Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Quest for authenticity - representation of the Sami image in Christmas tourism

Tourism is one of important livelihoods in Lapland. Christmas tourism was launched in the early 1980s and it became a success story - being labelled as the most epochal tourism product in Finland. Hence, today Christmas tourists are one of the most significant foreign groups arriving to Lapland during the winter season and contributing considerably to the economics of the northeastern periphery of the EU. Christmas tourism concentrates around Father Christmas who uses reindeer for transportation. The Sämi are the only indigenous people in the EU. They are all stereotypically perceived to be reindeer herders. Somehow these three, that is, Santa Claus, reindeer and the Sämi, have been incorporated into same fairytale dominion. In practice, this has happened by using the most visible cultural but also significant identity marker of the Sämi, the Sämi costume. This, in turn, has created controversy over authenticity due to manners in which the costume is used in tourism - often in imitational, mismatched forms by non-Sämi. In this thesis, after relevant literature review I intend to establish how the Sâmi are represented in Christmas tourism through visual data consisting of ten images from three foreign sources. Then I clarify why and to whom it matters of how the Sâmi are represented in Christmas tourism with the aid of 65 questionnaires and nineteen expert interviews collected mainly in the Finnish Sâmi Home Region in October 2009. Through the multiplicity of the voices of various interest and ethnic groups and by using critical discourse analysis I attempt to give an overview of the respondents' opinions and look at some preliminary solutions to the controversy. Based on my data, the non-Sami appear to accept the Sami costume usage in Christmas tourism most readily. Consequently, respect and attitudinal changes have become the respondents' propositions in addition to common set of rules of how the Sami image could be appropriated without violating the integrity of the Sami people, or a similar system of S¿m¡ Duodji trademark guaranteeing the authenticity of the tourism products. Additionally, though half of the interviewees explicate Sami presence in Christmas tourism by adding local flavour to otherwise commercial enterprise, the other half see no rationale to connect facts with fiction, that is, the Sami with Santa Claus.

Approximation of Internal Refractive Index Variation Improves Image Guided Diffuse Optical Tomography of Breast

Effective usage of image guidance by incorporating the refractive index (RI) variation in computational modeling of light propagation in tissue is investigated to assess its impact on optical-property estimation. With the aid of realistic patient breast three-dimensional models, the variation in RI for different regions of tissue under investigation is shown to influence the estimation of optical properties in image-guided diffuse optical tomography (IG-DOT) using numerical simulations. It is also shown that by assuming identical RI for all regions of tissue would lead to erroneous estimation of optical properties. The a priori knowledge of the RI for the segmented regions of tissue in IG-DOT, which is difficult to obtain for the in vivo cases, leads to more accurate estimates of optical properties. Even inclusion of approximated RI values, obtained from the literature, for the regions of tissue resulted in better estimates of optical properties, with values comparable to that of having the correct knowledge of RI for different regions of tissue.

Semi-Supervised Classification Using Sparse Gaussian Process Regression

Gaussian Processes (GPs) are promising Bayesian methods for classification and regression problems. They have also been used for semi-supervised learning tasks. In this paper, we propose a new algorithm for solving semi-supervised binary classification problem using sparse GP regression (GPR) models. It is closely related to semi-supervised learning based on support vector regression (SVR) and maximum margin clustering. The proposed algorithm is simple and easy to implement. It gives a sparse solution directly unlike the SVR based algorithm. Also, the hyperparameters are estimated easily without resorting to expensive cross-validation technique. Use of sparse GPR model helps in making the proposed algorithm scalable. Preliminary results on synthetic and real-world data sets demonstrate the efficacy of the new algorithm.

Change detection and controlling forest information using multi-temporal Landsat TM imagery.

A method was developed for relative radiometric calibration of single multitemporal Landsat TM image, several multitemporal images covering each others, and several multitemporal images covering different geographic locations. The radiometricly calibrated difference images were used for detecting rapid changes on forest stands. The nonparametric Kernel method was applied for change detection. The accuracy of the change detection was estimated by inspecting the image analysis results in field. The change classification was applied for controlling the quality of the continuously updated forest stand information. The aim was to ensure that all the manmade changes and any forest damages were correctly updated including the attribute and stand delineation information. The image analysis results were compared with the registered treatments and the stand information base. The stands with discrepancies between these two information sources were recommended to be field inspected.

