Articles

Recent Submissions

  • Bencsik, Otto; Berta, Mate; Papp, Tamas; Zana, Annamaria; Forgo, Peter; Dombi, György; Andersson, Maria; Salkinoja-Salonen, Mirja Sinikka; Vagvölgyi, Csaba (MDPI, 2014)
    Bipolaris oryzae is a phytopathogenic fungus causing a brown spot disease in rice, and produces substance that strongly perturbs motility and membrane integrities of boar spermatozoa. The substance was isolated from the liquid culture of the fungal strain using extraction and a multi-step semi-preparative HPLC procedures. Based on the results of mass spectrometric and 2D NMR techniques, the bioactive molecule was identified as ophiobolin A, a previously described sesterterpene-type compound. The purified ophiobolin A exhibited strong motility inhibition and viability reduction on boar spermatozoa. Furthermore, it damaged the sperm mitochondria significantly at sublethal concentration by the dissipation of transmembrane potential in the mitochondrial inner membrane, while the plasma membrane permeability barrier remained intact. The study demonstrated that the cytotoxicity of ophiobolin A toward somatic cell lines is higher by 1–2 orders of magnitude compared to other mitochondriotoxic mycotoxins, and towards sperm cells unique by replacing the progressive motility by shivering tail beating at low exposure concentration.
  • Tynkkynen, Veli-Pekka (Helsingin yliopisto, Aleksanteri-instituutti, 2015)
    Through its use of the Arctic, Russia tries to fortify the idea that it is a global Energy Superpower
  • Castagnoli, Emmanuelle; Mikkola, Raimo; Salo, Johanna; Andersson, Maria A; Sistonen, Esko; Vornanen-Winqvist, Camilla; Viljanen, Martti; Salkinoja-Salonen, Mirja Sinikka (2015)
    Suuren toimistokiinteistön työtiloista (11 kpl) mitattiin sisäilman mikrobilaskeumien lajistoa ja resistenssejä homeeenesto kemikaaleille, toksiineja tuottavia mikrobeja pölyissä ja rakenneavausnäytteissä; sisäpölyn toksisuutta ja sisäilmasta tiivistetyn veden toksisuutta, sekä monitoroitiin sisäilman 24/7 hengitettäviä hiukkasia (PM2.5, PM10), ilman painetta, lämpötilaa, suhteellista kosteutta sekä formaldehydiä, hiilidioksidia ja VOC aineita. Tavoitteena oli saada mittaustietoa niistä tekijöistä jotka ovat yhteydessä hyvinvointihaittaan. Tulokset osoittivat, että jokainen tutkittu, ongelmainen huone oli yksilöllinen mikrobiston, toksisuuksien, kemiallisten ja fysikaalisten parametrien suhteen, ja että useat 24/7 mitatut parametrit osoittivat viikkorytmiin, vuorokauden aikaan, tunti- tai jopa minuuttirytmiin kytkettyä syklisyyttä.
  • Kaasalainen, Ulla; Heinrichs, Jochen; Krings, Michael; Myllys, Leena; Grabenhorst, Heinrich; Rikkinen, Jouko; Schmidt, Alexander R. (Public Library of Science, 2015)
    One of the most important issues in molecular dating studies concerns the incorporation of reliable fossil taxa into the phylogenies reconstructed from DNA sequence variation in extant taxa. Lichens are symbiotic associations between fungi and algae and/or cyanobacteria. Several lichen fossils have been used as minimum age constraints in recent studies concerning the diversification of the Ascomycota. Recent evolutionary studies of Lecanoromycetes, an almost exclusively lichen-forming class in the Ascomycota, have utilized the Eocene amber inclusion Alectoria succinic as a minimum age constraint. However, a re-investigation of the type material revealed that this inclusion in fact represents poorly preserved plant remains, most probably of a root. Consequently, this fossil cannot be used as evidence of the presence of the genus Alectoria (Parmeliaceae, Lecanorales) or any other lichens in the Paleogene. However, newly discovered inclusions from Paleogene Baltic and Bitterfeld amber verify that alectorioid morphologies in lichens were in existence by the Paleogene. The new fossils represent either a lineage within the alectorioid group or belong to the genus Oropogon.
