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  • Eriksson, Sari (Suomen Venäjän ja Itä-Euroopan tutkimuksen seura, 2013)
  • Granqvist, Niko; Hanning, Anders; Eng, Lars; Tuppurainen, Jussi; Viitala, Tapani (Molecular Diversity Preservation International (MDPI), 2013)
  • Lindström, M.; Korkeala, H. (American Society for Microbiology, 2006)
    Botulism is a potentially lethal paralytic disease caused by botulinum neurotoxin. Human pathogenic neurotoxins of types A, B, E, and F are produced by a diverse group of anaerobic spore-forming bacteria, including Clostridium botulinum groups I and II, Clostridium butyricum, and Clostridium baratii. The routine laboratory diagnostics of botulism is based on the detection of botulinum neurotoxin in the patient. Detection of toxin-producing clostridia in the patient and/or the vehicle confirms the diagnosis. The neurotoxin detection is based on the mouse lethality assay. Sensitive and rapid in vitro assays have been developed, but they have not yet been appropriately validated on clinical and food matrices. Culture methods for C. botulinum are poorly developed, and efficient isolation and identification tools are lacking. Molecular techniques targeted to the neurotoxin genes are ideal for the detection and identification of C. botulinum, but they do not detect biologically active neurotoxin and should not be used alone. Apart from rapid diagnosis, the laboratory diagnostics of botulism should aim at increasing our understanding of the epidemiology and prevention of the disease. Therefore, the toxin-producing organisms should be routinely isolated from the patient and the vehicle. The physiological group and genetic traits of the isolates should be determined.
  • Lokki, A I; Järvelä, Irma; Israelsson, Elisabeth; Maiga, Bakary; Troye-Blomberg, Marita; Dolo, Amagana; Doumbo, Ogobara K; Meri, Seppo; Holmberg, Ville (BioMed Central Ltd, 2011)
    Abstract Background Fulani are a widely spread African ethnic group characterized by lower susceptibility to Plasmodium falciparum, clinical malaria morbidity and higher rate of lactase persistence compared to sympatric tribes. Lactase non-persistence, often called lactose intolerance, is the normal condition where lactase activity in the intestinal wall declines after weaning. Lactase persistence, common in Europe, and in certain African people with traditions of raising cattle, is caused by polymorphisms in the enhancer region approximately 14 kb upstream of the lactase gene. Methods To evaluate the relationship between malaria and lactase persistence genotypes, a 400 bp region surrounding the main European C/T-13910 polymorphism upstream of the lactase gene was sequenced. DNA samples used in the study originated from 162 Fulani and 79 Dogon individuals from Mali. Results Among 79 Dogon only one heterozygote of the lactase enhancer polymorphism was detected, whereas all others were homozygous for the ancestral C allele. Among the Fulani, the main European polymorphism at locus C/T-13910 was by far the most common polymorphism, with an allele frequency of 37%. Three other single-nucleotide polymorphisms were found with allele frequencies of 3.7%, 1.9% and 0.6% each. The novel DNA polymorphism T/C-13906 was seen in six heterozygous Fulani. Among the Fulani with lactase non-persistence CC genotypes at the C/T-13910 locus, 24% had malaria parasites detectable by microscopy compared to 18% for lactase persistent genotypes (P = 0.29). Pooling the lactase enhancer polymorphisms to a common presumptive genotype gave 28% microscopy positives for non-persistent and 17% for others (P = 0.11). Conclusions Plasmodium falciparum parasitaemia in asymptomatic Fulani is more common in individuals with lactase non-persistence genotypes, but this difference is not statistically significant. The potential immunoprotective properties of dietary cow milk as a reason for the partial malaria resistance of Fulani warrant further investigation.
  • Lyhs, Ulrike; Korkeala, Hannu; Vandamme, Peter; Björkroth, Johanna (Elsevier, 2001)
    Spoilage characterised by bulging of lids and gas formation affected various product lots of different marinated herring types. Microbiological analyses resulted in growth on MRS and Rogosa SL agar. Altogether, 206 randomly selected colonies from two unspoiled and ten spoiled samples were characterised using phenotypical key tests and a 16123S rRNA gene-based RFLP identification database. L. alimentarius was found to be the specific spoilage organism in all samples. All isolates obtained from the different product types were of the same clonal type. The slight rise in pH value together with marked gas production suggested a rare lactic acid bacteria spoilage type called ‘protein swell’. L. alimentarius has not been previously associated with herring spoilage.
