Integration of miRNA and mRNA expression with DNA copy number of Ewing sarcoma cell lines

Ewing sarcoma is an aggressive and poorly differentiated malignancy of bone and soft tissue. It primarily affects children, adolescents, and young adults, with a slight male predominance. It is characterized by a translocation between chromosomes 11 and 22 resulting in the EWSR1-FLI1fusion transcription factor. The aim of this study is to identify putative Ewing sarcoma target genes through an integrative analysis of three microarray data sets. Array comparative genomic hybridization is used to measure changes in DNA copy number, and analyzed to detect common chromosomal aberrations. mRNA and miRNA microarrays are used to measure expression of protein-coding and miRNA genes, and these results integrated with the copy number data. Chromosomal aberrations typically contain also bystanders in addition to the driving tumor suppressor and oncogenes, and integration with expression helps to identify the true targets. Correlation between expression of miRNAs and their predicted target mRNAs is also evaluated to assess the results of post-transcriptional miRNA regulation on mRNA levels. The highest frequencies of copy number gains were identified in chromosome 8, 1q, and X. Losses were most frequent in 9p21.3, which also showed an enrichment of copy number breakpoints relative to the rest of the genome. Copy number losses in 9p21.3 were found have a statistically significant effect on the expression of MTAP, but not on CDKN2A, which is a known tumor-suppressor in the same locus. MTAP was also down-regulated in the Ewing sarcoma cell lines compared to mesenchymal stem cells. Genes exhibiting elevated expression in association with copy number gains and up-regulation compared to the reference samples included DCAF7, ENO2, MTCP1, andSTK40. Differentially expressed miRNAs were detected by comparing Ewing sarcoma cell lines against mesenchymal stem cells. 21 up-regulated and 32 down-regulated miRNAs were identified, includingmiR-145, which has been previously linked to Ewing sarcoma. The EWSR1-FLI1 fusion gene represses miR-145, which in turn targets FLI1 forming a mutually repressive feedback loop. In addition higher expression linked to copy number gains and compared to mesenchymal stem cells, STK40 was also found to be a target of four different miRNAs that were all down-regulated in Ewing sarcoma cell lines compared to the reference samples. SLCO5A1 was identified as the only up-regulated gene within a frequently gained region in chromosome 8. This region was gained in over 90 % of the cell lines, and also with a higher frequency than the neighboring regions. In addition, SLCO5A1 was found to be a target of three miRNAs that were down-regulated compared to the mesenchymal stem cells.

Using a botanic garden collection to test a bioclimatic vegetation scheme

Vegetation maps and bioclimatic zone classifications communicate the vegetation of an area and are used to explain how the environment regulates the occurrence of plants on large scales. Many practises and methods for dividing the world’s vegetation into smaller entities have been presented. Climatic parameters, floristic characteristics, or edaphic features have been relied upon as decisive factors, and plant species have been used as indicators for vegetation types or zones. Systems depicting vegetation patterns that mainly reflect climatic variation are termed ‘bioclimatic’ vegetation maps. Based on these it has been judged logical to deduce that plants moved between corresponding bioclimatic areas should thrive in the target location, whereas plants moved from a different zone should languish. This principle is routinely applied in forestry and horticulture but actual tests of the validity of bioclimatic maps in this sense seem scanty. In this study I tested the Finnish bioclimatic vegetation zone system (BZS). Relying on the plant collection of Helsinki University Botanic Garden’s Kumpula collection, which according to the BZS is situated at the northern limit of the hemiboreal zone, I aimed to test how the plants’ survival depends on their provenance. My expectation was that plants from the hemiboreal or southern boreal zones should do best in Kumpula, whereas plants from more southern and more northern zones should show progressively lower survival probabilities. I estimated probability of survival using collection database information of plant accessions of known wild origin grown in Kumpula since the mid 1990s, and logistic regression models. The total number of accessions I included in the analyses was 494. Because of problems with some accessions I chose to separately analyse a subset of the complete data, which included 379 accessions. I also analysed different growth forms separately in order to identify differences in probability of survival due to different life strategies. In most analyses accessions of temperate and hemiarctic origin showed lower survival probability than those originating from any of the boreal subzones, which among them exhibited rather evenly high probabilities. Exceptionally mild and wet winters during the study period may have killed off hemiarctic plants. Some winters may have been too harsh for temperate accessions. Trees behaved differently: they showed an almost steadily increasing survival probability from temperate to northern boreal origins. Various factors that could not be controlled for may have affected the results, some of which were difficult to interpret. This was the case in particular with herbs, for which the reliability of the analysis suffered because of difficulties in managing their curatorial data. In all, the results gave some support to the BZS, and especially its hierarchical zonation. However, I question the validity of the formulation of the hypothesis I tested since it may not be entirely justified by the BZS, which was designed for intercontinental comparison of vegetation zones, but not specifically for transcontinental provenance trials. I conclude that botanic gardens should pay due attention to information management and curational practices to ensure the widest possible applicability of their plant collections.

