Laser processing of high-Tc superconducting thin films

High-Tc superconducting thin films can be deposited and processed by pulsed and CW lasers, and a respectable materials technology for the Y-Ba-Cu-O superconductor is rapidly emerging. The pulsed laser deposition technique is simple because it produces films with compositions nearly identical to those of the target pellets. A larger variety of substrates can be used, compared to other deposition technologies, because of the relatively low temperature requirements. The laser deposition mechanism has been investigated. As-deposited superconducting films, epitaxial films with smooth surfaces, and multilayer structures with abrupt interfaces have been produced. The electrical transport properties can be changed locally using a focused argon-ion laser by modifying the oxygen stoichiometry. This laser writing can be erased by room-temperature exposure to an oxygen plasma. Other laser patterning methods such as material removal, melt-quench, and direct pattern transfer are being developed.

Direct Synthesis of Terminally ``Clickable'' Linear and Hyperbranched Polyesters

1,3-Dipolar cycloaddition of an organic azide and an acetylenic unit,often referred to as the ``click reaction'', has become an important ligation tool both in the context of materials chemistry and biology. Thus, development of simple approaches to directly generate polymers that bear either an azide or an alkyne unit has gained considerable importance. We describe here a straightforward approach to directly prepare linear and hyperbranched polyesters that carry terminal propargyl groups. To achieve the former, we designed an AB-type monomer that carries a hydroxyl group and a propargyl ester, which upon self-condensation under standard transesterification conditions yielded a polyester that carries a single propargyl group at one of its chain-ends. Similarly, an AB(2) type monomer that carries one hydroxyl group and two propargyl ester groups, when polymerized under the same conditions yielded a hyperbranched polymer with numerous clickable'' propargyl groups at its molecular periphery. These propargyl groups can be readily clicked with different organic azides, such as benzyl azide, omega-azido heptaethyleneglycol monomethylether or 9-azidomethyl anthracene. When an anthracene chromophore is clicked, the molecular weight of the linear polyester could be readily estimated using both UV-visible and fluorescence spectroscopic measurements. Furthermore, the reactive propargyl end group could also provide an opportunity to prepare block copolymers in the case of linear polyesters and to generate nanodimensional scaffolds to anchor variety of functional units, in the case of the hyperbranched polymer. (C) 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 3200-3208, 2010.

Electronic absorption spectra of selenocarbonyl and thiocarbonyl compounds

Electronic absorption spectra of a variety of thiocarbonyl and selenocarbonyl compounds have been compared to point out their similarities. Interesting correlations between the absorption maxima and electronegativities of substituents in both the seleno- and thio-carbonyl compounds have been reported.

A finite element analysis of quasistatic crack growth in a pressure sensitive constrained ductile layer

Polymeric adhesive layers are employed for bonding two components in a wide variety of technological applications, It has been observed that, unlike in metals, the yield behavior of polymers is affected by the state of hydrostatic stress. In this work, the effect of pressure sensitivity of yielding and layer thickness on quasistatic interfacial crack growth in a ductile adhesive layer is investigated. To this end, finite deformation, finite element analyses of a cracked sandwiched layer are carried out under plane strain, small-scale yielding conditions for a wide range of mode mixities. The Drucker-Prager constitutive equations are employed to represent the behavior of the layer. Crack propagation is simulated through a cohesive zone model, in which the interface is assumed to follow a prescribed traction-separation law. The results show that for a given mode mixity, the steady state Fracture toughness [K](ss) is enhanced as the degree of pressure sensitivity increases. Further, for a given level of pressure sensitivity, [K](ss) increases steeply as mode Il loading is approached. (C) 2000 Elsevier Science Ltd. All rights reserved.

Improved procedures for the Beckmann rearrangement: the reaction of ketoxime carbonates with boron trifluoride etherate

A variety of ketoxime ethyl carbonates-easily prepared from the oximes and ethyl chloroformate-undergo the Beckmann rearrangement upon treatment with 1 equivalent of boron trifluoride etherate, in dichloromethane solution at room temperature in excellent yields (generally 75-99%). (C) 2000 Elsevier Science Ltd. All rights reserved.

