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  • Lindström, Jan Krister; Norrby, Catrin; Wide, Camilla; Nilsson, Jenny (2014)
    This paper presents the research program "Interaction and variation in pluricentric languages: Swedish communicative patterns in Sweden and Finland" and a specific study of address practices in doctor-patient conversations in Sweden and Finland. The comparison shows that address forms in second person singular are used more in the Sweden Swedish conversations. Moreover, in Finland Swedish conversations, there is some use of address in second person plural which counts as a formal mode of address. The results suggest that the doctors in Sweden are more personally oriented whereas the doctors in Finland may tone down personal orientation. In the former case, commonalities between the interlocutors are taken to the forefront; in the latter case, there is a tendency to respect the other participants space in the interaction.
  • Savanheimo, Nora; Vehkalahti, Miira M (BioMed Central Ltd, 2014)
    Abstract Background Dental general anesthesia (DGA) is part of public dental care in Finland, but the intention is to return the patient to routine dental care. The aims of this study were to describe the details of treatments under DGA given to generally healthy children and to explore the outcome of their dental care during a 5-year follow-up, with special focus on preventive care. In particular, we examined the return of the patients to routine dental care, of which, to our knowledge, little is known. Methods Our prospective 5-year follow-up of generally healthy children (aged 0–13 years) treated under DGA by the Helsinki Public Dental Service in 2004 was based on official dental and general anesthesia documents. The statistical analyses employed chi-square tests, t-tests, Pearson’s correlation coefficient (r), Fisher’s transformation to test r ≠ 0, and logistic regression modeling. Results The most common reason for DGA was uncooperation (82%), followed by dental fear (56%). Filling therapy predominated in the treatments given under anesthesia, and the mean number of treatments per patients was 9.5 (SD = 4.2). Throughout the follow-up, 54% of the patients continued to have co-operation problems and 53% expressed dental fear; 11% of the patients received repeat DGA. The mean follow-up time was 48 (median 52) months. The postoperative review visit was actualized within 1.5 (SD = 0.8) months and the first visit to the home dental clinic of the patients in 12.0 (SD = 11.8) months for the 0–5-year-olds and in 7.2 (SD = 5.9) months for the 6–13-year-olds (p < 0.001). The mean time elapsed to the first need for treatment was 18.5 (SD = 14.1) months. During the follow-up, the mean number of treatments per patient was 5.3 (SD = 4.9); almost all patients (97%) received preventive treatment at one of two visits, but the control of dental fear remained rare. Conclusions To return to routine dental care after DGA, most of the generally healthy children in our study still needed special attention due to their uncooperation and dental fear, thus calling for a renewal of practices to treat these patients.
  • Arponen, Heidi; Mäkitie, Outi; Waltimo-Sirén, Janna (BioMed Central Ltd, 2014)
    Abstract Background Joint hypermobility is a common clinical characteristic of patients with Osteogenesis imperfecta (OI), a disorder with serious comorbidities of scoliosis and cranial base anomalies. This study aimed at evaluating how prevalent joint hypermobility is in paediatric OI patients, and to find out whether it serves as a potential predictive marker of the different spinal complications; scoliosis and craniovertebral anomalies (basilar impression and basilar invagination). Methods In this cross-sectional one-center study we analysed retrospectively clinical patient records and radiographs of 47 OI patients, aged 1–19 years, some of whom were treated with bisphosphonates. Presence of joint hypermobility, scoliosis, and craniovertebral anomalies was recorded and possible connections between the phenomena were explored with correlation analysis. Results Joint hypermobility was found in 70% of the patients. Scoliosis and cranial base anomalies had developed in 26%. The presence of spinal complications was independent of the bisphosphonate treatment status and joint hypermobility. Conclusions Scoliosis and craniovertebral anomalies are strongly associated in paediatric OI patients. Joint hypermobility that is much more common appears, however, to be a poor predictor.
