361 research outputs found
Defective interaction between Pol2p and Dpb2p, subunits of DNA polymerase epsilon, contributes to a mutator phenotype in Saccharomyces cerevisiae.
No full textMost of the prokaryotic and eukaryotic replicative polymerases are multi-subunit complexes. There are several examples indicating that noncatalytic subunits of DNA polymerases may function as fidelity factors during replication process. In this work, we have further investigated the role of Dpb2p, a noncatalytic subunit of DNA polymerase epsilon holoenzyme from Saccharomyces cerevisiae in controlling the level of spontaneous mutagenesis. The data presented indicate that impaired interaction between catalytic Pol2p subunit and Dpb2p is responsible for the observed mutator phenotype in S. cerevisiae strains carrying different mutated alleles of the DPB2 gene. We observed a significant correlation between the decreased level of interaction between different mutated forms of Dpb2p towards a wild-type form of Pol2p and the strength of mutator phenotype that they confer. We propose that structural integrity of the Pol epsilon holoenzyme is essential for genetic stability in S. cerevisiae cells
Työntutkijan vaikutus maastotallentimella mitatun aikatutkimuksen mittaustarkkuuteen hakkuukonesimulaattorihakkuussa
No full textTutkimusselosteSeloste artikkelista: Nuutinen, Y., Väätäinen, K., Heinonen, J., Asikainen, A. & Röser, D. 2008. The accuracy of manually recorded time study data for harvester operation shown via simulator screen. Silva Fennica 42(1): 63–72
VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations
No full textDescription
This package contains a MATLAB toolbox for visual quality evaluation. If you use this software or part of it in your research, we kindly ask that you cite the following paper:
M. Nuutinen, T. Virtanen, O. Rummukainen, J. Häkkinen, "VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations" Behavior Research Methods, 2015, doi:10.3758/s13428-014-0555-y. [pdf].
Documentation
The pdf manual contains introduction to usage of the toolbox and the changelog. The toolbox is provided as is, no other instructions or additional training is not provided.
Download
The Toolbox was developed under Matlab R2012a in Windows 7 environment.
VersionTested Matlab DistributionTested OSFile
V0.1 7.14.0.739 (R2012a) Windows 7
List of our academic studies
Here is a list of our academic studies in which the VQone toolbox has been used for collecting subjective ratings:
Virtanen T., Nuutinen M., Leisti T., Radun J., Häkkinen J. (2015). Alternative performance metrics and target values for the CID2013 database. Proc. of SPIE/IS&T Electronic Imaging 2015, Image Quality and System Performance XII. San Francisco, California, USA, 8.-12.2.2015, [9396-0Q].
Virtanen, T., Nuutinen, M., Vaahteranoksa, M., Oittinen, P. & Häkkinen, J. (2015). CID2013: a database for evaluating no-reference image quality assessment algorithms. IEEE Transactions on Image Processing. 24(1), Pages 390-402.
Nuutinen M., Virtanen T., Leisti T., Mustonen T., Radun J., Häkkinen J. (2014). A new method for evaluating the subjective image quality of photographs: Dynamic Reference, Multimedia Tools and Applications. doi:10.1007/s11042-014-2410-7.
Nuutinen, M., Virtanen, T. & Oittinen, P. (2014). Image feature subsets for predicting the quality of consumer camera images and identifying quality dimensions. Journal of Electronic Imaging, 23(6), 061111.
Radun, J., Leisti, T., Virtanen, T., Nyman, G., & Häkkinen, J. (2014). Why is quality estimation judgment fast? Comparison of gaze control strategies in quality and difference estimation tasks. Journal of Electronic Imaging, 23(6), 061103.
Leisti T., Radun J., Virtanen, T., Nyman G., Häkkinen J. (2014). Explaining can enhance visual decision making. Acta Psychologica 145, Pages 65–74.
Nuutinen, M., Virtanen, T., Valkonen, V., & Oittinen, P. (2013). Automatic exposure and white balance control in video cameras: Time course characterization and preference. Proceedings of the 8th International Symposium on Image and Signal Processing and Analysis 2013, p. 25–29.
