Expression, Enzymatic Activities and Subcellular Localization of Hepatitis E Virus and Semliki Forest Virus Replicase Proteins

Viruses are submicroscopic, infectious agents that are obligate intracellular parasites. They adopt various types of strategies for their parasitic replication and proliferation in infected cells. The nucleic acid genome of a virus contains information that redirects molecular machinery of the cell to the replication and production of new virions. Viruses that replicate in the cytoplasm and are unable to use the nuclear transcription machinery of the host cell have developed their own transcription and capping systems. This thesis describes replication strategies of two distantly related viruses, hepatitis E virus (HEV) and Semliki Forest virus (SFV), which belong to the alphavirus-like superfamily of positive-strand RNA viruses. We have demonstrated that HEV and SFV share a unique cap formation pathway specific for alphavirus-like superfamily. The capping enzyme first acts as a methyltransferase, catalyzing the transfer of a methyl group from S-adenosylmethionine to GTP to yield m7GTP. It then transfers the methylated guanosine to the end of viral mRNA. Both reactions are virus-specific and differ from those described for the host cell. Therefore, these capping reactions offer attractive targets for the development of antiviral drugs. Additionally, it has been shown that replication of SFV and HEV takes place in association with cellular membranes. The origin of these membranes and the intracellular localization of the components of the replication complex were studied by modern microscopy techniques. It was demonstrated that SFV replicates in cytoplasmic membranes that are derived from endosomes and lysosomes. According to our studies, site for HEV replication seems to be the intermediate compartment which mediates the traffic between endoplasmic reticulum and the Golgi complex. As a result of this work, a unique mechanism of cap formation for hepatitis E virus replicase has been characterized. It represents a novel target for the development of specific inhibitors against viral replication.

Recognition, comorbidity, and outcome of DSM-IV bipolar I and II disorders in psychiatric care

This study is part of an ongoing collaborative bipolar research project, the Jorvi Bipolar Study (JoBS). The JoBS is run by the Department of Mental Health and Alcohol Research of the National Public Health Institute, Helsinki, and the Department of Psychiatry, Jorvi Hospital, Helsinki University Central Hospital (HUCH), Espoo, Finland. It is a prospective, naturalistic cohort study of secondary level care psychiatric in- and outpatients with a new episode of bipolar disorder (BD). The second report also included 269 major depressive disorder (MDD) patients from the Vantaa Depression Study (VDS). The VDS was carried out in collaboration with the Department of Psychiatry of the Peijas Medical Care District. Using the Mood Disorder Questionnaire (MDQ), all in- and outpatients at the Department of Psychiatry at Jorvi Hospital who currently had a possible new phase of DSM-IV BD were sought. Altogether, 1630 psychiatric patients were screened, and 490 were interviewed using a semistructured interview (SCID-I/P). The patients included in the cohort (n=191) had at intake a current phase of BD. The patients were evaluated at intake and at 6- and 18-month interviews. Based on this study, BD is poorly recognized even in psychiatric settings. Of the BD patients with acute worsening of illness, 39% had never been correctly diagnosed. The classic presentations of BD with hospitalizations, manic episodes, and psychotic symptoms lead clinicians to correct diagnosis of BD I in psychiatric care. Time of follow-up elapsed in psychiatric care, but none of the clinical features, seemed to explain correct diagnosis of BD II, suggesting reliance on cross- sectional presentation of illness. Even though BD II was clearly less often correctly diagnosed than BD I, few other differences between the two types of BD were detected. BD I and II patients appeared to differ little in terms of clinical picture or comorbidity, and the prevalence of psychiatric comorbidity was strongly related to the current illness phase in both types. At the same time, the difference in outcome was clear. BD II patients spent about 40% more time depressed than BD I patients. Patterns of psychiatric comorbidity of BD and MDD differed somewhat qualitatively. Overall, MDD patients were likely to have more anxiety disorders and cluster A personality disorders, and bipolar patients to have more cluster B personality disorders. The adverse consequences of missing or delayed diagnosis are potentially serious. Thus, these findings strongly support the value of screening for BD in psychiatric settings, especially among the major depressive patients. Nevertheless, the diagnosis must be based on a clinical interview and follow-up of mood. Comorbidity, present in 59% of bipolar patients in a current phase, needs concomitant evaluation, follow-up, and treatment. To improve outcome in BD, treatment of bipolar depression is a major challenge for clinicians.

