A fast method of comparing protein structures

Comparative studies on protein structures form an integral part of protein crystallography. Here, a fast method of comparing protein structures is presented. Protein structures are represented as a set of secondary structural elements. The method also provides information regarding preferred packing arrangements and evolutionary dynamics of secondary structural elements. This information is not easily obtained from previous methods. In contrast to those methods, the present one can be used only for proteins with some secondary structure. The method is illustrated with globin folds, cytochromes and dehydrogenases as examples.

Suomi ja Euroopan kirkollinen jälleenrakentaminen 1945-1948

The international aid that the Evangelical Lutheran Church of Finland received between 1945 and 1948 is the topic of this historical study, in which the process of reconstruction of the Evangelical Lutheran Church of Finland is examined in a European context. The key questions are related not only to the achievements of the reconstruction programs but also to the purposes and objectives of the donating churches. The study pays particular attention to the changes in the ecclesiastical, political and economic fields after the Second World War and asks how the tense political atmosphere of a divided world affected the reconstruction programs of the churches. It is possible to distinguish three periods within the European church reconstruction process. To begin with, the year 1945 was, in general, the year of organization. Many churches had started planning reconstruction work already during the war, but only after the conflict in Europe had ceased did they have a chance to renew contacts, assess the damage and begin operations. The years 1946 and 1947 were the main years of the work. Large reconstruction organizations from American churches donated money, food, clothes and vitamins worth millions of dollars to the European churches. The work started to diminish as early as 1948, partly because Marshall Plan aid and the rising standard of living had reduced the need for material assistance in many countries and partly because other problems overshadowed the reconstruction work of the World Council of Churches: for example, most WCC resources at this time were directed to refugee programs and to Third World churhces. The most important donors from the Evangelical Lutheran Church of Finland's point of view were the American Section of the Lutheran World Federation, the World Council of Churches and the Churches of Denmark, Sweden and England. The amount of money and value of goods received by the Evangelical Lutheran Church of Finland totaled approximately 2.5 million dollars, from which about 60 per cent came from the Lutheran churches of America. The importance of the Lutheran World Federation was even greater because of the productive financial arrangements that increased the American Lutheran funds. In addition the Evangelical Lutheran Church of Finland imported hundreds of tons of tax-free coffee and sold this to Finns. The money gained was used mostly to rebuild destroyed church buildings and to support the work of different ecclesiastical organizations. Smaller amounts were used for scholarship programs, youth work, and supporting sick and disabled church workers.

Viimeinen matka : Toimintatutkimus kirkollisen hautauskentän professiostruktuurista

This study is a qualitative examination of the professional structure of the ecclesias-tical funeral field. The research material is based on 13 funeral cases in the archdio-cese. The researcher participated in all the funerals and memorial events, interviewed the closest survivors, the officials of the funeral agency and the ecclesiastical actors. The material was collected by means of observation and recording of the interviews, and was later transcribed and analyzed. The actors in this study are the survivors, the funeral agencies and the church. The survivors act as the buyers and users of the products (funeral services) who require both the funeral agencies and the church to assist them with the problems that the death has caused. The numbers of actions related to the death and to the funerals - the rituals of death - are placed on the action field, which in this study is called the funeral field. In this field, the researchquestion focused space and power, and the actions on the funeral field are highly ritualized. The theoretical model comes from Pierre Bourdieu. The study showed an action structure on the funeral field in which the survivors first contacted a funeral agency, which then contacted the other actors of the field, re-served the date and place for the funeral, and organised the funeral arrangements. The funeral agencies arranged an opportunity for the survivors to have a last look at the deceased when he or she was placed in the coffin, and they held a moment of the prayer (if desired) before removing the deceased from the hospital's chapel. The sur-vivors contacted the pastor of the funeral much later. The pastor also participated in the memorial event. The survivors contacted the church musician through via pastor. In some cases, the survivors had neither met nor even seen the musician prior to the actual funeral service. Still, the music was of great importance to the survivors. In the research interviews, tensions emerged to some extent between the funeral agencies and the ecclesiastical actors; these actors attempted to resolve these tensions through organising negotiations. In the beginning of the 20th century, the family took an active part in the preparations of the deceased and in the arrangements of the funerals, whereas this study showed that these days, survivors often transfer the preparations to the funeral agencies. The professional side of the funeral field has grown. The funeral agencies can be seen as providers of full services that act on the survivors' behalf, aspiring to high individu-ality and aiming to fulfil the survivors' wishes. In practise, the role of the church in carrying out the last journey was reduced in the research cases to the actual funeral. In several cases, the pastor or the cantor of the funeral had never before seen the per-son in the coffin at any stage of life or death. The proportion of cremations in funeral cases has increased rapidly, however, special issues related to these cremations (such as the possibility of holding a funeral service for the already cremated deceased) have seen little consideration in the church. In the church's liturgies on funeral rites, cremation is frequently overlooked. The pastors or the cantors did not participate in either the burial of the funeral urn or in the scattering of the deceased's ashes. The verger took care of it. The parishes had no adopted standard practices for cremations, yet in each case for the survivors that moment was crucial.

