CsrA interacting small RNAs in Haemophilus spp genomes: a theoretical analysis

The csrA is a carbon storage regulator gene that encodes a protein with multiple RNA interaction sites. Bacterial non-coding small RNAs like csrB, csrC and their counterparts in diverse bacterial genus are identified to control the regulatory activities of CsrA and its orthologs. An attempt has been made in this study to identify 'novel' non-coding small RNAs that are involved in the regulatory activities of csrA gene. All CsrA-interacting small RNAs are computationally fingerprinted to have multiple occurrence of 7-nucleotide CsrA interacting repeats [CAGGA(U/A/C)G] along with a 18-nucleotide upstream binding site. However, in several of the genomes like Haemophilus spp, the upstream binding site is not identified. The current methodology overcomes this difficulty by identifying small RNA-specific orphan transcriptional units within the intergenic regions of the genome. The results could identify all known CsrA-interacting small RNAs in E. coli, Vibrio cholerae and Pseudomonas aeruginosa genomes and additionally has picked six new possible CsrA-interacting small RNA regions in E. coli. Our computational analysis indicates that known rygD and rprA sRNAs in E. coli could possibly interact with CsrA proteins. The study is extended to three of the Haemophilus genomes that could identify seven new possible CsrA interacting small RNAs.

Development of probabilistic understanding in fourth grade

We analyzed the development of 4th-grade students’ understanding of the transition from experimental relative frequencies of outcomes to theoretical probabilities with a focus on the foundational statistical concepts of variation and expectation. We report students’ initial and changing expectations of the outcomes of tossing one and two coins, how they related the relative frequency from their physical and computersimulated trials to the theoretical probability, and how they created and interpreted theoretical probability models. Findings include students’ progression from an initial apparent equiprobability bias in predicting outcomes of tossing two coins through to representing the outcomes of increasing the number of trials. After observing the decreasing variation from the theoretical probability as the sample size increased, students developed a deeper understanding of the relationship between relative frequency of outcomes and theoretical probability as well as their respective associations with variation and expectation. Students’ final models indicated increasing levels of probabilistic understanding.

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P (1) over bar and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H center dot center dot center dot(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H center dot center dot center dot S, one C-H center dot center dot center dot N, and one C-H center dot center dot center dot C-pi. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.

Estimation of thermal breakdown voltage of HVDC cables - A theoretical framework

The insulation in a dc cable is subjected to both thermal and electric stress at the same time. While the electric stress is generic to the cable, the temperature rise in the insulation is, by and large, due to the Ohmic losses in the conductor. The consequence of this synergic effect is to reduce the maximum operating voltage and causes a premature failure of the cable. The authors examine this subject in some detail and propose a comprehensive theoretical formulation relating the maximum thermal voltage (MTV) to the physical and geometrical parameters of the insulation. The heat flow patterns and boundary conditions considered by the authors here and those found in earlier literature are provided. The MTV of a dc cable is shown to be a function of the load current apart from the resistance of the insulation. The results obtained using the expressions, developed by the authors, are compared with relevant results published in the literature and found to be in close conformity.

On the mechanical behavior of compacted pack ice : A theoretical and numerical investigation

Pack ice is an aggregate of ice floes drifting on the sea surface. The forces controlling the motion and deformation of pack ice are air and water drag forces, sea surface tilt, Coriolis force and the internal force due to the interaction between ice floes. In this thesis, the mechanical behavior of compacted pack ice is investigated using theoretical and numerical methods, focusing on the three basic material properties: compressive strength, yield curve and flow rule. A high-resolution three-category sea ice model is applied to investigate the sea ice dynamics in two small basins, the whole Gulf Riga and the inside Pärnu Bay, focusing on the calibration of the compressive strength for thin ice. These two basins are on the scales of 100 km and 20 km, respectively, with typical ice thickness of 10-30 cm. The model is found capable of capturing the main characteristics of the ice dynamics. The compressive strength is calibrated to be about 30 kPa, consistent with the values from most large-scale sea ice dynamic studies. In addition, the numerical study in Pärnu Bay suggests that the shear strength drops significantly when the ice-floe size markedly decreases. A characteristic inversion method is developed to probe the yield curve of compacted pack ice. The basis of this method is the relationship between the intersection angle of linear kinematic features (LKFs) in sea ice and the slope of the yield curve. A summary of the observed LKFs shows that they can be basically divided into three groups: intersecting leads, uniaxial opening leads and uniaxial pressure ridges. Based on the available observed angles, the yield curve is determined to be a curved diamond. Comparisons of this yield curve with those from other methods show that it possesses almost all the advantages identified by the other methods. A new constitutive law is proposed, where the yield curve is a diamond and the flow rule is a combination of the normal and co-axial flow rule. The non-normal co-axial flow rule is necessary for the Coulombic yield constraint. This constitutive law not only captures the main features of forming LKFs but also takes the advantage of avoiding overestimating divergence during shear deformation. Moreover, this study provides a method for observing the flow rule for pack ice during deformation.

