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Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media.

mSphere

Sillanpää S, Kramna L, Oikarinen S, Sipilä M, Rautiainen M, Aittoniemi J, Laranne J, Hyöty H, Cinek O.
PMID: 28357413
mSphere. 2017 Mar 22;2(2). doi: 10.1128/mSphere.00006-17. eCollection 2017.

The aim of the study was to analyze the bacteriome of acute otitis media with a novel modification of next-generation sequencing techniques. Outpatient children with acute otitis media were enrolled in the study, and middle ear fluids were collected...

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Sillanpää S, Kramna L, Oikarinen S, et al. Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media. mSphere. 2017;2(2)doi: 10.1128/mSphere.00006-17.
Sillanpää, S., Kramna, L., Oikarinen, S., Sipilä, M., Rautiainen, M., Aittoniemi, J., Laranne, J., Hyöty, H., & Cinek, O. (2017). Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media. mSphere, 2(2), . https://doi.org/10.1128/mSphere.00006-17
Sillanpää, Saara, et al. "Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media." mSphere vol. 2,2 (2017). doi: https://doi.org/10.1128/mSphere.00006-17
Sillanpää S, Kramna L, Oikarinen S, Sipilä M, Rautiainen M, Aittoniemi J, Laranne J, Hyöty H, Cinek O. Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media. mSphere. 2017 Mar 22;2(2). doi: 10.1128/mSphere.00006-17. eCollection 2017. PMID: 28357413; PMCID: PMC5362748.
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Milk Products Containing Bioactive Tripeptides Have an Antihypertensive Effect in Double Transgenic Rats (dTGR) Harbouring Human Renin and Human Angiotensinogen Genes.

Journal of nutrition and metabolism

Jauhiainen T, Pilvi T, Cheng ZJ, Kautiainen H, Müller DN, Vapaatalo H, Korpela R, Mervaala E.
PMID: 20721338
J Nutr Metab. 2010;2010. doi: 10.1155/2010/287030. Epub 2009 Nov 30.

Tripeptides isoleucyl-prolyl-proline (IPP) and valyl-prolyl-proline (VPP) act as ACE inhibitors in vitro. Double transgenic rats (dTGR) harbouring human renin and human angiotensinogen genes develop malignant hypertension due to increased angiotensin II formation. The present study was aimed to evaluate...

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Jauhiainen T, Pilvi T, Cheng ZJ, et al. Milk Products Containing Bioactive Tripeptides Have an Antihypertensive Effect in Double Transgenic Rats (dTGR) Harbouring Human Renin and Human Angiotensinogen Genes. J Nutr Metab. 2009;2010doi: 10.1155/2010/287030.
Jauhiainen, T., Pilvi, T., Cheng, Z. J., Kautiainen, H., Müller, D. N., Vapaatalo, H., Korpela, R., & Mervaala, E. (2010). Milk Products Containing Bioactive Tripeptides Have an Antihypertensive Effect in Double Transgenic Rats (dTGR) Harbouring Human Renin and Human Angiotensinogen Genes. Journal of nutrition and metabolism, 2010. https://doi.org/10.1155/2010/287030
Jauhiainen, Tiina, et al. "Milk Products Containing Bioactive Tripeptides Have an Antihypertensive Effect in Double Transgenic Rats (dTGR) Harbouring Human Renin and Human Angiotensinogen Genes." Journal of nutrition and metabolism vol. 2010 (2010). doi: https://doi.org/10.1155/2010/287030
Jauhiainen T, Pilvi T, Cheng ZJ, Kautiainen H, Müller DN, Vapaatalo H, Korpela R, Mervaala E. Milk Products Containing Bioactive Tripeptides Have an Antihypertensive Effect in Double Transgenic Rats (dTGR) Harbouring Human Renin and Human Angiotensinogen Genes. J Nutr Metab. 2010;2010. doi: 10.1155/2010/287030. Epub 2009 Nov 30. PMID: 20721338; PMCID: PMC2915664.
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A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows.

Animal : an international journal of animal bioscience

Raussi S, Jauhiainen L, Saastamoinen S, Siivonen J, Hepola H, Veissier I.
PMID: 22445409
Animal. 2011 Mar;5(3):428-32. doi: 10.1017/S1751731110001928.

We developed a method for studying the synchrony of behaviour based on calculations of overdispersion of a binomial process. The lying behaviour of cows was investigated under two different housing units inside the same barn. The first unit housed...