Low reynolds number flow of a dilute suspension in slowly varying tubes

We have discussed here the flow of a dilute suspension of rigid particles in Newtonian fluid in slowly varying tubes characterized by a small parameter ε. Solutions are presented in the form of asymptotic expansions in powers of ε. The effect of the suspension on the fluid is described by two parameters β and γ which depend on the volume fraction of the particles which we assume to be small. It is found that the presence of the particles accelerate the process of eddy formation near the constriction and shifts the point of separation.

Cubicity of Interval Graphs and the Claw Number

Let G(V, E) be a simple, undirected graph where V is the set of vertices and E is the set of edges. A b-dimensional cube is a Cartesian product l(1) x l(2) x ... x l(b), where each l(i) is a closed interval of unit length on the real line. The cub/city of G, denoted by cub(G), is the minimum positive integer b such that the vertices in G can be mapped to axis parallel b-dimensional cubes in such a way that two vertices are adjacent in G if and only if their assigned cubes intersect. An interval graph is a graph that can be represented as the intersection of intervals on the real line-i.e. the vertices of an interval graph can be mapped to intervals on the real line such that two vertices are adjacent if and only if their corresponding intervals overlap. Suppose S(m) denotes a star graph on m+1 nodes. We define claw number psi(G) of the graph to be the largest positive integer m such that S(m) is an induced subgraph of G. It can be easily shown that the cubicity of any graph is at least log(2) psi(G)]. In this article, we show that for an interval graph G log(2) psi(G)-]<= cub(G)<=log(2) psi(G)]+2. It is not clear whether the upper bound of log(2) psi(G)]+2 is tight: till now we are unable to find any interval graph with cub(G)> (log(2)psi(G)]. We also show that for an interval graph G, cub(G) <= log(2) alpha], where alpha is the independence number of G. Therefore, in the special case of psi(G)=alpha, cub(G) is exactly log(2) alpha(2)]. The concept of cubicity can be generalized by considering boxes instead of cubes. A b-dimensional box is a Cartesian product l(1) x l(2) x ... x l(b), where each I is a closed interval on the real line. The boxicity of a graph, denoted box(G), is the minimum k such that G is the intersection graph of k-dimensional boxes. It is clear that box(G)<= cub(G). From the above result, it follows that for any graph G, cub(G) <= box(G)log(2) alpha]. (C) 2010 Wiley Periodicals, Inc. J Graph Theory 65: 323-333, 2010

