126 Works

Data from: Screen for mitochondrial DNA copy-number maintenance genes reveals essential role for ATP synthase

Atsushi Fukuoh, Giuseppe Cannino, Mike Gerards, Suzanne Buckley, Selena Kaziancioglu, Filippo Scialo, Eero Lihavainen, Andre Ribeiro, Eric Dufour, Howard T. Jacobs & S. Kazancioglu
The machinery of mitochondrial DNA (mtDNA) maintenance is only partially characterized and is of wide interest due to its involvement in disease. To identify novel components of this machinery, plus other cellular pathways required for mtDNA viability, we implemented a genome-wide RNAi screen in Drosophila S2 cells, assaying for loss of fluorescence of mtDNA nucleoids stained with the DNA-intercalating agent PicoGreen. In addition to previously characterized components of the mtDNA replication and transcription machineries, positives...

Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup

Cristina Palma, Vinodh Kandavalli, Mohamed N.M. Bahrudeen, Marco Minoia, Vatsala Chauhan, Suchintak Dash & Andre Ribeiro
Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a Line Weaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when...

Data from: Weighing trees with lasers: advances, challenges and opportunities

Mathias Disney, M. Boni Vicari, A. Burt, K. Calders, S. L. Lewis, P. Raumonen & P. Wilkes
Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements...

Data from: Porous poly-l-lactide-co-ε-caprolactone scaffold: a novel biomaterial for vaginal tissue engineering

Reetta Sartoneva, Kirsi Kuismanen, Miia Juntunen, Sanna Karjalainen, Markus Hannula, Laura Kyllönen, Jari Hyttinen, Heini Huhtala, Kaarlo Paakinaho & Susanna Miettinen
The surgical reconstruction of functional neovagina is challenging and susceptible to complications. Therefore, developing tissue engineering based treatment methods for vaginal defects is important. Our aim was to develop and test a novel supercritical carbon dioxide foamed poly-l-lactide-co-ε-caprolactone (scPLCL) scaffold for vaginal reconstruction. The scaffolds were manufactured and characterized for porosity (65±4%), pore size (350±150µm) and elastic modulus (2.8±0.4MPa). Vaginal epithelial (EC) and stromal cells (SC) were isolated, expanded, and characterized with flow cytometry. Finally,...

Can phones, syllables, and words emerge as side-products of cross-situational audiovisual learning? - A computational investigation

Khazar Khorrami & Okko Räsänen
Decades of research has studied how language learning infants learn to discriminate speech sounds, segment words, and associate words with their meanings. While gradual development of such capabilities is unquestionable, the exact nature of these skills and the underlying mental representations yet remains unclear. In parallel, computational studies have shown that basic comprehension of speech can be achieved by statistical learning between speech and concurrent referentially ambiguous visual input. These models can operate without prior...

A genome-wide association study of total child psychiatric problems scores: summary statistics

Alexander Neumann, Ilja M. Nolte, Irene Pappa, Tarunveer S. Ahluwalia, Erik Pettersson, Alina Rodriguez, Andrew J.O. Whitehouse, Catharina van Beijsterveldt, Beben Benyamin, Anke Hammerschlag, Quinta Helmer, Ville Karhunen, Eva Krapohl, Yi Lu, Peter van der Most, Teemu Palviainen, Beate St. Pourcain, Ilkka Seppälä, Anna Suarez, Natalia Vilor-Tejedor, Carla M. T. Tiesler, Carol Wang, Amanda Wills, Ang Zhou, Silvia Alemany … & Henning Tiemeier
Summary statistics for EAGLE GWAS on total child psychiatric problems scores.
Data is provided in R binary format and can be loaded within R with load("total_child_psychiatric_GWAS.Rdata").
snp: SNP RS ID effect_allele: Effect allele other_allele: Other allele beta: Change in total psychiatric problem score in SD per number of effect allele se: Standard Error p: p-value n: Sample Size
For more information, see PLOS ONE publication:
Neumann A, Nolte IM, [...], Hartman...

