Measuring and tracking quality factors in Free and Open Source Software projects

Free and Open Source Software (FOSS) has gained increased interest in the computer software industry, but assessing its quality remains a challenge. FOSS development is frequently carried out by globally distributed development teams, and all stages of development are publicly visible. Several product and process-level quality factors can be measured using the public data. This thesis presents a theoretical background for software quality and metrics and their application in a FOSS environment. Information available from FOSS projects in three information spaces are presented, and a quality model suitable for use in a FOSS context is constructed. The model includes both process and product quality metrics, and takes into account the tools and working methods commonly used in FOSS projects. A subset of the constructed quality model is applied to three FOSS projects, highlighting both theoretical and practical concerns in implementing automatic metric collection and analysis. The experiment shows that useful quality information can be extracted from the vast amount of data available. In particular, projects vary in their growth rate, complexity, modularity and team structure.

Population dynamics of blue mussels in a variable environment at the edge of their range

Spatial and temporal variation in the abundance of species can often be ascribed to spatial and temporal variation in the surrounding environment. Knowledge of how biotic and abiotic factors operate over different spatial and temporal scales in determining distribution, abundance, and structure of populations lies at the heart of ecology. The major part of the current ecological theory stems from studies carried out in central parts of the distributional range of species, whereas knowledge of how marginal populations function is inadequate. Understanding how marginal populations, living at the edge of their range, function is however in a key position to advance ecology and evolutionary biology as scientific disciplines. My thesis focuses on the factors affecting dynamics of marginal populations of blue mussels (Mytilus edulis) living close to their tolerance limits with regard to salinity. The thesis aims to highlight the dynamics at the edge of the range and contrast these with dynamics in more central parts of the range in order to understand the potential interplay between the central and the marginal part in the focal system. The objectives of the thesis are approached by studies on: (1) factors affecting regional patterns of the species, (2) long-term temporal dynamics of the focal species spaced along a regional salinity gradient, (3) selective predation by increasing populations of roach (Rutilus rutilus) when feeding on their main food item, the blue mussel, (4) the primary and secondary effects of local wave exposure gradients and (5) the role of small-scale habitat heterogeneity as determinants of large-scale pattern. The thesis shows that populations of blue mussels are largely determined by large scale changes in sea water salinity, affecting mainly recruitment success and longevity of local populations. In opposite to the traditional view, the thesis strongly indicate that vertebrate predators strongly affect abundance and size structure of blue mussel populations, and that the role of these predators increases towards the margin where populations are increasingly top-down controlled. The thesis also indicates that the positive role of biogenic habitat modifiers increases towards the marginal areas, where populations of blue mussels are largely recruitment limited. Finally, the thesis shows that local blue mussel populations are strongly dependent on high water turbulence, and therefore, dense populations are constrained to offshore habitats. Finally, the thesis suggests that ongoing sedimentation of rocky shores is detrimental for the species, affecting recruitment success and post-recruit survival, pushing stable mussel beds towards offshore areas. Ongoing large scale changes in the Baltic Sea, especially dilution processes with attendant effects, are predicted to substantially contract the distributional range of the mussel, but also affect more central populations. The thesis shows that in order to understand the functioning of marginal populations, research should (1) strive for multi-scale approaches in order to link ecosystem patterns with ecosystem processes, and (2) challenge the prevailing tenets that origin from research carried out in central areas that may not be valid at the edge.

The viral coat protein is regulated by HSP70 and HSP40 in Potato virus A infection

