Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

Effect of collection, transport, processing and storage of blood specimens on the activity of lysosomal enzymes in plasma and leukocytes

This study was designed to evaluate the effect of different conditions of collection, transport and storage on the quality of blood samples from normal individuals in terms of the activity of the enzymes ß-glucuronidase, total hexosaminidase, hexosaminidase A, arylsulfatase A and ß-galactosidase. The enzyme activities were not affected by the different materials used for collection (plastic syringes or vacuum glass tubes). In the evaluation of different heparin concentrations (10% heparin, 5% heparin, and heparinized syringe) in the syringes, it was observed that higher doses resulted in an increase of at least 1-fold in the activities of ß-galactosidase, total hexosaminidase and hexosaminidase A in leukocytes, and ß-glucuronidase in plasma. When the effects of time and means of transportation were studied, samples that had been kept at room temperature showed higher deterioration with time (72 and 96 h) before processing, and in this case it was impossible to isolate leukocytes from most samples. Comparison of heparin and acid citrate-dextrose (ACD) as anticoagulants revealed that ß-glucuronidase and hexosaminidase activities in plasma reached levels near the lower normal limits when ACD was used. In conclusion, we observed that heparin should be used as the preferable anticoagulant when measuring these lysosomal enzyme activities, and we recommend that, when transport time is more than 24 h, samples should be shipped by air in a styrofoam box containing wet ice.

The radio frequency identification technology in the supply chain management: a case of a big logistics company

Nowadays global business trends force the adoption of innovative ICTs into the supply chain management (SCM). Particularly, the RFID technology is on high demand among SCM professionals due to its business advantages such as improving of accuracy and veloc-ity of SCM processes which lead to decrease of operational costs. Nevertheless, a question of the RFID technology impact on the efficiency of warehouse processes in the SCM re-mains open. The goal of the present study is to experiment the possibility of improvement order picking velocity in a warehouse of a big logistics company with the use of the RFID technology. In order to achieve this goal the following objectives have been developed: 1) Defining the scope of the RFID technology applications in the SCM; 2) Justification of the RFID technology impact on the SCM processes; 3) Defining a place of the warehouse order picking process in the SCM; 4) Identification and systematization of existing meth-ods of order picking velocity improvement; 5) Choosing of the study object and gathering of the empirical data about number of orders, number of hours spent per each order line daily during 5 months; 6) Processing and analysis of the empirical data; 7) Conclusion about the impact of the RFID technology on the speed of order picking process. As a result of the research it has been found that the speed of the order picking processes has not been changed as time has gone after the RFID adoption. It has been concluded that in order to achieve a positive effect in the speed of order picking process with the use of the RFID technology it is necessary to simultaneously implement changes in logistics and organizational management in 3PL logistics companies. Practical recommendations have been forwarded to the management of the company for further investigation and procedure.

Developing purchase invoice processing through workflow automation

The aim of this master’s thesis is to research and analyze how purchase invoice processing can be automated and streamlined in a system renewal project. The impacts of workflow automation on invoice handling are studied by means of time, cost and quality aspects. Purchase invoice processing has a lot of potential for automation because of its labor-intensive and repetitive nature. As a case study combining both qualitative and quantitative methods, the topic is approached from a business process management point of view. The current process was first explored through interviews and workshop meetings to create a holistic understanding of the process at hand. Requirements for process streamlining were then researched focusing on specified vendors and their purchase invoices, which helped to identify the critical factors for successful invoice automation. To optimize the flow from invoice receipt to approval for payment, the invoice receiving process was outsourced and the automation functionalities of the new system utilized in invoice handling. The quality of invoice data and the need of simple structured purchase order (PO) invoices were emphasized in the system testing phase. Hence, consolidated invoices containing references to multiple PO or blanket release numbers should be simplified in order to use automated PO matching. With non-PO invoices, it is important to receive the buyer reference details in an applicable invoice data field so that automation rules could be created to route invoices to a review and approval flow. In the beginning of the project, invoice processing was seen ineffective both time- and cost-wise, and it required a lot of manual labor to carry out all tasks. In accordance with testing results, it was estimated that over half of the invoices could be automated within a year after system implementation. Processing times could be reduced remarkably, which would then result savings up to 40 % in annual processing costs. Due to several advancements in the purchase invoice process, business process quality could also be perceived as improved.

