BioMed Central -artikkelit


Uusimmat julkaisut

  • Kausar, Mehran; Siddiqi, Saima; Yaqoob, Muhammad; Mansoor, Sajid; Makitie, Outi; Mir, Asif; Khor, Chiea C; Foo, Jia N; Anees, Mariam (BioMed Central, 2018)
    Abstract Introduction Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disease with skeletal fragility and variable extra-skeletal manifestations. To date several point mutations in 18 different genes causing different types of OI have been identified. Mutations in WNT1 compromise activity of the osteoblasts leading to disturbed bone mass accrual, fragility fractures and progressive skeletal abnormalities. The present study was conducted to determine the underlying genetic cause of an autosomal recessive skeletal dysplasia in a large consanguineous family from Chinute, Pakistan. Materials and methods Blood was collected from 24 individuals of affected family along with clinical data. Homozygosity mapping was performed to confirm consanguinity. SNPs were identified, followed by whole exome and Sanger sequencing. In silico characterization of WNT1 mutation was performed using multiple platforms. Results Nine affected family members exhibited severe bone deformities, recurrent fractures, short stature and low bone mineral density. SNP array data revealed homozygous segments > 1 Mb in length accounting for 2.1–12.7% of the genome in affected individuals and their siblings and a single 6,344,821 bp homozygous region in all affected individuals on chromosome 12q12-q13. This region includes two potential OI candidate genes WNT1 and VDR. We did whole-exome sequencing for both genes in two patients and identified a novel damaging missense mutation in exon 4 of WNT1: c.1168G > T (NM_005430) resulting in p.G324C. Sanger sequencing confirmed segregation of mutation with the disease in family. Conclusion We report a novel mutation responsible for OI and our investigation expands the spectrum of disease-causing WNT1 mutations and the resulting OI phenotypes.
  • Haider, Najmul; Laaksonen, Sauli; Kjær, Lene J; Oksanen, Antti; Bødker, Rene (BioMed Central, 2018)
    Abstract Background In northern Finland (Lapland), reindeer are reared as semi-domesticated animals. The region has a short summer season of 2–3 months, yet reindeer are infected with the mosquito-borne filarioid parasite Setaria tundra. The infection causes peritonitis and perihepatitis, which cause significant economic losses due to reduced body weight of infected animals. The objective of this study was to: (i) describe the spatial and temporal pattern of outbreaks in three different areas across Finnish Lapland; and (ii) construct a temperature-driven mechanistic transmission model to quantify the potential role of temperature on intensity of S. tundra transmission in reindeer. Methods We developed a temperature-driven transmission model able to predict the number of S. tundra potentially transmitted from an infectious reindeer. We applied the model to the years 2004–2015, and compared the predictions to the proportion of reindeer whose livers were condemned due to S. tundra infection at the time of slaughter. Results The mean proportion of liver condemnation increased in reindeer slaughtered in late autumn/winter compared to earlier dates. The outbreaks were geographically clustered each year but there were no fixed foci where outbreaks occurred. Larger outbreaks were recorded in the southern regions of reindeer-herding areas compared to the central or northern parts of Lapland. Our model showed that temperatures never allowed for transmission of more than a single generation of S. tundra each season. In southern (Kuusamo) and central (Sodankylä) Lapland, our model predicted an increasing trend from 1979 to 2015 for both the duration of the effective transmission period of S. tundra (P < 0.001) and for the potential number of L3 S. tundra larvae being transmitted from an infectious reindeer (P < 0.001). Conclusions The effective transmission period for S. tundra in reindeer is very short in Lapland, but it increased over the period studied. Only one generation of S. tundra can be transmitted in one season among reindeer in Lapland. Increasing temperatures may facilitate a range expansion and increasing duration of effective transmission period for S. tundra.
  • Holopainen, Elina; Vakkilainen, Svetlana; Mäkitie, Outi (BioMed Central, 2018)
    Abstract Background Patients with cartilage-hair hypoplasia (CHH), a rare metaphyseal chondrodysplasia, manifest severe growth failure, variable immunodeficiency and increased risk of malignancies. The impact of CHH on gynecologic and reproductive health is unknown. Vulnerability to genital infections may predispose CHH patients to prolonged human papillomavirus (HPV) infections potentially leading to cervical, vaginal and vulvar cancer. Methods We carried out gynecologic evaluation, pelvic ultrasound and laboratory assessment in 19 women with genetically confirmed CHH. All patients were clinically examined and retrospective data were collected from hospital records. Results The women ranged in age from 19.2 to 70.8 years (median 40.8 years) and in height from 103 to 150 cm (median 123 cm). All women had undergone normal pubertal development as assessed by breast development according to Tanner scale and by age of menarche (mean 12.5 yrs., range 11–14 yrs). Despite significant short stature and potentially small pelvic diameters, a well-developed uterus with fairly normal size and shape was found by pelvic ultrasound in most of the patients. Ovarian follicle reserve, assessed by ultrasound was normal in relation to age in all premenopausal women it could be assessed (12 cases). Anti-Müllerian hormone was normal in relation to age in 17 women (89%). HPV was detected in 44% (8/18) and three women carried more than one HPV serotype; findings did not associate with immunological parameters. Three patients had a concurrent cell atypia in Pap smear. Conclusions Pubertal development, reproductive hormones and ovarian structure and function were usually normal in women with CHH suggesting fairly normal reproductive health. However, the immunodeficiency characteristic to CHH may predispose the patients to HPV infections. High prevalence of HPV infections detected in this series highlights the importance of careful gynecologic follow up of these patients.
