Non-surgical transfer of 4',6'-diamidino-2-phenylindole-stained equine embryos

Selostus: Hevosen alkioiden värjääminen DAPI:lla ennen vastaanottajaan siirtoa

Phosphorus saturation of Finnish soils : evaluating an easy oxalate extraction method

Selostus: Alumiini- ja rautaoksidien fosforikyllästysasteen arvioiminen suomalaisista peltomaista

Embedding, Extraction and Detection of Digital Watermark in Spectral Images

Tässä diplomityössä tutkitaan tekniikoita, joillavesileima lisätään spektrikuvaan, ja menetelmiä, joilla vesileimat tunnistetaanja havaitaan spektrikuvista. PCA (Principal Component Analysis) -algoritmia käyttäen alkuperäisten kuvien spektriulottuvuutta vähennettiin. Vesileiman lisääminen spektrikuvaan suoritettiin muunnosavaruudessa. Ehdotetun mallin mukaisesti muunnosavaruuden komponentti korvattiin vesileiman ja toisen muunnosavaruuden komponentin lineaarikombinaatiolla. Lisäyksessä käytettävää parametrijoukkoa tutkittiin. Vesileimattujen kuvien laatu mitattiin ja analysoitiin. Suositukset vesileiman lisäykseen esitettiin. Useita menetelmiä käytettiin vesileimojen tunnistamiseen ja tunnistamisen tulokset analysoitiin. Vesileimojen kyky sietää erilaisia hyökkäyksiä tarkistettiin. Diplomityössä suoritettiin joukko havaitsemis-kokeita ottamalla huomioon vesileiman lisäyksessä käytetyt parametrit. ICA (Independent Component Analysis) -menetelmää pidetään yhtenä mahdollisena vaihtoehtona vesileiman havaitsemisessa.

Local and Global Feature Extraction for Invariant Object Recognition

Perceiving the world visually is a basic act for humans, but for computers it is still an unsolved problem. The variability present innatural environments is an obstacle for effective computer vision. The goal of invariant object recognition is to recognise objects in a digital image despite variations in, for example, pose, lighting or occlusion. In this study, invariant object recognition is considered from the viewpoint of feature extraction. Thedifferences between local and global features are studied with emphasis on Hough transform and Gabor filtering based feature extraction. The methods are examined with respect to four capabilities: generality, invariance, stability, and efficiency. Invariant features are presented using both Hough transform and Gabor filtering. A modified Hough transform technique is also presented where the distortion tolerance is increased by incorporating local information. In addition, methods for decreasing the computational costs of the Hough transform employing parallel processing and local information are introduced.

On Option Price Information Content and Extraction of Implied Probability Distributions

In this study we used market settlement prices of European call options on stock index futures to extract implied probability distribution function (PDF). The method used produces a PDF of returns of an underlying asset at expiration date from implied volatility smile. With this method, the assumption of lognormal distribution (Black-Scholes model) is tested. The market view of the asset price dynamics can then be used for various purposes (hedging, speculation). We used the so called smoothing approach for implied PDF extraction presented by Shimko (1993). In our analysis we obtained implied volatility smiles from index futures markets (S&P 500 and DAX indices) and standardized them. The method introduced by Breeden and Litzenberger (1978) was then used on PDF extraction. The results show significant deviations from the assumption of lognormal returns for S&P500 options while DAX options mostly fit the lognormal distribution. A deviant subjective view of PDF can be used to form a strategy as discussed in the last section.

