Cutaneous porphyrias : Clinical and histopathological study

The prevalence of variegate porphyria (VP) (2.1:100 000, in 2006 n=108) was higher in Finland than elsewhere in European countries due to a founder effect (R152C). The incidence of VP was estimated at 0.2:1 000 000 based on the number of new symptomatic patients yearly. The prevalence of porphyria cutanea tarda (PCT) was 1.2:100 000 (in 2006 n=63), which is only one fourth of the numbers reported from other European countries. The estimated incidence of PCT was 0.5:1 000 000. Based on measurements of the uroporphyrinogen decarboxylase activity in erythrocytes, the proportion of familial PCT was 49% of the cases. The prevalence of erythropoietic protoporphyria (EPP) was at 0.8:100 000 (in 2006 n=39) including asymptomatic carriers of a mutation in the ferrochelatase (FECH) gene. The incidence of EPP was estimated at 0.1:1 000 000. After 1980 the penetrance was 37% among patients with VP. Of the mutation carriers (n=57) 30% manifested with skin symptoms. Frequency of skin symptom as only clinical sign was stable before or after 1980 (22% vs. 21%), but acute attacks became infrequent (29% vs. 7%). Of the symptomatic patients 30% had both acute attacks and skin symptoms and 80% had skin symptoms. Fragility (95%) and blistering (46%) of the skin in the backs of the hands were the most common skin symptoms. Transient correction of porphyrin metabolism using eight haem arginate infusions within five weeks had no effect on the skin symptoms in three of four patients with VP. In one case skin symptoms disappeared transiently. One patient with homozygous VP had severe photosensitivity since birth. Sensory polyneuropathy, glaucoma and renal failure developed during the 25-year follow-up without the presence of acute attacks. The I12T mutation was detected in both of his alleles in the protoporphyrinogen oxidase gene. Lack of skin symptoms and infrequency of acute attacks (1/9) in the patients with I12T mutation at the heterozygous stage indicate a mild phenotype (the penetrance 11%). Four mutations (751delGAGAA, 1122delT, C286T, C343T) in the FECH gene were characterised in four of 15 families with EPP. Burning pain (96%) and swelling (92%) of the sun-exposed skin were the major skin symptoms. Hepatopathy appeared in one of 25 symptomatic patients (4%). Clinical manifestations and associated factors of PCT were similar in the sporadic and familial types of PCT. The majority of the patients with PCT had one to three precipitating factors: alcohol intake (78%), mutations in hemochromatosis associated gene (50%), use of oestrogen (25% of women) and hepatitis B or C infections (25 %). Fatty liver disease (67%) and siderosis (67%) were commonly found in their liver biopsies. The major histopathological change of the sun-exposed skin in the patients with VP (n=20), EPP (n=8) and PCT (n=5) was thickening of the vessel walls of the upper dermis suggesting that the vessel wall is the primary site of the phototoxic reaction in each type of porphyria. The fine structure of the vessel walls was similar in VP, EPP and PCT consisting of the multilayered basement membrane and excess of finely granular substance between the layers which were surrounded by the band of homogenous material. EPP was characterised by amorphous perivascular deposits extending also to the extravascular space. In direct immunofluorescence study homogenous IgG deposits in the vessel walls of the upper dermis of the sun-exposed skin were demonstrated in each type of porphyria. In EPP the excess material around vessel walls consisted of other proteins such as serum amyloid protein, and kappa and lambda light chains in addition to the basement membrane constituents such as collagen IV and laminin. These results suggest that the alterations of the vessel walls are a consequence of the repeated damage and the repairing process in the vessel wall. The microscopic alterations could be demonstrated even in the normal looking but sun-exposed skin of the patients with EPP during the symptom-free phase suggesting that vascular change can be chronic. The stability of vascular changes in the patients with PCT after treatment indicates that circulating porphyrins are not important for the maintenance of the changes.

