Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Independent and mediating organizational commitment effects of trust in leadership on employees' job satisfaction and : a study within social and health care sector

The purpose of this study was to examine whether trust in supervisor and trust in senior management enhance employees' job satisfaction and organizational commitment, and whether trust mediates the relationship between perceived justice and these outcomes. Trust in supervisor was expected to mediate the effects of distributive justice and interactional justice, and trust in senior management was expected to mediate the effects of procedural justice. Theoretical background of the study is based on the framework for trust in leadership developed by Dirks and Ferrin (2002). According to the framework, perceived fairness of leaders' actions helps employees to draw inferences about the basis of the relationship and about leaders' characters. This allows trust formation. Reciprocation of care and concern in the relationship and confidence in leaders' characters are likely to enhance employees' job satisfaction and organizational commitment. This study was conducted with cross-sectional data (A/ = 960) of employees from social and health care sector. Hypotheses were studied using correlation analysis and several hierarchical regression analyses. Significances of the mediations were assessed using the Sobel test. Results partially supported the hypotheses. Trust in leadership was positively related to job satisfaction and organizational commitment. Trust in senior management mediated the relationship between procedural justice and the outcomes. Some support was also found for the mediating effect of trust in supervisor in the relationship between distributive justice and organizational commitment. Due to high correlation between trust in supervisor anil interactional justice, it wasn't possible to study the mediating e fleet of trust in supervisor in the relationship between interactional justice and the outcomes. Against expectations, results indicated that trust in senior management had a mediating effect in the relationship between distributive justice and organizational commitment, and in the relationship between interactional justice and organizational commitment. Results also indicated that trust in supervisor had a mediating effect in the relationship between procedural justice and organizational commitment.

Emerging bioenergy business at Finnish independent industrial sawmills

Finnish forest industry is in the middle of a radical change. Deepening recession and the falling demand of woodworking industry´s traditional products have forced also sawmilling industry to find new and more fertile solutions to improve their operational preconditions. In recent years, the role of bioenergy production has often been highlighted as a part of sawmills´ business repertoire. Sawmilling produces naturally a lot of by-products (e.g. bark, sawdust, chips) which could be exploited more effectively in energy production, and this would bring more incomes or maybe even create new business opportunities for sawmills. Production of bioenergy is also supported by government´s climate and energy policies favouring renewable energy sources, public financial subsidies, and soaring prices of fossil fuels. Also the decreasing production of domestic pulp and paper industry releases a fair amount of sawmills´ by-products for other uses. However, bioenergy production as a part of sawmills´ by-product utilization has been so far researched very little from a managerial point of view. The purpose of this study was to explore the relative significance of the main bioenergy-related processes, resources and factors at Finnish independent industrial sawmills including partnerships, cooperation, customers relationships and investments, and also the future perspectives of bioenergy business at these sawmills with the help of two resource-based approaches (resource-based view, natural-resource-based view). Data of the study comprised of secondary data (e.g. literature), and primary data which was attracted from interviews directed to sawmill managers (or equivalent persons in charge of decisions regarding bioenergy production at sawmill). While a literature review and the Delphi method with two questionnaires were utilized as the methods of the study. According to the results of the study, the most significant processes related to the value chain of bioenergy business are connected to raw material availability and procurement, and customer relationships management. In addition to raw material and services, the most significant resources included factory and machinery, personnel, collaboration, and geographic location. Long-term cooperation deals were clearly valued as the most significant form of collaboration, and especially in processes connected to raw material procurement. Study results also revealed that factors related to demand, subsidies and prices had highest importance in connection with sawmills´ future bioenergy business. However, majority of the respondents required that certain preconditions connected to the above-mentioned factors should be fulfilled before they will continue their bioenergy-related investments. Generally, the answers showed a wide divergence of opinions among the respondents which may refer to sawmills´ different emphases and expectations concerning bioenergy. In other words, bioenergy is still perceived as a quite novel and risky area of business at Finnish independent industrial sawmills. These results indicate that the massive expansion of bioenergy business at private sawmills in Finland is not a self-evident truth. The blocking barriers seem to be connected mainly to demand of bioenergy and money. Respondents´ answers disseminated a growing dissatisfaction towards the policies of authorities, which don´t treat equally sawmill-based bioenergy compared to other forms of bioenergy. This proposition was boiled down in a sawmill manager´s comment: “There is a lot of bioenergy available, if they just want to make use of it.” It seems that the positive effects of government´s policies favouring the renewables are not taking effect at private sawmills. However, as there anyway seems to be a lot of potential connected to emerging bioenergy business at Finnish independent industrial sawmills, there is also a clear need for more profound future studies over this topic.

