A novel polar-based human face recognition computational model

Motivated by a recently proposed biologically inspired face recognition approach, we investigated the relation between human behavior and a computational model based on Fourier-Bessel (FB) spatial patterns. We measured human recognition performance of FB filtered face images using an 8-alternative forced-choice method. Test stimuli were generated by converting the images from the spatial to the FB domain, filtering the resulting coefficients with a band-pass filter, and finally taking the inverse FB transformation of the filtered coefficients. The performance of the computational models was tested using a simulation of the psychophysical experiment. In the FB model, face images were first filtered by simulated V1- type neurons and later analyzed globally for their content of FB components. In general, there was a higher human contrast sensitivity to radially than to angularly filtered images, but both functions peaked at the 11.3-16 frequency interval. The FB-based model presented similar behavior with regard to peak position and relative sensitivity, but had a wider frequency band width and a narrower response range. The response pattern of two alternative models, based on local FB analysis and on raw luminance, strongly diverged from the human behavior patterns. These results suggest that human performance can be constrained by the type of information conveyed by polar patterns, and consequently that humans might use FB-like spatial patterns in face processing.

Induced maturation of hepatic progenitor cellsin vitro

Hepatic progenitor cells (HPCs) are a potential cell source for liver cell transplantation but do not function like mature liver cells. We sought an effective and reliable method to induce HPC maturation. An immortalized HP14.5 albumin promoter-driven Gaussian luciferase (ALB-GLuc) cell line was established from HPCs isolated from fetal mouse liver of post coitus day 14.5 mice to investigate the effect of induction factors on ALB promoter. HP14.5 parental cells were cultured in DMEM with different combinations of 2% horse serum (HS), 0.1 µM dexamethasone (DEX), 10 ng/mL hepatic growth factor (HGF), and/or 20 ng/mL fibroblast growth factor 4 (FGF4). Trypan blue and crystal violet staining were used to assess cell proliferation with different induction conditions. Expression of hepatic markers was measured by semi-quantitative RT-PCR, Western blot, and immunofluorescence. Glycogen storage and metabolism were detected by periodic acid-Schiff and indocyanine green (ICG) staining. GLuc activity indicated ALB expression. The combination of 2% HS+0.1 µM Dex+10 ng/mL HGF+20 ng/mL FGF4 induced the highest ALB-GLuc activity. Cell proliferation decreased in 2% HS but increased by adding FGF4. Upon induction, and consistent with hepatocyte development, DLK, AFP, and CK19 expression decreased, while ALB, CK18, and UGT1A expression increased. The maturity markers tyrosine aminotransferase and apolipoprotein B were detected at days 3 and 6 post-induction, respectively. ICG uptake and glycogen synthesis were detectable at day 6 and increased over time. Therefore, we demonstrated that HPCs were induced to differentiate into functional mature hepatocytes in vitro, suggesting that factor-treated HPCs may be further explored as a means of liver cell transplantation.

Tangential microfiltration of orange juice in bench pilot

The aim of this study was to introduce the tangential microfiltration (TMF) technique on the production of orange juice (TMFJ), and compare it with pasteurised juice (control) as regards chemical composition and sensorial characteristics. We used a TMF pilot equipped with four monotubular ceramic membranes (0.1, 0.2, 0.8 and 1.4mm) arranged in series with a filtering area of 0.005 m² each. Commercial flash-pasteurised orange juice was used as the initial product. Experiments were divided into three parts: a) the characterisation of the TMF pilot; b) optimisation of operational conditions; c) production of the TMFJ. In the second part, membrane with 0.8-mm pores presented best flux followed by those with 1.4-, 0.1-, and 0.2-mm pores. However, to guarantee permeate sterility, we chose the membrane with 0.1-mm pores for TMFJ production. Initially, the orange juice was sieved in order to separate part of the pulp, being subsequently submitted to TMF. A mixture of retentate and pulp was made, and was subsequently pasteurised. We obtained the TMFJ by adding the permeate to the mixture. TMFJ presented soluble solids content (°Brix), pulp, pH, and titrable acidity similar to the initial pasteurised juice (control). Nevertheless, 28% of vitamin C was lost during the TMFJ production. According to the juice taster panel, the control juice presented best sensorial characteristics (greater aroma intensity and fruity flavour) when compared with the TMJF.