Composite MR image reconstruction and unaliasing for general trajectories using neural networks

In rapid parallel magnetic resonance imaging, the problem of image reconstruction is challenging. Here, a novel image reconstruction technique for data acquired along any general trajectory in neural network framework, called ``Composite Reconstruction And Unaliasing using Neural Networks'' (CRAUNN), is proposed. CRAUNN is based on the observation that the nature of aliasing remains unchanged whether the undersampled acquisition contains only low frequencies or includes high frequencies too. Here, the transformation needed to reconstruct the alias-free image from the aliased coil images is learnt, using acquisitions consisting of densely sampled low frequencies. Neural networks are made use of as machine learning tools to learn the transformation, in order to obtain the desired alias-free image for actual acquisitions containing sparsely sampled low as well as high frequencies. CRAUNN operates in the image domain and does not require explicit coil sensitivity estimation. It is also independent of the sampling trajectory used, and could be applied to arbitrary trajectories as well. As a pilot trial, the technique is first applied to Cartesian trajectory-sampled data. Experiments performed using radial and spiral trajectories on real and synthetic data, illustrate the performance of the method. The reconstruction errors depend on the acceleration factor as well as the sampling trajectory. It is found that higher acceleration factors can be obtained when radial trajectories are used. Comparisons against existing techniques are presented. CRAUNN has been found to perform on par with the state-of-the-art techniques. Acceleration factors of up to 4, 6 and 4 are achieved in Cartesian, radial and spiral cases, respectively. (C) 2010 Elsevier Inc. All rights reserved.

A new classification and linear sequence of extant gymnosperms

A new classification and linear sequence of the gymnosperms based on previous molecular and morphological phylogenetic and other studies is presented. Currently accepted genera are listed for each family and arranged according to their (probable) phylogenetic position. A full synonymy is provided, and types are listed for accepted genera. An index to genera assists in easy access to synonymy and family placement of genera.

Functional outcome and health-related quality of life after traumatic brain injury in the framework of the International Classification of Functioning, Disability and Health (ICF)

Traumatic brain injury (TBI) affects people of all ages and is a cause of long-term disability. In recent years, the epidemiological patterns of TBI have been changing. TBI is a heterogeneous disorder with different forms of presentation and highly individual outcome regarding functioning and health-related quality of life (HRQoL). The meaning of disability differs from person to person based on the individual s personality, value system, past experience, and the purpose he or she sees in life. Understanding of all these viewpoints is needed in comprehensive rehabilitation. This study examines the epidemiology of TBI in Finland as well as functioning and HRQoL after TBI, and compares the subjective and objective assessments of outcome. The frame of reference is the International Classification of Functioning, Disability and Health (ICF). The subjects of Study I represent the population of Finnish TBI patients who experienced their first TBI between 1991 and 2005. The 55 Finnish subjects of Studies II and IV participated in the first wave of the international Quality of life after brain injury (QOLIBRI) validation study. The 795 subjects from six language areas of Study III formed the second wave of the QOLIBRI validation study. The average annual incidence of Finnish hospitalised TBI patients during the years 1991-2005 was 101:100 000 in patients who had TBI as the primary diagnosis and did not have a previous TBI in their medical history. Males (59.2%) were at considerably higher risk of getting a TBI than females. The most common external cause of the injury was falls in all age groups. The number of TBI patients ≥ 70 years of age increased by 59.4% while the number of inhabitants older than 70 years increased by 30.3% in the population of Finland during the same time period. The functioning of a sample of 55 persons with TBI was assessed by extracting information from the patients medical documents using the ICF checklist. The most common problems were found in the ICF components of Body Functions (b) and Activities and Participation (d). HRQoL was assessed with the QOLIBRI which showed the highest level of satisfaction on the Emotions, Physical Problems and Daily Life and Autonomy scales. The highest scores were obtained by the youngest participants and participants living independently without the help of other people, and by people who were working. The relationship between the functional outcome and HRQoL was not straightforward. The procedure of linking the QOLIBRI and the GOSE to the ICF showed that these two outcome measures cover the relevant domains of TBI patients functioning. The QOLIBRI provides the patients subjective view, while the GOSE summarises the objective elements of functioning. Our study indicates that there are certain domains of functioning that are not traditionally sufficiently documented but are important for the HRQoL of persons with TBI. This was the finding especially in the domains of interpersonal relationships, social and leisure activities, self, and the environment. Rehabilitation aims to optimize functioning and to minimize the experience of disability among people with health conditions, and it needs to be based on a comprehensive understanding of human functioning. As an integrative model, the ICF may serve as a frame of reference in achieving such an understanding.