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Raussi S, Jauhiainen L, Saastamoinen S, et al. A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows. Animal. 2011;5(3):428-32doi: 10.1017/S1751731110001928.
Raussi, S., Jauhiainen, L., Saastamoinen, S., Siivonen, J., Hepola, H., & Veissier, I. (2011). A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows. Animal : an international journal of animal bioscience, 5(3), 428-32. https://doi.org/10.1017/S1751731110001928
Raussi, S, et al. "A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows." Animal : an international journal of animal bioscience vol. 5,3 (2011): 428-32. doi: https://doi.org/10.1017/S1751731110001928
Raussi S, Jauhiainen L, Saastamoinen S, Siivonen J, Hepola H, Veissier I. A note on overdispersion as an index of behavioural synchrony: a pilot study in dairy cows. Animal. 2011 Mar;5(3):428-32. doi: 10.1017/S1751731110001928. PMID: 22445409.
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Sensitivity of barley varieties to weather in Finland.

The Journal of agricultural science

Hakala K, Jauhiainen L, Himanen SJ, Rötter R, Salo T, Kahiluoto H.
PMID: 22505777
J Agric Sci. 2012 Apr;150(2):145-160. doi: 10.1017/S0021859611000694. Epub 2011 Aug 11.

Global climate change is predicted to shift seasonal temperature and precipitation patterns. An increasing frequency of extreme weather events such as heat waves and prolonged droughts is predicted, but there are high levels of uncertainty about the nature of...

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Hakala K, Jauhiainen L, Himanen SJ, et al. Sensitivity of barley varieties to weather in Finland. J Agric Sci. 2011;150(2):145-160doi: 10.1017/S0021859611000694.
Hakala, K., Jauhiainen, L., Himanen, S. J., Rötter, R., Salo, T., & Kahiluoto, H. (2012). Sensitivity of barley varieties to weather in Finland. The Journal of agricultural science, 150(2), 145-160. https://doi.org/10.1017/S0021859611000694
Hakala, K, et al. "Sensitivity of barley varieties to weather in Finland." The Journal of agricultural science vol. 150,2 (2012): 145-160. doi: https://doi.org/10.1017/S0021859611000694
Hakala K, Jauhiainen L, Himanen SJ, Rötter R, Salo T, Kahiluoto H. Sensitivity of barley varieties to weather in Finland. J Agric Sci. 2012 Apr;150(2):145-160. doi: 10.1017/S0021859611000694. Epub 2011 Aug 11. PMID: 22505777; PMCID: PMC3320810.
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Temporal dynamics of albedo and climate in the sparse forests of Zagros.

The Science of the total environment

Alibakhshi S, Hovi A, Rautiainen M.
PMID: 30731407
Sci Total Environ. 2019 May 01;663:596-609. doi: 10.1016/j.scitotenv.2019.01.253. Epub 2019 Jan 23.

Land surface albedo is an important parameter affecting the climate locally and globally. A synthesis of current studies urgently calls for a better understanding of the impact of climate change on the surface albedo. The Middle East is expected...

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Alibakhshi S, Hovi A, Rautiainen M. Temporal dynamics of albedo and climate in the sparse forests of Zagros. Sci Total Environ. 2019;663:596-609doi: 10.1016/j.scitotenv.2019.01.253.
Alibakhshi, S., Hovi, A., & Rautiainen, M. (2019). Temporal dynamics of albedo and climate in the sparse forests of Zagros. The Science of the total environment, 663596-609. https://doi.org/10.1016/j.scitotenv.2019.01.253
Alibakhshi, Sara, et al. "Temporal dynamics of albedo and climate in the sparse forests of Zagros." The Science of the total environment vol. 663 (2019): 596-609. doi: https://doi.org/10.1016/j.scitotenv.2019.01.253
Alibakhshi S, Hovi A, Rautiainen M. Temporal dynamics of albedo and climate in the sparse forests of Zagros. Sci Total Environ. 2019 May 01;663:596-609. doi: 10.1016/j.scitotenv.2019.01.253. Epub 2019 Jan 23. PMID: 30731407.
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Estimation of leaf area index and its sunlit portion from DSCOVR EPIC data: Theoretical basis.

Remote sensing of environment

Yang B, Knyazikhin Y, Mõttus M, Rautiainen M, Stenberg P, Yan L, Chen C, Yan K, Choi S, Park T, Myneni RB.
PMID: 28867834
Remote Sens Environ. 2017 Sep 01;198:69-84. doi: 10.1016/j.rse.2017.05.033. Epub 2017 Jun 03.

