Browsing by Issue Date

Sort by: Order: Results:

Now showing items 21-40 of 2696
  • Baranova, Tatyana; Kalendar, Ruslan; Kalaev, V (V. N. Sukachev Institute of Forest, Russian Academy of Sciences, Siberian Branch, 2014)
    The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA and 5.8S rRNA gene from Rhododendron L. were analysed. This study reveals phylogenetic relationships and collation of data on the phylogeny of the genus Rhododendron L . according to the research of other authors using molecular and classical methods. Sequence analysis of ribosomal spacer showed low variability between species of the genus Rhododendron series of Dauricum. Rh. mucronulatum Turcz., Rh. dauricum L. and some other studied species had identical nucleotide ITS1-ITS2 sequence indicating the artificial division into separate species. Found species differing from each other by 1-2 or few nucleotides, which allows assuming their common phylogenetic affiliation or excluding one taxonomic unit. According to the analysis of ITS1-ITS2 sequences identified 16 groups of species with similar sequence ITS1-ITS2. When comparing the morphological descriptions of some species of the genus Rhododendron L. with a similar sequence of ITS1-ITS2 marked their small differences. Based on the results of molecular genetic analysis it has been assumed that Rhododendron dauricum L., Rh. ledebourii Pojark, Rh. sichotense Pojark and Rh. mucronulatum Turcz belong to the same species. The establishment phylogenetic relationships based on sequence ITS1-ITS2, applicable only in respect of highly isolated species Rhododendron L. To clarify the phylogenetic relationships of the genus Rhododendron L. necessary to expand the comparative analysis of the DNA sequences of universal genes or complex repeats elements (retrotransposons).
  • Stratula, Olga; Cockram, James; Kalendar, Ruslan (Novi Sad Institute of Field and Vegetable Crops, 2014)
    The proteins encoded by cereal β-amylase genes bamy1 and bamy2 genes play an important role in seedling germination and in the brewing process. Here, we use exon-primed intron-crossing (EPIC) to analyse Bmy1 and Bmy2 genetic diversity among 38 accessions belonging to six Poaceae tribes. DNA sequence alignment of multiple Poaceae species β-amylase sequences allowed design of EPIC primers that simultaneously amplify Bmy1 and Bmy2 in all the cereal species investigated. The genetic variation observed in the samples investigated is analysed and discussed, and illustrates the effectiveness of this approach for intra- and interspecific analysis in plant species.
  • Ylä-Anttila, Tuomas; Kukkonen, Anna (INDERSCIENCE PUBLISHERS, 2014)
    This paper examines the differences in the values that are evoked to justify arguments in the media debate on climate change in USA and France from 1997 to 2011. We find that climate change is more often discussed in terms of justice, democracy, and legal regulation in France, while monetary value plays a more important role as a justification for climate policy arguments in the USA. Technological and scientific arguments are more often made in France, and ecological arguments equally in both countries. We argue that understanding these national differences in argumentation at least partly as reflections of deep–seated cultural conceptions about what is worthy may help in understanding why disagreement persists in the global politics of climate change.
  • Sajantila, Antti (BioMed Central Ltd, 2014)
    Abstract No abstract
  • Peltola, Jari; Vainio, Markku; Fordell, Thomas; Hieta, Tuomas; Merimaa, Mikko; Halonen, Lauri (Optical Society of America, 2014)
    We report on a tunable continuous-wave mid-infrared optical parametric oscillator (OPO), which is locked to a fully stabilized near-infrared optical frequency comb using a frequency doubling scheme. The OPO is used for 40 GHz mode-hop-free, frequency-comb-locked scans in the wavelength region between 2.7 and 3.4 x03BC;m. We demonstrate the applicability of the method to high-precision cavity-ring-down spectroscopy of nitrous oxide (N2O) and water (H2O) at 2.85 x00B5;m and of methane (CH4) at 3.2 x03BC;m.
