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  • Ranki, Tuuli; Pesonen, Sari; Hemminki, Akseli; Partanen, Kaarina; Kairemo, Kalevi; Alanko, Tuomo; Lundin, Johan; Linder, Nina; Turkki, Riku; Ristimäki, Ari; Jäger, Elke; Karbach, Julia; Wahle, Claudia; Kankainen, Matti; Backman, Charlotta; von Euler, Mikael; Haavisto, Elina; Hakonen, Tiina; Heiskanen, Raita; Jaderberg, Magnus; Juhila, Juuso; Priha, Petri; Suoranta, Laura; Vassilev, Lotta; Vuolanto, Antti; Joensuu, Timo (BioMed Central, 2016)
    Abstract Background We conducted a phase I study with a granulocyte macrophage colony stimulating factor (GMCSF)-expressing oncolytic adenovirus, ONCOS-102, in patients with solid tumors refractory to available treatments. The objectives of the study were to determine the optimal dose for further use and to assess the safety, tolerability and adverse event (AE) profile of ONCOS-102. Further, the response rate and overall survival were evaluated as well as preliminary evidence of disease control. As an exploratory endpoint, the effect of ONCOS 102 on biological correlates was examined. Methods The study was conducted using a classic 3 + 3 dose escalation study design involving 12 patients. Patients were repeatedly treated intratumorally with ONCOS-102 plus daily low-dose oral cyclophosphamide (CPO). Tumor response was evaluated with diagnostic positron emission tomography (PET) and computed tomography (CT). Tumor biopsies were collected at baseline and after treatment initiation for analysis of immunological correlates. Peripheral blood mononuclear cells (PBMCs) were collected at baseline and during the study to assess antigen specificity of CD8+ T cells by interferon gamma (IFNγ) enzyme linked immunospot assay (ELISPOT). Results No dose limiting toxicity (DLT) or maximum tolerated dose (MTD) was identified for ONCOS-102. Four out of ten (40 %) evaluable patients had disease control based on PET/CT scan at 3 months and median overall survival was 9.3 months. A short-term increase in systemic pro-inflammatory cytokines and a prominent infiltration of TILs to tumors was seen post-treatment in 11 out of 12 patients. Two patients showed marked infiltration of CD8+ T cells to tumors and concomitant systemic induction of tumor-specific CD8+ T cells. Interestingly, high expression levels of genes associated with activated TH1 cells and TH1 type immune profile were observed in the post-treatment biopsies of these two patients. Conclusions ONCOS-102 is safe and well tolerated at the tested doses. All three examined doses may be used in further development. There was evidence of antitumor immunity and signals of clinical efficacy. Importantly, treatment resulted in infiltration of CD8+ T cells to tumors and up-regulation of PD-L1, highlighting the potential of ONCOS-102 as an immunosensitizing agent for combinatory therapies with checkpoint inhibitors. Trial registration NCT01598129 . Registered 19/04/2012
  • Calteau, Alexandra; Fewer, David P; Latifi, Amel; Coursin, Thérèse; Laurent, Thierry; Jokela, Jouni; Kerfeld, Cheryl A; Sivonen, Kaarina; Piel, Jörn; Gugger, Muriel (BioMed Central Ltd, 2014)
    Abstract Background Cyanobacteria are an ancient lineage of photosynthetic bacteria from which hundreds of natural products have been described, including many notorious toxins but also potent natural products of interest to the pharmaceutical and biotechnological industries. Many of these compounds are the products of non-ribosomal peptide synthetase (NRPS) or polyketide synthase (PKS) pathways. However, current understanding of the diversification of these pathways is largely based on the chemical structure of the bioactive compounds, while the evolutionary forces driving their remarkable chemical diversity are poorly understood. Results We carried out a phylum-wide investigation of genetic diversification of the cyanobacterial NRPS and PKS pathways for the production of bioactive compounds. 452 NRPS and PKS gene clusters were identified from 89 cyanobacterial genomes, revealing a clear burst in late-branching lineages. Our genomic analysis further grouped the clusters into 286 highly diversified cluster families (CF) of pathways. Some CFs appeared vertically inherited, while others presented a more complex evolutionary history. Only a few horizontal gene transfers were evidenced amongst strongly conserved CFs in the phylum, while several others have undergone drastic gene shuffling events, which could result in the observed diversification of the pathways. Conclusions Therefore, in addition to toxin production, several NRPS and PKS gene clusters are devoted to important cellular processes of these bacteria such as nitrogen fixation and iron uptake. The majority of the biosynthetic clusters identified here have unknown end products, highlighting the power of genome mining for the discovery of new natural products.