Inactivation of Staphylococcus aureus and Salmonella enteritidis in tryptic soy broth and caviar samples by high pressure processing

We studied the action of high pressure processing on the inactivation of two foodborne pathogens, Staphylococcus aureus ATCC 6538 and Salmonella enteritidis ATCC 13076, suspended in a culture medium and inoculated into caviar samples. The baroresistance of the two pathogens in a tryptic soy broth suspension at a concentration of 10(8)-10(9) colony-forming units/ml was tested for continuous and cycled pressurization in the 150- to 550-MPa range and for 15-min treatments at room temperature. The increase of cycle number permitted the reduction of the pressure level able to totally inactivate both microorganisms in the tryptic soy broth suspension, whereas the effect of different procedure times on complete inactivation of the microorganisms inoculated into caviar was similar.

Rapid test for the evaluation of the activity of the prodrug hydroxymethylnitrofurazone in the processing of Trypanosoma cruzi messenger RNAs

No fully effective treatment has been developed since the discovery of Chagas' disease by Carlos Chagas in 1909. Since drug-resistant Trypanosoma cruzi strains are occurring and the current therapy is effectiveness in the acute phase but with various adverse side effects, more studies are needed to characterize the susceptibility of T. cruzi to new drugs. Many natural and/or synthetic substances showing trypanocidal activity have been used, even though they are not likely to be turned into clinically approved drugs. Originally, drug screening was performed using natural products, with only limited knowledge of the molecular mechanism involved in the development of diseases. Trans-splicing, which is unusual RNA processing reaction and occurs in nematodes and trypanosomes, implies the processing of polycistronic transcription units into individual mRNAs; a short transcript spliced leader (SL RNA) is trans-spliced to the acceptor pre-mRNA, giving origin to the mature mRNA. In the present study, permeable cells of T. cruzi epimastigote forms (Y, BOL and NCS strains) were treated to evaluate the interference of two drugs (hydroxymethylnitrofurazone - NFOH-121 and nitrofurazone) in the trans-splicing reaction using silver-stained PAGE analysis. Both drugs induced a significant reduction in RNA processing at concentrations from 5 to 12.5 µM. These data agreed with the biological findings, since the number of parasites decreased, especially with NFOH-121. This proposed methodology allows a rapid and cost-effective screening strategy for detecting drug interference in the trans-splicing mechanism of T. cruzi.

Cost Reduction of Permanent Magnet Synchronous Machines

Electrical machine drives are the most electrical energy-consuming systems worldwide. The largest proportion of drives is found in industrial applications. There are, however many other applications that are also based on the use of electrical machines, because they have a relatively high efficiency, a low noise level, and do not produce local pollution. Electrical machines can be classified into several categories. One of the most commonly used electrical machine types (especially in the industry) is induction motors, also known as asynchronous machines. They have a mature production process and a robust rotor construction. However, in the world pursuing higher energy efficiency with reasonable investments not every application receives the advantage of using this type of motor drives. The main drawback of induction motors is the fact that they need slipcaused and thus loss-generating current in the rotor, and additional stator current for magnetic field production along with the torque-producing current. This can reduce the electric motor drive efficiency, especially in low-speed, low-power applications. Often, when high torque density is required together with low losses, it is desirable to apply permanent magnet technology, because in this case there is no need to use current to produce the basic excitation of the machine. This promotes the effectiveness of copper use in the stator, and further, there is no rotor current in these machines. Again, if permanent magnets with a high remanent flux density are used, the air gap flux density can be higher than in conventional induction motors. These advantages have raised the popularity of PMSMs in some challenging applications, such as hybrid electric vehicles (HEV), wind turbines, and home appliances. Usually, a correctly designed PMSM has a higher efficiency and consequently lower losses than its induction machine counterparts. Therefore, the use of these electrical machines reduces the energy consumption of the whole system to some extent, which can provide good motivation to apply permanent magnet technology to electrical machines. However, the cost of high performance rare earth permanent magnets in these machines may not be affordable in many industrial applications, because the tight competition between the manufacturers dictates the rules of low-cost and highly robust solutions, where asynchronous machines seem to be more feasible at the moment. Two main electromagnetic components of an electrical machine are the stator and the rotor. In the case of a conventional radial flux PMSM, the stator contains magnetic circuit lamination and stator winding, and the rotor consists of rotor steel (laminated or solid) and permanent magnets. The lamination itself does not significantly influence the total cost of the machine, even though it can considerably increase the construction complexity, as it requires a special assembly arrangement. However, thin metal sheet processing methods are very effective and economically feasible. Therefore, the cost of the machine is mainly affected by the stator winding and the permanent magnets. The work proposed in this doctoral dissertation comprises a description and analysis of two approaches of PMSM cost reduction: one on the rotor side and the other on the stator side. The first approach on the rotor side includes the use of low-cost and abundant ferrite magnets together with a tooth-coil winding topology and an outer rotor construction. The second approach on the stator side exploits the use of a modular stator structure instead of a monolithic one. PMSMs with the proposed structures were thoroughly analysed by finite element method based tools (FEM). It was found out that by implementing the described principles, some favourable characteristics of the machine (mainly concerning the machine size) will inevitable be compromised. However, the main target of the proposed approaches is not to compete with conventional rare earth PMSMs, but to reduce the price at which they can be implemented in industrial applications, keeping their dimensions at the same level or lower than those of a typical electrical machine used in the industry at the moment. The measurement results of the prototypes show that the main performance characteristics of these machines are at an acceptable level. It is shown that with certain specific actions it is possible to achieve a desirable efficiency level of the machine with the proposed cost reduction methods.

