Browsing by Subject "SAMPLES"

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  • Leskinen, Anumaija; Gautier, Celine; Räty, Antti; Kekki, Tommi; Laporte, Elodie; Giuliani, Margaux; Bubendorff, Jacques; Laurila, Julia Pauliina; Kurhela, Kristian Otto Aleksi; Fichet, Pascal; Salminen-Paatero, Susanna (2021)
    This paper reports the results obtained in a Nordic Nuclear Safety Research project during the second intercomparison exercise for the determination of difficult to measure radionuclides in decommissioning waste. Eight laboratories participated by carrying out radiochemical analysis of H-3, C-14, Cl-36, Ca-41, Fe-55 and Ni-63 in an activated concrete. In addition, gamma emitters, namely Eu-152 and Co-60, were analysed. The assigned values were derived from the submitted results according to ISO 13,528 standard and the performance assessments were determined using z scores. The measured results were compared with activation calculation result showing varying degree of comparability.
  • Svensson, Urban; Voutilainen, Mikko; Muuri, Eveliina; Ferry, Michel; Gylling, Björn (2019)
    A numerical reactive transport model for crystalline rocks is developed and evaluated. The model is based on mineral maps generated by X-ray micro computed tomography (X-μCT); the maps used have a resolution of approximately 30 μm and the rock samples are on the cm scale. A computational grid for the intergranular space is generated and a micro-DFN (Discrete Fracture Network) model governs the grid properties. A particle tracking method (Time Domain Random Walk) is used for transport simulations. The basic concept of the model can now be formulated as follows; “when a particle is close to a reactive mineral surface it has a certain probability to get sorbed during a certain time span. Once sorbed it will remain so a certain time”. The model requires a number of input parameters that represent the sorption properties of the reactive minerals. Attempts are made to relate the parameters to traditional distribution parameters. The model is evaluated by comparisons with recent laboratory experimental data. These experiments consider two rock types (veined gneiss and pegmatitic granite) and two radionuclides (cesium and barium). It is concluded that the new reactive transport model can simulate the experimental data in a consistent and realistic way.
  • Ambers, Angie; Turnbough, Meredith; Benjamin, Robert; Gill-King, Harrell; King, Jonathan; Sajantila, Antti; Budowle, Bruce (2016)
    Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors. Published by Elsevier Ireland Ltd.
  • Falgenhauer, Linda; Schwengers, Oliver; Schmiedel, Judith; Baars, Christian; Lambrecht, Oda; Hess, Stefanie; Berendonk, Thomas U.; Falgenhauer, Jane; Chakraborty, Trinad; Imirzalioglu, Can (2019)
    Water is considered to play a role in the dissemination of antibiotic-resistant Gram-negative bacteria including those encoding Extended-spectrum beta-lactamases (ESBL) and carbapenemases. To investigate the role of water for their spread in more detail, we characterized ESBL/Carbapenemase-producing bacteria from surface water and sediment samples using phenotypic and genotypic approaches. ESBL/Carbapenemase-producing isolates were obtained from water/sediment samples. Species and antibiotic resistance were determined. A subset of these isolates (n = 33) was whole-genome-sequenced and analyzed for the presence of antibiotic resistance genes and virulence determinants. Their relatedness to isolates associated with human infections was investigated using multilocus sequence type and cgMLST-based analysis. Eighty-nine percent of the isolates comprised of clinically relevant species. Fifty-eight percent exhibited a multidrug-resistance phenotype. Two isolates harbored the mobile colistin resistance gene mcr-1. One carbapenemase-producing isolate identified as Enterobacter kobei harbored bla(VIM-)(1). Two Escherichia coli isolates had sequence types (ST) associated with human infections (ST131 and ST1485) and a Klebsiella pneumoniae isolate was classified as hypervirulent. A multidrug-resistant (MDR) Pseudomonas aeruginosa isolate encoding known virulence genes associated with severe lung infections in cystic fibrosis patients was also detected. The presence of MDR and clinically relevant isolates in recreational and surface water underlines the role of aquatic environments as both reservoirs and hot spots for MDR bacteria. Future assessment of water quality should include the examination of the multidrug resistance of clinically relevant bacterial species and thus provide an important link regarding the spread of MDR bacteria in a One Health context.