  • Keto, Jaana; Jokelainen, Jari; Timonen, Markku; Linden, Kari; Ylisaukko-oja, Tero (BioMed Central, 2015)
    Abstract Background Our aim was to study the smoking cessation-related 1) attitudes & experiences and 2) consultation practices of Finnish physicians and to determine if there is a relationship between the two. Methods An online survey on smoking cessation was sent to 39 % of all Finnish physicians, with emphasis on physicians working in fields relevant to smoking cessation. A total of 1141 physicians (response rate 15 %) responded to the online survey, 53 % of whom were employed in primary health care. A total of 1066 respondents were eligible for the analysis. The questionnaire included questions on the physician’s own smoking status, their attitudes and experiences on smoking cessation, and the implementation of smoking cessation in clinical practice. Two sub-scales concerning smoking-related consultation activities were constructed: one for conversation, and another for practical actions. Results The most common consultation activities (respondents who reported doing the following actions “nearly always”) were asking how much the patient smokes (65 %), marking smoking status in patient records (58 %) and recommending quitting to the patient (55 %). The least common activity was prescribing withdrawal medication (4 %). Primary care physicians were more active than those working in secondary health care in nearly all activities mapped. A positive attitude and experiences on smoking cessation were associated with actively offering withdrawal support. Those who were familiar with the local treatment guidelines for tobacco addiction were 30 % more active in offering practical cessation help to their patient. The respondents were more active in discussing smoking with their patients than in offering practical cessation help. Conclusion Physicians offer their patients practical cessation support relatively infrequently. Practical cessation calls for continuous education of physicians about the nature of tobacco and nicotine addiction, the role of smoking as a risk factor for various diseases, and the practical measures needed for smoking cessation. Secondary care physicians should acknowledge the authority they pose toward smoking patients.
  • Guo, Baocheng; DeFaveri, Jacquelin; Sotelo, Graciela; Nair, Abhilash; Merilä, Juha (BioMed Central, 2015)
    Abstract Background The degree of genetic differentiation among populations experiencing high levels of gene flow is expected to be low for neutral genomic sites, but substantial divergence can occur in sites subject to directional selection. Studies of highly mobile marine fish populations provide an opportunity to investigate this kind of heterogeneous genomic differentiation, but most studies to this effect have focused on a relatively low number of genetic markers and/or few populations. Hence, the patterns and extent of genomic divergence in high-gene-flow marine fish populations remain poorly understood. Results We here investigated genome-wide patterns of genetic variability and differentiation in ten marine populations of three-spined stickleback (Gasterosteus aculeatus) distributed across a steep salinity and temperature gradient in the Baltic Sea, by utilizing >30,000 single nucleotide polymorphisms obtained with a pooled RAD-seq approach. We found that genetic diversity and differentiation varied widely across the genome, and identified numerous fairly narrow genomic regions exhibiting signatures of both divergent and balancing selection. Evidence was uncovered for substantial genetic differentiation associated with both salinity and temperature gradients, and many candidate genes associated with local adaptation in the Baltic Sea were identified. Conclusions The patterns of genetic diversity and differentiation, as well as candidate genes associated with adaptation, in Baltic Sea sticklebacks were similar to those observed in earlier comparisons between marine and freshwater populations, suggesting that similar processes may be driving adaptation to brackish and freshwater environments. Taken together, our results provide strong evidence for heterogenic genomic divergence driven by local adaptation in the face of gene flow along an environmental gradient in the post-glacially formed Baltic Sea.
  • Guo, Baocheng; DeFaveri, Jacquelin; Sotelo, Graciela; Nair, Abhilash; Merilä, Juha (BioMed Central, 2015)
    Abstract Background The degree of genetic differentiation among populations experiencing high levels of gene flow is expected to be low for neutral genomic sites, but substantial divergence can occur in sites subject to directional selection. Studies of highly mobile marine fish populations provide an opportunity to investigate this kind of heterogeneous genomic differentiation, but most studies to this effect have focused on a relatively low number of genetic markers and/or few populations. Hence, the patterns and extent of genomic divergence in high-gene-flow marine fish populations remain poorly understood. Results We here investigated genome-wide patterns of genetic variability and differentiation in ten marine populations of three-spined stickleback (Gasterosteus aculeatus) distributed across a steep salinity and temperature gradient in the Baltic Sea, by utilizing >30,000 single nucleotide polymorphisms obtained with a pooled RAD-seq approach. We found that genetic diversity and differentiation varied widely across the genome, and identified numerous fairly narrow genomic regions exhibiting signatures of both divergent and balancing selection. Evidence was uncovered for substantial genetic differentiation associated with both salinity and temperature gradients, and many candidate genes associated with local adaptation in the Baltic Sea were identified. Conclusions The patterns of genetic diversity and differentiation, as well as candidate genes associated with adaptation, in Baltic Sea sticklebacks were similar to those observed in earlier comparisons between marine and freshwater populations, suggesting that similar processes may be driving adaptation to brackish and freshwater environments. Taken together, our results provide strong evidence for heterogenic genomic divergence driven by local adaptation in the face of gene flow along an environmental gradient in the post-glacially formed Baltic Sea.
