Browsing by Subject "LONG-TERM"

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  • Varendi, Kärt; Mätlik, Kert; Andressoo, Jaan-Olle (2015)
    During the past decade, the identification of microRNA (miR) targets has become common laboratory practice, and various strategies are now used to detect interactions between miRs and their mRNA targets. However, the current lack of a standardized identification process often leads to incomplete and/or conflicting results. Here, we review the problems most commonly encountered when verifying miR-mRNA interactions, and we propose a workflow for future studies. To illustrate the challenges faced when validating a miR target, we discuss studies in which the regulation of brain-derived neurotrophic factor by miRs was investigated, and we highlight several controversies that emerged from these studies. Finally, we discuss the therapeutic use of miR inhibitors, and we discuss several questions that should be addressed before proceeding to preclinical testing.
  • Lan, Hangzhen; Holopainen, Jani; Hartonen, Kari; Jussila, Matti; Ritala, Mikko; Riekkola, Marja-Liisa (2019)
    Comprehensive and time-dependent information (e.g., chemical composition, concentration) of volatile organic compounds (VOCs) in atmospheric, indoor, and breath air is essential to understand the fundamental science of the atmosphere, air quality, and diseases diagnostic. Here, we introduced a fully automated online dynamic in-tube extraction (ITEX)-gas chromatography/mass spectrometry (GC/MS) method for continuous and quantitative monitoring of VOCs in air. In this approach, modified Cycle Composer software and a PAL autosampler controlled and operated the ITEX preconditioning, internal standard (ISTD) addition, air sampling, and ITEX desorption sequentially to enable full automation. Air flow passed through the ITEX with the help of an external pump, instead of plunger up-down strokes, to allow larger sampling volumes, exhaustive extraction, and consequently lower detection limits. Further, in order to evaluate the ITEX system stability and to develop the corresponding quantitative ITEX method, two laboratory-made permeation systems (for standard VOCs and ISTD) were constructed. The stability and suitability of the developed system was validated with a consecutive 19 day atmospheric air campaign under automation. By using an electrospun polyacrylonitrile nanofibers packed ITEX, selective extraction of some VOCs and durability of over 1500 extraction and desorption cycles were achieved. Especially, the latter step is critically important for on-site long-term application at remote regions. This ITEX method provided 2-3 magnitudes lower quantitation limits than the headspace dynamic ITEX method and other needle trap methods. Our results proved the excellence of the fully automated online dynamic ITEX-GC/MS system for tracking VOCs in the atmospheric air.
  • Mikola, Juha; Koikkalainen, Katariina; Rasehorn, Mira; Silfver, Tarja; Paaso, Ulla; Rousi, Matti (2021)
    Fast-growing and slow-growing plant species are suggested to show integrated economics spectrums and the tradeoffs of fast growth are predicted to emerge as susceptibility to herbivory and resource competition. We tested if these predictions also hold for fast-growing and slow-growing genotypes within a silver birch, Betula pendula population. We exposed cloned saplings of 17 genotypes with slow, medium or fast height growth to reduced insect herbivory, using an insecticide, and to increasing resource competition, using naturally varying field plot grass cover. We measured shoot and root growth, ectomycorrhizal (EM) fungal production using ergosterol analysis and soil N transfer to leaves using N-15-labelled pulse of NH4+. We found that fast-growing genotypes grew on average 78% faster, produced 56% and 16% more leaf mass and ergosterol, and showed 78% higher leaf N uptake than slow-growing genotypes. The insecticide decreased leaf damage by 83% and increased shoot growth, leaf growth and leaf N uptake by 38%, 52% and 76%, without differences between the responses of fast-growing and slow-growing genotypes, whereas root mass decreased with increasing grass cover. Shoot and leaf growth of fast-growing genotypes decreased and EM fungal production of slow-growing genotypes increased with increasing grass cover. Our results suggest that fast growth is genotypically associated with higher allocation to EM fungi, better soil N capture and greater leaf production, and that the tradeoff of fast growth is sensitivity to competition, but not to insect herbivory. EM fungi may have a dual role: to support growth of fast-growing genotypes under low grass competition and to maintain growth of slow-growing genotypes under intensifying competition.