  • Watzinger, Andrea; Schott, Katharina; Hood-Nowotny, Rebecca; Tamburini, Federica; Arppe, Laura; Cristini, Domiziana; Knoeller, Kay; Skrzypek, Grzegorz (2021)
    Rationale A silver phosphate reference material (Ag3PO4) for the measurement of stable oxygen isotope compositions is much needed; however, it is not available from the authorities distributing reference materials. This study aims to fill this gap by calibrating a new Ag3PO4 stable isotope comparison material produced by the University of Natural Resources and Life Sciences (BOKU). Methods Aliquots of Ag3PO4 were distributed to four laboratories who frequently measure the delta O-18 value in Ag3PO4; the University of Natural Resources and Life Sciences (BOKU), the University of Western Australia (UWA), the University of Helsinki (UH), and the Helmholtz Centre for Environmental Research (UFZ). The instruments used to perform the measurements were high-temperature conversion elemental analysers coupled with continuous flow isotope ratio mass spectrometers. The working gas delta O-18 value was set to 0 parts per thousand and the normalization was done by a three-point linear regression using the reference materials IAEA-601, IAEA-602, and NBS127. Results The mean delta O-18 value of the new BOKU Ag3PO4 comparison material on the VSMOW-SLAP scale is 13.71 parts per thousand and the combined uncertainty is estimated as +/- 0.34 parts per thousand. This estimated uncertainty is within the range typical for comparison materials of phosphates and sulphates. Consistent results from the different laboratories probably derived from similar instrumentation, and use of the same reference materials and normalization procedure. The matrix effect of the different reference materials used in this study was deemed negligible. Conclusions The BOKU Ag3PO4 can be used as an alternative comparison material for stable oxygen isotope analysis and is available for stable isotope research laboratories to facilitate calibration.
  • Granroth-Wilding, Hanna; Primmer, Craig; Lindqvist, Meri; Poutanen, Jenni; Thalmann, Olaf; Aspi, Jouni; Harmoinen, Jenni; Kojola, Ilpo; Laaksonen, Toni (2017)
    Background: Carnivores are re-establishing in many human-populated areas, where their presence is often contentious. Reaching consensus on management decisions is often hampered by a dispute over the size of the local carnivore population. Understanding the reproductive dynamics and individual movements of the carnivores can provide support for management decisions, but individual-level information can be difficult to obtain from elusive, wideranging species. Non-invasive genetic sampling can yield such information, but makes subsequent reconstruction of population history challenging due to incomplete population coverage and error-prone data. Here, we combine a collaborative, volunteer-based sampling scheme with Bayesian pedigree reconstruction to describe the pack dynamics of an establishing grey wolf (Canis lupus) population in south-west Finland, where wolf breeding was recorded in 2006 for the first time in over a century. Results: Using DNA extracted mainly from faeces collected since 2008, we identified 81 individual wolves and assigned credible full parentages to 70 of these and partial parentages to a further 9, revealing 7 breeding pairs. Individuals used a range of strategies to obtain breeding opportunities, including dispersal to established or new packs, long-distance migration and inheriting breeding roles. Gene flow occurred between all packs but inbreeding events were rare. Conclusions: These findings demonstrate that characterizing ongoing pack dynamics can provide detailed, locally-relevant insight into the ecology of contentious species such as the wolf. Involving various stakeholders in data collection makes these results more likely to be accepted as unbiased and hence reliable grounds for management decisions.
  • Youssef, Omar; Almangush, Alhadi; Zidi, Yossra H. S.; Loukola, Anu; Carpen, Olli (2020)
    Background:Archived formalin-fixed paraffin-embedded (FFPE) specimens from nonmalignant tissues derived from cancer patients are a vast and potentially valuable resource for high-quality genotyping analyses and could have a role in establishing inherited cancer risk. Methods:We systematically searched PubMed, Ovid MEDLINE, and Scopus databases for all articles that compared genotyping performance of DNA from nonmalignant FFPE tissue with blood DNA derived from cancer patients irrespective of tumor type. Two independent researchers screened the retrieved studies, removed duplicates, excluded irrelevant studies, and extracted genotyping data from the eligible studies. These studies included, but were not limited to, genotyping technique, reported call rate, and concordance. Results:Thirteen studies were reviewed, in which DNA from nonmalignant FFPE tissues derived from cancer patients was successfully purified and genotyped. All these studies used different approaches for genotyping of DNA from nonmalignant FFPE tissues to amplify single nucleotide polymorphisms (SNPs) and to estimate of loss of heterozygosity. The concordance between genotypes from nonmalignant FFPE tissues and blood derived from cancer patients was observed to be high, whereas the call rate of the tested SNPs was not reported in all included studies. Conclusion:This review illustrates that DNA from nonmalignant FFPE tissues derived from cancer patients can serve as an alternative and reliable source for assessment of germline DNA for various purposes, including assessment of cancer predisposition.
