The structures of ethyl 1,2,2-tricyano-3,3-dimethylcyclopropane-1-carboxylate and ethyl 2',3,3'-tricyanocyclohexanespirocyclopropane-2'-carboxylate

The crystal and molecular structures of C ,,H,IN302 (I) and C14HIsN302 (II) have been determined by direct methods using three-dimensional X-ray diffractometer data. Crystals of (I) are orthorhombic, space group Pna21, with a = 14.662(6), b = 10.492(5), c = 7.375 (3)A, Z = 4, V = 1134.5 A 3, D O = 1.25 (by flotation), D e = 1.269 Mgm -a, g(MoKa) = 0.085 mm -1. Crystals of (II) are monoclinic, space group P21/a, with a = 7.886 (5), b = 22.011 (8), c = 8.100 (3) A, fl = 103.12 (5) °, Z = 4, V = 1369.2 A 3, D O = 1.23 (by flotation), D e = 1.255 Mg m -3, g(Mo Kct) = 0.080 mm -1. Least-squares full-matrix refinement based on 782 (I) and 1400 independent reflections (II) converged at R = 0.040 (I) and 0.042 (II). The effect of electron-withdrawing substituents on the geometry of the cyclopropane ring is discussed.

Discovering hidden structures in molecular data using a Bayesian partition model approach

Advancements in the analysis techniques have led to a rapid accumulation of biological data in databases. Such data often are in the form of sequences of observations, examples including DNA sequences and amino acid sequences of proteins. The scale and quality of the data give promises of answering various biologically relevant questions in more detail than what has been possible before. For example, one may wish to identify areas in an amino acid sequence, which are important for the function of the corresponding protein, or investigate how characteristics on the level of DNA sequence affect the adaptation of a bacterial species to its environment. Many of the interesting questions are intimately associated with the understanding of the evolutionary relationships among the items under consideration. The aim of this work is to develop novel statistical models and computational techniques to meet with the challenge of deriving meaning from the increasing amounts of data. Our main concern is on modeling the evolutionary relationships based on the observed molecular data. We operate within a Bayesian statistical framework, which allows a probabilistic quantification of the uncertainties related to a particular solution. As the basis of our modeling approach we utilize a partition model, which is used to describe the structure of data by appropriately dividing the data items into clusters of related items. Generalizations and modifications of the partition model are developed and applied to various problems. Large-scale data sets provide also a computational challenge. The models used to describe the data must be realistic enough to capture the essential features of the current modeling task but, at the same time, simple enough to make it possible to carry out the inference in practice. The partition model fulfills these two requirements. The problem-specific features can be taken into account by modifying the prior probability distributions of the model parameters. The computational efficiency stems from the ability to integrate out the parameters of the partition model analytically, which enables the use of efficient stochastic search algorithms.

Paleomagnetic and rock magnetic study with emphasis on the Precambrian intrusions and impact structures in Fennoscandia and South Africa