Spectrally Tuned Lanthanide Photoluminescence for Point-of-Care Testing

Point-of-care (POC) –diagnostics is a field with rapidly growing market share. As these applications become more widely used, there is an increasing pressure to improve their performance to match the one of a central laboratory tests. Lanthanide luminescence has been widely utilized in diagnostics because of the numerous advantages gained by the utilization of time-resolved or anti-Stokes detection. So far the use of lanthanide labels in POC has been scarce due to limitations set by the instrumentation required for their detection and the shortcomings, e.g. low brightness, of these labels. Along with the advances in the research of lanthanide luminescence, and in the field of semiconductors, these materials are becoming a feasible alternative for the signal generation also in the future POC assays. The aim of this thesis was to explore ways of utilizing time-resolved detection or anti-Stokes detection in POC applications. The long-lived fluorescence for the time-resolved measurement can be produced with lanthanide chelates. The ultraviolet (UV) excitation required by these chelates is cumbersome to produce with POC compatible fluorescence readers. In this thesis the use of a novel light-harvesting ligand was studied. This molecule can be used to excite Eu(III)-ions at wavelengths extending up to visible part of the spectrum. An enhancement solution based on this ligand showed a good performance in a proof-of-concept -bioaffinity assay and produced a bright signal upon 365 nm excitation thanks to the high molar absorptivity of the chelate. These features are crucial when developing miniaturized readers for the time-resolved detection of fluorescence. Upconverting phosphors (UCPs) were studied as an internal light source in glucose-sensing dry chemistry test strips and ways of utilizing their various emission wavelengths and near-infrared excitation were explored. The use of nanosized NaYF :Yb3+,Tm3+-particles enabled the replacement of an external UV-light source with a NIR-laser and gave an additional degree of freedom in the optical setup of the detector instrument. The new method enabled a blood glucose measurement with results comparable to a current standard method of measuring reflectance. Microsized visible emitting UCPs were used in a similar manner, but with a broad absorbing indicator compound filtering the excitation and emission wavelengths of the UCP. This approach resulted in a novel way of benefitting from the non-linear relationship between the excitation power and emission intensity of the UCPs, and enabled the amplification of the signal response from the indicator dye.

Generative Part-Based Gabor Object Detector

Object detection is a fundamental task of computer vision that is utilized as a core part in a number of industrial and scientific applications, for example, in robotics, where objects need to be correctly detected and localized prior to being grasped and manipulated. Existing object detectors vary in (i) the amount of supervision they need for training, (ii) the type of a learning method adopted (generative or discriminative) and (iii) the amount of spatial information used in the object model (model-free, using no spatial information in the object model, or model-based, with the explicit spatial model of an object). Although some existing methods report good performance in the detection of certain objects, the results tend to be application specific and no universal method has been found that clearly outperforms all others in all areas. This work proposes a novel generative part-based object detector. The generative learning procedure of the developed method allows learning from positive examples only. The detector is based on finding semantically meaningful parts of the object (i.e. a part detector) that can provide additional information to object location, for example, pose. The object class model, i.e. the appearance of the object parts and their spatial variance, constellation, is explicitly modelled in a fully probabilistic manner. The appearance is based on bio-inspired complex-valued Gabor features that are transformed to part probabilities by an unsupervised Gaussian Mixture Model (GMM). The proposed novel randomized GMM enables learning from only a few training examples. The probabilistic spatial model of the part configurations is constructed with a mixture of 2D Gaussians. The appearance of the parts of the object is learned in an object canonical space that removes geometric variations from the part appearance model. Robustness to pose variations is achieved by object pose quantization, which is more efficient than previously used scale and orientation shifts in the Gabor feature space. Performance of the resulting generative object detector is characterized by high recall with low precision, i.e. the generative detector produces large number of false positive detections. Thus a discriminative classifier is used to prune false positive candidate detections produced by the generative detector improving its precision while keeping high recall. Using only a small number of positive examples, the developed object detector performs comparably to state-of-the-art discriminative methods.