Hakola, V. (2013). The Impact of Video Sequence Length and Distortion Position in Perceived Quality. MSc. Thesis, Aalto University School of Science, Degree Programme of Computer Science and Engineering, 2013. 71 pages.
Nuutinen, M., Orenius, O., Säämänen, T., Oittinen, P. (2012). A Framework for Measuring Sharpness in Natural Images Captured by Digital Cameras Based on Reference Image and Local Areas. EURASIP Journal on Image and Video Processing, 2012(8).
Nuutinen, M., Virtanen, T., Oittinen, P. (2012). Features for predicting quality of images captured by digital cameras. Proceedings of the IEEE International Symposium on Multimedia 2012. p. 165-168.
Nuutinen, M., Orenius, O., Säämänen, T., Oittinen, P. (2011). Potential of face area data for predicting sharpness of natural images. Proc. of SPIE/IS&T Electronic Imaging 2011, Image Quality and System Performance VIII. San Francisco, California, USA, 23.-27.1.2011, [7876-36].
Nuutinen, M., Orenius, O., Säämänen, T., Oittinen, P. (2011). Reference image method for measuring quality of photographs produced by digital cameras. Proc. of SPIE/IS&T Electronic Imaging 2011, Image Quality and System Performance VIII. San Francisco, California, USA, 23.-27.1.2011. [7876-22].
Copyright
The VQone software is Copyright © 2014 by Visual Cognition Research Group. Contact: Toni Virtanen, (firstname.lastname ( at ) helsinki.fi).
The software package is free software; you can redistribute it and/or modify it under terms of GNU General Public License as published by the Free Software Foundation. For more details see license at www.gnu.org.
As stated in the GNU General Public License it is not possible to include this software package or even parts of it in a proprietary program without written permission from the owners of the copyright.see our research group website: http://www.helsinki.fi/psychology/groups/visualcognition
Tubulointerstitial nephritis and uveitis syndrome : pathogenesis and long-term prognosis
No full textAbstract
Tubulointerstitial nephritis (TIN) and uveitis (TINU) syndrome are rare inflammatory conditions affecting the kidneys and eyes with uveitis in 30–80% of TIN patients. TIN, characterized by kidney tubulointerstitial inflammation and mostly sparing glomeruli, presents with systemic symptoms like fever, fatigue and malaise along with elevated inflammatory markers and abnormal kidney function as well as low molecular weight proteinuria. TIN may result from various factors, including infections, systemic diseases and medications, and there is some indication about genetic susceptibility to it. Usually, no predisposing factors are identified in children and TIN is considered to be idiopathic and probably of autoimmune origin.
This study focused on the role of inflammatory cytokines and regulatory cells in TIN/TINU syndrome. We identified FOXP3+ regulatory T-cells in kidney biopsies from TIN patients, noting a significant reduction in those TINU patients who had chronic uveitis. This suggests that altered regulatory T-cell dynamics might influence the disease progression. Additionally, our investigation into IL-10 single nucleotide polymorphisms (SNP) revealed an association with increased susceptibility to TINU syndrome, indicating a genetic predisposition.
In our relatively large pediatric cohort, 25% of the TIN/TINU patients exhibited reduced glomerular filtration rate (< 90 mL/min/1.73 m2) at the latest follow-up visit after a median follow-up of 5.7 years, with 24% experiencing relapses during glucocorticoid tapering. Uveitis was diagnosed in 63% of patients and uveitis was chronic in around 40% and persisted in 21% of cases at the latest follow-up visit. Based on our results, we suggest evidence-based follow-up protocols in TIN and TINU syndromes.
