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.

Multifrequency VLBI Observations of Selected Active Galactic Nuclei

In this dissertation, active galactic nuclei (AGN) are discussed, as they are seen with the high-resolution radio-astronomical technique called Very Long Baseline Interferometry (VLBI). This observational technique provides very high angular resolution (_ 10−300 = 1 milliarcsecond). VLBI observations, performed at different radio frequencies (multi-frequency VLBI), allow to penetrate deep into the core of an AGN to reveal an otherwise obscured inner part of the jet and the vicinity of the AGN’s central engine. Multi-frequency VLBI data are used to scrutinize the structure and evolution of the jet, as well as the distribution of the polarized emission. These data can help to derive the properties of the plasma and the magnetic field, and to provide constraints to the jet composition and the parameters of emission mechanisms. Also VLBI data can be used for testing the possible physical processes in the jet by comparing observational results with results of numerical simulations. The work presented in this thesis contributes to different aspects of AGN physics studies, as well as to the methodology of VLBI data reduction. In particular, Paper I reports evidence of optical and radio emission of AGN coming from the same region in the inner jet. This result was obtained via simultaneous observations of linear polarization in the optical and in radio using VLBI technique of a sample of AGN. Papers II and III describe, in detail, the jet kinematics of the blazar 0716+714, based on multi-frequency data, and reveal a peculiar kinematic pattern: plasma in the inner jet appears to move substantially faster that that in the large-scale jet. This peculiarity is explained by the jet bending, in Paper III. Also, Paper III presents a test of the new imaging technique for VLBI data, the Generalized Maximum Entropy Method (GMEM), with the observed (not simulated) data and compares its results with the conventional imaging. Papers IV and V report the results of observations of the circularly polarized (CP) emission in AGN at small spatial scales. In particular, Paper IV presents values of the core CP for 41 AGN at 15, 22 and 43 GHz, obtained with the help of the standard Gain transfer (GT) method, which was previously developed by D. Homan and J.Wardle for the calibration of multi-source VLBI observations. This method was developed for long multi-source observations, when many AGN are observed in a single VLBI run. In contrast, in Paper V, an attempt is made to apply the GT method to single-source VLBI observations. In such observations, the object list would include only a few sources: a target source and two or three calibrators, and it lasts much shorter than the multi-source experiment. For the CP calibration of a single-source observation, it is necessary to have a source with zero or known CP as one of the calibrators. If the archival observations included such a source to the list of calibrators, the GT could also be used for the archival data, increasing a list of known AGN with the CP at small spatial scale. Paper V contains also calculation of contributions of different sourced of errors to the uncertainty of the final result, and presents the first results for the blazar 0716+714.

People and the intertidal : human induced changes, biodiversity loss, livelihood implications and management in the Western Indian Ocean

Vad händer i tidvattenzonen? Var går gränsen mellan land och hav, vad händer i tidvattenzonen och vem ansvarar för detta? I västra Indiska oceanen (VIO) kan avståndet mellan den lägsta nivån för lågvattnet och den högsta nivån för högvattnet vara flera kilometer och nivåskillnaderna upp till 6 meter och detta skapar ett stort och föränderligt område. Syftet med min avhandling är att öka förståelsen för tidvattenzonen i tropiska och subtropiska västra Indiska oceanen. Sammanfattningsvis visar mina studier att det finns ett mycket stort värde i den komplexa tidvattenzonen, men också att det här området hotas från både land och hav, genom t.ex. överexploatering, erosion och föroreningar. Uttnyttjandet av tidvattenzonen är stort och min avhandling har visat att aktiviteter såsom fiske i form av plocking av musslor och andra ryggradslösa djur och hamnaktiviteter påverkar den biologiska mångfalden negativt, vilket leder till försämrad levnadsstandard för resursutnyttjande människor i regionen. För att förbättra situationen krävs det mer forskning, miljöövervakning och bättre förvaltning av tidvattenzonen. Experter i regionen har rangordnat förslag på förvaltningsstrategier som skulle kunna testas för att förbättra miljön och skapa ett mer hållbart nyttjande. Avhandlingen visar även att det är möjligt att använda fjärranalysteknik såsom satellitbildsanalys för att kvantifiera mängden sjögräsvegetation (i form av biomassa), vilket kan ha stor betydelse för att förbättra storskalig miljöövervakning av kustnära naturtyper (habitat). I avhandlingsarbetet har jag använt mig av ett multidisciplinärt tillvägagångssätt och använt metoder såsom ekologisk och biologisk provtagning, intervjuer, observationer, diskussionsgrupper, frågeformulär och fjärranalys. Resultaten presenterade i denna avhandling ger en ökad kunskap om tidvattenzonen i utvecklingsländerna inom VIO-regionen som kan användas för att initiera och fortsätta att utveckla hållbara förvaltningsstrategier av biologiska resurser.