Surgical treatment of hamstring injuries and disorders – the clinical spectrum from chronic tendinopathy to complete rupture

Hamstring muscle injuries and tendon disorders are common, especially in sports. They can be severe and difficult to treat, often resulting in impaired athletic performance and long rehabilitation times. Previous studies considering treatment of these problems are scarce. The current study was designed to investigate the effect of surgery on different types of hamstring muscle injuries and on proximal hamstring tendinopathy. In addition, we wanted to study the typical histopathological findings relating to proximal hamstring tendinopathy. In the study of complete (all three muscles torn) proximal hamstring avulsions (41 patients), our results showed that early operative treatment gives significantly better results than late surgery, and is therefore recommended. Despite this, considerable improvement of symptoms could also be achieved in chronic cases. In the study of partial (one or two muscles torn) proximal hamstring tears (47 patients), we observed that these injuries can cause significant functional deficit and impaired performance in athletes. The main finding was that after surgical repair most of the patients were able to return to their pre-injury level of sports. In the study of distal hamstring tears (18 patients), the results showed that surgical treatment had a good effect in the majority of these cases. In proximal hamstring tendinopathy, the main problem is pain which limits sports. In this study (90 patients), we found that after unsuccessful conservative treatment, surgery was a good treatment option resulting in full return to sports in most cases. In tendinopathic hamstring tendons, the morphological changes of tendinosis were largely identical to those previously described in other common (e.g. Achilles and patellar) tendinopathies. In chronic proximal hamstring avulsions, and also in reoperations, a large defect between distally retracted tendons and the ischial tuberosity may occasionally prevent anatomic reinsertion. We have described a reconstruction method using fascia lata autograft augmentation to be used in these most challenging repairs. This technique was utilized in the treatment of five patients, with encouraging results.

The Role of Surfactant Properties of Extractants in Hydrometallurgical LiquidLiquid Extraction Processes

The amphiphilic nature of metal extractants causes the formation of micelles and other microscopic aggregates when in contact with water and an organic diluent. These phenomena and their effects on metal extraction were studied using carboxylic acid (Versatic 10) and organophosphorus acid (Cyanex 272) based extractants. Special emphasis was laid on the study of phase behaviour in a pre neutralisation stage when the extractant is transformed to a sodium or ammonium salt form. The pre neutralised extractants were used to extract nickel and to separate cobalt and nickel. Phase diagrams corresponding to the pre neutralisation stage in a metal extraction process were determined. The maximal solubilisation of the components in the system water(NH3)/extractant/isooctane takes place when the molar ratio between the ammonia salt form and the free form of the extractant is 0.5 for the carboxylic acid and 1 for the organophosphorus acid extractant. These values correspond to the complex stoichiometry of NH4A•HA and NIi4A, respectively. When such a solution is contacted with water a microemulsion is formed. If the aqueous phase contains also metal ions (e.g. Ni²+), complexation will take place on the microscopic interface of the micellar aggregates. Experimental evidence showing that the initial stage of nickel extraction with pre neutralised Versatic 10 is a fast pseudohomogeneous reaction was obtained. About 90% of the metal were extracted in the first 15 s after the initial contact. For nickel extraction with pre neutralised Versatic 10 it was found that the highest metal loading and the lowest residual ammonia and water contents in the organic phase are achieved when the feeds are balanced so that the stoichiometry is 2NH4+(org) = Nit2+(aq). In the case of Co/Ni separation using pre neutralised Cyanex 272 the highest separation is achieved when the Co/extractant molar ratio in the feeds is 1 : 4 and at the same time the optimal degree of neutralisation of the Cyanex 272 is about 50%. The adsorption of the extractants on solid surfaces may cause accumulation of solid fine particles at the interface between the aqueous and organic phases in metal extraction processes. Copper extraction processes are known to suffer of this problem. Experiments were carried out using model silica and mica particles. It was found that high copper loading, aromacity of the diluent, modification agents and the presence of aqueous phase decrease the adsorption of the hydroxyoxime on silica surfaces.