This paper presents the theoretical basis of the algorithm designed for the generation of leaf area index and diurnal course of its sunlit portion from NASA's Earth Polychromatic Imaging Camera (EPIC) onboard NOAA's Deep Space Climate Observatory (DSCOVR). The...

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Yang B, Knyazikhin Y, Mõttus M, et al. Estimation of leaf area index and its sunlit portion from DSCOVR EPIC data: Theoretical basis. Remote Sens Environ. 2017;198:69-84doi: 10.1016/j.rse.2017.05.033.
Yang, B., Knyazikhin, Y., Mõttus, M., Rautiainen, M., Stenberg, P., Yan, L., Chen, C., Yan, K., Choi, S., Park, T., & Myneni, R. B. (2017). Estimation of leaf area index and its sunlit portion from DSCOVR EPIC data: Theoretical basis. Remote sensing of environment, 19869-84. https://doi.org/10.1016/j.rse.2017.05.033
Yang, Bin, et al. "Estimation of leaf area index and its sunlit portion from DSCOVR EPIC data: Theoretical basis." Remote sensing of environment vol. 198 (2017): 69-84. doi: https://doi.org/10.1016/j.rse.2017.05.033
Yang B, Knyazikhin Y, Mõttus M, Rautiainen M, Stenberg P, Yan L, Chen C, Yan K, Choi S, Park T, Myneni RB. Estimation of leaf area index and its sunlit portion from DSCOVR EPIC data: Theoretical basis. Remote Sens Environ. 2017 Sep 01;198:69-84. doi: 10.1016/j.rse.2017.05.033. Epub 2017 Jun 03. PMID: 28867834; PMCID: PMC5577800.
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Identification of Motor Symptoms Related to Parkinson Disease Using Motion-Tracking Sensors at Home (KÄVELI): Protocol for an Observational Case-Control Study.

JMIR research protocols

Jauhiainen M, Puustinen J, Mehrang S, Ruokolainen J, Holm A, Vehkaoja A, Nieminen H.
PMID: 30916665
JMIR Res Protoc. 2019 Mar 27;8(3):e12808. doi: 10.2196/12808.

BACKGROUND: Clinical characterization of motion in patients with Parkinson disease (PD) is challenging: symptom progression, suitability of medication, and level of independence in the home environment can vary across time and patients. Appointments at the neurological outpatient clinic provide...

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Jauhiainen M, Puustinen J, Mehrang S, et al. Identification of Motor Symptoms Related to Parkinson Disease Using Motion-Tracking Sensors at Home (KÄVELI): Protocol for an Observational Case-Control Study. JMIR Res Protoc. 2019;8(3):e12808doi: 10.2196/12808.
Jauhiainen, M., Puustinen, J., Mehrang, S., Ruokolainen, J., Holm, A., Vehkaoja, A., & Nieminen, H. (2019). Identification of Motor Symptoms Related to Parkinson Disease Using Motion-Tracking Sensors at Home (KÄVELI): Protocol for an Observational Case-Control Study. JMIR research protocols, 8(3), e12808. https://doi.org/10.2196/12808
Jauhiainen, Milla, et al. "Identification of Motor Symptoms Related to Parkinson Disease Using Motion-Tracking Sensors at Home (KÄVELI): Protocol for an Observational Case-Control Study." JMIR research protocols vol. 8,3 (2019): e12808. doi: https://doi.org/10.2196/12808
Jauhiainen M, Puustinen J, Mehrang S, Ruokolainen J, Holm A, Vehkaoja A, Nieminen H. Identification of Motor Symptoms Related to Parkinson Disease Using Motion-Tracking Sensors at Home (KÄVELI): Protocol for an Observational Case-Control Study. JMIR Res Protoc. 2019 Mar 27;8(3):e12808. doi: 10.2196/12808. PMID: 30916665; PMCID: PMC6456828.
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Author Correction: Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots.

Nature communications

Pärn J, Verhoeven JTA, Butterbach-Bahl K, Dise NB, Ullah S, Aasa A, Egorov S, Espenberg M, Järveoja J, Jauhiainen J, Kasak K, Klemedtsson L, Kull A, Laggoun-Défarge F, Lapshina ED, Lohila A, Lõhmus K, Maddison M, Mitsch WJ, Müller C, Niinemets Ü, Osborne B, Pae T, Salm JO, Sgouridis F, Sohar K, Soosaar K, Storey K, Teemusk A, Tenywa MM, Tournebize J, Truu J, Veber G, Villa JA, Zaw SS, Mander Ü.
PMID: 29700326
Nat Commun. 2018 Apr 26;9(1):1748. doi: 10.1038/s41467-018-04197-6.