  • Skrifvars, MB; Raj, R; Bendel, S; Selander, T; Kivisaari, R; Siironen, J; Reinikainen, M (BioMed Central Ltd, 2014)
  • Markkula, Ritva A; Kalso, Eija A; Kaprio, Jaakko A (BioMed Central, 2016)
    Abstract Background Fibromyalgia (FM) is a pain syndrome, the mechanisms and predictors of which are still unclear. We have earlier validated a set of FM-symptom questions for detecting possible FM in an epidemiological survey and thereby identified a cluster with “possible FM”. This study explores prospectively predictors for membership of that FM-symptom cluster. Methods A population-based sample of 8343 subjects of the older Finnish Twin Cohort replied to health questionnaires in 1975, 1981, and 1990. Their answers to the set of FM-symptom questions in 1990 classified them in three latent classes (LC): LC1 with no or few symptoms, LC2 with some symptoms, and LC3 with many FM symptoms. We analysed putative predictors for these symptom classes using baseline (1975 and 1981) data on regional pain, headache, migraine, sleeping, body mass index (BMI), physical activity, smoking, and zygosity, adjusted for age, gender, and education. Those with a high likelihood of having fibromyalgia at baseline were excluded from the analysis. In the final multivariate regression model, regional pain, sleeping problems, and overweight were all predictors for membership in the class with many FM symptoms. Results The strongest non-genetic predictor was frequent headache (OR 8.6, CI 95 % 3.8–19.2), followed by persistent back pain (OR 4.7, CI 95 % 3.3–6.7) and persistent neck pain (OR 3.3, CI 95 % 1.8–6.0). Conclusions Regional pain, frequent headache, and persistent back or neck pain, sleeping problems, and overweight are predictors for having a cluster of symptoms consistent with fibromyalgia.
  • Traoré, Oumar; Nyholm, Outi; Siitonen, Anja; Bonkoungou, Isidore J O; Traoré, Alfred S; Barro, Nicolas; Haukka, Kaisa (BioMed Central, 2015)
    Abstract Background This study investigated the prevalence, serotypes and antimicrobial sensitivity patterns of Salmonella enterica in environment in Ouagadougou, Burkina Faso. A total of 476 samples, consisting of 36 samples of tap water, 51 samples of well water, 87 samples of channel water, 44 samples of reservoir water, 238 samples of fish, and 20 samples of lettuce were examined using standard bacteriological procedures for Salmonella. Results Salmonella were isolated from 98 samples. Salmonella were rare in drinking water, since they were not found at all from the tap water, and only in 2 % of well water. Salmonella were more common in the water of reservoir of Tanghin (15 %), reservoir of Yamtenga (20 %), and in the water channels in the city (from 20 to 31 %). Salmonella were commonly isolated from the fish (24 %) caught from the reservoir of Tanghin and from the lettuce (50 %) irrigated with water from Tanghin. The Salmonella isolates were found to represent 50 different serotypes. The 11 most common serotypes were Salmonella Bredeney and S. Colindale (both 8.2 %), S. Muenster (6.1 %), S. Korlebu (5.1 %), S. Eastbourne and S. Poona (both 4.1 %), and S. Agona, S. Derby, S. Drac, S. Senftenberg, S. Waycross (each 3.1 %), accounting for 51.3 % of all the isolates. In general, the Salmonella strains were sensitive to the antimicrobials tested, but two strains were resistant to streptomycin and many more intermediate to streptomycin or sulphonamide. Conclusion This study highlights the common prevalence of Salmonella and the high diversity of Salmonella serotypes in aquatic environment in Ouagadougou, Burkina Faso. Therefore, various human activities linked to water and consumption of water-related products, such as fish and lettuce, can lead to human Salmonella infections.
  • Traoré, Oumar; Nyholm, Outi; Siitonen, Anja; Bonkoungou, Isidore J O; Traoré, Alfred S; Barro, Nicolas; Haukka, Kaisa (BioMed Central, 2015)
    Abstract Background This study investigated the prevalence, serotypes and antimicrobial sensitivity patterns of Salmonella enterica in environment in Ouagadougou, Burkina Faso. A total of 476 samples, consisting of 36 samples of tap water, 51 samples of well water, 87 samples of channel water, 44 samples of reservoir water, 238 samples of fish, and 20 samples of lettuce were examined using standard bacteriological procedures for Salmonella. Results Salmonella were isolated from 98 samples. Salmonella were rare in drinking water, since they were not found at all from the tap water, and only in 2 % of well water. Salmonella were more common in the water of reservoir of Tanghin (15 %), reservoir of Yamtenga (20 %), and in the water channels in the city (from 20 to 31 %). Salmonella were commonly isolated from the fish (24 %) caught from the reservoir of Tanghin and from the lettuce (50 %) irrigated with water from Tanghin. The Salmonella isolates were found to represent 50 different serotypes. The 11 most common serotypes were Salmonella Bredeney and S. Colindale (both 8.2 %), S. Muenster (6.1 %), S. Korlebu (5.1 %), S. Eastbourne and S. Poona (both 4.1 %), and S. Agona, S. Derby, S. Drac, S. Senftenberg, S. Waycross (each 3.1 %), accounting for 51.3 % of all the isolates. In general, the Salmonella strains were sensitive to the antimicrobials tested, but two strains were resistant to streptomycin and many more intermediate to streptomycin or sulphonamide. Conclusion This study highlights the common prevalence of Salmonella and the high diversity of Salmonella serotypes in aquatic environment in Ouagadougou, Burkina Faso. Therefore, various human activities linked to water and consumption of water-related products, such as fish and lettuce, can lead to human Salmonella infections.
