functions. In mammals there are five I-BAR domain containing proteins. Cell biological studies on ABBA revealed that it is highly expressed in radial glial cells during the development of the central nervous system and plays an important role in the extension process of radial glia-like C6R cells by regulating lamellipodial dynamics through its I-BAR domain. To reveal the role of these proteins in the context of animals, we analyzed MIM knockout mice and found that MIM is required for proper renal functions in adult mice. MIM deficient mice displayed a severe urine concentration defect due to defective intercellular junctions of the kidney epithelia. Consistently, MIM localized to adherens junctions in cultured kidney epithelial cells, where it promoted actin assembly through its I-BAR andWH2 domains. In summary, this thesis describes the mechanism how I-BAR proteins deform membranes and provides information about the biological role of these proteins, which to our knowledge are the first proteins that have been shown to directly deform plasma membrane to make cell protrusions.