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  • Lahelma, Marja (University of Helsinki, 2014)
    This study examines the dynamics of the self and art in the context of the Symbolist art and aesthetics of the fin-de-siècle. The purpose is to open new perspectives into how the self and its relationship with the world were understood and experienced, and to explore how these conceptions of selfhood suggest parallels with questions of art and creativity in ways that continue to affect our perceptions of these issues even today. The decades around the turn of the twentieth century were a period of intensifying preoccupation with questions of subjectivity as the coherence and autonomy of the self were constantly being threatened in the rapidly modernizing world. This issue is examined through an analysis and discussions of artworks by the Finnish artists Pekka Halonen and Ellen Thesleff, the Norwegian artist Edvard Munch, the Swedish author and artist August Strindberg, and the Danish artist Jens Ferdinand Willumsen. The artworks are considered as active participants in the discourses of the period and as sites of intellectual and artistic reflection. Self-portraits are the most obvious products of artistic self-examination, but the highly subjective attitude towards art indicates that in a way every work of art can be perceived as a self-portrait. Symbolism, therefore, constitutes a point in art history where old definitions of self-portraiture were no longer sufficient. Art came to be understood as a form of knowledge and a source of truth. Hence, the creative process turned into a method of self-exploration motivated by an attempt to transcend beyond everyday consciousness in order to achieve a heightened perception of the self and the world. At the same time, the focus of the artwork shifted towards an immaterial space of imagination. Hence, the work of art was no longer understood as a finite material object but rather as a revelation of an idea. The constant need for self-exploration was also related to an ever increasing questioning of traditional religiosity and a subsequent interest in religious syncretism, as well as in various mystical, spiritual, and occultist ideologies, which affected both the form and content of art. Subjectivity is often perceived as one of the defining features of Symbolist art. However, due to the content-oriented approach, which until recent years has dominated art historical research on Symbolism, the meaning of this subjective tendency has not been properly analysed. Although the emphasis on subjectivity obviously had a great impact on the content of the new art, which became increasingly concerned with mythological and fantastic material, it also worked on a more abstract level affecting the ways that the meaning and status of art were understood. The approach taken in this study is based on an idea of the interconnectedness of form and content. Through this critical perspective, this study takes part in an international current of research which seeks to redefine Symbolism and its relation to modernism.
  • Heikkinen, Mika Aatos; Kaitaniemi, Pekka; Karimäki, Veikko; Kortelainen, Matti J; Lampen, Pekka Tapio; Lehti, Sami Tapio; Linden, Tomas; Wendland, Lauri Andreas (2010)
  • Björkroth, Johanna; Vandamme, Peter; Korkeala, Hannu (American Society for Microbiology (ASM), 1998)
    Leuconostoc carnosum was shown to be the specific spoilage organism in vacuum-packaged, sliced, cooked ham showing spoilage during 3 weeks of shelf life. Identification of the specific spoilage organism was done by use of phenotypic data and ClaI, EcoRI, and HindIII reference strain ribopatterns. One hundred L. carnosum isolates associated with the production and spoilage of the ham were further characterized by pulsed-field gel electrophoresis (PFGE), together with some meat-associated Leuconostoc species: L. citreum, L. gelidum, L. mesenteroides subsp. dextranicum, and L. mesenteroides subsp. mesenteroides. ApaI and SmaI digests divided the industrial L. carnosum strains into 25 different PFGE types, ApaI and SmaI types being consistent. Only one specific PFGE type was associated with the spoiled packages. This type also was detected in air and raw-meat mass samples. The spoilage strain did not produce bacteriocins. Only seven isolates belonging to three different PFGE types produced bacteriocins. Similarity analysis of the industrial L. carnosum strains revealed a homogeneous cluster which could be divided into eight subclusters consisting of strains having at most three-fragment differences. The L. carnosum cluster was clearly distinguished from the other meatassociated leuconostoc clusters, with the exception of the L. carnosum type strain. Ribotyping can be very helpful in the identification of L. carnosum, but its discriminatory power is too weak for strain characterization. PFGE provides good discrimination for studies dealing with the properties of homogeneous L. carnosum strains.