Improved procedures for the Beckmann rearrangement: the reaction of ketoxime carbonates with boron trifluoride etherate

A variety of ketoxime ethyl carbonates-easily prepared from the oximes and ethyl chloroformate-undergo the Beckmann rearrangement upon treatment with 1 equivalent of boron trifluoride etherate, in dichloromethane solution at room temperature in excellent yields (generally 75-99%). (C) 2000 Elsevier Science Ltd. All rights reserved.

Computer simulation of protein—carbohydrate complexes: application to arabinose-binding protein and pea lectin

The CCEM method (Contact Criteria and Energy Minimisation) has been developed and applied to study protein-carbohydrate interactions. The method uses available X-ray data even on the native protein at low resolution (above 2.4 Å) to generate realistic models of a variety of proteins with various ligands.The two examples discussed in this paper are arabinose-binding protein (ABP) and pea lectin. The X-ray crystal structure data reported on ABP-β-l-arabinose complex at 2.8, 2.4 and 1.7 Å resolution differ drastically in predicting the nature of the interactions between the protein and ligand. It is shown that, using the data at 2.4 Å resolution, the CCEM method generates complexes which are as good as the higher (1.7 Å) resolution data. The CCEM method predicts some of the important hydrogen bonds between the ligand and the protein which are missing in the interpretation of the X-ray data at 2.4 Å resolution. The theoretically predicted hydrogen bonds are in good agreement with those reported at 1.7 Å resolution. Pea lectin has been solved only in the native form at 3 Å resolution. Application of the CCEM method also enables us to generate complexes of pea lectin with methyl-α-d-glucopyranoside and methyl-2,3-dimethyl-α-d-glucopyranoside which explain well the available experimental data in solution.

Molecular characterization of sediment bacterial communities affected by fish farming

Fish farming introduces nutrients, microbes and a wide variety of chemicals such as heavy metals, antifoulants and antibiotics to the surrounding environment. Introduction of antibiotics has been linked with the increased incidence of antibiotic resistant pathogenic bacteria in the farm vicinities. In this thesis molecular methods such as quantitative PCR and DNA sequencing were applied to analyze bacterial communities in sediments from fish farms and pristine locations. Altogether four farms and four pristine sites were sampled in the Baltic Sea. Two farm and two pristine locations were sampled over a surveillance period of four years. Furthermore, a new methodology was developed as a part of the study that permits amplifying single microbial genomes and capturing them according to any genetic traits, including antibiotic resistance genes. The study revealed that several resistance genes for tetracycline were found at the sediment underneath the aquaculture farms. The copy number of these genes remained elevated even at a farm that had not used any antibiotics since year 2000, six years before this study started. Similarly, an increase in the amount of mercury resistance gene merA was observed at the aquaculture sediment. The persistence of the resistance genes in absence of any selection pressure from antibiotics or heavy metals suggests that the genes may be introduced to the sediment by the farming process. This is also supported by the diversity pattern of the merA gene between farm and pristine sediments. The bacterial community-level changes in response to fish farming were very complex and no single phylogenetic groups were found that would be typical to fish farm sediments. However, the community structures had some correlation with the exposure to fish farming. Our studies suggest that the established approaches to deal with antibiotic resistance at the aquaculture, such as antibiotic cycling, are fundamentally flawed because they cannot prevent the introduction of the resistance genes and resistant bacteria to the farm area by the farming process. Further studies are required to study the entire fish farming process to identify the sources of the resistance genes and the resistant bacteria. The results also suggest that in order to prevent major microbiological changes in the surrounding aquatic environment, the farms should not be founded in shallow water where currents do not transport sedimenting matter from the farms. Finally, the technique to amplify and select microbial genomes will potentially have a considerable impact in microbial ecology and genomics.