To ask or not to ask? Investigating workers' flexibility requests and the phenomenon of discontented non-requesters

Flexible working arrangements have attracted growing attention in workplaces across Australia and in many other countries in recent years. This contribution utilises the results of two large Australian employee surveys to analyse who asks for flexibility, why, and with what effects on work-life interference. This analysis is set in the context of Australia’s ‘Right to Request’ (RTR) provisions which, at the time of the study, gave parents of preschool children and those with a disabled child aged up to 18 the RTR flexibility. The analysis also draws on a set of qualitative interviews of those we term ‘discontented non-requesters’ (that is, those who are not content with current arrangements but who do not ask for flexibility) to probe beneath the survey results to consider explanations about why some people do not ask for flexibility despite desiring different working arrangements. We conclude with the implications for policy and regulation.

Towards a Critique of the Concept of the Right to Self-Determination in Africa : A Conceptual Examination and the Cases of Western Sahara, Southern Sudan and Eritrea

This thesis examines the right to self-determination which is a norm used for numerous purposes by multiple actors in the field of international relations, with relatively little clarity or agreement on the actual and potential meaning of the right. In international practice, however, the main focus in applying the right has been in the context of decolonization as set by the United Nations in its early decades. Thus, in Africa the right to self-determination has traditionally implied that the colonial territories, and particularly the populations within these territories, were to constitute the people who were entitled to the right. That is, self-determination by decolonization provided a framework for the construction of independent nation-states in Africa whilst other dimensions of the right remained largely or totally neglected. With the objective of assessing the scope, content, developments and interpretations of the right to self-determination in Africa, particularly with regard to the relevance of the right today, the thesis proceeds on two fundamental hypotheses. The first is that Mervyn Frost s theory of settled norms, among which he lists the right to self-determination, assumes too much. Even if the right to self-determination is a human right belonging to all peoples stipulated, inter alia, in the first Article of the 1966 International Human Rights Covenants, it is a highly politicized and context-bound right instead of being settled and observed in a way that its denial would need special justification. Still, the suggested inconsistency or non-compliance with the norm of self-determination is not intended to prove the uselessness or inappropriateness of the norm, but, on the contrary, to invite and encourage debate on the potential use and coverage of the right to self-determination. The second hypothesis is that within the concept of self-determination there are two normative dimensions. One is to do with the idea and practice of statehood, the nation and collectivity that may decide to conduct itself as an independent state. The other one is to do with self-determination as a human right, as a normative condition, to be enjoyed by people and peoples within states that supersedes state authority. These external and internal dimensions need to be seen as complementary and co-terminous, not as mutually exclusive alternatives. The thesis proceeds on the assumption that the internal dimension of the right, with human rights and democracy at its core, has not been considered as important as the external. In turn, this unbalanced and selective interpretation has managed to put the true normative purpose of the right making the world better and bringing more just polity models into a somewhat peculiar light. The right to self-determination in the African context is assessed through case studies of Western Sahara, Southern Sudan and Eritrea. The study asks what these cases say about the right to self-determination in Africa and what their lessons learnt could contribute to the understanding and relevance of the right in today s Africa. The study demonstrates that even in the context of decolonization, the application of the right to self-determination has been far from the consistent approach supposedly followed by the international community: in many respects similar colonial histories have easily led to rather different destinies. While Eritrea secured internationally recognized right to self-determination in the form of retroactive independence in 1993, international recognition of distinct Western Sahara and Southern Sudan entities is contingent on complex and problematic conditions being satisfied. Overall, it is a considerable challenge for international legality to meet empirical political reality in a meaningful way, so that the universal values attached to the norm of self-determination are not overlooked or compromised but rather reinforced in the process of implementing the right. Consequently, this thesis seeks a more comprehensive understanding of the right to self-determination with particular