Extraction and Simultaneous Determination of Glyphosate, AMPA and Compounds of the Shikimic Acid Pathway in Plants

This study has aimed to develop a method for simultaneous extraction and determination by liquid chromatography and mass spectrometry (LC-MS/MS) of glyphosate, aminomethylphosphonic acid (AMPA), shikimic acid, quinic acid, phenylalanine, tyrosine and tryptophan. For the joint analysis of these compounds the best conditions of ionization in mass spectrometry and for chromatographic separation of the compounds were selected. Calibration curves and linearity ranges were also determined for each compound. Different extraction systems of the compounds were tested from plant tissues collected from sugarcane (Saccharum officinarum) and eucalyptus (Eucalyptus urophylla platiphylla) plants two days after the glyphosate application at the dose of 720 g a.e. ha-1. The plant material was dried in a forced air circulation drying oven and in a lyophilizer, and subsequently the extractions with acidified water (pH 2.5), acetonitrile-water (50:50) [v/v] and methanol-water (50:50) [v/v] were tested. To verify the recovery of the compounds in the plant matrix with acidified water as an extracting solution, the samples were fortified with a solution containing the mixture of the different analytical standards present so that this one presented the same levels of 50 and 100 μg L-1 of each compound. All experiments were conducted with three replicates. The analytical method developed was efficient for compounds quantifications. The extraction from the samples dried in an oven and using acidified water allowed better extraction levels for all compounds. The recovery levels of the compounds in the fortified samples with known amounts of each compound for both plants samples were rather satisfactory.

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.

Alternative procedures for parent choice in a breeding program for the common bean (Phaseolus vulgaris L.)

Six common bean cultivars were crossed in diallel and the segregant populations were assessed in the F2 and F3 generations to compare methodologies for parental selection in a breeding program based on hybridization. The cultivars involved in the diallel were A 114, A 77, ESAL 686, Milionário, Carioca, and Flor de Mayo. The segregant F2 and F3 generations were assessed on the experimental campus of the Universidade Federal de Larvas, in July 1994. It was found that the cultivars differed in their general combining ability (GCA). Flor de Mayo, which belongs to the Durango race, had the largest positive GCA estimate for grain field, and the cultivars from the Mesoamerican race, Milionário and A 114, the smallest GCA estimates. For flowering, the cultivar that most contributed to reduced plant cycle was ESAL 686. There was agreement among the results obtained from the diallel and the estimates of the parameter m + a of the populations. However, it was evident that the estimate of genetic variance of the populations should be considered as a condition to identify the hybrid population that will produce a line with high performance.

Use of a cysteine proteinase from Carica candamarcensis as a protective agent during DNA extraction

We describe the use of a plant cysteine proteinase isolated from latex of Carica candamarcensis as a protective agent during isolation of bacterial DNA following growth in culture of these cells. Between 100 to 720 units of proteinase (1 µg = 6 units) afforded good DNA protection when incubated with various kinds of microorganisms. Agarose gel electrophoresis showed that the resulting DNA was similar in size to DNA preparations obtained by treatment with proteinase K. The viability of the resulting material was checked by PCR amplification using species-specific primers. After standing at room temperature (25oC) for 35 days, the enzyme lost 10% of its initial activity. The enzyme stability and good yield of DNA suggest the use of this proteinase as an alternative to proteinase K.