  • Metsälä, Olli; Kreutzer, Joose; Högel, Heidi; Miikkulainen, Petra; Kallio, Pasi; Jaakkola, Panu M (BioMed Central, 2018)
    Abstract Background Cells in solid tumours are variably hypoxic and hence resistant to radiotherapy - the essential role of oxygen in the efficiency of irradiation has been acknowledged for decades. However, the currently available methods for performing hypoxic experiments in vitro have several limitations, such as a limited amount of parallel experiments, incapability of keeping stable growth conditions and dependence on CO2 incubator or a hypoxia workstation. The purpose of this study was to evaluate the usability of a novel portable system (Minihypoxy) in performing in vitro irradiation studies under hypoxia, and present supporting biological data. Materials and methods This study was conducted on cancer cell cultures in vitro. The cells were cultured in normoxic (~ 21% O2) or in hypoxic (1% O2) conditions either in conventional hypoxia workstation or in the Minihypoxy system and irradiated at dose rate 1.28 Gy/min ± 2.9%. The control samples were sham irradiated. To study the effects of hypoxia and irradiation on cell viability and DNA damage, western blotting, immunostainings and clonogenic assay were used. The oxygen level, pH, evaporation rate and osmolarity of the culturing media on cell cultures in different conditions were followed. Results The oxygen concentration in interest (5, 1 or 0% O2) was maintained inside the individual culturing chambers of the Minihypoxy system also during the irradiation. The radiosensitivity of the cells cultured in Minihypoxy chambers was declined measured as lower phosphorylation rate of H2A.X and increased clonogenic capacity compared to controls (OER~ 3). Conclusions The Minihypoxy system allows continuous control of hypoxic environment in multiple wells and is transportable. Furthermore, the system maintains the low oxygen environment inside the individual culturing chambers during the transportation and irradiation in experiments which are typically conducted in separate facilities.
  • Van Steenberge, Maarten; Raeymaekers, Joost A M; Hablützel, Pascal I; Vanhove, Maarten P M; Koblmüller, Stephan; Snoeks, Jos (BioMed Central, 2018)
    Abstract Background Species delineation is particularly challenging in taxa with substantial intra-specific variation. In systematic studies of fishes, meristics and linear measurements that describe shape are often used to delineate species. Yet, little is known about the taxonomic value of these two types of morphological characteristics. Here, we used Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika to test which of these types of characters best matched genetic lineages that could represent species in this group of stenotypic rock-dwelling cichlids. We further investigated intra-population variation in morphology. By linking this to a proxy of a population’s age, we could assess the evolutionary stability of different kinds of morphological markers. Results Morphological data was collected from 570 specimens originating from 86 localities. An AFLP approach revealed the presence of five lineages in the southern subbasin: T. moorii, T. brichardi, T. sp. ‘maculatus’, T. sp. ‘Mpimbwe’ and T. sp. ‘red’, which we consider to represent distinct species. Although both types of morphological data supported this classification, a comparison of PST-values that describe inter-population morphological differentiation, revealed a better correspondence between the taxon delineation based on AFLP data and the patterns revealed by an analysis of meristics than between the AFLP-based taxon delineation and the patterns revealed by an analysis of shape. However, classifying southern populations of Tropheus was inherently difficult as they contained a large amount of clinal variation, both in genetic and in morphological data, and both within and among species. A scenario is put forward to explain the current-day distribution of the species and colour varieties and the observed clinal variation across the subbasin’s shoreline. Additionally, we observed that variation in shape was larger in populations from shallow shores whereas populations from steep shores were more variable in meristics. This difference is explained in terms of the different timescales at which small and large scale lake level fluctuations affected populations of littoral cichlids at steep and shallow shores. Conclusions Our results showed meristics to be more evolutionary stable, and of higher taxonomic value for species delimitation in Tropheus, than linear measurements that describe shape. These results should be taken into account when interpreting morphological differences between populations of highly stenotypic species, such as littoral cichlids from the Great East African Lakes.