  • Alam, Syed Ariful (2012)
    Oats are a good source of protein and dietary fibre, especially β-glucan. Due to the health benefits of β-glucan, oats have gained popularity in snack food formulations. The literature review deals with oats and its components, removal of lipids and fractionation of oat products. The particular emphasis of the literature review was given to studies on the effects of different oat fractions and extrusion process variables on the properties of oat-containing extrudates. The aim of this study was to find out how different oat fractions and extrusion process variables (screw speed, water content and feed rate) affect the physical and chemical properties of the extrudates. The measured physical properties were expansion, hardness and water content. Extrusion trials were carried out by using defatted oat endosperm flour (EF) as the main ingredient. Whole grain oat flour (WF) was used as a reference. To improve the nutritional quality, defatted oat protein concentrate (PC) and defatted oat bran concentrate (OBC) were added to EF. The oat fractions were defatted by supercritical carbon dioxide (SC-CO2). Pregelatinised corn starch (CS) and waxy corn starch (WS) were added in some trials to increase the expansion of the extrudates. A co-rotating twin-screw extruder was used for the extrusion. Different process variables were: water content of the mass (16, 18 and 20%), screw speed (240, 370 and 500 rpm) and feed rate (68, 76 and 84 g/min). The temperature profile of the extruder barrel was held constant in all of the trials: 40, 70, 70, 100, 110, 130 and 130 °C (sections 1–6 and die). Screw speed had significant effect on the expansion and hardness. Expansion increased and hardness decreased with increasing screw speed. Water content of the mass affected all the response variables in WF extrudates and all but not hardness and torque in EF extrudates. Increased water content of mass decreased the expansion and hardness in WF extrudates. Feed rate did not have significant effect on the physical properties. When using EF, more expanded and less hard extrudates compared to the WF were obtained. Addition of PC or OBC (10%) decreased the expansion and increased the hardness. Mixing of EF with corn starch (CS or WS; 30%) gave less hard and more expanded extrudates compared to pure EF. The highest expansion was achieved by the addition of WS. Even addition of OBC (20%) in a presence of WS (30%) gave highly expanded and less hard extrudates with high β-glucan content 7.4% (dry weight). Decreasing the particle size of OBC (by ultra-fine milling) or the molecular weight of β-glucan (by enzymatic hydrolysis) did not affect the physical properties of the extrudates even though small decrease in hardness was observed in the trial with enzyme-hydrolysed OBC. The results showed that defatted oat fractions can successfully be used in extrusion when mixed with corn starch. Screw speed had the most profound effect on the physical properties of the oat-containing extrudates followed by the water content of mass.
  • Niemelä, Kati Marianne (SAGE PUBLICATIONS LTD., 2015)
    The prevailing attitude to the national churches in the Nordic countries has often been described as ‘believing in belonging’. Based on a longitudinal survey data, this article argues that this notion no longer applies to the younger generation, often referred to as Generation Y. Instead, they are challenging traditional reasons for belonging to national churches. The number of church-leavers has been unusually high in Finland since the beginning of the 21st century, the vast majority of them young adults. These same young adults were confirmed in the church only a few years earlier. This study aims to understand why such a high number of young people leave the Evangelical Lutheran Church soon after confirmation. The study shows that for Generation Y, the Church-leaving process is linked to personal beliefs and values. They leave the Church because they do not find it to be in line with their own beliefs. Tradition and culture alone are not enough to keep them as members.
  • Sobral-Leite, Marcelo; Wesseling, Jelle; Smit, Vincent T H B M; Nevanlinna, Heli; van Miltenburg, Martine H; Sanders, Joyce; Hofland, Ingrid; Blows, Fiona M; Coulson, Penny; Patrycja, Gazinska; Schellens, Jan H M; Fagerholm, Rainer; Heikkilä, Päivi; Aittomäki, Kristiina; Blomqvist, Carl; Provenzano, Elena; Ali, Hamid R; Figueroa, Jonine; Sherman, Mark; Lissowska, Jolanta; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Phillips, Kelly-Anne; Couch, Fergus J; Olson, Janet E; Vachon, Celine; Visscher, Daniel; Brenner, Hermann; Butterbach, Katja; Arndt, Volker; Holleczek, Bernd; Hooning, Maartje J; Hollestelle, Antoinette; Martens, John W M; van Deurzen, Carolien H M; van de Water, Bob; Broeks, Annegien; Chang-Claude, Jenny; Chenevix-Trench, Georgia; Easton, Douglas F; Pharoah, Paul D P; García-Closas, Montserrat; de Graauw, Marjo; Schmidt, Marjanka K (BioMed Central, 2015)