Characterizing and recognizing weak visibility polygons

A polygon is said to be a weak visibility polygon if every point of the polygon is visible from some point of an internal segment. In this paper we derive properties of shortest paths in weak visibility polygons and present a characterization of weak visibility polygons in terms of shortest paths between vertices. These properties lead to the following efficient algorithms: (i) an O(E) time algorithm for determining whether a simple polygon P is a weak visibility polygon and for computing a visibility chord if it exist, where E is the size of the visibility graph of P and (ii) an O(n2) time algorithm for computing the maximum hidden vertex set in an n-sided polygon weakly visible from a convex edge.

Helsingin lämpösaareke ajallisena ja paikallisena ilmiönä

The urban heat island phenomenon is the most well-known all-year-round urban climate phenomenon. It occurs in summer during the daytime due to the short-wave radiation from the sun and in wintertime, through anthropogenic heat production. In summertime, the properties of the fabric of city buildings determine how much energy is stored, conducted and transmitted through the material. During night-time, when there is no incoming short-wave radiation, all fabrics of the city release the energy in form of heat back to the urban atmosphere. In wintertime anthropogenic heating of buildings and traffic deliver energy into the urban atmosphere. The initial focus of Helsinki urban heat island was on the description of the intensity of the urban heat island (Fogelberg 1973, Alestalo 1975). In this project our goal was to carry out as many measurements as possible over a large area of Helsinki to give a long term estimate of the Helsinki urban heat island. Helsinki is a city with 550 000 inhabitants and located on the north shore of Finnish Bay of the Baltic Sea. Initially, comparison studies against long-term weather station records showed that our regular, but weekly, sampling of observations adequately describe the Helsinki urban heat island. The project covered an entire seasonal cycle over the 12 months from July 2009 to June 2010. The measurements were conducted using a moving platform following microclimatological traditions. Tuesday was selected as the measuring day because it was the only weekday during the one year time span without any public holidays. Once a week, two set of measurements, in total 104, were conducted in the heterogeneous temperature conditions of Helsinki city centre. In the more homogeneous suburban areas, one set of measurements was taken every second week, to give a total of 52.The first set of measurements took place before noon, and the second 12 hours, just prior to midnight. Helsinki Kaisaniemi weather station was chosen as the reference station. This weather station is located in a large park in the city centre of Helsinki. Along the measurement route, 336 fixed points were established, and the monthly air temperature differences to Kaisaniemi were calculated to produce monthly and annual maps. The monthly air temperature differences were interpolated 21.1 km by 18.1 km horizontal grid with 100 metre resolution residual kriging method. The following independent variables for the kriging interpolation method were used: topographical height, portion of sea area, portion of trees, fraction of built-up and not built-up area, volumes of buildings, and population density. The annual mean air temperature difference gives the best representation of the Helsinki urban heat island effect- Due to natural variability of weather conditions during the measurement campaign care must be taken when interpretation the results for the monthly values. The main results of this urban heat island research project are: a) The city centre of Helsinki is warmer than its surroundings, both on a monthly main basis, and for the annual mean, however, there are only a few grid points, 46 out of 38 191, which display a temperature difference of more than 1K. b) If the monthly spatial variation is air temperature differences is small, then usually the temperature difference between the city and the surroundings is also small. c) Isolated large buildings and suburban centres create their own individual heat island. d) The topographical influence on air temperature can generally be neglected for the monthly mean, but can be strong under certain weather conditions.

Processing maps for hot working of Cu-Ni-Zn alloys. Part I - Alpha-nickel silver

The constitutive behaviour of agr — nickel silver in the temperature range 700–950 °C and strain rate range 0.001–100 s–1 was characterized with the help of a processing map generated on the basis of the principles of the ldquodynamic materials modelrdquo of Prasadet al Using the flow stress data, processing maps showing the variation of the efficiency of power dissipation (given by 2m/(m+1) wherem is the strain-rate sensitivity) with temperature and strain rate were obtained, agr-nickel silver exhibits a single domain at temperatures greater than 750 °C and at strain rates lower than 1s–1, with a maximum efficiency of 38% occurring at about 950 °C and at a strain rate of 0.1 s–1. In the domain the material undergoes dynamic recrystallization (DRX). On the basis of a model, it is shown that the DRX is controlled by the rate of interface formation (nucleation) which depends on the diffusion-controlled process of thermal recovery by climb. At high strain rates (10 and 100s–1) the material undergoes microstructural instabilities, the manifestations of which are in the form of adiabatic shear bands and strain markings.