Pressurized hot water flow-through extraction of birch wood

Effective processes to fractionate the main compounds in biomass, such as wood, are a prerequisite for an effective biorefinery. Water is environmentally friendly and widely used in industry, which makes it a potential solvent also for forest biomass. At elevated temperatures over 100 °C, water can readily hydrolyse and dissolve hemicelluloses from biomass. In this work, birch sawdust was extracted using pressurized hot water (PHWE) flow-through systems. The hypothesis of the work was that it is possible to obtain polymeric, water-soluble hemicelluloses from birch sawdust using flow-through PHW extractions at both laboratory and large scale. Different extraction temperatures in the range 140–200 °C were evaluated to see the effect of temperature to the xylan yield. The yields and extracted hemicelluloses were analysed to obtain sugar ratios, the amount of acetyl groups, furfurals and the xylan yields. Higher extraction temperatures increased the xylan yield, but decreased the molar mass of the dissolved xylan. As the extraction temperature increased, more acetic acid was released from the hemicelluloses, thus further decreasing the pH of the extract. There were only trace amounts of furfurals present after the extractions, indicating that the treatment was mild enough not to degrade the sugars further. The sawdust extraction density was increased by packing more sawdust in the laboratory scale extraction vessel. The aim was to obtain extracts with higher concentration than in typical extraction densities. The extraction times and water flow rates were kept constant during these extractions. The higher sawdust packing degree decreased the water use in the extractions and the extracts had higher hemicellulose concentrations than extractions with lower sawdust degrees of packing. The molar masses of the hemicelluloses were similar in higher packing degrees and in the degrees of packing that were used in typical PHWE flow-through extractions. The structure of extracted sawdust was investigated using small angle-(SAXS) and wide angle (WAXS) x-ray scattering. The cell wall topography of birch sawdust and extracted sawdust was compared using x-ray tomography. The results showed that the structure of the cell walls of extracted birch sawdust was preserved but the cell walls were thinner after the extractions. Larger pores were opened inside the fibres and cellulose microfibrils were more tightly packed after the extraction. Acetate buffers were used to control the pH of the extracts during the extractions. The pH control prevented excessive xylan hydrolysis and increased the molar masses of the extracted xylans. The yields of buffered extractions were lower than for plain water extractions at 160–170 °C, but at 180 °C yields were similar to those from plain water and pH buffers. The pH can thus be controlled during extraction with acetate buffer to obtain xylan with higher molar mass than those obtainable using plain water. Birch sawdust was extracted both in the laboratory and pilot scale. The performance of the PHWE flow-through system was evaluated in the laboratory and the pilot scale using vessels with the same shape but different volumes, with the same relative water flow through the sawdust bed, and in the same extraction temperature. Pre-steaming improved the extraction efficiency and the water flow through the sawdust bed. The extracted birch sawdust and the extracted xylan were similar in both laboratory and pilot scale. The PHWE system was successfully scaled up by a factor of 6000 from the laboratory to pilot scale and extractions performed equally well in both scales. The results show that a flow-through system can be further scaled up and used to extract water-soluble xylans from birch sawdust. Extracted xylans can be concentrated, purified, and then used in e.g. films and barriers, or as building blocks for novel material applications.

DNA extraction and quantification from touch and scrape preparations obtained from autopsy liver cells

The objective of the present study was to develop a simplified low cost method for the collection and fixation of pediatric autopsy cells and to determine the quantitative and qualitative adequacy of extracted DNA. Touch and scrape preparations of pediatric liver cells were obtained from 15 cadavers at autopsy and fixed in 95% ethanol or 3:1 methanol:acetic acid. Material prepared by each fixation procedure was submitted to DNA extraction with the Wizard® genomic DNA purification kit for DNA quantification and five of the preparations were amplified by multiplex PCR (azoospermia factor genes). The amount of DNA extracted varied from 20 to 8,640 µg, with significant differences between fixation methods. Scrape preparation fixed in 95% ethanol provided larger amount of extracted DNA. However, the mean for all groups was higher than the quantity needed for PCR (50 ng) or Southern blot (500 ng). There were no qualitative differences among the different material and fixatives. The same results were also obtained for glass slides stored at room temperature for 6, 12, 18 and 24 months. We conclude that touch and scrape preparations fixed in 95% ethanol are a good source of DNA and present fewer limitations than cell culture, tissue paraffin embedding or freezing that require sterile material, culture medium, laboratory equipment and trained technicians. In addition, they are more practical and less labor intensive and can be obtained and stored for a long time at low cost.

Female pelvic floor disorders – outcome after mesh-augmented procedures and studies on vaginal connective tissue

Pelvic floor disorders, such as urinary incontinence (UI) and pelvic organ prolapse (POP), are common disorders in women. Because of the prolonged life expectancy the prevalence of UI and POP and the probability of ending up in surgery are increasing. However, the pathophysiology behind these disorders is still unsolved. The aim of this thesis is to study possible alterations in the connective tissue in the vaginal wall in patients with and without POP. The long-term outcome and complications of mid-urethral slings (MUS) and mesh-augmented POP surgery were studied in heterogenic patient populations. More elastin and a slight increase in immunostaining of type III and V collagens in tissue samples were obtained from patients with POP compared to controls in whom type I collagen was more prominent. The studies assessing the mesh-augmented procedures revealed good efficacy and high patient satisfaction after a long-term follow-up. Patients operated on because of mixed incontinence and with BMI >30 kg/m² reported significantly more urinary symptoms and a lower quality of life than the patients operated on because of stress urinary incontinence and the ones with BMI ≤30 kg/m². The objective outcome was equal between the groups. Mesh exposure through vaginal mucosa occurred in 23 % of the patients after POP surgery, most of these being asymptomatic. There are alterations in connective tissues in patients with POP. Mid-urethral sling procedures produced good long-term cure rates and patient satisfaction. As to the prolapse surgery, in spite of relatively high exposure rate, mesh-augmented procedure proved to be safe and effective method for the correction of POP.