The importance of supercontinents in our understanding of the geological evolution of the planet Earth has been recently emphasized. The role of paleomagnetism in reconstructing lithospheric blocks in their ancient paleopositions is vital. Paleomagnetism is the only quantitative tool for providing ancient latitudes and azimuthal orientations of continents. It also yields information of content of the geomagnetic field in the past. In order to obtain a continuous record on the positions of continents, dated intrusive rocks are required in temporal progression. This is not always possible due to pulse-like occurrences of dykes. In this work we demonstrate that studies of meteorite impact-related rocks may fill some gaps in the paleomagnetic record. This dissertation is based on paleomagnetic and rock magnetic data obtained from samples of the Jänisjärvi impact structure (Russian Karelia, most recent 40Ar-39Ar age of 682 Ma), the Salla diabase dyke (North Finland, U-Pb 1122 Ma), the Valaam monzodioritic sill (Russian Karelia, U-Pb 1458 Ma), and the Vredefort impact structure (South Africa, 2023 Ma). The paleomagnetic study of Jänisjärvi samples was made in order to obtain a pole for Baltica, which lacks paleomagnetic data from 750 to ca. 600 Ma. The position of Baltica at ca. 700 Ma is relevant in order to verify whether the supercontinent Rodinia was already fragmented. The paleomagnetic study of the Salla dyke was conducted to examine the position of Baltica at the onset of supercontinent Rodinia's formation. The virtual geomagnetic pole (VGP) from Salla dyke provides hints that the Mesoproterozoic Baltica - Laurentia unity in the Hudsonland (Columbia, Nuna) supercontinent assembly may have lasted until 1.12 Ga. Moreover, the new VGP of Salla dyke provides new constraint on the timing of the rotation of Baltica relative to Laurentia (e.g. Gower et al., 1990). A paleomagnetic study of the Valaam sill was carried out in order to shed light into the question of existence of Baltica-Laurentia unity in the supercontinent Hudsonland. Combined with results from dyke complex of the Lake Ladoga region (Schehrbakova et al., 2008) a new robust paleomagnetic pole for Baltica is obtained. This pole places Baltica on a latitude of 10°. This low latitude location is supported also by Mesoproterozoic 1.5 1.3 Ga red-bed sedimentation (for example the Satakunta sandstone). The Vredefort impactite samples provide a well dated (2.02 Ga) pole for the Kaapvaal Craton. Rock magnetic data reveal unusually high Koenigsberger ratios (Q values) in all studied lithologies of the Vredefort dome. The high Q values are now first time also seen in samples from the Johannesburg Dome (ca. 120 km away) where there is no impact evidence. Thus, a direct causative link of high Q values to the Vredefort impact event can be ruled out.

Homogeneous model theory of metric structures

This thesis studies homogeneous classes of complete metric spaces. Over the past few decades model theory has been extended to cover a variety of nonelementary frameworks. Shelah introduced the abstact elementary classes (AEC) in the 1980s as a common framework for the study of nonelementary classes. Another direction of extension has been the development of model theory for metric structures. This thesis takes a step in the direction of combining these two by introducing an AEC-like setting for studying metric structures. To find balance between generality and the possibility to develop stability theoretic tools, we work in a homogeneous context, thus extending the usual compact approach. The homogeneous context enables the application of stability theoretic tools developed in discrete homogeneous model theory. Using these we prove categoricity transfer theorems for homogeneous metric structures with respect to isometric isomorphisms. We also show how generalized isomorphisms can be added to the class, giving a model theoretic approach to, e.g., Banach space isomorphisms or operator approximations. The novelty is the built-in treatment of these generalized isomorphisms making, e.g., stability up to perturbation the natural stability notion. With respect to these generalized isomorphisms we develop a notion of independence. It behaves well already for structures which are omega-stable up to perturbation and coincides with the one from classical homogeneous model theory over saturated enough models. We also introduce a notion of isolation and prove dominance for it.

Mathematical models on the impact of noise and dyadic molecular structures on the properties of a cardiac myocyte

In cardiac myocytes (heart muscle cells), coupling of electric signal known as the action potential to contraction of the heart depends crucially on calcium-induced calcium release (CICR) in a microdomain known as the dyad. During CICR, the peak number of free calcium ions (Ca) present in the dyad is small, typically estimated to be within range 1-100. Since the free Ca ions mediate CICR, noise in Ca signaling due to the small number of free calcium ions influences Excitation-Contraction (EC) coupling gain. Noise in Ca signaling is only one noise type influencing cardiac myocytes, e.g., ion channels playing a central role in action potential propagation are stochastic machines, each of which gates more or less randomly, which produces gating noise present in membrane currents. How various noise sources influence macroscopic properties of a myocyte, how noise is attenuated and taken advantage of are largely open questions. In this thesis, the impact of noise on CICR, EC coupling and, more generally, macroscopic properties of a cardiac myocyte is investigated at multiple levels of detail using mathematical models. Complementarily to the investigation of the impact of noise on CICR, computationally-efficient yet spatially-detailed models of CICR are developed. The results of this thesis show that (1) gating noise due to the high-activity mode of L-type calcium channels playing a major role in CICR may induce early after-depolarizations associated with polymorphic tachycardia, which is a frequent precursor to sudden cardiac death in heart failure patients; (2) an increased level of voltage noise typically increases action potential duration and it skews distribution of action potential durations toward long durations in cardiac myocytes; and that (3) while a small number of Ca ions mediate CICR, Excitation-Contraction coupling is robust against this noise source, partly due to the shape of ryanodine receptor protein structures present in the cardiac dyad.