In conclusion, our findings suggest that TIN and TINU syndromes involve complex immune mechanisms, with genetic factors like IL-10 polymorphisms playing a role. Despite treatment, the long-term outcomes for pediatric TIN/TINU patients show variability, underlining the need for vigilant monitoring and tailored management strategies. Future research should focus on elucidating the pathomechanisms and on exploring new therapeutic targets. Original papers Rytkönen, S. H., Kulmala, P., Autio-Harmainen, H., Arikoski, P., Endén, K., Kataja, J., Karttunen, T., Nuutinen, M., & Jahnukainen, T. (2018). FOXP3+ T cells are present in kidney biopsy samples in children with tubulointerstitial nephritis and uveitis syndrome. Pediatric Nephrology, 33(2), 287–293. https://doi.org/10.1007/s00467-017-3796-z https://doi.org/10.1007/s00467-017-3796-z Self-archived version Rytkönen, S., Ritari, J., Peräsaari, J., Saarela, V., Nuutinen, M., & Jahnukainen, T. (2019). IL-10 polymorphisms +434T/C, +504G/T, and -2849C/T may predispose to tubulointersititial nephritis and uveitis in pediatric population. PLOS ONE, 14(2), e0211915. https://doi.org/10.1371/journal.pone.0211915 https://doi.org/10.1371/journal.pone.0211915 Self-archived version Rytkönen, S., Tainio, J., Saarela, V., Endén, K., Kataja, J., Arikoski, P., Nuutinen, M., & Jahnukainen, T. (2021). Long-term outcome of biopsy-proven idiopathic tubulointersitial nephritis with or without uveitis in children—A nationwide follow-up study. Pediatric Nephrology, 36(11), 3663–3671. https://doi.org/10.1007/s00467-021-05060-5 https://doi.org/10.1007/s00467-021-05060-5 Self-archived version Tiivistelmä
Tubulointerstitiaalinefriitti (TIN) on munuaisvälikudoksen ja munuaistubulusten tulehdus. TIN-potilaista 30–80 %:lle kehittyy myös silmän suonikalvoston tulehdus, uveiitti (TINU-syndrooma). Oireina esiintyy kuumetta, väsymystä ja pahoinvointia ja laboratoriokokeissa todetaan munuaistoiminnan häiriö sekä viitteitä tulehduksesta. Kaikilla potilailla esiintyy tubulaarista proteinuriaa. TIN voi johtua useista tekijöistä kuten infektioista, systeemisistä sairauksista ja lääkkeistä, ja on viitteitä geneettisestä alttiudesta sairastua TIN:iin. Pääsääntöisesti taudin syntymekanismit ja sille altistavat tekijät ovat kuitenkin tuntemattomia. Yleensä lapsilta ei löydetä altistavia tekijöitä, jolloin TIN katsotaan idiopaattiseksi ja todennäköisesti autoimmuuniperäiseksi.
Tutkimuksemme keskittyi tulehdussytokiinien ja tulehdusta säätelevien solujen rooliin TIN/TINU-oireyhtymässä. Havaitsimme FOXP3+ regulatorisia T-soluja munuaisbiopsioissa kaikilla TIN-potilailla ja niiden merkitsevän vähenemisen kroonista uveiittia sairastavilla potilailla. Tämä viittaa siihen, että regulatoristen T-solujen määrän muutokset voivat vaikuttaa taudin etenemiseen ja kroonistumiseen. Lisäksi tutkimuksemme IL-10-geneettisistä polymorfismeista (SNP) osoitti niiden yhteyden TIN- ja TINU-oireyhtymiin.
Seurantatutkimuksessamme 25 %:lla TIN/TINU-potilaista oli alentunut munuaispuhdistuma (< 90 ml/min/1,73 m2) viimeisellä seurantakäynnillä mediaaniseuranta-ajan ollessa 5,7 vuotta. Tautirelapseja ilmaantui 24 %:lla glukokortikoidihoidon vähentämisen aikana. Uveiitti diagnosoitiin 63 %:lla potilaista, ja uveiitti oli krooninen noin 40 %:lla. Jopa 21 %:lla tapauksista oli edelleen uveiittilöydöksiä viimeisellä raportoidulla seurantakäynnillä. Tuloksiimme pohjautuen teimme näyttöön perustuvan seurantaprotokollan TIN- ja TINU-oireyhtymissä.
