Probabilistic position and orientation estimation of rigid objects using an RGB-D sensor

The recent emergence of low-cost RGB-D sensors has brought new opportunities for robotics by providing affordable devices that can provide synchronized images with both color and depth information. In this thesis, recent work on pose estimation utilizing RGBD sensors is reviewed. Also, a pose recognition system for rigid objects using RGB-D data is implemented. The implementation uses half-edge primitives extracted from the RGB-D images for pose estimation. The system is based on the probabilistic object representation framework by Detry et al., which utilizes Nonparametric Belief Propagation for pose inference. Experiments are performed on household objects to evaluate the performance and robustness of the system.

Methods of genetic diversity creation and functional display for directed evolution experiments

Protein engineering aims to improve the properties of enzymes and affinity reagents by genetic changes. Typical engineered properties are affinity, specificity, stability, expression, and solubility. Because proteins are complex biomolecules, the effects of specific genetic changes are seldom predictable. Consequently, a popular strategy in protein engineering is to create a library of genetic variants of the target molecule, and render the population in a selection process to sort the variants by the desired property. This technique, called directed evolution, is a central tool for trimming protein-based products used in a wide range of applications from laundry detergents to anti-cancer drugs. New methods are continuously needed to generate larger gene repertoires and compatible selection platforms to shorten the development timeline for new biochemicals. In the first study of this thesis, primer extension mutagenesis was revisited to establish higher quality gene variant libraries in Escherichia coli cells. In the second study, recombination was explored as a method to expand the number of screenable enzyme variants. A selection platform was developed to improve antigen binding fragment (Fab) display on filamentous phages in the third article and, in the fourth study, novel design concepts were tested by two differentially randomized recombinant antibody libraries. Finally, in the last study, the performance of the same antibody repertoire was compared in phage display selections as a genetic fusion to different phage capsid proteins and in different antibody formats, Fab vs. single chain variable fragment (ScFv), in order to find out the most suitable display platform for the library at hand. As a result of the studies, a novel gene library construction method, termed selective rolling circle amplification (sRCA), was developed. The method increases mutagenesis frequency close to 100% in the final library and the number of transformants over 100-fold compared to traditional primer extension mutagenesis. In the second study, Cre/loxP recombination was found to be an appropriate tool to resolve the DNA concatemer resulting from error-prone RCA (epRCA) mutagenesis into monomeric circular DNA units for higher efficiency transformation into E. coli. Library selections against antigens of various size in the fourth study demonstrated that diversity placed closer to the antigen binding site of antibodies supports generation of antibodies against haptens and peptides, whereas diversity at more peripheral locations is better suited for targeting proteins. The conclusion from a comparison of the display formats was that truncated capsid protein three (p3Δ) of filamentous phage was superior to the full-length p3 and protein nine (p9) in obtaining a high number of uniquely specific clones. Especially for digoxigenin, a difficult hapten target, the antibody repertoire as ScFv-p3Δ provided the clones with the highest affinity for binding. This thesis on the construction, design, and selection of gene variant libraries contributes to the practical know-how in directed evolution and contains useful information for scientists in the field to support their undertakings.

Simulation of new p-type pixel strip detector with enhanced multiplication effect

This Master’s Thesis is dedicated to the simulation of new p-type pixel strip detector with enhanced multiplication effect. It is done for high-energy physics experiments upgrade such as Super Large Hadron Collider especially for Compact Muon Solenoid particle track silicon detectors. These detectors are used in very harsh radiation environment and should have good radiation hardness. The device engineering technology for developing more radiation hard particle detectors is used for minimizing the radiation degradation. New detector structure with enhanced multiplication effect is proposed in this work. There are studies of electric field and electric charge distribution of conventional and new p-type detector under reverse voltage bias and irradiation. Finally, the dependence of the anode current from the applied cathode reverse voltage bias under irradiation is obtained in this Thesis. For simulation Silvaco Technology Computer Aided Design software was used. Athena was used for creation of doping profiles and device structures and Atlas was used for getting electrical characteristics of the studied devices. The program codes for this software are represented in Appendixes.

Computer programs for analysis of droplets sprayed on water sensitive papers

The use of water-sensitive papers is an important tool for assessing the quality of pesticide application on crops, but manual analysis is laborious and time-consuming. Thus, this study aimed to evaluate and compare the results obtained from four software programs for spray droplet analysis in different scanned images of water-sensitive papers. After spraying, papers with four droplet deposition patterns (varying droplet spectra and densities) were analyzed manually and by means of the following computer programs: CIR, e-Sprinkle, DepositScan and Conta-Gotas. The diameter of the volume and number medians and the number of droplets per target area were studied. There is a strong correlation between the values measured using the different programs and the manual analysis, but there is a great difference between the numerical values measured for the same paper. Thus, it is not advisable to compare results obtained from different programs.