  • Chatrchyan, Serguei; Anttila, Erkki; Czellar, Sandor; Härkönen, Jaakko; Heikkinen, Mika Aatos; Karimäki, Veikko; Kinnunen, Ritva; Klem, Jukka; Kortelainen, Matti; Lampen, Pekka Tapio; Lassila-Perini, Katri Marjaana; Lehti, Sami Tapio; Linden, Tomas; Luukka, Panja; Mäenpää, Teppo H; Nysten, Jukka Sakari; Tuominen, Eija; Tuominiemi, Jorma; Ungaro, Donatella; Wendland, Lauri Andreas; CMS Collaboration (INSTITUTE OF PHYSICS PUBLISHING, 2010)
  • Koskinen, Lotta L E; Seppälä, Eija H; Belanger, Janelle M; Arumilli, Meharji; Hakosalo, Osmo; Jokinen, Päivi; Nevalainen, Elisa M; Viitmaa, Ranno; Jokinen, Tarja S; Oberbauer, Anita M; Lohi, Hannes (BioMed Central, 2015)
    Abstract Background Idiopathic epilepsy is a common neurological disease in human and domestic dogs but relatively few risk genes have been identified to date. The seizure characteristics, including focal and generalised seizures, are similar between the two species, with gene discovery facilitated by the reduced genetic heterogeneity of purebred dogs. We have recently identified a risk locus for idiopathic epilepsy in the Belgian Shepherd breed on a 4.4 megabase region on CFA37. Results We have expanded a previous study replicating the association with a combined analysis of 157 cases and 179 controls in three additional breeds: Schipperke, Finnish Spitz and Beagle (pc = 2.9e–07, pGWAS = 1.74E-02). A targeted resequencing of the 4.4 megabase region in twelve Belgian Shepherd cases and twelve controls with opposite haplotypes identified 37 case-specific variants within the ADAM23 gene. Twenty-seven variants were validated in 285 cases and 355 controls from four breeds, resulting in a strong replication of the ADAM23 locus (praw = 2.76e–15) and the identification of a common 28 kb-risk haplotype in all four breeds. Risk haplotype was present in frequencies of 0.49–0.7 in the breeds, suggesting that ADAM23 is a low penetrance risk gene for canine epilepsy. Conclusions These results implicate ADAM23 in common canine idiopathic epilepsy, although the causative variant remains yet to be identified. ADAM23 plays a role in synaptic transmission and interacts with known epilepsy genes, LGI1 and LGI2, and should be considered as a candidate gene for human epilepsies.
  • Tervahattu, H.; Juhanoja, J.; Kupiainen, K. (American Geophysical Union, 2002)
  • Seppälä, Eija; Koskinen, Lotta L. E.; Gullov, Christina H.; Jokinen, Paivi; Karlskov-Mortensen, Peter; Bergamasco, Luciana; Korberg, Izabella Baranowska; Cizinauskas, Sigitas; Oberbauer, Anita M.; Berendt, Mette; Fredholm, Merete; Lohi, Hannes (Public Library of Science, 2012)
  • Keto-Timonen, R.; Heikinheimo, A.; Eerola, E.; Korkeala, H. (American Society for Microbiology, 2006)
    An amplified fragment length polymorphism (AFLP) method was applied to 129 strains representing 24 different Clostridium species, with special emphasis on pathogenic clostridia of medical or veterinary interest, to assess the potential of AFLP for identification of clostridia. In addition, the ability of the same AFLP protocol to type clostridia at the strain level was assessed by focusing on Clostridium perfringens strains. All strains were typeable by AFLP, so the method seemed to overcome the problem of extracellular DNase production. AFLP differentiated all Clostridium species tested, except for Clostridium ramosum and Clostridium limosum, which clustered together with a 45% similarity level. Other Clostridium species were divided into species-specific clusters or occupied separate positions. Wide genetic diversity was observed among Clostridium botulinum strains, which were divided into seven species-specific clusters. The same AFLP protocol was also suitable for typing C. perfringens at the strain level. A total of 29 different AFLP types were identified for 37 strains of C. perfringens; strains initially originating from the same isolate showed identical fingerprinting patterns and were distinguished from unrelated strains. AFLP proved to be a highly reproducible, easy-to-perform, and relatively fast method which enables high throughput of samples and can serve in the generation of identification libraries. These results indicate that the AFLP method provides a promising tool for the identification and characterization of Clostridium species.
  • Lyhs, Ulrike; Korkeala, Hannu; Björkroth, Johanna (Elsevier, 2002)
    A total of 296 lactic acid bacteria (LAB) isolated from spoiled, vacuum-packaged ‘gravad’ rainbow trout stored at 3ºC and 8ºC were characterised and identified using a molecular approach. The isolates were initially grouped according to their HindIII restriction endonuclease profiles and further identified to species level using a rRNA gene restriction pattern (ribotype) identification database. Lactobacillus sakei, Lactobacillus curvatus and Carnobacterium piscicola were the three main species detected. Only one isolate was identified as Carnobacterium divergens. Most of the carnobacteria were found in the samples stored at 3ºC. The relative proportion of L. sakei was higher in the samples stored at 8ºC.