  • Honeyborne, Isobella; McHugh, Timothy D; Kuittinen, Iitu; Cichonska, Anna; Evangelopoulos, Dimitrios; Ronacher, Katharina; van Helden, Paul D; Gillespie, Stephen H; Fernandez-Reyes, Delmiro; Walzl, Gerhard; Rousu, Juho; Butcher, Philip D; Waddell, Simon J (BioMed Central, 2016)
    Abstract Background New treatment options are needed to maintain and improve therapy for tuberculosis, which caused the death of 1.5 million people in 2013 despite potential for an 86 % treatment success rate. A greater understanding of Mycobacterium tuberculosis (M.tb) bacilli that persist through drug therapy will aid drug development programs. Predictive biomarkers for treatment efficacy are also a research priority. Methods and Results Genome-wide transcriptional profiling was used to map the mRNA signatures of M.tb from the sputa of 15 patients before and 3, 7 and 14 days after the start of standard regimen drug treatment. The mRNA profiles of bacilli through the first 2 weeks of therapy reflected drug activity at 3 days with transcriptional signatures at days 7 and 14 consistent with reduced M.tb metabolic activity similar to the profile of pre-chemotherapy bacilli. These results suggest that a pre-existing drug-tolerant M.tb population dominates sputum before and after early drug treatment, and that the mRNA signature at day 3 marks the killing of a drug-sensitive sub-population of bacilli. Modelling patient indices of disease severity with bacterial gene expression patterns demonstrated that both microbiological and clinical parameters were reflected in the divergent M.tb responses and provided evidence that factors such as bacterial load and disease pathology influence the host-pathogen interplay and the phenotypic state of bacilli. Transcriptional signatures were also defined that predicted measures of early treatment success (rate of decline in bacterial load over 3 days, TB test positivity at 2 months, and bacterial load at 2 months). Conclusions This study defines the transcriptional signature of M.tb bacilli that have been expectorated in sputum after two weeks of drug therapy, characterizing the phenotypic state of bacilli that persist through treatment. We demonstrate that variability in clinical manifestations of disease are detectable in bacterial sputa signatures, and that the changing M.tb mRNA profiles 0–2 weeks into chemotherapy predict the efficacy of treatment 6 weeks later. These observations advocate assaying dynamic bacterial phenotypes through drug therapy as biomarkers for treatment success.
  • Örmälä-Odegrip, Anni-Maria; Ojala, Ville; Hiltunen, Teppo; Zhang, Ji; Bamford, Jaana K; Laakso, Jouni (BioMed Central, 2015)
    Abstract Background Consumer-resource interactions constitute one of the most common types of interspecific antagonistic interaction. In natural communities, complex species interactions are likely to affect the outcomes of reciprocal co-evolution between consumers and their resource species. Individuals face multiple enemies simultaneously, and consequently they need to adapt to several different types of enemy pressures. In this study, we assessed how protist predation affects the susceptibility of bacterial populations to infection by viral parasites, and whether there is an associated cost of defence on the competitive ability of the bacteria. As a study system we used Serratia marcescens and its lytic bacteriophage, along with two bacteriovorous protists with distinct feeding modes: Tetrahymena thermophila (particle feeder) and Acanthamoeba castellanii (surface feeder). The results were further confirmed with another study system with Pseudomonas and Tetrahymena thermophila. Results We found that selection by protist predators lowered the susceptibility to infections by lytic phages in Serratia and Pseudomonas. In Serratia, concurrent selection by phages and protists led to lowered susceptibility to phage infections and this effect was independent from whether the bacteria shared a co-evolutionary history with the phage population or not. Bacteria that had evolved with phages were overall more susceptible to phage infection (compared to bacteria with history with multiple enemies) but they were less vulnerable to the phages they had co-evolved with than ancestral phages. Selection by bacterial enemies was costly in general and was seen as a lowered fitness in absence of phages, measured as a biomass yield. Conclusions Our results show the significance of multiple species interactions on pairwise consumer-resource interaction, and suggest potential overlap in defending against predatory and parasitic enemies in microbial consumer-resource communities. Ultimately, our results could have larger scale effects on eco-evolutionary community dynamics.
