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Open access articles by University of Helsinki researchers. Contains final versions and manuscripts of research articles as well as professional publications and publications aimed at general public.

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  • Bello, Ibrahim O.; Almangush, Alhadi; Heikkinen, Ilkka; Haglund, Caj; Coletta, Ricardo D.; Kowalski, Luiz P.; Makitie, Antti A.; Nieminen, Pentti; Leivo, Ilmo; Salo, Tuula (2020)
    Little is known about the histopathological characteristics that may differentiate early oral tongue cancer (OTSCC) between young and older patients. From a total of 311 cases diagnosed with clinically early-stage OTSCC at 6 institutions, only 42 patients were young patients were aged 60 years old were matched for center of management, clinical stage and gender. We compared epithelial and stromal histopathologic parameters between the two groups. Most of the parameters were similar between the two groups, although the young patients appeared to have marginally higher intensity of tumor budding, histologic risk score, infiltrative pattern of invasion and tumor-stroma ratio. However, none of the factors showed significant difference when comparing the two groups. The histological parameters reflect mechanisms of invasive growth and tissue response to invasive growth, but not the etiological difference in OTSCC between young and older patients. Further investigations are necessary to compare the genetic background of early OTSCC in the two groups.
  • Zhang, Yansong; Zhang, Yu; Lu, Jiaheng; Wang, Shan; Liu, Zhuan; Han, Ruichen (2020)
    GPU has been considered as one of the next-generation platforms for real-time query processing databases. In this paper we empirically demonstrate that the representative GPU databases [e.g., OmniSci (Open Source Analytical Database & SQL Engine,, 2019)] may be slower than the representative in-memory databases [e.g., Hyper (Neumann and Leis, IEEE Data Eng Bull 37(1):3-11, 2014)] with typical OLAP workloads (with Star Schema Benchmark) even if the actual dataset size of each query can completely fit in GPU memory. Therefore, we argue that GPU database designs should not be one-size-fits-all; a general-purpose GPU database engine may not be well-suited for OLAP workloads without careful designed GPU memory assignment and GPU computing locality. In order to achieve better performance for GPU OLAP, we need to re-organize OLAP operators and re-optimize OLAP model. In particular, we propose the 3-layer OLAP model to match the heterogeneous computing platforms. The core idea is to maximize data and computing locality to specified hardware. We design the vector grouping algorithm for data-intensive workload which is proved to be assigned to CPU platform adaptive. We design the TOP-DOWN query plan tree strategy to guarantee the optimal operation in final stage and pushing the respective optimizations to the lower layers to make global optimization gains. With this strategy, we design the 3-stage processing model (OLAP acceleration engine) for hybrid CPU-GPU platform, where the computing-intensive star-join stage is accelerated by GPU, and the data-intensive grouping & aggregation stage is accelerated by CPU. This design maximizes the locality of different workloads and simplifies the GPU acceleration implementation. Our experimental results show that with vector grouping and GPU accelerated star-join implementation, the OLAP acceleration engine runs 1.9x, 3.05x and 3.92x faster than Hyper, OmniSci GPU and OmniSci CPU in SSB evaluation with dataset of SF = 100.
  • Raivio, Minna; Hartikainen, Sirpa (2020)
    Suomessa 75 vuotta täyttäneitä on tällä hetkellä yli 700 000, noin 14 % väestöstä. Heillä on enemmän sairauksia ja niihin lääkehoitoja kuin nuoremmilla. Lääkehaitat aiheuttavat viidesosan iäkkäiden päivystyskäynneistä sairaaloissa, mutta niistä merkittävä osa on ehkäistävissä. Perusterveydenhuollon tärkeä tehtävä on iäkkään lääkehoidon arviointi säännöllisesti vähintään kerran vuodessa. Kaikkein hauraimmille, kuten muistisairaille, lääkehoidon arviointi olisi syytä tehdä vielä tiheämmin. Iäkkään optimoidun lääkehoidon pitäisi olla rationaalista - oikea lääke oikeaan vaivaan - ja vanhenemismuutosten vaikutukset sekä yksilöllisesti iäkkään tarpeet ja elämäntilanne huomioon ottavaa. Kokonaisvaltainen hoito ja optimoitu lääkehoito sen osana on pitkäjänteistä työtä, jossa lääkärin tärkein kumppani on iäkäs ihminen itse läheisineen.