Mineraalien rikastusprosessin vesijalanjälki

Mineraalien rikastamiseen käytetään useita fysikaalisia ja kemiallisia menetelmiä. Prosessi sisältää malmin hienonnuksen, rikastuksen ja lopuksi vedenpoistamisen rikastelietteestä. Malmin rikastamiseen käytetään muun muassa vaahdotusta, liuotusta, magneettista rikastusta ja tiheyseroihin perustuvia rikastusmenetelmiä. Rikastuslietteestä voidaan poistaa vettä sakeuttamalla ja suodattamalla. Rikastusprosessin ympäristövaikutuksia voidaan arvioida laskemalla tuotteen vesijalanjälki, joka kertoo valmistamiseen kulutetun veden määrän. Tässä kirjallisuustyössä esiteltiin mineraalien käsittelymenetelmiä sekä prosessijätevesien puhdistusmenetelmiä. Kirjallisuuslähteiden pohjalta selvitettiin Pyhäsalmen kaivoksella valmistetun kuparianodin vesijalanjälki sekä esitettiin menetelmiä, joilla prosessiin tarvittavan raakaveden kulutusta voitaisiin vähentää. Pyhäsalmella kuparirikasteesta valmistetun kuparianodin vesijalanjälki on 240 litraa H2O ekvivalenttia tuotettua tonnia kohden. Pyhäsalmen prosessin raakaveden kulutusta voidaan vähentää lisäämällä sisäistä vedenkierrätystä. Kalsiumsulfaatin saostuminen putkiin ja pumppuihin on ilmentynyt ongelmaksi vedenkierrätyksen lisäämisessä. Kalsiumsulfaattia voidaan erottaa vedestä membraaneihin, ioninvaihtoon ja sähkökemiaan perustuvilla tekniikoilla. Vaihtoehdossa, jossa johdetaan kaikista kolmesta vaahdotuksesta saatavat rikastuslietteen ja rikastushiekan sakeutuksien ylitteet sekä suodatuksien suodosvedet samaan vedenkäsittelyyn voidaan kattaa arviolta noin 65 % koko veden tarpeesta. Raakavettä säästetään vuodessa 3,4 Mm^3 ja samalla rikastushiekka-altaiden tarvittava koko pienenee, joka vähentää ympäristöriskejä.

Use of airborne laser scanner data in demanding forest conditions

Most of the applications of airborne laser scanner data to forestry require that the point cloud be normalized, i.e., each point represents height from the ground instead of elevation. To normalize the point cloud, a digital terrain model (DTM), which is derived from the ground returns in the point cloud, is employed. Unfortunately, extracting accurate DTMs from airborne laser scanner data is a challenging task, especially in tropical forests where the canopy is normally very thick (partially closed), leading to a situation in which only a limited number of laser pulses reach the ground. Therefore, robust algorithms for extracting accurate DTMs in low-ground-point-densitysituations are needed in order to realize the full potential of airborne laser scanner data to forestry. The objective of this thesis is to develop algorithms for processing airborne laser scanner data in order to: (1) extract DTMs in demanding forest conditions (complex terrain and low number of ground points) for applications in forestry; (2) estimate canopy base height (CBH) for forest fire behavior modeling; and (3) assess the robustness of LiDAR-based high-resolution biomass estimation models against different field plot designs. Here, the aim is to find out if field plot data gathered by professional foresters can be combined with field plot data gathered by professionally trained community foresters and used in LiDAR-based high-resolution biomass estimation modeling without affecting prediction performance. The question of interest in this case is whether or not the local forest communities can achieve the level technical proficiency required for accurate forest monitoring. The algorithms for extracting DTMs from LiDAR point clouds presented in this thesis address the challenges of extracting DTMs in low-ground-point situations and in complex terrain while the algorithm for CBH estimation addresses the challenge of variations in the distribution of points in the LiDAR point cloud caused by things like variations in tree species and season of data acquisition. These algorithms are adaptive (with respect to point cloud characteristics) and exhibit a high degree of tolerance to variations in the density and distribution of points in the LiDAR point cloud. Results of comparison with existing DTM extraction algorithms showed that DTM extraction algorithms proposed in this thesis performed better with respect to accuracy of estimating tree heights from airborne laser scanner data. On the other hand, the proposed DTM extraction algorithms, being mostly based on trend surface interpolation, can not retain small artifacts in the terrain (e.g., bumps, small hills and depressions). Therefore, the DTMs generated by these algorithms are only suitable for forestry applications where the primary objective is to estimate tree heights from normalized airborne laser scanner data. On the other hand, the algorithm for estimating CBH proposed in this thesis is based on the idea of moving voxel in which gaps (openings in the canopy) which act as fuel breaks are located and their height is estimated. Test results showed a slight improvement in CBH estimation accuracy over existing CBH estimation methods which are based on height percentiles in the airborne laser scanner data. However, being based on the idea of moving voxel, this algorithm has one main advantage over existing CBH estimation methods in the context of forest fire modeling: it has great potential in providing information about vertical fuel continuity. This information can be used to create vertical fuel continuity maps which can provide more realistic information on the risk of crown fires compared to CBH.