Recovery of organic acids with liquid-liquid extraction contactors

Liquid-liquid extraction is a mass transfer process for recovering the desired components from the liquid streams by contacting it to non-soluble liquid solvent. Literature part of this thesis deals with theory of the liquid-liquid extraction and the main steps of the extraction process design. The experimental part of this thesis investigates the extraction of organic acids from aqueous solution. The aim was to find the optimal solvent for recovering the organic acids from aqueous solutions. The other objective was to test the selected solvent in pilot scale with packed column and compare the effectiveness of the structured and the random packing, the effect of dispersed phase selection and the effect of packing material wettability properties. Experiments showed that selected solvent works well with dilute organic acid solutions. The random packing proved to be more efficient than the structured packing due to higher hold-up of the dispersed phase. Dispersing the phase that is present in larger volume proved to more efficient. With the random packing the material that was wetted by the dispersed phase was more efficient due to higher hold-up of the dispersed phase. According the literature, the behavior is usually opposite.

Surgical Treatment of Colorectal Cancer. Controversial Issues

Aims: This study was carried out to evaluate surgical treatment of colorectal cancer (CRC) with special interest in present status and controversial issues: stenting as a palliative procedure for metastasized CRC (I), duration of thromboprophylaxis after the surgical treatment of CRC (II), treatment of the increasing population of elderly people (III) and the quality of life (QoL) after surgery for rectal cancer with special reference to pelvic floor dysfunction (IV). Materials and methods: The material consisted of patients with CRC operated on at Turku University Hospital between 2003 and 2008. In study II the data was collected retrospectively from electronic archives. In other studies the follow-up data was collected at postoperative control visits. In study IV the RAND-36 standardized questionnaire and additional questions assessing urinary, sexual and anorectal dysfunction were used. Results: The results of the current study showed that self-expanding metallic stents provided an alternative to palliative surgery in the treatment of obstructive CRC. Low molecular heparin given s.c. for a median of 11 days until hospital discharge seemed to provide sufficient thromboprophylaxis after surgery. With preoperative selection elderly patients with rectal cancer were suitable for major surgery for rectal cancer with morbidity and mortality rates comparable to those in younger patients. There was no difference between preoperative and one year postoperative general QoL for operated rectal cancer patients. Postoperative pelvic dysfunction was associated with an impaired QoL in some dimensions. Conclusions: Many individual factors regarding the patient and the disease must be taken into account when making treatment decisions in CRC to ensure successful treatment of CRC, patient satisfaction and QoL.

Quality of Abdominal Surgical Nursing Care

The study evaluates the quality of abdominal surgical nursing care. The data were collected from patients (n=1208) having undergone abdominal surgical operations on their last day of hospitalization and nurses (n=218) working in the same wards. Three instruments originally created in Finland and adapted to the Lithuanian context were used: (1) Good Nursing Care Scale for patients and nurses (GNCS-P, GNCS-N), (2) Nurse Competence Scale (NCS), and (3) Nurse Empowerment Scale (NES). Patient and nurses’ perceptions of the quality of nursing care were evaluated. In addition, nurses’ perceptions of their competence and empowerment were evaluated. The patient and nurses' perceptions of the quality of abdominal surgical nursing care were positive, with more criticism in the nurses’ perceptions. Both patients and nurses gave the lowest evaluation to the quality in the progress of nursing care and the co-operation with significant others. The nurses gave the highest evaluation to the self-assessed level of their competence and the frequency of using competences in practice, with the highest assessment given to situation management and their role at work and the lowest to teaching-coaching and ensuring quality. The nurse perceptions of their empowerment were positive in the qualities and performance of an empowered nurse and empowerment promoting factors, with the highest evaluation in moral principles and sociability and the lowest evaluation in the future-orientedness and expertise. The empowerment-impeding factors were evaluated as negative. The perceptions of the quality of nursing care of both patients and nurses had significant correlations with patient and nurse satisfaction and nurse job independence. The nurse perceptions of their competence and empowerment correlated with their education, the type of the nurse license, completed courses of development of their knowledge and skills, nurse job independence, and nurse satisfaction. The nurse perceptions of the quality of nursing care had a positive correlation with their perceptions of competence and empowerment. Generally, the quality of nursing care was evaluated as high and had correlations with the patients' demographic and satisfaction factors and with the nurse demographic, work-related, and satisfaction factors. The study produced the knowledge that the quality in co-operation with significant others and the progress of nursing process, surgical nurse competence in teaching-coaching, and future-orientedness of surgical nurse empowerment need to be improved in order to develop the quality of abdominal surgical nursing care. The knowledge may be used to offer better services for abdominal surgical patients and increase their satisfaction with nursing care, as well as to increase nurses' satisfaction with work and independence at work. The study suggests implications for clinical practice and management, nursing education, and nursing research.