  • Örmälä-Odegrip, Anni-Maria; Ojala, Ville; Hiltunen, Teppo; Zhang, Ji; Bamford, Jaana K; Laakso, Jouni (BioMed Central, 2015)
    Abstract Background Consumer-resource interactions constitute one of the most common types of interspecific antagonistic interaction. In natural communities, complex species interactions are likely to affect the outcomes of reciprocal co-evolution between consumers and their resource species. Individuals face multiple enemies simultaneously, and consequently they need to adapt to several different types of enemy pressures. In this study, we assessed how protist predation affects the susceptibility of bacterial populations to infection by viral parasites, and whether there is an associated cost of defence on the competitive ability of the bacteria. As a study system we used Serratia marcescens and its lytic bacteriophage, along with two bacteriovorous protists with distinct feeding modes: Tetrahymena thermophila (particle feeder) and Acanthamoeba castellanii (surface feeder). The results were further confirmed with another study system with Pseudomonas and Tetrahymena thermophila. Results We found that selection by protist predators lowered the susceptibility to infections by lytic phages in Serratia and Pseudomonas. In Serratia, concurrent selection by phages and protists led to lowered susceptibility to phage infections and this effect was independent from whether the bacteria shared a co-evolutionary history with the phage population or not. Bacteria that had evolved with phages were overall more susceptible to phage infection (compared to bacteria with history with multiple enemies) but they were less vulnerable to the phages they had co-evolved with than ancestral phages. Selection by bacterial enemies was costly in general and was seen as a lowered fitness in absence of phages, measured as a biomass yield. Conclusions Our results show the significance of multiple species interactions on pairwise consumer-resource interaction, and suggest potential overlap in defending against predatory and parasitic enemies in microbial consumer-resource communities. Ultimately, our results could have larger scale effects on eco-evolutionary community dynamics.
  • Hippeläinen, Eero; Tenhunen, Mikko; Mäenpää, Hanna; Sohlberg, Antti (Springer Berlin Heidelberg, 2016)
    Abstract Background In targeted radionuclide therapy (TRT), accurate quantification using SPECT/CT images is important for optimizing radiation dose delivered to both the tumour and healthy tissue. Quantitative SPECT images are regularly reconstructed using the ordered subset expectation maximization (OSEM) algorithm with various compensation methods such as attenuation (A), scatter (S) and detector and collimator response (R). In this study, different combinations of the compensation methods are applied during OSEM reconstruction and the effect on the 177Lu quantification accuracy is studied in an anthropomorphic torso phantom. In addition, the phantom results are reflected to (177)Lu-DOTA-Tyr3-octreotate (177Lu-DOTATATE)-treated patient data and kidney absorbed dose estimates. Methods The torso phantom was imaged with nine various sized (0.4–104.4 cm3) spherical inserts, filled with known 177Lu activity ranging from 0.5 to 105.5 MBq. Images were reconstructed using OSEM algorithm using A, AR and ARS compensation method combinations. The compensation method combinations were compared by calculating the concentration recovery coefficient (cRC) for each insert. In addition, ten 177Lu-DOTATATE-treated patient’s post-therapy dosimetry acquisitions were reconstructed, and the absorbed dose to kidneys was estimated. Results cRC values depend on the insert size for all compensation methods. AR and ARS produced significantly higher cRC values than attenuation correction alone. There were no cRC value differences between the methods for the smallest 1-cm-diameter insert, cRC being 0.18. However, the collimator and detector response compensation method (R) made the 1.3-cm-diameter insert clearly visible and improved cRC estimate from 0.19 to 0.43. ARS produced slightly higher cRC values for small- and medium-sized inserts than AR. On the patient data, a similar trend could be seen. AR and ARS produced higher kidney activities than using attenuation correction alone; the total absorbed doses to the right and left kidneys were on average 15 and 20 % higher for AR and 19 and 25 % higher for ARS, respectively. The effective half-life decay estimated from time-activity curves however showed no notable difference between the compensation methods. Conclusions The highest cRC values were achieved by applying ARS compensation during reconstruction. The results were notably higher than those using attenuation correction alone. Similarly, higher activity estimates and thus higher absorbed dose estimates were found in patient data when all compensation methods were applied. ARS improved cRC especially in small-sized sources, and it thus might aid tumour dosimetry for 177Lu PRRT treatments.
  • Pohjola, Leena; Rossow, Laila; Huovilainen, Anita; Soveri, Timo; Hänninen, Marja-Liisa; Fredriksson-Ahomaa, Maria (BioMed Central Ltd, 2015)
    Abstract Background Although modern commercial poultry production today is based on large farms and intensive husbandry, keeping backyard poultry has regained popularity in industrialized countries. However, the health status of backyard flocks is still relatively poorly documented. A questionnaire was sent to the owners of 376 backyard poultry flocks (<500 birds) in order to study health management procedures and characterize backyard poultry populations in Finland. Information was also collected on the postmortem findings from non-commercial flocks using necropsy data from the Finnish Food Safety Authority (Evira). Results Backyard flocks in Finland are small in size (<50 birds), comprising mainly chickens. Based on the results of the questionnaire, the health of such flocks is good, mortality low and vaccinations are not commonly used. Most of the flocks were registered in the national poultry register. The standard biosecurity practices are not generally applied and contact with wild birds, pets and farm animals is frequent, which can make the flocks more prone to infectious diseases. We conducted an 11-year retrospective study of the postmortem necropsy findings of the Evira in order to document the diseases, which caused mortality in backyard chickens in Finland. Necropsy was performed on a total of 132 non-commercial laying hens during 2000 – 2011. The most common postmortem findings were Marek’s disease (27%) and colibacillosis (17%). Conclusions This study is the first to report data on characteristics of and management practices for backyard chicken flocks in Finland. Close connections with commercial flocks are rare and farms are usually distantly located suggesting that the risk that these backyard flocks pose to commercial poultry is low.