Genetic background of bipolar disorder and related cognitive impairments

Bipolar disorder (BP) is a complex psychiatric disorder characterized by episodes of mania and depression. BP affects approximately 1% of the world’s population and shows no difference in lifetime prevalence between males and females. BP arises from complex interactions among genetic, developmental and environmental factors, and it is likely that several predisposing genes are involved in BP. The genetic background of BP is still poorly understood, although intensive and long-lasting research has identified several chromosomal regions and genes involved in susceptibility to BP. This thesis work aims to identify the genetic variants that influence bipolar disorder in the Finnish population by candidate gene and genome-wide linkage analyses in families with many BP cases. In addition to diagnosis-based phenotypes, neuropsychological traits that can be seen as potential endophenotypes or intermediate traits for BP were analyzed. In the first part of the thesis, we examined the role of the allelic variants of the TSNAX/DISC1 gene cluster to psychotic and bipolar spectrum disorders and found association of distinct allelic haplotypes with these two groups of disorders. The haplotype at the 5’ end of the Disrupted-in-Schizophrenia-1 gene (DISC1) was over-transmitted to males with psychotic disorder (p = 0.008; for an extended haplotype p = 0.0007 with both genders), whereas haplotypes at the 3’ end of DISC1 associated with bipolar spectrum disorder (p = 0.0002; for an extended haplotype p = 0.0001). The variants of these haplotypes also showed association with different cognitive traits. The haplotypes at the 5’ end associated with perseverations and auditory attention, while the variants at the 3’ end associated with several cognitive traits including verbal fluency and psychomotor processing speed. Second, in our complete set of BP families with 723 individuals we studied six functional candidate genes from three distinct signalling systems: serotonin-related genes (SLC6A4 and TPH2), BDNF -related genes (BDNF, CREB1 and NTRK2) and one gene related to the inflammation and cytokine system (P2RX7). We replicated association of the functional variant Val66Met of BDNF with BP and better performance in retention. The variants at the 5’ end of SLC6A4 also showed some evidence of association among males (p = 0.004), but the widely studied functional variants did not yield any significant results. A protective four-variant haplotype on P2RX7 showed evidence of association with BP and executive functions: semantic and phonemic fluency (p = 0.006 and p = 0.0003, respectively). Third, we analyzed 23 bipolar families originating from the North-Eastern region of Finland. A genome-wide scan was performed using the 6K single nucleotide polymorphism (SNP) array. We identified susceptibility loci at chromosomes 7q31 with a LOD score of 3.20 and at 9p13.1 with a LOD score of 4.02. We followed up both linkage findings in the complete set of 179 Finnish bipolar families. The finding on chromosome 9p13 was supported (maximum LOD score of 3.02), but the susceptibility gene itself remains unclarified. In the fourth part of the thesis, we wanted to test the role of the allelic variants that have associated with bipolar disorder in recent genome-wide association studies (GWAS). We could confirm findings for the DFNB31, SORCS2, SCL39A3, and DGKH genes. The best signal in this study comes from DFNB31, which remained significant after multiple testing corrections. Two variants of SORCS2 were allelic replications and presented the same signal as the haplotype analysis. However, no association was detected with the PALB2 gene, which was the most significantly associated region in the previous GWAS. Our results indicate that BP is heterogeneous and its genetic background may accordingly vary in different populations. In order to fully understand the allelic heterogeneity that underlies common diseases such as BP, complete genome sequencing for many individuals with and without the disease is required. Identification of the specific risk variants will help us better understand the pathophysiology underlying BP and will lead to the development of treatments with specific biochemical targets. In addition, it will further facilitate the identification of environmental factors that alter risk, which will potentially provide improved occupational, social and psychological advice for individuals with high risk of BP.