The original version of this Article contained an error in the first sentence of the Acknowledgements section, which incorrectly referred to the Estonian Research Council grant identifier as "PUTJD618". The correct version replaces the grant identifier with "PUTJD619". This...

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Pärn J, Verhoeven JTA, Butterbach-Bahl K, et al. Author Correction: Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots. Nat Commun. 2018;9(1):1748doi: 10.1038/s41467-018-04197-6.
Pärn, J., Verhoeven, J. T. A., Butterbach-Bahl, K., Dise, N. B., Ullah, S., Aasa, A., Egorov, S., Espenberg, M., Järveoja, J., Jauhiainen, J., Kasak, K., Klemedtsson, L., Kull, A., Laggoun-Défarge, F., Lapshina, E. D., Lohila, A., Lõhmus, K., Maddison, M., Mitsch, W. J., Müller, C., Niinemets, �. �., Osborne, B., Pae, T., Salm, J. O., Sgouridis, F., Sohar, K., Soosaar, K., Storey, K., Teemusk, A., Tenywa, M. M., Tournebize, J., Truu, J., Veber, G., Villa, J. A., Zaw, S. S., & Mander, �. �. (2018). Author Correction: Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots. Nature communications, 9(1), 1748. https://doi.org/10.1038/s41467-018-04197-6
Pärn, Jaan, et al. "Author Correction: Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots." Nature communications vol. 9,1 (2018): 1748. doi: https://doi.org/10.1038/s41467-018-04197-6
Pärn J, Verhoeven JTA, Butterbach-Bahl K, Dise NB, Ullah S, Aasa A, Egorov S, Espenberg M, Järveoja J, Jauhiainen J, Kasak K, Klemedtsson L, Kull A, Laggoun-Défarge F, Lapshina ED, Lohila A, Lõhmus K, Maddison M, Mitsch WJ, Müller C, Niinemets Ü, Osborne B, Pae T, Salm JO, Sgouridis F, Sohar K, Soosaar K, Storey K, Teemusk A, Tenywa MM, Tournebize J, Truu J, Veber G, Villa JA, Zaw SS, Mander Ü. Author Correction: Nitrogen-rich organic soils under warm well-drained conditions are global nitrous oxide emission hotspots. Nat Commun. 2018 Apr 26;9(1):1748. doi: 10.1038/s41467-018-04197-6. PMID: 29700326; PMCID: PMC5920078.
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MBG: Minimizer-based Sparse de Bruijn Graph Construction.

Bioinformatics (Oxford, England)

Rautiainen M, Marschall T.
PMID: 33475133
Bioinformatics. 2021 Jan 20; doi: 10.1093/bioinformatics/btab004. Epub 2021 Jan 20.

MOTIVATION: De Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally long read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided...

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Rautiainen M, Marschall T. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Bioinformatics. 2021;doi: 10.1093/bioinformatics/btab004.
Rautiainen, M., & Marschall, T. (2021). MBG: Minimizer-based Sparse de Bruijn Graph Construction. Bioinformatics (Oxford, England), . https://doi.org/10.1093/bioinformatics/btab004
Rautiainen, Mikko, and Marschall, Tobias. "MBG: Minimizer-based Sparse de Bruijn Graph Construction." Bioinformatics (Oxford, England) vol. (2021). doi: https://doi.org/10.1093/bioinformatics/btab004
Rautiainen M, Marschall T. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Bioinformatics. 2021 Jan 20; doi: 10.1093/bioinformatics/btab004. Epub 2021 Jan 20. PMID: 33475133; PMCID: PMC8521641.
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The enlargement of the maxillary ostium after balloon sinuplasty evaluated by a novel measuring technique from 3D CBCT images.

Scientific reports

Kalliomäki E, Bizaki-Vallaskangas AJ, Valtonen O, Rautiainen M.
PMID: 34880336
Sci Rep. 2021 Dec 08;11(1):23637. doi: 10.1038/s41598-021-03048-7.

Our aim was to evaluate the effects of balloon sinuplasty on the size of the ostium in the maxillary sinuses in patients with chronic rhinosinusitis from cone beam computer tomography (CBCT) scans of the sinus. This is a blinded...