Intensification of hemicellulose hot-water extraction from spruce wood by parameter tuning

The growing population on earth along with diminishing fossil deposits and the climate change debate calls out for a better utilization of renewable, bio-based materials. In a biorefinery perspective, the renewable biomass is converted into many different products such as fuels, chemicals, and materials, quite similar to the petroleum refinery industry. Since forests cover about one third of the land surface on earth, ligno-cellulosic biomass is the most abundant renewable resource available. The natural first step in a biorefinery is separation and isolation of the different compounds the biomass is comprised of. The major components in wood are cellulose, hemicellulose, and lignin, all of which can be made into various end-products. Today, focus normally lies on utilizing only one component, e.g., the cellulose in the Kraft pulping process. It would be highly desirable to utilize all the different compounds, both from an economical and environmental point of view. The separation process should therefore be optimized. Hemicelluloses can partly be extracted with hot-water prior to pulping. Depending in the severity of the extraction, the hemicelluloses are degraded to various degrees. In order to be able to choose from a variety of different end-products, the hemicelluloses should be as intact as possible after the extraction. The main focus of this work has been on preserving the hemicellulose molar mass throughout the extraction at a high yield by actively controlling the extraction pH at the high temperatures used. Since it has not been possible to measure pH during an extraction due to the high temperatures, the extraction pH has remained a “black box”. Therefore, a high-temperature in-line pH measuring system was developed, validated, and tested for hot-water wood extractions. One crucial step in the measurements is calibration, therefore extensive efforts was put on developing a reliable calibration procedure. Initial extractions with wood showed that the actual extraction pH was ~0.35 pH units higher than previously believed. The measuring system was also equipped with a controller connected to a pump. With this addition it was possible to control the extraction to any desired pH set point. When the pH dropped below the set point, the controller started pumping in alkali and by that the desired set point was maintained very accurately. Analyses of the extracted hemicelluloses showed that less hemicelluloses were extracted at higher pH but with a higher molar-mass. Monomer formation could, at a certain pH level, be completely inhibited. Increasing the temperature, but maintaining a specific pH set point, would speed up the extraction without degrading the molar-mass of the hemicelluloses and thereby intensifying the extraction. The diffusion of the dissolved hemicelluloses from the wood particle is a major part of the extraction process. Therefore, a particle size study ranging from 0.5 mm wood particles to industrial size wood chips was conducted to investigate the internal mass transfer of the hemicelluloses. Unsurprisingly, it showed that hemicelluloses were extracted faster from smaller wood particles than larger although it did not seem to have a substantial effect on the average molar mass of the extracted hemicelluloses. However, smaller particle sizes require more energy to manufacture and thus increases the economic cost. Since bark comprises 10 – 15 % of a tree, it is important to also consider it in a biorefinery concept. Spruce inner and outer bark was hot-water extracted separately to investigate the possibility to isolate the bark hemicelluloses. It was showed that the bark hemicelluloses comprised mostly of pectic material and differed considerably from the wood hemicelluloses. The bark hemicelluloses, or pectins, could be extracted at lower temperatures than the wood hemicelluloses. A chemical characterization, done separately on inner and outer bark, showed that inner bark contained over 10 % stilbene glucosides that could be extracted already at 100 °C with aqueous acetone.

Estimation procedures affect the center of pressure frequency analysis

Even though frequency analysis of body sway is widely applied in clinical studies, the lack of standardized procedures concerning power spectrum estimation may provide unreliable descriptors. Stabilometric tests were applied to 35 subjects (20-51 years, 54-95 kg, 1.6-1.9 m) and the power spectral density function was estimated for the anterior-posterior center of pressure time series. The median frequency was compared between power spectra estimated according to signal partitioning, sampling rate, test duration, and detrending methods. The median frequency reliability for different test durations was assessed using the intraclass correlation coefficient. When increasing number of segments, shortening test duration or applying linear detrending, the median frequency values increased significantly up to 137%. Even the shortest test duration provided reliable estimates as observed with the intraclass coefficient (0.74-0.89 confidence interval for a single 20-s test). Clinical assessment of balance may benefit from a standardized protocol for center of pressure spectral analysis that provides an adequate relationship between resolution and variance. An algorithm to estimate center of pressure power density spectrum is also proposed.