Environmental and climatic dependences of stable isotope ratios in tree rings on different temporal scales

This work examines stable isotope ratios of carbon, oxygen and hydrogen in annual growth rings of trees. Isotopic composition in wood cellulose is used as a tool to study past climate. The method benefits from the accurate and precise dating provided by dendrochronology. In this study the origin, nature and the strength of climatic correlations are studied on different temporal scales and at different sites in Finland. The origin of carbon isotopic signal is in photosynthetic fractionation. The basic physical and chemical fractionations involved are reasonably well understood. This was confirmed by measuring instantaneous photosynthetic discrimination on Scots pine (Pinus sylvestris L.). The internal conductance of CO2 was recognized to have a significant impact on the observed fractionation, and further investigations are suggested to quantify its role in controlling the isotopic signal of photosynthates. Isotopic composition of the produced biomass can potentially be affected by variety of external factors that induce physiological changes in trees. Response of carbon isotopic signal in tree ring cellulose to changes in resource availability was assessed in a manipulation experiment. It showed that the signal was relatively stable despite of changes in water and nitrogen availability to the tree. Palaeoclimatic reconstructions are typically based on functions describing empirical relationship between isotopic and climatic parameters. These empirical relationships may change depending on the site conditions, species and timeframe studied. Annual variation in Scots pine tree ring carbon and oxygen isotopic composition was studied in northern and in central eastern Finland and annual variation in tree ring latewood carbon, oxygen and hydrogen isotopic ratio in Oak (Quercus robur L.) was studied in southern Finland. In all of the studied sites at least one of the studied isotope ratios was shown to record climate strongly enough to be used in climatic reconstructions. Using the observed relationships, four-century-long climate reconstructions from living Scots pine were created for northern and central eastern Finland. Also temporal stability of the relationships between three proxy indicators, tree ring growth and carbon and oxygen isotopic composition was studied during the four-hundred-year period. Isotope ratios measured from tree rings in Finland were shown to be sensitive indicators of climate. Increasing understanding of environmental controls and physiological mechanisms affecting tree ring isotopic composition will make possible more accurate interpretation of isotope data. This study also demonstrated that by measuring multiple isotopes and physical proxies from the same tree rings, additional information on tree physiology can be obtained. Thus isotopic ratios measured from tree ring cellulose provide means to improve the reliability of climate reconstructions.

Frequency-Dependent Viscosity of Membrane Solutions

It is shown that dilute suspensions of membranes have strongly frequency-dependent viscosities. This behaviour should be seen in a variety of measurements such as capillary flow, mechanical impedance and ultrasound damping.