Plus-stranded (plus) RNA viruses multiply within a cellular environment as tightly integrated units and rely on the genetic information carried within their genomes for multiplication and, hence, persistence. The minimal genomes of plus RNA viruses are unable to encode the molecular machineries that are required for virus multiplication. This sets requisites for the virus, which must form compatible interactions with host components during multiplication to successfully utilize primary metabolites as building blocks or metabolic energy, and to divert the protein synthesis machinery for production of viral proteins. In fact, the emerging picture of a virus-infected cell displays tight integration with the virus, from simple host and virus protein interactions through to major changes in the physiological state of the host cell. This study set out to develop a method for the identification of host components, mainly host proteins, that interact with proteins of Potato virus A (PVA; Potyvirus) during infection. This goal was approached by developing affinity-tag based methods for the purification of viral proteins complexed with associated host proteins from infected plants. Using this method, host membrane-associated viral ribonucleoprotein (RNP) complexes were obtained, and several host and viral proteins could be identified as components of these complexes. One of the host proteins identified using this strategy was a member of the heat shock protein 70 (HSP70) family, and this protein was chosen for further analysis. To enable the analysis of viral gene expression, a second method was developed based on Agrobacterium-mediated virus genome delivery into plant cells, and detection of virally expressed Renilla luciferase (RLUC) as a quantitative measure of viral gene expression. Using this method, it was observed that down-regulation of HSP70 caused a PVA coat protein (CP)-mediated defect associated with replication. Further experimentation suggested that CP can inhibit viral gene expression and that a distinct translational activity coupled to replication, referred to as replication-associated translation (RAT), exists. Unlike translation of replication-deficient viral RNA, RAT was dependent on HSP70 and its co-chaperone CPIP. HSP70 and CPIP together regulated CP turnover by promoting its modification by ubiquitin. Based on these results, an HSP70 and CPIP-driven mechanism that functions to regulate CP during viral RNA replication and/or translation is proposed, possibly to prevent premature particle assembly caused by CP association with viral RNA.

The influence of eutrophication on sexual selection in sticklebacks

Jordens ekologiska system undergår för tillfället stora förändringar pga. människans aktiviteter. Ett växande antal studier visar att dessa förändringar påverkar naturliga och sexuella urvalet och därmed evolutiva processer. Målet med detta arbete var att undersöka effekterna av omgivningsförändringar på sexuella urvalet genom att använda den ökade övergödningen inom storpiggen Gasterosteus aculeatus lekområden som modell system. Sexuella urvalet är en viktig evolutiv kraft med följder på populations- och artnivå (Kapitel 1). Avhandlingens olika delar fokuserar på övergödningens effekter på upptäckandet av partners, användningen av visuella- och doftsignaler i partnersval, och fördelningen av parningsframgången mellan bobyggande hanar. I Kapitel II och III simuleras hur grumlighet orsakad av fytoplankton påverkar hastigheten med vilken potentiella partners påträffas, genom effekter på synligheten. Resultaten visar att normala algblomningar i Östersjön har en måttlig effekt på finnandet av potentiella partners. Detta tyder på att algblomningarna troligen inte kommer att minska på selektiva parningen pga. ökade sökkostnader. I Kapitel IV visas att storspiggen ändrar relativa användningen av olika signaler när vattnets grumlighet ökar; visuella signaler minskar i betydelse medan doftsignaler ökar i betydelse. Samtidigt underlättas användandet av doftsignaler av ändringar i vattnets kemiska sammansättning då fotosyntesen intensifieras (Kapitel V). Lek i övergödda vatten kan ändå vara kostsamt både på individ- och populationsnivån, då parasiterade hanar, som troligen är dåligt genetiskt anpassade till sin miljö, lyckas få mer ägg i sina bon än friskare hanar som troligen är av högre genetisk kvalitet (Kapitel VI). Övergödningen påverkar således partnersval och konkurrensen om partners genom att påverka upptäckandet av potentiella partners, evalueringen av partners och fördelningen av partners inom lekområdena. De följder detta kan ha för evolutionen av sexuellt selekterad egenskaper och för populationers dynamik och livskraft är dock oklara. Avhandlingen visar på svårigheten att förutse följderna av omgivningsförändringar för sexuella urvalet och effekterna på individ och populationsnivå.