  • Kivimies, Kristiina; Repo-Tiihonen, Eila; Kautiainen, Hannu; Tiihonen, Jari (BioMed Central, 2018)
    Abstract Background Substance use disorders are associated with poorer clinical outcomes in patients with schizophrenia. There is no specific treatment for amphetamine or cannabis use disorder, but methadone and buprenorphine are used as replacement therapy in the treatment of opioid dependence. Our aim was to study whether patients with schizophrenia have received opioid replacement therapy for their opioid use disorder. Methods The study sample consisted of 148 individuals diagnosed with schizophrenia who were in involuntary psychiatric treatment as forensic patients in Finland in 2012. The proportion of the study sample with comorbid opioid use disorder having received opioid replacement therapy prior to their forensic psychiatric treatment was compared to the available information of opioid dependent patients in general. The data were collected from forensic examination statements, patient files and other medical registers retrospectively. Results Of the study sample, 15.6% (23/148) had a history of opioid use disorder, of whom 8.7% (2/23) had received opioid replacement treatment (95% confidence interval (Cl): 1.1–28.0), even though opioid use disorder had been diagnosed in the treatment system. According the available information the corresponding proportion among patients with opioid use disorder and using substance use disorder services was 30.4% (565/1860, 95% Cl: 28.3–32.5). The fraction of patients receiving opioid replacement therapy was significantly lower among patients with schizophrenia (p = 0.022). Conclusions Opioid replacement therapy was seldom used among schizophrenia patients who were later ordered to involuntary forensic psychiatric treatment. More attention should be paid to the possible use of opioids when planning treatment for patients with schizophrenia. Trial registration Our study is not a randomized controlled trial (but a register-based study); thus the trial registration is not applicable.
  • Santos, Susana; Eekhout, Iris; Voerman, Ellis; Gaillard, Romy; Barros, Henrique; Charles, Marie-Aline; Chatzi, Leda; Chevrier, Cécile; Chrousos, George P; Corpeleijn, Eva; Costet, Nathalie; Crozier, Sarah; Doyon, Myriam; Eggesbø, Merete; Fantini, Maria P; Farchi, Sara; Forastiere, Francesco; Gagliardi, Luigi; Georgiu, Vagelis; Godfrey, Keith M; Gori, Davide; Grote, Veit; Hanke, Wojciech; Hertz-Picciotto, Irva; Heude, Barbara; Hivert, Marie-France; Hryhorczuk, Daniel; Huang, Rae-Chi; Inskip, Hazel; Jusko, Todd A; Karvonen, Anne M; Koletzko, Berthold; Küpers, Leanne K; Lagström, Hanna; Lawlor, Debbie A; Lehmann, Irina; Lopez-Espinosa, Maria-Jose; Magnus, Per; Majewska, Renata; Mäkelä, Johanna; Manios, Yannis; McDonald, Sheila W; Mommers, Monique; Morgen, Camilla S; Moschonis, George; Murínová, Ľubica; Newnham, John; Nohr, Ellen A; Andersen, Anne-Marie N; Oken, Emily; Oostvogels, Adriëtte J J M; Pac, Agnieszka; Papadopoulou, Eleni; Pekkanen, Juha; Pizzi, Costanza; Polanska, Kinga; Porta, Daniela; Richiardi, Lorenzo; Rifas-Shiman, Sheryl L; Roeleveld, Nel; Santa-Marina, Loreto; Santos, Ana C; Smit, Henriette A; Sørensen, Thorkild I A; Standl, Marie; Stanislawski, Maggie; Stoltenberg, Camilla; Thiering, Elisabeth; Thijs, Carel; Torrent, Maties; Tough, Suzanne C; Trnovec, Tomas; van Gelder, Marleen M H J; van Rossem, Lenie; von Berg, Andrea; Vrijheid, Martine; Vrijkotte, Tanja G M; Zvinchuk, Oleksandr; van Buuren, Stef; Jaddoe, Vincent W V (BioMed Central, 2018)
    Abstract Background Gestational weight gain differs according to pre-pregnancy body mass index and is related to the risks of adverse maternal and child health outcomes. Gestational weight gain charts for women in different pre-pregnancy body mass index groups enable identification of women and offspring at risk for adverse health outcomes. We aimed to construct gestational weight gain reference charts for underweight, normal weight, overweight, and grades 1, 2 and 3 obese women and to compare these charts with those obtained in women with uncomplicated term pregnancies. Methods We used individual participant data from 218,216 pregnant women participating in 33 cohorts from Europe, North America, and Oceania. Of these women, 9065 (4.2%), 148,697 (68.1%), 42,678 (19.6%), 13,084 (6.0%), 3597 (1.6%), and 1095 (0.5%) were underweight, normal weight, overweight, and grades 1, 2, and 3 obese women, respectively. A total of 138, 517 women from 26 cohorts had pregnancies with no hypertensive or diabetic disorders and with term deliveries of appropriate for gestational age at birth infants. Gestational weight gain charts for underweight, normal weight, overweight, and grade 1, 2, and 3 obese women were derived by the Box-Cox t method using the generalized additive model for location, scale, and shape. Results We observed that gestational weight gain strongly differed per maternal pre-pregnancy body mass index group. The median (interquartile range) gestational weight gain at 40 weeks was 14.2 kg (11.4–17.4) for underweight women, 14.5 kg (11.5–17.7) for normal weight women, 13.9 kg (10.1–17.9) for overweight women, and 11.2 kg (7.0–15.7), 8.7 kg (4.3–13.4) and 6.3 kg (1.9–11.1) for grades 1, 2, and 3 obese women, respectively. The rate of weight gain was lower in the first half than in the second half of pregnancy. No differences in the patterns of weight gain were observed between cohorts or countries. Similar weight gain patterns were observed in mothers without pregnancy complications. Conclusions Gestational weight gain patterns are strongly related to pre-pregnancy body mass index. The derived charts can be used to assess gestational weight gain in etiological research and as a monitoring tool for weight gain during pregnancy in clinical practice.