Hybrid Modelling of Titan's Interaction with the Magnetosphere of Saturn

In this dissertation we study the interaction between Saturn's moon Titan and the magnetospheric plasma and magnetic field. The method of research is a three-dimensional computer simulation model, that is used to simulate this interaction. The simulation model used is a hybrid model. Hybrid models enable individual tracking or tracing of ions and also take into account the particle motion in the propagation of the electromagnetic fields. The hybrid model has been developed at the Finnish Meteorological Institute. This thesis gives a general description of the effects that the solar wind has on Earth and other planets of our solar system. Planetary satellites can also have similar interactions with the solar wind but also with the plasma flows of planetary magnetospheres. Titan is clearly the largest among the satellites of Saturn and also the only known satellite with a dense atmosphere. It is the atmosphere that makes Titan's plasma interaction with the magnetosphere of Saturn so unique. Nevertheless, comparisons with the plasma interactions of other solar system bodies are valuable. Detecting charged plasma particles requires in situ measurements obtainable through scientific spacecraft. The Cassini mission has been one of the most remarkable international efforts in space science. Since 2004 the measurements and images obtained from instruments onboard the Cassini spacecraft have increased the scientific knowledge of Saturn as well as its satellites and magnetosphere in a way no one was probably able to predict. The current level of science on Titan is practically unthinkable without the Cassini mission. Many of the observations by Cassini instrument teams have influenced this research both the direct measurements of Titan as well as observations of its plasma environment. The theoretical principles of the hybrid modelling approach are presented in connection to the broader context of plasma simulations. The developed hybrid model is described in detail: e.g. the way the equations of the hybrid model are solved is shown explicitly. Several simulation techniques, such as the grid structure and various boundary conditions, are discussed in detail as well. The testing and monitoring of simulation runs is presented as an essential routine when running sophisticated and complex models. Several significant improvements of the model, that are in preparation, are also discussed. A main part of this dissertation are four scientific articles based on the results of the Titan model. The Titan model developed during the course of the Ph.D. research has been shown to be an important tool to understand Titan's plasma interaction. One reason for this is that the structures of the magnetic field around Titan are very much three-dimensional. The simulation results give a general picture of the magnetic fields in the vicinity of Titan. The magnetic fine structure of Titan's wake as seen in the simulations seems connected to Alfvén waves an important wave mode in space plasmas. The particle escape from Titan is also a major part of these studies. Our simulations show a bending or turning of Titan's ionotail that we have shown to be a direct result of the basic principles in plasma physics. Furthermore, the ion flux from the magnetosphere of Saturn into Titan's upper atmosphere has been studied. The modelled ion flux has asymmetries that would likely have a large impact in the heating in different parts of Titan's upper atmosphere.

Comparative study on damage identification from lso-Eigen-Value-Change contours and smeared damage model

The paper proposes two methodologies for damage identification from measured natural frequencies of a contiguously damaged reinforced concrete beam, idealised with distributed damage model. The first method identifies damage from Iso-Eigen-Value-Change contours, plotted between pairs of different frequencies. The performance of the method is checked for a wide variation of damage positions and extents. The method is also extended to a discrete structure in the form of a five-storied shear building and the simplicity of the method is demonstrated. The second method is through smeared damage model, where the damage is assumed constant for different segments of the beam and the lengths and centres of these segments are the known inputs. First-order perturbation method is used to derive the relevant expressions. Both these methods are based on distributed damage models and have been checked with experimental program on simply supported reinforced concrete beams, subjected to different stages of symmetric and un-symmetric damages. The results of the experiments are encouraging and show that both the methods can be adopted together in a damage identification scenario.

Optical and magnetic properties of the exact PPP states of biphenyl

The low-lying singlets and triplets of biphenyl are obtained exactly within the PPP model using the diagrammatic valence bond method. The energy gaps within the singlet manifold as well as the lowest singlet-triplet gap are found to be in good agreement with experimental results. The two weak absorptions between 4·1 and 4·2 eV reported experimentally are attributed to the two states lying below the optical gap that become weakly allowed on breaking electron-hole and inversion symmetries. The observed blue shift of the spectral lines, attributed to a change in dihedral angle, on going from crystalline to solution to vapour phase is also well reproduced within the PPP model. The bond orders show that the ground singlet state is benzenoidal while the dipole excited state as well as the lowest triplet state are quinonoidal and planar. Comparison with the experimental spin densities and the fine structure constants D and E in the triplet state point to slightly weaker correlations than assumed by the PPP model. The introduction of a 1-8 bond to mimic poly(paraphenylene)s gives an optical gap that is in good agreement with experiment.