  • Vehkala, Minna; Shubin, Mikhail; Connor, Thomas R.; Thomson, Nicholas R.; Corander, Jukka (2015)
    Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells' respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active and non-active bacteria manifest completely different metabolism and thus should be treated separately. Effect identification, in turn, provides new insights into detecting differing respiration patterns between experimental conditions, e.g. between different combinations of strains and temperatures, as not only the main effects but also their interactions can be evaluated. In the effect identification, the multilevel data are effectively processed by a hierarchical model in the Bayesian framework. The pipeline is tested on a data set of 12 phenotypic plates with bacterium Yersinia enterocolitica. Our pipeline is implemented in R language on the top of opm R package and is freely available for research purposes.
  • Salminen-Paatero, Susanna; Thölix, Laura E; Kivi, Rigel; Paatero, Jussi (2019)
    Radionuclides 137Cs and 90Sr and total beta activity were determined from air filters collected in Rovaniemi (Finnish Lapland) in1965–2011. Nuclear contamination sources present in the air filter samples as well as temporal changes in radionuclide concentrations were examined. Ozone observations and meteorological modeling were used in combination with radionuclide analyses to study the reasons behind the observed seasonal concentration variation. In general, the magnitude and variation in activity concentrations of 137Cs and 90Sr and total beta activity in the surface air of Rovaniemi in 1965–2011 corresponded well with values from other countries. However, the obtained results prove in practice that hardly any refractory or intermediate radionuclides from the destroyed Chernobyl reactor fuel were introduced to Finnish Lapland. The main source of 137Cs and 90Sr and total beta activity in the surface air of Rovaniemi in 1965–2011 has been intense atmospheric nuclear weapon testing in 1950s–1960s and later tests performed in 1965–1980, as well as leakages from underground nuclear tests in Semipalatinsk, 1966, and Novaya Zemlya, 1987. For 137Cs and total beta activity, the influence of Chernobyl and Fukushima accidents was detected.
  • Eriksson, Mats; Ämmälä, Kirsi; Levy, Isabelle; Gastaud, Janine; Lehto, Jukka; Scholten, Jan (2019)
    To analyze plutonium (Pu) in open ocean waters can be challenging due to the low seawater concentrations. In this study we compared two techniques for Pu determination, one in-situ MnO2 cartridge system and the more commonly used MnO2 precipitation technique. During the pre-pilot GEOTRACES cruise ANT XXX-1 (2005) we tested MnO2 cartridges for the pre-concentration of Pu from seawater at 19 sampling stations on a transect in the southeastern Atlantic Ocean between Vigo (Spain) and Cape Town (South Africa). Our in-situ sampling setup consisted of one particle cartridge followed by three MnO2 cartridges in a series. Through the system we pumped between 956 and 2700 I of surface seawater with a flow rate between 1.6 and 5.21/min. We found that the adsorption efficiency of a single MnO2 cartridge to adsorb Pu was rather constant and on average a 58 +/- 7%. The adsorption efficiency was also found to be independent of seawater: temperature in the range of 18.3-29.2 degrees C, salinity range 34.2-37.1 parts per thousand, and conductivity in the range of 46.8-58.4 mS/cm. In parallel with the in-situ sampling, discrete surface water samples between 259 and 281 I were taken and Pu was pre-concentrated using the MnO2 precipitation method. We find a good agreement between the Pu concentrations determined with the two different techniques. The in-situ pre-concentration technique requires more radiochemical work in the laboratory but has the advantage that large seawater volumes can be sampled without the necessity for radiochemical processing on-board the ship. The much larger volumes sampled with the in-situ technique compared with the precipitation technique, enables accurate determination of Pu-isotopic ratios with a low relative standard deviation. We have shown in this study that in-situ MnO2 cartridge technique can be used in a reliable way for the determination of dissolved Pu seawater concentration in open ocean waters.