reference to post-colonial Africa and with an emphasis on the internal, human rights and democracy dimensions of the norm. It is considered that the right to self-determination cannot be perceived only as an inter-state issue as it is also very much an intra-state issue, including the possibility of different sub-state arrangements exercised under the right, for example, in the form of autonomy. At the same time, the option of independent statehood achieved through secession remains a mode of exercising and part of the right to self-determination. But in whatever form or way applied, the right to self-determination, as a normative instrument, should constitute and work as a norm that comprehensively brings more added value in terms of the objectives of human rights and democracy. From a normative perspective, a peoples right should not be allowed to transform and convert itself into a right of states. Finally, in light of the case studies of Western Sahara, Southern Sudan and Eritrea, the thesis suggests that our understanding of the right to self-determination should now reach beyond the post-colonial context in Africa. It appears that both the questions and answers to the most pertinent issues of self-determination in the cases studied must be increasingly sought within the postcolonial African state rather than solely in colonial history. In this vein, the right to self-determination can be seen not only as a tool for creating states but also as a way to transform the state itself from within. Any such genuinely post-colonial approach may imply a judicious reconsideration, adaptation or up-dating of the right and our understanding of it in order to render it meaningful in Africa today.

Small State Cultures of Consensus : State Traditions and Consensus-Seeking in the Neo-Corporatist and Neutrality Policies in Post-1945 Austria and Finland

Austria and Finland are persistently referred to as the “success stories” of post-1945 European history. Notwithstanding their different points of departure, in the course of the Cold War both countries portrayed themselves as small and neutral border-states in the world dictated by superpower politics. By the 1970s, both countries frequently ranked at the top end in various international classifications regarding economic development and well-being in society. This trend continues today. The study takes under scrutiny the concept of consensus which figures centrally in the two national narratives of post-1945 success. Given that the two domestic contexts as such only share few direct links with one another and are more obviously different than similar in terms of their geographical location, historical experiences and politico-cultural traditions, the analogies and variations in the anatomies of the post-1945 “cultures of consensus” provide an interesting topic for a historical comparative and cross-national examination. The main research question concerns the identification and analysis of the conceptual and procedural convergence points of the concepts of the state and consensus. The thesis is divided into six main chapters. After the introduction, the second chapter presents the theoretical framework in more detail by focusing on the key concepts of the study – the state and consensus. Chapter two also introduces the comparative historical and cross-national research angles. Chapter three grounds the key concepts of the state and consensus in the historical contexts of Austria and Finland by discussing the state, the nation and democracy in a longer term comparative perspective. The fourth and fifth chapter present case studies on the two policy fields, the “pillars”, upon which the post-1945 Austrian and Finnish cultures of consensus are argued to have rested. Chapter four deals with neo-corporatist features in the economic policy making and chapter five discusses the building up of domestic consensus regarding the key concepts of neutrality policies in the 1950s and 1960s. The study concludes that it was not consensus as such but the strikingly intense preoccupation with the theme of domestic consensus that cross-cut, in a curiously analogous manner, the policy-making processes studied. The main challenge for the post-1945 architects of Austrian and Finnish cultures of consensus was to find strategies and concepts for consensus-building which would be compatible with the principles of democracy. Discussed at the level of procedures, the most important finding of the study concerns the triangular mechanism of coordination, consultation and cooperation that set into motion and facilitated a new type of search for consensus in both post-war societies. In this triangle, the agency of the state was central, though in varying ways. The new conceptions concerning a small state’s position in the Cold War world also prompted cross-nationally perceivable willingness to reconsider inherited concepts and procedures of the state and the nation. At the same time, the ways of understanding the role of the state and its relation to society remained profoundly different in Austria and Finland and this basic difference was in many ways reflected in the concepts and procedures deployed in the search for consensus and management of domestic conflicts. For more detailed information, please consult the author.