  • Koort, Joanna; Vandamme, Peter; Schillinger, Ulrich; Holzapfel, Wilhelm; Björkroth, Johanna (Society for General Microbiology, 2004)
    On the basis of phenotypic and DNA-DNA reassociation studies, strain CCUG 34545T has been considered to represent a distinct Lactobacillus curvatus subspecies, Lactobacillus curvatus subsp. melibiosus. However, in several independent studies dealing with Lactobacillus sakei and L. curvatus strains, the subspecies division of L. curvatus has been found to be controversial. The original study distinguishing the two subspecies within both L. curvatus and L. sakei also lacked 16S rRNA gene sequence analyses. Therefore, the taxonomic position of L. curvatus subsp. melibiosus CCUG 34545T was re-evaluated in a polyphasic taxonomy study that included 16S rRNA gene sequence analysis, DNA-DNA reassociation, DNA G+C content deternmination, numerical analysis of ribotypes and whole-cell protein patterns and the examination of some fundamental phenotypic properties. The results obtained indicate that strain CCUG 34545T and its duplicate, CCUG 41580T, are Lactobacillus sakei subsp. carnosus strains and that L. curvatus subsp. melibiosus is a later synonym of L. sakei subsp. carnosus.
  • Björkroth, Johanna; Korkeala, Hannu (International Association for Food Protection, 1997)
    Spoilage characterized by bulging as a result of gas formation in bottled ketchup was studied and resulted in growth on MRS and Rogosa selective Lactobacillus agar. Seventy randomly selected isolates were typed using restriction endonuclease analysis (ClaI, EcoRI, HindIII) and were found to have identical patterns. The strain was identified as Lactobacillus fructivorans using morphological, physiological and biochemical characteristics, combined with information obtained from rRNA gene restriction patterns. Factors affecting growth and survival of this L. fructivorans strain in production circumstances were also studied. Lactobacillus count of 105 CFU/g resulted in spoilage of inoculated ketchup samples. Spoilage occurred only in samples incubated at 15 to 30°C. L. fructivorans implicated in causing spoilage demonstrated heat resistance with a D-value of 1.2 min at 65°C. The strain did not show resistance against alkaline, active chloride containing detergent sanitizer, and also alkyldimethylbenzyl ammonium chloride and alkyldimethylethylbenzyl ammonium chloride containing sanitizer was found to be effective against it.
  • Koort, Joanna; Murros, Anna; Coenye, Tom; Eerola, Susanna; Vandamme, Peter; Sukura, Antti; Björkroth, Johanna (American Society for Microbiology (ASM), 2005)
    Unidentified lactic acid bacterium (LAB) isolates which had mainly been detected in spoiled, marinated, modified atmosphere packaged (MAP) broiler meat products during two previous studies were identified and analyzed for their phenotypic properties and the capability to produce biogenic amines. To establish the taxonomic position of these isolates, 16S rRNA gene sequence analysis, numerical analysis of ribopatterns, and DNA-DNA hybridization experiments were done. Unexpectedly for a meat spoilage associated LAB, the strains utilized glucose very weakly. According to the API 50 CHL test, arabinose and xylose were the only carbohydrates strongly fermented. None of the six strains tested for production of histamine, tyramine, tryptamine, phenylethylamine, putrescine and cadaverine were able to produce these main meat-associated biogenic amines in vitro. Polyphasic taxonomy approach showed that these strains represent a new Lactobacillus species. The six isolates sequenced for the 16S rRNA encoding genes shared the highest similarity (95.0 to 96.3%) with the sequence of the Lactobacillus durianis type strain. In the phylogenetic tree, these isolates formed a distinct cluster within the Lactobacillus reuteri -group which also includes L. durianis. Numerical analyses of HindIII/EcoRI ribotypes placed all isolates together in a cluster with seven subclusters well-separated from the L. reuteri group reference strains. The DNA-DNA hybridization levels between Lactobacillus sp. nov. isolates varied from 67 to 96% and low hybridization levels (3-15%) were obtained with the L. durianis type strain confirming that these isolates belong to same species different from L. durianis. The name Lactobacillus oligofermentans sp. nov. is proposed, with strain LMG 22743T (=DSM 15707T =AMKR18 T) as the type strain.
