Particle detector link system modifications in RE1/1 sector

The large hadron collider constructed at the European organization for nuclear research, CERN, is the world’s largest single measuring instrument ever built, and also currently the most powerful particle accelerator that exists. The large hadron collider includes six different experiment stations, one of which is called the compact muon solenoid, or the CMS. The main purpose of the CMS is to track and study residue particles from proton-proton collisions. The primary detectors utilized in the CMS are resistive plate chambers (RPCs). To obtain data from these detectors, a link system has been designed. The main idea of the link system is to receive data from the detector front-end electronics in parallel form, and to transmit it onwards in serial form, via an optical fiber. The system is mostly ready and in place. However, a problem has occurred with innermost RPC detectors, located in sector labeled RE1/1; transmission lines for parallel data suffer from signal integrity issues over long distances. As a solution to this, a new version of the link system has been devised, a one that fits in smaller space and can be located within the CMS, closer to the detectors. This RE1/1 link system has been so far completed only partially, with just the mechanical design and casing being done. In this thesis, link system electronics for RE1/1 sector has been designed, by modifying the existing link system concept to better meet the requirements of the RE1/1 sector. In addition to completion of the prototype of the RE1/1 link system electronics, some testing for the system has also been done, to ensure functionality of the design.

Evolutionary Ecology of Mountain Birch in Subarctic Stress Gradients: Interplay of Biotic and Abiotic Factors in Plant-Plant Interactions and Evolutionary Processes

In nature, variation for example in herbivory, wind exposure, moisture and pollution impact often creates variation in physiological stress and plant productivity. This variation is seldom clear-cut, but rather results in clines of decreasing growth and productivity towards the high-stress end. These clines of unidirectionally changing stress are generally known as ‘stress gradients’. Through its effect on plant performance, stress has the capacity to fundamentally alter the ecological relationships between individuals, and through variation in survival and reproduction it also causes evolutionary change, i.e. local adaptations to stress and eventually speciation. In certain conditions local adaptations to environmental stress have been documented in a matter of just a few generations. In plant-plant interactions, intensities of both negative interactions (competition) and positive ones (facilitation) are expected to vary along stress gradients. The stress-gradient hypothesis (SGH) suggests that net facilitation will be strongest in conditions of high biotic and abiotic stress, while a more recent ‘humpback’ model predicts strongest net facilitation at intermediate levels of stress. Plant interactions on stress gradients, however, are affected by a multitude of confounding factors, making studies of facilitation-related theories challenging. Among these factors are plant ontogeny, spatial scale, and local adaptation to stress. The last of these has very rarely been included in facilitation studies, despite the potential co-occurrence of local adaptations and changes in net facilitation in stress gradients. Current theory would predict both competitive effects and facilitative responses to be weakest in populations locally adapted to withstand high abiotic stress. This thesis is based on six experiments, conducted both in greenhouses and in the field in Russia, Norway and Finland, with mountain birch (Betula pubescens subsp. czerepanovii) as the model species. The aims were to study potential local adaptations in multiple stress gradients (both natural and anthropogenic), changes in plant-plant interactions under conditions of varying stress (as predicted by SGH), potential mechanisms behind intraspecific facilitation, and factors confounding plant-plant facilitation, such as spatiotemporal, ontogenetic, and genetic differences. I found rapid evolutionary adaptations (occurring within a time-span of 60 to 70 years) towards heavy-metal resistance around two copper-nickel smelters, a phenomenon that has resulted in a trade-off of decreased performance in pristine conditions. Heavy-metal-adapted individuals had lowered nickel uptake, indicating a possible mechanism behind the detected resistance. Seedlings adapted to heavy-metal toxicity were not co-resistant to others forms of abiotic stress, but showed co-resistance to biotic stress by being consumed to a lesser extent by insect herbivores. Conversely, populations from conditions of high natural stress (wind, drought etc.) showed no local adaptations, despite much longer evolutionary time scales. Due to decreasing emissions, I was unable to test SGH in the pollution gradients. In natural stress gradients, however, plant performance was in accordance with SGH, with the strongest host-seedling facilitation found at the high-stress sites in two different stress gradients. Factors confounding this pattern included (1) plant size / ontogenetic status, with seedling-seedling interactions being competition dominated and host-seedling interactions potentially switching towards competition with seedling growth, and (2) spatial distance, with competition dominating at very short planting distances, and facilitation being strongest at a distance of circa ¼ benefactor height. I found no evidence for changes in facilitation with respect to the evolutionary histories of plant populations. Despite the support for SGH, it may be that the ‘humpback’ model is more relevant when the main stressor is resource-related, while what I studied were the effects of ‘non-resource’ stressors (i.e. heavy-metal pollution and wind). The results have potential practical applications: the utilisation of locally adapted seedlings and plant facilitation may increase the success of future restoration efforts in industrial barrens as well as in other wind-exposed sites. The findings also have implications with regard to the effects of global change in subarctic environments: the documented potential by mountain birch for rapid evolutionary change, together with the general lack of evolutionary ‘dead ends’, due to not (over)specialising to current natural conditions, increase the chances of this crucial forest-forming tree persisting even under the anticipated climate change.