  • Kopra, Sanna (Palgrave Pivot, 2019)
  • Hämäläinen, Mika; Partanen, Niko; Alnajjar, Khalid (Association pour le Traitement Automatique des Langues, 2021)
  • de Hulster, Izaak J.; Nikolsky, Ronit; Nicolet, Valérie; Silverman, Jason M (2021)
  • Heikkinen, Liine; Äijälä, Mikko; Dällenbach, Kaspar; Chen, Gang; Garmash, Olga; Aliaga, Diego; Graeffe, Frans; Räty, Meri; Luoma, Krista; Aalto, Pasi; Kulmala, Markku; Petäjä, Tuukka; Worsnop, Douglas; Ehn, Mikael (2021)
  • de Hulster, Izaak J.; Nicolet, Valérie; Nikolsky, Ronit; Silverman, Jason M (2021)
  • Lecaudey, Laurene Alicia; Singh, Pooja; Sturmbauer, Christian; Duenser, Anna; Gessl, Wolfgang; Ahi, Ehsan Pashay (2021)
    BackgroundTeleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on an example of lip hypertrophy in the benthivorous Lake Tangnayika cichlid, Gnathochromis permaxillaris, considered to be a morphological adaptation to extract invertebrates out of the uppermost layer of mud bottom. We investigate the molecular and regulatory basis of lip hypertrophy in G. permaxillaris using a comparative transcriptomic approach.ResultsWe identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in lip formation in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression of foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation, and its function has been associated with hypertrophy of upper lip in human.ConclusionOur results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates. In the future, we advocate integrating gene regulatory networks of various craniofacial phenotypes to understand how they collectively govern trophic and behavioural adaptations.
  • Baalbaki, Rima; Pikridas, Michael; Jokinen, Tuija; Laurila, Tiia; Dada, Lubna; Bezantakos, Spyros; Ahonen, Lauri; Neitola, Kimmo; Maisser, Anne; Bimenyimana, Elie; Christodoulou, Aliki; Unga, Florin; Savvides, Chrysanthos; Lehtipalo, Katrianne; Kangasluoma, Juha; Biskos, George; Petäjä, Tuukka; Kerminen, Veli-Matti; Sciare, Jean; Kulmala, Markku (2021)
    To quantify the contribution of new particle formation (NPF) to ultrafine particle number and cloud condensation nuclei (CCN) budgets, one has to understand the mechanisms that govern NPF in different environments and its temporal extent. Here, we study NPF in Cyprus, an Eastern Mediterranean country located at the crossroads of three continents and affected by diverse air masses originating from continental, maritime, and desert-dust source areas. We performed 1-year continuous measurements of aerosol particles down to similar to 1 nm in diameter for the first time in the Eastern Mediterranean and Middle East (EMME) region. These measurements were complemented with trace gas data, meteorological variables, and retroplume analysis. We show that NPF is a very frequent phenomenon at this site and has higher frequencies of occurrence during spring and autumn. NPF events were both of local and regional origin, and the local events occurred frequently during the month with the lowest NPF frequency. Some NPF events exhibited multiple onsets, while others exhibited apparent particle shrinkage in size. Additionally, NPF events were observed during the nighttime and during episodes of high desert-dust loadings. Particle formation rates and growth rates were comparable to those in rological variables and trace gases played a role in explaining the intra-monthly variability of NPF events, but they did not explain why summer months had the least NPF frequency. Similarly, pre-existing aerosol loading did not explain the observed seasonality. The months with the least NPF frequency were associated with higher H2SO4 concentrations but lower NO2 concentrations, which is an indicator of anthropogenic influence. Air masses arriving from the Middle East were not observed during these months, which could suggest that precursor vapors important for nucleation and growth are transported to our site from the Middle East. Further comprehensive measurements of precursor vapors are required to prove this hypothesis.