How auditory temporal processing deficits relate to dyslexia

Studies have shown that dyslexic children present a deficiency in the temporal processing of auditory stimuli applied in rapid succession. However, discussion continues concerning the way this deficiency can be influenced by temporal variables of auditory processing tests. Therefore, the purpose of the present study was to analyze by auditory temporal processing tests the effect of temporal variables such as interstimulus intervals, stimulus duration and type of task on dyslexic children compared to a control group. Of the 60 children evaluated, 33 were dyslexic (mean age = 10.5 years) and 27 were normal controls (mean age = 10.8 years). Auditory processing tests assess the abilities of discrimination and ordering of stimuli in relation to their duration and frequency. Results showed a significant difference in the average accuracy of control and dyslexic groups considering each variable (interstimulus intervals: 47.9 ± 5.5 vs 37.18 ± 6.0; stimulus duration: 61.4 ± 7.6 vs 50.9 ± 9.0; type of task: 59.9 ± 7.9 vs 46.5 ± 9.0) and the dyslexic group demonstrated significantly lower performance in all situations. Moreover, there was an interactive effect between the group and the duration of stimulus variables for the frequency-pattern tests, with the dyslexic group demonstrating significantly lower results for short durations (53.4 ± 8.2 vs 48.4 ± 11.1), as opposed to no difference in performance for the control group (62.2 ± 7.1 vs 60.6 ± 7.9). These results support the hypothesis that associates dyslexia with auditory temporal processing, identifying the stimulus-duration variable as the only one that unequally influenced the performance of the two groups.

Effect of escitalopram on the processing of emotional faces

Serotonin has been implicated in the neurobiology of depressive and anxiety disorders, but little is known about its role in the modulation of basic emotional processing. The aim of this study was to determine the effect of the selective serotonin reuptake inhibitor, escitalopram, on the perception of facial emotional expressions. Twelve healthy male volunteers completed two experimental sessions each, in a randomized, balanced order, double-blind design. A single oral dose of escitalopram (10 mg) or placebo was administered 3 h before the task. Participants were presented to a task composed of six basic emotions (anger, disgust, fear, happiness, sadness, and surprise) that were morphed between neutral and each standard emotion in 10% steps. Escitalopram facilitated the recognition of sadness and inhibited the recognition of happiness in male, but not female faces. No drug effect on subjective measures was detected. These results confirm that serotonin modulates the recognition of emotional faces, and suggest that the gender of the face can have a role in this modulation. Further studies including female volunteers are needed.

Effect of auditory training on the middle latency response in children with (central) auditory processing disorder

The purpose of this study was to determine the middle latency response (MLR) characteristics (latency and amplitude) in children with (central) auditory processing disorder [(C)APD], categorized as such by their performance on the central auditory test battery, and the effects of these characteristics after auditory training. Thirty children with (C)APD, 8 to 14 years of age, were tested using the MLR-evoked potential. This group was then enrolled in an 8-week auditory training program and then retested at the completion of the program. A control group of 22 children without (C)APD, composed of relatives and acquaintances of those involved in the research, underwent the same testing at equal time intervals, but were not enrolled in the auditory training program. Before auditory training, MLR results for the (C)APD group exhibited lower C3-A1 and C3-A2 wave amplitudes in comparison to the control group [C3-A1, 0.84 µV (mean), 0.39 (SD - standard deviation) for the (C)APD group and 1.18 µV (mean), 0.65 (SD) for the control group; C3-A2, 0.69 µV (mean), 0.31 (SD) for the (C)APD group and 1.00 µV (mean), 0.46 (SD) for the control group]. After training, the MLR C3-A1 [1.59 µV (mean), 0.82 (SD)] and C3-A2 [1.24 µV (mean), 0.73 (SD)] wave amplitudes of the (C)APD group significantly increased, so that there was no longer a significant difference in MLR amplitude between (C)APD and control groups. These findings suggest progress in the use of electrophysiological measurements for the diagnosis and treatment of (C)APD.