Intracellular membrane trafficking in Osteoclasts The role of direct Rab protein – Rac 1 interactions in the targeting of intracellular vesicles

Osteoclasts are cells responsible for bone resorption. These cells undergo extensive membrane re-organization during their polarization for bone resorption and form four distinct membrane domains, namely the ruffled border, the basolateral membrane, the sealing zone and the functional secretory domain. The endocytic/biosynthetic pathway and transcytotic route(s) are important for the resorption process, since the endocytic/biosynthetic pathway brings the specific vesicles to the ruffled border whereas the transcytotic flow is believed to transport the degraded bone matrix away from the resorption lacuna to the functional secretory domain. In the present study, we found a new transcytotic route from the functional secretory domain to the ruffled border, which may compensate membrane loss from the ruffled border during the resorption process. We also found that lipid rafts are essential for the ruffled border-targeted late endosomal pathways. A small GTP-binding protein, Rab7, has earlier been shown to regulate the late steps of the endocytic pathway. In bone-resorbing osteoclasts it is involved in the formation of the ruffled border, which displays several features of late endosomal membranes. Here we discovered a new Rab7-interacting protein, Rac1, which is another small GTP-binding protein and binds to the GTP-form of Rab7 in vitro. We demonstrated further that Rab7 colocalizes with Rac1 at the fusion zone of the ruffled border in bone-resorbing osteoclasts. In other cell types, such as fibroblast-like cells, this colocalization is mainly perinuclear. Because Rac1 is known to control the actin cytoskeleton through its effectors, we suggest that the Rab7-Rac1 interaction may mediate late endosomal transport between microtubules and microfilaments, thus enabling endosomal vesicles to switch tracks from microtubules to microfilaments before their fusion to the ruffled border. We then studied the role of Rab-Rac1 interaction in the slow recycling pathway. We revealed that Rac1 also binds directly to Rab11 and to some other but not all Rab-proteins, suggesting that Rab-Rac1 interaction could be a general regulatory mechanism to direct the intracellular vesicles from microtubule mediated transport to actin filament mediated transport and vice versa. On the basis of our results we thus propose a new hypothesis for these GTPases in the regulation of intracellular membrane flow.

Designing features for supporting social interactions in online communities

This Master's thesis studies the development of interaction and socialization in online communities. A large number of online communities fade away even before they really get started. In many occasions the reason is that the community does not give anything new, or even if they do, the delivery does not satisfy the users. In this thesis guidelines were developed to help to see important things, which might be forgotten when developing an online community. The thesis goes through the characteristic of an online community and human behaviour related to them and also compares behaviour in the Internet and real life. In addition, usability is an important part of the online communities and thus it is also covered in this thesis. As a result of this thesis an 8-step guideline was developed to ease the design of an online community. Guidelines were also applied to two real life cases which are described as one part of this work.