Sequence-dependent model of genes with dual σ factor preference

Ines Baptista, Vinodh Kandavalli, Vatsala Chauhan, Mohamed Nasurudeen Mohamed Bahrudeen, Bilena Lima De Brito Almeida, Cristina Palma, Suchintak Dash & Andre Ribeiro
Escherichia coli uses s factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single s factor, approximately 5% of them have dual s factor preference. The most common are those responsive to both s70, which controls housekeeping genes, and s38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that ‘σ70+38 genes’ are nearly as upregulated in stationary growth as...

Self-perception of orofacial appearance: Brazil–Finland cross-national study

Lucas Arrais Campos, Juliana Alvares Duarte Bonini Campos, Minna Kämäräinen, Anna-Sofia Silvola, João Marôco & Timo Peltomäki
(i) To study the measurement invariance of Orofacial Esthetic Scale (OES) and Psychosocial Impact of Dental Aesthetics Questionnaire (PIDAQ), (ii) to compare the perception of orofacial appearance (OA) and (iii) to study the frequency of individuals who have sought or received aesthetic dental treatment between Brazil and Finland. This was a cross-sectional observational study with snowball non-probability sample selection. Students and staff from universities in Finland and Brazil were invited to participate. Data were collected...

Resting heart rate predicts cardiac autonomic modulation during passive head-up tilt in subjects without cardiovascular diseases

Jenni K. Koskela, Anna Tahvanainen, Antti J. Tikkakoski, Pauliina Kangas, Marko Uitto, Jari Viik, Mika Kähönen, Jukka Mustonen & Ilkka Pörsti
Background Resting heart rate (HR) and its variability (HRV) reflects the cardiac sympathovagal balance that is stimulated by head-up tilting. HRV is influenced by the level of HR, but how much HRV offers additional information about cardiac autonomic tone than HR alone remains unresolved. We examined the relation of resting HR with HRV during head-up tilt. Methods. Hemodynamics of 569 subjects without known cardiovascular diseases and medications with direct cardiovascular effects were recorded using whole-body...

Care pathways at end-of-life for cancer decedents: registry based analyses of the living situation, healthcare utilization and costs for all cancer decedents in Norway in 2009-2013 during their last 6 months of life

Gudrun Bjørnelv, Terje P. Hagen, Leena Forma & Eline Aas
Abstract Background Research on end-of-life care is often fragmented, focusing on one level of healthcare or on a particular patient subgroup. Our aim was to describe the complete care pathways of all cancer decedents in Norway during the last six months of life. Methods We used six national registries linked at patient level and including all cancer decedents in Norway between 2009-2013 to describe patient use of secondary, primary-, and home- and community-based care. We...

Methylation status of VTRNA2-1/nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Supplementary data

Emma Raitoharju, Miina Ollikainen, Aino Heikkinen, Eija K. Laakkonen, Elina Sillanpää, Jani Raitanen, Riitta Luoto, Winfried März, Marcus E. Kleber, Melanie Waldenberger, Annette Peters, Thomas Delerue, Sara Hägg, Juulia Jylhävä, Laura Kananen, Mika Kähönen, Olli Raitakari, Terho Lehtimäki, Pashupati P. Mishra, Sonja Rajić, Hely Tamminen & Saara Marttila
Supplementary Table 1. This study used 48 DNA methylation datasets, including DILGOM, FTC, ERMA, KORA, LURIC, NELLI, SATSA and YFS as well as 39 datasets available in the Gene Expression Omnibus (GEO) [29] consisting of >30 tissues and >30,000 individuals.
Supplementary Table 2. Differences in the proportion of individuals with imprinted nc886 locus between sexes or in a case–control setting.
Supplementary Table 3. Of these discordant pairs, one co-twin was always intermediately...