Protein folding: a perspective for biology, medicine and biotechnology

At the present time, protein folding is an extremely active field of research including aspects of biology, chemistry, biochemistry, computer science and physics. The fundamental principles have practical applications in the exploitation of the advances in genome research, in the understanding of different pathologies and in the design of novel proteins with special functions. Although the detailed mechanisms of folding are not completely known, significant advances have been made in the understanding of this complex process through both experimental and theoretical approaches. In this review, the evolution of concepts from Anfinsen's postulate to the "new view" emphasizing the concept of the energy landscape of folding is presented. The main rules of protein folding have been established from in vitro experiments. It has been long accepted that the in vitro refolding process is a good model for understanding the mechanisms by which a nascent polypeptide chain reaches its native conformation in the cellular environment. Indeed, many denatured proteins, even those whose disulfide bridges have been disrupted, are able to refold spontaneously. Although this assumption was challenged by the discovery of molecular chaperones, from the amount of both structural and functional information now available, it has been clearly established that the main rules of protein folding deduced from in vitro experiments are also valid in the cellular environment. This modern view of protein folding permits a better understanding of the aggregation processes that play a role in several pathologies, including those induced by prions and Alzheimer's disease. Drug design and de novo protein design with the aim of creating proteins with novel functions by application of protein folding rules are making significant progress and offer perspectives for practical applications in the development of pharmaceuticals and medical diagnostics.

The modulation of simple reaction time by the spatial probability of a visual stimulus

Simple reaction time (SRT) in response to visual stimuli can be influenced by many stimulus features. The speed and accuracy with which observers respond to a visual stimulus may be improved by prior knowledge about the stimulus location, which can be obtained by manipulating the spatial probability of the stimulus. However, when higher spatial probability is achieved by holding constant the stimulus location throughout successive trials, the resulting improvement in performance can also be due to local sensory facilitation caused by the recurrent spatial location of a visual target (position priming). The main objective of the present investigation was to quantitatively evaluate the modulation of SRT by the spatial probability structure of a visual stimulus. In two experiments the volunteers had to respond as quickly as possible to the visual target presented on a computer screen by pressing an optic key with the index finger of the dominant hand. Experiment 1 (N = 14) investigated how SRT changed as a function of both the different levels of spatial probability and the subject's explicit knowledge about the precise probability structure of visual stimulation. We found a gradual decrease in SRT with increasing spatial probability of a visual target regardless of the observer's previous knowledge concerning the spatial probability of the stimulus. Error rates, below 2%, were independent of the spatial probability structure of the visual stimulus, suggesting the absence of a speed-accuracy trade-off. Experiment 2 (N = 12) examined whether changes in SRT in response to a spatially recurrent visual target might be accounted for simply by sensory and temporally local facilitation. The findings indicated that the decrease in SRT brought about by a spatially recurrent target was associated with its spatial predictability, and could not be accounted for solely in terms of sensory priming.

Surface studies of limestones and dolostones : characterisation using various techniques and batch dissolution experiments with hydrochloric acid solutions