Tavallisuudesta tyylikkyyteen? : Sukupuoli ja maku kodinmuutosohjelmissa

The study focuses on the Finnish home makeover shows Inno (2004 , Nelonen) and Kodin kääntöpiiri (2001 2005; YLE TV2) and their episodes broadcast in spring 2004. The research material also includes the websites of both shows and messages concerning Inno from an online discussion forum. As people decorate their homes and reflect on them, they engage in negotiations of taste and in the construction of the ideal self. The main question of the study is: how are representations of the gendered self produced in home makeover shows? The broader theoretical and methodological context of the study is based on intersectionality, or simultaneous study of different identity categories. In this study, the main focus is on the intersections of gender, class and sexuality. Hence, the secondary research question is: how do ways of doing gender intersect with producing the ideas of class and sexuality in the representations of home makeover shows? The theoretical framework of the study combines Judith Butler s theory of gender performativity and Pierre Bourdieu s theory of taste. The analysis is founded upon a close reading focusing on the details and ambiguous meanings contained in the televisual representation. Home makeover shows are explored as a part of contemporary television culture, which is characterised by a significant increase in the number of both television channels and global television formats, as well as the hybridisation of programme types. Researchers on lifestyle television have paid attention to male designers and their ability to reconstruct meanings related to domesticity and home decoration as feminine spheres. The dissertation contributes to this discussion by analysing the representations of the male interior decorator in Inno and the four female interior decorators in Kodin kääntöpiiri. The focus is on the professional self and how it is both gendered and defined as an arbiter of taste. The programme concepts produce the impression that the makeover homes and their occupants are ordinary . The manufactured sense of ordinariness often conceals differences between the participants. One argument of the study is that the ordinariness of participants on lifestyle television should not be taken for granted without further reflection on the implications of labeling something as ordinary. Updating of interior decoration in home makeover shows can be interpreted as an area of doing gender that requires deliberation, effort, expert knowledge and a sufficient budget. The ideal lay decorator is portrayed as culturally omnivorous, brave and receptive to new ideas. The ability to reflect on ways of representing masculinity and femininity through decoration is also implied. In home makeover shows, greater self-awareness regarding the ways in which gender is produced does not lead to repeating gender differently. The idea of normative heterosexuality is in a hegemonic position in the representations of the participants. In Inno and Kodin kääntöpiiri questions of class are not made explicit. However, the idea of class is produced indirectly e.g. by describing the apartments and houses of the participants, by discussing their hobbies or interest in cultural products. In Inno, home decoration is primarily depicted as an individualistic consumer choice, while in Kodin kääntöpiiri it is often defined as a way to strengthen the ties of nuclear families. In Kodin kääntöpiiri, the ethos of familism is combined with pleasures gained from consumption and DIY activities. As a whole, the multidisciplinary study indicates a great number of differences between the two shows.

Liminal Belonging: West African male asylum seekers’ narratives of the asylum experience whilst in Finland

The dominant discourses on the issue of asylum have placed it on a uniquely higher level of scrutiny as a politically very sensitive area for social research. Today, member states within the EU have implemented stricter policies to control new arrivals, whilst instituting statutory procedures to manage the existing asylum claims. In 2010, the number of applicants for asylum in Finland totalled 5988, out of which 1784 were given positive decisions. This thesis endeavour to highlight asylum seekers in the discourses about them by adding their voices to the discussions of them in contemporary Finland. Studies, which has concentrated on asylum seekers in Finland, uses the living conditions within asylum reception centres to assess the impacts of structural barriers on asylum seekers’ efforts to deal with the asylum process. By highlighting the impacts of the entire asylum process, which I believe starts from the country of origin; I focus on examining narratives of dealing with the experience of liminality whilst waiting for asylum, and then explore areas of possible participation within informal social networks for West African asylum seekers in Finland. The overall aim is to place the current research within the broader sociological discussion of ‘belonging’ for asylum seekers who are yet to be recognized as refugees, and who exist in a state of limbo. Methodologically, oral interviews, self-written autobiographical narratives, and ethnographic field work are qualitatively combined as data in this thesis for an empirical study of West African male asylum seekers in Finland. Narrative analysis is employed to analyze the data for this thesis. The ethnographic research data for the study began in May 2009 and ended in August of 2010. Altogether, ten interviews and four self-written narratives were collected as data. In total seven hours of audio recording were made, along eleven pages of hand-written autobiographical narratives. Field observation notes are employed in the study to provide contexts to the active interactional processes of interpretation throughout the analysis. Findings from the study suggest that within the experience of liminality, which surrounds the entire asylum process, participations within informal social networks are found to be important to the process of re-making place and the sense of belonging. My study shows that this is necessary to countering the experience of boredom, stress and social isolation, which permeate all aspects of life for West African asylum seekers, whilst they wait for asylum decisions in Finland.

Fuzzy Coherence: Making Sense of Continuity in Hypertext Narratives

Hypertexts are digital texts characterized by interactive hyperlinking and a fragmented textual organization. Increasingly prominent since the early 1990s, hypertexts have become a common text type both on the Internet and in a variety of other digital contexts. Although studied widely in disciplines like hypertext theory and media studies, formal linguistic approaches to hypertext continue to be relatively rare. This study examines coherence negotiation in hypertext with particularly reference to hypertext fiction. Coherence, or the quality of making sense, is a fundamental property of textness. Proceeding from the premise that coherence is a subjectively evaluated property rather than an objective quality arising directly from textual cues, the study focuses on the processes through which readers interact with hyperlinks and negotiate continuity between hypertextual fragments. The study begins with a typological discussion of textuality and an overview of the historical and technological precedents of modern hypertexts. Then, making use of text linguistic, discourse analytical, pragmatic, and narratological approaches to textual coherence, the study takes established models developed for analyzing and describing conventional texts, and examines their applicability to hypertext. Primary data derived from a collection of hyperfictions is used throughout to illustrate the mechanisms in practice. Hypertextual coherence negotiation is shown to require the ability to cognitively operate between local and global coherence by means of processing lexical cohesion, discourse topical continuities, inferences and implications, and shifting cognitive frames. The main conclusion of the study is that the style of reading required by hypertextuality fosters a new paradigm of coherence. Defined as fuzzy coherence, this new approach to textual sensemaking is predicated on an acceptance of the coherence challenges readers experience when the act of reading comes to involve repeated encounters with referentially imprecise hyperlinks and discourse topical shifts. A practical application of fuzzy coherence is shown to be in effect in the way coherence is actively manipulated in hypertext narratives.

