Articles from TUHAT CRIS

 

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This collection contains Open Access articles deposited from the University of Helsinki TUHAT CRIS

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  • Kopotev, Mikhail; Pivovarova, Lidia; Kormacheva, Daria (Société Néophilologique de Helsinki, 2016)
    The CoCoCo project aims to model multi-word expressions (MWEs) of diverse natures in a unified fashion. The algorithm predicts the most stable features in an n-gram—morphological, lexical, or constructional. In this article, we focus more on lexical compatibility of extracted collocations. At one extreme are lexically stable idioms, where no generalization is possible, e.g., lo and behold. Other collocations appear to be stable on a more abstract level of generalization. They are constructions where lexical items are replaceable but belong to the same semantic class, e.g., sleight of [hand/mouth/mind]. In this case, prediction of the entire semantic class is possible. To confirm this idea, we present a qualitative analysis of automatically extracted Russian MWEs. We then use distributional semantics methods to find semantic classes automatically and demonstrate that these correspond with manually annotated classes. This implies that the semantic classes can be used in the collocation detection algorithm.
  • Jelenkovic, Aline; Sund, Reijo; Hur, Yoon-Mi; Yokoyama, Yoshie; Hjelmborg, Jacob V. B.; Moller, Soren; Honda, Chika; Magnusson, Patrik K. E.; Pedersen, Nancy L.; Ooki, Syuichi; Aaltonen, Sari; Stazi, Maria A.; Fagnani, Corrado; D'Ippolito, Cristina; Freitas, Duarte L.; Maia, Jose Antonio; Ji, Fuling; Ning, Feng; Pang, Zengchang; Rebato, Esther; Busjahn, Andreas; Kandler, Christian; Saudino, Kimberly J.; Jang, Kerry L.; Cozen, Wendy; Hwang, Amie E.; Mack, Thomas M.; Gao, Wenjing; Yu, Canqing; Li, Liming; Corley, Robin P.; Huibregtse, Brooke M.; Derom, Catherine A.; Vlietinck, Robert F.; Loos, Ruth J. F.; Heikkila, Kauko; Wardle, Jane; Llewellyn, Clare H.; Fisher, Abigail; McAdams, Tom A.; Eley, Thalia C.; Gregory, Alice M.; He, Mingguang; Ding, Xiaohu; Bjerregaard-Andersen, Morten; Beck-Nielsen, Henning; Sodemann, Morten; Tarnoki, Adam D.; Tarnoki, David L.; Knafo-Noam, Ariel; Mankuta, David; Abramson, Lior; Burt, S. Alexandra; Klump, Kelly L.; Silberg, Judy L.; Eaves, Lindon J.; Maes, Hermine H.; Krueger, Robert F.; McGue, Matt; Pahlen, Shandell; Gatz, Margaret; Butler, David A.; Bartels, Meike; van Beijsterveldt, Toos C. E. M.; Craig, Jeffrey M.; Saffery, Richard; Dubois, Lise; Boivin, Michel; Brendgen, Mara; Dionne, Ginette; Vitaro, Frank; Martin, Nicholas G.; Medland, Sarah E.; Montgomery, Grant W.; Swan, Gary E.; Krasnow, Ruth; Tynelius, Per; Lichtenstein, Paul; Haworth, Claire M. A.; Plomin, Robert; Bayasgalan, Gombojav; Narandalai, Danshiitsoodol; Harden, K. Paige; Tucker-Drob, Elliot M.; Spector, Timothy; Mangino, Massimo; Lachance, Genevieve; Baker, Laura A.; Tuvblad, Catherine; Duncan, Glen E.; Buchwald, Dedra; Willemsen, Gonneke; Skytthe, Axel; Kyvik, Kirsten O.; Christensen, Kaare; Oncel, Sevgi Y.; Aliev, Fazil; Rasmussen, Finn; Goldberg, Jack H.; Sorensen, Thorkild I. A.; Boomsma, Dorret I.; Kaprio, Jaakko; Silventoinen, Karri (NATURE PUBLISHING GROUP, 2016)
    Height variation is known to be determined by both genetic and environmental factors, but a systematic description of how their influences differ by sex, age and global regions is lacking. We conducted an individual-based pooled analysis of 45 twin cohorts from 20 countries, including 180,520 paired measurements at ages 1-19 years. The proportion of height variation explained by shared environmental factors was greatest in early childhood, but these effects remained present until early adulthood. Accordingly, the relative genetic contribution increased with age and was greatest in adolescence (up to 0.83 in boys and 0.76 in girls). Comparing geographic-cultural regions (Europe, North-America and Australia, and East-Asia), genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions. Our findings provide further insights into height variation during childhood and adolescence in populations representing different ethnicities and exposed to different environments.