  • Liu, Chengyu; Louhimo, Riku; Laakso, Marko; Lehtonen, Rainer; Hautaniemi, Sampsa (BioMed Central, 2015)
    Abstract Background Histologically similar tumors even from the same anatomical position may still show high variability at molecular level hindering analysis of genome-wide data. Leveling the analysis to a gene regulatory network instead of focusing on single genes has been suggested to overcome the heterogeneity issue although the majority of the network methods require large datasets. Network methods that are able to function at a single sample level are needed to overcome the heterogeneity and sample size issues. Methods We present a novel network method, Differentially Expressed Regulation Analysis (DERA) that integrates expression data to biological network information at a single sample level. The sample-specific networks are subsequently used to discover samples with similar molecular functions by identification of regulations that are shared between samples or are specific for a subgroup. Results We applied DERA to identify key regulations in triple negative breast cancer (TNBC), which is characterized by lack of estrogen receptor, progesterone receptor and HER2 expression and has poorer prognosis than the other breast cancer subtypes. DERA identified 110 core regulations consisting of 28 disconnected subnetworks for TNBC. These subnetworks are related to oncogenic activity, proliferation, cancer survival, invasiveness and metastasis. Our analysis further revealed 31 regulations specific for TNBC as compared to the other breast cancer subtypes and thus form a basis for understanding TNBC. We also applied DERA to high-grade serous ovarian cancer (HGS-OvCa) data and identified several common regulations between HGS-OvCa and TNBC. The performance of DERA was compared to two pathway analysis methods GSEA and SPIA and our results shows better reproducibility and higher sensitivity in a small sample set. Conclusions We present a novel method called DERA to identify subnetworks that are similarly active for a group of samples. DERA was applied to breast cancer and ovarian cancer data showing our method is able to identify reliable and potentially important regulations with high reproducibility. R package is available at http://csbi.ltdk.helsinki.fi/pub/czliu/DERA/ .
  • Kaur, Sippy; Lotsari, Johanna E; Al-Sohaily, Sam; Warusavitarne, Janindra; Kohonen-Corish, Maija R; Peltomäki, Päivi (BioMed Central, 2015)
    Abstract Background Altered expression of microRNAs (miRNAs) commonly accompanies colorectal (CRC) and endometrial carcinoma (EC) development, but the underlying mechanisms and clinicopathological correlations remain to be clarified. We focused on epigenetic mechanisms and aimed to explore if DNA methylation patterns in tumors depend on DNA mismatch repair (MMR) status, sporadic vs. Lynch-associated disease, and geographic origin (Finland vs. Australia). Treatment of cancer cell lines with demethylating agents revealed 109 significantly upregulated miRNAs. Seven met our stringent criteria for possible methylation-sensitive miRNAs and were used to screen patient specimens (205 CRCs and 36 ECs) by methylation-specific multiplex ligation-dependent probe amplification. Results Three miRNAs (129-2, 345, and 132) with low methylation levels in normal tissue and frequent hypermethylation in tumors were of particular interest. Hypermethylation of miR-345 and miR-132 associated with MMR deficiency in CRC regardless of geographic origin, and hypermethylation of miR-132 distinguished sporadic MMR-deficient CRC from Lynch-CRC. Finally, hypermethylation of miRNAs stratified 49 endometrial hyperplasias into low-methylator (simple hyperplasia) and high-methylator groups (complex hyperplasia with or without atypia) and suggested that miR-129-2 methylation in particular could serve as a marker of progression in early endometrial tumorigenesis. Conclusions Our study identifies miR-345 and miR-132 as novel differentially methylated miRNAs in CRC, thereby facilitating sub-classification of CRC and links miR-129-2 methylation to early endometrial tumorigenesis.