Theoretical modeling of ionospheric electrodynamics including induction effects

This thesis deals with theoretical modeling of the electrodynamics of auroral ionospheres. In the five research articles forming the main part of the thesis we have concentrated on two main themes: Development of new data-analysis techniques and study of inductive phenomena in the ionospheric electrodynamics. The introductory part of the thesis provides a background for these new results and places them in the wider context of ionospheric research. In this thesis we have developed a new tool (called 1D SECS) for analysing ground based magnetic measurements from a 1-dimensional magnetometer chain (usually aligned in the North-South direction) and a new method for obtaining ionospheric electric field from combined ground based magnetic measurements and estimated ionospheric electric conductance. Both these methods are based on earlier work, but contain important new features: 1D SECS respects the spherical geometry of large scale ionospheric electrojet systems and due to an innovative way of implementing boundary conditions the new method for obtaining electric fields can be applied also at local scale studies. These new calculation methods have been tested using both simulated and real data. The tests indicate that the new methods are more reliable than the previous techniques. Inductive phenomena are intimately related to temporal changes in electric currents. As the large scale ionospheric current systems change relatively slowly, in time scales of several minutes or hours, inductive effects are usually assumed to be negligible. However, during the past ten years, it has been realised that induction can play an important part in some ionospheric phenomena. In this thesis we have studied the role of inductive electric fields and currents in ionospheric electrodynamics. We have formulated the induction problem so that only ionospheric electric parameters are used in the calculations. This is in contrast to previous studies, which require knowledge of the magnetospheric-ionosphere coupling. We have applied our technique to several realistic models of typical auroral phenomena. The results indicate that inductive electric fields and currents are locally important during the most dynamical phenomena (like the westward travelling surge, WTS). In these situations induction may locally contribute up to 20-30% of the total ionospheric electric field and currents. Inductive phenomena do also change the field-aligned currents flowing between the ionosphere and magnetosphere, thus modifying the coupling between the two regions.

Mathematics, nature and cryptography: Insights from philosophy of information

One influential image that is popular among scientists is the view that mathematics is the language of nature. The present article discusses another possible way to approach the relation between mathematics and nature, which is by using the idea of information and the conceptual vocabulary of cryptography. This approach allows us to understand the possibility that secrets of nature need not be written in mathematics and yet mathematics is necessary as a cryptographic key to unlock these secrets. Various advantages of such a view are described in this article.

Synthesis and Characterization of a Class of Donor-Acceptor Conjugated Molecules: Experiments and Theoretical Calculations

A class of conjugated molecules containing donor (thiophene) and acceptor (malononitrile) is synthesized by Knoevenagel condensation reaction between 2-(2,6-dimethy1-4H-pyran-4-ylidene) malononitrile and thiophene carbaldehyde containing two and three thiophene units. The resulting molecules are characterized by H-1 and C-13 NMR. We have performed UV-vis absorption, fluorescence, and cyclic voltammetry measurements on these materials. The spectroscopic and electrochemical measurements proved beyond doubt that these materials possess lowexcitation gap and are suitable for being an active material in various electronic devices. We have also performed electronic structure calculations using density functional theory (DFT) and INDO/SCI methods to characterize the ground and excited states of this class of molecules. These donor-acceptor molecules show a strong charge transfercharacter that increases with the increase in the number of thiophene rings coupled to the malononitrile acceptor moiety. We have also calculated the pi-coherence length, Stoke's shift, and effect of solvents on excited states for this class of molecules, Our theoretical values agree well with experimental results.

