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  • Ruusuvuori, Johanna; Peräkylä, Anssi (Routledge, 2009)
  • Peräkylä, Anssi; Ruusuvuori, Johanna Elisabeth (Oxford University Press, 2012)
  • Peräkylä, Anssi; Ruusuvuori, Johanna (Peter Lang, 2006)
  • Zubizarreta-Gerendiain, Ane; Pellikka, Petri; Garcia-Gonzalo, Jordi; Ikonen, Veli-Pekka; Peltola, Heli (Finnish Society of Forest Science, 2012)
  • Berzins,-A; Horman,-A; Lunden,-J; Korkeala,-H (Amsterdam, Netherlands: Elsevier., 2007)
    A total of 312 samples of sliced, vacuum packaged, cold-smoked pork from 15 meat processing plants in Latvia and Lithuania, obtained over a 15-month period from 2003 until 2004, were analyzed for the presence of Listeria monocytogenes at the end of their shelf-life. Overall, 120 samples (38%) tested positive for L. monocytogenes. Despite the long storing period, the levels of L. monocytogenes in cold-smoked pork products were low. Manufacturing processes were studied at seven meat processing plants. A new approach with a logistic multivariable regression model was applied to identify the main factors associated with L. monocytogenes contamination during the manufacturing of cold-smoked pork products. Brining by injection was a significant factor (odds ratio 10.66; P<0.05) for contamination of product with L. monocytogenes. Moreover, long cold-smoking times (>=12 h) had a significant predictive value (odds ratio 24.38; P<0.014) for a sample to test positive for L. monocytogenes. Pulsed-field gel electrophoresis results indicated that various sources of L. monocytogenes contamination existed over periods of time in several meat processing plants. In two meat processing plants, persistent L. monocytogenes strains belonging to serotypes 1/2a and 1/2c were found.
  • Almeda-Valdes, Paloma; Cuevas-Ramos, Daniel; Mehta, Roopa; Muñoz-Hernandez, Liliana; Cruz-Bautista, Ivette; Perez-Mendez, Oscar; Tusie-Luna, Maria T; Gomez-Perez, Francisco J; Pajukanta, Päivi; Matikainen, Niina; Taskinen, Marja-Riitta; Aguilar-Salinas, Carlos A (BioMed Central Ltd, 2014)
    Abstract Background Alterations in postprandial metabolism have been described in familial combined hyperlipidemia (FCH); however, their underlying mechanisms are not well characterized. We aimed to identify factors related to the magnitude of postprandial lipemia and apolipoprotein (apo) A-V levels in subjects with FCH. Methods FCH cases (n&#8201;=&#8201;99) were studied using a standardized meal test. Abdominal obesity was assessed using the waist to hip ratio (WHR). A linear regression model was performed to investigate the variables associated with the triglycerides incremental area under the curve (iAUC). Independent associations between metabolic variables and apo A-V iAUC were also investigated in a randomly selected subgroup (n&#8201;=&#8201;44). The study sample was classified according to the presence of fasting hypertriglyceridemia (&#8805;150&#160;mg/dL) and abdominal obesity (WHR &#8805;0.92 in men and &#8805;0.85 in women) to explore differences in parameters. Results The fasting apo B-48 levels (r&#8201;=&#8201;0.404), and the WHR (r&#8201;=&#8201;0.359) were independent factors contributing to the triglycerides iAUC (r2&#8201;=&#8201;0.29, P&#8201;&lt;&#8201;0.001). The triglycerides iAUC was independently associated with the apo A-V iAUC (r2&#8201;=&#8201;0.54, P&#8201;&lt;&#8201;0.01). Patients with both hypertriglyceridemia and abdominal obesity showed the most robust triglycerides and apo A-V postprandial responses. Conclusions In patients with FCH the fasting apo B-48 level is the main factor associated with postprandial lipemia. Abdominal obesity also contributes to the magnitude of the postprandial response.The triglycerides postprandial increment is the principal factor associated with the apo A-V postprandial response.
  • Simonen, Outi; Viitanen, Elina; Blom, Marja (Emerald Group Publishing Limited, 2012)
  • Wacklin, Pirjo; Tuimala, Jarno; Nikkila, Janne; Tims, Sebastian; Makivuokko, Harri; Alakulppi, Noora; Laine, Pia; Rajilic-Stojanovic, Mirjana; Paulin, Lars; de Vos, Willem M.; Matto, Jaana (PUBLIC LIBRARY OF SCIENCE, 2014)
  • Marsh, John E.; Ljung, Robert; Nostl, Anatole; Threadgold, Emma; Campbell, Tom A. (Frontiers Media S.A, 2015)
    A dynamic interplay is known to exist between auditory processing and human cognition. For example, prior investigations of speech-in-noise have revealed there is more to learning than just listening: Even if all words within a spoken list are correctly heard in noise, later memory for those words is typically impoverished. These investigations supported a view that there is a "gap" between the intelligibility of speech and memory for that speech. Here, the notion was that this gap between speech intelligibility and memorability is a function of the extent to which the spoken message seizes limited immediate memory resources (e.g., Kiellberg et al., 2008). Accordingly, the more difficult the processing of the spoken message, the less resources are available for elaboration, storage, and recall of that spoken material. However, it was not previously known how increasing that difficulty affected the memory processing of semantically rich spoken material. This investigation showed that noise impairs higher levels of cognitive analysis. A variant of the Deese-Roediger-McDermott procedure that encourages semantic elaborative processes was deployed. On each trial, participants listened to a 36-item list comprising 12 words blocked by each of 3 different themes. Each of those 12 words (e.g., bed, tired, snore...) was associated with a "critical" lure theme word that was not presented (e.g., sleep). Word lists were either presented without noise or at a signal-to-noise ratio of 5 decibels upon an A-weighting. Noise reduced false recall of the critical words, and decreased the semantic clustering of recall. Theoretical and practical implications are discussed.