  • Laurila, Kirsti; Autio, Reija; Kong, Lingjia; Närvä, Elisa; Hussein, Samer; Otonkoski, Timo; Lahesmaa, Riitta; Lähdesmäki, Harri (BioMed Central Ltd, 2014)
    Abstract Background Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Several genome-wide studies have reported genomic variants that correlate with gene expression levels in various tissue and cell types. Results We studied human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) measuring the SNPs and CNVs with Affymetrix SNP 6 microarrays and expression values with Affymetrix Exon microarrays. We computed the linear relationships between SNPs and expression levels of exons, transcripts and genes, and the associations between gene CNVs and gene expression levels. Further, for a few of the resulted genes, the expression value was associated with both CNVs and SNPs. Our results revealed altogether 217 genes and 584 SNPs whose genomic alterations affect the transcriptome in the same cells. We analyzed the enriched pathways and gene ontologies within these groups of genes, and found out that the terms related to alternative splicing and development were enriched. Conclusions Our results revealed that in the human pluripotent stem cells, the expression values of several genes, transcripts and exons were affected due to the genomic variation.
  • Karkamo, Veera; Kaistinen, Anu; Näreaho, Anu; Dillard, Kati; Vainio-Siukola, Katri; Vidgrén, Gabriele; Tuoresmäki, Niina; Anttila, Marjukka (BioMed Central Ltd, 2014)
    Abstract Background Leishmania spp. are zoonotic protozoans that infect humans and other mammals such as dogs. The most significant causative species in dogs is L. infantum. In dogs, leishmaniosis is a potentially progressive, chronic disease with varying clinical outcomes. Autochthonous cases of canine leishmaniosis have not previously been reported in the Nordic countries. Results In this report we describe the first diagnosed autochthonous cases of canine leishmaniosis in Finland, in which transmission via a suitable arthropod vector was absent. Two Finnish boxers that had never been in endemic areas of Leishmania spp., had never received blood transfusions, nor were infested by ectoparasites were diagnosed with leishmaniosis. Another dog was found with elevated Leishmania antibodies. A fourth boxer dog that had been in Spain was considered to be the source of these infections. Transmission occurred through biting wounds and semen, however, transplacental infection in one of the dogs could not be ruled out. Two of the infected dogs developed a serious disease and were euthanized and sent for necropsy. The first one suffered from membranoproliferative glomerulonephritis and the second one had a chronic systemic disease. Leishmania sp. was detected from tissues by PCR and/or IHC in both dogs. The third infected dog was serologically positive for Leishmania sp. but remained free of clinical signs. Conclusions This case report shows that imported Leishmania-infected dogs may pose a risk for domestic dogs, even without suitable local arthropod vectors.
  • van de Bunt, Bert; Bron, Peter A; Sijtsma, Lolke; de Vos, Willem M; Hugenholtz, Jeroen (BioMed Central Ltd, 2014)
    Abstract Background Lactococcus lactis is a lactic acid bacterium that has been used for centuries in the production of a variety of cheeses, as these bacteria rapidly acidify milk and greatly contribute to the flavour of the fermentation end-products. After a short growth phase during cheese ripening L. lactis enters an extended non-growing state whilst still strongly contributing to amino acid-derived flavour formation. Here, a research approach is presented that allows investigation of strain- and amino acid-specific flavour formation during the non-growing state. Results Non-growing cells of five selected L. lactis strains were demonstrated to degrade amino acids into flavour compounds that are relevant in food fermentations and differs greatly from production of flavour compounds using growing cells. As observed earlier in other research set-ups and with other microorganisms, addition of NADH, α-ketoglutarate and pyridoxal-5-phosphate was demonstrated to be essential for optimal flavour formation, suggesting that intracellular pools of these substrates are too low for the significant production of the flavour compounds. Production of flavours during the non-growing phase strongly depends on the individual amino acids that were supplied, on the presence of other amino acids (mixtures versus single compounds), and on the strain used. Moreover, we observed that the plasmid-free model strains L. lactis MG1363 and IL1403 produce relatively low amounts of flavour components under the various conditions tested. Conclusions By using this simplified and rapid approach to study flavour formation by non-growing lactic acid bacteria, lengthy ripening periods are no longer required to assess the capacity of strains to produce flavours in the long, non-growing state of dairy fermentation. In addition, this method also provides insight into the conversion of single amino acids versus the conversion of a mixture of amino acids as produced during protein degradation. The generated results are complementary to earlier generated datasets using growing cells, allowing assessment of the full flavour forming potential of strains used as starter cultures in industrial food fermentation processes.