  • Kaunisto, Jaana; Kelloniemi, K.; Sutinen, E.; Hodgson, U.; Piilonen, A.; Kaarteenaho, R.; Mäkitaro, R.; Purokivi, M.; Lappi-Blanco, E.; Saarelainen, S.; Kankaanranta, H.; Mursu, A.; Kanervisto, M.; Salomaa, E-R.; Myllärniemi, M. (BioMed Central, 2015)
    Abstract Background The FinnishIPF registry is a prospective, longitudinal national registry study on the epidemiology of idiopathic pulmonary fibrosis (IPF). It was designed to describe the characteristics, management and prognosis of prevalent and incident IPF patients. The study was initiated in 2012. Methods We present here results limited to five university hospitals. Patients with IPF were screened from hospital registries using ICD-10 diagnosis codes J84.1 and J84.9. All patients who gave informed consent were included and evaluated using novel diagnostic criteria. Point prevalence on the 31st of December in 2012 was calculated using the reported population in each university hospital city as the denominator. Results Patients with ICD-10 codes J84.1 and J84.9 yielded a heterogeneous group – on the basis of patient records assessed by pulmonologists only 20–30 % of the cases were IPF. After clinical, radiological and histological re-evaluation 111 of 123 (90 %) of patients fulfilled the clinical criteria of IPF. The estimated prevalence of IPF was 8.6 cases/100 000. 60.4 % were men. Forty four percent of the patients were never-smokers. At diagnosis, the patients’ mean age was 73.5 years and mean FVC was 80.4 % and DLCO 57.3 % of predicted. Conclusions Our results suggest that hospital registries are inaccurate for epidemiological studies unless patients are carefully re-evaluated. IPF is diagnosed in Finland at a stage when lung function is still quite well preserved. Smoking in patients with IPF was less common than in previous reports.
  • Kaunisto, Jaana; Kelloniemi, K.; Sutinen, E.; Hodgson, U.; Piilonen, A.; Kaarteenaho, R.; Mäkitaro, R.; Purokivi, M.; Lappi-Blanco, E.; Saarelainen, S.; Kankaanranta, H.; Mursu, A.; Kanervisto, M.; Salomaa, E-R.; Myllärniemi, M. (BioMed Central, 2015)
    Abstract Background The FinnishIPF registry is a prospective, longitudinal national registry study on the epidemiology of idiopathic pulmonary fibrosis (IPF). It was designed to describe the characteristics, management and prognosis of prevalent and incident IPF patients. The study was initiated in 2012. Methods We present here results limited to five university hospitals. Patients with IPF were screened from hospital registries using ICD-10 diagnosis codes J84.1 and J84.9. All patients who gave informed consent were included and evaluated using novel diagnostic criteria. Point prevalence on the 31st of December in 2012 was calculated using the reported population in each university hospital city as the denominator. Results Patients with ICD-10 codes J84.1 and J84.9 yielded a heterogeneous group – on the basis of patient records assessed by pulmonologists only 20–30 % of the cases were IPF. After clinical, radiological and histological re-evaluation 111 of 123 (90 %) of patients fulfilled the clinical criteria of IPF. The estimated prevalence of IPF was 8.6 cases/100 000. 60.4 % were men. Forty four percent of the patients were never-smokers. At diagnosis, the patients’ mean age was 73.5 years and mean FVC was 80.4 % and DLCO 57.3 % of predicted. Conclusions Our results suggest that hospital registries are inaccurate for epidemiological studies unless patients are carefully re-evaluated. IPF is diagnosed in Finland at a stage when lung function is still quite well preserved. Smoking in patients with IPF was less common than in previous reports.