  • Kinnula, Sohvi; Hemminki, Kaisa; Kotilainen, Hannele; Ruotsalainen, Eeva; Tarkka, Eveliina; Salmenlinna, Saara; Hallanvuo, Saija; Leinonen, Elina; Jukka, Ollgren; Rimhanen-Finne, Ruska (2018)
    In August 2016, an outbreak of Shiga toxin-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) with 237 cases occurred in the Helsinki metropolitan area, Finland. Gastroenteritis cases were reported at 11 events served by one catering company. Microbiological and epidemiological investigations suggested rocket salad as the cause of the outbreak. STEC ONT:H-11 and EPEC O-111:H8 strains isolated from food samples containing rocket were identical to the patient isolates. In this outbreak, the reported symptoms were milder than considered before for STEC infection, and the guidelines for STEC control measures need to be updated based on the severity of the illness. Based on our experience in this outbreak, national surveillance criteria for STEC have been updated to meet the practice in reporting laboratories covering both PCR-positive and culture-confirmed findings. We suggest that EPEC could be added to the national surveillance since diagnostics for EPEC are routinely done in clinical laboratories.
  • van der Meijden, Els; Horvath, Barbara; Nijland, Marcel; de Vries, Karin; Raez, Emoke; Diercks, Gilles F.; de Weerd, Annelies E.; Clahsen-van Groningen, Marian C.; van der Blij-de Brouwer, Caroline S.; van der Zon, Arnulfo J.; Kroes, Aloys C. M.; Hedman, Klaus; van Kampen, Jeroen J. A.; Riezebos-Brilman, Annelies; Feltkamp, Mariet C. W. (2017)
    Classic human polyomaviruses (JC and BK viruses) become pathogenic when reactivating from latency. For the rare skin disease trichodysplasia spinulosa, we show that manifestations of the causative polyomavirus (TSPyV) occur during primary infection of the immunosuppressed host. High TSPyV loads in blood and cerebrospinal fluid, sometimes coinciding with cerebral lesions and neuroendocrine symptoms, marked the acute phase of trichodysplasia spinulosa, whereas initiation and maturation of TSPyV seroresponses occurred in the convalescent phase. TSPyV genomes lacked the rearrangements typical for reactivating polyomaviruses. These findings demonstrate the clinical importance of primary infection with this rapidly expanding group of human viruses and explain the rarity of some novel polyomavirus-associated diseases.
  • GoT2D T2D-GENES Consortium; SIGMA Consortium Helmsley IBD Exom; FinMetSeq Consortium; iPSYCH-Broad Consortium; Ganna, Andrea; Kurki, Mitja; Havulinna, Aki S.; Saarentaus, Elmo; Ripatti, Samuli; Hämäläinen, Eija; Moilanen, Jukka S.; Kuismin, Outi; Palotie, Aarno; Neale, Benjamin M. (2018)
    There is a limited understanding about the impact of rare protein-truncating variants across multiple phenotypes. We explore the impact of this class of variants on 13 quantitative traits and 10 diseases using whole-exome sequencing data from 100,296 individuals. Protein-truncating variants in genes intolerant to this class of mutations increased risk of autism, schizophrenia, bipolar disorder, intellectual disability, and ADHD. In individuals without these disorders, there was an association with shorter height, lower education, increased hospitalization, and reduced age at enrollment. Gene sets implicated from GWASs did not show a significant protein-truncating variants burden beyond what was captured by established Mendelian genes. In conclusion, we provide a thorough investigation of the impact of rare deleterious coding variants on complex traits, suggesting widespread pleiotropic risk.
  • Jian, Ching; Luukkonen, Panu; Yki-Järvinen, Hannele; Salonen, Anne; Korpela, Katri (2020)
    The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.
  • Dieckmann, Linda; Cruceanu, Cristiana; Lahti-Pulkkinen, Marius; Lahti, Jari; Kvist, Tuomas; Laivuori, Hannele; Sammallahti, Sara; Villa, Pia M.; Suomalainen-König, Sanna; Rancourt, Rebecca C.; Plagemann, Andreas; Henrich, Wolfgang; Eriksson, Johan G.; Kajantie, Eero; Entringer, Sonja; Braun, Thorsten; Räikkönen, Katri; Binder, Elisabeth B.; Czamara, Darina (2022)
    The placenta is a central organ during early development, influencing trajectories of health and disease. DNA methylation (DNAm) studies of human placenta improve our understanding of how its function relates to disease risk. However, DNAm studies can be biased by cell type heterogeneity, so it is essential to control for this in order to reduce confounding and increase precision. Computational cell type deconvolution approaches have proven to be very useful for this purpose. For human placenta, however, an assessment of the performance of these estimation methods is still lacking. Here, we examine the performance of a newly available reference-based cell type estimation approach and compare it to an often-used reference-free cell type estimation approach, namely RefFreeEWAS, in placental genome-wide DNAm samples taken at birth and from chorionic villus biopsies early in pregnancy using three independent studies comprising over 1000 samples. We found both reference-free and reference-based estimated cell type proportions to have predictive value for DNAm, however, reference-based cell type estimation outperformed reference-free estimation for the majority of data sets. Reference-based cell type estimations mirror previous histological knowledge on changes in cell type proportions through gestation. Further, CpGs whose variation in DNAm was largely explained by reference-based estimated cell type proportions were in the proximity of genes that are highly tissue-specific for placenta. This was not the case for reference-free estimated cell type proportions. We provide a list of these CpGs as a resource to help researchers to interpret results of existing studies and improve future DNAm studies of human placenta.