  • Töyräänvuori, Joanna (2021)
    This article discusses the iconography of the deified Mediterranean Sea in Syrian glyptic from the Middle and Late Bronze Ages in light of textual evidence from the city of Ugarit (Ras Shamra). Building on the work of Paolo Matthiae in recognizing the visual vocabulary of the representation of the deity, the article argues that the reason for the depiction of the sea god as a winged deity was due to its role as a mediator between the celestial and terrestial oceans in ancient semitic conception. The article also provides a heuristic for separating depictions of the winged sea god from the representations of the winged goddess in the presence of water birds and fish in its visual vocabulary.
  • Blujdea, Viorel N. B.; Viskari, Toni; Kulmala, Liisa; Garbacea, George; Dutca, Ioan; Miclaus, Mihaela; Marin, Gheorghe; Liski, Jari (2021)
    We investigated the effects of forest management on the carbon (C) dynamics in Romanian forest soils, using two model simulations: CBM-CFS3 and Yasso15. Default parametrization of the models and harmonized litterfall simulated by CBM provided satisfactory results when compared to observed data from National Forest Inventory (NFI). We explored a stratification approach to investigate the improvement of soil C prediction. For stratification on forest types only, the NRMSE (i.e., normalized RMSE of simulated vs. NFI) was approximately 26%, for both models; the NRMSE values reduced to 13% when stratification was done based on climate only. Assuming the continuation of the current forest management practices for a period of 50 years, both models simulated a very small C sink during simulation period (0.05 MgC ha(-1) yr(-1)). Yet, a change towards extensive forest management practices would yield a constant, minor accumulation of soil C, while more intensive practices would yield a constant, minor loss of soil C. For the maximum wood supply scenario (entire volume increment is removed by silvicultural interventions during the simulated period) Yasso15 resulted in larger emissions (-0.3 MgC ha(-1) yr(-1)) than CBM (-0.1 MgC ha(-1) yr(-1)). Under 'no interventions' scenario, both models simulated a stable accumulation of C which was, nevertheless, larger in Yasso15 (0.35 MgC ha(-1) yr(-1)) compared to CBM-CSF (0.18 MgC ha(-1) yr(-1)). The simulation of C stock change showed a strong "start-up" effect during the first decade of the simulation, for both models, explained by the difference in litterfall applied to each scenario compared to the spinoff scenario. Stratification at regional scale based on climate and forest types, represented a reasonable spatial stratification, that improved the prediction of soil C stock and stock change.
  • Ahi, Ehsan Pashay; Tsakoumis, Emmanouil; Brunel, Mathilde; Schmitz, Monika (2021)
    The signal mediated by leptin hormone and its receptor is a major regulator of body weight, food intake and metabolism. In mammals and many teleost fish species, leptin has an anorexigenic role and inhibits food intake by influencing the appetite centres in the hypothalamus. However, the regulatory connections between leptin and downstream genes mediating its appetite-regulating effects are still not fully explored in teleost fish. In this study, we used a loss of function leptin receptor zebrafish mutant and real-time quantitative PCR to assess brain expression patterns of several previously identified anorexigenic genes downstream of leptin signal under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-h refeeding). These downstream factors include members of cart genes, crhb and gnrh2, as well as selected genes co-expressed with them based on a zebrafish co-expression database. Here, we found a potential gene expression network (GRN) comprising the abovementioned genes by a stepwise approach of identifying co-expression modules and predicting their upstream regulators. Among the transcription factors (TFs) predicted as potential upstream regulators of this GRN, we found expression pattern of sp3a to be correlated with transcriptional changes of the downstream gene network. Interestingly, the expression and transcriptional activity of Sp3 orthologous gene in mammals have already been implicated to be under the influence of leptin signal. These findings suggest a potentially conserved regulatory connection between leptin and sp3a, which is predicted to act as a transcriptional driver of a downstream gene network in the zebrafish brain.