Spatial variability of soil fertility and its relationship with seed physiological potential in a soybean production area

The correlation of soil fertility x seed physiological potential is very important in the area of seed technology but results published with that theme are contradictory. For this reason, this study to evaluate the correlations between soil chemical properties and physiological potential of soybean seeds. On georeferenced points, both soil and seeds were sampled for analysis of soil fertility and seed physiological potential. Data were assessed by the following analyses: descriptive statistics; Pearson's linear correlation; and geostatistics. The adjusted parameters of the semivariograms were used to produce maps of spatial distribution for each variable. Organic matter content, Mn and Cu showed significant effects on seed germination. Most variables studied presented moderate to high spatial dependence. Germination and accelerated aging of seeds, and P, Ca, Mg, Mn, Cu and Zn showed a better fit to spherical semivariogram: organic matter, pH and K had a better fit to Gaussian model; and V% and Fe showed a better fit to the linear model. The values for range of spatial dependence varied from 89.9 m for P until 651.4 m for Fe. These values should be considered when new samples are collected for assessing soil fertility in this production area.

Loistehon kompensoinnin ja yliaaltosuodattimien nykytila sekä kehityskohteet Kemira Chemicals Oy:n Joutsenon tehtaalla

Tutkimuksessa käsitelty kemikaalitehdas on 110 kV:n kantaverkkoon liittyvä tehointensiivinen teollisuuslaitos. Prosessien käyttöön mukautetut sähkönjakeluverkon yliaaltosuodattimet ja niiden käyttökytkennät ovat tärkeässä asemassa loistehon tuoton hallitsemiseksi liittymän loistehoikkunaan ja riittävän yliaaltosuodatuksen järjestämiseksi häviöt minimoiden. Kohteena olleen kemikaalitehtaan sähkönjakeluverkon kompensointia ja yliaaltosuodatusta on viimeksi tutkittu vuonna 2003. Tämän jälkeen verkostokomponentit ovat ikääntyneet, prosessien käyttö sekä pienjänniteverkko ovat muuttuneet ja tehdasta käyttävät osittain eri henkilöt. Nykytilaselvitykselle ja verkon kehityskohteiden analysoinnille on tullut tarve edellisen selvityksen jatkoksi. Tutkimus painottuu vahvasti kenttämittauksiin, joiden perusteella sekä kirjallisuutta ja tehtaan järjestelmiä hyödyntäen määritetään loistehotasot verkon keskeisimmissä kohteissa pien-, keski- ja suurjännitetasoilla. Tutkimuksessa esitetään lipeätehtaan suotimien uudelleenjärjestely 4. yliaallon vähentämiseksi ja yksikkökoon pienentämiseksi. Kantaverkon liittymäpisteen tilanne oli hyväksyttävä. Tutkimus esittää pienjännitekompensointia KF-4-100 keskukseen varayhteyden kapasiteettia lisäten. Tutkimus tuotti yleistietoutta verkon käytöstä ja selvitti parhaat käyttökytkennät loistehoikkunan hallitsemiseksi ilman loistehokustannuksia.