Epidemiology and Treatment Options of Primary Biliary Cirrhosis

Primary biliary cirrhosis (PBC) is caused by an autoimmune inflammation of the small bile ducts. It results to destruction of bile ducts, accumulation of the bile in the liver, and cirrhosis. The prevalence and incidence of PBC is increasing in the Western world. The prevalence is highest in the USA (402 per million) and incidence in Scotland (49/million/year). Our aim was to assess the epidemiology of PBC in Finland. Patients for the epidemiological study were searched from the hospital discharge records from year 1988 to 1999.The prevalence rose from 103 to 180/million from 1988 to 1999, an annual increase of 5.1%. The incidence rose from 12 to 17 /million/year, an annual increase of 3.5%. The age at death increased markedly from 65 to 76 years. The risk of liver related deaths diminished over time. The treatment of PBC is based on Ursodeoxycholic acid (UDCA). During 20 years 50% of patients end up with cirrhosis. Our treatment option was to combine budesonide, a potent corticosteroid with a high first pass metabolism in the liver, to UDCA and evaluate the liver effects and systemic effects such as bone mass density (BMD) changes. Our aim was to find out if combination of laboratory tests would serve as a surrogate marker for PBC and help reducing the need for liver biopsy. Non-cirrhotic PBC patients were randomized to receive budesonide 6 mg/day combined to UDCA 15 mg /kg/day or UDCA alone for three years. The combination therapy with UDCA and budesonide was effective: stage improved 22%, fibrosis 25%, and inflammation 32%. In the UDCA group the changes were: 20% deterioriation in stage and 70% in fibrosis, but a 10% improvement in inflammation. BMD in femoral neck decreased by 3.6% in the combination group and by 1.9% in the UDCA group. The reductions in lumbar spine were 2.8% and 0.7%. Pharmacokinetics did not differ between the stages of PBC. HA, PIIINP, bile acids, and AST were significantly different within stages I-III and could differentiate the mild fibrosis (F0F1) from the moderate (F2F3). The combination of these individual markers (PBC-score) further improved the accuracy. The area under the ROC of the PBC score, using a cut of value 66, had a sensitivity of 81.4% and a specificity of 65.2% to classify the stage of PBC. The prevalence of PBC in Finland increases, which results from increasing incidence and improved survival. The combination of budesonide and UDCA improves liver histology compared to UDCA alone in non-cirrhotic stages of PBC. The treatment may reduce BMD. Hyaluronic acid, PIIINP, AST, and bile acids may serve as tools to monitor the treatment response in the early stages of PBC. The budesonide and UDCA combination therapy is an option for those patients who do not receive full response from UDCA and are still at the non-cirrhotic stage of PBC.

Macroseismology as a Component of Seismicity Assessments in an Intraplate Region: Studies of Northern Europe with Emphasis on Finland

This work focuses on the role of macroseismology in the assessment of seismicity and probabilistic seismic hazard in Northern Europe. The main type of data under consideration is a set of macroseismic observations available for a given earthquake. The macroseismic questionnaires used to collect earthquake observations from local residents since the late 1800s constitute a special part of the seismological heritage in the region. Information of the earthquakes felt on the coasts of the Gulf of Bothnia between 31 March and 2 April 1883 and on 28 July 1888 was retrieved from the contemporary Finnish and Swedish newspapers, while the earthquake of 4 November 1898 GMT is an example of an early systematic macroseismic survey in the region. A data set of more than 1200 macroseismic questionnaires is available for the earthquake in Central Finland on 16 November 1931. Basic macroseismic investigations including preparation of new intensity data point (IDP) maps were conducted for these earthquakes. Previously disregarded usable observations were found in the press. The improved collection of IDPs of the 1888 earthquake shows that this event was a rare occurrence in the area. In contrast to earlier notions it was felt on both sides of the Gulf of Bothnia. The data on the earthquake of 4 November 1898 GMT were augmented with historical background information discovered in various archives and libraries. This earthquake was of some concern to the authorities, because extra fire inspections were conducted in three towns at least, i.e. Tornio, Haparanda and Piteå, located in the centre of the area of perceptibility. This event posed the indirect hazard of fire, although its magnitude around 4.6 was minor on the global scale. The distribution of slightly damaging intensities was larger than previously outlined. This may have resulted from the amplification of the ground shaking in the soft soil of the coast and river valleys where most of the population was found. The large data set of the 1931 earthquake provided an opportunity to apply statistical methods and assess methodologies that can be used when dealing with macroseismic intensity. It was evaluated using correspondence analysis. Different approaches such as gridding were tested to estimate the macroseismic field from the intensity values distributed irregularly in space. In general, the characteristics of intensity warrant careful consideration. A more pervasive perception of intensity as an ordinal quantity affected by uncertainties is advocated. A parametric earthquake catalogue comprising entries from both the macroseismic and instrumental era was used for probabilistic seismic hazard assessment. The parametric-historic methodology was applied to estimate seismic hazard at a given site in Finland and to prepare a seismic hazard map for Northern Europe. The interpretation of these results is an important issue, because the recurrence times of damaging earthquakes may well exceed thousands of years in an intraplate setting such as Northern Europe. This application may therefore be seen as an example of short-term hazard assessment.

