Inferring molecular function: contributions from functional linkages

In the current era of high-throughput sequencing and structure determination, functional annotation has become a bottleneck in biomedical science. Here, we show that automated inference of molecular function using functional linkages among genes increases the accuracy of functional assignments by >= 8% and enriches functional descriptions in >= 34% of top assignments. Furthermore, biochemical literature supports >80% of automated inferences for previously unannotated proteins. These results emphasize the benefit of incorporating functional linkages in protein annotation.

Synthesis of plane linkages to generate functions of two variables using point-position reduction—Part 1. Rotary inputs and output

The paper presents simple graphical procedures for position synthesis of plane linkage mechanisms to generate functions of two independent variables. The procedures are based on point-position reduction and permit synthesis of the linkage to satisfy up to six arbitrarily selected precision positions.

Synthesis of plane linkages to generate functions of two variables using point position reduction—II. Sliding inputs and outputs

The paper presents simple graphical procedures for the position synthesis of plane linkage mechanisms with sliding inputs and output to generate functions of two independent variables. The procedures are based on point position reduction and permit synthesis of the linkage to satisfy up to five arbitrarily selected precision positions.

Essays on the Linkages Between Financial Markets, and Risk Asymmetries (summary section only)

During the last few decades there have been far going financial market deregulation, technical development, advances in information technology, and standardization of legislation between countries. As a result, one can expect that financial markets have grown more interlinked. The proper understanding of the cross-market linkages has implications for investment and risk management, diversification, asset pricing, and regulation. The purpose of this research is to assess the degree of price, return, and volatility linkages between both geographic markets and asset categories within one country, Finland. Another purpose is to analyze risk asymmetries, i.e., the tendency of equity risk to be higher after negative events than after positive events of equal magnitude. The analysis is conducted both with respect to total risk (volatility), and systematic risk (beta). The thesis consists of an introductory part and four essays. The first essay studies to which extent international stock prices comove. The degree of comovements is low, indicating benefits from international diversification. The second essay examines the degree to which the Finnish market is linked to the “world market”. The total risk is divided into two parts, one relating to world factors, and one relating to domestic factors. The impact of world factors has increased over time. After 1993, when foreign investors were allowed to freely invest in Finnish assets, the risk level has been higher than previously. This was also the case during the economic recession in the beginning of the 1990’s. The third essay focuses on the stock, bond, and money markets in Finland. According to a trading model, the degree of volatility linkages should be strong. However, the results contradict this. The linkages are surprisingly weak, even negative. The stock market is the most independent, while the money market is affected by events on the two other markets. The fourth essay concentrates on volatility and beta asymmetries. Contrary to many international studies there are only few cases of risk asymmetries. When they occur, they tend to be driven by the market-wide component rather than the portfolio specific element.

The Organisation of Policy Meets the Commercialisation of Sex - Global Linkages, Policies, Technologies

During recent years the commercialisation of sex has increased and intensified both locally and globally. This thesis explores the commercialisation of bodies, sex and sexualities, particularly the sex trade, and the impact of rapidly evolving information and communication technologies on this globalising trade. The main focus of this work is on the policies, discourses and policy developments in the area especially in the Finnish context. The study is based on multidisciplinary theoretical sources through which the framework of multiple linkages relevant to the commercialisation of sex is conceptualised. The sex trade functions through a web of intersecting linkages of a substantive, economic, organisational, temporal, spatial, cultural, technological, as well as of legislative and policy nature. This framework of linkages forms the basis for the analysis of the main empirical data, namely qualitative interviews with thirty key managers and professionals, who are responsible for the preparation and implementation of policies on commercial sex. In addition, the thesis addresses the policies and policy practices on the sex trade through the analysis of national and international policy instruments. In addition to analysing the processes of the commercialisation of sex and its effects, the study also discusses their further implications for organisational policy-making, research, and society more generally. The thesis thus seeks to contribute to practice, research and theory on gender, management and organisations.

Intraday Linkages across International Equity Markets

Utilizing concurrent 5-minute returns, the intraday dynamics and inter-market dependencies in international equity markets were investigated. A strong intraday cyclical autocorrelation structure in the volatility process was observed to be caused by the diurnal pattern. A major rise in contemporaneous cross correlation among European stock markets was also noticed to follow the opening of the New York Stock Exchange. Furthermore, the results indicated that the returns for UK and Germany responded to each other’s innovations, both in terms of the first and second moment dependencies. In contrast to earlier research, the US stock market did not cause significant volatility spillover to the European markets.

Functional linkages can reveal protein complexes for structure determination

The study of molecular machines, and protein complexes in general, is a growth area of biology. Is there a computational method for inferring which combinations of proteins in an organism are likely to form a crystallizable complex? We use the Protein Data Bank (PDB) to assess the usefulness of inferred functional protein linkages for this task. We find that of 242 nonredundant prokaryotic protein complexes (complexes excluding structural variants of the same protein) from organisms that are shared between the current PDB and the Prolinks functional linkage database, 44% (107/242) contain proteins that are linked at high-confidence by one or more methods of computed functional linkages. This suggests that computing functional linkages will be useful in defining protein complexes for structural studies. We offer a database of such inferred linkages corresponding to likely protein complexes for some 629,952 pairs of proteins in 154 prokaryotes and archea.