    Abstract Background Annexin A1 (ANXA1) is a protein related with the carcinogenesis process and metastasis formation in many tumors. However, little is known about the prognostic value of ANXA1 in breast cancer. The purpose of this study is to evaluate the association between ANXA1 expression, BRCA1/2 germline carriership, specific tumor subtypes and survival in breast cancer patients. Methods Clinical-pathological information and follow-up data were collected from nine breast cancer studies from the Breast Cancer Association Consortium (BCAC) (n = 5,752) and from one study of familial breast cancer patients with BRCA1/2 mutations (n = 107). ANXA1 expression was scored based on the percentage of immunohistochemical staining in tumor cells. Survival analyses were performed using a multivariable Cox model. Results The frequency of ANXA1 positive tumors was higher in familial breast cancer patients with BRCA1/2 mutations than in BCAC patients, with 48.6 % versus 12.4 %, respectively; P <0.0001. ANXA1 was also highly expressed in BCAC tumors that were poorly differentiated, triple negative, EGFR-CK5/6 positive or had developed in patients at a young age. In the first 5 years of follow-up, patients with ANXA1 positive tumors had a worse breast cancer-specific survival (BCSS) than ANXA1 negative (HRadj = 1.35; 95 % CI = 1.05–1.73), but the association weakened after 10 years (HRadj = 1.13; 95 % CI = 0.91–1.40). ANXA1 was a significant independent predictor of survival in HER2+ patients (10-years BCSS: HRadj = 1.70; 95 % CI = 1.17–2.45). Conclusions ANXA1 is overexpressed in familial breast cancer patients with BRCA1/2 mutations and correlated with poor prognosis features: triple negative and poorly differentiated tumors. ANXA1 might be a biomarker candidate for breast cancer survival prediction in high risk groups such as HER2+ cases.
  • Virtanen, Jorma I; Vehkalahti, Kimmo I; Vehkalahti, Miira M (BioMed Central, 2015)
    Abstract Background Health behaviors play a major role in the prevention of the most common oral diseases. To investigate health behaviors related to the potential transmission of oral bacteria from mother to child using novel multiple correspondence analysis (MCA). Methods Mothers (n = 313) with children under three years attending two municipal child health clinics in Finland completed a self-administered questionnaire on health knowledge and behaviors such as sharing a spoon with their child, kissing on the lips, and the mothers’ tooth brushing, smoking, age, and level of education. We used MCA to reveal the relationships between the mothers’ behaviors and background factors, along with unconditional, binary, multivariable logistic regression models, odds ratios (OR) and their 95 % confidence intervals (95 %CI). Results Of the mothers, 38 % kissed their child on the lips and 14 % shared a spoon with their child; 11 % believed that oral bacteria cannot be transmitted from mother to child. Two-thirds (68 %) of them reported tooth brushing twice daily, and 80 % were non-smokers. MCA revealed two diverging dimensions of the mothers’ behaviors: a ‘horizontal’ one showing clear evidence of relationships between tooth brushing, smoking, age and education, whereas the ‘vertical’ one revealed the mothers’ habits of kissing the child on the lips and sharing a spoon related to each other. Spoon sharing was related to the kissing on lips (OR 10.3), a higher level of education (OR 3.1), and, inversely, older age (OR 0.1), whereas kissing on lips behavior was inversely related to a higher level of education (OR 0.5). Conclusion The study revealed two diverging dimensions of the mothers’ health behaviors. More emphasis in health education ought to be put to how to avoid bacterial transmission from caregiver to child during feeding.
  • Fagerholm, Fabian; Ikonen, Marko; Kettunen, Petri; Münch, Jürgen; Roto, Virpi; Abrahamsson, Pekka (ELSEVIER BV, 2015)
    Context: Companies increasingly strive to adapt to market and ecosystem changes in real time. Gauging and understanding team performance in such changing environments present a major challenge. Objective: This paper aims to understand how software developers experience the continuous adaptation of performance in a modern, highly volatile environment using Lean and Agile software development methodology. This understanding can be used as a basis for guiding formation and maintenance of high-performing teams, to inform performance improvement initiatives, and to improve working conditions for software developers. Method: A qualitative multiple-case study using thematic interviews was conducted with 16 experienced practitioners in five organisations. Results: We generated a grounded theory, Performance Alignment Work, showing how software developers experience performance. We found 33 major categories of performance factors and relationships between the factors. A cross-case comparison revealed similarities and differences between different kinds and different sizes of organisations. Conclusions: Based on our study, software teams are engaged in a constant cycle of interpreting their own performance and negotiating its alignment with other stakeholders. While differences across organisational sizes exist, a common set of performance experiences is present despite differences in context variables. Enhancing performance experiences requires integration of soft factors, such as communication, team spirit, team identity, and values, into the overall development process. Our findings suggest a view of software development and software team performance that centres around behavioural and social sciences.