The Soviet Union, Finland and the Cold War : The Finnish Card in Soviet Foreign Policy, 1956-1959

From the Soviet point of view the actual substance of Soviet-Finnish relations in the second half of 1950s clearly differed from the contemporary and later public image, based on friendship and confidence rhetoric. As the polarization between the right and the left became more underlined in Finland in the latter half of the 1950s, the criticism towards the Soviet Union became stronger, and the USSR feared that this development would have influence on Finnish foreign policy. From the Soviet point of view, the security commitments of FCMA-treaty needed additional guarantees through control of Finnish domestic politics and economic relations, especially during international crises. In relation to Scandinavia, Finland was, from the Soviet point of view, the model country of friendship or neutrality policy. The influence of the Second Berlin Crisis or the Soviet-Finnish Night Frost Crisis in 1958-1959 to Soviet policy towards Scandinavia needs to be observed from this point of view. The Soviet Union used Finland as a tool, in agreement with Finnish highest political leadership, for weakening of the NATO membership of Norway and Denmark, and for maintaining Swedish non-alliance. The Finnish interest to EFTA membership in the summer of 1959, at the same time with the Scandinavian countries, seems to have caused a panic reaction in the USSR, as the Soviets feared that these economic arrangements would reverse the political advantages the country had received in Finland after the Night Frost Crisis. Together with history of events, this study observes the interaction of practical interests and ideologies, both in individuals and in decision-making organizations. The necessary social and ideological reforms in the Soviet Union after 1956 had influence both on the legitimacy of the regime, and led to contradictions in the argumentation of Soviet foreign policy. This was observed both in the own camp as well as in the West. Also, in Finland a breakthrough took place in the late 1950's: as the so-called counter reaction lost to the K-line, "a special relationship" developed with the Soviet Union. As a consequence of the Night Frost Crisis the Soviet relationship became a factor decisively defining the limits of domestic politics in Finland, a part of Finnish domestic political argumentation. Understood from this basis, finlandization is not, even from the viewpoint of international relations, a special case, but a domestic political culture formed by the relationship between a dominant state, a superpower, and a subordinate state, Finland.

Statutory licences and third party dealings: Property analysis v statutory interpretation

Statutory licensing schemes are proliferating as a means of regulating commercial activity, resource exploitation and activities harmful to the environment. Statutes often declare that entitlements are non-transferable or are transferable only with approval or subject to conditions. Some entitlements, such as resource consents issued under the Resource Management Act 1991 (NZ), are declared not to be property. Despite these statutory declarations, entitlements are often held to be transferable in equity or to be property for the purposes of resolving private disputes. Recently, in Greenshell New Zealand Ltd v Tikapa Moana Enterprises Ltd, the High Court of New Zealand indicated that a resource consent was property that could support a claim for relief against forfeiture, continuing the trend in earlier cases that appear to depart from the statute. In this article we examine the juridical treatment of entitlements in private law. We identify factors influencing the courts’ enforcement of private arrangements which may circumvent the statutory intent. Our analysis will guide legislators in the design of provisions to implement new schemes.