In this thesis, stepwise titration with hydrochloric acid was used to obtain chemical reactivities and dissolution rates of ground limestones and dolostones of varying geological backgrounds (sedimentary, metamorphic or magmatic). Two different ways of conducting the calculations were used: 1) a first order mathematical model was used to calculate extrapolated initial reactivities (and dissolution rates) at pH 4, and 2) a second order mathematical model was used to acquire integrated mean specific chemical reaction constants (and dissolution rates) at pH 5. The calculations of the reactivities and dissolution rates were based on rate of change of pH and particle size distributions of the sample powders obtained by laser diffraction. The initial dissolution rates at pH 4 were repeatedly higher than previously reported literature values, whereas the dissolution rates at pH 5 were consistent with former observations. Reactivities and dissolution rates varied substantially for dolostones, whereas for limestones and calcareous rocks, the variation can be primarily explained by relatively large sample standard deviations. A list of the dolostone samples in a decreasing order of initial reactivity at pH 4 is: 1) metamorphic dolostones with calcite/dolomite ratio higher than about 6% 2) sedimentary dolostones without calcite 3) metamorphic dolostones with calcite/dolomite ratio lower than about 6% The reactivities and dissolution rates were accompanied by a wide range of experimental techniques to characterise the samples, to reveal how different rocks changed during the dissolution process, and to find out which factors had an influence on their chemical reactivities. An emphasis was put on chemical and morphological changes taking place at the surfaces of the particles via X-ray Photoelectron Spectroscopy (XPS) and Scanning Electron Microscopy (SEM). Supporting chemical information was obtained with X-Ray Fluorescence (XRF) measurements of the samples, and Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) and Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) measurements of the solutions used in the reactivity experiments. Information on mineral (modal) compositions and their occurrence was provided by X-Ray Diffraction (XRD), Energy Dispersive X-ray analysis (EDX) and studying thin sections with a petrographic microscope. BET (Brunauer, Emmet, Teller) surface areas were determined from nitrogen physisorption data. Factors increasing chemical reactivity of dolostones and calcareous rocks were found to be sedimentary origin, higher calcite concentration and smaller quartz concentration. Also, it is assumed that finer grain size and larger BET surface areas increase the reactivity although no certain correlation was found in this thesis. Atomic concentrations did not correlate with the reactivities. Sedimentary dolostones, unlike metamorphic ones, were found to have porous surface structures after dissolution. In addition, conventional (XPS) and synchrotron based (HRXPS) X-ray Photoelectron Spectroscopy were used to study bonding environments on calcite and dolomite surfaces. Both samples are insulators, which is why neutralisation measures such as electron flood gun and a conductive mask were used. Surface core level shifts of 0.7 ± 0.1 eV for Ca 2p spectrum of calcite and 0.75 ± 0.05 eV for Mg 2p and Ca 3s spectra of dolomite were obtained. Some satellite features of Ca 2p, C 1s and O 1s spectra have been suggested to be bulk plasmons. The origin of carbide bonds was suggested to be beam assisted interaction with hydrocarbons found on the surface. The results presented in this thesis are of particular importance for choosing raw materials for wet Flue Gas Desulphurisation (FGD) and construction industry. Wet FGD benefits from high reactivity, whereas construction industry can take advantage of slow reactivity of carbonate rocks often used in the facades of fine buildings. Information on chemical bonding environments may help to create more accurate models for water-rock interactions of carbonates.

Measurement of epidermal thickness in a patient with psoriasis by computer-supported image analysis

The aim of the present study was to measure full epidermal thickness, stratum corneum thickness, rete length, dermal papilla widening and suprapapillary epidermal thickness in psoriasis patients using a light microscope and computer-supported image analysis. The data obtained were analyzed in terms of patient age, type of psoriasis, total body surface area involvement, scalp and nail involvement, duration of psoriasis, and family history of the disease. The study was conducted on 64 patients and 57 controls whose skin biopsies were examined by light microscopy. The acquired microscopic images were transferred to a computer and measurements were made using image analysis. The skin biopsies, taken from different body areas, were examined for different parameters such as epidermal, corneal and suprapapillary epidermal thickness. The most prominent increase in thickness was detected in the palmar region. Corneal thickness was more pronounced in patients with scalp involvement than in patients without scalp involvement (t = -2.651, P = 0.008). The most prominent increase in rete length was observed in the knees (median: 491 µm, t = 10.117, P = 0.000). The difference in rete length between patients with a positive and a negative family history was significant (t = -3.334, P = 0.03), being 27% greater in psoriasis patients without a family history. The differences in dermal papilla distances among patients were very small. We conclude that microscope-supported thickness measurements provide objective results.

Assessing negative priming by attended distractors in a paper-and-pencil task

The paper-and-pencil digit-comparison task for assessing negative priming (NP) was introduced, using a referent-size-selection procedure that was demonstrated to enhance the effect. NP is indicated by slower responses to recently ignored items, and proposed within the clinical-experimental framework as a major cognitive index of active suppression of distracting information, critical to executive functioning. The digit-comparison task requires circling digits of a list with digit-asterisk pairs (a baseline measure for digit-selection), and the larger of two digits in each pair of the unrelated (with different digits in successive digit-pairs) and related lists (in which the smaller digit subsequently became a target). A total of 56 students (18-38 years) participated in two experiments that explored practice effects across lists and demonstrated reliable NP, i.e., slowing to complete the related list relative to the unrelated list, (F(2, 44) = 52.42, P < 0.0001). A 3rd experiment examined age-related effects. In the paper-and-pencil digit-comparison task, NP was reliable for the younger (N = 8, 18-24 years) and middle-aged adults (N = 8, 31-54 years), but absent for the older group (N = 8, 68-77 years). NP was also reduced with aging in a computer-implemented digit-comparison task, and preserved in a task typically used to test location-specific NP, accounting for the dissociation between identity- and spatial-based suppression of distractors (Rao R(3, 12) = 16.02, P < 0.0002). Since the paper-and-pencil digit-comparison task can be administered easily, it can be useful for neuropsychologists seeking practical measures of NP that do not require cumbersome technical equipment.