  • Lienemann, Taru; Kyyhkynen, Aino; Halkilahti, Jani; Haukka, Kaisa; Siitonen, Anja (BioMed Central, 2015)
    Abstract Background Salmonella enterica spp. enterica serotype Typhimurium (STM) is the most common agent of domestically acquired salmonellosis in Finland. Subtyping methods which allow the characterization of STM are essential for effective laboratory-based STM surveillance and for recognition of outbreaks. This study describes the diversity of Finnish STM isolates using phage typing, antimicrobial susceptible testing, pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA), and compares the discriminatory power and the concordance of these methods. Results A total of 375 sporadic STM isolates were analysed. The isolates were divided into 31 definite phage (DT) types, dominated by DT1 (47 % of the isolates), U277 (9 % of the isolates) and DT104 (8 % of the isolates). Of all the isolates, 62 % were susceptible to all the 12 antimicrobials tested and 11 % were multidrug resistant. Subtyping resulted in 83 different XbaI-PFGE profiles and 111 MLVA types. The three most common XbaI-PFGE profiles (STYM1, STYM7 and STYM8) and one MLVA profile with three single locus variants accounted for 56 % and 49 % of the STM isolates, respectively. The studied isolates showed a genetic similarity of more than 70 % by XbaI-PFGE. In MLVA, 71 % of the isolates lacked STTR6 and 77 % missed STTR10p loci. Nevertheless, the calculated Simpson’s diversity index for XbaI-PFGE was 0.829 (95 % CI 0.792−0.865) and for MLVA 0.867 (95 % CI 0.835−0.898). However, the discriminatory power of the 5-loci MLVA varied among the phage types. The highest concordance of the results was found between XbaI-PFGE and phage typing (adjusted Wallace coefficient was 0.833 and adjusted Rand coefficient was 0.627). Conclusions In general, the calculated discriminatory power was higher for genotyping methods (MLVA and XbaI-PFGE) than for phenotyping methods (phage typing). Overall, comparable diversity indices were calculated for PFGE and MLVA (both DI > 0.8). However, MLVA was phage type dependent providing better discrimination of the most common phage types. Furthermore, 5-loci MLVA was a less laborious method and easier to interpret than XbaI-PFGE. Thus, the laboratory-based surveillance of the Finnish human STM infections has been conducted with a combination of phage typing, antimicrobial susceptibility testing and 5-loci MLVA since January 2014.
  • Lehtisaari, Katja (SUOMEN VENÄJÄN JA ITÄ-EUROOPAN TUTKIMUKSEN SEURA., 2014)
  • Lehtisaari, Katja (SUOMEN VENÄJÄN JA ITÄ-EUROOPAN TUTKIMUKSEN SEURA., 2014)
  • Kreutz, Andreas; Aakala, Tuomas; Grenfell, Russell; Kuuluvainen, Timo (Finnish Society of Forest Science, 2015)
    Development of species composition during succession is well studied in natural boreal forests, but empirical assessments of how within-stand spatial structure develops in late-successional stages are few. Here, we quantified spatial patterns in three unmanaged stands consisting of Picea abies (L.) Karst. and Betula pubescens Ehrh. and Betula pendula Roth (hereafter Betula spp.) in northern boreal Fennoscandia. We conducted a comprehensive analysis of small-scale spatial point patterns in three fully mapped 1.2-ha sample plots, representing different forest developmental stages: mid-successional, late-successional and old-growth forest. We used several variants of Ripley’s K-function to analyze the spatial point patterns along the successional gradient. Univariate analyses showed that mature trees of both species were either randomly distributed or clumped. P. abies saplings were clumped, and Betula spp. saplings occurred in a random or clumped manner. In the bivariate analyses, saplings were more likely to be found in the surroundings of mature trees of the same species, but occurred independent of the individuals of other tree species. Mature trees showed interspecific repulsion. Only modest differences occurred in the univariate patterns between the three successional stages, but in the bivariate analyses the most evident patterns, i.e. intraspecific attraction and interspecific repulsion, were stronger in the older successional stages. Overall, the studied stands appear structured as species-specific mosaics. These mosaics, along with mixed species composition, seem to be maintained by species self-replacement, which contrasts with findings from earlier studies.