Liquid transportation and distribution during (re)wetting : impact on coated papers in printing

In many industrial applications, such as the printing and coatings industry, wetting of porous materials by liquids includes not only imbibition and permeation into the bulk but also surface spreading and evaporation. By understanding these phenomena, valuable information can be obtained for improved process control, runnability and printability, in which liquid penetration and subsequent drying play important quality and economic roles. Knowledge of the position of the wetting front and the distribution/degree of pore filling within the structure is crucial in describing the transport phenomena involved. Although exemplifying paper as a porous medium in this work, the generalisation to dynamic liquid transfer onto a surface, including permeation and imbibition into porous media, is of importance to many industrial and naturally occurring environmental processes. This thesis explains the phenomena in the field of heatset web offset printing but the content and the analyses are applicable in many other printing methods and also other technologies where water/moisture monitoring is crucial in order to have a stable process and achieve high quality end products. The use of near-infrared technology to study the water and moisture response of porous pigmented structures is presented. The use of sensitive surface chemical and structural analysis, as well as the internal structure investigation of a porous structure, to inspect liquid wetting and distribution, complements the information obtained by spectroscopic techniques. Strong emphasis has been put on the scale of measurement, to filter irrelevant information and to understand the relationship between interactions involved. The near-infrared spectroscopic technique, presented here, samples directly the changes in signal absorbance and its variation in the process at multiple locations in a print production line. The in-line non-contact measurements are facilitated by using several diffuse reflectance probes, giving the absolute water/moisture content from a defined position in the dynamic process in real-time. The nearinfrared measurement data illustrate the changes in moisture content as the paper is passing through the printing nips and dryer, respectively, and the analysis of the mechanisms involved highlight the roles of the contacting surfaces and the relative liquid carrier properties of both non-image and printed image areas. The thesis includes laboratory studies on wetting of porous media in the form of coated paper and compressed pigment tablets by mono-, dual-, and multi-component liquids, and paper water/moisture content analysis in both offline and online conditions, thus also enabling direct sampling of temporal water/moisture profiles from multiple locations. One main focus in this thesis was to establish a measurement system which is able to monitor rapid changes in moisture content of paper. The study suggests that near-infrared diffuse reflectance spectroscopy can be used as a moisture sensitive system and to provide accurate online qualitative indicators, but, also, when accurately calibrated, can provide quantification of water/moisture levels, its distribution and dynamic liquid transfer. Due to the high sensitivity, samples can be measured with excellent reproducibility and good signal to noise ratio. Another focus of this thesis was on the evolution of the moisture content, i.e. changes in moisture content referred to (re)wetting, and liquid distribution during printing of coated paper. The study confirmed different wetting phases together with the factors affecting each phase both for a single droplet and a liquid film applied on a porous substrate. For a single droplet, initial capillary driven imbibition is followed by equilibrium pore filling and liquid retreat by evaporation. In the case of a liquid film applied on paper, the controlling factors defining the transportation were concluded to be the applied liquid volume in relation to surface roughness, capillarity and permeability of the coating giving the liquid uptake capacity. The printing trials confirmed moisture gradients in the printed sheet depending on process parameters such as speed, fountain solution dosage and drying conditions as well as the printed layout itself. Uneven moisture distribution in the printed sheet was identified to be one of the sources for waving appearance and the magnitude of waving was influenced by the drying conditions.