  • Trevisan, Chiara; Sotiraki, Smaragda; Laranjo-González, Minerva; Dermauw, Veronique; Wang, Ziqi; Kärssin, Age; Cvetkovikj, Aleksandar; Winkler, Andrea S; Abraham, Annette; Bobić, Branko; Lassen, Brian; Cretu, Carmen M; Vasile, Cozma; Arvanitis, Dimitris; Deksne, Gunita; Boro, Ilievski; Kucsera, István; Karamon, Jacek; Stefanovska, Jovana; Koudela, Břetislav; Pavlova, Maja J; Varady, Marian; Pavlak, Marina; Šarkūnas, Mindaugas; Kaminski, Miriam; Djurković-Djaković, Olgica; Jokelainen, Pikka; Jan, Dagny S; Schmidt, Veronika; Dakić, Zorica; Gabriël, Sarah; Dorny, Pierre; Devleesschauwer, Brecht (BioMed Central, 2018)
    Abstract Background Taenia solium and Taenia saginata are food-borne parasites of global importance. In eastern Europe only fragmented information is available on the epidemiology of these zoonotic parasites in humans and animal populations. In particular for T. solium, on-going transmission is suspected. The aim of this systematic review was to collect the available data and describe the current knowledge on the epidemiology of T. solium and T. saginata in eastern Europe. Methods Literature published in international databases from 1990 to 2017 was systematically reviewed. Furthermore, local sources and unpublished data from national databases were retrieved from local eastern European experts. The study area included 22 countries. Results Researchers from 18 out of the 22 countries provided data from local and unpublished sources, while no contacts could be established with researchers from Belarus, Kosovo, Malta and Ukraine. Taeniosis and human cysticercosis cases were reported in 14 and 15 out of the 22 countries, respectively. Estonia, the Former Yugoslav Republic of Macedonia, Lithuania, Moldova, Poland, Romania, Serbia, and Slovakia reported cases of porcine cysticercosis. Croatia, Czech Republic, Estonia, Former Yugoslav Republic of Macedonia, Moldova, Poland, Romania, Serbia, Slovakia, and Ukraine reported bovine cysticercosis. Conclusions There is indication that taeniosis and cysticercosis are present across eastern Europe but information on the occurrence of T. solium and T. saginata across the region remains incomplete. Available data are scarce and species identification is in most cases absent. Given the public health impact of T. solium and the potential economic and trade implications due to T. saginata, notification of taeniosis and human cysticercosis should be implemented and surveillance and notification systems in animals should be improved.
  • Pajunen, Tuulia; Vuori, Erkki; Lunetta, Philippe (Springer International Publishing, 2018)
    Abstract Background Post-mortem (PM) ethanol production may hamper the interpretation of blood alcohol concentration (BAC) in victims of drowning. Different exclusion criteria (e.g. cases with low BAC or with protracted interval between death and toxicological analysis) have been proposed with no factual figures to reduce the potential bias due to PM ethanol production when examining the prevalence rates for alcohol-related drowning. The aim of this study is to verify the extent to which PM alcohol production may affect the accuracy of studies on drowning and alcohol. Findings Unintentional fatal drowning cases (n = 967) for which a full medico-legal autopsy and toxicological analysis was performed, in Finland, from 2000 to 2013, and relevant variables (demographic data of the victims, month of incident, PM submersion time, blood alcohol concentration, urine alcohol concentration (UAC), vitreous humour alcohol concentration (VAC) were available. Overall, out of 967 unintentional drownings, 623 (64.4%) were positive for alcohol (BAC > 0 mg/dL), 595 (61.5%) had a BAC ≥ 50 mg/dL, and 567 (58.6%) a BAC ≥ 100 mg/dL. Simultaneous measurements, in each victim, of BAC, UAC, and VAC revealed PM ethanol production in only 4 victims (BAC: 25 mg/dL – 48 mg/dL). These false positive cases represented 0.4% of drownings with BAC > 0 mg/dL and 14.3% of drownings with BAC > 0 mg/dL and < 50 mg/dL. Conclusions The present study suggests that PM ethanol production has a limited impact on research addressing the prevalence rate for alcohol-related drowning and that the use of too rigorous exclusion criteria, such as those previously recommended, may led to a significant underestimation of actual alcohol-positive drowning cases.