  • Ruuska, Satu Maria; Laaperi, Mitja Tapani; Hukkinen, Maria; Jalanko, Hannu; Kolho, Kaija-Leena; Pakarinen, Mikko P. (2019)
    We addressed growth of biliary atresia (BA) patients living with native livers between ages 0-6 and effects of post-surgical corticosteroid treatment on growth. Growth charts of 28 BA patients born in Finland between 1987 and 2017 were retrospectively evaluated. Dosage and length of corticosteroid treatment and hydrocortisone substitution were reviewed. At birth, BA patients were shorter (median height -0.6 (interquartile range (IQR) -1.3 to -0.1) SDS, n=28, P
  • Manninen, Hanna E.; Mirme, Sander; Mirme, Aadu; Petäjä, Tuukka; Kulmala, Markku (2016)
    To understand the very first steps of atmospheric particle formation and growth processes, information on the size where the atmospheric nucleation and cluster activation occurs, is crucially needed. The current understanding of the concentrations and dynamics of charged and neutral clusters and particles is based on theoretical predictions and experimental observations. This paper gives a standard operation procedure (SOP) for Neutral cluster and Air Ion Spectrometer (NAIS) measurements and data processing. With the NAIS data, we have improved the scientific understanding by (1) direct detection of freshly formed atmospheric clusters and particles, (2) linking experimental observations and theoretical framework to understand the formation and growth mechanisms of aerosol particles, and (3) parameterizing formation and growth mechanisms for atmospheric models. The SOP provides tools to harmonize the world-wide measurements of small clusters and nucleation mode particles and to verify consistent results measured by the NAIS users. The work is based on discussions and interactions between the NAIS users and the NAIS manufacturer.
  • Haggblom, Olle; Salo, Heidi; Turunen, Mika; Nurminen, Jyrki; Alakukku, Laura; Myllys, Merja; Koivusalo, Harri (2019)
    In northern clay soils, field drainage is needed to ensure suitable moisture conditions for crop growth and farming operations. Supplementary drainage installations improve the efficiency of old drainage systems, but the hydrological impacts of the drainage procedures are not comprehensively understood or quantified. The objective was to simulate the hydrological behavior of a clay field section and to quantify the effects of a supplementary drainage on the water balance of the field section. The study site, in southern Finland, was originally subsurface drained in 1952 with 32 m drain spacing. Supplementary drainage was installed in 2014, decreasing the drain spacing to 10.7 m. Simulations were carried out with a dual-permeability hydrological model and two model parametrizations describing the field hydrology (1) before and (2) after the supplementary drainage installation. The parameterizations were used for simulations of a nine-year period to quantify the hydrological impacts of the supplementary drainage. For the periods without snow on the ground, the modified Nash-Sutcliffe efficiency for daily drain discharge and topsoil layer runoff values ranged from 0.43 to 0.53 and from 0.44 to 0.53, respectively. During the original drainage setup scenario, the average annual drain discharge was lower (7.8% of precipitation) than topsoil layer runoff and groundwater outflow (10.3% and 26.4%, respectively). For the supplementary drainage scenario, most of the water outflow was through drain discharge and groundwater outflow (20.4% and 21.9%, respectively). The supplementary drainage installation increased the average annual drain discharge by a factor of 2.6, while the annual average topsoil layer runoff and groundwater outflow decreased by 75% and 18%, respectively. The supplementary drainage setup was found to expedite the drying of the field section in spring by 8 days on average compared to the original drainage setup.