Sediment Volume Tests for Expansive Soil Identification and Classification

Equilibrium sediment volume tests are conducted on field soils to classify them based on their degree of expansivity and/or to predict the liquid limit of soils. The present technical paper examines different equilibrium sediment volume tests, critically evaluating each of them. It discusses the settling behavior of fine-grained soils during the soil sediment formation to evolve a rationale for conducting the latest version of equilibrium sediment volume test. Probable limitations of equilibrium sediment volume test and the possible solution to overcome the same have also been indicated.

A Parallel Progressive Refinement Image Rendering Algorithm on a Scalable Multithreaded VLSI Processor Array

In this paper we develop a multithreaded VLSI processor linear array architecture to render complex environments based on the radiosity approach. The processing elements are identical and multithreaded. They work in Single Program Multiple Data (SPMD) mode. A new algorithm to do the radiosity computations based on the progressive refinement approach[2] is proposed. Simulation results indicate that the architecture is latency tolerant and scalable. It is shown that a linear array of 128 uni-threaded processing elements sustains a throughput close to 0.4 million patches/sec.

Dual-DSP system for signal and image processing

The design of a dual-DSP microprocessor system and its application for parallel FFT and two-dimensional convolution are explained. The system is based on a master-salve configuration. Two ADSP-2101s are configured as slave processors and a PC/AT serves as the master. The master serves as a control processor to transfer the program code and data to the DSPs. The system architecture and the algorithms for the two applications, viz. FFT and two-dimensional convolutions, are discussed.

Monumenttikuvista elämyskuviin : Helsinki matkaesitteiden kuvituksessa 1895 - 2005

The purpose of this study is to define how Helsinki has been presented in the pictures of tourist brochures and how their illustration has changed over time. Attention is also paid to the values and meanings that the pictures mediate, as well as their historical and societal connections. The pictures are approached as representations selectively interpreting and illustrating the reality of Helsinki, while constructing mental images of it. An iconological framework structures the study. It proceeds from the description and classification of the physical features towards an analysis of time- and culture-specific meanings. The emergence of meanings and their historical and cultural underpinnings are examined from the perspectives of humanistic geography, semiotics and constructionism. In the analysis attention is paid to the discourses, myths and ideologies that underlie the representations. Information on the physical features of the pictures and their changes is collected with a content analysis. The classified data consists of 1377 photographs. These pictures are collected from 75 tourist brochures of Helsinki that have been published between 1895 and 2005. The deeper meanings of the pictures are studied qualitatively, by paying attention to the mental images that the content elements and visual effects evoke. Research studies, contemporary literature and the texts of the tourist brochures are utilised in the interpretation of the meanings. There has been a permanent core to objects of the pictures during the entire study period. It has consisted mainly of sights that are located close to the Senate and Market Squares. In addition, marine elements have been popular. The area of Helsinki represented in the brochures has extended from the Senate Square towards Töölö Bay. Pictures of monumental buildings and statues have been complemented with snapshots and portraits. In the beginning of the 20th century, brochures were mainly produced for the travelling, educated elite. The style of the pictures was declaratory and educative. They aimed at medating an objective image of the reality that prevailed in Helsinki. In practice, the pictures were connected to a patriotic ideology and the corresponding myth of Finnishness. In the second half of the 20th century the improvement of the standard of living led to a democratisation of consumers and an increase in the tourism demand. Local culture and the everyday life of "ordinary" people became popular themes in the pictures. A new welfare ideology manifested itself in the people of the local residential areas, for instance. The increase in the cultural diversity has led to the recognition of new target groups, expecially since the 1980s. The human figures in the pictures have started to function as objects of identification and a means of constructing mental images. A pronounced emphasis on experience and individuality in the illustration of the tourist brochures mirrors the post-modern change and a new ideology based on consumption. The construction and consumption of the pictures in the tourist brochures is governed by the conventions of representation and interpretaion that are typical of the genre of tourist brochures. The pictures emphasize the perceived positive characteristics of Helsinki and thus construct a skewed view of the reality. However, consumers can knowingly use the pictures as a means of dreaming and detaching themselves from their everyday reality.