Seeking continuity: Educational strategy in and for mobile ADF families

This report shares findings and insights from an interview study conducted in 2009, with 34 ADF families. These families were identified in the communities of primary schools in both state and Catholic systems with high ADF family enrolments in 3 towns across 2 states, with the assistance of the DCO and their embedded Defence School Transition Aides (DSTAs). In the interviews the parents were invited to describe their history of ADF relocations, and how they managed transitions for each member in terms of school choice, child care arrangements, spouse employment, and educational transitions. Parallel interviews were conducted with 12 teachers and 6 DSTAs across the identified schools to describe how schools cater for mobile ADF families flowing through their classes. Parents were invited to tell the story of their family’s sequence of moves and how each member made the transition, then reflect more generally on what advice they’d give other mobile families. Teachers were asked to describe how they respond to the mobile families in their school community, and to illustrate some of the issues and challenges from the institutional perspective. By offering perspectives from both parents and teachers, the report hopes to facilitate a dialogue between parties to address their common goal – promoting productive continuities in education for children in mobile families.

Environmental applications of inorganic-organic clays for recalcitrant organic pollutants removal: Bisphenol A

Bisphenol-A (BPA) adsorption onto inorganic-organic clays (IOCs) was investigated. For this purpose, IOCs synthesised using octadecyltrimethylammonium bromide (ODTMA, organic modifier) and hydroxy aluminium (Al13, inorganic modifier) were used. Three intercalation methods were employed with varying ODTMA concentration in the synthesis of IOCs. Molecular interactions of clay surfaces with ODTMA and Al13 and their arrangements within the interlayers were determined using Fourier transform infrared spectroscopy (FTIR). Surface area and porous structure of IOCs were determined by applying Brunauer, Emmett, and Teller (BET) method to N2 adsorption-desorption isotherms. Surface area decreased upon ODTMA intercalation while it increased with Al13 pillaring. As a result, BET specific surface area of IOCs was considerably higher than those of organoclays. Initial concentration of BPA, contact time and adsorbent dose significantly affected BPA adsorption into IOCs. Pseudo-second order kinetics model is the best fit for BPA adsorption into IOCs. Both Langmuir and Freundlich adsorption isotherms were applicable for BPA adsorption (R2 > 0.91) for IOCs. Langmuir maximum adsorption capacity for IOCs was as high as 109.89 mg g‒1 and it was closely related to the loaded ODTMA amount into the clay. Hydrophobic interactions between long alkyl chains of ODTMA and BPA are responsible for BPA adsorption into IOCs.

Assessing taxpayer response to legislative changes: A case study of ‘in-house’ fringe benefits rules

On 22 October 2012, the Australian Federal Government announced the removal of the $1,000 in-house fringe benefits concession when used as part of a salary packaging arrangement. At the time of the announcement, the Federal Government predicted that the removal of the concession would contribute additional tax revenue of $445 million over the following four years as well as an increase of GST payments to the States and Territories. However, anecdotal evidence at the same time indicated that the Australian employer response was to immediately stop providing employees with such in-house fringe benefits via salary sacrificing arrangements. Data presented in this article, collected from a combination of interviews with tax managers of four Australian entities as well as a review of the published archival data, confirms that the abolition of the $1,000 in-house fringe benefits concession was perceived as a negative change, whereby employees were considered the ‘big losers’ despite assertions by the Federal Government to the contrary. Using a conceptual map of tax rule change developed by Oats and Sadler, this article seeks to understand the reasons for this fringe benefits tax change and taxpayer response. In particular, the economic and political factors, and the responses of the relevant taxpayers (employers) are explored. Drawing on behavioural economic concepts, the actions, attitudes and response of employers to the rule change are also examined. The research findings suggest that the decision by Australian employers to cease providing the in-house fringe benefits as part of a salary-packaging arrangement after the legislative amendment was impacted by more than simple rational behaviour.