  • Kolmeder, Carolin A.; de Vos, Willem M. (2021)
    It is known for more than 100 years that the intestinal microbes are important for the host's health and the last decade this is being intensely studied with a focus on the mechanistic aspects. Among the fundamental functions of the intestinal microbiome are the priming of the immune system, the production of essential vitamins and the energy harvest from foods. By now, several dozens of diseases, both intestinal and non-intestinal related, have been associated with the intestinal microbiome. Initially, this was based on the description of the composition between groups of different health status or treatment arms based on phylogenetic approaches based on the 16S rRNA gene sequences. This way of analysis has mostly moved to the analysis of all the genes or transcripts of the microbiome i.e. metagenomics and meta-transcriptomics. Differences are regularly found but these have to be taken with caution as we still do not know what the majority of genes of the intestinal microbiome are capable of doing. To circumvent this caveat researchers are studying the proteins and the metabolites of the microbiome and the host via metaproteomics and metabolomics approaches. However, also here the complexity is high and only a fraction of signals obtained with high throughput instruments can be identified and assigned to a known protein or molecule. Therefore, modern microbiome research needs advancement of existing and development of new analytical techniques. The usage of model systems like intestinal organoids where samples can be taken and processed rapidly as well as microfluidics systems may help. This review aims to elucidate what we know about the functionality of the human intestinal microbiome, what technologies are advancing this knowledge, and what innovations are still required to further evolve this actively developing field. (C) 2020 The Authors. Published by Elsevier B.V.
  • Lan, Hangzhen; Zhang, Wenzhong; Smått, Jan-Henrik; Koivula, Risto; Hartonen, Kari; Riekkola, Marja-Liisa (2019)
    Mesoporous silica-coated solid phase microextraction (SPME) Arrow systems were developed for capturing of low-molecular-weight aliphatic amines (LMWAAs) from complicated sample matrices. Specifically, silicas of type MCM-41, SBA-15 and KIT-6 were chosen as substrates to afford size-exclusion selectivity. They possess ordered multidimensional pore-channel structures and mesopore sizes between 3.8 and 8.2 nm. Their surface acidity was enhanced by grafting them with a layer of titanium hydrogenphosphate (-TP). This enhanced the chemical selectivity for basic LMWAAs. The siliceous coatings increased the extraction of ethylamine, diethylamine (DEA) and triethylamine (TEA) by factors of 18.6–102.5, 4.8–10.8 and 2.6–4.0, respectively, when compared to the commercial SPME Arrow with polydimethylsiloxane/divinylbenzene coating. Among them, the MCM-41 and MCM-41-TP coated SPME Arrows demonstrated exceptional selectivity towards LMWAAs that were quantified by gas chromatography-mass spectrometry (GC-MS). The total peak area ratios of LMWAAs/ten competing compounds were 25.4 and 36.3, respectively. The extraction equilibrium was reached within 20–30 min. The MCM-41 and MCM-41-TP derived SPME Arrows gave very similar results (18.4 ± 2.1–376 ± 12 ng g−1 to DEA and TEA) when applied to urban mushroom samples. SPME Arrow with MCM-41 coatings followed by GC-MS was applied also to the analysis of atmospheric air and urine samples resulting in high selectivity due to the size and mesoporous structure of the functionalized silica, and its chemical interactions with the LMWAAs.