Additional file 1 of Randomized controlled trials in de-implementation research: a systematic scoping review

Aleksi J. Raudasoja, Petra Falkenbach, Robin W. M. Vernooij, Jussi M. J. Mustonen, Arnav Agarwal, Yoshitaka Aoki, Marco H. Blanker, Rufus Cartwright, Herney A. Garcia-Perdomo, Tuomas P. Kilpeläinen, Olli Lainiala, Tiina Lamberg, Olli P. O. Nevalainen, Eero Raittio, Patrick O. Richard, Philippe D. Violette, Jorma Komulainen, Raija Sipilä & Kari A. O. Tikkinen
Additional file 1: eFigure1. Flow diagram. eFigure 2. Published studies per medical content area. eFigure 3. Risk of bias per question. eFigure 4. Risk of bias inside intervention categories. eFigure 5. Intervention components in single-component interventions. eMethods 1. Search strategies. eMethods 2. Risk of Bias Tool for RCTs of complex interventions. eMethods 3. Refined version of intervention taxonomy for de-implementation interventions. eMethods 4. Rationale for refined intervention taxonomy. eMethods 5. Rationale for outcome hierarchy of...

Additional file 3 of Facilitating conditions for staff’s confidence to enforce school tobacco policies: qualitative analysis from seven European cities

Anu Linnansaari, Michael Schreuders, Anton E. Kunst & Pirjo Lindfors
Additional file 3. English interview guide.

Additional file 5 of Facilitating conditions for staff’s confidence to enforce school tobacco policies: qualitative analysis from seven European cities

Anu Linnansaari, Michael Schreuders, Anton E. Kunst & Pirjo Lindfors
Additional file 5. Field notes.

Additional file 1 of Factors associated with body size perception among adolescent goal-oriented sports participants and non-participants: a cross-sectional Finnish study

Leevi Mäkituomas, Laura Heikkilä, Marjukka Nurkkala, Raija Korpelainen, Lauri Alanko, Olli J. Heinonen, Sami Kokko, Urho Kujala, Jari Parkkari, Kai Savonen, Maarit Valtonen, Tommi Vasankari, Jari Villberg & Marja Vanhala
Additional file 1: Supplementary Table 1. Motives to exercise by competitive goals in sports. Supplementary Table 2. Motives to exercise by body size perception.

Additional file 3 of The choice of reference chart affects the strength of the association between malaria in pregnancy and small for gestational age: an individual participant data meta-analysis comparing the Intergrowth-21 with a Tanzanian birthweight chart

George Mtove, Daniel T. R. Minja, Omari Abdul, Samwel Gesase, Kenneth Maleta, Titus H. Divala, Noel Patson, Ulla Ashorn, Miriam K. Laufer, Mwayiwawo Madanitsa, Per Ashorn, Don Mathanga, Jobiba Chinkhumba, Julie R. Gutman, Feiko O. ter Kuile, Sofie Lykke Møller, Ib C. Bygbjerg, Michael Alifrangis, Thor Theander, John P. A. Lusingu & Christentze Schmiegelow
Additional file 3: Figure S2. The birth weight z-scores comparing STOPPAM vs. Intergrowth (IG21) references. The dash line indicates the mean birthweight z-scores.

Use of antibiotics and risk of type 2 diabetes, overweight and obesity: the Cardiovascular Risk in Young Finns Study and the national FINRISK study

Joel Nuotio, Teemu Niiranen, Tomi T. Laitinen, Jessica Miller, Matthew A. Sabin, Aki S. Havulinna, Jorma S. A. Viikari, Tapani Rönnemaa, Nina Hutri-Kähönen, Tomi P. Laitinen, Päivi Tossavainen, Veikko Salomaa, Olli T. Raitakari, David P. Burgner & Markus Juonala
Abstract Purpose To investigate whether exposure to systemic antibiotics influences the risk of developing type 2 diabetes and overweight/obesity. Methods The study sample comprised 2209 (110 with incident diabetes) participants from the population-based Cardiovascular Risk in Young Finns Study (YFS) aged 24–39 years in 2001. The exposure was national linked register data on purchased antibiotic courses between 1993 and 2001. Clinical examinations including BMI were conducted in 2001, 2007 and 2011. Participants with prevalent diabetes...