Making Sense of Value and Value Co-Creation in Service Logic

In order to further develop the logic of service, value creation, value co-creation and value have to be formally and rigorously defined, so that the nature, content and locus of value and the roles of service providers and customers in value creation can be unambiguously assessed. In the present article, following the underpinning logic of value-in-use, it is demonstrated that in order to achieve this, value creation is best defined as the customer’s creation of value-in-use. The analysis shows that the firm’s and customer’s processes and activities can be divided into a provider sphere, closed for the customer, and a customer sphere, closed for the firm. Value creation occurs in the customer sphere, whereas firms in the provider sphere facilitate value creation by producing resources and processes which represent potential value or expected value-in use for their customers. By getting access to the closed customer sphere, firms can create a joint value sphere and engage in customers’ value creation as co-creators of value with them. This approach establishes a theoretically sound foundation for understanding value creation in service logic, and enables meaningful managerial implications, for example as to what is required for co-creation of value, and also further theoretical elaborations.

Squeezed states, photon-number distributions, and U(l) invariance

We study the photon-number distribution in squeezed states of a single-mode radiation field. A U(l)-invariant squeezing criterion is compared and contrasted with a more restrictive criterion, with the help of suggestive geometric representations. The U(l) invariance of the photon-number distribution in a squeezed coherent state, with arbitrary complex squeeze and displacement parameters, is explicitly demonstrated. The behavior of the photon-number distribution for a representative value of the displacement and various values of the squeeze parameter is numerically investigated. A new kind of giant oscillation riding as an envelope over more rapid oscillations in this distribution is demonstrated.

Improved mechanical properties of polymer nanocomposites incorporating graphene-like BN: Dependence on the number of BN layers

The mechanical properties of composites of polymethylmethacrylate (PMMA) with two-dimensional graphene-like boron nitride (BN) have been investigated to explore the dependence of the properties on the number of BN layers. This study demonstrates that significantly improved mechanical properties are exhibited by the composite with the fewest number of BN layers. Thus, with incorporation of three BN layers, the hardness and elastic modulus of the composite showed an increase of 125% and 130%, respectively, relative to pure PMMA. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Five-level inverter scheme for an open-end winding induction machine with less number of switches

Higher level of inversion is achieved with a less number of switches in the proposed scheme. The scheme proposes a five-level inverter for an open-end winding induction motor which uses only two DC-link rectifiers of voltage rating of Vdc/4, a neutral-point clamped (NPC) three-level inverter and a two-level inverter. Even though the two-level inverter is connected to the high-voltage side, it is always in square-wave operation. Since the two-level inverter is not switching in a pulse width modulated fashion and the magnitude of switching transient is only half compared to the convention three-level NPC inverter, the switching losses and electromagnetic interference is not so high. The scheme is experimentally verified on a 2.5 kW induction machine.

Unsteady nonsimilar two-dimensional and axisymmetric water boundary layers with variable viscosity and prandtl number

The influence of temperature-dependent viscosity and Prandtl number on the unsteady laminar nonsimilar forced convection flow over two-dimensional and axisymmetric bodies has been examined where the unsteadiness and (or) nonsimilarity are (is) due to the free stream velocity, mass transfer, and transverse curvature. The partial differential equations governing the flow which involve three independent variables have been solved numerically using an implicit finite-difference scheme along with a quasilinearization technique. It is found that both the skin friction and heat transfer strongly respond to the unsteady free stream velocity distributions. The unsteadiness and injection cause the location of zero skin friction to move upstream. However, the effect of variable viscosity and Prandtl number is to move it downstream. The heat transfer is found to depend strongly on viscous dissipation, but the skin friction is little affected by it. In general, the results pertaining to variable fluid properties differ significantly, from those of constant fluid properties.