  • Spurdle, Amanda B; Couch, Fergus J; Parsons, Michael T; McGuffog, Lesley; Barrowdale, Daniel; Bolla, Manjeet K; Wang, Qin; Healey, Sue; Schmutzler, Rita K; Wappenschmidt, Barbara; Rhiem, Kerstin; Hahnen, Eric; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Plendl, Hansjoerg; Niederacher, Dieter; Sutter, Christian; Wang-Gohrke, Shan; Steinemann, Doris; Preisler-Adams, Sabine; Kast, Karin; Varon-Mateeva, Raymonda; Ellis, Steve; Frost, Debra; Platte, Radka; Perkins, Jo; Evans, D G; Izatt, Louise; Eeles, Ros; Adlard, Julian; Davidson, Rosemarie; Cole, Trevor; Scuvera, Giulietta; Manoukian, Siranoush; Bonanni, Bernardo; Mariette, Frederique; Fortuzzi, Stefano; Viel, Alessandra; Pasini, Barbara; Papi, Laura; Varesco, Liliana; Balleine, Rosemary; Nathanson, Katherine L; Domchek, Susan M; Offitt, Kenneth; Jakubowska, Anna; Lindor, Noralane; Thomassen, Mads; Jensen, Uffe B; Rantala, Johanna; Borg, Åke; Andrulis, Irene L; Miron, Alexander; Hansen, Thomas V; Caldes, Trinidad; Neuhausen, Susan L; Toland, Amanda E; Nevanlinna, Heli; Montagna, Marco; Garber, Judy; Godwin, Andrew K; Osorio, Ana; Factor, Rachel E; Terry, Mary B; Rebbeck, Timothy R; Karlan, Beth Y; Southey, Melissa; Rashid, Muhammad U; Tung, Nadine; Pharoah, Paul D; Blows, Fiona M; Dunning, Alison M; Provenzano, Elena; Hall, Per; Czene, Kamila; Schmidt, Marjanka K; Broeks, Annegien; Cornelissen, Sten; Verhoef, Senno; Fasching, Peter A; Beckmann, Matthias W; Ekici, Arif B; Slamon, Dennis J; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Aittomäki, Kristiina; Muranen, Taru A; Heikkilä, Päivi; Blomqvist, Carl; Figueroa, Jonine; Chanock, Stephen J; Brinton, Louise; Lissowska, Jolanta; Olson, Janet E; Pankratz, Vernon S; John, Esther M; Whittemore, Alice S; West, Dee W; Hamann, Ute; Torres, Diana; Ulmer, Hans U; Rüdiger, Thomas; Devilee, Peter; Tollenaar, Robert A; Seynaeve, Caroline; Van Asperen, Christi J; Eccles, Diana M; Tapper, William J; Durcan, Lorraine; Jones, Louise; Peto, Julian; dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Dwek, Miriam; Swann, Ruth; Bane, Anita L; Glendon, Gord; Mulligan, Anna M; Giles, Graham G; Milne, Roger L; Baglietto, Laura; McLean, Catriona; Carpenter, Jane; Clarke, Christine; Scott, Rodney; Brauch, Hiltrud; Brüning, Thomas; Ko, Yon-Dschun; Cox, Angela; Cross, Simon S; Reed, Malcolm W; Lubinski, Jan; Jaworska-Bieniek, Katarzyna; Durda, Katarzyna; Gronwald, Jacek; Dörk, Thilo; Bogdanova, Natalia; Park-Simon, Tjoung-Won; Hillemanns, Peter; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Burwinkel, Barbara; Marme, Frederik; Surovy, Harald; Yang, Rongxi; Anton-Culver, Hoda; Ziogas, Argyrios; Hooning, Maartje J; Collée, J M; Martens, John W; Tilanus-Linthorst, Madeleine M; Brenner, Hermann; Dieffenbach, Aida K; Arndt, Volke; Stegmaier, Christa; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Grip, Mervi; Lindblom, Annika; Margolin, Sara; Joseph, Vijai; Robson, Mark; Rau-Murthy, Rohini; González-Neira, Anna; Arias, José I; Zamora, Pilar; Benítez, Javier; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Peterlongo, Paolo; Zaffaroni, Daniela; Barile, Monica; Capra, Fabio; Radice, Paolo; Teo, Soo H; Easton, Douglas F; Antoniou, Antonis C; Chenevix-Trench, Georgia; Goldgar, David E (BioMed Central, 2014)
    Abstract Introduction The distribution of histopathological features of invasive breast tumors in BRCA1 or BRCA2 germline mutation carriers differs from that of individuals with no known mutation. Histopathological features thus have utility for mutation prediction, including statistical modeling to assess pathogenicity of BRCA1 or BRCA2 variants of uncertain clinical significance. We analyzed large pathology datasets accrued by the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC) to reassess histopathological predictors of BRCA1 and BRCA2 mutation status, and provide robust likelihood ratio (LR) estimates for statistical modeling. Methods Selection criteria for study/center inclusion were estrogen receptor (ER) status or grade data available for invasive breast cancer diagnosed younger than 70 years. The dataset included 4,477 BRCA1 mutation carriers, 2,565 BRCA2 mutation carriers, and 47,565 BCAC breast cancer cases. Country-stratified estimates of the likelihood of mutation status by histopathological markers were derived using a Mantel-Haenszel approach. Results ER-positive phenotype negatively predicted BRCA1 mutation status, irrespective of grade (LRs from 0.08 to 0.90). ER-negative grade 3 histopathology was more predictive of positive BRCA1 mutation status in women 50 years or older (LR = 4.13 (3.70 to 4.62)) versus younger than 50 years (LR = 3.16 (2.96 to 3.37)). For BRCA2, ER-positive grade 3 phenotype modestly predicted positive mutation status irrespective of age (LR = 1.7-fold), whereas ER-negative grade 3 features modestly predicted positive mutation status at 50 years or older (LR = 1.54 (1.27 to 1.88)). Triple-negative tumor status was highly predictive of BRCA1 mutation status for women younger than 50 years (LR = 3.73 (3.43 to 4.05)) and 50 years or older (LR = 4.41 (3.86 to 5.04)), and modestly predictive of positive BRCA2 mutation status in women 50 years or older (LR = 1.79 (1.42 to 2.24)). Conclusions These results refine likelihood-ratio estimates for predicting BRCA1 and BRCA2 mutation status by using commonly measured histopathological features. Age at diagnosis is an important variable for most analyses, and grade is more informative than ER status for BRCA2 mutation carrier prediction. The estimates will improve BRCA1 and BRCA2 variant classification and inform patient mutation testing and clinical management.