  • Eriksson, Britas Klemens; Yanos, Casey; Bourlat, Sarah J.; Donadi, Serena; Fontaine, Michael C.; Hansen, Joakim P.; Jakubaviciute, Egle; Kiragosyan, Karine; Maan, Martine E.; Merilä, Juha; Austin, Åsa N.; Olsson, Jens; Reiss, Katrin; Sundblad, Göran; Bergström, Ulf; Eklöf, Johan S. (2021)
    Declines of large predatory fish due to overexploitation are restructuring food webs across the globe. It is now becoming evident that restoring these altered food webs requires addressing not only ecological processes, but evolutionary ones as well, because human-induced rapid evolution may in turn affect ecological dynamics. We studied the potential for niche differentiation between different plate armor phenotypes in a rapidly expanding population of a small prey fish, the three-spined stickleback (Gasterosteus aculeatus). In the central Baltic Sea, three-spined stickleback abundance has increased dramatically during the past decades. The increase in this typical mesopredator has restructured near-shore food webs, increased filamentous algal blooms, and threatens coastal biodiversity. Time-series data covering 22 years show that the increase coincides with a decline in the number of juvenile perch (Perca fluviatilis), the most abundant predator of stickleback along the coast. We investigated the distribution of different stickleback plate armor phenotypes depending on latitude, environmental conditions, predator and prey abundances, nutrients, and benthic production; and described the stomach content of the stickleback phenotypes using metabarcoding. We found two distinct lateral armor plate phenotypes of stickleback, incompletely and completely plated. The proportion of incompletely plated individuals increased with increasing benthic production and decreasing abundances of adult perch. Metabarcoding showed that the stomach content of the completely plated individuals more often contained invertebrate herbivores (amphipods) than the incompletely plated ones. Since armor plates are defense structures favored by natural selection in the presence of fish predators, the phenotype distribution suggests that a novel low-predation regime favors stickleback with less armor. Our results suggest that morphological differentiation of the three-spined stickleback has the potential to affect food web dynamics and influence the persistence and resilience of the stickleback take-over in the Baltic Sea.
  • Ercan, Fabian E. Z.; Mikola, Juha; Silfver, Tarja; Myller, Kristiina; Vainio, Elina; Slowinska, Sandra; Slowinski, Michal; Lamentowicz, Mariusz; Blok, Daan; Wagner-Cremer, Friederike (2021)
    Numerous long-term, free-air plant growth facilities currently explore vegetation responses to the ongoing climate change in northern latitudes. Open top chamber (OTC) experiments as well as the experimental set-ups with active warming focus on many facets of plant growth and performance, but information on morphological alterations of plant cells is still scarce. Here we compare the effects of in-situ warming on leaf epidermal cell expansion in dwarf birch, Betula nana in Finland, Greenland, and Poland. The localities of the three in-situ warming experiments represent contrasting regions of B. nana distribution, with the sites in Finland and Greenland representing the current main distribution in low and high Arctic, respectively, and the continental site in Poland as a B. nana relict Holocene microrefugium. We quantified the epidermal cell lateral expansion by microscopic analysis of B. nana leaf cuticles. The leaves were produced in paired experimental treatment plots with either artificial warming or ambient temperature. At all localities, the leaves were collected in two years at the end of the growing season to facilitate between-site and within-site comparison. The measured parameters included the epidermal cell area and circumference, and using these, the degree of cell wall undulation was calculated as an Undulation Index (UI). We found enhanced leaf epidermal cell expansion under experimental warming, except for the extremely low temperature Greenland site where no significant difference occurred between the treatments. These results demonstrate a strong response of leaf growth at individual cell level to growing season temperature, but also suggest that in harsh conditions other environmental factors may limit this response. Our results provide evidence of the relevance of climate warming for plant leaf maturation and underpin the importance of studies covering large geographical scales.