  • Sun, Weilun; Suzuki, Kunimichi; Toptunov, Dmytro; Stoyanov, Stoyan; Yuzaki, Michisuke; Khiroug, Leonard; Dilyatev, Alexander (2019)
    Two-photon imaging of fluorescently labeled microglia in vivo provides a direct approach to measure motility of microglial processes as a readout of microglial function that is crucial in the context of neurodegenerative diseases, as well as to understand the neuroinflammatory response to implanted substrates and brain-computer interfaces. In this longitudinal study, we quantified surveilling and photodamage-directed microglial processes motility in both acute and chronic cranial window preparations and compared the motility under isoflurane and ketamine anesthesia to an awake condition in the same animal. The isoflurane anesthesia increased the length of surveilling microglial processes in both acute and chronic preparations, while ketamine increased the number of microglial branches in acute preparation only. In chronic (but not acute) preparation, the extension of microglial processes toward the laser-ablated microglial cell was faster under isoflurane (but not ketamine) anesthesia than in awake mice, indicating distinct effects of anesthetics and of preparation type. These data reveal potentiating effects of isoflurane on microglial response to damage, and provide a framework for comparison and optimal selection of experimental conditions for quantitative analysis of microglial function using two-photon microscopy in vivo.
  • Salmi, Samuli J.; Nieminen, Tuomo; Hartikainen, Juha; Biancari, Fausto; Lehto, Joonas; Nissinen, Maunu; Malmberg, Markus; Yannopoulos, Fredrik; Savolainen, Jyri; Airaksinen, Juhani; Kiviniemi, Tuomas (2020)
    OBJECTIVES: We sought to study the indications, long-term occurrence, and predictors of permanent pacemaker implantation (PPI) after isolated surgical aortic valve replacement with bioprostheses. METHODS: The CAREAVR study included 704 patients (385 females, 54.7%) without a preoperative PPI (mean +/- standard deviation age 75 +/- 7years) undergoing isolated surgical aortic valve replacement at 4 Finnish hospitals between 2002 and 2014. Data were extracted from electronic patient records. RESULTS: The follow-up was median 4.7years (range 1day to 12.3years). Altogether 56 patients received PPI postoperatively, with the median 507days from the operation (range 6days to 10.0years). The PPI indications were atrioventricular block (31 patients, 55%) and sick sinus syndrome (21 patients, 37.5%). For 4 patients, the PPI indication remained unknown. A competing risks regression analysis (Fine-Gray method), adjusted with age, sex, diabetes, coronary artery disease, preoperative atrial fibrillation (AF), left ventricular ejection fraction, New York Heart Association class, AF at discharge and urgency of operation, was used to assess risk factors for PPI. Only AF at discharge (subdistribution hazard ratio 4.34, 95% confidence interval 2.34-8.03) was a predictor for a PPI. CONCLUSIONS: Though atrioventricular block is the major indication for PPI after surgical aortic valve replacement, >30% of PPIs are implanted due to sick sinus syndrome during both short-term follow-up and long-term follow-up. Postoperative AF versus sinus rhythm conveys >4-fold risk of PPI.
  • Arzel, Celine; Nummi, Petri; Arvola, Lauri; Pöysä, Hannu; Davranche, Aurélie; Rask, Martti; Olin, Mikko; Holopainen, Sari; Viitala, Risto; Einola, Eeva; Manninen-Johansen, Sanni (2020)
    Surface water browning affects boreal lakes in the Northern Hemisphere. This process is expected to increase with global warming. Boreal lakes are the most numerous lakes on Earth. These ecosystems are particularly sensitive to disturbances due to their low biodiversity compared to other aquatic environments. The recent darkening of surface water is expected to hinder key ecosystem processes, particularly through lower primary productivity and loss of biodiversity. However, studies based on long-term data collections have rarely been conducted on the ecological consequences of water browning on aquatic food webs, especially concerning its impacts on invertebrate communities. For the first time, our analysis based on two decades of data collection in Finnish lakes highlighted a relation between water browning and a decline in aquatic macroinvertebrate abundances. Aquatic invertebrates are the main food resource for many secondary predators such as fish and waterbirds, hence such effect on their populations may have major consequences for boreal ecosystem functioning.