Molecular genetics of Usher syndrome -inherited deafness and blindness

Usher syndrome (USH) is an inherited blindness and deafness disorder with variable vestibular dysfunction. The syndrome is divided into three subtypes according to the progression and severity of clinical symptoms. The gene mutated in Usher syndrome type 3 (USH3), clarin 1 (CLRN1), was identified in Finland in 2001 and two mutations were identified in Finnish patients at that time. Prior to this thesis study, the two CLRN1 gene mutations were the only USH mutations identified in Finnish USH patients. To further clarify the Finnish USH mutation spectrum, all nine USH genes were studied. Seven mutations were identified: one was a previously known mutation in CLRN1, four were novel mutations in myosin VIIa (MYO7A) and two were a novel and a previously known mutation in usherin (USH2A). Another aim of this thesis research was to further study the structure and function of the CLRN1 gene, and to clarify the effects of mutations on protein function. The search for new splice variants resulted in the identification of eight novel splice variants in addition to the three splice variants that were already known prior to this study. Studies of the possible promoter regions for these splice variants showed the most active region included the 1000 bases upstream of the translation start site in the first exon of the main three exon splice variant. The 232 aa CLRN1 protein encoded by the main (three-exon) splice variant was transported to the plasma membrane when expressed in cultured cells. Western blot studies suggested that CLRN1 forms dimers and multimers. The CLRN1 mutant proteins studied were retained in the endoplasmic reticulum (ER) and some of the USH3 mutations caused CLRN1 to be unstable. During this study, two novel CLRN1 sequence alterations were identified and their pathogenicity was studied with cell culture protein expression. Previous studies with mice had shown that Clrn1 is expressed in mouse cochlear hair cells and spiral ganglion cells, but the expression profile in mouse retina remained unknown. The Clrn1 knockout mice display cochlear cell disruption/death, but do not have a retinal phenotype. The zebrafish, Danio rerio, clrn1 was found to be expressed in hair cells associated with hearing and balance. Clrn1 expression was also found in the inner nuclear layer (INL), photoreceptor layer and retinal pigment epithelium layer (RPE) of the zebrafish retina. When Clrn1 production was knocked down with injected morpholino oligonucleotides (MO) targeting Clrn1 translation or correct splicing, the zebrafish larvae showed symptoms similar to USH3 patients. These larvae had balance/hearing problems and reduced response to visual stimuli. The knowledge this thesis research has provided about the mutations in USH genes and the Finnish USH mutation spectrum are important in USH patient diagnostics. The extended information about the structure and function of CLRN1 is a step further in exploring USH3 pathogenesis caused by mutated CLRN1 as well as a step in finding a cure for the disease.

Is tetramethyleneethane a ground state triplet?

We have examined a number of possible ways by which tetramethyleneethane (TME) can be a ground state triplet, as claimed by experimental studies, in violation of Ovchinnikov’s theorem for alternant hydrocarbons of equal bond lengths. Model exact π calculations of the low-lying states of TME, 3,4-dimethylenefuran and 3,4-dimethylenepyrrole were carried out using a diagrammatic valence bond approach. The calculations failed to yield a triplet ground state even after (a) tuning of electron correlation, (b) breaking alternancy symmetry, and (c) allowing for geometric distortions. In contrast to earlier studies of fine structure constants in other conjugated systems, the computedD andE values of all the low-lying triplet states of TME for various geometries are at least an order of magnitude different from the experimentally reported values. Incorporation of σ-π mixing by means of UHF MNDO calculations is found to favour a singlet ground state even further. A reinterpretation of the experimental results of TME is therefore suggested to resolve the conflict.

Altered ultrastructure of rinderpest virus and its nucleocapsids induced by 5-fluorouracil

he ultrastructure of purified rinderpest virus and intracellular viral nucleocapsids from infected vero cells treated with a subtoxic dose of 5-fluorouracil (5-Fu) (1 mug/ml), has been analysed by transmission electron microscopy, and compared with that of normal virus particle and nucleocapsids. The results reveal dramatic alterations in the structure of both virions and nucleocapsids. The surface glycoprotein projection of virions was not seen or present at a much reduced level. The intracellular nucleocapsids showed pronounced structural changes,with respect to size, shape and fine structure. The length of treated nucleocapsids is much smaller as compared to the control. The central hollow core is missing in case of drug-treated nucleocapsid and the herring bone structure is replaced by a 'beads on string' structure. The presence of N protein, which is a major structural component of nucleocapsids was seen in 5-Fu-treated cells, but it was associated with a predominantly diffused form of nucleocapsids as seen by immunoelectron microscopy. We report here the first definitive and visual evidence of altered structure of virions and their nucleocapsids after 5-Fu treatment