  • Delgado, M M; Tikhonov, G; Meyke, E; Babushkin, M; Bespalova, T; Bondarchuk, S; Esengeldenova, A; Fedchenko, I; Kalinkin, Y; Knorre, A; Kosenkov, G; Kozsheechkin, V; Kuznetsov, A; Larin, E; Mirsaitov, D; Prokosheva, I; Rozhkov, Y; Rykov, A; Seryodkin, I V; Shubin, S; Sibgatullin, R; Sikkila, N; Sitnikova, E; Sultangareeva, L; Vasin, A; Yarushina, L; Kurhinen, J; Penteriani, V (BioMed Central, 2018)
    Abstract Background For brown bears (Ursus arctos), hibernation is a critical part of the annual life cycle because energy savings during hibernation can be crucial for overwintering, and females give birth to cubs at that time. For hibernation to be a useful strategy, timing is critical. However, environmental conditions vary greatly, which might have a negative effect on the functionality of the evolved biological time-keeping. Here, we used a long-term dataset (69 years) on brown bear denning phenology recorded in 12 Russian protected areas and quantified the phenological responses to variation in temperature and snow depth. Previous studies analyzing the relationship between climate and denning behavior did not consider that the brown bear response to variation in climatic factors might vary through a period preceding den entry and exit. We hypothesized that there is a seasonal sensitivity pattern of bear denning phenology in response to variation in climatic conditions, such that the effect of climatic variability will be pronounced only when it occurs close to den exit and entry dates. Results We found that brown bears are most sensitive to climatic variations around the observed first den exit and last entry dates, such that an increase/decrease in temperature in the periods closer to the first den exit and last entry dates have a greater influence on the denning dates than in other periods. Conclusions Our study shows that climatic factors are modulating brown bear hibernation phenology and provide a further structuring of this modulation. The sensitivity of brown bears to changes in climatic factors during hibernation might affect their ability to cope with global climate change. Therefore, understanding these processes will be essential for informed management of biodiversity in a changing world.
  • Cruz, Cristina D; Shah, Shreya; Tammela, Päivi (BioMed Central, 2018)
    Abstract Background Biofilms are formed by a complex bacterial community encapsulated by a polymeric matrix, with strong adherent properties and persistent phenotype. Biofilms are considered one of the most challenging areas of modern medicine. Existing antibiotics have been developed against free-floating bacterial cells, and thus, many treatments of biofilm-related infection fail. In this study, we compared the effects of different media on biofilm growth of clinical reference strains of Staphylococci and Enterococci, including multi-drug resistant representatives. Further, we optimized the resazurin-based assay for determining the minimal biofilm inhibitory concentration (MBIC) of standard antibiotics, and evaluated its use for the determination of minimal biofilm eradication concentration (MBEC). Results We showed that tryptic soy broth supplemented with 1% glucose was an optimal media for maximum biofilm growth of all strains tested, with an extended incubation time for Enterococci. A range of parameters were tested for the resazurin assay, including concentration, temperature and time of incubation. Using quality parameters to analyze the assay’s performance, the conditions for the resazurin assay were set as follows: 4 μg/mL and 8 μg/mL, with incubation at 25 °C for 20 min and 40 min for Staphylococci and Enterococci, respectively. Conclusions In summary, we defined conditions for optimal biofilm growth and for standardized resazurin assay for MBIC determination against six Gram-positive clinical reference strains. We also observed that MBEC determination by the resazurin-based assay is limited due to the poor detection limit of the assay. Complementary cell counting data is needed for precise determination of MBEC.