Facilitatory effects of an auditory warning stimulus in a visual location identification task and a visual shape identification task

The occurrence of a weak auditory warning stimulus increases the speed of the response to a subsequent visual target stimulus that must be identified. This facilitatory effect has been attributed to the temporal expectancy automatically induced by the warning stimulus. It has not been determined whether this results from a modulation of the stimulus identification process, the response selection process or both. The present study examined these possibilities. A group of 12 young adults performed a reaction time location identification task and another group of 12 young adults performed a reaction time shape identification task. A visual target stimulus was presented 1850 to 2350 ms plus a fixed interval (50, 100, 200, 400, 800, or 1600 ms, depending on the block) after the appearance of a fixation point, on its left or right side, above or below a virtual horizontal line passing through it. In half of the trials, a weak auditory warning stimulus (S1) appeared 50, 100, 200, 400, 800, or 1600 ms (according to the block) before the target stimulus (S2). Twelve trials were run for each condition. The S1 produced a facilitatory effect for the 200, 400, 800, and 1600 ms stimulus onset asynchronies (SOA) in the case of the side stimulus-response (S-R) corresponding condition, and for the 100 and 400 ms SOA in the case of the side S-R non-corresponding condition. Since these two conditions differ mainly by their response selection requirements, it is reasonable to conclude that automatic temporal expectancy influences the response selection process.

Evaluation of total carotenoids, alpha- and beta-carotene in carrots (Daucus carota L.) during home processing

This study aims to analyze the influence of dehydration and different preparation methods during home processing related toalpha-carotene, beta-carotene and total carotenoids stability in carrots. Vitamin A values were evaluated after different treatments. Thus, carrots were submitted to steam cooking, water cooking with and without pressure, moist/dry cooking and conventional dehydration. Determination of alpha- and beta-carotenes was made by High-Performance Liquid Chromatography (HPLC) (conditions were developed by us) using spectrophotometric detection visible-UV at 470 nm; a RP-18 column and methanol: acetonitrile: ethyl acetate (80: 10: 10) as mobile phase. Total carotenoids quantification was made by 449 nm spectrophotometer. The retention of the analyzed carotenoids ranged from 60.13 to 85.64%. Water cooking without pressure promoted higher retention levels of alpha- and beta-carotene and vitamin A values, while water cooking with pressure promoted higher retention levels of total carotenoids. Dehydration promoted the highest carotenoid losses. The results showed that, among the routinely utilized methods under domestic condition, cooking without pressure, if performed under controlled time and temperature, is the best method as it reduces losses in the amount of alpha- and beta-carotene, the main carotenoids present in the carrots. Despite the significant carotenoid losses, carrots prepared through domestic methods, remain a rich source of provitamin A.

Processing of spent nickelcatalyst for fat recovery

Spent nickel catalyst (SNC) has the potential of insulting the quality of the environment in a number of ways. Its disposal has a pollution effect. Optimum recovery of fat from SNC, could save the environment and reduce the oil loss. Hexane has been the solvent of choice for oil extraction. Alternative solvents considered to have been safer have been evaluated. Hexane, isopropanol, ethanol and heptane were examined using soxhlet extraction. While hexane is more efficient in oil recovery from SNC, isopropanol proved to be very good in clear separation of oil from waste material and also provides high solvent recovery compared to other solvents. Isopropanol extraction with chill separation of miscella into lower oil-rich phase, and an upper, solvent-rich recyclable phase save mush energy of vaporization for distilling. An aqueous extraction process with immiscible solvent assisted was tested. Solvent like hexane added to SNC, and water added later with continuous stirring. The mixture was stirred for about 30 minutes, prior to centrifugation. Aqueous process extracted less amount of oil compared to solvent extraction.

Effect of processing and roasting on the antioxidant activity of coffee brews

The aim of this work was to evaluate the effect of processing and roasting on the antioxidant activity of coffee brews. Brews prepared with light, medium and dark roasted coffees were analyzed. The pH, total solids content, polyphenols content, reducing substances and chlorogenic acids content were determined. The antioxidant activity of aqueous extracts, the guaicol decolorizing and the capacity to inhibit lipid peroxidation were also analyzed. The antioxidant activity of coffee brews were concentration-dependent. A progressive antioxidant activity and polyphenols content was observed decreasing with roasting. The light roasted coffee showed the highest antioxidant activity and dark roasted coffee showed the lowest antioxidant activity. The results indicate that the ingestion of coffee brews prepared with light and medium roasted coffees might protect cells from oxidative stress damages.