Mode B ultrasonography and abdominal Doppler in crab-eating-foxes ( Cerdocyon thous )

Abstract: Annually hundreds of crab-eating foxes (Cerdocyon thous) are referred to rehabilitation centers and zoos in Brazil. The ultrasonographic study of wildlife species is an important tool for a non-invasive and accurate anatomical description and provides important information for wildlife veterinary care. The aim of the present study was to determine the characteristics of the main abdominal organs as well as the vascular indexes of the abdominal aorta and renal arteries of crab-eating foxes (Cerdocyon thous) using mode B ultrasonography and Doppler ultrasonography, respectively. Ultrasonographic features of the main abdominal organs were described and slight differences were noticed between ultrasound imaging of abdominal organs of crab-eating foxes and other species. The bladder presented wall thickness of 12±0.01mm, with three defined layers. Both, the right and left kidneys presented corticomedullary ratio of 1:1 and similarly to the adrenals and the liver, they were homogeneous and hypoechoic compared to the spleen. The spleen was homogeneous and hyperechoic compared to the kidneys. The stomach presented 3 to 5 peristaltic movements per minute, wall thickness of 39±0.05mm and lumen and mucosa with hyperechoic and hypoechoic features, respectively. Small and large intestines presented 2 to 3 peristaltic movements per minute, wall thickness of 34±0.03mm and three defined layers with hyperechogenic (submucosa and serosa) and hypoechogenic (muscular) features. Ovaries of the female crab-eating fox were hypoechoic compared to the spleen and with heterogeneous parenchyma due to the presence of 2x2mm ovarian follicles. Prostates of the six males were regular and with a well defined boundary, with a homogeneous and hyperechoic parenchyma compared to the spleen. Vascular indexes of the abdominal aorta (PSV: 25.60±0.32cm/s; EDV: 6.96±1.68cm/s; PI: 1.15±0.07 e RI: 0.73±0.07) and right (PSV: 23.08±3.34cm/s; EDV: 9.33±2.36cm/s; PI: 1.01±0.65 e RI: 0.65±0.16) and left renal arteries (PSV: 23.74±3.94cm/s; EDV: 9.07±3.02cm/s; PI: 1.04±0.31 e RI: 0.64±0.10) were determined. Thus, conventional and Doppler ultrasonographic imaging provides basic information that can be used as reference for the species as well for other wild canids and it is a precise and non-invasive method that can be safely used to evaluate and diagnose abdominal injuries in these patients.

Panel Method Formulation for Oscillating Airfoils in Sonic Flow

The mathematical model for two-dimensional unsteady sonic flow, based on the classical diffusion equation with imaginary coefficient, is presented and discussed. The main purpose is to develop a rigorous formulation in order to bring into light the correspondence between the sonic, supersonic and subsonic panel method theory. Source and doublet integrals are obtained and Laplace transformation demonstrates that, in fact, the source integral is the solution of the doublet integral equation. It is shown that the doublet-only formulation reduces to a Volterra integral equation of the first kind and a numerical method is proposed in order to solve it. To the authors' knowledge this is the first reported solution to the unsteady sonic thin airfoil problem through the use of doublet singularities. Comparisons with the source-only formulation are shown for the problem of a flat plate in combined harmonic heaving and pitching motion.

Adaptation of TRIZ Method for Problem Solving in Process Engineering

TRIZ is one of the well-known tools, based on analytical methods for creative problem solving. This thesis suggests adapted version of contradiction matrix, a powerful tool of TRIZ and few principles based on concept of original TRIZ. It is believed that the proposed version would aid in problem solving, especially those encountered in chemical process industries with unit operations. In addition, this thesis would help fresh process engineers to recognize importance of various available methods for creative problem solving and learn TRIZ method of creative problem solving. This thesis work mainly provides idea on how to modify TRIZ based method according to ones requirements to fit in particular niche area and solve problems efficiently in creative way. Here in this case, the contradiction matrix developed is based on review of common problems encountered in chemical process industry, particularly in unit operations and resolutions are based on approaches used in past to handle those issues.