  • Inkinen, Tommi (Springer Singapore, 2015)
    Abstract This paper combines three location-based cases with literature background focusing on knowledge bases and cities. The paper considers the regional context of the city of Helsinki and its surrounding area (HMA). Analyzed cases include three specific locations highlighting urban form, connectivity and knowledge-intensive production. Conceptually innovative cities are experiencing extensive change as they transform and change in order to become competitive providers of first class living for highly skilled global work-force. The integration of spatial characteristics into analyses of knowledge intensiveness of cities brings forth new theoretical openings for urban analysis setting platforms for open innovation and economy. The paper focuses on extensive material resources collected in numerous projects. The data gives more reliable picture of the knowledge-intensive locations compared to single interviews or survey studies. The total data includes work and education statistics, stakeholder interviews and observation field work. Provided reflections are classified according to key issues presented in urban studies and economic geography.
  • Hemilä, Harri; Al-Biltagi, Mohammed; Baset, Ahmed A (BioMed Central Ltd, 2012)
    AbstractWe reported that the effect of vitamin C on asthma in Egyptian children was modified by age, exposure to dampness and the severity of asthma, Clinical & Translational Allergy 2011, 1:9. After our paper was published, we found out severe problems in the data set. There were 60 children in the study. The ages were by accident duplicated between the upper and lower halves of the database. Thus, the ages for the first 30 children in the data set were identical and in the same order with the ages for the second set of 30 children. Similar duplication was also found for C-ACT and FEV1 measurements after vitamin C supplementation and for exposure to dampness. This duplication thus directly invalidates the second part of the data set, and thus the reported outcome. We have not been able to sort out the reason for this duplication. The files with the original data are not available any more, making it impossible to reconstruct a valid data set for reanalysis. Therefore we have to retract our paper. The authors deeply regret the inconvenience this has caused to the journal and the scientific community.
  • Castellsagué, Xavier; Paavonen, Jorma; Jaisamrarn, Unnop; Wheeler, Cosette M; Skinner, S Rachel; Lehtinen, Matti; Naud, Paulo; Chow, Song-Nan; Del Rosario-Raymundo, Maria R; Teixeira, Julio C; Palmroth, Johanna; de Carvalho, Newton S; Germar, Maria JV; Peters, Klaus; Garland, Suzanne M; Szarewski, Anne; Poppe, Willy AJ; Romanowski, Barbara; Schwarz, Tino F; Tjalma, Wiebren AA; Bosch, F X; Bozonnat, Marie-Cecile; Struyf, Frank; Dubin, Gary; Rosillon, Dominique; Baril, Laurence; for the HPV PATRICIA Study Group (BioMed Central Ltd, 2014)
    Abstract Background More information is needed about time between sexual initiation and human papillomavirus (HPV) infection and development of cervical precancer. Methods The objectives were to investigate the time between first sexual activity and detection of first cervical HPV infection or development of first cervical intraepithelial neoplasia (CIN), and associated factors in women from the double-blind, multinational, 4-year PATRICIA trial. PATRICIA enroled women aged 15–25 years with no more than 6 lifetime sexual partners. Women were randomized 1:1 to the HPV-16/18 AS04-adjuvanted vaccine or to control, but only women from the control arm who began sexual intercourse during the study or within 6 months before enrolment, and had no HPV infection detected before the recorded date of their first sexual intercourse, were included in the present analysis. The time between onset of sexual activity and detection of the first cervical HPV infection or development of the first CIN lesion was analyzed using Kaplan-Meier and univariate and multivariable Cox proportional-hazards models. Results A total of 9337 women were enroled in the control arm of PATRICIA of whom 982 fulfilled the required inclusion criteria for analysis. A cumulative total of 28%, 44%, and 62% of the subjects had HPV infection within 12, 24, and 48 months, respectively. The overall incidence rate was 27.08 per 100 person-years. The most common oncogenic types associated with 6-month persistent infection were HPV-16 (incidence rate: 2.74 per 100 person-years), HPV-51 (2.70), HPV-52 (1.66), HPV-66 (1.14), and HPV-18 (1.09). Increased infection risk was associated with more lifetime sexual partners, being single, Chlamydia trachomatis history, and duration of hormone use. CIN1+ and CIN2+ lesions were most commonly associated with HPV-16, with an overall incidence rate of 1.87 and 1.07 per 100 person-years, respectively. Previous cervical HPV infection was most strongly associated with CIN development. Conclusions More than 25% of women were infected with HPV within 1 year of beginning sexual activity. Without underestimating the value of vaccination at older ages, our findings emphasize its importance before sexual initiation. Trial registration clinicaltrials.gov: NCT00122681.