  • Tiira, Timo Ensio; Uski, Marja Riitta; Kortström, Jari Tapio; Kaisko, Outi Sinikka; Korja, Annakaisa (Springer Netherlands, 2016)
    This study presents a plan for seismic monitoring of a region around a potential nuclear power plant. Seismic monitoring is needed to evaluate seismic risk. The International Atomic Energy Agency has set guidelines on seismic hazard evaluation and monitoring of such areas. According to these guidelines, we have made a plan for a local network of seismic stations to collect data for seismic source characterization and seismotectonic interpretations, as well as to monitor seismic activity and natural hazards. The detection and location capability of the network were simulated using different station configurations by computing spatial azimuthal coverages and detection threshold magnitudes. Background noise conditions around Pyhäjoki were analyzed by comparing data from different stations. The annual number of microearthquakes that should be detected with a dense local network centered around Pyhäjoki was estimated. The network should be dense enough to fulfill the requirements of azimuthal coverage better than 180° and automatic event location capability down to ML ∼ 0 within a distance of 25 km from the site. A network of 10 stations should be enough to reach these goals. With this setup, the detection threshold magnitudes are estimated to be ML = −0.1 and ML = 0.1 within a radius of 25 and 50 km from Pyhäjoki, respectively. The annual number of earthquakes detected by the network is estimated to be 2 (ML ≥ ∼ −0.1) within 25 km radius and 5 (ML ≥ ∼−0.1 to ∼0.1) within 50 km radius. The location accuracy within 25 km radius is estimated to be 1–2 and 4 km for horizontal coordinates and depth, respectively. Thus, the network is dense enough to map out capable faults with horizontal accuracy of 1–2 km within 25 km radius of the site. The estimation is based on the location accuracies of five existing networks in northern Europe. Local factors, such as seismic noise sources, geology and infrastructure might limit the station configuration and detection and location capability of the network.
  • Bona, Silvia; Cattaneo, Zaira; Silvanto, Juha (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2016)
    Background: The right occipital face area (rOFA) is known to be involved in face discrimination based on local featural information. Whether this region is also involved in global, holistic stimulus processing is not known. Objective: We used fMRI-guided transcranial magnetic stimulation (TMS) to investigate whether rOFA is causally implicated in stimulus detection based on holistic processing, by the use of Mooney stimuli. Methods: Two studies were carried out: In Experiment 1, participants performed a detection task involving Mooney faces and Mooney objects; Mooney stimuli lack distinguishable local features and can be detected solely via holistic processing (i.e. at a global level) with top-down guidance from previously stored representations. Experiment 2 required participants to detect shapes which are recognized via bottom-up integration of local (collinear) Gabor elements and was performed to control for specificity of rOFA's implication in holistic detection. Results: In Experiment 1, TMS over rOFA and rLO impaired detection of all stimulus categories, with no category-specific effect. In Experiment 2, shape detection was impaired when TMS was applied over rLO but not over rOFA. Conclusions: Our results demonstrate that rOFA is causally implicated in the type of top-down holistic detection required by Mooney stimuli and that such role is not face-selective. In contrast, rOFA does not appear to play a causal role in detection of shapes based on bottom-up integration of local components, demonstrating that its involvement in processing non-face stimuli is specific for holistic processing. (C) 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
  • Gabay, Cem; Riek, Myriam; Hetland, Merete Lund; Hauge, Ellen-Margrethe; Pavelka, Karel; Tomsic, Matija; Canhao, Helena; Chatzidionysiou, Katerina; Lukina, Galina; Nordstrom, Dan C.; Lie, Elisabeth; Ancuta, Ioan; Victoria Hernandez, M.; van Riel, Piet L. M. C.; van Vollenhoven, Ronald; Kvien, Tore K. (BMJ PUBLISHING GROUP, 2016)
    Objectives To examine the effectiveness of tocilizumab (TCZ) with and without synthetic disease-modifying antirheumatic drugs (sDMARDs) in a large observational study. Methods Patients with rheumatoid arthritis treated with TCZ who had a baseline visit and information on concomitant sDMARDs were included. According to baseline data, patients were considered as taking TCZ as monotherapy or combination with sDMARDs. Main study outcomes were the change of Clinical Disease Activity Index (CDAI) and TCZ retention. The prescription of TCZ as monotherapy was analysed using logistic regression. CDAI change was analysed with a mixed-effects model for longitudinal data. TCZ retention was analysed with a stratified extended Cox model. Results Multiple-adjusted analysis suggests that prescription of TCZ as monotherapy varied according to age, corticosteroid use, country of the registry and year of treatment initiation. The change of disease activity assessed by CDAI as well as the likelihood to be in remission were not significantly different whether TCZ was used as monotherapy or in combination with sDMARDs in a covariate-adjusted analysis. Estimates for unadjusted median TCZ retention were 2.3 years (95% CI 1.8 to 2.7) for monotherapy and 3.7 years (lower 95% CI limit 3.1, upper limit not estimable) for combination therapies. In a covariate-adjusted analysis, TCZ retention was also reduced when used as monotherapy, with an increasing difference between mono and combination therapy over time after 1.5 years (p=0.002). Conclusions TCZ with or without concomitant sDMARDs resulted in comparable clinical response as assessed by CDAI change, but TCZ retention was shorter under monotherapy of TCZ.