Additional file 5 of The biological activity of serum bacterial lipopolysaccharides associates with disease activity and likelihood of achieving remission in patients with rheumatoid arthritis

J. Parantainen, G. Barreto, R. Koivuniemi, H. Kautiainen, D. Nordström, E. Moilanen, M. Hämäläinen, M. Leirisalo-Repo, K. Nurmi & K. K. Eklund
Additional file 5: Supplementary table 5a-b. Serum TLR4 activity and LPS bioactivity determined after neutralization by polymyxin B.

Additional file 1 of The socioeconomic impact of tuberculosis on children and adolescents: a scoping review and conceptual framework

S. Atkins, L Heimo, DJ Carter, M. Ribas Closa, L. Vanleeuw, L. Chenciner, P. Wambi, K. Sidney-Annerstedt, U Egere, S Verkuijl, A Brands, T Masini, K Viney, T. Wingfield, K Lönnroth & D. Boccia
Additional file 1: Appendix 1. Search strategy.

The Scene of Experience

Minna Harjula & Heikki Kokko

Framework of the outreach after a school shooting and the students perceptions of the provided support

Tuija Turunen, Henna Haravuori, Jaakko J. Pihlajamäki, Mauri Marttunen & Raija-Leena Punamäki
A large number of bereaved family members, surviving students, and their relatives as well as school staff and the wider community were in need of psychosocial support as a result of a school shooting in Kauhajoki, Finland, 2008. A multilevel outreach project provided psychosocial care to the trauma-affected families, students, schools staff, and wider community for 2 years and 4 months. This article is twofold. First, it presents the theoretical rationale behind the psychosocial support...

Data from: Genome-wide meta-analysis of sciatica in Finnish population

Susanna Lemmelä, Svetlana Solovieva, Rahman Shiri, Christian Benner, Markku Heliövaara, Johannes Kettunen, Verneri Anttila, Samuli Ripatti, Markus Perola, Ilkka Seppälä, Markus Juonala, Mika Kähönen, Veikko Salomaa, Jorma Viikari, Olli Raitakari, Terho Lehtimäki, Aarno Palotie, Eira Viikari-Juntula, Kirsti Husgafvel-Pursiainen, Olli T. Raitakari & Eira Viikari-Juntura
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291...

A genome-wide association study of total child psychiatric problems scores: summary statistics

Alexander Neumann, Ilja M. Nolte, Irene Pappa, Tarunveer S. Ahluwalia, Erik Pettersson, Alina Rodriguez, Andrew J.O. Whitehouse, Catharina van Beijsterveldt, Beben Benyamin, Anke Hammerschlag, Quinta Helmer, Ville Karhunen, Eva Krapohl, Yi Lu, Peter van der Most, Teemu Palviainen, Beate St. Pourcain, Ilkka Seppälä, Anna Suarez, Natalia Vilor-Tejedor, Carla M. T. Tiesler, Carol Wang, Amanda Wills, Ang Zhou, Silvia Alemany … & Henning Tiemeier
Summary statistics for EAGLE GWAS on total child psychiatric problems scores.
Data is provided in R binary format and can be loaded within R with load("total_child_psychiatric_GWAS.Rdata").
snp: SNP RS ID effect_allele: Effect allele other_allele: Other allele beta: Change in total psychiatric problem score in SD per number of effect allele se: Standard Error p: p-value n: Sample Size
For more information, see PLOS ONE publication:
Neumann A, Nolte IM, [...], Hartman...

Analytical kinetic model of native tandem promoters in E. coli

Vatsala Chauhan, Mohamed N.M. Bahrudeen, Cristina S.D. Palma, Ines S.C. Baptista, Bilena L.B. Almeida, Suchintak Dash, Vinodh Kandavalli & Andre S. Ribeiro
Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites ‘dTSS’, pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression...

Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli

Cristina Palma, Suchintak Dash, Ines Baptista, Bilena Almeida, Mohamed Bahrudeen, Vatsala Chauhan, Rahul Jagadeesan & Andre Ribeiro
Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers’ variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered...

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