  • Nascimento-Carvalho, Amanda C.; Vilas-Boas, Ana-Luisa; Fontoura, Maria-Socorro H.; Xu, Man; Vuorinen, Tytti; Söderlund-Venermo, Maria; Ruuskanen, Olli; Nascimento-Carvalho, Cristiana M.; PNEUMOPAC-Efficacy Study Grp (2018)
    AimTo assess the role of human bocavirus 1 (HBoV1) as a causative agent of non-severe community-acquired pneumonia (CAP) in children. MethodsPatients aged 2-59 months with non-severe CAP (respiratory complaints and radiographic pulmonary infiltrate/consolidation) attending a University Hospital in Salvador, Brazil were enrolled in a prospective cohort. From 820 recruited children in a clinical trial ( NCT01200706), nasopharyngeal aspirate (NPA), and acute and convalescent serum samples were obtained from 759 (92.6%) patients. NPAs were tested for 16 respiratory viruses by PCR. Acute HBoV1 infection was confirmed by measuring specific IgM and IgG responses in paired serum samples. ResultsRespiratory viruses were detected in 693 (91.3%; 95%CI: 89.1-93.2) CAP cases by PCR. HBoV1-DNA was detected in 159 (20.9%; 95%CI: 18.2-24.0) cases. Of these 159 PCR positive cases, acute HBoV1 infection was confirmed serologically in 38 cases (23.9%; 95%CI: 17.8-31.0). Overall, acute HBoV1 infection was confirmed in 5.0% (38/759) of non-severe CAP patients. HBoV1 was detected in 151 cases with at least one other virus making 31.7% of all multiple virus (n=477) detections. Among all 759 cases, 216 had one respiratory virus detected, and sole HBoV1 was detected in only 8 (3.7%). Acute HBoV1 infection was serologically diagnosed in 34 (22.5%) HBoV1-DNA-positive cases with another virus, compared to 4 (50.0%) cases with sole virus detection (p=0.09). ConclusionHBoV1 was detected by PCR in one fifth of the children with non-severe CAP and acute HBoV1 infection was serologically confirmed in one quarter of these cases.
  • Ojanpera, Ilkka; Mesihää, Samuel; Rasanen, Ilpo; Pelander, Anna; Ketola, Raimo A. (2016)
    A novel platform is introduced for simultaneous identification and quantification of new psychoactive substances (NPS) in blood matrix, without the necessity of using authentic reference standards. The instrumentation consisted of gas chromatography (GC) coupled to nitrogen chemiluminescence detection (NCD) and atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (APCI-QTOFMS). In this concept, the GC flow is divided in appropriate proportions between NCD for single-calibrant quantification, utilizing the detector's equimolar response to nitrogen, and QTOFMS for accurate mass-based identification. The principle was proven by analyzing five NPS, bupropion, desoxypipradrol (2-DPMP), mephedrone, methylone, and naphyrone, in sheep blood. The samples were spiked with the analytes post-extraction to avoid recovery considerations at this point. All the NPS studies produced a protonated molecule in APCI resulting in predictable fragmentation with high mass accuracy. The N-equimolarity of quantification by NCD was investigated by using external calibration with the secondary standard caffeine at five concentration levels between 0.17 and 1.7 mg/L in blood matrix as five replicates. The equimolarity was on average 98.7 %, and the range of individual equimolarity determinations was 76.7-130.1 %. The current analysis platform affords a promising approach to instant simultaneous qualitative and quantitative analysis of drugs in the absence of authentic reference standards, not only in forensic and clinical toxicology but also in other bioanalytical applications.
  • El Fellah, Samira; Duporte, Geoffroy; Siren, Heli (2017)
    Steroid hormones, botrydial, and inorganic ions were studied from cold and hot tap water samples with capillary electrophoresis techniques using UV detection. Identification of the steroids and botrydial was made with ultra-high -performance liquid chromatography (UHPLC) coupled to electrospray ionization orbitrap high-resolution mass spectrometry. Solid phase extraction with nonpolar and ion-exchange sorbents was needed to enrich the compounds for CE and UHPLC studies. The steroids identified from the drinking water samples were estradiol glucoside, androstenedione, testosterone, and progesterone. However, only progesterone could be quantified in both cold and hot tap water samples from Helsinki households. Its concentration varied from 0.031 ng/L to 0.135 ng/L and from 0.054 ng/L to 0.191 ng/L, respectively. Chloride and nitrate amounts were 25 mg/L. Calcium, potassium, magnesium, and sodium were 20, 1, 1, and 17 mg/L at the highest, respectively. Copper, iron, sulphate, and ammonium were below the methods concentration limits. Botrydial from Botrytis cinerea mould was identified in all drinking waters. In both cold and hot tap waters its concentration was 861-3900% higher than in a drilled well water that was also used as the household tap water. The mould was also confirmed by identification of its metabolite abscisic acid. (C) 2017 Elsevier B.V. All rights reserved.