  • Glaus, Peter; Honkela, Antti; Rattray, Magnus (Oxford University Press, 2012)
    Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression (DE) estimation requires a probabilistic approach to properly account for ambiguity caused by shared exons and finite read sampling as well as the intrinsic biological variance of transcript expression. Results: We present Bayesian inference of transcripts from sequencing data (BitSeq), a Bayesian approach for estimation of transcript expression level from RNA-seq experiments. Inferred relative expression is represented by Markov chain Monte Carlo samples from the posterior probability distribution of a generative model of the read data. We propose a novel method for DE analysis across replicates which propagates uncertainty from the sample-level model while modelling biological variance using an expression-level-dependent prior. We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with technical and biological replication for both studied conditions. Availability: The implementation of the transcriptome expression estimation and differential expression analysis, BitSeq, has been written in C++ and Python. The software is available online from http://code.google.com/p/bitseq/, version 0.4 was used for generating results presented in this article.
  • Oza, Nilay; Münch, Jürgen; Garbajosa, Juan; Yague, Agustin; Gonzalez Ortega, Eloy (2013)
    Cloud-based infrastructure has been increasingly adopted by the industry in distributed software development (DSD) environments. Its proponents claim that its several benefits include reduced cost, increased speed and greater productivity in software development. Empirical evaluations, however, are in the nascent stage of examining both the benefits and the risks of cloud-based in-frastructure. The objective of this paper is to identify potential benefits and risks of using cloud in a DSD project conducted by teams based in Helsinki and Ma-drid. A cross-case qualitative analysis is performed based on focus groups con-ducted at the Helsinki and Madrid sites. Participants’ observations are used to supplement the analysis. The results of the analysis indicated that the main ben-efits of using cloud are rapid development, continuous integration, cost savings, code sharing, and faster ramp-up. The key risks determined by the project are dependencies, unavailability of access to the cloud, code commitment and inte-gration, technical debt, and additional support costs. The results revealed that if such environments are not planned and set up carefully, the benefits of using cloud in DSD projects might be overshadowed by the risks associated with it.
  • Oza, Nilay; Münch, Jürgen; Garbajosa, Juan; Yague, Agustin; Gonzalez Ortega, Eloy (2013)
    Cloud-based infrastructure has been increasingly adopted by the industry in distributed software development (DSD) environments. Its proponents claim that its several benefits include reduced cost, increased speed and greater productivity in software development. Empirical evaluations, however, are in the nascent stage of examining both the benefits and the risks of cloud-based in-frastructure. The objective of this paper is to identify potential benefits and risks of using cloud in a DSD project conducted by teams based in Helsinki and Ma-drid. A cross-case qualitative analysis is performed based on focus groups con-ducted at the Helsinki and Madrid sites. Participants’ observations are used to supplement the analysis. The results of the analysis indicated that the main ben-efits of using cloud are rapid development, continuous integration, cost savings, code sharing, and faster ramp-up. The key risks determined by the project are dependencies, unavailability of access to the cloud, code commitment and inte-gration, technical debt, and additional support costs. The results revealed that if such environments are not planned and set up carefully, the benefits of using cloud in DSD projects might be overshadowed by the risks associated with it.
  • Titsias, Michalis K; Honkela, Antti; Lawrence, Neil D; Rattray, Magnus (BIOMED CENTRAL LTD., 2012)
    Background Complete transcriptional regulatory network inference is a huge challenge because of the complexity of the network and sparsity of available data. One approach to make it more manageable is to focus on the inference of context-specific networks involving a few interacting transcription factors (TFs) and all of their target genes. Results We present a computational framework for Bayesian statistical inference of target genes of multiple interacting TFs from high-throughput gene expression time-series data. We use ordinary differential equation models that describe transcription of target genes taking into account combinatorial regulation. The method consists of a training and a prediction phase. During the training phase we infer the unobserved TF protein concentrations on a subnetwork of approximately known regulatory structure. During the prediction phase we apply Bayesian model selection on a genome-wide scale and score all alternative regulatory structures for each target gene. We use our methodology to identify targets of five TFs regulating Drosophila melanogaster mesoderm development. We find that confident predicted links between TFs and targets are significantly enriched for supporting ChIP-chip binding events and annotated TF-gene interations. Our method statistically significantly outperforms existing alternatives. Conclusions Our results show that it is possible to infer regulatory links between multiple interacting TFs and their target genes even from a single relatively short time series and in presence of unmodelled confounders and unreliable prior knowledge on training network connectivity. Introducing data from several different experimental perturbations significantly increases the accuracy.
  • Ylä-Anttila, Tuukka (Tutkijaliitto, 2013)
  • Unknown author (Venäjän ja Itä-Euroopan tutkimuksen seura, 2003)
  • Piirainen, Timo (Venäjän ja Itä-Euroopan tutkimuksen seura, 1994)
  • Saarinen, Risto (Suomalainen teologinen kirjallisuusseura, 2014)