Suicidal behaviour in bipolar disorder

The Jorvi Bipolar Study (JoBS) is a collaborative ongoing bipolar research project between the Department of Mental Health and Alcohol Research of the National Public Health Institute, Helsinki, and the Department of Psychiatry, Jorvi Hospital, Helsinki University Central Hospital (HUCH), Espoo, Finland. The JoBS is a prospective, naturalistic cohort study of secondary level care psychiatric out-and inpatients with a new episode of Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) bipolar disorder (BD). Altogether, 1630 patients (aged 18-59) years were screened using the Mood Disorder Questionnaire (MDQ) for a possible new episode of DSM-IV BD. 490 patients were interviewed with semi-structured interview [the Structured Clinical Interview for DSM-IV Disorders, research version with Psychotic Screen (SCID-I/P)]. 191 patients with new episode of DSM-IV BD were included in the bipolar cohort study. Psychiatric comorbidity was evaluated using semi-structured interviews. At 6- and 18-month follow-up, the interviews were repeated and life-chart methodology was used to integrate all available information about nature and duration of all different phases. Suicidal behaviour was examined both at intake and follow-up by psychometric scale [Scale for Suicidal Ideation (SSI)], interviewer s questions and medical and psychiatric records. The aim of this thesis was to evaluate prevalence of suicidal behaviour and incidence of suicide attempts, and examine the wide range of risk factors for attempted suicide both, at intake and follow-up, in representative secondary-level sample of psychiatric in- and outpatients with BD. In this study suicidal behaviour was common among psychiatric patients with BD. During the episode when patients were included into cohort study (index episode), 20% of the patients had attempted suicide and 61% had suicidal ideation. Severity of depressive episode and hopelessness were independent risk factors for suicidal ideation, whereas hopelessness, comorbid personality disorder and previous suicide attempt predicted suicide attempts during the index episode. There were no differences in prevalence of suicidal behaviour between bipolar I and II disorder; the risk factors were overlapping but not identical. During the index episode, suicide attempts took place during depressive, mixed and depressive mixed phases. Furthermore, there were marked differences regarding level of suicidal ideation during different phases, with the highest levels during the mixed phases of the illness. Hopelessness was independently associated with suicidal behaviour during the depressive phase. A subjective rating of severity of depression (Beck Depression Inventory) and younger age predicted suicide attempts during mixed phases. During the 18-month follow-up 20% of patients attempted suicide. Previous suicide attempts, hopelessness, depressive phase at index episode and younger age at intake were independent risk factors for suicide attempts during follow-up. Taken altogether, 55% patients attempted suicide before index episode, during index episode or during follow-up. The incidence of suicide attempts was 37-fold during combined mixed and depressive mixed states and 18-fold during major depressive phase as compared with other phases. Prior suicide attempt and time spent in combined mixed phases - mixed and depressive mixed - and depressive phases independently predicted the suicide attempt during follow-up. More than half of the patients have attempted suicide during their lifetime, a finding which highlights the public health importance of suicidal behaviour in bipolar disorder. Clinically, it is crucial to recognize BD and manage the mixed and depressive phases of bipolar patients fast and effectively, as time spent in depressive and mixed phases involves a remarkably high risk of suicide attempts.

Localization of handwritten text in documents using moment invariants and Delaunay triangulation

This paper describes an approach based on Zernike moments and Delaunay triangulation for localization of hand-written text in machine printed text documents. The Zernike moments of the image are first evaluated and we classify the text as hand-written using the nearest neighbor classifier. These features are independent of size, slant, orientation, translation and other variations in handwritten text. We then use Delaunay triangulation to reclassify the misclassified text regions. When imposing Delaunay triangulation on the centroid points of the connected components, we extract features based on the triangles and reclassify the text. We remove the noise components in the document as part of the preprocessing step so this method works well on noisy documents. The success rate of the method is found to be 86%. Also for specific hand-written elements such as signatures or similar text the accuracy is found to be even higher at 93%.