Tuloksemme viittaavat siihen, että TIN- ja TINU-oireyhtymiin liittyy monimutkaisia immuunimekanismeja, joissa voivat vaikuttaa geneettiset tekijät, kuten IL-10-polymorfismit. Hoidosta huolimatta TIN/TINU-lapsipotilaiden pitkäaikaistulokset vaihtelevat, mikä korostaa strukturoidun seurannan ja hoitostrategioiden tarpeellisuutta. Tulevaisuudessa tutkimuksen tulisi keskittyä edelleen syntymekanismien selvittämiseen sekä uusien hoitomuotojen tutkimiseen. Osajulkaisut Rytkönen, S. H., Kulmala, P., Autio-Harmainen, H., Arikoski, P., Endén, K., Kataja, J., Karttunen, T., Nuutinen, M., & Jahnukainen, T. (2018). FOXP3+ T cells are present in kidney biopsy samples in children with tubulointerstitial nephritis and uveitis syndrome. Pediatric Nephrology, 33(2), 287–293. https://doi.org/10.1007/s00467-017-3796-z https://doi.org/10.1007/s00467-017-3796-z Rinnakkaistallennettu versio Rytkönen, S., Ritari, J., Peräsaari, J., Saarela, V., Nuutinen, M., & Jahnukainen, T. (2019). IL-10 polymorphisms +434T/C, +504G/T, and -2849C/T may predispose to tubulointersititial nephritis and uveitis in pediatric population. PLOS ONE, 14(2), e0211915. https://doi.org/10.1371/journal.pone.0211915 https://doi.org/10.1371/journal.pone.0211915 Rinnakkaistallennettu versio Rytkönen, S., Tainio, J., Saarela, V., Endén, K., Kataja, J., Arikoski, P., Nuutinen, M., & Jahnukainen, T. (2021). Long-term outcome of biopsy-proven idiopathic tubulointersitial nephritis with or without uveitis in children—A nationwide follow-up study. Pediatric Nephrology, 36(11), 3663–3671. https://doi.org/10.1007/s00467-021-05060-5 https://doi.org/10.1007/s00467-021-05060-5 Rinnakkaistallennettu versio Academic dissertation to be presented with the assent of the Doctoral Programme Committee of Health and Biosciences of the University of Oulu for public defence in Auditorium F202 of the Faculty of Medicine (Aapistie 5 B), on 11 April 2025, at 12 noonAbstract
Tubulointerstitial nephritis (TIN) and uveitis (TINU) syndrome are rare inflammatory conditions affecting the kidneys and eyes with uveitis in 30–80% of TIN patients. TIN, characterized by kidney tubulointerstitial inflammation and mostly sparing glomeruli, presents with systemic symptoms like fever, fatigue and malaise along with elevated inflammatory markers and abnormal kidney function as well as low molecular weight proteinuria. TIN may result from various factors, including infections, systemic diseases and medications, and there is some indication about genetic susceptibility to it. Usually, no predisposing factors are identified in children and TIN is considered to be idiopathic and probably of autoimmune origin.
This study focused on the role of inflammatory cytokines and regulatory cells in TIN/TINU syndrome. We identified FOXP3+ regulatory T-cells in kidney biopsies from TIN patients, noting a significant reduction in those TINU patients who had chronic uveitis. This suggests that altered regulatory T-cell dynamics might influence the disease progression. Additionally, our investigation into IL-10 single nucleotide polymorphisms (SNP) revealed an association with increased susceptibility to TINU syndrome, indicating a genetic predisposition.
In our relatively large pediatric cohort, 25% of the TIN/TINU patients exhibited reduced glomerular filtration rate (< 90 mL/min/1.73 m2) at the latest follow-up visit after a median follow-up of 5.7 years, with 24% experiencing relapses during glucocorticoid tapering. Uveitis was diagnosed in 63% of patients and uveitis was chronic in around 40% and persisted in 21% of cases at the latest follow-up visit. Based on our results, we suggest evidence-based follow-up protocols in TIN and TINU syndromes.