  • Laaksonen, Maija; Klemola, Tero; Feuth, Eeva; Sormunen, Jani J; Puisto, Anna; Mäkelä, Satu; Penttinen, Ritva; Ruohomäki, Kai; Hänninen, Jari; Sääksjärvi, Ilari E; Vuorinen, Ilppo; Sprong, Hein; Hytönen, Jukka; Vesterinen, Eero J (BioMed Central, 2018)
    Abstract Background Almost 3500 tick samples, originally collected via a nationwide citizen science campaign in 2015, were screened to reveal the prevalence and distribution of a wide spectrum of established and putative tick-borne pathogens vectored by Ixodes ricinus and I. persulcatus in Finland. The unique geographical distribution of these two tick species in Finland allowed us to compare pathogen occurrence between an I. ricinus-dominated area (southern Finland), an I. persulcatus-dominated area (northern Finland), and a sympatric area (central Finland). Results Of the analysed ticks, almost 30% carried at least one pathogen and 2% carried more than one pathogen. A higher overall prevalence of tick-borne pathogens was observed in I. ricinus than in I. persulcatus: 30.0% (604/2014) versus 24.0% (348/1451), respectively. In addition, I. ricinus were more frequently co-infected than I. persulcatus: 2.4% (49/2014) versus 0.8% (12/1451), respectively. Causative agents of Lyme borreliosis, i.e. bacterial genospecies in Borrelia burgdorferi (sensu lato) group, were the most prevalent pathogens (overall 17%). “Candidatus Rickettsia tarasevichiae” was found for the first time in I. ricinus ticks and in Finnish ticks in general. Moreover, Babesia divergens, B. venatorum and “Candidatus Neoehrlichia mikurensis” were reported for the first time from the Finnish mainland. Conclusions The present study provides valuable information on the prevalence and geographical distribution of various tick-borne pathogens in I. ricinus and I. persulcatus ticks in Finland. Moreover, this comprehensive subset of ticks revealed the presence of rare and potentially dangerous pathogens. The highest prevalence of infected ticks was in the I. ricinus-dominated area in southern Finland, while the prevalence was essentially equal in sympatric and I. persulcatus-dominated areas. However, the highest infection rates for both species were in areas of their dominance, either in south or north Finland.
  • Korpela, Katri; Salonen, Anne; Vepsäläinen, Outi; Suomalainen, Marjo; Kolmeder, Carolin; Varjosalo, Markku; Miettinen, Sini; Kukkonen, Kaarina; Savilahti, Erkki; Kuitunen, Mikael; de Vos, Willem M (BioMed Central, 2018)
    Abstract Background Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches. Results The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant’s diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced. Conclusions The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding. Trial registration NCT00298337 . Registered March 2, 2006.
  • Brenner, Stephan; Mazalale, Jacob; Wilhelm, Danielle; Nesbitt, Robin C; Lohela, Terhi J; Chinkhumba, Jobiba; Lohmann, Julia; Muula, Adamson S; De Allegri, Manuela (BioMed Central, 2018)
    Abstract Background Results-based financing (RBF) describes health system approaches addressing both service quality and use. Effective coverage is a metric measuring progress towards universal health coverage (UHC). Although considered a means towards achieving UHC in settings with weak health financing modalities, the impact of RBF on effective coverage has not been explicitly studied. Methods Malawi introduced the Results-Based Financing For Maternal and Neonatal Health (RBF4MNH) Initiative in 2013 to improve quality of maternal and newborn health services at emergency obstetric care facilities. Using a quasi-experimental design, we examined the impact of the RBF4MNH on both crude and effective coverage of pregnant women across four districts during the two years following implementation. Results There was no effect on crude coverage. With a larger proportion of women in intervention areas receiving more effective care over time, the overall net increase in effective coverage was 7.1%-points (p = 0.07). The strongest impact on effective coverage (31.0%-point increase, p = 0.02) occurred only at lower cut-off level (60% of maximum score) of obstetric care effectiveness. Design-specific and wider health system factors likely limited the program’s potential to produce stronger effects. Conclusion The RBF4MNH improved effective coverage of pregnant women and seems to be a promising reform approach towards reaching UHC. Given the short study period, the full potential of the current RBF scheme has likely not yet been reached.
  • Pänkäläinen, Mikko; Fogelholm, Mikael; Valve, Raisa; Kampman, Olli; Kauppi, Markku; Lappalainen, Erja; Hintikka, Jukka (BioMed Central, 2018)
    Abstract Background Dietary habits have a great influence on physiological health. Even though this fact is generally recognized, people do not eat as healthily as they know they should. The factors that support a healthy diet, on the other hand, are not well known. It is supposed that there is a link between personal traits and dietary habits. Personal traits may also partially explain why some people manage to make healthy dietary changes while some fail to do so or are not able to try to make changes even when they desire to do so. There is some information suggesting that dispositional optimism plays a role in succeeding in improving dietary habits. The aim of this study was to determine the role of optimism and pessimism in the process of dietary changes. Methods Dispositional optimism and pessimism were determined using the revised Life Orientation Test in 2815 individuals (aged 52–76 years) participating in the GOAL study in the region of Lahti, Finland. The dietary habits of the study subjects were analysed. After 3 years, the subjects’ dietary habits and their possible improvements were registered. The associations between dispositional optimism and pessimism, dietary habits at baseline, and possible changes in dietary habits during the follow-up were studied with logistic regression. We also studied if the dietary habits or certain lifestyle factors (e.g. physical exercising and smoking) at baseline predicted success in improving the diet. Results Pessimism seemed to correlate clearly negatively with the healthiness of the dietary habits at baseline – i.e. the higher the level of pessimism, the unhealthier the diet. Optimism also showed a correlation with dietary habits at baseline, although to a lesser extent. Those who managed to improve their dietary habits during follow-up or regarded their dietary habits as healthy enough even without a change were less pessimistic at baseline than those who failed in their attempts to improve their diet or did not even try, even when they recognized the need for a change. Conclusions Pessimistic people are more likely to eat an unhealthy diet than others. Pessimism reduces independently the possibilities to improve dietary patterns.