Isolation of an 800 kb contiguous DNA fragment encompassing a 3.5-cM region of chromosome 1 in Arabidopsis using YAC clones

The apetalal mutation of Arabidopsis affects floral meristem identity and the development of sepal and petal primordia of the flower. We mapped the available RFLP markers on chromosome 1 that are in the general vicinity of apetalal on a fine structure map and then chose the closest RFLP as a starting point for contiguous DNA (contig) generation. We report here a contig of about 800 kilobases (kb) that spans a 3.5 cM region of chromosome 1. We used genomic libraries of Arabidopsis prepared in yeast artificial chromosome (YAC) vectors and the detailed characterization of 19 YACs is reported. RFLPs displayed by the end fragments from the walk were mapped to align and correlate the genetic and physical maps for this region of chromosome 1. In this segment of the genome, 1 cM corresponds to a little over 200 kb of physical distance.

Probing the structural changes in the phase transitions of a Bi2MoO6 catalyst: the nature of the intermediate-temperature phase

The nature of the phase transitions of Bi2MoO6 has been investigated by the combined use of X-ray diffraction and Xray absorption spectroscopy. The distorted MoO6 octahedra in the low-temperature form are shown to undergo further distortion in the intermediate-temperature form before transforming to MoO4 tetrahedra in the high-temperature phase. (C) 1995 Academic Press, Inc.

Predictive uncertainty of chaotic daily streamflow using ensemble wavelet networks approach

Perfect or even mediocre weather predictions over a long period are almost impossible because of the ultimate growth of a small initial error into a significant one. Even though the sensitivity of initial conditions limits the predictability in chaotic systems, an ensemble of prediction from different possible initial conditions and also a prediction algorithm capable of resolving the fine structure of the chaotic attractor can reduce the prediction uncertainty to some extent. All of the traditional chaotic prediction methods in hydrology are based on single optimum initial condition local models which can model the sudden divergence of the trajectories with different local functions. Conceptually, global models are ineffective in modeling the highly unstable structure of the chaotic attractor. This paper focuses on an ensemble prediction approach by reconstructing the phase space using different combinations of chaotic parameters, i.e., embedding dimension and delay time to quantify the uncertainty in initial conditions. The ensemble approach is implemented through a local learning wavelet network model with a global feed-forward neural network structure for the phase space prediction of chaotic streamflow series. Quantification of uncertainties in future predictions are done by creating an ensemble of predictions with wavelet network using a range of plausible embedding dimensions and delay times. The ensemble approach is proved to be 50% more efficient than the single prediction for both local approximation and wavelet network approaches. The wavelet network approach has proved to be 30%-50% more superior to the local approximation approach. Compared to the traditional local approximation approach with single initial condition, the total predictive uncertainty in the streamflow is reduced when modeled with ensemble wavelet networks for different lead times. Localization property of wavelets, utilizing different dilation and translation parameters, helps in capturing most of the statistical properties of the observed data. The need for taking into account all plausible initial conditions and also bringing together the characteristics of both local and global approaches to model the unstable yet ordered chaotic attractor of a hydrologic series is clearly demonstrated.

EPR and photoluminescence studies of ZnO:Mn nanophosphors prepared by solution combustion route

Nanocrystalline ZnO:Mn (0.1 mol%) phosphors have been successfully prepared by self propagating, gas producing solution combustion method. The powder X-ray diffraction of as-formed ZnO:Mn sample shows, hexagonal wurtzite phase with particle size of similar to 40 nm. For Mn doped ZnO, the lattice parameters and volume of unit cell (a=3.23065 angstrom, c=5.27563 angstrom and V=47.684 (angstrom)(3)) are found to be greater than that of undoped ZnO (a=3.19993 angstrom, c=5.22546 angstrom and V=46.336 (angstrom)(3)). The SEM micrographs reveal that besides the spherical crystals, the powders also contained several voids and pores. The TEM photograph also shows the particles are approximately spherical in nature. The FTIR spectrum shows two peaks at similar to 3428 and 1598 cm(-1) which are attributed to O-H stretching and H-O-H bending vibration. The PL spectra of ZnO:Mn indicate a strong green emission peak at 526 nm and a weak red emission at 636 nm corresponding to T-4(1) -> (6)A(1) transition of Mn2+ ions. The EPR spectrum exhibits fine structure transition which will be split into six hyperfine components due to Mn-55 hyperfine coupling giving rise to all 30 allowed transitions. From EPR spectra the spin-Hamiltonian parameters have been evaluated and discussed. The magnitude of the hyperfine splitting (A) constant indicates that there exists a moderately covalent bonding between the Mn2+ ions and the surrounding ligands. The number of spins participating in resonance (N), its paramagnetic susceptibility (chi) have been evaluated. (C) 2011 Elsevier B.V. All rights reserved.