Theoretical and computational approaches on heterogeneous nucleation

Nucleation is the first step of a first order phase transition. A new phase is always sprung up in nucleation phenomena. The two main categories of nucleation are homogeneous nucleation, where the new phase is formed in a uniform substance, and heterogeneous nucleation, when nucleation occurs on a pre-existing surface. In this thesis the main attention is paid on heterogeneous nucleation. This thesis wields the nucleation phenomena from two theoretical perspectives: the classical nucleation theory and the statistical mechanical approach. The formulation of the classical nucleation theory relies on equilibrium thermodynamics and use of macroscopically determined quantities to describe the properties of small nuclei, sometimes consisting of just a few molecules. The statistical mechanical approach is based on interactions between single molecules, and does not bear the same assumptions as the classical theory. This work gathers up the present theoretical knowledge of heterogeneous nucleation and utilizes it in computational model studies. A new exact molecular approach on heterogeneous nucleation was introduced and tested by Monte Carlo simulations. The results obtained from the molecular simulations were interpreted by means of the concepts of the classical nucleation theory. Numerical calculations were carried out for a variety of substances nucleating on different substances. The classical theory of heterogeneous nucleation was employed in calculations of one-component nucleation of water on newsprint paper, Teflon and cellulose film, and binary nucleation of water-n-propanol and water-sulphuric acid mixtures on silver nanoparticles. The results were compared with experimental results. The molecular simulation studies involved homogeneous nucleation of argon and heterogeneous nucleation of argon on a planar platinum surface. It was found out that the use of a microscopical contact angle as a fitting parameter in calculations based on the classical theory of heterogeneous nucleation leads to a fair agreement between the theoretical predictions and experimental results. In the presented cases the microscopical angle was found to be always smaller than the contact angle obtained from macroscopical measurements. Furthermore, molecular Monte Carlo simulations revealed that the concept of the geometrical contact parameter in heterogeneous nucleation calculations can work surprisingly well even for very small clusters.

Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

The Media and the Academic Globalization Debate : Theoretical Analysis and Critique

This study offers a reconstruction and critical evaluation of globalization theory, a perspective that has been central for sociology and cultural studies in recent decades, from the viewpoint of media and communications. As the study shows, sociological and cultural globalization theorists rely heavily on arguments concerning media and communications, especially the so-called new information and communication technologies, in the construction of their frameworks. Together with deepening the understanding of globalization theory, the study gives new critical knowledge of the problematic consequences that follow from such strong investment in media and communications in contemporary theory. The book is divided into four parts. The first part presents the research problem, the approach and the theoretical contexts of the study. Followed by the introduction in Chapter 1, I identify the core elements of globalization theory in Chapter 2. At the heart of globalization theory is the claim that recent decades have witnessed massive changes in the spatio-temporal constitution of society, caused by new media and communications in particular, and that these changes necessitate the rethinking of the foundations of social theory as a whole. Chapter 3 introduces three paradigms of media research the political economy of media, cultural studies and medium theory the discussion of which will make it easier to understand the key issues and controversies that emerge in academic globalization theorists treatment of media and communications. The next two parts offer a close reading of four theorists whose works I use as entry points into academic debates on globalization. I argue that we can make sense of mainstream positions on globalization by dividing them into two paradigms: on the one hand, media-technological explanations of globalization and, on the other, cultural globalization theory. As examples of the former, I discuss the works of Manuel Castells (Chapter 4) and Scott Lash (Chapter 5). I maintain that their analyses of globalization processes are overtly media-centric and result in an unhistorical and uncritical understanding of social power in an era of capitalist globalization. A related evaluation of the second paradigm (cultural globalization theory), as exemplified by Arjun Appadurai and John Tomlinson, is presented in Chapter 6. I argue that due to their rejection of the importance of nation states and the notion of cultural imperialism for cultural analysis, and their replacement with a framework of media-generated deterritorializations and flows, these theorists underplay the importance of the neoliberalization of cultures throughout the world. The fourth part (Chapter 7) presents a central research finding of this study, namely that the media-centrism of globalization theory can be understood in the context of the emergence of neoliberalism. I find it problematic that at the same time when capitalist dynamics have been strengthened in social and cultural life, advocates of globalization theory have directed attention to media-technological changes and their sweeping socio-cultural consequences, instead of analyzing the powerful material forces that shape the society and the culture. I further argue that this shift serves not only analytical but also utopian functions, that is, the longing for a better world in times when such longing is otherwise considered impracticable.