  • Moilanen, Ulla; Kellock, Miriam; Várnai, Anikó; Andberg, Martina; Viikari, Liisa (BioMed Central Ltd, 2014)
    Abstract Background The recalcitrance of softwood to enzymatic hydrolysis is one of the major bottlenecks hindering its profitable use as a raw material for platform sugars. In softwood, the guaiacyl-type lignin is especially problematic, since it is known to bind hydrolytic enzymes non-specifically, rendering them inactive towards cellulose. One approach to improve hydrolysis yields is the modification of lignin and of cellulose structures by laccase-mediator treatments (LMTs). Results LMTs were studied to improve the hydrolysis of steam pre-treated spruce (SPS). Three mediators with three distinct reaction mechanisms (ABTS, HBT, and TEMPO) and one natural mediator (AS, that is, acetosyringone) were tested. Of the studied LMTs, laccase-ABTS treatment improved the degree of hydrolysis by 54%, while acetosyringone and TEMPO increased the hydrolysis yield by 49% and 36%, respectively. On the other hand, laccase-HBT treatment improved the degree of hydrolysis only by 22%, which was in the same order of magnitude as the increase induced by laccase treatment without added mediators (19%). The improvements were due to lignin modification that led to reduced adsorption of endoglucanase Cel5A and cellobiohydrolase Cel7A on lignin. TEMPO was the only mediator that modified cellulose structure by oxidizing hydroxyls at the C6 position to carbonyls and partially further to carboxyls. Oxidation of the reducing end C1 carbonyls was also observed. In contrast to lignin modification, oxidation of cellulose impaired enzymatic hydrolysis. Conclusions LMTs, in general, improved the enzymatic hydrolysis of SPS. The mechanism of the improvement was shown to be based on reduced adsorption of the main cellulases on SPS lignin rather than cellulose oxidation. In fact, at higher mediator concentrations the advantage of lignin modification in enzymatic saccharification was overcome by the negative effect of cellulose oxidation. For future applications, it would be beneficial to be able to understand and modify the binding properties of lignin in order to decrease unspecific enzyme binding and thus to increase the mobility, action, and recyclability of the hydrolytic enzymes.
  • Tikkinen, Kari AO; Agarwal, Arnav; Craigie, Samantha; Cartwright, Rufus; Gould, Michael K; Haukka, Jari; Naspro, Richard; Novara, Giacomo; Sandset, Per M; Siemieniuk, Reed A; Violette, Philippe D; Guyatt, Gordon H (BioMed Central Ltd, 2014)
    Abstract Background Pharmacological thromboprophylaxis in the peri-operative period involves a trade-off between reduction in venous thromboembolism (VTE) and an increase in bleeding. Baseline risks, in the absence of prophylaxis, for VTE and bleeding are known to vary widely between urological procedures, but their magnitude is highly uncertain. Systematic reviews and meta-analyses addressing baseline risks are uncommon, needed, and require methodological innovation. In this article, we describe the rationale and methods for a series of systematic reviews of the risks of symptomatic VTE and bleeding requiring reoperation in urological surgery. Methods/design We searched MEDLINE from January 1, 2000 until April 10, 2014 for observational studies reporting on symptomatic VTE or bleeding after urological procedures. Additional studies known to experts and studies cited in relevant review articles were added. Teams of two reviewers, independently assessed articles for eligibility, evaluated risk of bias, and abstracted data. We derived best estimates of risk from the median estimates among studies rated at the lowest risk of bias. The primary endpoints were 30-day post-operative risk estimates of symptomatic VTE and bleeding requiring reoperation, stratified by procedure and patient risk factors. Discussion This series of systematic reviews will inform clinicians and patients regarding the trade-off between VTE prevention and bleeding. Our work advances standards in systematic reviews of surgical complications, including assessment of risk of bias, criteria for arriving at best estimates of risk (including modeling of timing of events and dealing with suboptimal data reporting), dealing with subgroups at higher and lower risk of bias, and use of the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to rate certainty in estimates of risk. The results will be incorporated in the upcoming European Association Urology Guideline on Thromboprophylaxis. Systematic review registration PROSPERO CRD42014010342.
  • Lappalainen, Anu K; Vaittinen, Elina; Junnila, Jouni; Laitinen-Vapaavuori, Outi (BioMed Central Ltd, 2014)
    Abstract Background Intervertebral disc disease (IDD) is a very common neurological disease, Dachshunds being the breed most often affected. In this breed, IDD has a hereditary background and is associated with intervertebral disc calcification (IDC), an indicator of severe intervertebral disc degeneration. In Finland, spinal radiography is used, when screening for IDC before breeding Dachshunds. We evaluated the association between IDC and IDD in Finnish Dachshunds radiographically screened for IDC. A questionnaire was sent to owners of 193 radiographically screened Dachshunds aged at least ten years. Clinical signs indicative of IDD were compared with IDC grade (grade 0 = no calcifications, grade 1 = 1 – 2 calcifications, grade 2 = 3 – 4 calcifications and grade 3 = 5 or more calcifications) and with age at the time of the radiographic examination. The diagnosis of IDD was confirmed by a veterinarian. Results IDD was common in the study population with 31% of dogs being affected. IDD and IDC were clearly connected (P < 0.001); IDD was rare in dogs with no calcifications (grade 0) and common in dogs with severe IDC (grade 3). The IDC grade was strongly positively associated with frequency of back pain periods (P < 0.001), and dogs with IDC grade 3 had frequent periods of pain. Reluctance to jump onto a sofa had a strong positive association with back pain. No association existed between age of the dog at the time of the radiographic examination and clinical signs indicative of IDD. Conclusions Radiographically detected IDC and IDD are common in Finnish Dachshunds and are strongly associated with one another. Spinal radiography is an appropriate screening tool for breeders attempting to diminish IDC and IDD in Dachshunds. A breeding program that screens dogs and selects against IDC can be expected to reduce the occurrence of IDD in future. Twenty-four to 48 months of age is a suitable age for screening.