Binaural Localization and Masking

Binaural experiments are described which indicate that the ability of the brain to localize a desired sound and to suppress undesired sounds coming from other directions can be traced in part to the different times of arrival of a sound at the two ears. It is suggested that the brain inserts a time delay in one of the two nerve paths associated with the ears so as to be able to compare, and thus concentrate on, those sounds arriving at the ears with this particular time of arrival distance.The ability to perceive weak sounds binaurally in the presence of noise is shown to be a simple function of the direction of the desired sound and noise. An explanation is given for the effect reported by Koenig that front and rear confusion is avoided by head movements.

Intrinsic Electron localization in manganites

We mention here an unusual disorder effect in manganites, namely the ubiquitous hopping behavior for electron transport observed in them over a wide range of doping. We argue that the implied Anderson localization is intrinsic to manganites, because of the existence of polarons in them which are spatially localized, generally at random sites (unless there is polaron ordering). We have developed a microscopic two fluid lb model for manganites, where l denotes lattice site localized l polarons, and b denotes band electrons. Using this, and the self-consistent theory of localization, we show that the occupied b states are Anderson localized in a large range of doping due to the scattering of b electrons from l polarons. Numerical simulations which further include the effect of long range Coulomb interactions support this, as well the existence of a novel polaronic Coulomb glass. A consequence is the inevitable hopping behaviour for electron transport observed in doped insulating manganites.

Text localization and extraction from complex gray images

We propose two texture-based approaches, one involving Gabor filters and the other employing log-polar wavelets, for separating text from non-text elements in a document image. Both the proposed algorithms compute local energy at some information-rich points, which are marked by Harris' corner detector. The advantage of this approach is that the algorithm calculates the local energy at selected points and not throughout the image, thus saving a lot of computational time. The algorithm has been tested on a large set of scanned text pages and the results have been seen to be better than the results from the existing algorithms. Among the proposed schemes, the Gabor filter based scheme marginally outperforms the wavelet based scheme.

Binarization and localization of text images captured on a mobile phone camera

This paper proposes and compares four methods of binarzing text images captured using a camera mounted on a cell phone. The advantages and disadvantages(image clarity and computational complexity) of each method over the others are demonstrated through binarized results. The images are of VGA or lower resolution.

Analysis of effects of ambients (temperature and light intensity) on the electrical breakdown in bipolar transistors

This paper presents an analysis of the effects of ambients-temperature and light intensity on the V-l characteristics of bipolar transistors under electrical breakdown. The analysis is based on the transportation and storage of majority carriers in the base region. It is shown that this analysis can explain the observed shift in the V-l characteristics to lower voltages with increase in either temperature or light intensity.

Angle-resolved photoemission spectroscopy of the insulating NaxWO3: Anderson localization, polaron formation, and remnant Fermi surface

The electronic structure of the insulating sodium tungsten bronze, Na0.025WO3, is investigated by high-resolution angle-resolved photoemission spectroscopy. We find that near-E-F states are localized due to the strong disorder arising from random distribution of Na+ ions in the WO3 lattice, which makes the system insulating. The temperature dependence of photoemission spectra provides direct evidence for polaron formation. The remnant Fermi surface of the insulator is found to be the replica of the real Fermi surface in the metallic system

Rapid localization of damage using a circular sensor array and Lamb wave based triangulation

A damage detection and imaging methodology based on symmetry of neighborhood sensor path and similarity of signal patterns with respect to radial paths in a circular array of sensors has been developed It uses information regarding Limb wave propagation along with a triangulation scheme to rapidly locate and quantify the severity of damage without using all of the sensor data. In a plate like structure, such a scheme can be effectively employed besides full field imaging of wave scattering pattern from the damage, if present in the plate. This new scheme is validated experimentally. Hole and corrosion type damages have been detected and quantified using the proposed scheme successfully. A wavelet based cumulative damage index has been studied which shows monotonic sensitivity against the severity of the damage. which is most desired in a Structural Health Monitoring system. (C) 2010 Elsevier Ltd. All rights reserved.