  • Rahe-Meyer, N.; Levy, J. H.; Mazer, C. D.; Schramko, A.; Klein, A. A.; Brat, R.; Okita, Y.; Ueda, Y.; Schmidt, D. S.; Ranganath, R.; Gill, R. (Oxford University Press, 2016)
    Background: Single-dose human fibrinogen concentrate (FCH) might have haemostatic benefits in complex cardiovascular surgery. Methods: Patients undergoing elective aortic surgery requiring cardiopulmonary bypass were randomly assigned to receive FCH or placebo. Study medication was administered to patients with a 5 min bleeding mass of 60-250 g after separation from bypass and surgical haemostasis. A standardized algorithm for allogeneic blood product transfusion was followed if bleeding continued after study medication. Results: 519 patients from 34 centres were randomized, of whom 152 (29%) met inclusion criteria for study medication. Median (IQR) pretreatment 5 min bleeding mass was 107 (76-138) and 91 (71-112) g in the FCH and placebo groups, respectively (P=0.13). More allogeneic blood product units were administered during the first 24 h after FCH, 5.0 (2.0-11.0), when compared with placebo, 3.0 (0.0-7.0), P=0.026. Fewer patients avoided transfusion in the FCH group (15.4%) compared with placebo (28.4%), P=0.047. The FCH immediately increased plasma fibrinogen concentration and fibrin-based clot strength. Adverse event rates were comparable in each group. Conclusions: Human fibrinogen concentrate was associated with increased allogeneic blood product transfusion, an unexpected finding contrary to previous studies. Human fibrinogen concentrate may not be effective in this setting when administered according to 5-minute bleeding mass. Low bleeding rates and normal-range plasma fibrinogen concentrations before study medication, and variability in adherence to the complex transfusion algorithm, may have contributed to these results.
  • Rissanen, Antti-Pekka E.; Koskela-Koivisto, Tiina; Hägglund, Harriet; Koponen, Anne S.; Aho, Jyrki M.; Pöyhönen-Alho, Maritta; Tiitinen, Aila; Tikkanen, Heikki O.; Peltonen, Juha E. (Wiley, 2016)
    In polycystic ovary syndrome (PCOS), cardiovascular risk is increased. Peak O2 uptake (V˙O2peak) predicts the cardiovascular risk. We were the first to examine the contribution of systemic O2 delivery and arteriovenous O2 difference to V˙O2peak in overweight and obese women with PCOS. Fifteen overweight or obese PCOS women and 15 age-, anthropometry-, and physical activity-matched control women performed a maximal incremental cycling exercise test. Alveolar gas exchange (volume turbine and mass spectrometry), arterial O2 saturation (pulse oximetry), and cardiac output (CO) (impedance cardiography) were monitored. Hb concentration was determined. Arterial O2 content and arteriovenous O2 difference (C(a-v)O2) (Fick equation) were calculated. Insulin resistance was evaluated by homeostasis model assessment (HOMA-IR). PCOS women had lower V˙O2peak than controls (40 ± 6 vs. 46 ± 5 mL/min/kg fat-free mass [FFM], P = 0.011). Arterial O2 content was similarly maintained in the groups throughout the exercise test (P > 0.05). Linear regression analysis revealed a pronounced response of CO to increasing V˙O2 in PCOS women during the exercise test: A ∆CO/∆V˙O2 slope was steeper in PCOS women than in controls (β = 5.84 vs. β = 5.21, P = 0.004). Eventually, the groups attained similar peak CO and peak CO scaled to FFM (P > 0.05). Instead, C(a-v)O2 at peak exercise was lower in PCOS women than in controls (13.2 ± 1.6 vs. 14.8 ± 2.4 mL O2/100 mL blood, P = 0.044). HOMA-IR was similar in the groups (P > 0.05). The altered cardiorespiratory responses to exercise in overweight and obese PCOS women indicate that PCOS per se is associated with alterations in peripheral adjustments to exercise rather than with limitations of systemic O2 delivery.