Looking for the GAP effect in manual responses and the role of contextual influences in reaction time experiments

When the offset of a visual stimulus (GAP condition) precedes the onset of a target, saccadic reaction times are reduced in relation to the condition with no offset (overlap condition) - the GAP effect. However, the existence of the GAP effect for manual responses is still controversial. In two experiments using both simple (Experiment 1, N = 18) and choice key-press procedures (Experiment 2, N = 12), we looked for the GAP effect in manual responses and investigated possible contextual influences on it. Participants were asked to respond to the imperative stimulus that would occur under different experimental contexts, created by varying the array of warning-stimulus intervals (0, 300 and 1000 ms) and conditions (GAP and overlap): i) intervals and conditions were randomized throughout the experiment; ii) conditions were run in different blocks and intervals were randomized; iii) intervals were run in different blocks and conditions were randomized. Our data showed that no GAP effect was obtained for any manipulation. The predictability of stimulus occurrence produced the strongest influence on response latencies. In Experiment 1, simple manual responses were shorter when the intervals were blocked (247 ms, P < 0.001) in relation to the other two contexts (274 and 279 ms). Despite the use of choice key-press procedures, Experiment 2 produced a similar pattern of results. A discussion addressing the critical conditions to obtain the GAP effect for distinct motor responses is presented. In short, our data stress the relevance of the temporal allocation of attention for behavioral performance.

Effects of estragole on the compound action potential of the rat sciatic nerve

Estragole, a relatively nontoxic terpenoid ether, is an important constituent of many essential oils with widespread applications in folk medicine and aromatherapy and known to have potent local anesthetic activity. We investigated the effects of estragole on the compound action potential (CAP) of the rat sciatic nerve. The experiments were carried out on sciatic nerves dissected from Wistar rats. Nerves, mounted in a moist chamber, were stimulated at a frequency of 0.2 Hz, with electric pulses of 50-100-µs duration at 10-20 V, and evoked CAP were monitored on an oscilloscope and recorded on a computer. CAP control parameters were: peak-to-peak amplitude (PPA), 9.9 ± 0.55 mV (N = 15), conduction velocity, 92.2 ± 4.36 m/s (N = 15), chronaxy, 45.6 ± 3.74 µs (N = 5), and rheobase, 3.9 ± 0.78 V (N = 5). Estragole induced a dose-dependent blockade of the CAP. At 0.6 mM, estragole had no demonstrable effect. At 2.0 and 6.0 mM estragole, PPA was significantly reduced at the end of 180-min exposure of the nerve to the drug to 85.6 ± 3.96 and 13.04 ± 1.80% of control, respectively. At 4.0 mM, estragole significantly altered PPA, conduction velocity, chronaxy, and rheobase (P <= 0.05, ANOVA; N = 5) to 49.3 ± 6.21 and 77.7 ± 3.84, 125.9 ± 10.43 and 116.7 ± 4.59%, of control, respectively. All of these effects developed slowly and were reversible upon a 300-min wash-out. The data show that estragole dose-dependently blocks nerve excitability.

The terrestrial Gastropoda Megalobulimus abbreviatus as a useful model for nociceptive experiments: effects of morphine and naloxone on thermal avoidance behavior