Eläke- ja vammaisetuuksien, maahanmuuttajan erityistuen ja eläkkeensaajan asumistuen muutokset 1.1.2011

Kansaneläkeindeksi 1 508, elinkustannusindeksi 1 749 (pistelukujen keskiarvo heinäsyyskuulta 2010) Vuoden 2011 alusta kansaneläkkeisiin, perhe-eläkkeisiin, lapsikorotuksiin, rintamalisiin, vammaisetuuksiin (pl. ruokavaliokorvaukset) ja maahanmuuttajan erityistukiin tehtiin 0,4 prosentin indeksitarkistus. Eläke-etuusmenot kasvoivat 9,7 milj. euroa (0,4 %), vammaisetuusmenot 1,9 milj. euroa (0,4 %) ja maahanmuuttajan erityistukimenot 0,1 milj. euroa (0,3 %). Laskelmat perustuvat joulukuun 2010 etuuskantaan.

Asumistuensaajien vuokranylityksiin toimeentulotukea

Kela maksoi asumistukia 1 214,5 milj. euroa vuoden 2010 aikana. Kasvua edelliseen vuoteen oli 7 %. Taloustilanteen aiheuttaman työllisyyden huononemisen seurauksena asumistukien maksatus on kahtena peräkkäisenä vuotena kasvanut reilusti. Asumistukea saaneita perheitä tai ruokakuntia oli vuoden lopussa 498 000.

Population projection for Namibia 2011-2020 - With an estimation of the impact of HIV/AIDS

This study presents a population projection for Namibia for years 2011–2020. In many countries of sub-Saharan Africa, including Namibia, the population growth is still continuing even though the fertility rates have declined. However, many of these countries suffer from a large HIV epidemic that is slowing down the population growth. In Namibia, the epidemic has been severe. Therefore, it is important to assess the effect of HIV/AIDS on the population of Namibia in the future. Demographic research on Namibia has not been very extensive, and data on population is not widely available. According to the studies made, fertility has been shown to be generally declining and mortality has been significantly increasing due to AIDS. Previous population projections predict population growth for Namibia in the near future, yet HIV/AIDS is affecting the future population developments. For the projection constructed in this study, data on population is taken from the two most recent censuses, from 1991 and 2001. Data on HIV is available from HIV Sentinel Surveys 1992–2008, which test pregnant women for HIV in antenatal clinics. Additional data are collected from different sources and recent studies. The projection is made with software (EPP and Spectrum) specially designed for developing countries with scarce data. The projection includes two main scenarios which have different assumptions concerning the development of the HIV epidemic. In addition, two hypothetical scenarios are made: the first considering the case where HIV epidemic would never have existed and the second considering the case where HIV treatment would never have existed. The results indicate population growth for Namibia. Population in the 2001 census was 1.83 million and is projected to result in 2.38/2.39 million in 2020 in the first two scenarios. Without HIV, population would be 2.61 million and without treatment 2.30 million in 2020. Urban population is growing faster than rural. Even though AIDS is increasing mortality, the past high fertility rates still keep young adult age groups quite large. The HIV epidemic shows to be slowing down, but it is still increasing the mortality of the working-aged population. The initiation of HIV treatment in 2004 in the public sector seems to have had an effect on many projected indicators, diminishing the impact of HIV on the population. For example, the rise of mortality is slowing down.