Pharmacokinetics of Oxycodone and Paracetamol in the Elderly. Clinical Pharmacokinetic Study on Orthopaedic Surgical Patients and Healthy Volunteers

The proportion of elderly people over 65 years of age in Finland is expected to grow to over 25% by the 2025. It has been estimated that elderly people today consume nearly 40% of all drugs. Age brings about number of physiological changes that may affect the disposition, metabolism and excretion of drugs. The function of heart, lungs, liver and kidneys decreases even in healthy people, as they get older. The proportion of total body water decreases and the relative fat percentage increases. Also several other factors such as concurrent diseases, concomitant medication and nutritional factors have an effect on drug therapy in elderly. Age increases the risk of adverse drug reactions, which most often are dose-dependent. Despite all this there are not enough studies involving the elderly people and the elderly are most often excluded from clinical trials. Oxycodone is a strong opioid analgesic, which is used to treat moderate or severe pain. Paracetamol is a widely used nonopioid analgesic, which has become popular in the treatment of pain in many patient groups. In this series of studies the pharmacokinetics of oral and intravenous oxicodone as well as intravenous paracetamol in the elderly and young adult patients were investigated. Also a study investigating the interaction of oral antibiotic clarityhromycin, a known cytochrome P450 (CYP) 3A4 inhibitor, with oxycodone pharmacokinetics and pharmacodynamics in elderly and young healthy volunteers was carried out. The pharmacokinetics of oxycodone showed a clear age depency. Patients over 70 years had 50-80% higher mean exposure to oral oxycodone and a twofold greater plasma concentration than young adults 12 h after ingestion of the drug. Elderly patients had 40-80% greater exposure to intravenous oxycodone and patients over 80 years had over twofold greater plasma concentrations 8 h post dose than the young adults. The elderly patients had also greater exposure to intra venous paracetamol compared to young adults. Clarithromycin increased the exposure to oral oxycodone in both young and elderly volunteers. The elderly had marked interindividual variation in the pharmacokinetics and pharmacodynamics when clarithromycin was given concomitantly with oxycodone. Because the pharmacokinetics of oxycodone and intravenous paracetamol depend on the age of the subject, it is important to titrate the analgesic dose individually in the elderly.

Recovery of carboxylic acids from aqueous streams by extraction and back extraction

Separation of carboxylic acids from aqueous streams is an important part of their manufacturing process. The aqueous solutions are usually dilute containing less than 10 % acids. Separation by distillation is difficult as the boiling points of acids are only marginally higher than that of water. Because of this distillation is not only difficult but also expensive due to the evaporation of large amounts of water. Carboxylic acids have traditionally been precipitated as calcium salts. The yields of these processes are usually relatively low and the chemical costs high. Especially the decomposition of calcium salts with sulfuric acid produces large amounts of calcium sulfate sludge. Solvent extraction has been studied as an alternative method for recovery of carboxylic acids. Solvent extraction is based on mixing of two immiscible liquids and the transfer of the wanted components form one liquid to another due to equilibrium difference. In the case of carboxylic acids, the acids are transferred from aqueous phase to organic solvent due to physical and chemical interactions. The acids and the extractant form complexes which are soluble in the organic phase. The extraction efficiency is affected by many factors, for instance initial acid concentration, type and concentration of the extractant, pH, temperature and extraction time. In this paper, the effects of initial acid concentration, type of extractant and temperature on extraction efficiency were studied. As carboxylic acids are usually the products of the processes, they are wanted to be recovered. Hence the acids have to be removed from the organic phase after the extraction. The removal of acids from the organic phase also regenerates the extractant which can be then recycled in the process. The regeneration of the extractant was studied by back-extracting i.e. stripping the acids form the organic solution into diluent sodium hydroxide solution. In the solvent regeneration, the regenerability of different extractants and the effect of initial acid concentration and temperature were studied.