Chelating Adsorbents in Purification of Hydrometallurgical Solutions

In this thesis, equilibrium and dynamic sorption properties of weakly basic chelating adsorbents were studied to explain removal of copper, nickel from a concentrated zinc sulfate solution in a hydrometallurgical process. Silica-supported chelating composites containing either branched poly(ethyleneimine) (BPEI) or 2-(aminomethyl)pyridine (AMP) as a functional group were used. The adsorbents are commercially available from Purity Systems Inc, USA as WP-1® and CuWRAM®, respectively. The fundamental interactions between the adsorbents, sulfuric acid and metal sulfates were studied in detail and the results were used to find the best conditions for removal of copper and nickel from an authentic ZnSO4 process solution. In particular, the effect of acid concentration and temperature on the separation efficiency was considered. Both experimental and modeling aspectswere covered in all cases. Metal sorption is considerably affected by the chemical properties of the studied adsorbents and by the separation conditions. In the case of WP-1, acid affinity is so high that column separation of copper, nickel and zinc has to be done using the adsorbent in base-form. On the other hand, the basicity of CuWRAM is significantly lower and protonated adsorbent can be used. Increasing temperature decreases the basicity and the metals affinity of both adsorbents, but the uptake capacities remain practically unchanged. Moreover, increasing temperature substantially enhances intra-particle mass transport and decreases viscosities thus allowing significantly higher feed flow rates in the fixed-bed separation. The copper selectivity of both adsorbents is very high even in the presence of a 250-fold excess of zinc. However, because of the basicity of WP-1, metal precipitation is a serious problem and therefore only CuWRAM is suitable for the practical industrial application. The optimum temperature for copper removal appears to be around 60 oC and an alternative solution purification method is proposed. The Ni/Zn selectivity of both WP-1 and CuWRAM is insufficient for removal of the very small amounts of nickel present in the concentrated ZnSO4 solution.

Multi-Eruption Solar Energetic Particle Events Observed by SOHO/ERNE

In the last two decades of studying the Solar Energetic Particle (SEP) phenomenon, intensive emphasis has been put on how and when and where these SEPs are injected into interplanetary space. It is well known that SEPs are related to solar flares and CMEs. However, the role of each in the acceleration of SEPs has been under debate since the major role was taken from flares ascribed to CMEs step by step after the skylab mission, which started the era of CME spaceborn observations. Since then, the shock wave generated by powerful CMEs in between 2-5 solar radii is considered the major accelerator. The current paradigm interprets the prolonged proton intensity-time profile in gradual SEP events as a direct effect of accelerated SEPs by shock wave propagating in the interplanetary medium. Thus the powerful CME is thought of as a starter for the acceleration and its shock wave as a continuing accelerator to result in such an intensity-time profile. Generally it is believed that a single powerful CME which might or might not be associated with a flare is always the reason behind such gradual events.

In this work we use the Energetic and Relativistic Nucleus and Electrons ERNE instrument on board Solar and Heliospheric Observatory SOHO to present an empirical study to show the possibility of multiple accelerations in SEP events. In the beginning we found 18 double-peaked SEP events by examining 88 SEP events. The peaks in the intensity-time profile were separated by 3-24 hours. We divided the SEP events according to possible multiple acceleration into four groups and in one of these groups we find evidence for multiple acceleration in velocity dispersion and change in the abundance ratio associated at transition to the second peak. Then we explored the intensity-time profiles of all SEP events during solar cycle 23 and found that most of the SEP events are associated with multiple eruptions at the Sun and we call those events as Multi-Eruption Solar Energetic Particles (MESEP) events. We use the data available by Large Angle and Spectrometric Coronograph LASCO on board SOHO to determine the CME associated with such events and YOHKOH and GOES satellites data to determine the flare associated with such events. We found four types of MESEP according to the appearance of the peaks in the intensity-time profile in large variation of energy levels. We found that it is not possible to determine whether the peaks are related to an eruption at the Sun or not, only by examining the anisotropy flux, He/p ratio and velocity dispersion. Then we chose a rare event in which there is evidence of SEP acceleration from behind previous CME. This work resulted in a conclusion which is inconsistent with the current SEP paradigm. Then we discovered through examining another MESEP event, that energetic particles accelerated by a second CME can penetrate a previous CME-driven decelerating shock. Finally, we report the previous two MESEP events with new two events and find a common basis for second CME SEPs penetrating previous decelerating shocks. This phenomenon is reported for the first time and expected to have significant impact on modification of the current paradigm of the solar energetic particle events.

A generalized 1D particle transport method for convection diffusion reaction model

This work is devoted to the development of numerical method to deal with convection diffusion dominated problem with reaction term, non - stiff chemical reaction and stiff chemical reaction. The technique is based on the unifying Eulerian - Lagrangian schemes (particle transport method) under the framework of operator splitting method. In the computational domain, the particle set is assigned to solve the convection reaction subproblem along the characteristic curves created by convective velocity. At each time step, convection, diffusion and reaction terms are solved separately by assuming that, each phenomenon occurs separately in a sequential fashion. Moreover, adaptivities and projection techniques are used to add particles in the regions of high gradients (steep fronts) and discontinuities and transfer a solution from particle set onto grid point respectively. The numerical results show that, the particle transport method has improved the solutions of CDR problems. Nevertheless, the method is time consumer when compared with other classical technique e.g., method of lines. Apart from this advantage, the particle transport method can be used to simulate problems that involve movingsteep/smooth fronts such as separation of two or more elements in the system.