  • Rapo-Pylkkö, Susanna; Haanpää, Maija; Liira, Helena (TAYLOR & FRANCIS LTD, 2016)
    Objective: To present the occurrence, characteristics, etiology, interference, and medication of chronic pain among the elderly living independently at home. Design/setting: A total of 460 subjects in three cohorts aged 75, 80 and 85 years respectively received visits by communal home-care department nurses for a cross-sectional survey. Of them, 175 had chronic (duration 3 months) pain with an average intensity of 4/10 and/or moderate interference in daily life. Main outcome measures: Clinical assessment was performed for consenting subjects to define the location, intensity, etiology, type, interference and medications of chronic pain. Results: According to home visits, elderly people with chronic pain rated their health and mobility worse and felt sadder, lonelier and more tired than those without chronic pain. A geriatrician made clinical assessments for 106 patients with chronic pain in 2009-2013. Of them, 66 had three, 35 had two and 5 had one pain condition. The worst pain was musculoskeletal in 88 (83%) of patients. Pain was pure nociceptive in 61 (58%), pure neuropathic in 9 (8%), combined nociceptive and neuropathic pain in 34 (32%), and idiopathic in 2 (2%) patients. On a numerical rating scale from 0 to 10, the mean and maximal intensity of the worst pain was 5.7 and 7.7, respectively, while the mean pain interference was 5.9. Mean pain intensity and maximal pain intensity decreased by age. Duration of pain was longer than 5 years in 51 (48%) patients. Regular pain medication was used by 82 (77%) patients, most commonly paracetamol or NSAIDs. Although pain limited the lives of the elderly with chronic pain, they were as satisfied with their lives as those without chronic pain. Conclusions: Elderly people in our study often suffered from chronic pain, mostly musculoskeletal pain, and the origin of pain was neuropathic in up to 40% of these cases. However, elderly people with chronic pain rarely used the medications specifically for neuropathic pain. Based on increased loneliness, sadness and tiredness, as well as decreased subjective health and mobility, the quality of life was decreased among those with chronic pain compared with those without pain.
  • Liira, Helena (TAYLOR & FRANCIS LTD, 2016)
  • Gu, Yuexi; Helenius, Mikko; Vaananen, Kristiina; Bulanova, Daria; Saarela, Jani; Sokolenko, Anna; Martens, John; Imyanitov, Evgeny; Kuznetsov, Sergey (NATURE PUBLISHING GROUP, 2016)
    Germ-line or somatic inactivation of BRCA1 is a defining feature for a portion of human breast cancers. Here we evaluated the anti-proliferative activity of 198 FDA-approved and experimental drugs against four BRCA1-mutant (HCC1937, MDA-MB-436, SUM1315MO2, and SUM149PT) and four BRCA1-wild-type (MDA-MB-231, SUM229PE, MCF10A, and MCF7) breast cancer cell lines. We found that all BRCA1-mutant cell lines were insensitive to inhibitors of mitogen-activated protein kinase kinase 1 and 2 (MEK1/2) Selumetinib and Pimasertib in contrast to BRCA1-wildtype control cell lines. However, unexpectedly, only two BRCA1-mutant cell lines, HCC1937 and MDA-MB-436, were hypersensitive to a nucleotide analogue 6-thioguanine (6-TG). SUM149PT cells readily formed radiation-induced RAD51-positive nuclear foci indicating a functional homologous recombination, which may explain their resistance to 6-TG. However, the reason underlying 6-TG resistance of SUM1315MO2 cells remains unclear. Our data reveal a remarkable heterogeneity among BRCA1-mutant cell lines and provide a reference for future studies.