  • Timmermans, Martijn J. T. N.; Barton, Christopher; Haran, Julien; Ahrens, Dirk; Culverwell, C. Lorna; Ollikainen, Alison; Dodsworth, Steven; Foster, Peter G.; Bocak, Ladislav; Vogler, Alfried P. (Oxford University Press, 2016)
    Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML ("nonhomogeneous") algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.
  • Räsänen, Pajari (Gaudeamus Helsinki University Press, 2010)
  • Raumonen, Pasi; Kaasalainen, Mikko; Akerblom, Markku; Kaasalainen, Sanna; Kaartinen, Harri; Vastaranta, Mikko; Holopainen, Markus; Disney, Mathias; Lewis, Philip (MDPI, Molecular Diversity Preservation International, 2013)
  • Kasari, Melissa; Toivonen, Hannu; Hintsanen, Petteri (2010)
    Lecture Notes in Artificial Intelligence
  • Hintsanen, Petteri; Toivonen, Hannu; Sevon, Petteri (2010)
  • Åstrand, Matti; Suomela, Jukka (2010)
    We present a distributed algorithm that finds a maximal edge packing in O(Δ + log* W) synchronous communication rounds in a weighted graph, independent of the number of nodes in the network; here Δ is the maximum degree of the graph and W is the maximum weight. As a direct application, we have a distributed 2-approximation algorithm for minimum-weight vertex cover, with the same running time. We also show how to find an f-approximation of minimum-weight set cover in O(f2k2 + fk log* W) rounds; here k is the maximum size of a subset in the set cover instance, f is the maximum frequency of an element, and W is the maximum weight of a subset. The algorithms are deterministic, and they can be applied in anonymous networks.
  • Lemström, Kjell; Mikkilä, Niko; Mäkinen, Veli (2008)
    We consider two content-based music retrieval problems where the music is modeled as sets of points in the Euclidean plane, formed by the (on-set time, pitch) pairs. We introduce fast filtering methods based on indexing the underlying database. The filters run in a sublinear time in the length of the database, and they are lossless if a quadratic space may be used. By taking into account the application, the search space can be narrowed down, obtaining practically lossless filters using linear size index structures. For the checking phase, which dominates the overall running time, we exploit previously designed algorithms suitable for local checking. In our experiments on a music database, our best filter-based methods performed several orders of a magnitude faster than previous solutions.
  • Arroyuelo, Diego; Claude, Francisco; Maneth, Sebastian; Mäkinen, Veli; Navarro, Gonzalo; Nguyen, Kim; Sirén, Jouni; Välimäki, Niko (2010)
    A large fraction of an XML document typically consists of text data. The XPath query language allows text search via the equal, contains, and starts-with predicates. Such predicates can be efficiently implemented using a compressed self-index of the document's text nodes. Most queries, however, contain some parts querying the text of the document, plus some parts querying the tree structure. It is therefore a challenge to choose an appropriate evaluation order for a given query, which optimally leverages the execution speeds of the text and tree indexes. Here the SXSI system is introduced. It stores the tree structure of an XML document using a bit array of opening and closing brackets plus a sequence of labels, and stores the text nodes of the document using a global compressed self-index. On top of these indexes sits an XPath query engine that is based on tree automata. The engine uses fast counting queries of the text index in order to dynamically determine whether to evaluate top-down or bottom-up with respect to the tree structure. The resulting system has several advantages over existing systems: (1) on pure tree queries (without text search) such as the XPathMark queries, the SXSI system performs on par or better than the fastest known systems MonetDB and Qizx, (2) on queries that use text search, SXSI outperforms the existing systems by 1-3 orders of magnitude (depending on the size of the result set), and (3) with respect to memory consumption, SXSI outperforms all other systems for counting-only queries.
  • Kalendar, Ruslan; Lee, David; Schulman, Alan (Humana Press, 2014)
    Methods in Molecular Biology
    This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a programme to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with GC or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyses sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html.
  • Salmela, Leena; Mäkinen, Veli; Välimäki, Niko; Ylinen, Johannes; Ukkonen, Esko (Oxford University Press, 2011)
  • Tiškina, Valentina; Capligina, Valentina; Must, Külli; Berzina, Inese; Ranka, Renate; Jokelainen, Pikka (BioMed Central, 2016)
    Abstract A previously splenectomized dog from Estonia was presented with a sudden lack of appetite and discoloration of the urine. Despite supportive therapy, its condition deteriorated dramatically during 1 day. Severe thrombocytopenia and high numbers of protozoan hemoparasites were evident in blood smears, and the hematocrit dropped from 46 to 33 %. The dog was euthanized before specific antibabesial treatment was initiated. Blood samples from the dog and from two other dogs in the same household tested positive for Babesia using molecular methods, and the sequences of partial 18S rRNA gene confirmed the causative species as Babesia canis canis. The risk of severe, rapidly progressing babesiosis in splenectomized dogs merits awareness.