Real-time Image-based RGB-D Camera Motion Tracking and Environment Mapping

In this work, image based estimation methods, also known as direct methods, are studied which avoid feature extraction and matching completely. Cost functions use raw pixels as measurements and the goal is to produce precise 3D pose and structure estimates. The cost functions presented minimize the sensor error, because measurements are not transformed or modified. In photometric camera pose estimation, 3D rotation and translation parameters are estimated by minimizing a sequence of image based cost functions, which are non-linear due to perspective projection and lens distortion. In image based structure refinement, on the other hand, 3D structure is refined using a number of additional views and an image based cost metric. Image based estimation methods are particularly useful in conditions where the Lambertian assumption holds, and the 3D points have constant color despite viewing angle. The goal is to improve image based estimation methods, and to produce computationally efficient methods which can be accomodated into real-time applications. The developed image-based 3D pose and structure estimation methods are finally demonstrated in practise in indoor 3D reconstruction use, and in a live augmented reality application.

Blade and rod coating of low solid dispersions

Työn aiheena oli tehdä ohut barrierkalvo terä- tai sauvapäällystys menetelmällä. Erilaisissa elintarvikepakkauksissa käytetään hyviä barrier-ominaisuuksia omaavia ohuita päällysteitä. Elintarvikepakkauksen tehtävä on suojata pakattua tuotetta ympäristöltä, mahdollistaa helppo kuljetus ja säilytys sekä antaa tarvittavat tiedot tuotteesta tuotteen käsittelijöille ja loppukäyttäjille. Diplomityön teoriaosuudessa keskityttiin barrierpäällystykseen, eri päällystysmenetelmiin, niiden erityisvaatimuksiin ja ominaisuuksiin. Teoriaosuudessa käsiteltiin myös vaadittavia barrier-ominaisuuksia ja haasteita niiden saavuttamisessa. Kirjallisuuden perusteella haasteiksi nousivat helposti muodostuvat mikroreiät. Kokeellinen osa jakautui kahteen osakokonaisuuteen: laboratoriokokeisiin ja pilot-koeajoon. Laboratoriokokeita tehtiin ennen pilot-ajoa, jotta pilot-koeajoon voitiin valita parhaat päällystereseptit. Pilot-koeajonäytteiden päällystemäärät osoittautuivat liian pieniksi ja siksi laboratoriossa tehtiin jatkotutkimuksia riittävän päällystemäärän saavuttamiseksi. Tämän työnperusteella pohjakartongin ominaisuuksilla, erityisesti karheudella, on merkittävä vaikutus päällystyksen onnistumisessa ja yksinkertaisilla resepteillä ja päällystysmenetelmillä ei saada tarpeeksi laadukasta kalvoa.

Backpacker 2.0 - Contemporary backpackers and their use of social media as an information and communication platform

Long-term independent budget travel to countries far away has become increasingly common over the last few decades, and backpacking has now entered the tourism mainstream. Nowadays, backpackers are a very important segment of the global travel market. Backpacking is a type of tourism that involves a lot of information search activities. The Internet has become a major source of information as well as a platform for tourism business transactions. It allows travelers to gain information very effortlessly and to learn about tourist destinations and products directly from other travelers in the form of electronic word-of-mouth (eWOM). Social media has penetrated and changed the backpacker market, as now modern travelers can stay connected to people at home, read online recommendations, and organize and book their trips very independently. In order to create a wider understanding on modern-day backpackers and their information search and share behavior in the Web 2.0 era, this thesis examined contemporary backpackers and their use of social media as an information and communication platform. In order to achieve this goal, three sub-objectives were identified: 1. to describe contemporary backpacker tourism 2. to examine contemporary backpackers’ travel information search and share behavior 3. to explore the impacts of new information and communications technologies and Web 2.0 on backpacker tourism The empirical data was gathered with an online survey, thus the method of analysis was mainly quantitative, and a qualitative method was used for a brief analysis of open questions. The research included both descriptive and analytical approaches, as the goal was to describe modern-day backpackers, and to examine possible interdependencies between information search and share behavior and background variables. The interdependencies were tested for statistical significance with the help of five research hypotheses. The results suggested that backpackers no longer fall under the original backpacker definitions described some decades ago. Now, they are mainly short-term travelers, whose trips resemble more those of mainstream tourists. They use communication technologies very actively, and particularly social media. Traditional information sources, mainly guide books and recommendations from friends, are of great importance to them but also eWOM sources are widely used in travel decision making. The use of each source varies according to the stage of the trip. All in all, Web 2.0 and new ICTs have transformed the backpacker tourism industry in many ways. Although the experience has become less authentic in some travelers’ eyes, the backpacker culture is still recognizable.