  • Grote, Anne; Abbas, Mahmoud; Linder, Nina; Kreipe, Hans H; Lundin, Johan; Feuerhake, Friedrich (BioMed Central Ltd, 2014)
    Abstract Background Comprehensive spatial assessment of hormone receptor immunohistochemistry staining in digital whole slide images of breast cancer requires accurate detection of positive nuclei within biologically relevant regions of interest. Herein, we propose a combination of automated region labeling at low resolution and subsequent detailed tissue evaluation of subcellular structures in lobular structures adjacent to breast cancer, as a proof of concept for the approach to analyze estrogen and progesterone receptor expression in the spatial context of surrounding tissue. Methods Routinely processed paraffin sections of hormone receptor-negative ductal invasive breast cancer were stained for estrogen and progesterone receptor by immunohistochemistry. Digital whole slides were analyzed using commercially available image analysis software for advanced object-based analysis, applying textural, relational, and geometrical features. Mammary gland lobules were targeted as regions of interest for analysis at subcellular level in relation to their distance from coherent tumor as neighboring relevant tissue compartment. Lobule detection quality was evaluated visually by a pathologist. Results After rule set optimization in an estrogen receptor-stained training set, independent test sets (progesterone and estrogen receptor) showed acceptable detection quality in 33% of cases. Presence of disrupted lobular structures, either by brisk inflammatory infiltrate, or diffuse tumor infiltration, was common in cases with lower detection accuracy. Hormone receptor detection tended towards higher percentage of positively stained nuclei in lobules distant from the tumor border as compared to areas adjacent to the tumor. After adaptations of image analysis, corresponding evaluations were also feasible in hormone receptor positive breast cancer, with some limitations of automated separation of mammary epithelial cells from hormone receptor-positive tumor cells. Conclusions As a proof of concept for object-oriented detection of steroid hormone receptors in their spatial context, we show that lobular structures can be classified based on texture-based image features, unless brisk inflammatory infiltration disrupts the normal morphological structure of the tubular gland epithelium. We consider this approach as prototypic for detection and spatial analysis of nuclear markers in defined regions of interest. We conclude that advanced image analysis at this level of complexity requires adaptation to the individual tumor phenotypes and morphological characteristics of the tumor environment.
  • Lindström, Jan Krister; Londen, Anne-Marie (DI P P - N R W, 2014)
    Concessive practices are a recurrent phenomenon in conversation. This paper investigates one variant of them: tripartite sequences which involve a first assertion, an inserted concession, and a reassertion of the original standpoint. This interactional practice may be produced by one speaker only or in a dialogue with another participant whose contribution triggers a conceding move from the speaker. The argument is made that the practice in question, Insertion Concessive, has such distinct sequential and formal properties that they warrant an account of the practice as a discourse grammatical construction. The tripartite sequences follow recurrent polarity and subjectivity patterns and are operated with a finite set of linguistic markers which signal concession (in the conceding part) and contrast (in the reasserting part). The study relates directly to interactional approaches to Construction Grammar, accounting for formal and semantic regularities which go beyond the limits of a single sentence. The data is drawn from corpora of everyday and institutional conversations in Swedish.
  • Kulhánová, Ivana; Menvielle, Gwenn; Bopp, Matthias; Borrell, Carme; Deboosere, Patrick; Eikemo, Terje A; Hoffmann, Rasmus; Leinsalu, Mall; Martikainen, Pekka; Regidor, Enrique; Rodríguez-Sanz, Maica; Rychtaříková, Jitka; Wojtyniak, Bogdan; Mackenbach, Johan P (BioMed Central Ltd, 2014)
    Abstract Background Cause-of-death data linked to information on socioeconomic position form one of the most important sources of information about health inequalities in many countries. The proportion of deaths from ill-defined conditions is one of the indicators of the quality of cause-of-death data. We investigated educational differences in the use of ill-defined causes of death in official mortality statistics. Methods Using age-standardized mortality rates from 16 European countries, we calculated the proportion of all deaths in each educational group that were classified as due to “Symptoms, signs and ill-defined conditions”. We tested if this proportion differed across educational groups using Chi-square tests. Results The proportion of ill-defined causes of death was lower than 6.5% among men and 4.5% among women in all European countries, without any clear geographical pattern. This proportion statistically significantly differed by educational groups in several countries with in most cases a higher proportion among less than secondary educated people compared with tertiary educated people. Conclusions We found evidence for educational differences in the distribution of ill-defined causes of death. However, the differences between educational groups were small suggesting that socioeconomic inequalities in cause-specific mortality in Europe are not likely to be biased.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.