Conserving Biodiversity as If People Matter: A Case Study from India

India has rich traditions of nature conservation as well as a vigorous official program of protection of nature reserves developed over the last 40 years. However, the officialp rograms uffers fromt otal relianceo n authoritarianm anagement arrangements in which decisions are made centrally and coercion is used to implement them. At the same time, the state apparatus organises subsidized resource flows to the urbanindustrial- intensivea griculturalc omplex which promote inefficient,n on-sustainable resource-use patterns that are inimical to conservation of biodiversity. These processes are illustrated within the concrete setting of the district of Uttara Kannada in southern India. It is suggested that the interests of conservation would be served far better by an approach that withdraws the subsidies to the elite so that a much more efficient, sustainable and equitable pattern of resource use, compatible with conservation of biodiversity, can be instituted. In conjunction with this, the larger society should involve local people in working out detailed plans for conservation of biodiversity and offer them adequate authority as well as appropriate financial incentives to implement these plans. The paper goes on to illustrate how such an approach may be implemented in the case of Uttara Kannada.

Non-preferential trading clubs

This paper examines the welfare implications of non-discriminatory tariff reforms by a subset of countries, which we term a non-preferential trading club. We show that there exist coordinated tariff reforms, accompanied by appropriate income transfers between the member countries, that unambiguously increase the welfare of these countries while leaving the welfare of non-members unaltered. In terms of economic policy implications, our results show that there exist regional, MFN-consistent arrangements that lead to Pareto improvements in world welfare.

Theoretical calculations of base-base interactions in nucleic acids: II Stacking interactions in polynucleotides

Base-base interactions were computed for single- and double- stranded polynucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interaction energies of a regular duplex and the alternative structures3 were compared. It was found that the type II model3 is energetically more favourable than the rest.

Diffusive and ship-mediated spread of dinoflagellates in the Baltic Sea with Prorocentrum minimum as a special case

In this thesis the role played by expansive and introduced species in the phytoplankton ecology of the Baltic Sea was investigated. The aims were threefold. First, the studies investigated the resting stages of dinoflagellates, which were transported into the Baltic Sea via shipping and were able to germinate under the ambient, nutrient-rich, brackish water conditions. The studies also estimated which factors favoured the occurrence and spread of P. minimum in the Baltic Sea and discussed the identification of this morphologically variable species. In addition, the classification of phytoplankton species recently observed in the Baltic Sea was discussed. Incubation of sediments from four Finnish ports and 10 ships ballast tanks revealed that the sediments act as sources of living dinoflagellates and other phytoplankton. Dinoflagellates germinated from all ports detected and from 90% of ballast tanks. The concentrations of cells germinating from ballast tank sediments were mostly low compared with the acceptable cell concentrations set by the International Maritime Organization s (IMO s) International Convention for the Control and Management of Ships Ballast Water and Sediments. However, the IMO allows such high concentrations of small cells in the discharged ballast water that the total number of cells in large ballast water tanks can be very high. Prorocentrum minimum occurred in the Baltic Sea annually but with no obvious trend in the 10-year timespan from 1993 to 2002. The species occurred under wide ranges of temperatures and salinities and the abundance of the species was positively related especially to the presence of organic nitrogen and phosphorus. This indicated that the species was favoured by increased organic nutrient loading and runoff from land and rivers. The cell shape of P. minimum varied from triangular to oval-round, but morphological fine details indicated that only one morphospecies was present. P. minimum also is, according to present knowledge, the only potentially harmful phytoplankton species that has recently expanded widely into new areas of the Baltic Sea.