  • Almeida, Diana Abondano; Mappes, Johanna; Gordon, Swanne (2021)
    Predator-induced plasticity in life-history and antipredator traits during the larval period has been extensively studied in organisms with complex life-histories. However, it is unclear whether different levels of predation could induce warning signals in aposematic organisms. Here, we investigated whether predator-simulated handling affects warning coloration and life-history traits in the aposematic wood tiger moth larva, Arctia plantaginis. As juveniles, a larger orange patch on an otherwise black body signifies a more efficient warning signal against predators but this comes at the costs of conspicuousness and thermoregulation. Given this, one would expect that an increase in predation risk would induce flexible expression of the orange patch. Prior research in this system points to plastic effects being important as a response to environmental changes for life history traits, but we had yet to assess whether this was the case for predation risk, a key driver of this species evolution. Using a full-sib rearing design, in which individuals were reared in the presence and absence of a non-lethal simulated bird attack, we evaluated flexible responses of warning signal size (number of orange segments), growth, molting events, and development time in wood tiger moths. All measured traits except development time showed a significant response to predation. Larvae from the predation treatment developed a more melanized warning signal (smaller orange patch), reached a smaller body size, and molted more often. Our results suggest plasticity is indeed important in aposematic organisms, but in this case may be complicated by the trade-off between costly pigmentation and other life-history traits.
  • Zheng, Guoqiao; Chattopadhyay, Subhayan; Sundquist, Kristina; Sundquist, Jan; Forsti, Asta; Hemminki, Akseli; Hemminki, Kari (2020)
    The increased survival in malignant cutaneous melanoma (melanoma) is probably due to early diagnosis combined with improved treatment most recently. National health campaigns and screening programs for melanoma detection were started in Sweden several decades ago. We want to assess the influence of tumor characteristics, based on the TNM classification, and of second primary cancers on overall survival in melanoma. We used the Swedish Cancer Registry to assess all-cause survival in melanoma from 2003 to 2015. Hazard ratios (HRs) were estimated using multivariable Cox regression models. A total of 19,773 melanoma patients were diagnosed with TNM data. Survival showed a strong improving trend over time (p-trend
  • Demyanenko, Svetlana; Gantsgorn, Elena; Rodkin, Stanislav; Sharifulina, Svetlana (2020)
    Sirtuins, class III histone deacetylases, are involved in the regulation of tissue repair processes and brain functions after a stroke. The ability of some isoforms of sirtuins to circulate between the nucleus and cytoplasm may have various pathophysiological effects on the cells. In present work, we focused on the role of non-mitochondrial sirtuins SIRT1, SIRT2, and SIRT6 in the restoration of brain cells following ischemic stroke. Here, using a photothrombotic stroke (PTS) model in mice, we studied whether local stroke affects the level and intracellular localization of SIRT1, SIRT2, and SIRT6 in neurons and astrocytes of the intact cerebral cortex adjacent to the ischemic ipsilateral hemisphere and in the analogous region of the contralateral hemisphere at different time points during the recovery period after a stroke. We evaluated the co-localization of sirtuins with growth-associated protein-43 (GAP 43), the presynaptic marker synaptophysin (SYN) and acetylated a-tubulin (Aca-Tub), that are associated with brain plasticity and are known to be involved in brain repair after a stroke. The results show that during the recovery period, an increase in SIRT1 and SIRT2 levels occurred. The increase of SIRT1 level was associated with an increase in synaptic plasticity proteins, whereas the increase of SIRT2 level was associated with an acetylated of a-tubulin, that can reduce the mobility of neurites. SIRT6 co-localized with GAP-43, but not with SYN. Moreover, we showed that SIRT1, SIRT2, and SIRT6 are not involved in the PTS-induced apoptosis of pen umbra cells. Taken together, our results suggest that sirtuins functions differ depending on cell type, intracellular localization, specificity of sirtuins isoforms to different substrates and nature of post-translational modifications of enzymes.

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