Epidemiology of Cytochrome P450-mediated Drug-Drug Interactions

Drug-drug interactions (DDIs) comprise an important cause of adverse drug reactions leading to excess hospitalizations. Drug metabolism is catalyzed by 75% by cytochrome P450 (CYP) enzymes and thus they are often involved in pharmacokinetic DDIs. In general, DDIs are studied in randomized controlled clinical trials in selected study populations. The overall aim of the present studies was to perform observational pharmacoepidemiological surveys on CYP-mediated DDIs in diseases important at the population level. The prevalence of co-administrations of four prodrugs (losartan, codeine, tramadol, and clopidogrel), three sulphonylureas (glibenclamide, glimepiride, and glipizide), or two statins (lovastatin and simvastatin) with well established agents altering CYP activity, as well as of statins with fibrates, was studied in Finland utilizing data from a university hospital medication database (inpatients) and the National Prescription Register of the Social Insurance Institution of Finland, Kela (outpatients). Clinical consequences of potential DDIs were estimated by reviewing laboratory data, and information from hospital care and cause-of-death registers. Concomitant use of study substrates with interacting medication was detected in up to one fifth of patients in both hospital and community settings. Potential CYP3A4 interactions in statin users did not manifest in clear adverse laboratory values but pharmacodynamic DDIs between statins and fibrates predisposed patients to muscular toxicity. Sulphonylurea DDIs with CYP2C9 inhibitors increased the risk of hypoglycaemia. CYP3A4 inhibitor use with clopidogrel was not associated with significant changes in mortality but non-fatal thrombosis and haemorrhage complications were seen less often in this group. Concomitant administration of atorvastatin with clopidogrel moderately attenuated the antithrombotic effect by clopidogrel. The overall mortality was increased in CYP3A4 inducer and clopidogrel co-users. Atorvastatin used concomitantly with prodrug clopidogrel seems to be beneficial in terms of total and LDL cholesterol concentrations, and overall mortality compared with clopidogrel use without interacting medication. In conclusion, CYP-mediated DDIs are a common and often unrecognized consequence of irrational drug prescribing.

Interactions between Polyunsaturated Fatty Acids and Probiotics

The prevalence of inflammatory based diseases has increased in industrialized countries over the last decades. For allergic diseases, two primary hypotheses have been proposed to explain this phenomenon, namely the hygiene and dietary evolution based hypothesis. Particularly, the reduced early exposure to microbes and an increase in the amount of polyunsaturated fatty acids (especially n-6 PUFA) in the diet have been discussed. Often, these two factors have been studied independently, even though both factors have been shown to possess potential health benefits and their mode of action to share similar mechanisms. The hypothesis of the present study was that demonstrate that PUFA and probiotics are not separate entities as such but do interact with each other. In the present study, we investigated whether maternal diet and atopic status influence the PUFA composition of breast milk and serum fatty acids of infants, and whether the fatty acid absorption and utilization of infant formula fatty acids is affected by supplementation of infant formula with probiotic bacteria (Lactobacillus GG and Bifidobacterium lactis Bb-12). Moreover, we investigated the mechanisms by which different PUFA influence the physicochemical and functional properties of probiotics as well as functionality of epithelial cells in vitro. We demonstrated a carry-over effect of dietary fatty acids from maternal diet via breast milk into infants’ serum lipid fatty acids. Our data confirmed the previously shown allergy –related PUFA level imbalances, though it did not fully support the impaired desaturation and elongation capacity hypothesis. We also showed that PUFA incorporation into phospholipids of infants was influenced by probiotics in infant formula in a strain dependent manner. Especially,Bifidobacterium lactis Bb-12 in infant formula promoted the utilization of n-3 PUFA. Mechanistically, we demonstrated that probiotics (Lactobacillus GG, Lactobacillus casei Shirota and Lactobacillus bulgaricus) did incorporate and interconvert exogenous free PUFA in the growth medium into bacterial fatty acids strain and PUFA dependently. In general, high concentrations of free PUFA inhibited the growth and mucus adhesion of probiotics, whereas low concentrations of specific long chain PUFA were found to promote the growth and mucus adhesion of Lactobacillus casei Shirota. These effects were paralleled with only minor alterations in hydrophobicity and electron donor – electron acceptor properties of lactobacilli. Furthermore, free PUFA were also demonstrated to alter the adhesion capacity of the intestinal epithelial cells; n-6 PUFA tended to inhibit the Caco-2 adhesion of probiotics, whereas n-3 PUFA had either no or minor effects or even promote the bacterial adhesion (especially Lactobacillus casei Shirota) to PUFA treated Caco-2 cells. The results of this study demonstrate the close and bilateral interactions between dietary PUFA and probiotics. Probiotics were shown to influence the absorption and utilization of dietary PUFA, whereas PUFA were shown to alter the functional properties of both probiotics and mucosal epithelia. These findings suggest that a more thorough understanding of interactions between PUFA and intestinal microbiota is a prerequisite, when the beneficial effects of new functional foods containing probiotics are designed and planned for human intervention studies.

