99 Works

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...

Supplemental Material - Dementia and Related Comorbidities in the Population Aged 90 and Over in the Vitality 90+ Study, Finland: Patterns and Trends From 2001 to 2018

Pauliina Halonen, Linda Enroth, Esa Jämsen, Saritha Vargese & Marja Jylhä
Supplemental Material for Dementia and Related Comorbidities in the Population Aged 90 and Over in the Vitality 90+ Study, Finland: Patterns and Trends From 2001 to 2018 by Pauliina Halonen, Linda Enroth, Esa Jämsen, Saritha Vargese, and Marja Jylhä in Journal of Aging and Health

Additional file 1 of Transplantation of maternal intestinal flora to the newborn after elective cesarean section (SECFLOR): study protocol for a double blinded randomized controlled trial

Noora Carpén, Petter Brodin, Willem M. de Vos, Anne Salonen, Kaija-Leena Kolho, Sture Andersson & Otto Helve
Additional file 1.

Additional file 1 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 1: Table S1. Comparison of the Intergrowth-21 and STOPPAM standard charts. Table S2. Quality of studies using Cochrane’s Risk of Bias 2 tool (ROB-2) for randomized trials. Table S3. Risk of Bias assessment by Newcastle scale for cohort studies. Table S4. Prevalence of small for gestational age by gestational age and birthweight. Table S5. Prevalence of small for gestational age when applying the inclusion criteria for each reference chart. Table S6. Sensitivity analysis...

Additional file 4 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 4: Figure S3. Association between small for gestational age (SGA) and malaria in pregnancy excluding all HIV seropositive women. Panels A and B shows the unadjusted odds ratio (uOR) for SGA when using STOPPAM (SGASTOPPAM) and Intergrowth-21 (SGAIG21) references. Panels C and D shows the adjusted odds ratio (aOR).

Additional file 6 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 6: Figure S5. Funnel plots for meta-analysis. The closed dots indicate the observed studies, panel A indicate the trim and fill funnel plot for STOPPAM (P = 0.10) and panel B for Intergrowth-21 reference (P = 0.35). The contour enhanced funnel plot for STOPPAM (panel C) and Intergrowth-21 (panel D) show the distribution of studies in both the small and large p-values contours, hence no publication bias.

Additional file 2 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 2. Overview of interviewees.

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.

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...

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...

Additional file 1 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 1: Supplementary table 1. Patient cohort characteristics at baseline.

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
Abstract Background Dysbiotic intestinal and oral microbiota have been implicated in the pathogenesis of rheumatoid arthritis (RA), but the mechanisms how microbiota could impact disease activity have remained elusive. The aim of this study was to assess the association of the biological activity of serum lipopolysaccharides (LPS) with disease activity and likelihood of achieving remission in RA patients. Methods We measured Toll-like receptor (TLR) 4-stimulating activity of sera of 58 RA patients with a reporter...

Additional file 3 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 3: Supplementary table 3a-e. Correlations of LPS-related biomarkers with RA disease activity, inflammatory biomarkers, and metabolic factors.

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 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
Additional file 1.

Additional file 1 of Healthcare workers’ heterogeneous mental-health responses to prolonging COVID-19 pandemic: a full year of monthly follow up in Finland

Tom Rosenström, Katinka Tuisku, Jaana Suvisaari, Eero Pukkala, Kristiina Junttila, Henna Haravuori, Marko Elovainio, Toni Haapa, Pekka Jylhä & Tanja Laukkala
Additional file 1. Supplementary Material. Healthcare workers’ heterogeneous mental-health responses to prolonging Covid-19 pandemic: A full year of monthly follow up in Finland. Supplementary data on a Logistic regression mixed model and on the latent class mixture models.

Additional file 1 of The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis

Antonio Federico, Alisa Pavel, Lena Möbus, David McKean, Giusy del Giudice, Vittorio Fortino, Hanna Niehues, Joe Rastrick, Kilian Eyerich, Stefanie Eyerich, Ellen van den Bogaard, Catherine Smith, Stephan Weidinger, Emanuele de Rinaldis & Dario Greco
Additional file 1. Additional material including supplemetary figures and tables.

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...

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...

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...

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...

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...

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.

Registration Year

  • 2022
    99

Resource Types

  • Text
    48
  • Collection
    26
  • Image
    16
  • Dataset
    9

Affiliations

  • Tampere University
    99
  • University of Helsinki
    43
  • Tampere University Hospital
    34
  • London School of Hygiene & Tropical Medicine
    18
  • Liverpool School of Tropical Medicine
    18
  • University of Eastern Finland
    17
  • Kuopio University Hospital
    17
  • University of Oulu
    17
  • Oulu University Hospital
    17
  • Malawi University of Science and Technology
    13