Comparative efficacy and safety of the left versus right radial approach for percutaneous coronary procedures: a meta-analysis including 6870 patients

The radial approach is widely used in the treatment of patients with coronary artery disease. We conducted a meta-analysis of published results on the efficacy and safety of the left and right radial approaches in patients undergoing percutaneous coronary procedures. A systematic search of reference databases was conducted, and data from 14 randomized controlled trials involving 6870 participants were analyzed. The left radial approach was associated with significant reductions in fluoroscopy time [standardized mean difference (SMD)=-0.14, 95% confidence interval (CI)=-0.19 to -0.09; P<0.00001] and contrast volume (SMD=-0.07, 95%CI=-0.12 to -0.02; P=0.009). There were no significant differences in rate of procedural failure of the left and the right radial approaches [risk ratios (RR)=0.98; 95%CI=0.77-1.25; P=0.88] or procedural time (SMD=-0.05, 95%CI=0.17-0.06; P=0.38). Tortuosity of the subclavian artery (RR=0.27, 95%CI=0.14-0.50; P<0.0001) was reported more frequently with the right radial approach. A greater number of catheters were used with the left than with the right radial approach (SMD=0.25, 95%CI=0.04-0.46; P=0.02). We conclude that the left radial approach is as safe as the right radial approach, and that the left radial approach should be recommended for use in percutaneous coronary procedures, especially in percutaneous coronary angiograms.

EXTRACTION OF OIL FROM PRESSED PALM OIL (Elaes guineensis) FIBERS USING SUPERCRITICAL CO2

Residual fibers from palm oil production are a good source of carotene, since they contain more than 5% of the original oil, with about 5000 ppm of carotenoids. As carotenoids are thermosensitive molecules, supercritical CO2 can be used for oil recovery, because this technique employs low temperatures. In this work results of oil extraction experiments from pressed palm oil fibers are shown. Fibers were from AGROPALMA, an industry which is located in Tailândia (Pará, Brazil). Extractions were carried out at 200, 250 and 300 bar and at temperatures of 45 and 55oC. Oil was analyzed by UV/vis spectrophotometry for total carotene determination. Results showed a large increase in extraction rate from 200 to 250 bar and a small variation from 250 to 300 bar. The total amount of carotenes did not increase in the course of extraction at 300 bar, but it showed a large increase at 200 and at 250 bar. Free fatty acids are present in amounts larger than those found in commercial oils.

Effect of blanching time on selective mineral elements extraction from the spinach substitute (Tetragonia expansa) commonly used in Brazil

The true spinach (Spinacia oleracea) does not grow well in warm climates and for that reason is not commercialized in Brazil. Instead, a spinach substitute (Tetragonia expansa), originally from New Zealand, is widely used in the country. There is scant information on the mineral profile and none on the soluble mineral fraction of this vegetable. The solubility of a mineral is one of the important factors for its absorption. For this reason, the calcium, magnesium, iron, manganese, copper, zinc, potassium, and sodium soluble fractions in the raw spinach substitute were determined and the effect of blanching times on the solubility of these minerals was investigated. Blanching times of 1, 5, and 15 minutes were employed. The magnesium, manganese, potassium, and sodium soluble fractions increased sizably with shorter blanching time. Longer blanching time (15 minutes) caused large losses of minerals. The soluble mineral fractions can contribute poorly to diet in terms of potassium, magnesium, manganese, and zinc. The spinach substitute cannot be considered a dietary source of calcium, iron and copper due to the insolubility of these minerals in the vegetable, possibly caused by the large oxalate content.

Collective redundancies in the State of California of the United States and in the Republic of Finland. Procedures and Provisions