  • Weitschek, Emanuel; Cunial, Fabio; Felici, Giovanni (BioMed Central, 2015)
    Abstract Alignment-free algorithms can be used to estimate the similarity of biological sequences and hence are often applied to the phylogenetic reconstruction of genomes. Most of these algorithms rely on comparing the frequency of all the distinct substrings of fixed length (k-mers) that occur in the analyzed sequences. In this paper, we present Logic Alignment Free (LAF), a method that combines alignment-free techniques and rule-based classification algorithms in order to assign biological samples to their taxa. This method searches for a minimal subset of k-mers whose relative frequencies are used to build classification models as disjunctive-normal-form logic formulas (if-then rules). We apply LAF successfully to the classification of bacterial genomes to their corresponding taxonomy. In particular, we succeed in obtaining reliable classification at different taxonomic levels by extracting a handful of rules, each one based on the frequency of just few k-mers. State of the art methods to adjust the frequency of k-mers to the character distribution of the underlying genomes have negligible impact on classification performance, suggesting that the signal of each class is strong and that LAF is effective in identifying it.
  • Alaspää, Katariina; Muukkonen, Petteri; Mäkipää, Raisa (Metsäntutkimuslaitos, 2015)
    Tutkimuksen tarkoituksena oli selvittää lahopuun merkitystä kuusivaltaisen luonnonmetsän uudistumisessa. Tutkimme tätä mittaamalla kuusentaimien määrää ja kasvua lahopuulla ja muilla metsän kasvualustoilla. Muut kasvualustaluokat olivat sammal sekä karike/muu. Lisäksi analysoimme lahopuun vedenpidätysominaisuuksia ja hiili-typpisuhdetta (C/N), jotka kuvaavat eri lahovaiheessa olevan lahopuun laatua kasvualustana. Osoitimme, että vanhassa kuusivaltaisessa metsässä lahopuulla kasvaa lähes kolmannes taimista vaikka lahopuukasvualustan osuus pinta-alasta on vain 2%. Lahopuulla on siis tärkeä merkitys luonnonmetsän uudistumisessa. Erityisen runsaasti taimia kasvoi lahoasteen 4 maapuilla (lahoasteluokittelu 1–5, jossa 5 on pisimmälle lahonnut). Pitkälle lahonneet maapuut ovat siis taimille hyviä itämisalustoja ja taimien pituuskasvu pitkälle lahonneella puulla ei poikennut muilla kasvualustoilla havaitusta. Muiden lahoasteiden maapuilla taimien keskipituus ja pituuden keskimääräinen vuosikasvu olivat puolestaan pienempää kuin ympäröivällä metsänpohjalla kasvavilla taimilla. Lahopuu on hyvin typpiköyhä kasvualusta, mutta sillä on hyvät vedenpidätysominaisuudet. Lahoamisen edetessä sekä vedenpidätyskyky että typpipitoisuus kasvavat.
  • Belikov, Nikolai; Yakovleva, Marina; Feldman, Tatiana; Demina, Olga; Khodonov, Andrei; Lindström, Magnus; Donner, Kristian; Ostrovsky, Mikhail (PUBLIC LIBRARY OF SCIENCE, 2014)
  • Pareyon, Gabriel (2007)
    In Aztec mythology and religion, Xipe Totec ("our lord the flayed one") was a life-death-rebirth deity, god of agriculture, vegetation, the east, disease, spring, goldsmiths, silversmiths and the seasons. The music used for his worship has been described by a diversity of documents (carved stones, depicted codices, and chronicles made by the first European friars arrived to Mexico). This article explores the symbolic content of these descriptions, especially in association with Xochipilli Macuilxochitl, master of music and poetry.
  • Aalto, Daniel; Simko, Juraj; Vainio, Martti (2013)
    The fundamental frequency of a complex sound modulates the perceived duration of a sound. Higher pitch sounds are perceived longer compared to lower pitch sounds as shown by several independent studies since 1973. In this paper, the effect of language background is studied: native speakers of Finnish and German participated in a two alternative forced choice duration discrimination experiment where the duration and frequency of two sounds are randomly varied. The overall duration discrimination sensitivity was similar to both groups but the speakers of Finnish were influenced more by the pitch in their judgements. In addition, the difference in the two sounds’ pitch period explained the response data better than the difference in pitch frequencies or the pitch interval. As the Finnish quantity system is known to employ both duration and pitch cues, the present results suggest that the speakers are shaped by the language environment even when the task is purely non-linguistic.