  • Visala, Aku; Vainio, Olli-Pekka (de Gruyter, 2016)
  • Peltomäki, Päivi (Springer, 2016)
    Four main DNA mismatch repair (MMR) genes have been identified, MLH1, MSH2, MSH6, and PMS2, which when mutated cause susceptibility to Lynch syndrome (LS). LS is one of the most prevalent hereditary cancer syndromes in man and accounts for 1-3 % of unselected colorectal carcinomas and some 15 % of those with microsatellite instability and/or absent MMR protein. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) maintains a database for LS-associated mutations since 1996. The database was recently reorganized to efficiently gather published and unpublished data and to classify the variants according to a five-tiered scheme linked to clinical recommendations. This review provides an update of germline mutations causing susceptibility to LS based on information available in the InSiGHT database and the latest literature. MMR gene mutation profiles, correlations between genotype and phenotype, and possible mechanisms leading to the characteristic spectrum of tumors in LS are discussed in light of the different functions of MMR proteins, many of which directly serve cancer avoidance.
  • Tolonen, Anna-Liisa (de Gruyter, 2016)
    Two opposing opinions about “the Maccabees” feature in the homily On Eleazar and the Seven Boys. According to the homilist, “the Maccabees” can be recognized as martyrs; yet, many others fail to see it. The construction of this conflict relies heavily on another confrontation identifiable in the same text: a dialogue between the homilist and “the Jew”, who thinks differently and, in the opinion of the homilist, incorrectly. These tensions in the source may be taken to reflect “identity-political” issues of the time and evaluated accordingly. My analysis challenges this view by emphasizing how difficult it is to reconstruct historical encounters between persons/groups based on such a source. I suggest, instead, that the conflict and dialogue should be considered parallel examples of how, in the context of late antiquity, a Christian intellectual mind conceptualizes “difference” (of opinions or between identities) and how it deals with it. The analysis shows that the homilist’s argumentation is built on seemingly commonsensical or authoritative fair-to-all “facts”. Yet, interactions with others provide the homilist with ways to govern and re-produce those very facts. Rather than social struggles, the interactions reflect and represent the level of otherness contained in the discourse of the homilist.
  • Nieminen, Markku Sakari; Buerke, Michael; Cohen-Solal, Alain; Costa, Susana; Edes, Istvan; Erlikh, Alexey; Franco, Fatima; Gibson, Charles; Gorjuph, Vojka; Guarracino, Fabio; Gustafsson, Finn; Harjola, Veli-Pekka; Husebye, Trygve; Karason, Kristjan; Katsytadze, Igor; Kaul, Sundeep; Kivikko, Matti; Marenzi, Giancarlo; Masip, Josep; Matskeplishvili, Simon; Mebazaa, Alexandre; Moller, Jacob E.; Nessler, Jadwiga; Nessler, Bohdan; Ntalianis, Argyrios; Oliva, Fabrizio; Pichler-Cetin, Emel; Poder, Pentti; Recio-Mayoral, Alejandro; Rex, Steffen; Rokyta, Richard; Strasser, Ruth H.; Zima, Endre; Pollesello, Piero (ELSEVIER IRELAND LTD, 2016)
  • SePIA 
    Icay, Katherine; Chen, Ping; Cervera Taboada, Alejandra; Rantanen, Ville; Lehtonen, Rainer; Hautaniemi, Sampsa (BIOMED CENTRAL LTD, 2016)
    Background: Large-scale sequencing experiments are complex and require a wide spectrum of computational tools to extract and interpret relevant biological information. This is especially true in projects where individual processing and integrated analysis of both small RNA and complementary RNA data is needed. Such studies would benefit from a computational workflow that is easy to implement and standardizes the processing and analysis of both sequenced data types. Results: We developed SePIA (Sequence Processing, Integration, and Analysis), a comprehensive small RNA and RNA workflow. It provides ready execution for over 20 commonly known RNA-seq tools on top of an established workflow engine and provides dynamic pipeline architecture to manage, individually analyze, and integrate both small RNA and RNA data. Implementation with Docker makes SePIA portable and easy to run. We demonstrate the workflow's extensive utility with two case studies involving three breast cancer datasets. SePIA is straightforward to configure and organizes results into a perusable HTML report. Furthermore, the underlying pipeline engine supports computational resource management for optimal performance. Conclusion: SePIA is an open-source workflow introducing standardized processing and analysis of RNA and small RNA data. SePIA's modular design enables robust customization to a given experiment while maintaining overall workflow structure.