De novo transcriptome assembly and annotation of the isopod Idotea balthica

The Baltic Sea is a unique environment that contains unique genetic populations. In order to study these populations on a genetic level basic molecular research is needed. The aim of this thesis was to provide a basic genetic resource for population genomic studies by de novo assembling a transcriptome for the Baltic Sea isopod Idotea balthica. RNA was extracted from a whole single adult male isopod and sequenced using Illumina (125bp PE) RNA-Seq. The reads were preprocessed using FASTQC for quality control, TRIMMOMATIC for trimming, and RCORRECTOR for error correction. The preprocessed reads were then assembled with TRINITY, a de Bruijn graph-based assembler, using different k-mer sizes. The different assemblies were combined and clustered using CD-HIT. The assemblies were evaluated using TRANSRATE for quality and filtering, BUSCO for completeness, and TRANSDECODER for annotation potential. The 25-mer assembly was annotated using PANNZER (protein annotation with z-score) and BLASTX. The 25-mer assembly represents the best first draft assembly since it contains the most information. However, this assembly shows high levels of polymorphism, which currently cannot be differentiated as paralogs or allelic variants. Furthermore, this assembly is incomplete, which could be improved by sampling additional developmental stages.

Fluorescence spectra and ab initio theoretical studies of HCOOH /

A fluorescence excitation spectrum of formic acid monomer (HCOOH) , has been recorded in the 278-246 nm region and has been attributed to an n >7r* electron promotion in the anti conformer. The S^< S^ electronic origins of the HCOOH/HCOOD/DCOOH/DCOOD isotopomers were assigned to weak bands observed at 37431.5/37461.5/37445.5/37479.3 cm'''. From a band contour analysis of the 0°^ band of HCOOH, the rotational constants for the excited state were estimated: A'=1.8619, B'=0.4073, and C'=0.3730 cm'\ Four vibrational modes, 1/3(0=0), j/^(0-C=0) , J/g(C-H^^^) and i/,(0-H^yJ were observed in the spectrum. The activity of the antisymmetric aldehyde wagging and hydroxyl torsional modes in forming progressions is central to the analysis, leading to the conclusion that the two hydrogens are distorted from the molecular plane, 0-C=0, in the upper S. state. Ab initio calculations were performed at the 6-3 IG* SCF level using the Gaussian 86 system of programs to aid in the vibrational assignments. The computations show that the potential surface which describes the low frequency OH torsion (twisting motion) and the CH wagging (molecular inversion) motions is complex in the S^ excited electronic state. The OH and CH bonds were calculated to be twisted with respect to the 0-C=0 molecular frame by 63.66 and 4 5.76 degrees, respectively. The calculations predicted the existence of the second (syn) rotamer which is 338 cm'^ above the equilibrium configuration with OH and CH angles displaced from the plane by 47.91 and 41.32 degrees.

Heterogeneity of photosystem II as it occurs in domain specific regions of the thylakoid membrane of spinach (spinacia oleracia L.)

Thylakoid membrane fractions were prepared from specific regions of thylakoid membranes of spinach (Spinacia oleracea). These fractions, which include grana (83), stroma (T3), grana core (8S), margins (Ma) and purified stroma (Y100) were prepared using a non-detergent method including a mild sonication and aqueous two-phase partitioning. The significance of PSlla and PSII~ centres have been described extensively in the literature. Previous work has characterized two types of PSII centres which are proposed to exist in different regions of the thylakoid membrane. a-centres are suggested to aggregate in stacked regions of grana whereas ~-centres are located in unstacked regions of stroma lamellae. The goal of this study is to characterize photosystem II from the isolated membrane vesicles representing different regions of the higher plant thylakoid membrane. The low temperature absorption spectra have been deconvoluted via Gaussian decomposition to estimate the relative sub-components that contribute to each fractions signature absorption spectrum. The relative sizes of the functional PSII antenna and the fluorescence induction kinetics were measured and used to determine the relative contributions of PSlla and PSII~ to each fraction. Picosecond chlorophyll fluorescence decay kinetics were collected for each fraction to characterize and gain insight into excitation energy transfer and primary electron transport in PSlla and PSII~ centres. The results presented here clearly illustrate the widely held notions of PSII/PS·I and PSlIa/PSII~ spatial separation. This study suggests that chlorophyll fluorescence decay lifetimes of PSII~ centres are shorter than those of PSlIa centres and, at FM, the longer lived of the two PSII components renders a larger yield in PSlIa-rich fractions, but smaller in PSIlr3-rich fractions.