We describe the behavior of the snail Megalobulimus abbreviatus upon receiving thermal stimuli and the effects of pretreatment with morphine and naloxone on behavior after a thermal stimulus, in order to establish a useful model for nociceptive experiments. Snails submitted to non-functional (22ºC) and non-thermal hot-plate stress (30ºC) only displayed exploratory behavior. However, the animals submitted to a thermal stimulus (50ºC) displayed biphasic avoidance behavior. Latency was measured from the time the animal was placed on the hot plate to the time when the animal lifted the head-foot complex 1 cm from the substrate, indicating aversive thermal behavior. Other animals were pretreated with morphine (5, 10, 20 mg/kg) or naloxone (2.5, 5.0, 7.5 mg/kg) 15 min prior to receiving a thermal stimulus (50ºC; N = 9 in each group). The results (means ± SD) showed an extremely significant difference in response latency between the group treated with 20 mg/kg morphine (63.18 ± 14.47 s) and the other experimental groups (P < 0.001). With 2.5 mg/kg (16.26 ± 3.19 s), 5.0 mg/kg (11.53 ± 1.64 s) and 7.5 mg/kg naloxone (7.38 ± 1.6 s), there was a significant, not dose-dependent decrease in latency compared to the control (33.44 ± 8.53 s) and saline groups (29.1 ± 9.91 s). No statistically significant difference was found between the naloxone-treated groups. With naloxone plus morphine, there was a significant decrease in latency when compared to all other groups (minimum 64% in the saline group and maximum 83.2% decrease in the morphine group). These results provide evidence of the involvement of endogenous opioid peptides in the control of thermal withdrawal behavior in this snail, and reveal a stereotyped and reproducible avoidance behavior for this snail species, which could be studied in other pharmacological and neurophysiological studies.

Pyörivän keskiökärjen rakenteen kehittäminen työstövärähtelyjen välttämiseksi sorvauksessa

Tässä diplomityössä käsitellään sorvauksen työstövärähtelyjen ja sorvin keskiökärjen rakenteen yhteyttä. Työ on osa Lappeenrannan teknillisen yliopiston VMAX-projektia, ja sen taustalla on pyrkimys uudenlaisen, sorvin kärkipylkän puristusvoiman ajonaikaiseen säätämiseen perustuvan työstövärähtelyjen välttämismenetelmän kehittämiseen. Tämän menetelmän toiminnan todentaminen oli työn ensimmäinen tavoite. Menetelmän toteuttaminen asettaa kuitenkin käytetyn keskiökärjen rakenteelle tiettyjä vaatimuksia. Työn toisena tavoitteena oli nämä vaatimukset täyttävän keskiökärjen prototyypin kehittäminen. Tutkimus eteni seuraavasti. Ensimmäiseksi ongelma määriteltiin tutustumalla työn teoreettiseen taustaan ja aiheeseen liittyvään tutkimukseen Lappeenrannan teknillisestä yliopistosta ja muualta. Myös keskiökärkiä valmistavien yritysten tuotekatalogeja tarkasteltiin. Seuraavaksi siirryttiin alustavaan suunnitteluvaiheeseen, jossa verifioitiin menetelmän toiminta ja luotiin konsepteja keskiökärjen rakenteen kehittämistä varten. Tämän alustavan vaiheen jälkeen suoritettiin suunnitteluprosessi keskiökärjen prototyypille. Lopuksi, suunnitellun prototyypin rakenteen käyttäytymistä arvioitiin tietokonemallinnuksen avulla. Lisätuloksena tutkimuksen aikana johdettiin yksinkertaistettu elementtimenetelmään perustuva laskentamalli järjestelmän ominaistaajuuksien selvittämiseksi. Laskentamallin tarkkuutta arvoitiin. Suunnitteluprosessin tuloksena saatiin kaikki menetelmän toiminnan sekä normaalin käytön asettamat vaatimukset täyttävä rakenne keskiökärjen prototyypille. Myös johdetun laskentamallin tulokset ovat varsin lähellä 3D-elementtimallinnuksen antamia tuloksia. Tutkimuksen tavoitteiden voidaan siis sanoa toteutuneen. Koska prototyyppiä ja laskentamallia ei kuitenkaan ole vielä kokeellisesti verifioitu, tämä ei ole täysin varmaa.

Automatic image-based identification of Saimaa ringed seals

The Saimaa ringed seal is one of the most endangered seals in the world. It is a symbol of Lake Saimaa and a lot of effort have been applied to save it. Traditional methods of seal monitoring include capturing the animals and installing sensors on their bodies. These invasive methods for identifying can be painful and affect the behavior of the animals. Automatic identification of seals using computer vision provides a more humane method for the monitoring. This Master's thesis focuses on automatic image-based identification of the Saimaa ringed seals. This consists of detection and segmentation of a seal in an image, analysis of its ring patterns, and identification of the detected seal based on the features of the ring patterns. The proposed algorithm is evaluated with a dataset of 131 individual seals. Based on the experiments with 363 images, 81\% of the images were successfully segmented automatically. Furthermore, a new approach for interactive identification of Saimaa ringed seals is proposed. The results of this research are a starting point for future research in the topic of seal photo-identification.