Transcriptional analysis of persistent Chlamydia pneumoniae infection in vitro

Chlamydia pneumoniae can cause acute respiratory infections including pneumonia. Repeated and persistent Chlamydia infections occur and persistent C. pneumoniae infection may have a role in the pathogenesis of atherosclerosis and coronary heart disease and may also contribute to the development of chronic inflammatory lung diseases like chronic obstructive pulmonary disease (COPD) and asthma. In this thesis in vitro models for persistent C. pneumonia infection were established in epithelial and monocyte/macrophage cell lines. Expression of host cell genes in the persistent C. pneumoniae infection model of epithelial cells was studied by microarray and RT-PCR. In the monocyte/macrophage infection model expression of selected C. pneumoniae genes were studied by RT-PCR and immunofluorescence microscopy. Chlamydia is able to modulate host cell gene expression and apoptosis of host cells, which may assist Chlamydia to evade the host cells' immune responses. This, in turn, may lead to extended survival of the organism inside epithelial cells and promote the development of persistent infection. To simulate persistent C. pneumoniae infection in vivo, we set up a persistent infection model exposing the HL cell cultures to IFN-gamma. When HL cell cultures were treated with moderate concentration of IFN-gamma, the replication of C. pneumoniae DNA was unaffected while differentiation into infectious elementary bodies (EB) was strongly inhibited. By transmission electron microscopy small atypical inclusions were identified in IFN-gamma treated cultures. No second cycle of infection was observed in cells exposed to IFN-gamma , whereas C. pneumoniae was able to undergo a second cycle of infection in unexposed HL cells. Although monocytic cells can naturally restrict chlamydial growth, IFN-gamma further reduced production of infectious C. pneumoniae in Mono Mac 6 cells. Under both studied conditions no second cycle of infection could be detected in monocytic cell line suggesting persistent infection in these cells. As a step toward understanding the role of host genes in the development and pathogenesis of persistent C. pneumoniae infection, modulation of host cell gene expression during IFN-gamma induced persistent infection was examined and compared to that seen during active C. pneumoniae infection or IFN-gamma treatment. Total RNA was collected at 6 to 150 h after infection of an epithelial cell line (HL) and analyzed by a cDNA array (available at that time) representing approximately 4000 human transcripts. In initial analysis 250 of the 4000 genes were identified as differentially expressed upon active and persistent chlamydial infection and IFN-gamma treatment. In persistent infection more potent up-regulation of many genes was observed in IFN-gamma induced persistent infection than in active infection or in IFN-gamma treated cell cultures. Also sustained up-regulation was observed for some genes. In addition, we could identify nine host cell genes whose transcription was specifically altered during the IFN-gamma induced persistent C. pneumoniae infection. Strongest up-regulation in persistent infection in relation to controls was identified for insulin like growth factor binding protein 6, interferon-stimulated protein 15 kDa, cyclin D1 and interleukin 7 receptor. These results suggest that during persistent infection, C. pneumoniae reprograms the host transcriptional machinery regulating a variety of cellular processes including adhesion, cell cycle regulation, growth and inflammatory response, all of which may play important roles in the pathogenesis of persistent C. pneumoniae infection. C. pneumoniae DNA can be detected in peripheral blood mononuclear cells indicating that the bacterium can also infect monocytic cells in vivo and thereby monocytes can assist the spread of infection from the lungs to other anatomical sites. Persistent infection established at these sites could promote inflammation and enhance pathology. Thus, the mononuclear cells are in a strategic position in the development of persistent infection. To investigate the intracellular replication and fate of C. pneumoniae in mononuclear cells we analyzed the transcription of 11 C. pneumoniae genes in Mono Mac 6 cells during infection by real time RT-PCR. Our results suggest that the transcriptional profile of the studied genes in monocytes is different from that seen in epithelial cells and that IFN-gamma has a less significant effect on C. pneumoniae transcription in monocytes. Furthermore, our study shows that type III secretion system (T3SS) related genes are transcribed and that Chlamydia possesses a functional T3SS during infection in monocytes. Since C. pneumoniae infection in monocytes has been implicated to have reduced antibiotic susceptibility, this creates opportunities for novel therapeutics targeting T3SS in the management of chlamydial infection in monocytes.

Genetic Heterogeneity in Wild Isolates of Cellular Slime Mold Social Groups

This study addresses the issues of spatial distribution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil amoebae with an unusual life cycle that consists of alternating solitary and social phases. Because the social phase involves division of labor with what appears to be an extreme form of "altruism", the CSMs raise interesting evolutionary questions regarding the origin and maintenance of sociality. Knowledge of the genetic structure of social groups in the wild is necessary for answering these questions. We confirm that CSMs are widespread in undisturbed forest soil from South India. They are dispersed over long distances via the dung of a variety of large mammals. Consistent with this mode of dispersal, most social groups in the two species examined for detailed study, Dictyostelium giganteum and Dictyostelium purpureum, are multi-clonal.

Surface diffusion driven nanoshell formation by controlled sintering of mesoporous nanoparticle aggregates

We report a general method for the synthesis of hollow structures of a variety of functional inorganics by partial sintering of mesoporous nanocrystal aggregates. The formation of a thin shell initiates the transport of mass from the interior leading to growth of the shell. The principles are general and the hollow structures thus produced are attractive for many applications including catalysis, drug delivery and biosensing.