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Kalliomäki E, Bizaki-Vallaskangas AJ, Valtonen O, et al. The enlargement of the maxillary ostium after balloon sinuplasty evaluated by a novel measuring technique from 3D CBCT images. Sci Rep. 2021;11(1):23637doi: 10.1038/s41598-021-03048-7.
Kalliomäki, E., Bizaki-Vallaskangas, A. J., Valtonen, O., & Rautiainen, M. (2021). The enlargement of the maxillary ostium after balloon sinuplasty evaluated by a novel measuring technique from 3D CBCT images. Scientific reports, 11(1), 23637. https://doi.org/10.1038/s41598-021-03048-7
Kalliomäki, Eerika, et al. "The enlargement of the maxillary ostium after balloon sinuplasty evaluated by a novel measuring technique from 3D CBCT images." Scientific reports vol. 11,1 (2021): 23637. doi: https://doi.org/10.1038/s41598-021-03048-7
Kalliomäki E, Bizaki-Vallaskangas AJ, Valtonen O, Rautiainen M. The enlargement of the maxillary ostium after balloon sinuplasty evaluated by a novel measuring technique from 3D CBCT images. Sci Rep. 2021 Dec 08;11(1):23637. doi: 10.1038/s41598-021-03048-7. PMID: 34880336; PMCID: PMC8655076.
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Corrigendum: Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate.

Frontiers in microbiology

Palojärvi A, Kellock M, Parikka P, Jauhiainen L, Alakukku L.
PMID: 34093513
Front Microbiol. 2021 May 20;12:693341. doi: 10.3389/fmicb.2021.693341. eCollection 2021.

[This corrects the article on p. 534786 in vol. 11, PMID: 33193124.].

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Palojärvi A, Kellock M, Parikka P, et al. Corrigendum: Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate. Front Microbiol. 2021;12:693341doi: 10.3389/fmicb.2021.693341.
Palojärvi, A., Kellock, M., Parikka, P., Jauhiainen, L., & Alakukku, L. (2021). Corrigendum: Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate. Frontiers in microbiology, 12693341. https://doi.org/10.3389/fmicb.2021.693341
Palojärvi, Ansa, et al. "Corrigendum: Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate." Frontiers in microbiology vol. 12 (2021): 693341. doi: https://doi.org/10.3389/fmicb.2021.693341
Palojärvi A, Kellock M, Parikka P, Jauhiainen L, Alakukku L. Corrigendum: Tillage System and Crop Sequence Affect Soil Disease Suppressiveness and Carbon Status in Boreal Climate. Front Microbiol. 2021 May 20;12:693341. doi: 10.3389/fmicb.2021.693341. eCollection 2021. PMID: 34093513; PMCID: PMC8173252.
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Children with familial hypercholesterolemia display changes in LDL and HDL function: A cross-sectional study.

Journal of internal medicine

Christensen JJ, Narverud I, Ruuth M, Heier M, Jauhiainen M, Ulven SM, Bogsrud MP, Kovanen PT, Halvorsen B, Oda MN, Wium C, Retterstøl K, Öörni K, Holven KB.
PMID: 34506681
J Intern Med. 2021 Nov;290(5):1083-1097. doi: 10.1111/joim.13383.

BACKGROUND: The functional status of lipoprotein particles contributes to atherogenesis. The tendency of plasma low-density lipoprotein (LDL) particles to aggregate and the ability of igh-density lipoprotein (HDL) particles to induce and mediate reverse cholesterol transport associate with high and...

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Christensen JJ, Narverud I, Ruuth M, et al. Children with familial hypercholesterolemia display changes in LDL and HDL function: A cross-sectional study. J Intern Med. 2021;290(5):1083-1097doi: 10.1111/joim.13383.
Christensen, J. J., Narverud, I., Ruuth, M., Heier, M., Jauhiainen, M., Ulven, S. M., Bogsrud, M. P., Kovanen, P. T., Halvorsen, B., Oda, M. N., Wium, C., Retterstøl, K., Öörni, K., & Holven, K. B. (2021). Children with familial hypercholesterolemia display changes in LDL and HDL function: A cross-sectional study. Journal of internal medicine, 290(5), 1083-1097. https://doi.org/10.1111/joim.13383
Christensen, Jacob J, et al. "Children with familial hypercholesterolemia display changes in LDL and HDL function: A cross-sectional study." Journal of internal medicine vol. 290,5 (2021): 1083-1097. doi: https://doi.org/10.1111/joim.13383
Christensen JJ, Narverud I, Ruuth M, Heier M, Jauhiainen M, Ulven SM, Bogsrud MP, Kovanen PT, Halvorsen B, Oda MN, Wium C, Retterstøl K, Öörni K, Holven KB. Children with familial hypercholesterolemia display changes in LDL and HDL function: A cross-sectional study. J Intern Med. 2021 Nov;290(5):1083-1097. doi: 10.1111/joim.13383. PMID: 34506681.
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