  • Heliste, Juho; Jokilammi, Anne; Paatero, Ilkka; Chakroborty, Deepankar; Stark, Christoffer; Savunen, Timo; Laaksonen, Maria; Elenius, Klaus (BioMed Central, 2018)
    Abstract Background Receptor tyrosine kinases (RTK) are potential targets for the treatment of ischemic heart disease. The human RTK family consists of 55 members, most of which have not yet been characterized for expression or activity in the ischemic heart. Methods RTK gene expression was analyzed from human heart samples representing healthy tissue, acute myocardial infarction or ischemic cardiomyopathy. As an experimental model, pig heart with ischemia-reperfusion injury, caused by cardiopulmonary bypass, was used, from which phosphorylation status of RTKs was assessed with a phospho-RTK array. Expression and function of one RTK, ROR1, was further validated in pig tissue samples, and in HL-1 cardiomyocytes and H9c2 cardiomyoblasts, exposed to hypoxia and reoxygenation. ROR1 protein level was analyzed by Western blotting. Cell viability after ROR1 siRNA knockdown or activation with Wnt-5a ligand was assessed by MTT assays. Results In addition to previously characterized RTKs, a group of novel active and regulated RTKs was detected in the ischemic heart. ROR1 was the most significantly upregulated RTK in human ischemic cardiomyopathy. However, ROR1 phosphorylation was suppressed in the pig model of ischemia-reperfusion and ROR1 phosphorylation and expression were down-regulated in HL-1 cardiomyocytes subjected to short-term hypoxia in vitro. ROR1 expression in the pig heart was confirmed on protein and mRNA level. Functionally, ROR1 activity was associated with reduced viability of HL-1 cardiomyocytes in both normoxia and during hypoxia-reoxygenation. Conclusions Several novel RTKs were found to be regulated in expression or activity in ischemic heart. ROR1 was one of the most significantly regulated RTKs. The in vitro findings suggest a role for ROR1 as a potential target for the treatment of ischemic heart injury.
  • Tsai, Pei-Chien; Glastonbury, Craig A; Eliot, Melissa N; Bollepalli, Sailalitha; Yet, Idil; Castillo-Fernandez, Juan E; Carnero-Montoro, Elena; Hardiman, Thomas; Martin, Tiphaine C; Vickers, Alice; Mangino, Massimo; Ward, Kirsten; Pietiläinen, Kirsi H; Deloukas, Panos; Spector, Tim D; Viñuela, Ana; Loucks, Eric B; Ollikainen, Miina; Kelsey, Karl T; Small, Kerrin S; Bell, Jordana T (BioMed Central, 2018)
    Abstract Background Tobacco smoking is a risk factor for multiple diseases, including cardiovascular disease and diabetes. Many smoking-associated signals have been detected in the blood methylome, but the extent to which these changes are widespread to metabolically relevant tissues, and impact gene expression or metabolic health, remains unclear. Methods We investigated smoking-associated DNA methylation and gene expression variation in adipose tissue biopsies from 542 healthy female twins. Replication, tissue specificity, and longitudinal stability of the smoking-associated effects were explored in additional adipose, blood, skin, and lung samples. We characterized the impact of adipose tissue smoking methylation and expression signals on metabolic disease risk phenotypes, including visceral fat. Results We identified 42 smoking-methylation and 42 smoking-expression signals, where five genes (AHRR, CYP1A1, CYP1B1, CYTL1, F2RL3) were both hypo-methylated and upregulated in current smokers. CYP1A1 gene expression achieved 95% prediction performance of current smoking status. We validated and replicated a proportion of the signals in additional primary tissue samples, identifying tissue-shared effects. Smoking leaves systemic imprints on DNA methylation after smoking cessation, with stronger but shorter-lived effects on gene expression. Metabolic disease risk traits such as visceral fat and android-to-gynoid ratio showed association with methylation at smoking markers with functional impacts on expression, such as CYP1A1, and at tissue-shared smoking signals, such as NOTCH1. At smoking-signals, BHLHE40 and AHRR DNA methylation and gene expression levels in current smokers were predictive of future gain in visceral fat upon smoking cessation. Conclusions Our results provide the first comprehensive characterization of coordinated DNA methylation and gene expression markers of smoking in adipose tissue. The findings relate to human metabolic health and give insights into understanding the widespread health consequence of smoking outside of the lung.