In conclusion, our findings suggest that TIN and TINU syndromes involve complex immune mechanisms, with genetic factors like IL-10 polymorphisms playing a role. Despite treatment, the long-term outcomes for pediatric TIN/TINU patients show variability, underlining the need for vigilant monitoring and tailored management strategies. Future research should focus on elucidating the pathomechanisms and on exploring new therapeutic targets.Tiivistelmä
Tubulointerstitiaalinefriitti (TIN) on munuaisvälikudoksen ja munuaistubulusten tulehdus. TIN-potilaista 30–80 %:lle kehittyy myös silmän suonikalvoston tulehdus, uveiitti (TINU-syndrooma). Oireina esiintyy kuumetta, väsymystä ja pahoinvointia ja laboratoriokokeissa todetaan munuaistoiminnan häiriö sekä viitteitä tulehduksesta. Kaikilla potilailla esiintyy tubulaarista proteinuriaa. TIN voi johtua useista tekijöistä kuten infektioista, systeemisistä sairauksista ja lääkkeistä, ja on viitteitä geneettisestä alttiudesta sairastua TIN:iin. Pääsääntöisesti taudin syntymekanismit ja sille altistavat tekijät ovat kuitenkin tuntemattomia. Yleensä lapsilta ei löydetä altistavia tekijöitä, jolloin TIN katsotaan idiopaattiseksi ja todennäköisesti autoimmuuniperäiseksi.
Tutkimuksemme keskittyi tulehdussytokiinien ja tulehdusta säätelevien solujen rooliin TIN/TINU-oireyhtymässä. Havaitsimme FOXP3+ regulatorisia T-soluja munuaisbiopsioissa kaikilla TIN-potilailla ja niiden merkitsevän vähenemisen kroonista uveiittia sairastavilla potilailla. Tämä viittaa siihen, että regulatoristen T-solujen määrän muutokset voivat vaikuttaa taudin etenemiseen ja kroonistumiseen. Lisäksi tutkimuksemme IL-10-geneettisistä polymorfismeista (SNP) osoitti niiden yhteyden TIN- ja TINU-oireyhtymiin.
Seurantatutkimuksessamme 25 %:lla TIN/TINU-potilaista oli alentunut munuaispuhdistuma (< 90 ml/min/1,73 m2) viimeisellä seurantakäynnillä mediaaniseuranta-ajan ollessa 5,7 vuotta. Tautirelapseja ilmaantui 24 %:lla glukokortikoidihoidon vähentämisen aikana. Uveiitti diagnosoitiin 63 %:lla potilaista, ja uveiitti oli krooninen noin 40 %:lla. Jopa 21 %:lla tapauksista oli edelleen uveiittilöydöksiä viimeisellä raportoidulla seurantakäynnillä. Tuloksiimme pohjautuen teimme näyttöön perustuvan seurantaprotokollan TIN- ja TINU-oireyhtymissä.
Tuloksemme viittaavat siihen, että TIN- ja TINU-oireyhtymiin liittyy monimutkaisia immuunimekanismeja, joissa voivat vaikuttaa geneettiset tekijät, kuten IL-10-polymorfismit. Hoidosta huolimatta TIN/TINU-lapsipotilaiden pitkäaikaistulokset vaihtelevat, mikä korostaa strukturoidun seurannan ja hoitostrategioiden tarpeellisuutta. Tulevaisuudessa tutkimuksen tulisi keskittyä edelleen syntymekanismien selvittämiseen sekä uusien hoitomuotojen tutkimiseen
Gas-Phase Ion-Molecule Reactions Between a Series of Protonated Diastereomeric Cavitands and Neutral Amines Studied by ESI-FTICRMS: Gas-Phase Inclusion Complex Formation
No full textScience Capital: Results from a Finnish Population Survey
No full textThis project is created for storing the materials, data and analysis code of the Finnish Science Capital Population Survey 2021 reported in Kaakinen, J. K., Havu-Nuutinen, S., Häikiö, T., Julku, H., Koskela, T., Mikkilä-Erdmann, M., ... & Wikström, V. (2025). Science capital: Results from a Finnish population survey. Public Understanding of Science, https://doi.org/10.1177/0963662524131075
Biliary alpha 1-acid glycoprotein concentrations in gallstone-free controls and in patients with multiple or solitary cholesterol gallstones.