Processing maps for hot working of Cu-Ni-Zn alloys Part II Alpha-Beta nickel silver

The constitutive behaviour of agr-beta nickel silver in the temperature range 600�850 °C and strainrate range 0.001�100s�1 was characterized with the help of a processing map generated on the principles of the dynamic materials model. On the basis of the flow-stress data, processing maps showing the variation of the efficiency of power dissipation (given by [2m/(m+1)], wherem is the strain-rate sensitivity) with temperature and strain rate were obtained, agr-beta nickel silver exhibits a single domain at temperatures greater than 700 °C and at strain rates lower than 1 s�1 with a maximum efficiency of power dissipation of about 42% occurring at about 850 °C and at 0.1 s�1. In the domain, the agr phase undergoes dynamic recrystallization and controls the deformation of the alloy, while the beta phase deforms superplastically. Optimum conditions for the processing of agr-beta nickel silver are 850 °C and 0.1 s�1. The material undergoes unstable flow at strain rates of 10 and 100 s�1 and in the temperature range 600�750 °C, manifestated in the form of adiabatic shear bands.

Maximum-entropy calculation of the electron density at 4 A resolution of Pf1 filamentous bacteriophage

A 4 A electron-density map of Pf1 filamentous bacterial virus has been calculated from x-ray fiber diffraction data by using the maximum-entropy method. This method produces a map that is free of features due to noise in the data and enables incomplete isomorphous-derivative phase information to be supplemented by information about the nature of the solution. The map shows gently curved (banana-shaped) rods of density about 70 A long, oriented roughly parallel to the virion axis but slewing by about 1/6th turn while running from a radius of 28 A to one of 13 A. Within these rods, there is a helical periodicity with a pitch of 5 to 6 A. We interpret these rods to be the helical subunits of the virion. The position of strongly diffracted intensity on the x-ray fiber pattern shows that the basic helix of the virion is right handed and that neighboring nearly parallel protein helices cross one another in an unusual negative sense.

Minimum weight design of fiber-reinforced laminated composite structures with maximum stress and Tsai-Wu failure criteria

In this article, a minimum weight design of carbon/epoxy laminates is carried out using genetic algorithms. New failure envelopes have been developed by the combination of two commonly used phenomenological failure criteria, namely Maximum Stress (MS) and Tsai-Wu (TW) are used to obtain the minimum weight of the laminate. These failure envelopes are the most conservative failure envelope (MCFE) and the least conservative failure envelope (LCFE). Uniaxial and biaxial loading conditions are considered for the study and the differences in the optimal weight of the laminate are compared for the MCFE and LCFE. The MCFE can be used for design of critical load-carrying composites, while the LCFE could be used for the design of composite structures where weight reduction is much more important than safety such as unmanned air vehicles.

The decline of malaria in Finland – the impact of the vector and social variables

Background: Malaria was prevalent in Finland in the 18th century. It declined slowly without deliberate counter-measures and the last indigenous case was reported in 1954. In the present analysis of indigenous malaria in Finland, an effort was made to construct a data set on annual malaria cases of maximum temporal length to be able to evaluate the significance of different factors assumed to affect malaria trends. Methods: To analyse the long-term trend malaria statistics were collected from 1750–2008. During that time, malaria frequency decreased from about 20,000 – 50,000 per 1,000,000 people to less than 1 per 1,000,000 people. To assess the cause of the decline, a correlation analysis was performed between malaria frequency per million people and temperature data, animal husbandry, consolidation of land by redistribution and household size. Results: Anopheles messeae and Anopheles beklemishevi exist only as larvae in June and most of July. The females seek an overwintering place in August. Those that overwinter together with humans may act as vectors. They have to stay in their overwintering place from September to May because of the cold climate. The temperatures between June and July determine the number of malaria cases during the following transmission season. This did not, however, have an impact on the longterm trend of malaria. The change in animal husbandry and reclamation of wetlands may also be excluded as a possible cause for the decline of malaria. The long-term social changes, such as land consolidation and decreasing household size, showed a strong correlation with the decline of Plasmodium. Conclusion: The indigenous malaria in Finland faded out evenly in the whole country during 200 years with limited or no counter-measures or medication. It appears that malaria in Finland was basically a social disease and that malaria trends were strongly linked to changes in human behaviour. Decreasing household size caused fewer interactions between families and accordingly decreasing recolonization possibilities for Plasmodium. The permanent drop of the household size was the precondition for a permanent eradication of malaria.