  • Turkia, Tytti; Jousimo, Jussi; Tiainen, Juha; Helle, Pekka; Rintala, Jukka; Hokkanen, Tatu; Valkama, Jari; Selonen, Vesa (2020)
    Spatial synchrony between populations emerges from endogenous and exogenous processes, such as intra- and interspecific interactions and abiotic factors. Understanding factors contributing to synchronous population dynamics help to better understand what determines abundance of a species. This study focuses on spatial and temporal dynamics in the Eurasian red squirrel (Sciurus vulgaris) using snow-track data from Finland from 29 years. We disentangled the effects of bottom-up and top-down forces as well as environmental factors on population dynamics with a spatiotemporally explicit Bayesian hierarchical approach. We found red squirrel abundance to be positively associated with both the abundance of Norway spruce (Picea abies) cones and the predators, the pine marten (Martes martes) and the northern goshawk (Accipiter gentilis), probably due to shared habitat preferences. The results suggest that red squirrel populations are synchronized over remarkably large distances, on a scale of hundreds of kilometres, and that this synchrony is mainly driven by similarly spatially autocorrelated spruce cone crop. Our research demonstrates how a bottom-up effect can drive spatial synchrony in consumer populations on a very large scale of hundreds of kilometres, and also how an explicit spatiotemporal approach can improve model performance for fluctuating populations.
  • Tanislav, Christian; Grittner, Ulrike; Misselwitz, Bjoern; Jungehuelsing, Gerhard Jan; Enzinger, Christian; von Sarnowski, Bettina; Putaala, Jukka; Kaps, Manfred; Kropp, Peter; Rolfs, Arndt; Tatlisumak, Turgut; Fazekas, Franz; Kolodny, Edwin; Norrving, Bo (2014)
  • Rose, C.; Sellegri, K.; Asmi, E.; Hervo, M.; Freney, E.; Colomb, A.; Junninen, H.; Duplissy, J.; Sipilä, Mikko; Kontkanen, J.; Lehtipalo, K.; Kulmala, Markku (2015)
    The formation of new aerosol particles in the atmosphere is a key process influencing the aerosol number concentration as well as the climate, in particular at high altitude, where the newly formed particles directly influence cloud formation. However, free tropospheric new particle formation (NPF) is poorly documented due to logistic limitations and complex atmospheric dynamics around high-altitude stations that make the observation of this day-time process challenging. Recent improvements in measurement techniques make now possible the detection of neutral clusters down to similar to 1 nm sizes, which opens new horizons in our understanding of the nucleation process. Indeed, only the charged fraction of clusters has been reported in the upper troposphere up to now. Here we report day-time concentrations of charged and neutral clusters (1 to 2.5 nm mobility diameter) recorded at the interface between the boundary layer (BL) and the FT as well as in the FT at the altitude site of Puy de Dome (1465 m a.s.l.), central France, between 10 and 29 February 2012. Our findings demonstrate that in the FT, and especially at the interface between the BL and the FT, the formation of 1.5 nm neutral clusters significantly exceeds the one of ionic clusters during NPF events, clearly indicating that they dominate in the nucleation process. We also observe that the total cluster concentration significantly increases during NPF events compared to the other days, which was not clearly observed for the charged cluster population in the past. During the studied period, the nucleation process does not seem to be sulfuric acid-limited and could be promoted by the transport of pollutants to the upper troposphere, coupled with low temperatures.