Generalised regression estimation for domain class frequencies

This study examines the properties of Generalised Regression (GREG) estimators for domain class frequencies and proportions. The family of GREG estimators forms the class of design-based model-assisted estimators. All GREG estimators utilise auxiliary information via modelling. The classic GREG estimator with a linear fixed effects assisting model (GREG-lin) is one example. But when estimating class frequencies, the study variable is binary or polytomous. Therefore logistic-type assisting models (e.g. logistic or probit model) should be preferred over the linear one. However, other GREG estimators than GREG-lin are rarely used, and knowledge about their properties is limited. This study examines the properties of L-GREG estimators, which are GREG estimators with fixed-effects logistic-type models. Three research questions are addressed. First, I study whether and when L-GREG estimators are more accurate than GREG-lin. Theoretical results and Monte Carlo experiments which cover both equal and unequal probability sampling designs and a wide variety of model formulations show that in standard situations, the difference between L-GREG and GREG-lin is small. But in the case of a strong assisting model, two interesting situations arise: if the domain sample size is reasonably large, L-GREG is more accurate than GREG-lin, and if the domain sample size is very small, estimation of assisting model parameters may be inaccurate, resulting in bias for L-GREG. Second, I study variance estimation for the L-GREG estimators. The standard variance estimator (S) for all GREG estimators resembles the Sen-Yates-Grundy variance estimator, but it is a double sum of prediction errors, not of the observed values of the study variable. Monte Carlo experiments show that S underestimates the variance of L-GREG especially if the domain sample size is minor, or if the assisting model is strong. Third, since the standard variance estimator S often fails for the L-GREG estimators, I propose a new augmented variance estimator (A). The difference between S and the new estimator A is that the latter takes into account the difference between the sample fit model and the census fit model. In Monte Carlo experiments, the new estimator A outperformed the standard estimator S in terms of bias, root mean square error and coverage rate. Thus the new estimator provides a good alternative to the standard estimator.

Communicative and Anticipatory Decision-making Supported by Bayesian Networks

The purpose of this research is to draw up a clear construction of an anticipatory communicative decision-making process and a successful implementation of a Bayesian application that can be used as an anticipatory communicative decision-making support system. This study is a decision-oriented and constructive research project, and it includes examples of simulated situations. As a basis for further methodological discussion about different approaches to management research, in this research, a decision-oriented approach is used, which is based on mathematics and logic, and it is intended to develop problem solving methods. The approach is theoretical and characteristic of normative management science research. Also, the approach of this study is constructive. An essential part of the constructive approach is to tie the problem to its solution with theoretical knowledge. Firstly, the basic definitions and behaviours of an anticipatory management and managerial communication are provided. These descriptions include discussions of the research environment and formed management processes. These issues define and explain the background to further research. Secondly, it is processed to managerial communication and anticipatory decision-making based on preparation, problem solution, and solution search, which are also related to risk management analysis. After that, a solution to the decision-making support application is formed, using four different Bayesian methods, as follows: the Bayesian network, the influence diagram, the qualitative probabilistic network, and the time critical dynamic network. The purpose of the discussion is not to discuss different theories but to explain the theories which are being implemented. Finally, an application of Bayesian networks to the research problem is presented. The usefulness of the prepared model in examining a problem and the represented results of research is shown. The theoretical contribution includes definitions and a model of anticipatory decision-making. The main theoretical contribution of this study has been to develop a process for anticipatory decision-making that includes management with communication, problem-solving, and the improvement of knowledge. The practical contribution includes a Bayesian Decision Support Model, which is based on Bayesian influenced diagrams. The main contributions of this research are two developed processes, one for anticipatory decision-making, and the other to produce a model of a Bayesian network for anticipatory decision-making. In summary, this research contributes to decision-making support by being one of the few publicly available academic descriptions of the anticipatory decision support system, by representing a Bayesian model that is grounded on firm theoretical discussion, by publishing algorithms suitable for decision-making support, and by defining the idea of anticipatory decision-making for a parallel version. Finally, according to the results of research, an analysis of anticipatory management for planned decision-making is presented, which is based on observation of environment, analysis of weak signals, and alternatives to creative problem solving and communication.

Methodological perspectives for register-based health system performance assessment : Developing a hip fracture monitoring system in Finland

The resources of health systems are limited. There is a need for information concerning the performance of the health system for the purposes of decision-making. This study is about utilization of administrative registers in the context of health system performance evaluation. In order to address this issue, a multidisciplinary methodological framework for register-based data analysis is defined. Because the fixed structure of register-based data indirectly determines constraints on the theoretical constructs, it is essential to elaborate the whole analytic process with respect to the data. The fundamental methodological concepts and theories are synthesized into a data sensitive approach which helps to understand and overcome the problems that are likely to be encountered during a register-based data analyzing process. A pragmatically useful health system performance monitoring should produce valid information about the volume of the problems, about the use of services and about the effectiveness of provided services. A conceptual model for hip fracture performance assessment is constructed and the validity of Finnish registers as a data source for the purposes of performance assessment of hip fracture treatment is confirmed. Solutions to several pragmatic problems related to the development of a register-based hip fracture incidence surveillance system are proposed. The monitoring of effectiveness of treatment is shown to be possible in terms of care episodes. Finally, an example on the justification of a more detailed performance indicator to be used in the profiling of providers is given. In conclusion, it is possible to produce useful and valid information on health system performance by using Finnish register-based data. However, that seems to be far more complicated than is typically assumed. The perspectives given in this study introduce a necessary basis for further work and help in the routine implementation of a hip fracture monitoring system in Finland.