Multi-source ingestion of publisher articles - The SCOAP3 repository experience

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

How and why to measure the germination process?

In the last two centuries, papers have been published including measurements of the germination process. High diversity of mathematical expressions has made comparisons between papers and some times the interpretation of results difficult. Thus, in this paper is included a review about measurements of the germination process, with an analysis of the several mathematical expressions included in the specific literature, recovering the history, sense, and limitations of some germination measurements. Among the measurements included in this paper are the germinability, germination time, coefficient of uniformity of germination (CUG), coefficient of variation of the germination time (CVt), germination rate (mean rate, weighted mean rate, coefficient of velocity, germination rate of George, Timson’s index, GV or Czabator’s index; Throneberry and Smith’s method and its adaptations, including Maguire’s rate; ERI or emergence rate index, germination index, and its modifications), uncertainty associated to the distribution of the relative frequency of germination (U), and synchronization index (Z). The limits of the germination measurements were included to make the interpretation and decisions during comparisons easier. Time, rate, homogeneity, and synchrony are aspects that can be measured, informing the dynamics of the germination process. These characteristics are important not only for physiologists and seed technologists, but also for ecologists because it is possible to predict the degree of successful of a species based on the capacity of their harvest seed to spread the germination through time, permitting the recruitment in the environment of some part of the seedlings formed.

Segmentation of overlapping convex objects

This thesis presents a framework for segmentation of clustered overlapping convex objects. The proposed approach is based on a three-step framework in which the tasks of seed point extraction, contour evidence extraction, and contour estimation are addressed. The state-of-art techniques for each step were studied and evaluated using synthetic and real microscopic image data. According to obtained evaluation results, a method combining the best performers in each step was presented. In the proposed method, Fast Radial Symmetry transform, edge-to-marker association algorithm and ellipse fitting are employed for seed point extraction, contour evidence extraction and contour estimation respectively. Using synthetic and real image data, the proposed method was evaluated and compared with two competing methods and the results showed a promising improvement over the competing methods, with high segmentation and size distribution estimation accuracy.

Plant height reduction in populations of triticale (X triticosecale Wittmack) by induced mutations and artificial crosses

Induced mutations by gamma radiation (0, 5, 10, 20 and 40 kR doses) and reciprocal crosses were tested as mechanisms of enhancing genetic variability for plant height in two triticale cultivars, BR4 and EMBRAPA18. The reciprocal crosses and all doses of radiation showed similar increase in genetic amplitude for this trait, being suitable for increasing variability in breeding programs. Genotypes showed different responses as the gamma ray doses were increased, expressing shorter plant height. The decision of using induced mutations or artificial crosses depends on the resources available and the selection method to be used

Alternative oxidase in the branched mitochondrial respiratory network: an overview on structure, function, regulation, and role

Plants and some other organisms including protists possess a complex branched respiratory network in their mitochondria. Some pathways of this network are not energy-conserving and allow sites of energy conservation to be bypassed, leading to a decrease of the energy yield in the cells. It is a challenge to understand the regulation of the partitioning of electrons between the various energy-dissipating and -conserving pathways. This review is focused on the oxidase side of the respiratory chain that presents a cyanide-resistant energy-dissipating alternative oxidase (AOX) besides the cytochrome pathway. The known structural properties of AOX are described including transmembrane topology, dimerization, and active sites. Regulation of the alternative oxidase activity is presented in detail because of its complexity. The alternative oxidase activity is dependent on substrate availability: total ubiquinone concentration and its redox state in the membrane and O2 concentration in the cell. The alternative oxidase activity can be long-term regulated (gene expression) or short-term (post-translational modification, allosteric activation) regulated. Electron distribution (partitioning) between the alternative and cytochrome pathways during steady-state respiration is a crucial measurement to quantitatively analyze the effects of the various levels of regulation of the alternative oxidase. Three approaches are described with their specific domain of application and limitations: kinetic approach, oxygen isotope differential discrimination, and ADP/O method (thermokinetic approach). Lastly, the role of the alternative oxidase in non-thermogenic tissues is discussed in relation to the energy metabolism balance of the cell (supply in reducing equivalents/demand in energy and carbon) and with harmful reactive oxygen species formation.