Tannakian Formalism Applied to the Category of Mixed Hodge Structures

Many problems in analysis have been solved using the theory of Hodge structures. P. Deligne started to treat these structures in a categorical way. Following him, we introduce the categories of mixed real and complex Hodge structures. Category of mixed Hodge structures over the field of real or complex numbers is a rigid abelian tensor category, and in fact, a neutral Tannakian category. Therefore it is equivalent to the category of representations of an affine group scheme. The direct sums of pure Hodge structures of different weights over real or complex numbers can be realized as a representation of the torus group, whose complex points is the Cartesian product of two punctured complex planes. Mixed Hodge structures turn out to consist of information of a direct sum of pure Hodge structures of different weights and a nilpotent automorphism. Therefore mixed Hodge structures correspond to the representations of certain semidirect product of a nilpotent group and the torus group acting on it.

Mining Sequential Data – in Search of Segmental Structures

Segmentation is a data mining technique yielding simplified representations of sequences of ordered points. A sequence is divided into some number of homogeneous blocks, and all points within a segment are described by a single value. The focus in this thesis is on piecewise-constant segments, where the most likely description for each segment and the most likely segmentation into some number of blocks can be computed efficiently. Representing sequences as segmentations is useful in, e.g., storage and indexing tasks in sequence databases, and segmentation can be used as a tool in learning about the structure of a given sequence. The discussion in this thesis begins with basic questions related to segmentation analysis, such as choosing the number of segments, and evaluating the obtained segmentations. Standard model selection techniques are shown to perform well for the sequence segmentation task. Segmentation evaluation is proposed with respect to a known segmentation structure. Applying segmentation on certain features of a sequence is shown to yield segmentations that are significantly close to the known underlying structure. Two extensions to the basic segmentation framework are introduced: unimodal segmentation and basis segmentation. The former is concerned with segmentations where the segment descriptions first increase and then decrease, and the latter with the interplay between different dimensions and segments in the sequence. These problems are formally defined and algorithms for solving them are provided and analyzed. Practical applications for segmentation techniques include time series and data stream analysis, text analysis, and biological sequence analysis. In this thesis segmentation applications are demonstrated in analyzing genomic sequences.

Gas-crystal photoreaction: the structures of 4,4'-dimethoxy(thiobenzophenone) (I), C15H14O2S, and 4,4'-bis(dimethylamino)thiobenzophenone (II), C17H20N2S

(I): M r = 258.34, triclinic, Pi, a = 9.810 (3), b=9.635(3), e=15.015(4)A, a=79.11(2), #= 102.38 (3), y = 107.76 (3) o, V= 1308.5 A 3, Z = 4, Din= 1.318 (3) (by flotation in KI solution), D x = 1.311 g cm -3, Cu Ka, 2 = 1.5418/~, g = 20-05 cm -1, F(000) = 544, T---- 293 K, R = 0.074 for 2663 reflections. (II): M r = 284.43, monoclinic, P2~/c, a= 17.029 (5), b=6.706 (5), c= 14.629 (4), t= 113.55 (2) ° , V=1531.4A 3, Z=4, Dm=1.230(5) (by flotation in KI solution), Dx= 1.234gem -3, Mo Ka, 2 = 0.7107 A, g = 1.63 cm-1; F(000) = 608, T= 293 K, R = 0.062 for 855 reflections. The orientation of the C=S chromophores in the crystal lattice and their reactivity in the crystalline state are discussed. The C--S bonds are much shorter than the normal bond length [1.605 (4) (I), 1.665 (8) A (II) cf. 1.71 A].