Wegener's granulomatosis in Finland in 1981-2000

Objectives: Wegener s granulomatosis (WG) is a vasculitis with a predilection for the airways and kidneys. An increasing incidence and improved prognosis of WG has been shown. The aim of this study was to evaluate the incidence, clinical presentation, diagnostic delay, risk of dialysis-dependent renal insufficiency and mortality of WG in 1981-2000. Patients and methods: Data was retrieved from the Finnish hospital discharge register and hospital case reports. Patients diagnosed with WG in 1981-2000 were included, and their demographic and clinical data recorded. The patients were crossed with the national kidney dialysis register and the national mortality statistics. Results: A total of 492 patients (243 ♂ , 249 ♀) were diagnosed at a mean age of 54 years (SD 18). The incidence increased from 1.9 to 9.3/ million/ year. The median diagnostic delay decreased from 17 to 4 months. Patients presented most often with symptoms of the ear, nose and throat (ENT) (45%), lung (36%), musculoskeletal system (22%) and kidney (11%). Initial lung involvement, constitutional symptoms, high erythrocyte sedimentation rate (ESR) and high ELK scores [(number of simultaneously involved organ groups (ENT, Lung, Kidney)] were associated with a shorter diagnostic delay. Medical treatment of WG patients remained similar in the 1980s and 1990s. Almost 90% of patients received cyclophosphamide (CYC) and more than 90% glucocorticoid medication at some point during the course of the disease. Eighty-four patients (17%) needed dialysis. Initial renal involvement and elevated serum creatinine values were related to an increased risk of dialysis-dependent kidney disease. In two-thirds of the patients, renal impairment was reversible. Dialysis became chronic (>3 months) in 32 patients (6.5%). Nineteen patients (3.9%) received a kidney transplant. Altogether 203 patients (99 men, 104 women) died before 30 June 2005. WG was the underlying cause of death in 37%. The crude one-year and five-year survival rates were 83.3% and 74.2%, respectively. The standardized mortality ratio was 3.43 (95% CI = 2.98 to 3.94). Older age and elevated creatinine level at diagnosis predicted shorter survival. ENT symptoms at presentation and treatment with CYC were associated with better outcome. There was no additional risk associated with male gender or with either of the decades (1981-1990 and 1991-2000) Conclusions: In 1981-2000, the incidence of WG increased ca. 4.5-fold and diagnostic delay decreased to ca. one-fourth, reflecting increased recognition of the disease and improved diagnostic means. WG patients are at great risk of developing dialysis-dependent renal insufficiency and an increased risk of dying. During the study period the treatment of WG did not change markedly, nor did the prognosis improve.

Asukkaan Helsinki? : Tapaustutkimus vuorovaikutteisuudesta kaupunkisuunnittelussa

This study examines the interaction between inhabitants and urban planning. In addition to traditional methods of participation there can be seen an increasing need to find new channels and means to influence on one´s environment. Hearing of inhabitants during planning is hoped to decrease the amount of claims and this way to speed up the planning process. Discussion that emphasizes competitiveness and innovativeness in planning has brought out the role of inhabitants as selective consumers and end users. This extension of civil perspective completes the thought of participation in city planning and adds the pressure on developing the interaction and user orientation. The aim of the study is to point out the present situation of inhabitant´s participation and influencing in Helsinki. Helsinki City Planning Department opened a new information and exhibiotion hall called Laituri in 2008. Laituri provides the latest information about planning projects in Helsinki and temporary exhibitions as well as it operates as communication channel and information point for the department. In this study Laituri is examined as a case study of interaction between citizen and planner. The study is divided into two principal themes. The aim is to research action and interactivity at Laituri from the inhabitants´and planners´point of view. The qualitative study has inquiries, interview surveys and observation as research methods. Empiricial data of the study consists of three parts which complement each other: Laituri operational reseach, inquiry directed to the members of Laituri team and interviews of three experts. The aim is to find answers to questions like, does Laituri reach the citizens and will the opportunities to participate improve along Laituri. The study examines also how the local knowledge of inhabitants will come across to planners and further to planning. The study combines discussions of inhabitants´ influencing in Finnish society and science community. Cornerstones of the study are inhabitant participation, interaction and local knowledge in urban planning. The theory behind the study is communicative planning theory. In addition the theory consists of key concepts. The study introduces a concept of Inhabitant´s Helsinki, which reflects the inhabitant as customer-citizen who is an active product developer in participative urban planning. According to the research results the experts of Laituri and majority of inhabitants in Helsinki experience that the inhabitant´s possibilities to participate will improve along Laituri. However half of the citizens in Helsinki believe that local knowledge and ideas will only have minor impact on the final plan. According to city dwellers the present practise used by Helsinki City Planning Department supports only partially adequate interaction. The experts of Laituri experience that the role of Laituri is first of all forum of communication and discussion channel instead of effective local data collector. Based on the results the study introduces a model of inhabitant´s participation field. According to the model Laituri can be seen as phenomenom in Helsinki urban planning which has the elements of network municipality. The planner is more like diplomatic trend-setter and visionary. The inhabitant of Helsinki is an expert in city living and participative producer of local knowledge. Participation methods are increasingly segmented and tailored in every plan and project. The study argues that Inhabitant´s Helsinki is a pluralistic milieu in constant pressure for change. Therefore reaching the everyday life experiencies of inhabintants should be at higher degree in Helsinki City Planning Department´s operations.