  • Rosenblatt, Alana J; Lappalainen, Anu K; James, Nina A; Webster, Natalie S L; Caraguel, Charles G B (BioMed Central, 2018)
    Abstract Background The Dachshund is a chondrodystrophic breed of dog predisposed to premature degeneration and calcification, and subsequent herniation, of intervertebral discs (IVDs). This condition is heritable in Dachshunds and breeding candidates are screened for radiographically detectable intervertebral disc calcification (RDIDC), a feature of advanced disc degeneration and a prognostic factor for clinical disease. RDIDC scoring has been previously shown to be consistent within scorers; however, strong scorer effect (subjectivity) was also reported. The aim of this study was to estimate the within- and between-scorer agreement (repeatability and reproducibility, respectively) of computed tomography (CT) scanning and magnetic resonance imaging (MRI) for scoring IVD calcification, and to compare these modalities with radiographic scoring. Results Twenty-one Dachshund dogs were screened for IVD calcification using the three imaging modalities. Three scorers scored each case twice, independently. Repeatability was highest for radiography (95.4%), and significantly higher than for CT (90.4%) but not MRI (93.8%). Reproducibility was also highest for radiography (92.9%), but not significantly higher than for CT or MRI (89.4% and 86.4%, respectively). Overall, CT scored IVDs differently than radiography and MRI (64.8% and 62.7% agreement, respectively), while radiography and MRI scored more similarly (85.7% agreement). Conclusions Despite high precision for radiography, previous evidence of scorer subjectivity was confirmed, which was not generally observed with CT and MRI. The increased consistency of radiography may be related to prior scorer experience with the modality and RDIDC scoring. This study does not support replacing radiography with CT or MRI to screen for heritable IVD calcification in breeding Dachshunds; however, evaluation of dog-level precision and the accuracy of each modality is recommended.
  • Soukkio, Paula; Suikkanen, Sara; Kääriä, Sanna; Kautiainen, Hannu; Sipilä, Sarianna; Kukkonen-Harjula, Katriina; Hupli, Markku (BioMed Central, 2018)
    Abstract Background Health concerns, such as frailty and osteoporotic fractures decrease functional capacity and increase use of health and social care services in the aging population. The ability to continue living at home is dependent on functional capacity, which can be enhanced by rehabilitation. We study the effects of a 12-month home-based physiotherapy program with 12-month follow-up on duration of living at home, functional capacity, and the use of social and health care services among older persons with signs of frailty, or with a recently operated hip fracture. Methods This is a non-blinded, parallel group, randomized controlled trial performed in South Karelia Social and Health Care District, Finland (population 131,000). Three hundred community-dwelling older persons with signs of frailty (age ≥ 65) and 300 persons with a recent hip fracture (age ≥ 60) will be recruited. Frailty is screened by FRAIL questionnaire and verified by modified Fried’s frailty criteria. Both patient groups will be randomized separately to a physiotherapy and a usual care arm. Individualized, structured and progressive physiotherapy will be carried out for 60 min, twice a week for 12 months at the participant’s home. The primary outcome at 24 months is duration of living at home. Our hypothesis is that persons assigned to the physiotherapy arm will live at home for six months longer than those in the usual care arm. Secondary outcomes are functional capacity, frailty status, health-related quality-of-life, falls, use and costs of social and health care services, and mortality. Assessments, among others Short Physical Performance Battery, Functional Independence Measure, Mini Nutritional Assessment, and Mini-Mental State Examination will be performed at the participant’s home at baseline, 3, 6, and 12 months. Register data on the use and costs of social and health care services, and mortality will be monitored for 24 months. Discussion Our trial will provide new knowledge on the potential of intensive, long-term home-based physiotherapy among older persons at risk for disabilities, to enhance functional capacity and thereby to postpone the need for institutional care, and diminish the use of social and health care services. Trial registration Identifier: NCT02305433 , Registered Nov 28, 2014.
  • Topa, Hande; Honkela, Antti (BioMed Central, 2018)
    Abstract Background Genome-wide high-throughput sequencing (HTS) time series experiments are a powerful tool for monitoring various genomic elements over time. They can be used to monitor, for example, gene or transcript expression with RNA sequencing (RNA-seq), DNA methylation levels with bisulfite sequencing (BS-seq), or abundances of genetic variants in populations with pooled sequencing (Pool-seq). However, because of high experimental costs, the time series data sets often consist of a very limited number of time points with very few or no biological replicates, posing challenges in the data analysis. Results Here we present the GPrank R package for modelling genome-wide time series by incorporating variance information obtained during pre-processing of the HTS data using probabilistic quantification methods or from a beta-binomial model using sequencing depth. GPrank is well-suited for analysing both short and irregularly sampled time series. It is based on modelling each time series by two Gaussian process (GP) models, namely, time-dependent and time-independent GP models, and comparing the evidence provided by data under two models by computing their Bayes factor (BF). Genomic elements are then ranked by their BFs, and temporally most dynamic elements can be identified. Conclusions Incorporating the variance information helps GPrank avoid false positives without compromising computational efficiency. Fitted models can be easily further explored in a browser. Detection and visualisation of temporally most active dynamic elements in the genome can provide a good starting point for further downstream analyses for increasing our understanding of the studied processes.

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