Sequence effects in structures of the dinucleotides d-pApT AND d-pTpA

The H1',H2' and H2″ regions of the 270-MHz PMR spectra of two deoxydinucleotides, d-pTpA and d-pApT, have been analyzed. The coupling constants in the sugar ring indicate that both A and T sugars have a tendency to acquire 2E conformations. There is also a marginal difference in the 2E populations of the T sugar in the two dinucleotides. The trends in the chemical shifts of base protons indicate different stacking of the bases in d-pApT and d-pTpA. The sequence effects on base stacking and pentose conformation are discussed.

Molecular structures of cytidine-5-diphosphate and cytidine-5-diphospho-choline, and their role in intermediary metabolism

The nucleotide coenzyme cytidine-5-diphospho-choline is highly folded. The CMP-5 parts of the molecules in the crystal structure are strongly linked by metal ligation and hydrogen bonds leaving the phosphoryl-choline residues relatively free. Cytidine-5-diphosphoric acid exists as a zwitterion with N31 protonated. The P−O bond lengths from the anhydride bridging oxygen in the pyrophosphate are significantly different.

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.

On reconsideration of IT governance structures to govern cloud computing services

There is an increase in the uptake of cloud computing services (CCS). CCS is adopted in the form of a utility, and it incorporates business risks of the service providers and intermediaries. Thus, the adoption of CCS will change the risk profile of an organization. In this situation, organisations need to develop competencies by reconsidering their IT governance structures to achieve a desired level of IT-business alignment and maintain their risk appetite to source business value from CCS. We use the resource-based theories to suggest that collaborative board oversight of CCS, competencies relating to CCS information and financial management, and a CCS-related continuous audit program can contribute to business process performance improvements and overall firm performance. Using survey data, we find evidence of a positive association between these IT governance considerations and business process performance. We also find evidence of positive association between business process performance improvements and overall firm performance. The results suggest that the suggested considerations on IT governance structures can contribute to CCS-related IT-business alignment and lead to anticipated business value from CCS. This study provides guidance to organizations on competencies required to secure business value from CCS.

Governing cloud computing services: Reconsideration of IT governance structures

There is an increase in the uptake of cloud computing services (CCS). CCS is adopted in the form of a utility, and it incorporates business risks of the service providers and intermediaries. Thus, the adoption of CCS will change the risk profile of an organization. In this situation, organizations need to develop competencies by reconsidering their IT governance structures to achieve a desired level of IT-business alignment and maintain their risk appetite to source business value from CCS. We use the resource-based theories to suggest that collaborative board oversight of CCS, competencies relating to CCS information and financial management, and a CCS-related continuous audit program can contribute to business process performance improvements and overall firm performance. Using survey data, we find evidence of a positive association between these IT governance considerations and business process performance. We also find evidence of positive association between business process performance improvements and overall firm performance. The results suggest that the suggested considerations on IT governance structures can contribute to CCS-related IT-business alignment and lead to anticipated business value from CCS. This study provides guidance to organizations on competencies required to secure business value from CCS.

On information technology competencies for collaborative organizational structures

There is an uptake of organizations involvement in collaborative organizational structures (COS). As the nature and level of information technology (IT) investment in COS will be similar, the COS IT competencies will leverage the IT investments to create the collaborative rent generating potential of the COS, which would then improve the business value of the COS members. Consistent with the resource-centric views of the firm, we suggest that the COS members need to contribute their managed IT competencies to their COS, whose synergies would create COS IT competencies. We suggest three key IT competencies for COS; proactive top management decision synergy, collaborative and agile IT infrastructure, and cross-functional tactical management synergy. Using survey data, we find evidence of a positive association between these COS IT competencies and the collaborative rent generating potential of the COS. We also find a positive association between the collaborative rent generating potential of the COS and the business value of the COS members. The results suggest that developing COS IT competencies add value to a COS and its members. This study provides guidance for organizations looking to leverage their involvement in a COS.