Modification of commercial poly-lactide for extrusion coated food packaging applications

Poly-L-lactide (PLLA) is a widely used sustainable and biodegradable alternative to replace synthetic non-degradable plastic materials in the packaging industry. Conversely, its processing properties are not always optimal, e.g. insufficient melt strength at higher temperatures (necessary in extrusion coating processes). This thesis reports on research to improve properties of commercial PLLA grade (3051D from NatureWorks), to satisfy and extend end-use applications, such as food packaging by blending with modified PLLA. Adjustment of the processability by chain branching of commercial poly-L-lactide initiated by peroxide was evaluated. Several well-defined branched structures with four arms (sPLLA) were synthesized using pentaerythritol as a tetra-functional initiator. Finally, several block copolymers consisting of polyethylene glycol and PLLA (i.e. PEGLA) were produced to obtain a well extruded material with improved heat sealing properties. Reactive extrusion of poly-L-lactide was carried out in the presence of 0.1, 0.3 and 0.5 wt% of various peroxides [tert-butyl-peroxybenzoate (TBPB), 2,5-dimethyl-2,5-(tert-butylperoxy)-hexane (Lupersol 101; LOL1) and benzoyl peroxide (BPO)] at 190C. The peroxide-treated PLLAs showed increased complex viscosity and storage modulus at lower frequencies, indicating the formation of branched/cross linked architectures. The material property changes were dependent on the peroxide, and the used peroxide concentration. Gel fraction analysis showed that the peroxides, afforded different gel contents, and especially 0.5 wt% peroxide, produced both an extremely high molar mass, and a cross linked structure, not perhaps well suited for e.g. further use in a blending step. The thermal behavior was somewhat unexpected as the materials prepared with 0.5 wt% peroxide showed the highest ability for crystallization and cold crystallization, despite substantial cross linking. The peroxide-modified PLLA, i.e. PLLA melt extruded with 0.3 wt% of TBPB and LOL1 and 0.5 wt% BPO was added to linear PLLA in ratios of 5, 15 and 30 wt%. All blends showed increased zero shear viscosity, elastic nature (storage modulus) and shear sensitivity. All blends remained amorphous, though the ability of annealing was improved slightly. Extrusion coating on paperboard was conducted with PLLA, and peroxide-modified PLLA blends (90:10). All blends were processable, but only PLLA with 0.3 wt% of LOL1 afforded a smooth high quality surface with improved line speed. Adhesion levels between fiber and plastic, as well as heat seal performance were marginally reduced compared with pure 3051D. The water vapor transmission measurements (WVTR) of the blends containing LOL1 showed acceptable levels, only slightly lower than for comparable PLLA 3051D. A series of four-arm star-shaped poly-L-lactide (sPLLA) with different branch length was synthesized by ring opening polymerization (ROP) of L-lactide using pentaerythritol as initiator and stannous octoate as catalyst. The star-shaped polymers were further blended with its linear resin and studied for their melt flow and thermal properties. Blends containing 30 wt% of sPLLA with low molecular weight (30 wt%; Mwtotal: 2500 g mol-1 and 15000 g mol-1) showed lower zero shear viscosity and significantly increased shear thinning, while at the same time slightly increased crystallization of the blend. However, the amount of crystallization increased significantly with the higher molecular weight sPLLA, therefore the star-shaped structure may play a role as nucleating agent. PLLA-polyethylene glycol–PLLA triblock copolymers (PEGLA) with different PLLA block length were synthesized and their applicability as blends with linear PLLA (3051D NatureWorks) was investigated with the intention of improving heat-seal and adhesion properties of extrusion-coated paperboard. PLLA-PEG-PLLA was obtained by ring opening polymerization (ROP) of L-lactide using PEG (molecular weight 6000 g mol-1) as an initiator, and stannous octoate as catalyst. The structures of the PEGLAs were characterized by proton nuclear magnetic resonance spectroscopy (1H-NMR). The melt flow and thermal properties of all PEGLAs and their blends were evaluated using dynamic rheology, and differential scanning calorimeter (DSC). All blends containing 30 wt% of PEGLAs showed slightly higher zero shear viscosity, higher shear thinning and increased melt elasticity (based on tan delta). Nevertheless, no significant changes in thermal properties were distinguished. High molecular weight PEGLAs were used in extrusion coating line with 3051D without problems.