Seasonal prediction of the Indian monsoon

Under the project `Seasonal Prediction of the Indian Monsoon' (SPIM), the prediction of Indian summer monsoon rainfall by five atmospheric general circulation models (AGCMs) during 1985-2004 was assessed. The project was a collaborative effort of the coordinators and scientists from the different modelling groups across the country. All the runs were made at the Centre for Development of Advanced Computing (CDAC) at Bangalore on the PARAM Padma supercomputing system. Two sets of simulations were made for this purpose. In the first set, the AGCMs were forced by the observed sea surface temperature (SST) for May-September during 1985-2004. In the second set, runs were made for 1987, 1988, 1994, 1997 and 2002 forced by SST which was obtained by assuming that the April anomalies persist during May-September. The results of the first set of runs show, as expected from earlier studies, that none of the models were able to simulate the correct sign of the anomaly of the Indian summer monsoon rainfall for all the years. However, among the five models, one simulated the correct sign in the largest number of years and the second model showed maximum skill in the simulation of the extremes (i.e. droughts or excess rainfall years). The first set of runs showed some common bias which could arise either from an excessive sensitivity of the models to El Nino Southern Oscillation (ENSO) or an inability of the models to simulate the link of the Indian monsoon rainfall to Equatorial Indian Ocean Oscillation (EQUINOO), or both. Analysis of the second set of runs showed that with a weaker ENSO forcing, some models could simulate the link with EQUINOO, suggesting that the errors in the monsoon simulations with observed SST by these models could be attributed to unrealistically high sensitivity to ENSO.

Boxicity and Poset Dimension

Let G be a simple, undirected, finite graph with vertex set V(G) and edge set E(C). A k-dimensional box is a Cartesian product of closed intervals a(1), b(1)] x a(2), b(2)] x ... x a(k), b(k)]. The boxicity of G, box(G) is the minimum integer k such that G can be represented as the intersection graph of k-dimensional boxes, i.e. each vertex is mapped to a k-dimensional box and two vertices are adjacent in G if and only if their corresponding boxes intersect. Let P = (S, P) be a poset where S is the ground set and P is a reflexive, anti-symmetric and transitive binary relation on S. The dimension of P, dim(P) is the minimum integer l such that P can be expressed as the intersection of t total orders. Let G(P) be the underlying comparability graph of P. It is a well-known fact that posets with the same underlying comparability graph have the same dimension. The first result of this paper links the dimension of a poset to the boxicity of its underlying comparability graph. In particular, we show that for any poset P, box(G(P))/(chi(G(P)) - 1) <= dim(P) <= 2box(G(P)), where chi(G(P)) is the chromatic number of G(P) and chi(G(P)) not equal 1. The second result of the paper relates the boxicity of a graph G with a natural partial order associated with its extended double cover, denoted as G(c). Let P-c be the natural height-2 poset associated with G(c) by making A the set of minimal elements and B the set of maximal elements. We show that box(G)/2 <= dim(P-c) <= 2box(G) + 4. These results have some immediate and significant consequences. The upper bound dim(P) <= 2box(G(P)) allows us to derive hitherto unknown upper bounds for poset dimension. In the other direction, using the already known bounds for partial order dimension we get the following: (I) The boxicity of any graph with maximum degree Delta is O(Delta log(2) Delta) which is an improvement over the best known upper bound of Delta(2) + 2. (2) There exist graphs with boxicity Omega(Delta log Delta). This disproves a conjecture that the boxicity of a graph is O(Delta). (3) There exists no polynomial-time algorithm to approximate the boxicity of a bipartite graph on n vertices with a factor of O(n(0.5-epsilon)) for any epsilon > 0, unless NP=ZPP.

A canonical formulation of the direct position kinematics problem for a general 6-6 stewart platform

This paper deals with the direct position kinematics problem of a general 6-6 Stewart platform, the complete solution of which is not reported in the literature until now and even establishing the number of possible solutions for the general case has remained an unsolved problem for a long period. Here a canonical formulation of the direct position kinematics problem for a general 6-6 Stewart platform is presented. The kinematic equations are expressed as a system of six quadratic and three linear equations in nine unknowns, which has a maximum of 64 solutions. Thus, it is established that the mechanism, in general, can have up to 64 closures. Further reduction of the system is shown arriving at a set of three quartic equations in three unknowns, the solution of which will yield the assembly configurations of the general Stewart platform with far less computational effort compared to earlier models.