Video games industry has recently bonded California and Finland in a new way and where the employers are recruiting they also need to be aware of the provisions and procedures related to terminations. In general, collective dismissals are on a relatively high level both in Finland and in California. In California, collective redundancies are regulated under the WARN law. The WARN obligates employers with 75 or more employees to give a 60-day notice prior to a mass lay off and some other similar events. Employers with less than 75 employees are free to administer the terminations without the WARN notice period. Generally, the California at-will presumption allows employment relationship to be terminated any day with or without reason and without notice period if conditions of collective agreements or employment contract do not limit this right. Termination cannot anyhow be in violation of the anti-discrimination law. In Finland the termination related provisions are part of the Employment Contracts Act and the Act on Co-operation within Undertakings. Collective redundancies are allowed under financial and production related grounds. Small employers with less than 20 employees follow the termination provisions of the Employment Contracts Act and are obligated to inform the employee to be terminated on the details of the termination itself and also the services of the Employment and Economic Development Office. Employers with 20 or more employees are to initiate co-operation procedure under the Act on Co-operation within Undertakings when reducing personnel. The co- operation negotiations are to inform employees on the employer’s plans and financial situation as well as to involve them in the decision making regarding the terminations. The employer’s duty to inform the employees of the services of Employment and Economic Development Office needs to be fulfilled also in terminations under the co-operation procedure. Discrimination is prohibited in Finland in terminations of employment. As an alternative for terminations, employees can for example be transferred to another position or be temporarily laid off. Employer’s duties related to search of alternatives for layoff are broader in Finland than in California. The recent development of the labor laws in Finland and in California suggests that the labor law is not static in either one of these environments but changes can be expected as the needs of the business life so require.

Continuous Counter-current Solvent Extraction of Magnesium and Calcium from Lithium-rich Brine

Solvent extraction of calcium and magnesium impurities from a lithium-rich brine (Ca ~ 2,000 ppm, Mg ~ 50 ppm, Li ~ 30,000 ppm) was investigated using a continuous counter-current solvent extraction mixer-settler set-up. The literature review includes a general review about resources, demands and production methods of Li followed by basics of solvent extraction. Experimental section includes batch experiments for investigation of pH isotherms of three extractants; D2EHPA, Versatic 10 and LIX 984 with concentrations of 0.52, 0.53 and 0.50 M in kerosene respectively. Based on pH isotherms LIX 984 showed no affinity for solvent extraction of Mg and Ca at pH ≤ 8 while D2EHPA and Versatic 10 were effective in extraction of Ca and Mg. Based on constructed pH isotherms, loading isotherms of D2EHPA (at pH 3.5 and 3.9) and Versatic 10 (at pH 7 and 8) were further investigated. Furthermore based on McCabe-Thiele method, two extraction stages and one stripping stage (using HCl acid with concentration of 2 M for Versatic 10 and 3 M for D2EHPA) was practiced in continuous runs. Merits of Versatic 10 in comparison to D2EHPA are higher selectivity for Ca and Mg, faster phase disengagement, no detrimental change in viscosity due to shear amount of metal extraction and lower acidity in stripping. On the other hand D2EHPA has less aqueous solubility and is capable of removing Mg and Ca simultaneously even at higher Ca loading (A/O in continuous runs > 1). In general, shorter residence time (~ 2 min), lower temperature (~23 °C), lower pH values (6.5-7.0 for Versatic 10 and 3.5-3.7 for D2EHPA) and a moderately low A/O value (< 1:1) would cause removal of 100% of Ca and nearly 100% of Mg while keeping Li loss less than 4%, much lower than the conventional precipitation in which 20% of Li is lost.

Effectiveness of cleaning and sanitizing procedures in controlling the adherence of Pseudomonas fluorescens, Salmonella Enteritidis, and Staphylococcus aureus to domestic kitchen surfaces

The effectiveness of cleaning and sanitizing procedures in controlling Staphylococcus aureus, Salmonella Enteritidis, and Pseudomonasfluorescens adhered to granite and stainless steel was evaluated. There was no significant difference (p > 0.05) in the adherence of pure cultures of these microorganisms to stainless steel. The numbers of P. fluorescens and S. Enteritidis adhered to granite were greater (p < 0.05) than the numbers of S. aureus. Additionally, the adherence of P. fluorescens was similar to the adherence of S. Enteritidis on granite surface. In a mixed culture with P. fluorescens, S aureus adhered less (p < 0.05) to stainless steel surfaces (1.31 log CFU.cm-2) than when in a pure culture (6.10 log CFU.cm-2). These results suggest that P. fluorescens inhibited the adherence of S. aureus. However, this inhibition was not observed in the adherence process for granite. There was a significant difference (p < 0.05) between the number of adhered cells before and after pre-washing for S. aureus on stainless steel and granite surfaces, and after washing with detergent for all microorganisms and surfaces. The efficiency of the cleaning plus sanitizing procedures was not significantly different (p > 0.05) between the surfaces. However, a significant difference was observed (p < 0.05) between the sanitizer solutions. Sodium hypochlorite and peracetic acid were more bactericidal (p < 0.05) than a quaternary ammonium compound. With regard to microorganisms, S. aureus was the least resistant to the sanitizers. These results show the importance of good cleaning and sanitization procedures to prevent bacterial adherence and biofilm formation.