Models of Dispersal and Diversification

Ecology and evolutionary biology is the study of life on this planet. One of the many methods applied to answering the great diversity of questions regarding the lives and characteristics of individual organisms, is the utilization of mathematical models. Such models are used in a wide variety of ways. Some help us to reason, functioning as aids to, or substitutes for, our own fallible logic, thus making argumentation and thinking clearer. Models which help our reasoning can lead to conceptual clarification; by expressing ideas in algebraic terms, the relationship between different concepts become clearer. Other mathematical models are used to better understand yet more complicated models, or to develop mathematical tools for their analysis. Though helping us to reason and being used as tools in the craftmanship of science, many models do not tell us much about the real biological phenomena we are, at least initially, interested in. The main reason for this is that any mathematical model is a simplification of the real world, reducing the complexity and variety of interactions and idiosynchracies of individual organisms. What such models can tell us, however, both is and has been very valuable throughout the history of ecology and evolution. Minimally, a model simplifying the complex world can tell us that in principle, the patterns produced in a model could also be produced in the real world. We can never know how different a simplified mathematical representation is from the real world, but the similarity models do strive for, gives us confidence that their results could apply. This thesis deals with a variety of different models, used for different purposes. One model deals with how one can measure and analyse invasions; the expanding phase of invasive species. Earlier analyses claims to have shown that such invasions can be a regulated phenomena, that higher invasion speeds at a given point in time will lead to a reduction in speed. Two simple mathematical models show that analysis on this particular measure of invasion speed need not be evidence of regulation. In the context of dispersal evolution, two models acting as proof-of-principle are presented. Parent-offspring conflict emerges when there are different evolutionary optima for adaptive behavior for parents and offspring. We show that the evolution of dispersal distances can entail such a conflict, and that under parental control of dispersal (as, for example, in higher plants) wider dispersal kernels are optimal. We also show that dispersal homeostasis can be optimal; in a setting where dispersal decisions (to leave or stay in a natal patch) are made, strategies that divide their seeds or eggs into fractions that disperse or not, as opposed to randomized for each seed, can prevail. We also present a model of the evolution of bet-hedging strategies; evolutionary adaptations that occur despite their fitness, on average, being lower than a competing strategy. Such strategies can win in the long run because they have a reduced variance in fitness coupled with a reduction in mean fitness, and fitness is of a multiplicative nature across generations, and therefore sensitive to variability. This model is used for conceptual clarification; by developing a population genetical model with uncertain fitness and expressing genotypic variance in fitness as a product between individual level variance and correlations between individuals of a genotype. We arrive at expressions that intuitively reflect two of the main categorizations of bet-hedging strategies; conservative vs diversifying and within- vs between-generation bet hedging. In addition, this model shows that these divisions in fact are false dichotomies.

'... the walls fell down but the blokes just coded ...' - Varieties of stability in software product development during organizational restructurings

Many Finnish IT companies have gone through numerous organizational changes over the past decades. This book draws attention to how stability may be central to software product development experts and IT workers more generally, who continuously have to cope with such change in their workplaces. It does so by analyzing and theorizing change and stability as intertwined and co-existent, thus throwing light on how it is possible that, for example, even if ‘the walls fall down the blokes just code’ and maintain a sense of stability in their daily work. Rather than reproducing the picture of software product development as exciting cutting edge activities and organizational change as dramatic episodes, the study takes the reader beyond the myths surrounding these phenomena to the mundane practices, routines and organizings in product development during organizational change. An analysis of these ordinary practices offers insights into how software product development experts actively engage in constructing stability during organizational change through a variety of practices, including solidarity, homosociality, close relations to products, instrumental or functional views on products, preoccupations with certain tasks and humble obedience. Consequently, the study shows that it may be more appropriate to talk about varieties of stability, characterized by a multitude of practices of stabilizing rather than states of stagnation. Looking at different practices of stability in depth shows the creation of software as an arena for micro-politics, power relations and increasing pressures for order and formalization. The thesis gives particular attention to power relations and processes of positioning following organizational change: how social actors come to understand themselves in the context of ongoing organizational change, how they comply with and/or contest dominant meanings, how they identify and dis-identify with formalization, and how power relations often are reproduced despite dis-identification. Related to processes of positioning, the reader is also given a glimpse into what being at work in a male-dominated and relatively homogeneous work environment looks like. It shows how the strong presence of men or “blokes” of a particular age and education seems to become invisible in workplace talk that appears ‘non-conscious’ of gender.