An EDC-based turbulent premixed combustion model

In the present study, a new turbulent premixed combustion model is proposed by integrating the Coherent Flame Model with the modified eddy dissipation concept, and relating the fine structure mass fraction to the flame surface density. First, experimental results of turbulent flame speed available from literature are compared with the predicted results at different turbulence intensities to validate the flame surface density model. It is observed that the model is able to predict the turbulent burning speeds accurately. Then, a comprehensive validation is carried out utilizing data on a turbulent lifted methane flame issuing into a vitiated co-flow. Detailed comparison of temperature and species concentrations between experiment and simulation is performed at different heights of the flame. Overall, the model is found to predict both the spatial variation and peak values of the scalars at various heights satisfactorily.

Optical frequency metrology with an Rb-stabilized ring-cavity resonator-study of cavity-dispersion errors

We have developed a technique to measure the absolute frequencies of optical transitions by using an evacuated Rb-stabilized ring-cavity resonator as a transfer cavity. The absolute frequency of the Rb D-2 line (at 780 nm) used to stabilize the cavity is known and allows us to determine the absolute value of the unknown frequency. We study wavelength-dependent errors due to dispersion at the cavity mirrors by measuring the frequency of the same transition in the Cs D-2 line (at 852 nm) at three cavity lengths. The spread in the values shows that dispersion errors are below 30 kHz, corresponding to a relative precision of 10(-10). We give an explanation for reduced dispersion errors in the ring-cavity geometry by calculating errors due to the lateral shift and the phase shift at the mirrors, and show that they are roughly equal but occur with opposite signs. We have earlier shown that diffraction errors (due to Guoy phase) are negligible in the ring-cavity geometry compared to a linear cavity; the reduced dispersion error is another advantage. Our values are consistent with measurements of the same transition using the more expensive frequency-comb technique. Our simpler method is ideally suited for measuring hyperfine structure, fine structure, and isotope shifts, up to several hundreds of gigahertz.

Spatially Adaptive Kernel Regression Using Risk Estimation

An important question in kernel regression is one of estimating the order and bandwidth parameters from available noisy data. We propose to solve the problem within a risk estimation framework. Considering an independent and identically distributed (i.i.d.) Gaussian observations model, we use Stein's unbiased risk estimator (SURE) to estimate a weighted mean-square error (MSE) risk, and optimize it with respect to the order and bandwidth parameters. The two parameters are thus spatially adapted in such a manner that noise smoothing and fine structure preservation are simultaneously achieved. On the application side, we consider the problem of image restoration from uniform/non-uniform data, and show that the SURE approach to spatially adaptive kernel regression results in better quality estimation compared with its spatially non-adaptive counterparts. The denoising results obtained are comparable to those obtained using other state-of-the-art techniques, and in some scenarios, superior.

Enhanced sunlight photocatalytic activity of Ag3PO4 decorated novel combustion synthesis derived TiO2 nanobelts for dye and bacterial degradation

This study demonstrates the synthesis of TiO2 nanobelts using solution combustion derived TiO2 with enhanced photocatalytic activity for dye degradation and bacterial inactivation. Hydrothermal treatment of combustion synthesized TiO2 resulted in unique partially etched TiO2 nanobelts and Ag3PO4 was decorated using the co-precipitation method. The catalyst particles were characterized using X-ray diffraction analysis, BET surface area analysis, diffuse reflectance and electron microscopy. The photocatalytic properties of the composites of Ag3PO4 with pristine combustion synthesized TiO2 and commercial TiO2 under sunlight were compared. Therefore the studies conducted proved that the novel Ag3PO4/unique combustion synthesis derived TiO2 nanobelt composites exhibited extended light absorption, better charge transfer mechanism and higher generation of hydroxyl and hole radicals. These properties resulted in enhanced photodegradation of dyes and bacteria when compared to the commercial TiO2 nanocomposite. These findings have important implications in designing new photocatalysts for water purification.