Extraction of polymeric galactoglucomannans from spruce wood by pressurized hot water

The major type of non-cellulosic polysaccharides (hemicelluloses) in softwoods, the partly acetylated galactoglucomannans (GGMs), which comprise about 15% of spruce wood, have attracted growing interest because of their potential to become high-value products with applications in many areas. The main objective of this work was to explore the possibilities to extract galactoglucomannans in native, polymeric form in high yield from spruce wood with pressurised hot-water, and to obtain a deeper understanding of the process chemistry involved. Spruce (Picea abies) chips and ground wood particles were extracted using an accelerated solvent extractor (ASE) in the temperature range 160 – 180°C. Detailed chemical analyses were done on both the water extracts and the wood residues. As much as 80 – 90% of the GGMs in spruce wood, i.e. about 13% based on the original wood, could be extracted from ground spruce wood with pure water at 170 – 180°C with an extraction time of 60 min. GGMs comprised about 75% of the extracted carbohydrates and about 60% of the total dissolved solids. Other substances in the water extracts were xylans, arabinogalactans, pectins, lignin and acetic acid. The yields from chips were only about 60% of that from ground wood. Both the GGMs and other non-cellulosic polysaccharides were extensively hydrolysed at severe extraction conditions when pH dropped to the level of 3.5. Addition of sodium bicarbonate increased the yields of polymeric GGMs at low additions, 2.5 – 5 mM, where the end pH remained around 3.9. However, at higher addition levels the yields decreased, mainly because the acetyl groups in GGMs were split off, leading to a low solubility of GGMs. Extraction with buffered water in the pH range 3.8 – 4.4 gave similar yields as with plain water, but gave a higher yield of polymeric GGMs. Moreover, at these pH levels the hydrolysis of acetyl groups in GGMs was significantly inhibited. It was concluded that hot-water extraction of polymeric GGMs in good yields (up to 8% of wood) demands appropriate control of pH, in a narrow range about 4. These results were supported by a study of hydrolysis of GGM at constant pH in the range of 3.8 – 4.2 where a kinetic model for degradation of GGM was developed. The influence of wood particle size on hot-water extraction was studied with particles in the range of 0.1 – 2 mm. The smallest particles (< 0.1 mm) gave 20 – 40% higher total yield than the coarsest particles (1.25 – 2 mm). The difference was greatest at short extraction times. The results indicated that extraction of GGMs and other polysaccharides is limited mainly by the mass transfer in the fibre wall, and for coarse wood particles also in the wood matrix. Spruce sapwood, heartwood and thermomechnical pulp were also compared, but only small differences in yields and composition of extracts were found. Two methods for isolation and purification of polymeric GGMs, i.e. membrane filtration and precipitation in ethanol-water, were compared. Filtration through a series of membranes with different pore sizes separated GGMs of different molar masses, from polymers to oligomers. Polysaccharides with molar mass higher than 4 kDa were precipitated in ethanol-water. GGMs comprised about 80% of the precipitated polysaccharides. Other polysaccharides were mainly arabinoglucuronoxylans and pectins. The ethanol-precipitated GGMs were by 13C NMR spectroscopy verified to be very similar to GGMs extracted from spruce wood in low yield at a much lower temperature, 90°C. The obtained large body of experimental data could be utilised for further kinetic and economic calculations to optimise technical hot-water extractionof softwoods.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.