  • Pirie, Ailith; Guo, Qi; Kraft, Peter; Canisius, Sander; Eccles, Diana M; Rahman, Nazneen; Nevanlinna, Heli; Chen, Constance; Khan, Sofia; Tyrer, Jonathan; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Michailidou, Kyriaki; Lush, Michael; Dunning, Alison M; Shah, Mitul; Czene, Kamila; Darabi, Hatef; Eriksson, Mikael; Lambrechts, Dieter; Weltens, Caroline; Leunen, Karin; van Ongeval, Chantal; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Rudolph, Anja; Seibold, Petra; Flesch-Janys, Dieter; Blomqvist, Carl; Aittomäki, Kristiina; Fagerholm, Rainer; Muranen, Taru A; Olsen, Janet E; Hallberg, Emily; Vachon, Celine; Knight, Julia A; Glendon, Gord; Mulligan, Anna M; Broeks, Annegien; Cornelissen, Sten; Haiman, Christopher A; Henderson, Brian E; Schumacher, Frederick; Le Marchand, Loic; Hopper, John L; Tsimiklis, Helen; Apicella, Carmel; Southey, Melissa C; Cross, Simon S; Reed, Malcolm W; Giles, Graham G; Milne, Roger L; McLean, Catriona; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Hooning, Maartje J; Hollestelle, Antoinette; Martens, John W; van den Ouweland, Ans M; Marme, Federick; Schneeweiss, Andreas; Yang, Rongxi; Burwinkel, Barbara; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Brenner, Hermann; Butterbach, Katja; Holleczek, Bernd; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Li, Jingmei; Brand, Judith S; Humphreys, Keith; Devilee, Peter; Tollenaar, Robert A; Seynaeve, Caroline; Radice, Paolo; Peterlongo, Paolo; Manoukian, Siranoush; Ficarazzi, Filomena; Beckmann, Matthias W; Hein, Alexander; Ekici, Arif B; Balleine, Rosemary; Phillips, Kelly-Anne; Benitez, Javier; Zamora, M P; Perez, Jose I A; Menéndez, Primitiva; Jakubowska, Anna; Lubinski, Jan; Gronwald, Jacek; Durda, Katarzyna; Hamann, Ute; Kabisch, Maria; Ulmer, Hans U; Rüdiger, Thomas; Margolin, Sara; Kristensen, Vessela; Nord, Siljie; Evans, D G; Abraham, Jean; Earl, Helena; Poole, Christopher J; Hiller, Louise; Dunn, Janet A; Bowden, Sarah; Yang, Rose; Campa, Daniele; Diver, W R; Gapstur, Susan M; Gaudet, Mia M; Hankinson, Susan; Hoover, Robert N; Hüsing, Anika; Kaaks, Rudolf; Machiela, Mitchell J; Willett, Walter; Barrdahl, Myrto; Canzian, Federico; Chin, Suet-Feung; Caldas, Carlos; Hunter, David J; Lindstrom, Sara; Garcia-Closas, Montserrat; Couch, Fergus J; Chenevix-Trench, Georgia; Mannermaa, Arto; Andrulis, Irene L; Hall, Per; Chang-Claude, Jenny; Easton, Douglas F; Bojesen, Stig E; Cox, Angela; Fasching, Peter A; Pharoah, Paul D; Schmidt, Marjanka K (BioMed Central, 2015)
    Abstract Introduction Previous studies have identified common germline variants nominally associated with breast cancer survival. These associations have not been widely replicated in further studies. The purpose of this study was to evaluate the association of previously reported SNPs with breast cancer-specific survival using data from a pooled analysis of eight breast cancer survival genome-wide association studies (GWAS) from the Breast Cancer Association Consortium. Methods A literature review was conducted of all previously published associations between common germline variants and three survival outcomes: breast cancer-specific survival, overall survival and disease-free survival. All associations that reached the nominal significance level of P value <0.05 were included. Single nucleotide polymorphisms that had been previously reported as nominally associated with at least one survival outcome were evaluated in the pooled analysis of over 37,000 breast cancer cases for association with breast cancer-specific survival. Previous associations were evaluated using a one-sided test based on the reported direction of effect. Results Fifty-six variants from 45 previous publications were evaluated in the meta-analysis. Fifty-four of these were evaluated in the full set of 37,954 breast cancer cases with 2,900 events and the two additional variants were evaluated in a reduced sample size of 30,000 samples in order to ensure independence from the previously published studies. Five variants reached nominal significance (P <0.05) in the pooled GWAS data compared to 2.8 expected under the null hypothesis. Seven additional variants were associated (P <0.05) with ER-positive disease. Conclusions Although no variants reached genome-wide significance (P <5 x 10−8), these results suggest that there is some evidence of association between candidate common germline variants and breast cancer prognosis. Larger studies from multinational collaborations are necessary to increase the power to detect associations, between common variants and prognosis, at more stringent significance levels.
  • Gel'man, Vladimir (Russian Analytical Digest, 2015)