Pohjavesivarat aktiiviseen hyötykäyttöön eteläisessä Satakunnassa ja Laitilassa

Pohjavedet aktiiviseen hyötykäyttöön eteläisessä Satakunnassa ja Laitilassa kehittämissuunnitelma laadittiin Varsinais-Suomen ELY-keskuksen koordinoimana yhdessä Euran, Köyliön ja Säkylän kuntien sekä Harjavallan, Kokemäen, Laitilan ja Rauman kaupunkien, Satakuntaliiton, Varsinais-Suomen liiton ja Pyhäjärvi-instituutin yhteishankkeena. Suunnittelu tehtiin Sweco Ympäristö Oy:n sekä alikonsultteina toimineiden Vesi-instituutti Wanderin ja Suomen Pohjavesitekniikka Oy:n toimesta. Kehittämissuunnitelman tavoitteena on yhdyskuntien vedentarpeen turvaaminen määrällisesti ja laadullisesti myös tulevaisuudessa, hyvälaatuisen pohjaveden käytön lisääminen alueella (korvata huonolaatuiset pohjavesilähteet ja mahdollisesti myös pintavesilähteet)sekä hyvien pohjavesivarojen hyödyntäminen niin, että se antaisi mahdollisuudet teollisuuden ja erityisesti biotalouden kehittämiselle koko suunnittelualueella. Suunnitelmassa on löydetty sekä yhdyskuntien vedenhankintaa että elinkeinoelämän turvaamista ja kehittämistä palveleva ratkaisu. Vedenhankinnan kehittämisen ensimmäisessä vaiheessa turvataan yhdyskuntien lisäveden- ja varavedentarpeet rakentamalla kolmeuutta vedenottamoa; Kokemäen Risteelle, Köyliön Ristolaan ja Säkylän Porsaanharjulle. Lisäksi toteutetaan näihin liittyvät uudet vesijohtoyhteydet mukaan lukien varavesiyhteys Harjavallan ja Kokemäen välille. Ratkaisu parantaa nykyisen elinkeinoelämän toimintaedellytyksiä alueella ja mahdollistaa myös yritysten kehittymistä ja kasvua jo lähitulevaisuudessa. Ensimmäinen vaihe mahdollistaa lisäksi uudenlaisen vesibisneksen käynnistämisen suunnittelualueella. Ensimmäisen vaiheen rakentamiskustannukset ovat 11,0 milj. € ja toteutusaikataulu 2 – 5 vuotta. Alueellista yhteistyötä kehitetään perustamalla Ristolan ottamoa varten kuntien yhteinen osakeyhtiömuotoinen tukkuvesilaitos. Vedenhankinnan jatkokehittelyllä kohti tekopohjavesilaitosta vedenhankintaa saadaan entisestään alueellistettua ja optimoitua. Tekopohjavesilaitos mahdollistaa pintaveden käytöstä luopumisen ja turvaa vedenhankinnan varmuutta jopa alueen ulkopuolella. Alueelliseen tekopohjavesilaitoksen käyttöön siirtyminen luo alueen elinkeinoelämälle uusia toimintamahdollisuuksia. Laitoksenkapasiteetista riippuen mahdollisuuksia on jopa veden laajamittaiseen vientiin asti. Tähän tarkoitukseen juuri eteläisen Satakunnan ja Laitilan muodostama alue on yksi vahvimpia alueita Suomessa. Tekopohjavesilaitoksen rakentamiskustannukset ovat noin 24 – 53 milj. €. Alueen pitkäjännitteinen kehittäminen vaatii toimivaa yhteistyöorganisaatiota, jolle on tämän suunnitelman puitteissa luotu hyvät lähtökohdat jatkaa aloitettua työtä.