  • Pietiläinen, Jukka (Helsingin yliopisto, Aleksanteri-instituutti, 2014)
  • Kiljunen, Saija; Pajunen, Maria I; Dilks, Kieran; Storf, Stefanie; Pohlschroder, Mechthild; Savilahti, Harri (BioMed Central Ltd, 2014)
    Abstract Background Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Results Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. Conclusions We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea.
  • Choi, Jaeyoung; Kim, Ki-Tae; Jeon, Jongbum; Wu, Jiayao; Song, Hyeunjeong; Asiegbu, Fred O; Lee, Yong-Hwan (BioMed Central Ltd, 2014)
    Abstract Background RNA interference (RNAi) is involved in genome defense as well as diverse cellular, developmental, and physiological processes. Key components of RNAi are Argonaute, Dicer, and RNA-dependent RNA polymerase (RdRP), which have been functionally characterized mainly in model organisms. The key components are believed to exist throughout eukaryotes; however, there is no systematic platform for archiving and dissecting these important gene families. In addition, few fungi have been studied to date, limiting our understanding of RNAi in fungi. Here we present funRNA, a fungal kingdom-wide comparative genomics platform for putative genes encoding Argonaute, Dicer, and RdRP. Description To identify and archive genes encoding the abovementioned key components, protein domain profiles were determined from reference sequences obtained from UniProtKB/SwissProt. The domain profiles were searched using fungal, metazoan, and plant genomes, as well as bacterial and archaeal genomes. 1,163, 442, and 678 genes encoding Argonaute, Dicer, and RdRP, respectively, were predicted. Based on the identification results, active site variation of Argonaute, diversification of Dicer, and sequence analysis of RdRP were discussed in a fungus-oriented manner. funRNA provides results from diverse bioinformatics programs and job submission forms for BLAST, BLASTMatrix, and ClustalW. Furthermore, sequence collections created in funRNA are synced with several gene family analysis portals and databases, offering further analysis opportunities. Conclusions funRNA provides identification results from a broad taxonomic range and diverse analysis functions, and could be used in diverse comparative and evolutionary studies. It could serve as a versatile genomics workbench for key components of RNAi.
  • Ojala, Teija; Kankainen, Matti; Castro, Joana; Cerca, Nuno; Edelman, Sanna; Westerlund-Wikström, Benita; Paulin, Lars; Holm, Liisa; Auvinen, Petri (BioMed Central Ltd, 2014)
    Abstract Background Lactobacillus crispatus is a ubiquitous micro-organism encountered in a wide range of host-associated habitats. It can be recovered from the gastrointestinal tract of animals and it is a common constituent of the vaginal microbiota of humans. Moreover, L. crispatus can contribute to the urogenital health of the host through competitive exclusion and the production of antimicrobial agents. In order to investigate the genetic diversity of this important urogenital species, we performed a comparative genomic analysis of L. crispatus. Results Utilizing the completed genome sequence of a strain ST1 and the draft genome sequences of nine other L. crispatus isolates, we defined the scale and scope of the pan- and core genomic potential of L. crispatus. Our comparative analysis identified 1,224 and 2,705 ortholog groups present in all or only some of the ten strains, respectively. Based on mathematical modeling, sequencing of additional L. crispatus isolates would result in the identification of new genes and functions, whereas the conserved core of the ten strains was a good representation of the final L. crispatus core genome, estimated to level at about 1,116 ortholog groups. Importantly, the current core was observed to encode bacterial components potentially promoting urogenital health. Using antibody fragments specific for one of the conserved L. crispatus adhesins, we demonstrated that the L. crispatus core proteins have a potential to reduce the ability of Gardnerella vaginalis to adhere to epithelial cells. These findings thereby suggest that L. crispatus core proteins could protect the vagina from G. vaginalis and bacterial vaginosis. Conclusions Our pan-genome analysis provides insights into the intraspecific genome variability and the collective molecular mechanisms of the species L. crispatus. Using this approach, we described the differences and similarities between the genomes and identified features likely to be important for urogenital health. Notably, the conserved genetic backbone of L. crispatus accounted for close to 60% of the ortholog groups of an average L. crispatus strain and included factors for the competitive exclusion of G. vaginalis, providing an explanation on how this urogenital species could improve vaginal health.