Microscopic simulation of pigment coating consolidation

The control of coating layer properties is becoming increasingly important as a result of an emerging demand for novel coated paper-based products and an increasing popularity of new coating application methods. The governing mechanisms of microstructure formation dynamics during consolidation and drying are nevertheless, still poorly understood. Some of the difficulties encountered by experimental methods can be overcome by the utilisation of numerical modelling and simulation-based studies of the consolidation process. The objective of this study was to improve the fundamental understanding of pigment coating consolidation and structure formation mechanisms taking place on the microscopic level. Furthermore, it is aimed to relate the impact of process and suspension properties to the microstructure of the coating layer. A mathematical model based on a modified Stokesian dynamics particle simulation technique was developed and applied in several studies of consolidation-related phenomena. The model includes particle-particle and particle-boundary hydrodynamics, colloidal interactions, Born repulsion, and a steric repulsion model. The Brownian motion and a free surface model were incorporated to enable the specific investigation of consolidation and drying. Filter cake stability was simulated in various particle systems, and subjected to a range of base substrate absorption rates and system temperatures. The stability of the filter cake was primarily affected by the absorption rate and size of particles. Temperature was also shown to have an influence. The consolidation of polydisperse systems, with varying wet coating thicknesses, was studied using imposed pilot trial and model-based drying conditions. The results show that drying methods have a clear influence on the microstructure development, on small particle distributions in the coating layer and also on the mobility of particles during consolidation. It is concluded that colloidal properties can significantly impact coating layer shrinkage as well as the internal solids concentration profile. Visualisations of particle system development in time and comparison of systems at different conditions are useful in illustrating coating layer structure formation mechanisms. The results aid in understanding the underlying mechanisms of pigment coating layer consolidation. Guidance is given regarding the relationship between coating process conditions and internal coating slurry properties and their effects on the microstructure of the coating.

Quantification of Proteins and Cells: Luminometric Nonspecific Particle-Based Methods

New luminometric particle-based methods were developed to quantify protein and to count cells. The developed methods rely on the interaction of the sample with nano- or microparticles and different principles of detection. In fluorescence quenching, timeresolved luminescence resonance energy transfer (TR-LRET), and two-photon excitation fluorescence (TPX) methods, the sample prevents the adsorption of labeled protein to the particles. Depending on the system, the addition of the analyte increases or decreases the luminescence. In the dissociation method, the adsorbed protein protects the Eu(III) chelate on the surface of the particles from dissociation at a low pH. The experimental setups are user-friendly and rapid and do not require hazardous test compounds and elevated temperatures. The sensitivity of the quantification of protein (from 40 to 500 pg bovine serum albumin in a sample) was 20-500-fold better than in most sensitive commercial methods. The quenching method exhibited low protein-to-protein variability and the dissociation method insensitivity to the assay contaminants commonly found in biological samples. Less than ten eukaryotic cells were detected and quantified with all the developed methods under optimized assay conditions. Furthermore, two applications, the method for detection of the aggregation of protein and the cell viability test, were developed by utilizing the TR-LRET method. The detection of the aggregation of protein was allowed at a more than 10,000 times lower concentration, 30 μg/L, compared to the known methods of UV240 absorbance and dynamic light scattering. The TR-LRET method was combined with a nucleic acid assay with cell-impermeable dye to measure the percentage of dead cells in a single tube test with cell counts below 1000 cells/tube.