  • Qi, Ximeng; Ding, Aijun; Roldin, Pontus; Xu, Zhengning; Zhou, Putian; Sarnela, Nina; Nie, Wei; Huang, Xin; Rusanen, Anton; Ehn, Mikael; Rissanen, Matti P.; Petäjä, Tuukka; Kulmala, Markku; Boy, Michael (2018)
    Highly oxygenated multifunctional compounds (HOMs) play a key role in new particle formation (NPF), but their quantitative roles in different environments of the globe have not been well studied yet. Frequent NPF events were observed at two "flagship" stations under different environmental conditions, i.e. a remote boreal forest site (SMEAR II) in Finland and a suburban site (SORPES) in polluted eastern China. The averaged formation rate of 6 nm particles and the growth rate of 6-30 nm particles were 0.3 cm(-3) s(-1) and 4.5 nm h(-1) at SMEAR II compared to 2.3 cm(-3) s(-1) and 8.7 nm h(-1) at SORPES, respectively. To explore the differences of NPF at the two stations, the HOM concentrations and NPF events at two sites were simulated with the MALTE-BOX model, and their roles in NPF and particle growth in the two distinctly different environments are discussed. The model provides an acceptable agreement between the simulated and measured concentrations of sulfuric acid and HOMs at SMEAR II. The sulfuric acid and HOM organonitrate concentrations are significantly higher but other HOM monomers and dimers from monoterpene oxidation are lower at SORPES compared to SMEAR II. The model simulates the NPF events at SMEAR II with a good agreement but underestimates the growth of new particles at SORPES, indicating a dominant role of anthropogenic processes in the polluted environment. HOMs from monoter-pene oxidation dominate the growth of ultrafine particles at SMEAR II while sulfuric acid and HOMs from aromatics oxidation play a more important role in particle growth. This study highlights the distinct roles of sulfuric acid and HOMs in NPF and particle growth in different environmental conditions and suggests the need for molecular-scale measurements in improving the understanding of NPF mechanisms in polluted areas like eastern China.
  • Velmala, William; Helle, Samuli; Ahola, Markus P.; Klaassen, Marcel; Lehikoinen, Esa; Rainio, Kalle; Sirkiä, Päivi; Laaksonen, Toni (2015)
    For migratory birds, the earlier arrival of males to breeding grounds is often expected to have fitness benefits. However, the selection differential on male arrival time has rarely been decomposed into the direct effect of male arrival and potential indirect effects through female traits. We measured the directional selection differential on male arrival time in the pied flycatcher (Ficedula hypoleuca) using data from 6years and annual number of fledglings as the fitness proxy. Using structural equation modeling, we were able to take into account the temporal structure of the breeding cycle and the hierarchy between the examined traits. We found directional selection differentials for earlier male arrival date and earlier female laying date, as well as strong selection differential for larger clutch size. These selection differentials were due to direct selection only as indirect selection for these traits was nonsignificant. When decomposing the direct selection for earlier male arrival into direct and indirect effects, we discovered that it was almost exclusively due to the direct effect of male arrival date on fitness and not due to its indirect effects via female traits. In other words, we showed for the first time that there is a direct effect of male arrival date on fitness while accounting for those effects that are mediated by effects of the social partner. Our study thus indicates that natural selection directly favored earlier male arrival in this flycatcher population.
  • Castren, Eero; Hen, Rene (2013)
  • Valtonen, Jussi; Gregory, Emma; Landau, Barbara; McCloskey, Michael (2014)
  • Hukkinen, Maria; Lohi, Jouko; Heikkilä, Päivi; Kivisaari, Reetta; Jahnukainen, Timo; Jalanko, Hannu; Pakarinen, Mikko P. (2019)
    We investigated noninvasive follow-up markers for histologic liver fibrosis and portal hypertension (PH) in patients with biliary atresia after successful portoenterostomy (PE). Among children with bilirubin 11 mu mol/L in the youngest tertile (AUROC, 0.91; P <0.001), bile acids was >80 mu mol/L in the middle tertile (AUROC, 0.81; P = 0.009), and liver stiffness was >24 kPa in the oldest age tertile (AUROC, 0.96; P = 0.002). Conclusion: After successful PE, development of PH associates with progression of liver fibrosis and can be accurately detected by APRI and stiffness. Liver stiffness most accurately identified cirrhosis in older children, whereas biochemical markers of cholestasis closely reflected histologic cirrhosis in younger children.