  • Paassilta, Marita; Kuusela, Elina; Korppi, Matti; Lemponen, Riina; Kaila, Minna; Nikkari, Seppo T (BioMed Central Ltd, 2014)
    Abstract Background Elevated serum Mead acid as a proportion of total fatty acids is an indirect marker of a deficiency of essential fatty acids (EFA). The aim of the study was to evaluate the symptoms and nutrition of food-allergic children with elevated or normal serum Mead acid. Methods Serum fatty acid compositions from 400 children were studied by clinical indications, mostly by suspicion of deficiency of EFA due to inadequate nutrition. A Mead acid level exceeding 0.21% (percentage of total fatty acids) was considered to be a specific sign of an insufficient EFA supply. From a total of 31 children with elevated Mead acid (MEADplus group), 23 (74%) had food allergy. The symptoms and dietary restrictions of this MEADplus group of food allergic children were compared to 54 age-and sex-matched controls with food allergy but normal Mead acid proportions (MEADminus group) before and 6 months after the serum fatty acid determination. Results At the beginning of the 6-month follow-up, 44% of the food allergic children in both MEADplus and MEADminus groups were on an elimination diet. These diets did not differ between the two groups and we were not able to document an association between the severity of elimination diet and elevated Mead acid proportion. However, the MEADplus children were on average more symptomatic than MEADminus children. In the MEADplus group, food allergy presented with skin symptoms in 100% (vs. 70% in the MEADminus group, p < 0.001) and with vomiting or diarrhea in 70% (vs. 44% in the MEADminus group, p < 0.05). Clinical suspicion of malnutrition resulted in increase in the use of vegetable oil and milk-free margarine in both groups from <50% to 65-74% during the follow-up. After 6 months, 64% of the MEADplus children with food allergy had been sent to a control serum fatty acid analysis. Of these children, Mead acid had declined to normal level in 69%, and remained elevated in 31%. Conclusions Severe symptoms of food allergy combined with elimination diets in children may lead to insufficient nutrition presenting with elevated serum Mead acid. Adding of supplementary polyunsaturated fat to the diet should be considered in these children.
  • Härmänmaa, Marja (Euroopan Kulttuurisäätiön Suomen Osasto EKSO ry, 2014)
  • Sorsa, Ville-Pekka (ELÄKETURVAKESKUS., 2014)
  • Tandefelt, Henrika (Helsinki Collegium for Advanced Studies, 2014)
    This article sets out to study the entanglement of different political, ideological and moral ideals and traditions in the Kingship of Gustav III, King of Sweden 1772–1792. Political thinking and practice in Eighteenth-Century Europe offered many elements and examples that different monarchs could apply in their own particular circumstances. Gustav III was one of the European Kings that openly supported the French enlightened thinkers fashioning himself as a Reformer-King. He was also very influenced by the French culture over all, and the culture of the traditional royal court in particular. In addition the Swedish political history with a fifty-year period of decreased royal power before the coup d’état of Gustav III in 1772 influenced how the European trends and traditions were put into practice. The article pursues to understand the way different elements were bound up together and put to action by the King in his coup d’état 1772, his law reforms in the 1770s and in the establishment of a court of appeal in the town Vasa in Ostrobothnia in 1776 and the ceremonial, pictorial and architectural projects linked to this.
  • Hakkarainen, Minna; Jari Järviluoma; Petri Muje (Saimaan ammattikorkeakoulu, 2014)
    Tutkimusraportti käsittelee eri näkökulmista venäläisten Itä-Suomeen suuntautuvaa matkailua. Alueellisesti tarkastelun kohteena ovat erityisesti Etelä-Karjala, Pohjois-Karjala sekä Kainuu. Tutkimus luotaa myös matkailun nousevia trendejä ja tarkastelee niiden luomia uusia mahdollisuuksia matkailuelinkeinolle Itä-Suomessa.
  • Tolonen, Mikko Sakari (ACADEMIC PRINTING AND PUBLISHING., 2014)
  • Van der Vet, Freek (Laboratorium: Russian Review of Social Research, 2014)