3-D Warping in Four-Bar Laminated Linkages

This paper deals with the evaluation of the component-laminate load-carrying capacity, i.e., to calculate the loads that cause the failure of the individual layers and the component-laminate as a whole in four-bar mechanism. The component-laminate load-carrying capacity is evaluated using the Tsai-Wu-Hahn failure criterion for various layups. The reserve factor of each ply in the component-laminate is calculated by using the maximum resultant force and the maximum resultant moment occurring at different time steps at the joints of the mechanism. Here, all component bars of the mechanism are made of fiber reinforced laminates and have thin rectangular cross-sections. They could, in general, be pre-twisted and/or possess initial curvature, either by design or by defect. They are linked to each other by means of revolute joints. We restrict ourselves to linear materials with small strains within each elastic body (beam). Each component of the mechanism is modeled as a beam based on geometrically nonlinear 3-D elasticity theory. The component problems are thus split into 2-D analyses of reference beam cross-sections and nonlinear 1-D analyses along the three beam reference curves. For the thin rectangular cross-sections considered here, the 2-D cross-sectional nonlinearity is also overwhelming. This can be perceived from the fact that such sections constitute a limiting case between thin-walled open and closed sections, thus inviting the nonlinear phenomena observed in both. The strong elastic couplings of anisotropic composite laminates complicate the model further. However, a powerful mathematical tool called the Variational Asymptotic Method (VAM) not only enables such a dimensional reduction, but also provides asymptotically correct analytical solutions to the nonlinear cross-sectional analysis. Such closed-form solutions are used here in conjunction with numerical techniques for the rest of the problem to predict more quickly and accurately than would otherwise be possible. Local 3-D stress, strain and displacement fields for representative sections in the component-bars are recovered, based on the stress resultants from the 1-D global beam analysis. A numerical example is presented which illustrates the failure of each component-laminate and the mechanism as a whole.

Polymers containing disulfide, tetrasulfide, diselenide and ditelluride linkages in the main chain

The present review articulates the syntheses and properties of industrially important disulfide and tetrasulfide polymers. The diselenide and ditelluride polymers have also been reviewed, for the first time, so that a comprehensive view on the polymers containing group VIA elements can be obtained. The latter two polymers are gaining considerable current attention due to their semi-conducting properties. The emphasis has been made to sift through the developments in the last ten years or so to get the latest flavour in these rapidly developing polymers. We have also attempted to bring to the fore several contradicting results, like, for example, the crystallinity of ditelluride polymers, to clear the mist in such reports. We hope that this review will help those working in the field to assess the progress achieved in this area and that it may also provide useful orientation for those who wish to become involved.

Synthesis of novel cationic lipids with fully or partially non-scissile linkages between the hydrocarbon chains and pseudoglyceryl backbone

Five novel cationic lipids with fully or partially non-scissile linkage regions between the pseudoglyceryl backbone and the hydrocarbon chains have been synthesized. The membrane-forming properties of these new lipids are briefly presented.

Static Balancing of Spring-loaded Planar Revolute-joint Linkages without Auxiliary Links

We present a method to statically balance a general treestructured,planar revolute-joint linkage loaded with linear springs or constant forces without using auxiliary links. The balancing methods currently documented in the literature use extra links; some do not apply when there are spring loads and some are restricted to only two-link serial chains. In our method, we suitably combine any non-zero-free-length load spring with another spring to result in an effective zero-free-length spring load. If a link has a single joint (with the parent link), we give a procedure to attach extra zero-free-length springs to it so that forces and moments are balanced for the link. Another consequence of this attachment is that the constraint force of the joint on the parent link becomes equivalent to a zero-free-length spring load. Hence, conceptually,for the parent link, the joint with its child is removed and replaced with the zero-free-length spring. This feature allows recursive application of this procedure from the end-branches of the tree down to the root, satisfying force and moment balance of all the links in the process. Furthermore, this method can easily be extended to the closed-loop revolute-joint linkages, which is also illustrated in the paper.

Perfect Static Balance of Linkages by Addition of Springs But Not Auxiliary Bodies

A linkage of rigid bodies under gravity loads can be statically counter-balanced by adding compensating gravity loads. Similarly, gravity loads or spring loads can be counterbalanced by adding springs. In the current literature, among the techniques that add springs, some achieve perfect static balance while others achieve only approximate balance. Further, all of them add auxiliary bodies to the linkage in addition to springs. We present a perfect static balancing technique that adds only springs but not auxiliary bodies, in contrast to the existing techniques. This technique can counter-balance both gravity loads and spring loads. The technique requires that every joint that connects two bodies in the linkage be either a revolute joint or a spherical joint. Apart from this, the linkage can have any number of bodies connected in any manner. In order to achieve perfect balance, this technique requires that all the spring loads have the feature of zero-free-length, as is the case with the existing techniques. This requirement is neither impractical nor restrictive since the feature can be practically incorporated into any normal spring either by modifying the spring or by adding another spring in parallel. DOI: 10.1115/1.4006521]