No full textAbstract: We recently identified a promoting glycoprotein in the concanavalin A-bound fraction of gallbladder bile as a biliary form of alpha 1-acid glycoprotein (AAG), The concentration of biliary AAG appears to exert an important promoting effect on the speed of cholesterol nucleation in many patients with cholesterol gallstone disease, In the current study, we provide information about the biliary concentration of AAG as well as the amount and comparative potency of its subfractions in patients with and without cholesterol gallstone disease, The amount of total biliary AAG and the amounts of its different isoforms separated by concanavalin A affinity chromatography were measured by ELISA, Estimates of absolute concentrations of AAG for each sample were normalized to the sample total protein content to give relative AAG values. The promoting activity (potency) of immunopurified biliary AAG from gallstone patients and gallstone-free controls on cholesterol crystallization was compared by a crystal growth assay. The mean absolute concentration of AAG in gallstone-free controls was not significantly different from multiple stone patients. The relative concentration of AAG (micrograms per milligram total protein) was significantly increased in patients with multiple stones when compared to controls (P < 0.05), and both the absolute and relative concentrations of AAG (micrograms per milligram bile), were three- and to five fold higher in a number of these patients. The functional activity and distribution of AAG in different subfractions was similar in gallstone patients and gallstone-free controls, The relative concentration of biliary AAG is significantly greater in cholesterol gallstone patients with multiple stones than in gallstone-free controls, These observations suggest that raised levels of AAG may be of pathogenetic importance in a subgroup of patients with multiple gallstones
Techno-Economic Comparative Analysis of Innovative Combined Cycle Power Plant Layouts Integrated With Heat Pumps and Thermal Energy Storage
No full textIn the pursuit of increasing their profitability, the design and operation of combined cycle power plants needs to be optimized for new liberalized markets with large penetration of renewables. A clear consequence of such renewable integration is the need for these plants for being more flexible in terms of ramping-up periods and higher part-load efficiencies. Flexibility becomes an even clearer need for combined heat and power plants to be more competitive, particularly when simultaneously following the market hourly price dynamics and varying demands for both the heat and the electricity markets. In this paper, three new plant layouts have been investigated by integrating different storage concepts and heat-pump units in key sections of a traditional plant layout. The study analyses the influence that market has on determining the optimum layouts for maximizing profits in energy-only markets (in terms of plant configuration, sizing and operation strategies). The study is performed for a given location nearby Turin, Italy, for which hourly electricity and heat prices, as well as meteorological data, have been gathered. A multi parameter modeling approach was followed using KTH's in house teclmo-economic modeling tool, which uses time dependent market data, e.g. price and weather, to determine the trade-off curves between minimizing investment and maximizing profits when varying critical size-related power plant parameters e.g. installed power capacities and storage size, for pre-defined layouts and operating strategies. A comparative analysis between the best configurations found for each of the proposed layouts and the reference plant is presented in the discussion section of the results. For the specific case study set in northern Italy, it is shown that the integration of a pre-cooling loop into baseload-like power-oriented combined cycle plants is not justified, calling for investigating new markets and different operating strategies. Only the integration of a heat pump alone was shown to improve the profitability, but within the margin of error of the study. Alternatively, a layout where district heating supply water is preheated with a combination of a heat pump with hot thermal tank was able to increase the internal rate of return of the plant by up to 0.5%, absolute, yet within the error margin and thus not justifying the added complexity in operation and in investment costs. All in all, the analysis shows that even when considering energy-only market revenue streams (i.e. heat and electricity sells) the integration of heat pump and storage units could increase the profitability of plants by making them more flexible in terms of power output levels and load variations. The latter is shown true even when excluding other flexibilityrelated revenue streams. It is therefore conclusively suggested to further investigate the proposed layouts in markets with larger heat and power price variations, as well as to investigate the impact of additional control logics and dispatch strategies.</p
Demo Report 4 - Efficiency of integrated grinding and screening of stump wood for fuel at roadside landing with a Crambo 6000 grinder equipped with a star screen. Julkaisussa:
No full textALPHA(1)-ACID GLYCOPROTEIN (AAG) AS A PROMOTER OF CHOLESTEROL CRYSTALLIZATION IN GALLSTONE DISEASE - CORRELATION BETWEEN THE CONCENTRATION OF AAG AND NUCLEATION TIME
No full text- …