  • Nevalainen, Terttu; Vartiainen, Turo; Säily, Tanja; Kesäniemi, Joonas; Dominowska, Agata; Öhman, Emily (NORWEGIAN COMPUTING CENTRE FOR THE HUMANITIES, 2016)
    We introduce the Language Change Database (LCD), which provides access to the results of previous corpus-based research dealing with change in the English language. The LCD will be published on an open-access linked data platform that will allow users to enter information about their own publications into the database and to conduct searches based on linguistic and extralinguistic parameters. Both metadata and numerical data from the original publications will be available for download, enabling systematic reviews, meta-analyses, replication studies and statistical modelling of language change. The LCD will be of interest to scholars, teachers and students of English.
  • Jauhiainen, Tommi Sakari; Linden, Krister; Jauhiainen, Heidi Annika (2015)
    In this paper, we reconsider the problem of language identification of multilingual documents. Automated language identification algorithms have been improving steadily from the seventies until recent years. The current state-of-the-art language identifiers are quite efficient even with only a few characters and this gives us enough reason to again evaluate the possibility to use existing language identifiers for monolingual text to detect the language set of a multilingual document. We are using a previously developed language identifier for monolingual documents with the multilingual documents from the WikipediaMulti dataset published in a recent study. Our method outperforms previous methods tested with the same data, achieving an F 1-score of 97.6 when classifying between 44 languages.
  • Snellman, Hanna (Oulun Historiaseura, 2008)
    Scripta Historica;33
    Aloittaessani tutkimushankkeen "Göteborg - Sallan suurin kylä" vuonna 2000 olin astumassa maailmaan, joka oli minulle vieras.' Saadakseni esiymmärrystä tutkimuskohteestani, ruotsinsuomalaisista, aloin seurata Ruotsissa ilmestyvää suomenkielistä sanomalehteä Viikkoviestiä. Luin niin artikkeleita, mainoksia kuin ilmoituksiakin. Lehteä säännöllisesti lukiessani kiinnitin melko pian huomiota siihen, että sana Lappi esiintyi lehden henkilökohtaista- palstalla kumppaninhakuilmoituksissa useammin kuin mikään muu alue Suomessa. Karjala tuli hyvänä kakkosena. Vuosien varrella lehden nimi muuttui Ruotsin Sanomiksi. Alun lyhyen tauon jälkeen lehden välityksellä oli edelleen kerran viikossa mahdollisuus hakea ystävää. Kun Ruotsin Sanomat -lehden ilmestyminen päättyi, päättyi myös aineistonkeruuni. Vuosina 2000-2005 poimin systemaattisesti lehden henkilökohtaista-palstalta kaikki ne ilmoitukset, joissa mainitaan tavalla tai toisella Matillekin niin rakas Pohjois-Suomi. Näitä ilmoituksia on yhteensä 23 kappaletta, joista 13:ssa mies etsii naista ja kymmenessä nainen miestä. Tässä artikkelissa esittelen ilmoitusten tyypillisiä piirteitä ja pohdin sitä, miksi juuri Lappi kaikista Suomen maakunnista esiintyy ilmoituksissa niin usein.
  • Lignell, Antti; Khriachtchev, Leonid; Pettersson, Mika; Räsänen, Markku (American Institute of Physics, 2002)
  • Merilä, Juha; Lakka, Hanna-Kaisa; Eloranta, Antti (BioMed Central, 2013)
    Background Little is known about variation in catch per unit of effort (CPUE) in stickleback fisheries, or the factors explaining this variation. We investigated how nine-spined stickleback (Pungitius pungitius) CPUE was influenced by trap model by comparing the CPUEs of two very similar minnow trap models fished side-by-side in a paired experimental design. Results The galvanized trap type (mean CPUE = 1.31 fish h–1) out-fished the black trap type (mean CPUE = 0.20 fish h–1) consistently, and yielded on average 81% more fish. Conclusions The results demonstrate that small differences in trap appearance can have large impacts on CPUE. This has implications for studies designed to investigate abundance and occurrence of fish using minnow traps.
  • Kauppi, Pekka E.; Posch, Maximilian; Pirinen, Pentti (PUBLIC LIBRARY OF SCIENCE, 2014)
  • Grönthal, Thomas; Moodley, Arshnee; Nykäsenoja, Suvi; Junnila, Jouni; Guardabassi, Luca; Thomson, Katariina; Rantala, Merja (PUBLIC LIBRARY OF SCIENCE, 2014)