  • Pryazhnikov, Evgeny; Kislin, Mikhail; Tibeykina, Marina; Toptunov, Dmytro; Ptukha, Anna; Shatillo, Artem; Gröhn, Olli; Giniatullin, Rashid; Khiroug, Leonard (2014)
  • Janket, Sok-Ja; Benwait, Jaspreet; Isaac, Paul; Ackerson, Leland K.; Meurman, Jukka H. (2019)
    Recent results of randomized trials testing the efficacy of xylitol in caries prevention have been conflicting. This narrative review reveals the sources of discrepancy. The following databases were searched for the terms xylitol or artificial sweeteners restricted to the English language: PubMed, Web of Science, Evidenced-Based Medicine, Scopus, and the Cochrane database. In a separate search, the terms dental caries or cariogenicity or glucosyltransferase or low glycemic or low insulinemic or dysbiosis or gut microbiome were used and then combined. In section I, findings regarding the role of xylitol in dental caries prevention, the appropriateness of research methods, and the causes for potential biases are summarized. In section II, the systemic effects of xylitol on gut microbiota as well as low-glycemic/insulinogenic systemic effects are evaluated and summarized. The substitution of a carbonyl group with an alcohol radical in xylitol hinders its absorption and slowly releases sugar into the bloodstream. This quality of xylitol is beneficial for diabetic patients to maintain a constant glucose level. Although this quality of xylitol has been proven in in vitro and animal studies, it has yet to be proven in humans. Paradoxically, recent animal studies reported hyperglycemia and intestinal dysbiosis with artificial sweetener consumption. Upon careful inspection of evidence, it was revealed that these reports may be due to misinterpretation of original references or flaws in study methodology. Any systemic benefits of xylitol intake must be weighed in consideration with the well-established adverse gastrointestinal consequences. The contribution of xylitol to gut dysbiosis that may affect systemic immunity warrants further research.
  • Kajosaari, Lauri; Pennanen, Juhani; Klockars, Tuomas (2017)
    Introduction: Prominent ears are seen in approximately 5% of the population. This benign condition can be treated surgically to reduce or prevent psychological and social problems, most commonly in children before the start of school. Our aim was to examine the demographic characteristics of patients undergoing prominent ear surgery in Finland, and compare findings with international data. Methods: A retrospective study of all the patients treated for prominent ears in our academic tertiary care referral center during 2007-2011 was performed to gather demographic details of operated patients. A systematic review of published series of prominent ear surgery after the year 2000 was performed to gather demographic details for international comparison. Results: A total of 180 patients were operated in our institution for prominent ears, most of the cases (78.9%) were bilateral. Age at operation ranged between 3 and 36 years, with mean of 9.2 y and median of 7 y. The most common reason for seeking operative treatment was aesthetic complaint, followed by bullying. Review process gathered 20 publications, describing a total of 4433 patients who had been operated for prominent ears. There was wide variation the mean age at operation, ranging 7-38 y while the mean overall was 15.0y. Gender distribution of patient samples was also very variable, with percentage of females ranging from 38 to 71% (overall 52%). There was also considerable variation in the tendency to perform unilateral operations: from 0% up to 21% of the reported population. There were no statistically significant correlations linking these demographic variables, though there was a trend that females are more likely to have this operation performed at an older age. Conclusions: The treatment culture of prominent ear surgery varies substantially in international comparison. The age at which this operation is performed showed most variation. Omitting some of the basic demographic variables while reporting the results of surgery was common in the reviewed publications. (C) 2017 Published by Elsevier Ireland Ltd.